Phylogeny, Character Evolution and the Systematics of Psilochilus (Triphoreae)

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THE PRIMITIVE EPIDENDROIDEAE (ORCHIDACEAE): PHYLOGENY, CHARACTER EVOLUTION AND THE SYSTEMATICS OF PSILOCHILUS (TRIPHOREAE)

A Dissertation

Presented in Partial Fulfillment of the Requirements for

The Degree Doctor of Philosophy in the

Graduate School of the Ohio State University

Erik Paul Rothacker, M.Sc.

*****

The Ohio State University

2007

Doctoral Dissertation Committee: Approved by

Dr. John V. Freudenstein, Adviser

Dr. John Wenzel ______

Dr. Andrea Wolfe Adviser

Evolution, Ecology and Organismal Biology

Graduate Program

ABSTRACT

Considering the significance of the basal Epidendroideae in understanding patterns of morphological evolution within the subfamily, it is surprising that no fully resolved hypothesis of historical relationships has been presented for these orchids. This is the first study to improve both taxon and character sampling. The phylogenetic study of the basal Epidendroideae consisted of two components, molecular and morphological.

A molecular phylogeny using three loci representing each of the plant genomes including gap characters is presented for the basal Epidendroideae. Here we find Neottieae sister to

Palmorchis at the base of the Epidendroideae, followed by Triphoreae. Tropidieae and

Sobralieae form a clade, however the relationship between these, Nervilieae and the advanced Epidendroids has not been resolved.

A morphological matrix of 40 taxa and 30 characters was constructed and a phylogenetic analysis was performed. The results support many of the traditional views of tribal composition, but do not fully resolve relationships among many of the tribes. A robust hypothesis of relationships is presented based on the results of a total evidence analysis using three molecular loci, gap characters and morphology. Palmorchis is placed at the base of the tree, sister to Neottieae, followed successively by Triphoreae sister to

Epipogium, then Sobralieae. Tropidieae form a clade with the advanced Epidendroideae,

ii and this sister to Nervilieae and Gastrodieae. Diceratostele gabonensis groups within this clade. These results support a primitive condition of plicate leaves with absent or reduced leaves evolving a minimum of five times. An objective of this study was to investigate anther evolution. Among the basal members we find anthers that are erect or exhibit varying degrees of incumbency. It is clear that the erect anthers of some orchids evolved independently from those observed in the Orchidoideae, and the primitive condition among the basal Epidendroideae is suberect/subincumbent. Epidendroid incumbency is achieved via combinations of bending in different regions of the anther, with the primitive condition being in the column region and to a lesser extent, the basal region of the anther. The primitive condition for pollinia is free monads with tetrads evolving twice, and sectile pollinia four times. Some authors have suggested that the type III stigma of Cephalanthera, possessing other primitive features, was evidence that it was intermediate between Neottieae and advanced Epidendroideae. Given its position in the

Neottieae, this condition in Cephalanthera is a case of convergence.

Based on the results of other studies using nonorchids, it was expected that we would find higher rates of nucleotide substitutions and divergence rates in taxa that lack chlorophyll when compared to green relatives. This study confirms this for both nuclear

ITS and mitochondrial nad1 for which there were significant numbers of achlorophyllous taxa represented. These taxa had lower transition:transversion ratios (TI:TV) than chlorophyllous taxa in the same clade and generally lower than other taxa.

As part of the study of the basal Epidendroideae, a monograph of the orchid genus

Psilochilus (Triphoreae) was prepared in order to better understand the natural variation within the genus. Based on this work, there are seven species recognized, of which one is

iii a newly described species, Psilochilus ecuadoriensis, from lowlands of western Ecuador.

A molecular phylogenetic study of the genus, representing five of the seven species, was performed using the plastid trnL-F intergenic spacer. Psilochilus physurifolius is at the base of the genus. A grouping is formed between Psilochilus modestus and P. macrophyllus and a clade of P. mollis and P. ecuadoriensis.

Conditions of the labellum and vegetative leaf characters were mapped onto the strict consensus of the parsimony analysis including gaps. In the Triphoreae the primitive condition is to have clasping or apetiolate ovate leaves and a labellum with acute lateral lobes and three calli. Psilochilus has two calli and a petiolate leaf, with apetiolate leaves evolving again in P. macrophyllus; elliptic leaves evolved in P. physurifolius. The lateral lobes of the labellum are acute in most of the taxa with rounded or blunted lateral lobes evolving in the clade of P. mollis and P. ecuadoriensis. The clade of Psilochilus modestus and P. macrophyllus is distinguished from the clade of P. mollis and P. ecuadoriensis by a labellum with acute lateral lobes and ovate leaves.

This is the first significant study of the basal Epidendroideae in which both taxon and locus sampling were increased. It had been previously suggested by other authors that the diversity of the Epidendroideae might be the result of a rapid evolutionary radiation, as indicated by the short branch lengths and low support obtained. The implication was that a hypothesis of relationships among the basal tribes of the

Epidendroideae might not be possible to obtain. These results prove that the epidendroid problem is not intractable, and while still showing low support, there is considerable structure to the topology obtained.

Dedicated to my loving wife, Birgit, who has stood by me from the beginning, gave me encouragement and support, worried for me when I did not, and deserves this as much as me. To my son, Nathan, who is my muse and my inspiration for enjoying the little things, and to my parents, who fostered a love of nature and learning.

ACKNOWLEDGMENTS

I wish to thank my adviser, Dr. John V. Freudenstein for the intellectual support, guidance and love of orchids, which gave me the encouragement to pursue this.

Moreover his patience, and endless hours of draft corrections were greatly appreciated, and have helped to make this document the best that it could be.

I would also like to thank my committee members, Dr. John Wenzel and Dr.

Andrea Wolfe for their support and constructive criticism, and the members of the

Phylogenetic Discussion Group for stimulating debate and a forum for the working out intellectual and philosophical issues.

In addition, there are a number people that have helped in so many ways. Thanks to my colleague and friend Lou Jost for his help in Ecuador and his efforts in finding populations of Psilochilus; I am glad that he finally took his eyes from the trees and took time to look down at the ground. I greatly appreciate the assistance of Sr. Andres Maduro for his hospitality and assistance in working in Panama and Vladimir Melgarejo and Eric

Olmos for field assistance, the staff of the Smithsonian Tropical Research Institute for making Barro Colorado islands long steps and big tree available to me. Thanks to: Dr.

Mark Chase, Dr. Meg Daly, Dr. Robert Dressler, Dr. Emerson R. Pansarin, Dr. Mark

vi Whitten and lab, and Dr. Mesfin Tedesse, all of whom have provided material and intellectual support, without which this may not have been possible; and finally, my lab partners and colleagues, Dr. Shawn Krosnick, Jeff Morrawetz, and Craig Barrett for coffee, moral support and discussion.

I would also like to acknowledge funding from the Janice Carson Beatley Fund for funding research travel to Panama and Ecuador.

vii

VITA

December 10, 1971 …………….……...…. Born, Charleston, South Carolina, USA

2000 ………………………………………. M.Sc. Biology, Department of Biology, DePaul University, Chicago IL.

1997 ……………………………………….. B.Sc. Department of Biology, DePaul University, Chicago IL.

2001-present ……………………………….. Graduate Teaching associate, The Ohio State University

1997-2000 …………………………………. Graduate Teaching Associate, DePaul University, Chicago, IL.

1996 – 2000 ……………………………….. Intern, Field Museum of Natural History, Chicago, IL.

PUBLICATIONS

1. Rothacker. 2005. Triphoreae. Pp. 605-616 in Pridgeon, A. M., P. J. Cribb, M. W. Chase and F. N. Rasmussen (eds.), Genera Orchidacearum. Oxford Univ. Press, Oxford.

2. Rothacker. 2000. Stable isotopic and morphometric characterization of Peregrine migration with an emphasis on determining the importance of particular habitat types. June 2000. MSc. Thesis. DePaul University, Chicago, IL.

3. Kharas, Karras, Michna, Grajzer, Karins, Kontzias, Rothacker, McManigal, Dian, and Watson. 2001. Novel Copolymers of Trisubstituted Ethylenes with Styrene - 1. 2- Halophenyl-1,1-dicyanoethylenes, J. Macromol. Sci., A38, 889-896.

viii 4. Kharas, Karras, Michna, Grajzar, Karins, Rothacker, McManigal, and Watson. 1999. Novel copolymers of halogen ring substituted 2-Phenyl-1,1-Dicyanoethylenes and styrene. Polymer Preprints. Vol. 40:1.

FIELDS OF STUDY

Major Field: Evolution, Ecology and Organismal Biology

TABLE OF CONTENTS

Page

Abstract ……………………………………………………………………………… ii

Dedication ………………………………………………………………………….... v

Acknowledgments ………………………………………………………………….... vi

Vita …………………………………………………………………………………... vii

List of Tables ………………………………………………………………………… xiv

List of Figures ……………………………………………………………………….. xvi

Chapters: 1. Systematic history and current hypotheses of relationships among the basal Epidendroideae ………………………………………………………………. 1 The Basal Epidendroids in Current Classifications …………………… 3 A Brief History of Epidendroid Classification …….………………….. 5 Tribal treatments ……………………………………………...... 7 Neottieae ...... 7 Tropideae ……………………………………………… 8 Sobralieae ……………………………………...... 8 Triphoreae …………………………………………….. 9 Gastrodieae ………………………………………….... 10 Nervilieae ……………………………………………… 11 Outstanding taxa …………………………………….... 11 Current Classifications …………………………………………… 14 Cladistic Morphological Hypotheses ………………..... 14 x Molecular Hypotheses ……………………………….. 15 2. Towards a phylogenetic hypothesis of the basal Epidendroideae (Orchidaceae) inferred from 3 loci and 3 genomes ………………………… 21 Introduction ………………………………………………….……….. 21 Purpose of this study ………………………………..………… 22 Materials and methods ……………………………………….………. 24 Materials- Taxon sampling ….……………………………...... 24 Methods -DNA extraction and purification ………………...... 25 Amplification and sequencing ………………………... 25 Alignment …………………………...………………... 27 Outgroup choice ……….……………………………… 28 Gap coding ….………………………………………… 28 Parsimony ………………………………………...... 28 Maximum likelihood ………..…………………………. 29 Branch support ….……………………………………. 29 Results …………………………………………………….….. 30 ITS partition ……………………………………...... 30 trnL-F partition ………………………………………. 32 nadb-c partition ………………………………………. 34 Parsimony combined analysis ....…………….……….. 35 Maximum likelihood combined analysis ....…..……… 39 Discussion ……………………………………………………. 40 Conflicting signals using different optimality criteria ………………………………………………………… 41 Topology ……………………………………………… 43 Tribal composition ……….…………………………… 48 The loss of chlorophyll …...…………………………... 57 The utility of nad1B-C ………………………………... 60 Conclusions …………………………………………………… 61

xi 3. A phylogenetic hypothesis of basal Epidendroideae from morphology and molecular data: a total evidence approach ………………………………. 86 Introduction …………………………………………………… 86 Materials and methods ………………………………………… 89 Results ………………………………………………………… 94 Discussion …………………………………………………….. 110 Conclusion ……………………………………………………. 132 4. A Monograph of the Orchid Genus Psilochilus (Triphoreae, Epidendroideae) …………………………………………….…………………………………... 162 Introduction ………………….……………………………………….. 162 Materials and methods …….…………………………………………. 164 Taxonomy ……………………………………………………………. 165 Psilochilus …………………………………………………… 165 Artificial Key to the species of Psilochilus .………………………….. 168 P. carinatus ………………………………………………….. 169 P. dusenianus ………………………………………………… 170 P. ecuadoriensis ……………………………………………… 171 P. macrophyllus ……………………………………………… 173 P. modestus …………………………………………………... 179 P. mollis ……………………………………………………… 183 P. physurifolius ……………………………………………… 186 Specimens examined with uncertain placement ……..…….………… 189 Uncertain names …………………………………………………….. 190 5. Phylogeny of Psilochilus (Triphoreae, Epidendroideae) using the plastid trnL-F intergenic spacer …………………………….……………………….. 215 Introduction ………………………………………………………..... 215 Materials and methods ………………………………………………. 216 Results ……………………………………………………………….. 220 Discussion ……………………………………………………………. 222 Conclusions …………………………………………………………. 227

xii Appendix A: Nuclear, Chloroplast, Mitochondrial DNA Sequences And Gap

Matrices Used In Chapter 2 …………………………………..……… 236

Appendix B: Nuclear, Chloroplast, Mitochondrial DNA Sequences And Gap

Matrices Including 30 Morphological Characters Used In Chapter 3

……………………………………………………………………….. 367

Appendix C: DNA Alignments For The Chloroplast trnL-F Intergenic Spacers

Regions And Gap Matrices Used In Chapter 5 …………...……....…. 422

Appendix D: Table Of Accessions Used In The Molecular Analyses Of Chapters

2, 3 And 5 ………………………………………………….……….... 430

Literature cited ……………………………………………………………….. 437

xiii

LIST OF TABLES

TABLE PAGE

1.1 Historical treatment of the genera of the primitive Epidendroideae used in this study……………………………………………………………...... 18

2.1 ITS sequence information including sequence length, % gaps and transition / transversion ratios…....………………………………….…………………. 64

2.2 Sequence characteristics for nad1b-c including length variation, % gaps, transition/ transversion ratios……………………...………………………... 66

3.1 Morphological matrix consisting of 30 characters coded for 40 taxa…….… 136

A.1 Primitive Epidendroideae analysis. ITS molecular matrix………….………. 237

A.2 Primitive Epidendroideae analysis. trnL-F +gaps molecular matrix.………. 247

A.3 Primitive Epidendroideae analysis. nad1 +gaps molecular matrix.………… 267

A.4 Primitive Epidendroideae analysis. Combined molecular matrix for ITS (281 characters already excluded), trnL-F +gaps, nad1 +gaps.…………….. 310

xiv B.1 Primitive Epidendroideae combined Total Evidence analysis ……………. 368

C.1 Alignment of the trnL-F sequences data including gap characters coded using simple gaps methods. ….…………………………………………….. 422

D.1 List of Accessions used in the molecular analyses…………………………. 431

LIST OF FIGURES

FIGURE PAGE

1.1 Tree presented for the Epidendroideae redrawn from the summary tree of Chase et al. (2003).………………………………………………………….. 20

2.1 Strict consensus tree returned from an analysis of the nuclear ITS locus calculated from 3 MPTs of length 2307 (CI=0.412, RI=0.649)...... 68

2.2 Phylogram of 1 of 3 most parsimonious trees. Numbers indicate character changes along the branch……………………………………………………. 70

2.3 Strict consensus tree for trnL-F including gaps coded using simple gap method.………..…………………………………………………………….. 72

2.4 Adams consensus for the portion of the trnL-F strict consensus for which there was a lack of resolution……………………………………...... 74

2.5 Strict consensus tree for nad1, returned from 640 most parsimonious trees of length 3236 (CI=0.735, RI=0.536)……………………………………..… 75

2.6 Portion of the nad1 Adams consensus tree; * indicates node not obtained in strict consensus………………………….....…….………..……. 77

xvi

2.7 Strict consensus tree returned from the parsimony analysis of the combined data from three loci: trnLF, trnLF gaps, ITS, and nad1, nad1 gap …………… 78

2.8 The strict consensus calculated from 6 MPTs of length 5570 (CI=0.663, RI=0.546) returned from the combined analysis excluding Gastrodia procera & Triphora amazonica, but including all partial sequences of Wullschlaegelia, Epipogium and Gastrodia species...... 80

2.9 Topology from the Maximum likelihood combined analysis of the three data partitions, ITS, nad1, and trnL-F.………..….………………………………… 82

2.10 Maximum Likelihood topology returned from the combined analysis excluding Gastrodia procera and Triphora amazonica, but including all partial sequences of Wullschlaegelia, Epipogium and Gastrodia species….…….…… 84

3. 1 A) Epilyna hirtzii (Sobralieae), B) Didymoplexis pallens bud just prior to opening showing granular pollinia, C) Palmorchis trilobulata, D) Gastrodia procera with distinctly sectile pollinia, inset showing stigmatic surface cells …………………………………………………………………………………. 138

3.2 The columns of the Triphoreae…….………………………………………….. 140

3.3 Column morphology of Diceratostele gabonensis (ER44) showing an erect anther with distinct staminoda and concave stigma.………………...... 142

xvii 3.4 Diagram of a longitudinal cross section of typical orchid column illustrating an epidendroid incumbent anther and delineating the three zones of bending as described and illustrated in Freudenstein et al. (2002)………………………………………………………………….……… 144

3.5 Strict consensus tree of 4 MPTs (L= 123, CI= 0.333, RI= 0.657) returned from the analysis of the parsimony analysis of the morphological matrix ………………….…………………………………………………………….. 145

3.6 Portion of the Adams consensus tree returned from the morphological analysis………….……………………………………………………………. 147

3.7 1 of 4 MPTs obtained from the analysis of the morphological matrix with character distributions mapped.…………………………………………. 148

3. 8 A portion of 1of 4 MPTs derived from the analysis of the morphological matrix………………………………………………………………………..... 150

3.9 Single most parsimonious tree obtained from the successively weighted analysis of 30 morphological characters ……………………………………... 151

3.10 The single most parsimonious tree of 4196 steps (CI= 0.712, RI= 0.461) returned from the parsimony analysis of the total evidence matrix including all Gastrodia species except Gastrodia procera………………...... 152

3.11 Single MPT obtained using total evidence with unambiguious changes mapped onto branches...... 154

xviii 3.12 Distribution of leaf morphology mapped onto the single MPT obtained from total evidence analysis of 4858 characters from ITS, nad1b-c+gaps, trnL-F +gaps and 30 morphological characters……………………………… 155

3.13 Distribution of sporogenous and basal zone anther bending onto the single MPT obtained from total evidence analysis of 4858 characters from ITS, nad1b-c+gaps, trnL-F +gaps and 30 morphological characters…………..… 156

3.14 Distribution of column zone bending mapped onto the single MPT obtained from total evidence analysis of 4858 ITS, nad1b-c+gaps, trnL-F +gaps and 30 morphological characters………………………………………………… 157

3.15 Distribution of monads /tetrads and sectile pollinia mapped onto the single MPT obtained from total evidence analysis of 4858 ITS, nad1b-c+gaps, trnL-F +gaps and 30 morphological characters…………………………….. 158

3.16 Distribution of caudicles mapped onto the single MPT obtained from total evidence analysis of 4858 ITS, nad1b-c+gaps, trnL-F +gaps and 30 morphological characters……………………………………………………. 159

3.17 Distribution of stipe and stigmatic cell shape mapped onto the single MPT obtained from total evidence analysis of 4858 ITS, nad1b-c +gaps, trnL-F +gaps and 30 morphological characters…………………………….. 160

3.18 Distribution of pollinium number mapped onto the single MPT obtained from total evidence analysis of 4858 ITS, nad1b-c +gaps, trnL-F +gaps and 30 morphological characters…………………………………………... 161

4.1 A generalized distribution map of Psilochilus…………………………….. 191

xix 4.2 Dissection light microscope images of Psilochilus macrophyllus seeds….. 192

4.3 Species level variation in lablellum morphology for the genus Psilochilus ...... 194

4.4 Distribution map of Psilochilus carinatus…………………………………. 196

4.5 Distribution map of Psilochilus dusenianus……………………………..… 197

4. 6 Illustration of Psilochilus ecuadoriensis ined. drawn from LJ7955….……. 198

4. 7 Psilochilus ecuadoriensis sp. nov. showing flower…...……………………. 200

4.8 Distribution map of Psilochilus ecuadoriensis…………………………….. 201

4.9 Distribution map of Psilochilus macrophyllus…………………………….. 202

4.10 Psilochilus modestus A. flower B. in habitat.……………………………… 203

4.11 Distribution map of Psilochilus modestus………………………………….. 205

4.12 Variation in the labelum of Psilochilus mollis...... 206

4.13 Distribution map of Psilochilus mollis……………………………………… 208

4.14 Variation in the flower color observed in Psilochilus mollis..………………. 209

4.15 Distribution of Psilochilus physurifolius……………………………………. 213

4.16 Illustration of Psilochilus LJ5414………….……………………………….... 214

5.1 Strict consensus of 5MPTs of the matrix of nucleotide sequences...... 228

5.2 Strict consensus topology of 7 MPTs returned from the analysis of nucleotide sequence data and gaps coded. ..……………………………………………… 229

5.3 Topology of the maximum likelihood analysis with the likelihood score of –ln L= 3567.74558………………………………………………………….... 232

5.4 Labellum characters mapped on to simplified parsimony strict consensus tree……………………………………………………………………………. 234

5.5 Vegetative characters mapped on to simplified parsimony strict consensus tree…………………...……………………………………………………….. 235

xxi

CHAPTER 1

SYSTEMATIC HISTORY AND CURRENT HYPOTHESES OF RELATIONSHIPS

AMONG THE BASAL EPIDENDROIDEAE

INTRODUCTION

The Orchidaceae is one of the largest flowering plant families with as many as 20-

30 thousand species. The Epidendroideae contains as much as 80% of the diversity within the family (Dressler 1990, 1993; Chase et al. 2003). The Epidendroideae are a major component of orchid diversity, and may represent the fundamental evolutionary radiation

of the family. A clearer understanding of the phylogenetic relationships as well as the

natural variation within the subfamily is essential for understanding orchid evolution in

general. However, in many phylogenetic analyses of orchids, and specifically those

looking at epidendroids, resolution of tribal level relationships among the basal

epidendroids is poor (Cameron et al. 1999; Chase et al. 2003) owing to combinations of

plesiomorphic and apomorphic traits and insufficient uncontested synapomorphies

1 making it difficult to resolve nested sets of relationships (Rasmussen 2000). Ironically, it is among these basal taxa that there is the greatest need for a strong phylogenetic hypothesis of relationships given their significance in understanding patterns of evolution in the Epidendroideae.

In nearly all of the molecular phylogenetic studies of the Orchidaceae, taxa from the tribes Palmorchideae, Neottieae, Sobralieae, Tropidieae, Nervilieae, Gastrodieae,

Xerorchideae (Pridgeon et al. 2005) and Triphoreae (Table 1.1, sensu Dressler 1993,) have been observed forming a basal polytomy within the Epidendroideae. It has been hypothesized that the Epidendroideae underwent a rapid radiation (Cameron et al. 1999,

Chase et al. 2003), probably associated with specialization in pollination syndromes. As a consequence these taxa are a mosaic of primitive and derived traits, morphologically and molecularly, with a few autapomorphies, and fewer synapomorphies. Additionally, there are many achlorophyllous taxa. The loss of chlorophyll often results in a convergence in floral morphology associated with a loss of specialized pollination syndromes and increased autogamy, as well as numerous convergences in the reductions of anatomical and morphological features such as the loss of leaves and associated structures (Molvray et al. 2000). At the genomic level, many authors have suggested that organellar functional constraints are reduced in plants lacking chlorophyll. As such many loci used in plant molecular phylogenetics often exhibit accelerated nucleotide substitution rates and an increased occurrence of indel events relative to closely related chlorophyllous or green taxa (Duff and Nickrent 1994, Nickrent and Star 1994, Nickrent and Duff 1996, and

Nickrent et al. 1998).

2 THE BASAL EPIDENDROIDS IN CURRENT CLASSIFICATIONS- The most

recent widely accepted family classification was that of Dressler (1993), and while there

are more recent molecular studies primarily focusing on the phylogenetic relationships,

the taxonomy of Dressler (1993) provides the taxonomic foundation of all subsequent

treatments and will be used here as the basis for discussion of the basal epidendroid

groups (Table 1.1).

In Dressler’s (1993) classification, the subfamily Spiranthoideae includes three

tribes: Diceratosteleae (Diceratostele), Tropidieae (Corymborkis and Tropidia), and

Cranichideae. The Spiranthoideae were characterized as possessing a terminal viscidium,

a trait that is absent in Diceratostele. Both Diceratostele and Tropidieae are also

characterized as having “woody” stems, a trait absent in the remainder of the subfamily.

Both Diceratostele and Tropidieae possess a “spiranthoid” type column in that the anther

is erect, or nearly so, and subequal to the rostellum, supporting its inclusion in this

Spiranthoideae. However, numerous molecular and morphological studies support an

epidendroid affinity for both Tropidieae and Diceratostele (Cameron et al. 1999,

Freudenstein and Rasmussen 1999), therefore it has been argued, for Tropidieae based on

morphology, that this is a convergent trait. With the exception of the column, neither

Diceratostele nor Tropidieae has flowers resembling any of the spiranthoid orchids.

Because Triphoreae, Neottieae, Gastrodieae, Nervilieae and Palmorchis have monandrous anthers and soft pollinia, Dressler placed them among the primitive

Epidendroideae. Neottieae (Neottia, Limodorum, Aphyllorchis, Cephalanthera, Epipactis

and Listera) and Triphoreae (Triphora, Psilochilus, and Monophyllorchis) were difficult

3 to place, given so few morphological and anatomical similarities with the other taxa.

Triphoreae resembles Neottieae in the form of the anther and Cephalanthera most closely agrees with Triphoreae in the structure of the column; both Triphora (and to a lesser extent Psilochilus) and Cephalanthera possess recurved anthers. Dressler also suggests that Triphoreae may be closely related to Palmorchis, as they tend to share the features of gregarious blooming and similarity in floral morphology. It should be pointed out here that gregarious blooming is a characteristic of many terrestrial orchid species order to increase the chances of outcrossing (Dressler 1981).

In the narrow sense, Neottieae as it is currently circumscribed is probably a monophyletic group (Dressler 1993, Pridegon 2005, R. Bateman pers. com.). Palmorchis was removed from Sobralieae (Dressler and Dodoson 1960) and given tribal status

(Palmorchideae) because of significant morphological differences between it and the other members Sobralieae (Sobralia, Elleanthus, Epilyna, and Sertifera) such as seed

type, pollinium number (4 vs. 8), and the lack of a viscidium. More recent classifications

(Chase et al. 2003; Table 1.1 and Fig.1.1) suggest that a subfamilial rank is not warranted

and have tentatively placed Palmorchis in Neottieae (see section Molecular hypotheses

for a more comprehensive discussion). Palmorchis has 4 pollinia that are unique in that

they are firmer than those found in many of the basal taxa yet are softer than pollinia

from more advanced orchids; given the recent results of molecular studies (Bateman et al

unpublished, Cameron et al. 1999, and Chase et al 2003) which support the tentative

placement of Palmorchis with Neottieae, however, given morphology it does not seem

that this is an appropriate place for it here either.

4 Other tribes recognized by Dressler (1993) were Gastrodieae, including

Wullschlaegelia, and the monotypic Nervilieae (Nervilia). Gastrodieae have traditionally

been the repository for many of those orchids that lack chlorophyll, thus it is possibly a

paraphyletic assemblage when you consider that convergences in morphology have been

observed in plants with increased achlorophylly (Molvray et al 2000). Dressler also

included Vanilleae (Vanilla, Galeola, Erythorchis, Crytosia among others) among these

primitive epidendroid orchids; recent molecular research points to a subfamilial status for

vanilloid orchids, somewhere near the base of the orchid phylogeny (Kores et al. 1997,

Cameron et al.1999). Finally, Sobraliinae (Sobralia, Elleanthus, Sertifera, and Epilyna) were put in the “epidendroid 1” phylad of the advanced epidendroids as they were considered to have many derived characters of the more “advanced” epidendroid orchids

by Dressler (1993). Of note is the uncertain placement of the genus Xerorchis, which was left as a primitive monandrous orchid, close to Pogoniinae (now Vanillioideae, sensu

Cameron et al. 1999) due to terrestrial habit, persistent leaves, and seed type; however because it had 8 pollina, it could have been more closely related to Arethuseae or

Epidendreae sensu Dressler (1993).

A BRIEF HISTORY OF EPIDENDROID CLASSIFICATION- The tribes of the basal Epidendroideae have been variously conceptualized depending upon the author, state of knowledge and degree of importance placed upon assorted key characteristics. In all orchid classifications, many monandrous orchids closely allied to Neottia, have been associated on the basis of possessing many primitive characters and have been collectively called the “neottioid” orchids. These characters include soft mealy pollinia,

5 plicate leaves, suberect to subincumbent anthers. Lindley (1830-40; see Table 1.1 for

summary) was the first substantial work to give a full account of all orchid genera known

at the time in which he placed the “neottioid” orchids and the other basal epidendroid

orchids (sensu Dressler 1993) into two “tribes”, Neottieae and Arethuseae with

equivalence to the subfamilial rank used today. While both subfamilies had some variant

of sectile pollinium, they were distinguished based on dorsal (sub-incumbent) vs.

opercular anthers (distinctly incumbent with a detachable pollinia). Bentham (1881) accepted much of Lindley’s work with a few exceptions (Table 1.1). Arethuseae was subsumed into Neottieae, which was maintained as a subfamily. Of the more recent classifications, the works of Schlechter (1911-1926) were the most influential from early in the 1900’s. All of the orchids of the basal Epidendroideae, as well as the whole of the

Orchidoideae and “vanilloid” orchids, were put into the subfamily Monandrae, as they possessed single fertile anthers. These subfamilies were then subdivided into tribes.

Schlechter placed orchids with mealy or sectile pollinia into subdivision Polychondreae

(containing 23 groups or subtribes) and those with more hard or firm waxy pollinia into

Kerosphaereae (containing 43 groups), the former containing all the basal epidendroid orchids in this study. Abandoning the higher-level nomenclature of Lindley and others, the names that Schlechter used were based on the classifications of Ernst Pfitzer (1877, not presented here in detail) with modifications to relationships and groupings. By 1926,

Schlechter had revised his classification scheme (Table 1.1). While other works were being published concurrently, the work of Schlechter was by far the most influential for the first half of the twentieth century.

6 The modern era in orchid classifications began with the work of Dressler and

Dodson (1960). Dressler and Dodson accepted some of Schlechter (1911-1914; 1926)

and the revisions of this work by Mansfeld (1934, 1937a, 1937b, 1954), but they went

back to the nomenclature of Lindley and Bentham (Table 1.1). While Dressler and others

continued to publish many orchid classifications at different ranks over the subsequent

decades, this work represents one of the most comprehensive and influential

classifications of orchids up until that time, and provided a foundation for all future work

leading to the culmination of Dressler (1993).

TRIBAL TREATMENTS- Neottieae- With the exception of Lindley, who was able to see only a relatively small percentage of the diversity of Neottieae (sensu Dressler

1993), Neottieae as it is currently recognized is much more narrowly defined then that used in many previous classifications. With Lindley’s (1830-1840) circumscription of the subfamily Neottieae he included taxa such as Neottia, Listera, and Epipactis, and into the

Arethuseae were placed Cephalanthera and Limodorum. Bentham (1881) placed Listera and Neottia into Spiranthieae (Table 1.1), suggested by a terminal erect anther on top of or interiorly inclined behind the rostellum, with pollen affixed to a gland. Bentham

(1881) included Aphyllorchis in his Diurideae (Neottieae), on the basis of an erect or inclined anther, an abbreviated rostellum and powdery or granular to semi-solid pollinia.

Cephalanthera, Epipactis, and Limodorum were listed in Limodoreae (Neottieae). The conditions for this were an operculate anther, incumbent or suberect, with a short rostellum and powdery and granular pollinia, with dorsal anther dehiscence. In Schlechter

(1911-1914) Aphyllorchis was placed in Vanillinae (Polychondreae) with the remaining

7 Neottieae treated in two subtribes of the Polychondreae, the Listerinae and

Cephalantherinae. In the 1926 classification, Schlechter combined all these taxa under the

Polychondreae (Monandrae). Listera and Neottia were placed in Listereae, while into

Cepahalanthereae went Aphyllorchis, Cephalanthera, Epipactis, and Limodorum. The

work of Dressler and Dodson (1960) accepted some of Schlechter’s classification (with

revisions). Neottieae were placed into the subfamily Orchidoideae, and divided among

the subtribes Limodorinae (Aphyllorchis, Cephalanthera, Epipactis, and Limodorum)

and Neottieae (Neottia, and Listera). The later were defined as having a sensitive

rostellum (which exudes a viscid substance when stimulated), and cauline leaves spirally

arranged (when present).

TROPIDIEAE- it is clear from a survey of the literature that the two genera in this

tribe have had a long history together based on floral similarity. Lindley (1830-1840)

placed Tropidia (Tropidieae) in the subfamily Neottieae based on having loose pollen and an erect anther. Bentham (1881) treated Corymborkis (called Corymbis) and Tropidia at

the level of tribe, Corymbideae (Neottieae), given a parallel or erect anther atop the

rostellum and granular pollinia. Schlechter (1911-1914, 1926) included both Tropidia and

Corymborkis (as Corymbis) as members of the Tropidiinae (Polychondreae). Dressler and

Dodson (1960) transferred Tropidia and Corymborkis to the Tropidia alliance under the

Spiranthoideae.

SOBRALIEAE-Lindley (1830-1840) placed Sobralia into the subfamily

Arethuseae. Bentham (1881) moved Sobralia and Sertifera into the Vanilleae given a

long column, short rostellum, and an incumbent sub-operculate anther possessing lax

8 granular pollinia and a rostellum or gland. Based on Schlechter’s work (1911-1914,

1926), Sobralia, Elleanthus, Epilyna and Sertifera were placed in the Sobraliinae

(Polychondreae). Dressler and Dodson (1960) transferred the Sobraliinae (Sobralia,

Elleanthus and Sertifera) to Epidendreae (Orchidoideae) with the rank of subtribe.

TRIPHOREAE- In Lindley’s treatment (1830-1840), Triphora gentianoides and

Psilochilus macrophyllus were the only species of this tribe that were discussed, and were

placed in Arethuseae as Pogonia gentianoides and P. macrophylla respectively. Until

Schlechter, members of this tribe were treated as related to Pogonia (for examples see

Reichenbach 1859; Cogniaux 1906; Williams 1970), however Schlechter (1911-1914)

used the name Nerviliinae (Polychondreae) for the taxa of Triphoreae, but by 1926, he

moved Triphora, Psilochilus and Monophyllorchis to Vanillieae. Dressler and Dodson

(1960) included the three genera of this tribe again as belonging to Pogoniinae.

Interestingly, Nervilia was also included here, implying a relationship to Triphoreae

based on similarity in flower structure. Ames (1922) was the first to suggest that

Triphoreae were not members of Pogoniinae, and Baldwin and Speese (1957)

subsequently established that Triphoreae have 44 chromosomes while Pogoniinae have

only 18, thus further supporting the hypothesis that this relationship is not correct. Using the system of Schlechter, Breiger (1975) segregated Triphora and Nervilia into

Nerviliinae but kept Psilochilus and Monophyllorchis in Pogoniinae. The reason for this

segregation, Brieger argued, was that there were significance differences in habit, citing the rhizome, which was not sympodial, but rather a stolon from which new growth emerges and an apical inflorescence forms. Triphoreae was originally circumscribed by

9 Dressler (1979) in which he segregated these taxa from Pogoniinae on the basis of the

fact that the three taxa of Triphoreae lacked a clearly incumbent anther, sinuous

epidermal cell walls, and an abcission layer between the ovary and perianth, all

characteristics observed in Pogoniinae. In this original description, Dressler included the

genera Monophyllorchis, Psilochilus, and Triphora. Dressler stated he believed that this tribe may be most closely related to the Orchidoideae, but pointed out that

Monophyllorchis and Psilochilus both have subsidiary cells, which are lacking in the orchidoid orchids, finally suggesting that Triphoreae were most likely related to or sister to Epidendroideae s.s, but did not state what characters he used to make this decision. In a reversal of this opinion Dressler (1981) later treated Triphoreae as an anomalous tribe of the Orchidoideae, arguing that the position of the anthers was not consistent with the epidendroid line of evolution. His position on this was later revised again, and by the

1993 publication he placed the tribe among the primitive orchids with a single fertile anther.

GASTRODIEAE- Lindley (1830-1840) treated Epipogium, Stereosandra and

Gastrodia as Arethuseae. As with the genus Aphyllorchis (Neottieae), Bentham placed

Stereosandra into the Diurideae on the basis of an erect or inclined anther and an abbreviated rostellum sometimes equivalent in length to the anther, and pollinia that were powdery or granular to semi-solid. At the rank of subdivision (subtribe), Schlechter, in his 1911-1914, treatment treated Gastrodieae to include Didymoplexis, Epipogium,

Gastrodia, and Auxopus. However by 1926, he revised this so that Gastrodieae only included Gastrodia and Didymoplexis, and the other taxa were moved to Epipogoneae, in

10 which he included Stereosandra. In the traditional sense, Gastrodieae has been a repository for those orchids without chlorophyll and having a single anther while lacking additional characters that could suggest other affinities. Dressler and Dodson (1960) placed Silvorchis into the Satryum alliance of the subtribe Coryciinae (Orchideae,

Orchidoideae) with question. Into the subtribe Epipogiinae (Orchideae, Orchidoideae) were placed Epipogium and Stereosandra based on a persistent anther and sectile pollinia with basal caudicles; Auxopus, Didymoplexis, Didymoplexiella, Gastrodia, and

Uleiorchis were put into the subtribe Gastrodiinae (Epidendreae).

NERVILIEAE- For much of its history, Nervilieae was considered either a

monogeneric tribe or Nervilia was subsumed into Pogonia or closely allied to it. In

Lindley (1830-1840), Nervilia aragoana (as Pogonia aragoana) was placed into the tribe

Arethuseae. Pfitzer (1891) placed Nervilia into the subtribe Pogoniinae. Schlechter

(1911-1914, 1926) used the subtribe Nerviliineae (Gastrodiinae), in which he placed

Nervilia, and in 1926, it was moved to Polychondreae. Dressler (1960) treated Nervilia as

Pogoniinae with Triphora, Psilochilus and Monophyllorchis. Brieger (1975) segregated

Triphora and Nervilia into Nervilinae (see Triphoreae for discussion). Dressler (1990)

raised Nervilia to the rank of tribe. Nervilia possesses a corm and similar floral

morphology to that of Arethuseae, which appeared to be a natural place for it.

OUTSTANDING TAXA- Authors have variously treated the outstanding taxa

Diceratostele, Palmorchis and Xerorchis. Palmorchis was originally described by

Rodrigues (1877). There are approximately 21 species currently recognized, found in

west central South America and Central America into the Isthmus of Tehuantepec,

between the Mexican states of Oaxaca and Veracruz (Salazar per com.). The only recent

treatment was by Schweinfurth and Correll (1940) in which they addressed nomenclature,

history of the genus and described the 6 known taxa. Palmorchis has traditionally been

difficult to place into a higher taxonomy. These orchids are terrestrial (except P.

imuyanensis, a terrestrial/marginal herb of ephemeral wetlands [Dodson and Romero

1993]) having reed-like stems, with broad plicate, spirally arranged or alternating leaves

resembling those of palm-seedlings. Each of these characters is plesiomorphic. The

flowers are often small, borne on short terminal or lateral inflorescences. Like many

terrestrial orchids they exhibit gregarious blooming. In appearance, Palmorchis

resembles Sobralia and Elleanthus (Sobralieae) or Diceratostele and at one time or

another, Palmorchis was attributed in part or as a whole to Sobralieae, or allied with

Diceratostele or Vanilla (Vanilloideae; Ames 1922; Dressler and Dodson 1960;

Freudenstein and Rasmussen 1999). With the exception of Vanilla, the other taxa are all

very similar in appearance and habit, which may be a plesiomorphic condition.

Palmorchis is similar to Vanilla in that each has a hard seed coat, something also seen in

Apostasioideae (Dressler 1993), thus suggesting that this trait is also convergently

derived. Palmorchis is not vanilloid based vegetative morphology and growth habit, and

differs also in a well developed, sculptured seed-coat, and the medial union of the lip with the column; molecular analyses support this conclusion as well (Cameron and Chase

2000). Exactly where it belongs has not been conclusively determined. Palmorchis can be

distinguished from the Apostasioid orchids on the basis of being monandrous and having

an incumbent anther. Dressler and Dodson (1960) moved Palmorchis into Sobraliinae where it was associated with Sobralia until 1993 (Dressler 1993) when it was placed into a monotypic tribe, Palmorchideae, of the Epidendroideae.

Diceratostele was originally described by Summerhayes (1938). In this work the author suggested that based on morphology and habit, this genus was most closely related to Palmorchis. This relationship was again argued by Dressler and Dodson (1960) in which Diceratostele, Palmorchis and Xerorchis were put in the Sobraliineae.

Diceratostele was considered sister to the rest of Sobralieae by Rasmussen and

Rasmussen (1979) but latter placed into the monogeneric Diceratosteleae

(Spiranthoideae) by Dressler (1990, 1993). As it is currently understood, Diceratostele is

a monspecific genus of the subtribe Diceratostelinae (Triphoreae) based on the results of

Cameron et al. (1999). It is found in the old world tropics, in western Africa from Liberia,

Ivory Coast, Gabon, Cameroon, and Congo.

Dressler (1981) placed Xerorchis in the Sobraliinae given similarity in floral

morphology (i.e. entire lip with a single linear callus on the labellum, column with apical

wings) because it also had eight (superposed) pollinia. By 1993, Dressler removed it and

placed it among a group of monandrous primitive orchids of unknown affinities. He

suggested that it may be related to Arethuseae or Epidendrae given its eight pollinia, but its terrestrial habit, the presence of persistent leaves, and seed type seem to suggest an affinity to Pogoniinae. Nearly all of these conditions are plesiomorphic, and therefore not of phylogenetic utility.

CURRENT CLASSIFICATIONS-Cladistic Morphological hypotheses-

Morphological synapomorphies for the epidendroid subfamily include a single incumbent anther (Freudenstein and Rasmussen 1999; Pridgeon et al. 1999), a type III stigma

(Dannenbaum et al. 1989), and distinct hard or firm pollinia (except some basal taxa).

Dressler (1993), while an influential work, was not cladistic; therefore any phylogenetic relationships presented were more or less speculative. One of the first substantial classifications based on a significant number of morphological characters was that of

Burns-Balogh and Funk (1986). While their study was founded in cladistic methodology, it is not clear that their taxonomy was based on that methodology. The basal epidendroid taxa (sensu Dressler 1993) were distributed between the orchidoid and epidendroid orchids of Dressler. The only cladistic morphological study to include any significant numbers of basal Epidendroideae was performed by Freudenstein and Rasmussen (1999).

Freudenstein and Rasmussen (1999) failed to resolve basal relationships among the primitive Epidendroideae, obtaining a basal polytomy in the consensus. Epidendroid taxa such as Triphora grouped with orchidoids and Palmorchis with vanilloids (Vanillioideae,

14 Cameron and Chase 2000, Cameron et al. 1999). Explanations given for their results were convergence or that many of these basal taxa possess more plesiomorphic character states relative to more advanced epidendroids, but given the data, neither of these explanations is testable.

Molecular hypotheses-The number of molecular analyses in systematics has increased in response to the diverse array of methods, the quality and quantity of readily available information, and the speed with which data can be obtained (Soltis and Soltis

1998). While molecular studies are helping to resolve many of the issues of orchid phylogeny, one perennial problem is that they, like morphology, have failed to resolve tribal relationships of the basal Epidendroideae. The most comprehensive molecular study containing a significant sampling of the subfamily used a single plastid locus, rbcL

(Cameron et al. 1999). In this study the authors found Nervilieae + Xerorchis to be sister to the whole of Epidendroideae, followed on successive branches by a clade of

Triphoreae + Diceratostele, then Tropidieae, Neottieae (+ Palmorchis), and finally

Sobralieae (these basal clades sister to the remaining Epidendroideae). However in the strict consensus the nodes collapse and relationships are unresolved. Chase et al. (2003) argued that the lack of resolution among these orchids is due to low sequence divergence, as indicated by the short branch lengths and low branch support. Perhaps this suggests a rapid evolutionary radiation as argued by the authors; nevertheless only one gene was used in this analysis, which assumes that the tree obtained from a single sequence can faithfully reflect the species tree.

15 The current molecular phylogenetic hypothesis of the orchids by Chase et al.

(2003; Fig.1.1) is based on a summary tree constructed from the results of molecular studies using the plastid (atpB, rbcL, matK, psaB, trnL-F intron and spacer), the nuclear

(26S rDNA), and the mitochondrial genomes. The summary tree shows Neottieae,

Sobralieae, Tropidieae, Triphoreae (Triphorinae and Diceratostelinae; see Pridgeon et al.

2005), Nervilieae, and Gastrodieae within the primitive Epidendroideae (Cameron et al.

1999, Chase et al. 2003). Most of the tribal level relationships among the basal

Epidendroideae are still unresolved, with the exception of Neottieae (including

Palmorchis) which is found at the base of the tree followed by a clade of Sobralieae and

Tropidieae, this sister to the rest of the Epidendroideae.

Goldman et al. (2001) included Xerorchis in their study of Arethuseae, where it was found unrelated to both this tribe and Sobralieae to which it was also suggested that it was related. In this study, Neottieae (Listera and Epipactis) were at the base of the

Epidendroideae, followed successively by Xerorchis and a clade of Sobralieae sister to

Tropidieae. As this study was not focusing on the basal Epidendroideae, their sampling of these taxa was limited. On the basis of the work by Cameron et al. (1999), Xerorchis was placed as a member of Nervilieae; also included in this tribe were Nervilia, Silvorchis and Stereosandra (the latter two not included in this study, but see Chase et al. 2003), and

Epipogium. Xerorchis shares with Nervilieae in this sense some aspects of floral morphology, but differs from it with respect to the habit; in Pridgeon et al. (2005) it was treated as a monotypic tribe, Xerorchideae, due to its unique morphology.

16 In many of these analyses, one or two exemplar species may have been included

in the phylogenetic analysis, acting as placeholders for tribes and even in some cases the whole of the diversity among the basal Epidendroideae. Additionally, even when sampling was improved, as in the case of Cameron’s (1999) rbcL analysis, the use of a

single locus, especially one which is uniparentally inherited, to infer phylogenetic

relationships may not be appropriate given the issues of using a single locus in

phylogenetic inference (Goodman et al. 1979, Olmstead and Sweere 1994, Pamilo and

Nei 1988).

17 Lindley (1830- Schlechter Genus Bentham (1881) Genus Genus 1840) (1926) Neottieae Neottia, Listera Neottieae Monandrae Vanilleae Sobralia, Sertifera Polychondreae Corymbis Corymbieae (Corymborkis), Listereae Listera, Neottia Cephalanthera, Tropidia Epipogium, Gastrodia, Arethuseae Limodorum, Nervilia Spirantheae Listera, Neottia, Cephalanthereae Aphyllorchis, Cephalanthera, Epipactis, aragoana (Pogonia Wullschlaegelia Limodorum aragoana), Triphora gentianoides (Pogonia Diruidaeae Aphyllorchis, Triphora, Psilochilus, Monophyllorchis, gentianoides), Psilochilus Stereosandra Vanillieae Xerorchis (Pogonia macrophylla), Sobralia Cephalanthera, Limodoreae Didymoplexis, Gastrodia Epipactis, Limodorum Gastrodieae

Corymborkis, Tropidia Tropidiinae

Epipogoneae Epipogium, Stereosandra 18

Sobralieae Elleanthus, Epilyna, Sertifera, Sobralia

Nervilieae Nervilia

Continued Table 1.1: Historical treatment of the genera of the primitive Epidendroideae used in this study.

Genus Cephalanthera, Aphyllorchis, Epipactis, Limodorum, Neottia/Listera, Palmorchis Elleanthus, Epilyna, Sertifera, Sobralia Corymborkis, Tropidia Triphora, Psilochilus, Diceratostele Monophyllorchis, Nervilia, Silvorchis, Stereosandra, Xerorchis Epipogium, Didymoplexis, Auxopus, Gastrodia, Didymoplexiella, Neoclemensia Wullschlaegelia

Neottieae Nervilieae Tropidieae Sobralieae Arethuseae (2003) Triphoreae Gastrodieae Chaseal. et Epidendroideae Genus Diceratostele Corymborkis, Tropidia Neottia, Aphyllorchis, Epipactis, Cephalanthera, Listera Limodorum, Palmorchis Triphora, Psilochilus, Vanilleae Monophyllorchis, Nervilia Didymoplexis, Auxopus, Didymoplexiella, Gastrodia, Neoclemensia , Silvorchis, Epipogium, Stereosandra, Wullschlaegelia Sobralia, Sertifera, Epilyna, Elleanthus Xerorchis

Nervilieae Triphoreae Gastrodieae Uncertain Diceratosteleae Neottieae Epidendreae 1 Dressler (1993) Dressler Tropidieae Spiranthoideae Epidendroideae Palmorchideae Genus Epipogium, Stereosandra Silvorchis Aphyllorchis, Cephalanthera, Epipactis, Limodorum Listera, Neottia Corymborkis, Tropidia Auxopus, Didymoplexis, Didymoplexiella, Uleiorchis Gastrodia, Monophyllorchis, Nervilia, Psilochilus, Triphora Diceratostele, Elleanthus, Palmorchis, Sobralia, Sertifera, Xerorchis Disinae Disinae Neottinae Neottinae Pogoniinae Pogoniinae Epipogiinae Epipogiinae Sobraliinae Dressler and Limodorinae Spiranthinae Gastrodiinae Dodson (1960) Dodson Continued Table 1.1 Neottieae Epidendreae

Neottieae + Palmorchis

Tropidieae

Sobralieae

Triphoreae Nervilieae Gastrodieae

Calypsoeae Malaxideae Dendrobiinae

Arethuseae Podochilinae Collabiinae

Epidendreae

Vandeae,

Cymbidieae

Figure. 1.1: Tree presented for the Epidendroideae redrawn from summary tree of Chase et al. (2003). Arrow indicates Orchidoideae, taxa in bold are in the scope of this study.

CHAPTER 2

TOWARDS A PHYLOGENETIC HYPOTHESIS OF THE BASAL

EPIDENDROIDEAE (ORCHIDACEAE) INFERRED FROM 3 LOCI AND 3

GENOMES.

INTRODUCTION

As a taxonomic unit, orchids have had a long history, dating back to the works of the Greek philosopher Theophrastus (ca. 370-285 BC), primarily the manuscript

“Enquiry into plants” (Reinikka 1995). All classical classifications were primarily based on medicinal use of the plants, a largely artificial method of classification. Numerous attempts to make a classification of the Orchidaceae and lower order relationships have been made since Lindley (1830-1840) first formulated a more natural classification. As more orchid species were discovered, more detailed classifications emerged, and associations changed, although relationships remained intuitive, based on a few key morphological or vegetative characters. Increasingly over the last century, systematists

21 have tried to establish a natural classification based on an understanding of historical phylogenetic patterns of relatedness between taxa. Three of the most recent comprehensive classifications of the orchids are based largely on intuitive schemes

(Dressler 1981, 1993, Szlatchetko 1995).

Orchid relationships at the level of the family have only recently been resolved with the use of cladistic methods (Cameron et al 1999). All of the current hypotheses of orchid relationships have failed to retrieve robust or even resolved phylogenetic relationships among the tribes of the basal Epidendroideae (Kores et al 1997, Cameron

1999, Freudenstein and Rasmussen 1999, Goldberg et al. 2001, Chase et al. 2003,

Freudenstein et al. 2004, Van den Berg et al. 2005). All were limited in both taxon sampling and locus sampling, relying instead on a few exemplars taxa to represent whole tribes or even the diversity of the basal Epidendroideae. Admittedly however, many of these were not focusing on lower order relationships within the Epidendroideae, especially many of the earliest.

Given the results of these studies it has been argued that the Epidendroideae may be the result of a rapid radiation as indicated by short internodes subtending clades and low branch support, such that resolving relationships may be nearly intractable (Chase et al 2003). However, given the significance of the basal epidendroids for understanding evolution of particular traits within the subfamily, there is a significant need for an improved understanding of relationships among the most primitive members of this the largest subfamily of orchids.

22 PURPOSE OF THIS STUDY- The purpose of any phylogenetic systematic study is to provide an hypothesis of historical relationships among the organisms being studied, and further provide a point from which to assess the evolution of particular characters of interest. With a robust hypothesis of evolutionary relationships among these orchids,

more fundamental evolutionary questions regarding the origin and evolution of the

Epidendroideae may be addressed. Using both a more comprehensive taxon and

increased locus sampling in a combined analysis, a phylogenetic hypothesis of

relationships among the basal Epidendroideae is presented here. For this study three loci

were used, the nuclear ITS1, ITS2 and 5.8S region, the plastid trnL-F and the one

mitochondrial marker, NADH dehydrogenase subunit 1 (nad1) intron between the B and

C exons (nad1b-c).

Achlorophyllous orchids are similar for many ecological or adaptive strategies and morphological features. For example, among orchids one observes floral convergences such as soft mealy pollen, short column, and fused perianth parts (Molvray et al. 2000) and reduction or absence in vegetative structures such as leaves and

associated structures. Such a reduced phenotype results in few or no phylogenetically

informative morphological characters that are unique homologies. As a consequence,

many of these taxa have traditionally been grouped together because they appear to share

many characters that are the result of convergence. One tribe, Gastrodieae, has

historically been the repository for many epidendroid taxa that lack chlorophyll (Dressler

1993) and also lack characters that point to other affinities. As part of this study, the

concept of Gastrodieae under both the Dressler (1993) and Chase et al. (2003)

classifications will be tested using a broader sample of taxa than previously included.

23 With reduced dependence on chlorophyll and increased mycoheterotrophy, it is expected that sequence evolution should increase as functional constraints on genomes decrease. This hypothesis is based on the results of numerous studies in which it was observed that achlorophyllous taxa exhibited a transversion bias relative to green sister taxa (eg. Nickrent and Starr 1994, Nickrent and Duff 1996). Orchids for at least some point in their life history are dependent upon fungi for carbon, and with the loss of chlorophyll, this relationship is expected to increase (Rasmussen 1995). Furthermore, the basal Epidendroideae have a large number of achlorophyllous or transitional taxa, consequently orchids are an excellent model for testing this hypothesis.

MATERIALS AND METHODS

MATERIALS-Taxon sampling- Where possible, two species of each genus were used as representatives of the tribe. Sampling was increased through field collections where possible and in collaboration with the DNA banks at Royal Botanical Gardens

Kew and the New York Botanical Garden. Additional sequences were obtained from

Genbank (Benson et al. 2006) and from colleagues at the University of Florida and the

Departamento de Botânica, Universidad de Campinas, Brazil.

Because of the scope and geographical distribution of the taxa in this study, fresh material was obtained with the help of researchers in Brazil, Ecuador, Panama, Mexico,

Cameroon, Australia, Singapore, and Japan. Fieldwork was performed throughout the

24 eastern United States in late July/August of 2001, Florida in June/July 2002, Panama and

central and northern Ecuador in June and July of 2003, and central and southern Ecuador

during December of 2005.

METHODS-DNA Extraction and Purification- Total DNA extraction from fresh

or silica dried material was performed using either the CTAB method of Doyle and Doyle

(1987) or DNeasy Plant Mini Kit (QIAGEN, Valencia, California, USA) for very small

quantities of tissue. These extractions were stored at –20°C. In some instances where

weak amplifications were seen further purification of the total DNA was performed using

the Elu-Quik DNA purification kit (Schleicher and Schuell, Keene, New Hampshire,

USA).

Amplification and Sequencing- All amplifications were performed initially using

standard PCR protocol methods as follows: 50 L reactions were prepared using 40L

HPLC water, 1 L of each of 10 M primer, 5 L buffer (100mM tris –HCL [pH 8.8], 35 mM MgCl2, and 250mM KCL), 0.5L of 0.20 M dNTPs, 0.5 L Taq polymerase, and

0.5L of 10 g/L of bovine serum albumen. Each reaction had between 1L to 2.5L of

template. For weak amplicons, a second round of amplification was performed in order to

increase overall yield.

In nearly all instances, the internal transcribed spacer region (ITS) was amplified

using the universal primer pairs of White et al. (1990, but also see Baldwin 1992 and

Baldwin et al. 1994), ITS 1 (5’TCCGTAGGTGAACCTGCGG3’) and ITS 4

(5’TCCTCCGCTTATTGATATGC3’). In those instances where amplifications yielded

messy or non-orchid sequences or multiple bands, a reamplifaction using a nested primer

approach was performed using the Sun et al. (1994) primers, 17SE and 26SE, followed

25 by a second round of PCR using ITS1 and ITS2; the Sun et al. (1994) primer pairs

preferentially amplify angiosperms, thus reducing the occurrence of secondary signals

due to other contaminating plant materials and the nested approach helps to increase the

yield when an initial reaction resulted in weak bands. ITS1 and ITS4 were used internally

for the second amplification and all sequencing. Amplification was performed under the

following PCR conditions: an initial denaturation step of 95°C for 5 min, followed by 35

cycles of 95°C for 1 min, 48/52°C for 2 min and 72°C for 2 min; a final 7 min extension

at 72°C was performed.

The primers of Taberlet (1991) were used in the amplification and sequencing of

trnL-F. These primers were “C” (5’ CGAAATCGGTAGACGCTACG 3’) and “F” (5’

ATTTGAACTGGTGACACGAG 3’); amplification was performed under the following

PCR conditions: an initial denaturation step of 96°C for 3 min, followed by 29 cycles of

96°C for 45s, 64°C for 45s and 72°C for 2 min.; a final 5 min extension at 72°C.

Even though the nad1bc mitochondrial locus is highly conserved, it was chosen

rather than any of the more extensively studied chloroplast or nuclear loci because of the

inaccessibility of chloroplast genes in achlorophyllous orchids. Secondly, nad1bc is

relatively easy to align. However, being a Type II intron, it is variable in length

(Freudenstein et al. 1998, Freudenstein and Chase 2001, and Kelchner 2002) making it

ideal for the use of indels in a phylogenetic study. For the mitochondrial nad1b-c intron, the primers nad1B (5’ GCATTACGATCTGCAGCTCA 3’) and nad1C

(5’ GGAGCTCGATT AGTTTCTGC 3’) were used (Demesure et al. 1995). Because of the large indels and extreme sequence length variation the nadM primer

(5’ GGTGACAGATCGGCCAT AGG 3’) was used internally in order to obtain

26 complete sequences (Freudenstein and Chase 2001). PCR conditions were as follows: an

initial denaturation step of 94°C for 4 min, followed by 34 cycles of 92°C for 45s, 52°C

for 45s and 72°C for 2 min; a final 5 min extension at 72°C was performed.

PCR products were quantified visually using an agarose gel. Products were

cleaned using the Wizard PCR Prep DNA Purification system (Promega Corporation,

Madison, Wisconsin, USA), Ampure (Agencourt Bioscience Corporation, Beverly,

Maine, USA), or 50 L of 20% polyethylene glycol–2.5 M NaCl and sequenced directly using the amplification primers. Sequencing reactions were performed using BigDye

Terminator v3.1 chemistry (Applied Biosystems, Foster City, California, USA) in 5 L

reactions: 3.32L distilled water, 0.025L DMSO, 1L Big Dye, and 1L ABI buffer.

These were combined into a master mix and aliquoted at 4.5 L to which 0.5L of the

PCR product was added. The following cycle sequencing protocol was followed: initial denaturation step of 96°C for 1min, followed by 24 cycles of 96°C for 10s, 50°C for 5s and extension phase at 60°C for 4min. Sequences were cleaned using ethanol purification, Sephadex (Sigma-Aldrich, St. Louis, MO USA.) spin columns or Cleanseq

(Agencourt Bioscience Corporation, Beverly, Maine, USA). All reactions were run on an

ABI Prism 3100 automated sequencer (PE Biosystems, Foster City, California, USA).

Alignment - Contigs were assembled using Sequencher 3.1.1 (Gene Codes, Ann

Arbor, Michigan, USA) and aligned using Clustal X (Thompson et al., 1994). In Clustal

X, an initial gap opening /extension costs of 6/3 (ITS), 6/4 (trnL-F and nad1bc) was applied in order to estimate alignments. Being a type II intron, nad1 is generally easy to align regardless of the gap costs assigned. This is true at least for the 5’ region of the locus, however there is considerable sequence length variation between taxa. This is due

27 to the presence of several hairpin loop regions in which there are a number of indel

events making it difficult to align using the algorithms implemented in programs

currently in use. It is well known that Clustal X does not perform well in regions with

large numbers of gaps, therefore for all loci, the Clustal alignments were manually adjusted using the program Se-Al v 2.0.11 (Rambaut, 1996).

Outgroup Choice- Based on previous studies of the Orchidaceae, the

Epidendroideae are monophyletic, and included all the genera designated as

Epidendroideae in this study. Therefore based on these previous results, representatives

from across the Orchidoideae were chosen to serve as outgroups thereby rooting the tree

by outgroup comparison; this provides the best method for establishing polarity and

ancestor descendent relationships.

Gap Coding- given the sequence length variation observed in nad1bc and trnL-F,

gaps were coded for these two loci and included in the analysis. Gaps were coded using

the simple gap coding method of Simmons and Ochoterena (2000) as implemented in

SeqState (Müller 2005).

Parsimony- Cladistic phylogenetic analyses were performed on each dataset and

the combined data using cladistic methodology in a parsimony framework. Parsimony

analysis was implemented in the program PAUP* version 4.0b.10 (Swofford, 2002). Data

sets were combined in 4 different searches, ITS + trnL-F, ITS + nad1bc, trnl-F+ nad1,

and all three together. This was done to explore which if any of the datasets may be

contributing the most signal and thus is providing the hierarchy observed in the combined

tree. The following approach was taken for all searches; an initial heuristic search was

28 performed on 1000 random taxon addition replicates using TBR, with settings to hold

two trees per random addition sequence, saving only two trees, multrees in effect, and

swapping on best trees only. The best trees from this search were used as starting trees

for a second, exhaustive heuristic search in order to search the tree space as thoroughly as

possible.

Maximum Likelihood- Model-based methods are advocated as a means to

integrate knowledge regarding the processes of evolution including transition to

transversion ratios, base frequency, etc. Maximum likelihood was performed and

implement in PAUP*. A parsimony heuristic search was used following the above

methods to obtain an initial starting tree. From this starting parsimony tree, likelihood

parameters were estimated from the data in order to determine the best substitution model

for the analysis. The estimated values were then applied, and a maximum likelihood

heuristic search was performed using the same search settings as in the parsimony search.

Branch Support- Following the jackknife search parameter recommendations by

Freudenstein et al. (2003), branch support was evaluated on all trees using jackknife as performed in PAUP* set to run 5000 jackknife replicate iterations and with 1 addition

sequence replicate in each. Two random addition sequences per replication were used,

saving only two trees per random addition sequence, and tree bisection reconnection

(TBR) branch swapping was employed for all analyses with Multrees in effect, and

swapping on best trees only. With regards to the maximum likelihood analysis, a jackknife search was performed with settings as in the parsimony jackknife, and let run for 1 week; during this time it performed 20 jackknife replicates.

In subsequent discussions of the results, support for the data was considered weak from 50% jackknife support to 70%; strong support ranged from 71%-85%, and very strong 86-100%. No support was considered for anything less then 50%. These values are not significant in terms other than to provide a method for discussion.

RESULTS

ITS PARTITION-the ITS region is a commonly used locus for phylogenetic inference given its high copy number and relative range of phylogenetic utility (Soltis and Soltis 1998). The ITS matrix of 64 taxa and 900 molecular characters (see Appendix

A.1) was submitted for a parsimony heuristic search. Characters were excluded based on the relative amount (i.e. >50%) of missing data for the character position, or regions determined to be so variable that homology assessment was not possible; on this basis I excluded 281 (31%) characters from the analysis leaving 619 positions, and 400 parsimony informative sites. The analysis returned 3 most parsimonious trees (MPTs) of length 2307 (CI=0.412, RI=0.649). A strict consensus was calculated in order to summarize all the MPTs. (Fig. 2.1). The strict consensus was well resolved with a considerable amount of structure, but failed to receive strong support for tribal level relationships, however the monophyly of each of the tribes was supported. Palmorchis and Neottieae were found successively branching at the base of the tree sister to the remaining Epidendroideae. As the next clade to branch, Epipogium united with

30 Triphoreae and this clade sister to Sobralieae followed on successive branches by

Wullschlaegelia, Nervilieae+ Didymoplexis+ Xerorchis +Diceratostele, Tropidieae and the advanced Epidendroideae.

A phylogram showing branch lengths was calculated (Figs. 2.2). Many of the branches are short, with 42 changes between the Orchidoideae and Epidendroideae.

Comparatively, some taxa were observed to be subtended by long branches, so in order to test whether these were due to the effects of long branch attraction, a series of experiments were performed in which taxa appearing on long branches were systematically removed and the analyses repeated (Siddall and Whiting 1999). The clade of Triphoreae and Epipogium is subtended by a long branch, with each taxon also on long branches (Fig. 2.2); given that this relationship is an unexpected finding, Epipogium was deactivated and dataset reanalyzed. This returned 15 trees of length 2169 steps

(CI=0.430, RI =0.665). The resulting topology of the strict consensus (not shown) found

Triphoreae sister to Wullschlaegelia, and with the exception of a loss in structure, it was otherwise unremarkable. Therefore this does not appear to be a case of long branch attraction. On successive branches, Palmorchis and Neottieae were still observed sister to the remaining Epidendroideae with remaining tribes forming a polytomy. Triphoreae

(including T. amazonica) was deactivated and Epipogium reactivated. This resulted in eight trees of 2199 steps (CI=0.416, RI= 0.660). In the strict consensus (not shown), both

Epipogium and Sobralieae were in a basal polytomy sister to the rest of the

Epidendroideae including Neottieae and Palmorchis. Based on the results of these experimental manipulations, the relationship of Epipogium to Triphoreae does not appear to be a case of long branch attraction.

Another set of manipulations was performed looking at the effects of

Didymoplexis pallens and Xerorchis amazonica; the branch subtending this clade is

relatively long compared to other clades (Fig. 2.2b) and receiving moderately weak

support in the jackknife analysis (69%). The deactivation of Didymoplexis resulted in the

retention of 1 MPT of 2189 steps (CI= 0.417, RI=0.661). The topology of this tree was

unaffected when compared to the strict consensus of the complete data set, as such this

does not appear to be a case of long branch attraction.

TRNL-F PARTITION- Numerous attempts were made to amplify the plastid trnL-

F region from species of Gastrodia, Epipogium and other achlorophyllous epidendroid

taxa but without success. A trnL-F sequence from Wullschlaegelia was obtained by

Molvray et al. (M.Chase pers. com) and was initially included in this study but regarded with optimistic skepticism given the numerous unsuccessful attempts to amplify it for both W. aphylla and W. calcarata, as well as the overall difficulty in obtaining plastid

sequences from achlorophyllous orchids (Cameron et al. 1999, Cameron 2001, Goldman

et al 2001). The resulting strict consensus (not presented) of the heuristic search found a

very well supported (89%) relationship of Wullschlaegelia sister to Corallorhiza

(Calypsoeae). Based on the results of a study using the plastid matK locus, others have

suggested a relationship of the Wullschlaegelia with Aplectrum and Govenia in

Calyposeae (see Freudenstein et al. 2004) but this is regarded as not likely given the lack of morphological synapomorphies to support such a group. Arguably a morphological

synapomorphy is not needed to validate the results of a molecular study, however, in

conjunction with the difficulty in obtaining chloroplast loci for achlorophyllous orchids,

and the numerous attempts to amplify this genus using different optimizations and

protocols, this sequence was removed from all subsequent analyses of this locus.

With the removal of the accession of Wullschlaegelia, the matrix (Appendix A.2) consisted of 53 taxa. During the alignment process, it was observed that there were indels that may have phylogenetic utility; therefore gaps were coded using simple gap coding.

An analysis with and without gaps was conducted. Including gaps in the analysis increased consistency and retention index values as well as improved resolution and increased support for clades. The parsimony heuristic search of trnL-F including gaps

(1326 characters) resulted in 32 MPTs being retained of length 1495 (CI= 0.78, RI=

0.714). There were 400 invariant characters, and 466 parsimony informative characters

(35%). Since the analysis returned multiple MPTs, a strict consensus was calculated in order to summarize the results (Fig. 2.3). In general, there was good resolution for most tribal level relationships. While support for each of the tribes was observed, with some exceptions tribal level relationships were unsupported. The Epidendroideae receives very good support. The first clades to branch off within the Epidendroideae are a clade containing Palmorchis sister to Neottieae with weak support (66%), this sister to the remaining Epidendroids with weak support. Neottieae sensu stricto are resolved as monophyletic with weak support. Among the remaining Epidendroid taxa, Triphoreae

(100%) and a clade of Tropidia + Xerorchis (without support) form a polytomy followed by a clade of the advanced epidendroid outgroups (55%) and Sobralieae, Nervilia

and Diceratostele gabonensis. In order to determine which taxa are in conflict, an Adams

consensus was also calculated; the topology agreed with that of the strict consensus, but

resolved Sobralieae (Fig. 2.4), which received very good support (76%) in the jackknife

analysis.

NAD1BC PARTITION- Being a type II intron, the nad1 locus is highly conserved,

and easily aligned sequence with the exception of a number of variable sized gaps

primarily located in loop regions. Analyses of DNA sequence data with and without gaps

coded as simple gap characters were performed. The resulting consensus tree of the

sequence characters without gaps (not shown) resolved the Epidendroideae, but generally failed to resolve any of the lower order relationships.

Previous studies have suggested the utility of gaps for phylogenetic analysis in

orchids (Freudenstein et al. 1998, Freudenstein and Chase 2001). In order to test the

utility of nad1 gap characters at this level, simple gap characters were coded using

SeqState (Müller 2005). The output matrix was imported into PAUP*, and executed

implementing parsimony. Both matrices, without gaps and with gaps, were submitted for analysis. The results of the search without gaps (not presented) returned an unstructured tree in which the Epidendroideae was resolved, however internal relationships were not.

The matrix (Appendix A.3) consisted of 58 taxa for 2602 characters (710 characters or

27% of the matrix was parsimony informative) consisting of both sequence (1480, 57%) and gap characters (1122, 43%) was submitted for heuristic analysis. This returned 800

34 trees that were subsequently filtered using “best trees”; this resulted in 640 MPTs being

retained of length 3236 (CI=0.735, RI= 0.536). Strict and Adams consensus trees were

calculated (Fig. 2.5 and Fig. 2.6).

The strict consensus returned a very highly resolved topology however there is

little jackknife support for any of the relationships (Fig. 2.5). The Epidendroideae is

supported with 100% jackknife support. Neottieae and Palmorchis form a clade at the base of the Epidendroideae with Palmorchis sister to Neottieae s.s. This clade is sister to the remaining Epidendroideae in which a clade of the advanced Epidendroids (50%) is next to branch, sister a polytomy of Tropidieae (57%), Triphoreae, Sobralieae (including

Nervilia plicata) and a clade of Xerorchis amazonica + Diceratostele gabonensis sister to

Gastrodieae (including Epipogium aphyllum and Nervilia shirensis with very good

support). The Adams topology differed from that of the strict consensus in uniting

Triphoreae and Sobralieae, but was otherwise identical (Fig. 2.6).

PARSIMONY COMBINED ANALYSIS- The combined analysis included three loci

(trnL-F, ITS, and nad1) and two gap partitions (trnL-F and nad1). The matrix (Appendix

A.4) was constructed with 43 taxa and 4828 characters consisting of 1686 (35%) variable

parsimony uninformative characters, 1659 (32%) constant and 1202 (26.4%) parsimony

informative characters. Eight trees were retained of 5452 steps (CI=0.66, RI= 0.553).

Both a strict and an Adams consensus were calculated; the topologies did not differ,

therefore the strict consensus is presented for discussion (Fig. 2.7). The resulting

topology was fairly well resolved, with each of the tribes receiving some support.

Palmorchis was sister to Neottieae; these were sister to the remaining tribes with weak

support. Triphoreae formed a clade with Epipogium. Tropidieae and Sobralieae form a

clade, this a part of a polytomy with the advanced Epidendroideae, and a weakly

supported clade of Nervilia + Diceratostele sister to Didymoplexis + Xerorchis.

In order to explore which data partition may be influencing the topology of the

combined analysis, three analyses were conducted looking at each of the data partitions in

combination with one of the other datasets. The ITS +trnL-F+ gaps combined dataset

(results not presented) returned a highly structured strict consensus tree with high support

for the all the tribes except Triphoreae. Palmorchis and Neottieae branched successively

as the first two clades at the base of the Epidendroideae. An unsupported Triphoreae is

pulled down sister to Palmorchis. This is sister to the remaining taxa, which form an unresolved polytomy of Nervilieae (including Diceratostele, Xerorchis and

Didymoplexis), Sobralieae (including Epipogium unsupported) and a clade of Tropidieae

and the advanced epidendroids.

The combined trnL-F +gaps and nad1+gaps analysis retrieved a supported

Epidendroideae, however there was a lack of tribal level resolution within the

Epidendroideae. This analysis recovered Palmorchis sister to Neottieae with weak

support (75%). The results of the nad1+gaps and ITS analysis returned Palmorchis and

Neottieae successively branching at the base of the Epidendroideae. Sobralieae was

recovered, as was Tropidieae and the advanced Epidendroideae. However the

relationships between these tribes and the remaining taxa remained unresolved.

36 A Partition Homogeneity Test (Swofford 1995; also ILD sensu Farris et al. 1994) was performed using parsimony to measure the amount of incongruence in the individual partitions in the combined analysis. This was performed in PAUP* using 100 partition homogeneity replicates; the results indicated considerable incongruence between the data partitions (P=0.01).

In the combined parsimony analysis, Gastrodia procera is observed uniting with

Palmorchis, which was seen only in the ITS analysis. Even though there are two complete sequences represented in the combined matrix (ITS and nad1 +gaps) for

Gastrodia, the suggestion is that the position of Gastrodia procera may be greatly influenced by the ITS dataset. When analyzed with the other taxa in the nad1 partition analysis, G. procera comes out within Nervilieae sister to G. sesamoides. In order to see whether the position of G. procera in the combined analysis was an artifact of the ITS partition influencing the placement of this genus, two manipulations were performed on the dataset. The nad1 dataset was the only locus for which there were four additional accessions of Gastrodia (Fig. 2.5-2.6). These accessions were included and missing data were added for the other two outstanding loci. With Epipogium uniting with Triphoreae, an ITS sequence of Epipogium roseum was added in order to improve sampling within the genus. In addition an ITS sequence of Wullschlaegelia aphylla was included because of its importance (either Gastrodieae sensu Dressler [1993], or Arethuseae sensu Chase et al. [2003]) in more fully understanding what are the relationships among the basal epidendroids.

37 A matrix of 49 taxa was created and the analysis was rerun including all taxa.

This returned two MPTs L= 5903, CI=0.651 RI=0.540; the Adams consensus did not differ from the strict consensus (results not presented). Gastrodia was found to be polyphyletic, Gastrodia sp. ER214, G. seamoides, and G. confusa united with G. procera in Palmorchis as in the ITS analysis. Gastrodia zeylanica, on the other hand, was seen in a position consistent with that seen in the nad1 analysis, sister to Didymoplexis (91% jackknife) in Nervilieae. To determine whether or not G. procera was influencing these results, it was removed from the analysis and the analysis was rerun. The removal of G. procera produced the expected results, Gastrodia species reuniting with Gastrodia zeylanica in Nervilieae (not presented). The relationships of the remaining taxa also differed between the two manipulations with and without G. procera. The inclusion of all taxa produced a more resolved topology, but when G. procera was removed, Triphoreae comes out in a polytomy with Neottieae and Palmorchis, which also fail to unite. In both analyses Epipogium species are sister to the whole of the Epidendroideae. When analyzed with all taxa, Palmorchis was sister to Neottieae followed on successive branches by

Triphoreae, Sobralieae, Tropidieae, and Nervilieae sister to the advanced epidendroids.

Wullschlaegelia, in both analyses, was sister to the advanced epidendroids orchids.

As a result of the loss of resolution observed when G. procera was removed it was of interest to determine what could cause Triphoreae to fall back to an equivocal position in this second analysis. The ITS sequence of Triphora amazonica was considerably more divergent than the other sequences within the genus, and in the ITS analysis it came out with Palmorchis and Gastrodia procera. While this relationship failed to be retrieved in any other analysis, this conflict could influence both support and

38 resolution of this combined analysis, resulting in the position of Triphoreae being unresolved. In order to test this hypothesis, using the dataset with both G. procera and

Triphora amazonica deactivated, the analysis was rerun. The resulting topology (Fig. 2.8) is presented as a strict consensus of 6MPTs of 5570 steps (CI=0.663 RI= 0.546). With the removal of both G. procera and T. amazonica, both with conflicting ITS sequences,

Palmorchis and Neottieae are recovered as sister groups with strong support, these sister to the remaining Epidendroideae. The next clade was Tropidieae followed by a pair of sister clades: Triphoreae (including Epipogium) and Sobralieae, and Nervilieae (including

Gastrodieae) and Wullschlaegelia and the advanced epidendroids.

MAXIMUM LIKELIHOOD COMBINED ANALYSIS- Due to the methodological and technical limitations of applying this optimality criterion, gap characters were excluded (1466 characters from trnL-F and nad1). The matrix (Appendix A.4) contained

3081 characters from three data partitions (ITS, trnL-F and nad1). The parameters were estimated as follows: two substitution types; TI:TV =0.96732; nucleotide frequencies estimated as A=0.26931, C= 0.22914, G=0.23322, T=0.26833; Shape (alpha)=0.5; 4 rate categories. From these values, a model of HYK85+G+I was selected, and a maximum likelihood heuristic search was performed. This analysis resulted in a single ML tree (Fig.

2.9). The resulting topology was highly structured with good support for most clades, and agreed in principle with the combined parsimony analysis regarding tribal level composition.

In order to compare topologies without G. procera and T. amazonica to those obtained using parsimony, an ML analysis was performed using the same matrix prepared to test the effects of these taxa on topology reconstruction using parsimony.

39 Given the observed effects in parsimony, the analysis was performed with both taxa removed. An initial parsimony search was performed from which from the following ML parameters were estimated: two substitution types, TI:TV= 0.984639, nucleotide frequencies estimated as A= 0.26650, C= 0.22982, G= 0.23482, T= 0.26886, Shape

(alpha)= 0.5, and four rate categories. These values correspond to a model of HYK85+G.

Using these model parameters a maximum likelihood heuristic search was run. The analysis was run for six days, during which time 48 replicates were performed. The topology (Fig. 2.10) is identical to the one obtained using whole dataset, with two notable exceptions. The four Gastrodia accessions are found in clade sister to Nervilieae

(including Diceratostele) and Wullschlaegelia branched off after Tropidieae and the advanced Epidendroideae, subtending the clade of Nervilieae, Triphoreae, and

Sobralieae. Likelihood jackknife scores were not calculated due to time limitations for computer access.

DISCUSSION

There have been a number of recent molecular studies of the orchid family, subfamily and tribes that have included members of the basal Epidendroideae (Cameron et al. 1999, Goldman et al. 2001, Freudenstein et al. 2004, Van den Berg et al. 2005).

Some authors, particularly those using morphology alone, placed some of the taxa used in the current study in either Orchidoideae or in their own subfamilies (see Chapter 1, but also Dressler 1981, 1993, Szlachetko 1995, Szlachetko and Rutkowski 2000). Based on the results of the current study, the Epidendroideae (sensu Chase et al. 2003) is strongly supported. This is the first study of the Epidendroideae in which there is a significant

40 improvement in taxon sampling of the primitive grade of orchids at the base of this

subfamily. Furthermore, sample choice greatly influences the patterns of relationships,

such that poor sampling increases the probability of obtaining spurious relationships due

to unrelated taxa being coded as homologous for the same character. Within the

Epidendroideae, it is apparent that the results of the parsimony combined analysis support a more defensible hypothesis of relationships. This study supports many of the tribes as outlined by Dressler and confirms the results of previous authors that Tropidieae and

Diceratostele belong in the Epidendroideae (Cameron et al.1999, and Chase 2003), however the monophyly of Gastrodieae is questioned.

CONFLICTING SIGNALS USING DIFFERENT OPTIMALITY CRITERIA- The

parsimony combined analysis found Gastrodia procera nested within Palmorchis.

Removing it caused Triphoreae to become polyphyletic, with Triphora amazonica

uniting with Palmorchis. The only other instance these relationships were observed was

in the ITS analysis. The implications are that the ITS sequences for these two taxa are

contributing conflicting signals, but at least for T. amazonica there is additional signal

which unites it with the rest of Triphoreae in the parsimony combined analysis. Although

the ML analyses with and without T. amazonica and G. procera did not differ greatly in

the overall topologies returned, the removal of these taxa resulted in some very

interesting changes in the parsimony topology. There is topological agreement between

the two methods when these taxa are removed. Both retain a clade of Triphoreae

(including Epipogium) sister to Sobralieae, and a clade of Nervilieae, Diceratostele

gabonensis, Xerorchis amazonica, and Gastrodieae. Furthermore, Palmorchis and

41 Neottieae are both at the base of the Epidendroideae either with Palmorchis the first to branch off, or sister to Neottieae and this clade the first to branch; but as in previous analyses in this study, the relationships of these taxa to each other are as yet not clear.

The only major difference between the two topologies using the different optimality criteria is the placement of the advanced Epidendroideae. In previous studies,

Tropidieae and Sobralieae have been seen at the base of the Epidendroideae branching off after Neottieae (Chase et al. 2003). However, when T. amazonica and G. procera are included, Triphoreae (including T. amazonica) is found branching after Neottieae, something not previously suggested, and not found in any other analysis in this study except ITS. When Triphora amazonica and Gastrodia procera are removed, Tropidia is again seen in this at the base of the tree branching after Neottieae. In the parsimony analysis, after Tropidieae, Wullschlaegelia unites with the advanced Epidendroideae this sister to a clade of Nervilieae and Gastrodieae, however, there is no clear reason to support Tropidieae sister to the advanced epidendroid orchids, near the base of the tree as observed in the ML analysis. While this manipulation added more taxa, it included more missing data, which can affect topologies in ways similar to poor taxon sampling resulting in spurious associations from long branch attraction (see Wiens 1998). Given these results, there is nothing to suggest this is the case. The analysis including both

Triphora amazonica and Gastrodia procera is more complete for the loci used and will be the results discussed from this point forward. It must be pointed out however that further study is warranted given these results, especially focusing on improving locus sampling.

42 TOPOLOGY –One issue with topology reconstruction using combined data is whether any single data partition is having a greater influence on the topology than the other partitions. The results of the experimental analysis looking at different partition combinations found that other than the instance of Triphoreae uniting with Palmorchis in

the analysis of ITS + trnL-F(+ gaps), there were no groupings of relationships not supported by another analysis and returned in the combined analysis, therefore, the combined parsimony analysis does not appear to be influenced by any single data partition. In addition, these results suggest that ITS and trnL-F may have greater phylogenetic signal at the level of the tribe when combined than nad1, which when included reduced the resolution.

Topological congruence between trees obtained from independent data partitions and using different optimality criteria is often touted as evidence for the “truth” of relationships which are not otherwise supported using traditional support measures

(Kelchner 2006). Proponents of the total evidence approach argue that the tree obtained from multiple independent partitions obtained from different loci and different genomes is more indicative of the phylogeny of the taxa then any one partition might be

(Grandcolas et al.2001, Kluge 1989, 2004, Kluge and Wolfe 1993). In recent years there has been extensive discussion regarding the use of multiple genes in phylogeny reconstruction (e.g. Goodman et al. 1979, Olmstead and Sweere 1994, Pamilo and Nei

1988). These discussions have focused on instances where there is topological incongruence between gene trees and species trees, which may arise if different genomes and individual genes have different evolutionary rates or histories as consequences of lineage sorting, introgression or modes of inheritance (Wendel and Doyle 1998). By

43 using multiple independent genes in a combined analysis in a total evidence approach

(Grandcolas et al.2001, Kluge 1989, 2004, Kluge and Wolfe 1993), the processes that

affect single genes are outweighed by the collective information content of the combined

data set allowing secondary signal to interact in tree construction. In addition, Wenzel and Siddall (1999) argued that homology is additive whereas homoplasy is averaged when datasets are combined, consequently combining datasets should improve phylogenetic signal and provide better evidence for relationships. The total evidence philosophy is the one taken in this study.

Moreover there is a considerable amount of homoplasy in the dataset as indicated by the low CI values and the results of the partion homogeneity test. It is important to clarify that this does not mean that these datasets are not combinable, the combined data or total evidence philosophy is that different processes drive evolution in each partition of the matrix, therefore different trees can be returned by each partition when analyzed separately. As parsimony methods are interested in the shortest tree given the data, and as homoplasy tends to add length to a branch, preserving the pattern is preferred over throwing out data. By combining data, secondary signal may be revealed which is not affected by independent processes and histories, and therefore may reflect the species tree.

In this study, all of the analyses returned resolved topologies with support for tribes, but lacked support (>50%) for tribal level relationships at deeper nodes. An assessment of support is desirable to some as it is a measure of the confidence of a clade given the data, but support values, regardless of support measure, are not a measure of the

“truth” of any given results so much as a measure of the relative support of the clade

44 given the dataset. The choice of using Jackknife rather than other measures of support such as Bootstrap or Bremer support (Bremer Decay Index) is because it minimizes the effects of invariant and phylogenetically uninformative positions by assigning a probability of 1/e (i.e. 37% deletion) of being excluded; therefore using this approach a fraction of the matrix is resampled with each replicate and any character has an assigned probability of being included (63%) in the jackknife matrix. PAUP* was set at 37% deletion in using the ‘‘emulate Jac’’ command; this is consistent with the sampling strategy of Farris et al. (1996) in which a each character has a probability of 1/e to be included in the jackknife matrix. Support is often low in data sets with high levels of homoplasy. The fact that we obtained well-resolved topologies with low CI values, but relatively higher RI values indicates that many of the nodes are supported by homoplasious characters.

The topologies of the trees have some agreement regarding tribal level relationships with much of the conflict between the topologies from the placement of clades with low jackknife support. Many of these are clades with achlorophyllous taxa which are lacking for chloroplast markers in this analysis and are thought to have higher divergence rates as indicated by higher frequency of indel events or a TI:TV bias (see discussion below). For the remainder of the discussion, the total evidence combined trees will be evaluated, particularly the parsimony tree (Fig. 2.7) as this methodology presents the most testable hypothesis of relationships as it assumes the fewest ad hoc hypotheses of homoplasy.

45 While the position of Palmorchis is not as yet unequivocal, it is clearly found at the base of the Epidendroideae in all analyses with Neottieae s.s. and these are sister to the rest of the Epidendroideae with good support. On successive branches at the base of the Epidendroideae, Palmorchis (Palmorchideae sensu Dressler 1993) is followed by

Neottieae, each clade very well supported; the relationship between these two groups

fails to receive support in the parsimony analysis but does receive high support in the ML

analysis as sister taxa. On the basis of these findings, I propose to maintain Neottieae to

include Palmorchis (sensu Chase et al. 2003).

A basal position of Sobralieae sister to Tropidieae and branching after Neottieae

had been suggested by Cameron (1999, but also see Chase et al. 2003). The relationships

among the other tribes of the basal Epidendroideae failed to resolve in the strict

consensus. In the current study, after Neottieae, the next clade observed is Epipogium

sister to Triphoreae. Although the position of this clade fails to receive support in the

parsimony analysis, the relationship of these two taxa to each other is observed in both

the combined parsimony and ML analyses, the latter with jackknife support of 76%.

Triphoreae observed at or near the base of the Epidendroideae is not a new observation

among molecular phylogenies of these orchids. Cameron (1999) found Triphoreae

(including Diceratostele) in a grade with Nervilieae at the base of the Epidendroideae

sister to everything including Neottieae. However, this, like most of the relationships

among the basal Epidendroideae, failed to receive support and was not recovered in the

strict consensus. Dressler (1993) stated that Triphoreae was superficially similar to

Neottieae in the flower and that Cephalanthera in particular resembled Triphoreae in the

46 column. Cephalanthera (Rasmussen 1982), Triphora, and Psilochilus (see Fig. 3.2) each possesses recurved anther locules and rather prominent apical beaks on the anther.

Of the remaining three tribes, the clade of Nervilieae + Diceratostele and

Xerorchis + Didymoplexis forms a polytomy with the advanced Epidendroideae and a clade of Sobralieae and Tropideae (Fig. 2.7). Morphologically, Nervilieae could easily be justified in a position near Triphoreae at the base of the tree. Nervilia and Triphora have at times been associated due to similar flower morphology and for much of their history

Triphora, Psilochilus and Nervilia have been included together (Chapter 1, Table 1.1).

In this analysis Gastrodieae were observed to be polyphyletic, with Gastrodia

procera uniting with Palmorchis (this being the result of influence from the ITS

partition) and Didymoplexis pallens in Nervilieae. In the morphological analysis of

Freudenstein and Rasmussen (1999), Nervilia and Gastrodieae were united, and Chase et

al. (2003) moved Epipogium, Stereosandra and Silvorchis to Nervilieae. In the current

study when all Gastrodia accessions were included, with the exception of Gastrodia

zeylanica, the species were pulled down to a position sister to Palmorchis, consistent

with the observation of ITS and the combined analysis. Gastrodia zeylanica came out

among Nervilieae sister to Didymoplexis pallens in the clade of Xerorchis. Removal of

Gastrodia procera (Fig. 2.8) moves all the Gastrodia together in a polytomy with

Didymoplexis pallens, this sister to Xerorchis, which is consistent with the results

obtained from the nad1 analysis. However based on these results and previous findings, it

appears that there is a close relationship between these tribes. My results do not clarify

47 the question of relationships between Nervilieae and Gastrodieae with any certainty, as

there is low support for this clade as well as a large amount of missing data for Gastrodia

(2 of three loci, but with better sampling within Nervilieae and Gastrodieae using more

taxa and additional loci, a more robust hypothesis among these orchids can be presented.

In both of the combined analyses (Fig. 2.7 and Fig. 2.9), Tropidieae was observed

either sister to or in an equivocal association with the advanced Epidendroideae in a

position very near Sobralieae. Morphologically, Sobralieae and Tropidieae share derived

features such as reed-stem habit and large fibrous plicate leaves, characteristics observed

in a few other taxa among the basal epidendroids such as Xerorchis and Diceratostele

(Nervilieae). Based on characters such as these as well as having eight firm pollinia,

Dressler included Sobralieae among with the more derived taxa in the so-called reed-stem

epidendroid Phylad. Tropidia and Corymborkis both have hamular stipes, which is a trait not observed in other basal taxa, but found in more advanced epidendroids. Sobralieae and Tropidieae are observed as sister groups in the parsimony analysis, consistent with the observations of Chase et al. (2003) however they are in disagreement regarding their position within the Epidendroideae, and given the presence of derived traits found in the advanced epidendroids, these results support a position closer to the more derived taxa.

TRIBAL COMPOSITION –In Dressler’s taxonomy (1993; also see Chapter 1 table

1.1), the tribe consisted of Neottia, Listera, Aphyllorchis, Cephalanthera, Epipactis, and

Limodorum. Chase et al. (2003) tentatively placed Palmorchis in Neottieae on the basis

of molecular work by Cameron et al. (1999). Neottieae s.s. is clearly supported by this

study. In three of the five analyses (trnLF, nad1, and parsimony combined) Palmorchis

was sister to Neottieae, receiving support (66%) in the trnL-F analysis. In both the ITS

48 analysis and ML combined analysis, it received very high support as the first clade to

branch off within the Epidendroideae and sister to everything else, and both the ML

combined and the parsimony combined analysis are incongruent with regards to this.

Palmorchis is clearly closely related to Neottieae. Given the results of these parsimony

analyses, Palmorchis should be included within Neottieae following the classification of the orchids proposed by Chase et al. (2003).

Tropidieae are considered a natural group on the basis of morphological

synapomorphies of an erect anther subequal to the rostellum and a hamular stipe as well

as similar habit and floral morphology. With the exception of the trnL-F analysis in

which Tropidia remained united but Corymborkis verticilata came out in a distant

polytomy composed of members of Sobralieae and Nervilieae, all the other analyses returned a monophyletic Tropidieae. Based on these findings, the Tropidieae should be considered monophyletic. Internal organization of the terminals within the tribe suggests more sampling may be required within in order to resolve these relationships.

Dressler’s (1993) concept of Nervilieae was somewhat narrower than that proposed by Chase et al. (2003) who in addition to Nervilia included Xerorchis,

Epipogium, Silvorchis, and Stereosandra. The concept of a monogeneric Nervilieae suggested by Dressler (1993) is not supported here. In all the analyses a clade of Nervilia,

Xerorchis and Diceratostele gabonensis is found. With the exception of this latter species, these findings support a concept of Nervilieae sensu Chase et al. (2003). These results can neither support nor contradict the inclusion of Silvorchis or Stereosandra

given they were not included due to a lack of material for these taxa. The nad1 results are

the only results that fail to support the monophyly of Nervilia. In this case Nervilia

49 included was polyphyletic with Nervilia plicata observed in Sobralieae, and Nervilia

shirenesis in a position consistent with other results of this study. Observation of the

sequences for each indicated they are highly divergent, which could result in spurious

associations, which could be corrected for with better taxon sampling within Nervilia.

Chase et al. (2003) recommended that Epipogium be transferred out of

Gastrodieae and placed into Nervilieae based on the findings of Molvray et al. (2000) in

which it was seen sister to Nervilia. The result of the current study do not support this

given the sister relationship recovered for Epipogium and Triphoreae. In addition,

Nervilia is deep in a clade with Diceratostele gabonensis sister to a clade of Xerorchis amazonica and Didymoplexis pallens. There is evidence based on these results that

Xerorchis should be included in Nervilieae as suggested by Chase et al. (2003). My results are the first study to suggest that there is a relationship between Xerorchis and

Didymoplexis, let alone that Didymoplexis is not closely related to Gastrodia as previously thought hypothesized on morphology. Clearly further study is needed to examine these associations more thoroughly.

Given the results of two recent molecular studies (Cameron et al. 1999, Molvray et al.1997), Diceratostele was tentatively in Triphoreae by Chase et al. (2003), and put in a subtribe Diceratostelinae by Rothacker and Rasmussen (see Pridgeon et al. 2005). This decision was based on the results obtained from a single gene, and relatively poor sampling of primitive epidendroid orchids. In terms of vegetative morphology and habit,

Diceratostele is not similar to any other member of Triphoreae appearing more closely related to taxa such as Tropidia or Sobralia. Dressler (1993) suggested that

Diceratostele resembled Tropidia or Corymborkis in habit; additionally, no

50 morphological synapomorphies support a relationship with Triphoreae. For example,

Diceratostele seeds are considered to be Goodyera type (Dressler 1993, Tohda 1995) while other members of this tribe are referred to the Eulophia type (Barthlott 1979).

Goodyera type seeds are characterized as dust-like, ca. 5 cells wide, with testa cells isodiametric or slightly elongate with intercellular spaces. Eulophia type seeds are club- shaped balloons to threads, whitish-brown, with elongate testa cells, lacking intercellular

spaces, and a cell border covered by a cuticle. The current study indicates that

Diceratostele is more closely related to Nervilieae and in particular Nervilia, and should

probably be transferred to that tribe as consequence; Nervilia has a similar seed type to

the Goodyera seed type (Dressler 1993). This raises some rather interesting biogeographical questions as Diceratostele is Old World African, Nervilia is also Old

World, but found in Asia, and Xerorchis is New World. Diceratostele and Xerorchis are

both are tropical species with plicate, fibrous leaves and reed-stem habits. Interestingly,

they also seem to share a feature of “sympodial” branching (term used in Rasmussen and

Rasmussen [1979]), a characteristic not seen in other basal epidendroid orchids. Yet the

nad1 tree (Fig. 2.5 -2.6) is the only analysis that places Diceratostele and Xerorchis

together, while in all the other analysis’s Diceratostele was seen at the base of Nervilia.

Given the similarity in habit, a relationship to Xerorchis cannot yet be ruled out, and

requires further investigation including the use of morphology and an increased sampling

within the tribe.

Sobralieae has often been considered more derived than the other primitive

epidendroids, and is composed of three to four genera (Elleanthus + Epilyna, Sobralia,

and Sertifera). Dressler (1993) considered Sobralieae to be part of an advanced group of

51 orchids he called the Epidendroid Phylad given Bletia seed type and eight solid pollinia.

The Bletia seed type is characterized as dust-like or balloon seeds to thread-like, with flat trough-shaped elongate testa cells with a smooth surface (Dressler 1993). Moreover,

Sobralieae have a reed-stem habit and an operculate anther; morphology alone suggests that it might be more closely related to the advanced epidendroid outgroups, than the more primitive taxa of the basal Epidendroideae. The trnL-F analysis was the only analysis that failed to recover a resolved Sobralieae, however the Adams consensus

(Fig.2.4) shows there is conflict between terminal relationships, and as such the strict consensus presented does not resolve the tribe.

The monophyly of Triphoreae (sensu Dressler 1979,1993) is supported by this study. Psilochilus could not be amplified for ITS and was not included in the analysis of that locus. Moreover, this was the only analysis that recovered a polyphyletic Triphoreae, where Triphora amazonica was found in Palmorchis. This sequence was complete, yet highly divergent relative to other members of this tribe, nevertheless there was no reason seen to exclude it from the analysis. That sequence was provided by E. R. Pansarin from material collected in Brazil and amplified as part of work related research being conducted by that individual. Additional amplification attempts of an accession (ER73) of this species from the same population as that of Pansarin were made, however no useable sequences were obtained. With the exception of T. amazonica, the remaining

Triphoreae were recovered in the ITS analysis with high support. Resembling the ITS results, the ML analysis recovered a polyphyletic Triphoreae, with T. amazonica and

Gastrodia uniting among Palmorchis which suggests that the ITS partition may have a greater influence on the ML than on parsimony which recovered a monophyletic

52 Triphoreae. One explanation for this lies with the technical limitations of the ML

methodology in which gaps are excluded from the analysis; the parsimony combined

analyses were performed with both sequence and gap characters. The nad1 locus is

highly conserved, with most of the phylogenetic signal at the level of interest coming

from gap characters. Given the lack of sufficient tribal level signal when using nad1

sequence data only, the effects of excluding gaps on the ML analysis are evident in the

recovery of a polyphyletic Triphoreae.

Members of Triphoreae are found exclusively in the Western Hemisphere, from

northern South America, Central America, the Caribbean, and eastern North America,

with the highest diversity found in tropical and subtropical Americas. In all analyses,

Monophyllorchis, which is found in South and Central America, is seen to be the first

genus to branch off within the tribe, followed by Psilochilus and Triphora. Psilochilus is

also found throughout South America and the Caribbean. Within Triphora, the South

American/Amazonian, T. amazonica is at the base of the clade followed by a clade of the pan-Caribbean, T. gentianoides and the temperate T. trianthophora. Based on these results, given the sampling, it appears that the tribe evolved in the Southern Hemisphere and expanded its range into North America.

No previous study has suggested that Epipogium might be related to Triphoreae.

Both ML and parsimony combined analyses support a sister relationship between

Epipogium and Triphoreae (Figs. 2.7-2.10). The only analysis that failed to recover this relationship was the nad1 partition including gaps in which Epipogium was sister to

Nervilia with high support, a position consistent with that argued by Chase et al (2003).

The results of the trnL-F analysis can neither support nor refute these relationships,

53 because this locus did not amplify for Epipogium. Both Triphoreae and Epipogium

possess monads, pollen grains with smooth tectum, irregular sectile massulae, columnar

stigmatic cells, prominent undetached viscidium, and a prominent apical thick anther

beak similar to that observed in Triphora trianthophora (Rasmussen 1981, Freudenstein

and Rasmussen 1999, and this study [see Chapter 3 for discussion]). Epipogium has a

rather unique tuberous rhizome and villous, reduced roots superficially similar to those

observed in Triphora, especially T. gentianoides, but also present in T. trianthophora.

With the exception of vegetative characters such as reduced or absent leaves, which is associated with a lack of chlorophyll (some achlorophyllous Triphora), the flower of

Epipogium is so highly derived that there are no apparent floral synapomorphies. Dressler

(1981) reported that Epipogium possessed an erect anther but revised this by 1993 where he reported that it possessed an incumbent or sub-erect anther, most likely referring to the somewhat recurved appearance of the anther; Epipogium aphyllum is clearly incumbent as shown in Rasmussen (1982, Fig. 28) and Vermeulen (1965), but the anther of E. roseum is sub-erect (Rasmussen 1982, Fig. 30). The flower and column of Epipogium are highly derived in that the perianth is fused and the column is much reduced, characteristic features both of self- pollination and a loss of chlorophyll. The loss of chlorophyll and associated increase in mycoheterotrophy also reduce vegetative characters such as leaves and habit. Yet no single morphological character could be considered a unique synapomorphy for the relationship of Epipogium and Triphoreae and moreover, many are symplesiomorphies seen in other primitive Epidendroideae. In addition, Epipogium is Old

54 World, found throughout Europe, Africa, and Southeast Asia. Given the current

distribution of Triphoreae, there exists a geographic disjunction between sister taxa.

Because of the complex tectonic and geological history of the regions to which these taxa

are currently found, biogeographic relationships may also be complex.

The Orchidaceae as a family began to evolve rapidly in response to the evolution

of the bees, a major pollinator group (Chase 2001), for which long tongue bees are at

least 65 mya old (Michener and Grimaldi 1988). This places diversification of the orchids

during the late Cretaceous period, and after the breakup of Gondwana had begun.

Triphoreae, based on the results presented here, evolved in South America and expanded

its range northward, therefore, the most recent common ancestor to both Epipogium and

Triphoreae must have been present in both Africa and South America prior to 65mya.

The implication is that the most recent common ancestor diverged as a result of this

vicariance event. Other orchids exhibit similar patterns of associations between Africa

and South America, some in support of long distance dispersal and others ancestral distributions separated by vicariance. Oeceoclades maculata in the Western Hemisphere

may be the result of long dispersal from Africa to South America after the breakup of

Gondwana (Stern 1988), arriving in the Caribbean and Florida during the mid 1970’s (Nir

2000). Vanilla, Campylocentrum, Polystachya, as well some members of the Angraecinae

are all taxa with current distributions in South America, Asia, and Africa which can also

be attributed to vicariance as a result of the breakup of Gondwana (Chase 2001).

Gastrodieae have traditionally been the repository for many of those orchids with

epidendroid affinities lacking chlorophyll, but without definitive associations to other

tribes based on some other set of characteristics. Dressler (1993) suggested that the taxa

55 of Gastrodiinae were united based on the characters of petal fusion, Gastrodia seed type,

and the habit of “saprophytism”. The Gastrodia seed type is characterized as small dust

or thread seeds from 1.5 x 10-100m, white or light brown with isodiametric testa cells

with reticulate thickenings and a covered cell border (Dressler 1993). Given the results of

this study Gastrodieae, as sampled in here, is not consistent with Dressler’s (1993)

concept of the tribe, nor is it monophyletic based on the taxonomy of Chase et al. (2003).

The condition of achlorophylly also affects molecular markers, such as resulting in a

reduced plastid genome (Cameron et al. 2000, Cameron 1999, Freudenstein 2000) and

the work of Nickrent, Duff and others (see below for discussion) found increased rates of

evolution in the other genomes as well.

The observation that Wullschlaegelia is inconsistent in its affinities in the various manipulations is not surprising given that it is achlorophyllous and has a higher rate of evolution as indicated by the long branch subtending it. The results of both analyses show the importance of taxon sampling in obtaining spurious relationships between taxa. In the ITS analysis in which Epipogium was removed, Triphoreae unites with

Wullschlaegelia. This may be an indication of long branch attraction between Triphoreae and Wullschlaegelia as each is subtended by long branches. Furthermore, it is interesting to note that the position of Wullschlaegelia can be greatly affected by the removal of a single taxon (e.g., Didymoplexis or Xerorchis), which shows the importance of taxon sampling in preventing the resolution of spurious relationships. Improving taxon sampling, such as including sequences from both species of Wullschlaegelia and adding sequences for the closely related genus Uleiorchis, should help resolve these relationships.

56 THE LOSS OF CHLOROPHYLL- As a character, the loss of chlorophyll has been discussed as being a convergent condition by a number of authors. Within the angiosperms, it is evident that the condition of being green (presence of chlorophyll) is a symplesiomorphy, with the loss of chlorophyll being the derived condition. By some estimates, achlorophylly and holoparasitism have evolved a minimum of 400 times in different families of flowering plants (Furman and Trappe 1971). Dressler (1993) reports that saprophytism (i.e. mycoheterotrophy associated with achlorophylly) arose at a minimum of 10 times in the orchids. There is no doubt that this is a conservative estimate given that Gastrodieae as circumscribed by most authors is a repository for achlorophyllous, leafless, mycoheterotrophic orchids with epidendroid affinities and as such is probably not a natural group. Molvray et al. (2000) reported a high level of convergence for achlorophylly when it was mapped onto an 18S topology and is associated with some combination of a reduction in pollinator specificity and complex pollinator/flower interactions, or increased autogamy when associated with a reduced or absent rostellum. Based on these results it appears that achlorophylly evolved a minimum of 5 times (Fig. 2.7) among the basal Epidendroideae.

Putatively achlorophyllous angiosperms have been reported to have at least some small amount of chlorophyll present in their tissues (Cummings and Welschmeyer 1998).

In orchids, Cephalanthera austiniae and Corallorhiza maculata are reported to possess low, but detectable levels of both chlorophylls a and b. Cephalanthera austinae is pigment free while Corallorhiza maculata contains additional pigments and higher levels of chlorophyll. This is consistent with more recent observations made of different species of Corallorhiza (C. F. Barrett pers com.). The implications of these findings are

57 that for terrestrial achlorophyllous taxa, the incomplete absence of chlorophyll may be masked by the presence of other pigments such as anthocyanins or carotenoids, and

therefore while their concentrations are much reduced, chlorophyll and hence

chloroplasts, still occur in some taxa and could therefore contribute photosynthates. The

lack of pigmentation all together may be the end result of holomycoheterotrophy and

reduced/absent functional chloroplast genomes, as indicated in some studies of

holoparastic angiosperms.

Duff and Nickrent (1997) found that mitochondrial 19S rDNA sequences from

holoparasitic plants expressed higher rates of substitutions and a transversion bias

indicated by lower transition to transversion (TI:TV) ratios than related, non-

holoparasitic green plants. This is consistent with findings made in earlier studies of the

same holoparasitic non-asterid taxa in which both nuclear (18S rRNA) and chloroplast

(16S rRNA) loci were studied (Nickrent and Starr 1994, Nickrent and Duff 1996, and

Nickrent et al. 1998). As a general rule the results of these studies indicate that one

should expect higher rates of nucleotide substitutions and subsequent divergence rates in

those taxa that lack chlorophyll as functional constraints of the genomes is reduced. This

is measured by lower TI:TV and nucleotide base substitutions (e.g. longer branches)

when compared to green relatives. The absolute rate of transitions is higher than that of

transversions; therefore transversion bias is observed when transitions become saturated

making transversions appear more frequent (Moore and DeFilippis 1997).

Given the results of this previous work, it was expected that achlorophyllous taxa

would express higher rates of evolution as observed by higher substitution rates and

lower TI:TV ratios. This study confirms this for the nuclear ITS (Table 2.1) and the

58 mitochondrial nad1 locus (Table 2.2) for which there were significant numbers of achlorophyllous taxa represented. The difficulty in obtaining plastid sequences from taxa suspected of lacking chlorophyll is indirect evidence for a reduced or absent plastid genome in these plants. In addition, achlorophyllous or nearly achlorophyllous species tended to be on longer branches than green taxa, signifying higher rates of sequence change along these branches. Furthermore, TI:TV ratios were relatively lower in achlorophyllous species than chlorophyllous ones in the same clade and generally lower than other taxa. Moreover, achlorophyllous, pigment-free taxa such as Epipogium and

Wullschlaegelia had lower TI:TV than other achlorophyllous pigmented taxa such as

Gastrodia procera and Neottia. Further evidence for greater evolutionary change among achlorophyllous taxa comes from sequence length changes. Achlorophyllous taxa on average had shorter sequences and higher percentages of gaps than other taxa (Tables

2.1- 2.2). The wholly achlorophyllous pigment-free Epipogium aphyllum, is the only representative of this type of achlorophylly in the nad1 dataset, therefore broad conclusions from this observation cannot be made, however it was considerably lower than other achlorophyllous taxa.

Some anomalous results were observed for pigmented taxa such as Nervilia for nad1 and Triphoreae (Triphora trianthophora and Monophyllorchis maculata) for ITS.

These had much lower TI:TV scores than other taxa to which they are putatively related.

One explanation for this is that these taxa are in transition to becoming achlorophyllous holoparasites. Triphora trianthophora for example is found with some plants in a population being green while others are wholly achlorophyllous (T. trianthophora forma rossiii) with a gradient in the middle. Additionally, both Nervilia and Monophyllorchis

59 are found in dense tropical understories where photosynthesis is greatly reduced. While not presented because achlorophyllous taxa failed to amplify for the trnL-F locus, pairwise base comparisons show that Triphora trianthophora exhibits ratios similar to green taxa, whereas species of Psilochilus and Monophyllorchis maculata both exhibited low ratios (by as much as 50%) consistent with the hypothesis that taxa without chlorophyll or those that are becoming holoparasitic should have lower values. It is apparent that further investigation is needed in order to study this more thoroughly.

THE UTILITY OF NAD1B-C- The mitochondrial marker used in this study was the NADH dehydrogenase subunit 1 (nad1) intron between the B and C exons (nad1b-c).

In plants, the mitochondrion generally has low rates of nucleotide sequence evolution compared to the other two genomes (Soltis and Soltis 1998). The results of both the nuclear ITS and mitochondrial nad1b-c intron datasets are consistent with this general observation in that there was an observable difference in rates of evolution between the two loci. This is best observed in the lower number of nucleotide substitutions calculated for the nad1b-c locus (Table 1.4) than those calculated for the same taxa using ITS.

Intron families are characterized by their conserved secondary RNA structure consisting of stems and loops regions associated with exon/intron borders (Michel and

Dujon 1983, Michel et al. 1989, Kelchner 2002). As a type II intron, the nad1 mitochondrial locus is highly conserved making alignment relatively easy with the exception of a number of variable length mutations found primarily in loop regions. Most of the length variation observed was seen in the large 781bp loop of the IV domain.

Functionally, stem regions are more conserved than loop regions. Kelchner (2002) argued that stem regions will most likely be sites of transition mutations as these, while not being

60 synonymous substitutions per se, are less likely to cause a structural change in the secondary structure. Loops on the other hand are under less functional constraint and exhibit a greater degree of length change.

In terms of the overall performance of nad1 in this analysis, it is clear that nucleotide data alone did not have enough signal to sufficiently resolve relationships at the level of interest. The proportion of parsimony informative sites went from 15% to

27% with the inclusion of gaps even though the absolute number of sequence positions was much lower when gaps were coded. In addition, there were a high number of constant characters (21%) and parsimony uninformative (64%) characters relative to parsimony informative characters in the matrix. Wenzel and Siddall (1999) reported that you need a lot of “noise” (i.e. homoplasy) in a data set in order to swamp out the phylogenetic signal (see also Källersjö et al. 1999). Gaps when included in a phylogenetic analysis significantly improved the overall signal and increased phylogenetic resolution. Given the relatively high CI values, including nad1 gaps still did not resolve tribal level relationships among the basal Epidendroideae. Therefore the nad1 locus is not adequate for studies below the level of the subfamily.

CONCLUSIONS

This is the first study of these taxa in which there has been a significant improvement in both taxon and locus sampling, providing a first look at historical patterns of relationships among the basal epidendroid orchids from which further investigation can proceed. In addition, my results show that the basal epidendroid problem is not intractable. Combining data in phylogenetic analysis permits secondary

61 phylogenetic signal to contribute to topology reconstruction, essentially reducing the

effect of different histories, and evolutionary processes that may affect different partitions

of the data. This approach provides the best evidence of phylogenetic relationships. The

“basal epidendroid problem” in resolving historical relationships is that, given the

apparent rapid radiation of the subfamily, there are often short branches with few

characters supporting them. The issues of differing gene and genome histories compound

this, and together results in a lack of strong support for deeper nodes, and different

topologies observed in analyses of the individual partitions. Therefore in order to come

up with a hypothesis of relationships for these orchids, “statistical” support will have to

be secondarily important, giving way to congruence between topologies in a combined

analysis using different methods.

There are still some issues with regard to defining Nervilieae in the sense of any

of the previous classifications. My results support moving Diceratostele out of

Triphoreae into Nervilieae (sensu Chase et al. 2003) or into an association with Nervilia.

Also, Nervilieae is in some way closely associated with Gastrodia and Didymoplexis, but given the ambiguities with the placement of Gastrodia into this higher-level organization, further work is needed to work out the details. Epipogium, which was included in the

Nervilieae by Chase et al. (2003), appears in all the analyses to be sister to Triphoreae or to Monophyllorchis within Triphoreae. In either case, the implications are that it should be moved. Further work at the tribe level will be need in order to determine whether or not to include Epipogium in Triphoreae or put it into a monotypic tribe sister to

Triphoreae.

62 The affinities of the achlorophyllous Wullschlaegelia remain somewhat unclear.

An exemplar of this genus appears in only a single partition, ITS sister to a clade containing Nervilieae + Didymoplexis, Tropidieae, and the advanced epidendroids, while in the combined analysis in which it was included, it is observed sister the advanced epidendroids. The ITS sequence of this accession is highly divergent from all of the other sequences as indicated by the long branches subtending it. It is suggested that additional accessions be amplified for these loci, as well as obtaining a sample of the closely related

Uleiorchis (Born et al. 1999).

The parsimony analysis (Fig. 2.7) places Neottieae sister to Palmorchis at the base of the Epidendroideae, followed by Triphoreae. Tropidieae and Sobralieae form a clade, however the relationship between these, Nervilieae and the advanced Epidendroids has not been resolved. This is the first step towards a phylogenetic hypothesis of relationships among the basal tribes of the Epidendroideae, and there is still a lot of work to be done. Greater taxon sampling has already improved the resolution of relationships among the basal epidendroid orchids, and the combined analyses were able to recover relationships not seen in the analyses of the individual partitions, and improve the resolution some, as a result of secondary signal coming through. These first steps, although tentative, are finding that patterns of relationships may not be intractable given enough data.

% ti/tv Taxon Length Gaps ratio Corycium nigrescens 631 29.9 - Codonorchis lessonii 611 32.1 - Goodyera macrantha 439 51.2 - Pterygodium catholicum 628 30.2 - Brownleea coerilea 561 37.7 - Monandenia bracteata 605 32.8 - Palmorchis trilobulata 578 35.8 - Palmorchis trilobulata 578 35.8 1.5 Palmorchis powellii 585 35 1.58 Palmorchis sp.1 ER110 587 34.8 1.5 Palmorchis sp.2 ER110E 587 34.8 1.5 Palmorchis sp. ER129 585 35 1.39 Palmorchis sp. 462 579 35.7 1.51 Gastrodia procera 543 39.7 1.53 Cephalanthera austiniae 550 38.9 1.68 Cephalanthera damasonium 551 38.8 1.7 Cephalanthera longifolia 552 38.7 1.66 Epipactis helleborine 557 38.1 1.94 Epipactis fageticola 557 38.1 1.94 Epipactis lusitanica 557 38.1 1.92 Limodorum abortivum 554 38.4 1.75 Listera smallii 551 38.8 1.74 Neottia nidus-avis 553 38.6 1.66 Corymborkis sp. 591 34.3 1.56 Corymborkis verticilata 547 39.2 1.46

Continued

Table 2.1: ITS sequence information including sequence length, % gaps and transition/ transversion ratios. Bold entries indicate achlorophyllous or holomycoheterotrophs.

64 Table 2.1 Continued

% ti/tv Taxon Length Gaps ratio Tropidia effusa 585 35 1.63 Tropidia graminae 473 47.4 1.42 Tropidia polystachya 587 34.8 1.58 Epilyna jimenzeii 585 35 1.94 Epilyna hirtzii 618 31.3 1.82 Sertifera columbiana 590 34.4 1.49 Sertifera sp. 589 34.6 1.49 Elleanthus sp. 591 34.3 1.71 Elleanthus lancifolius 588 34.7 1.86 Elleanthus cynarocephalus 595 33.9 2 Ellianthus oliganthus 591 34.3 1.71 Elleanthus tricallosus 595 33.9 2.03 Sobralia amabilis 583 35.2 1.83 Sobralia fimbriata 595 33.9 1.87 Sobralia crocea 593 34.1 1.81 Sobralia mucronata 592 34.2 1.84 Diceratostele gabonensis 541 39.9 1.91 Epipogium aphyllum 527 41.4 1.36 Epipogium roseum 542 39.8 1.2 Nervilia shirensis 561 37.7 1.72 Nervilia plicata 555 38.3 1.66 Nervilia holochila 572 36.4 1.68 Didymoplexis pallens 561 37.7 1.45 Xerorchis amazonica 500 44.4 1.94 Monophyllorchis maculata 537 40.3 0.96 Triphora trianthophora 551 38.8 0.92 Triphora gentianoides 526 41.6 1.13 Triphora amazonica 582 35.3 1.38 Calypso bulbosa 581 35.4 1.5 Ephippianthus schmidtii 499 44.6 1.3 Chysis bractescens 581 35.4 1.47 Coelia triptera 587 34.8 1.19 Corallorhiza trifida 564 37.3 1.51 Eulophia sp. 592 34.2 1.41 Wullschlaegelia aphylla 554 38.4 1.24 Isochilus amparoana 598 33.6 1.13 Leptotes bicolor 576 36 1.37 Oreorchis patens 575 36.1 1.56 Govenia sp 585 35 1.53 Avg.= 36.92 1.58

% ti/tv Taxon Length Gaps ratio Brownleea caerulea 1469 53.3 - Altensteinia palacea 1030 67.2 - Disperis lindleyana 1393 55.7 - Goodyera pubescens 1506 52.1 - Habenaria repens 1117 64.5 - Orchis quadripunctata 1152 63.3 - Pachyplectron arifolium 1595 49.3 - Spiranthes cernua 1520 51.6 - Stenoglottis longifolia 1089 65.4 - Palmorchis trilobulata 1553 50.6 0.32 Palmorchis powellii 1343 57.3 0.26 Epipactis helleborine 1526 51.4 0.30 Limodorum abortivum 1492 52.5 0.34 Cephalanthera damasonium 1570 50 0.27 Cepahalanthera austiniae 1478 52.9 0.35 Neottia nidus-avis 1014 67.7 0.24 Listera smallii 1583 49.6 0.29 Listera convol 1504 52.1 0.49 Listera cordata 1028 67.3 0.38 Aphyllorchis montana 1381 56.1 0.32 Corymborkis verticilata 1309 58.4 0.35 Tropidia effusia 1425 54.7 0.25 Tropidia curculigoides 1400 55.5 0.36 Tropidia bambusifolia 1408 55.2 0.38 Sertifera columbiana 1022 67.5 0.20 Sertifera sp. 1023 67.5 0.22 Elleanthus sp. 1533 51.2 0.18 Epilyna jemenzii 494 84.3 0.38 Epilyna hirtzii 1542 50.9 0.37 Sobralia mucroanta 580 81.5 0.25 Sobralia crocea 1058 66.3 0.19 Xerorchis amazonica 1174 62.6 0.52 Epipogium aphyllum 941 70.1 0.17 Nervilia plicata 736 76.6 0.17 Nervilia shirensis 483 84.6 0.00

Continued

Table 2.2: Sequence characteristics for nad1 including length variation, % gaps, and transition/ transversion ratios. Bold entries indicate achlorophyllous/holomycohetrotrophs.

Table 2.2 Continued

% ti/tv Taxon Length Gaps ratio Gastrodia sesamoides 1353 56.9 0.32 Gastrodia procera 749 76.2 0.24 Gastrodia sp. Reunion Island 888 71.7 0.35 Gastrodia confusa 1037 67 0.51 Gastrodia zeylanica 820 73.9 0.37 Diceratostele gabonensis 1530 51.3 0.31 Didymoplexis pallens 1313 58.2 0.35 Psilochilus macrophyllus 1390 55.8 0.37 Psilochilus sp. LJ6914 1402 55.4 0.45 Triphora trianthophora 1206 61.6 0.35 Triphora gentianoides 1339 57.4 0.42 Triphora amazonica 782 75.1 0.49 Monophyllorchis sp. 1506 52.1 0.33 Aplectrum hyemale 1191 62.1 0.37 Bletilla striata 1532 51.3 0.23 Isochilus amparoana 1338 57.4 0.35 Calypso bulbosa 1564 50.2 0.33 Leptotes bicolor 1247 60.3 0.34 Ephippianthus schmidtii 1541 50.9 0.32 Chysis bractescens 1637 47.9 0.26 Coelia triptera 1285 59.1 0.20 Avg.= 60.56 0.32

Figure 2.1: Strict consensus tree returned from an analysis of the nuclear ITS locus calculated from 3 MPTs of length 2307 (CI=0.412, RI=0.649). Numbers below branches are jackknife support values > 50%.

Corycium nigrescense Pterygodium catholicum Codonorchis lessonii Goodyera macrantha Brownleea coerilea Monadenia bracteata Palmorchis Sp ER110 Palmorchis sp1 ER110E Palmorchis powellii 100 Gastrodia procera Palmorchis sp ER129 Palmorchis Palmorchis O- 462 Triphora amazonica Palmorchis trilobulata Palmorchis trilobulata Cepahalanthera austiniae C. damasonium Cephalanthera longifolia Limodorum abortivum Neottieae Listera smallii 98 100 NeottiaNeottia nidusnidus-avis avis Epipactis lusitanica Epipactis helleborine Epipactis fageticola Epipogium aphyllum Epipogium roseum 90 Monophyllorchis maculta Triphora trianthophora Triphoreae Triphora gentianoides 98 Sobralia amabilis Sobralia fimbriata Sobralia crocea Sobralia mucronata Sertifera columbiana 100 Sertifera n546 Epilyna jimenzeii Sobralieae Epilyna hirtzii Elleanthus tricallosus Elleanthus sp Elleanthus oliganthus Elleanthus lancifolius E. cynarocephalus Wullschlae gelia aphylla Didymoplexis pallens 69 Xerorchis amazonica Diceratostele gabonensis Nervilia plicata 56 58 Nervilia shirensis 100 Nervilia holochila Nervilia Corymborkis sp 0542 Corymborkis verticillata Tropidia gramgraminae Tropidieae 100 Tropidia effusa Tropidia polystachya Eulophia sp Chysis bractescens Isochilus amparoana Leptotes bicolor Advanced Coelia triptera Epidendroids 86 Calypso bulbosa Ephippianthus schmidtii Govenia sp Corallorhiza trifida Oreorchis patens

Figure 2.1

57 Corycium nigrescense AJ000126 38 Pterygodium catholicum 39 33 Codonorchis lessonii 36 Goodyera macrantha 40 34 Brownleea coerilea AJ000138 38 Monadenia bracteata 14 Palmorchis Sp ER110 32 24 Palmorchis sp1 ER110E 12 Palmorchis powelllii 4 Gastrodia procera ER64 9 12 Palmorchis sp ER129 30 Palmorchis 462 9 Triphora amazonica Palmorchis trilobulata Palmorchis trilobulata ER68 8 19 Cephalanthera austiniae 4 4 Cephalanthera damasonium 8 42 21 Cephalanthera longifolia 17 Limodorum abortivum 14 25 15 Listera smallii 23 Neottia nidus-avis 2 10 changes 26 Epipactis lusitanica 10 1 Epipactis helleborine 8 Epipactis fageticola

Continued

Figure 2.2: Phylogram of 1 of 3 most parsimonious trees. Numbers indicate character changes along the branch.

Figure 2.2 Continued

28 35 Epipogium aphyllum 50 49 Epipogium roseum 60 47 Monophyllorchis maculata 55 34 Triphora trianthophora 26 Triphora gentianoides 2 4 Sobralia amabilis 28 8 4 Sobralia fimbriata 1 9 Sobralia crocea Sobralia mucronata 19 1 20 Sertifera columbiana Sertifera n546 8 14 12 Epilyna jimenzeii 12 Epilyna hirtzii 17 14 20 Elleanthus tricallosus 16 Elleanthus sp 10 Elleanthus oliganthus 11 6 Elleanthus lancifolius Elleanthus cynarocephalus 102 2 8 Wullschlaegelia aphylla 43 87 Didymoplexis pallens 34 Xerorchis amazonica 29 22 Diceratostele gabonensis 18 20 42 Nervilia plicata 12 18 Nervilia shirensis 16 Nervilia holochila 2 14 Corymborkis sp 0542 23 Corymborkis verticillata 2 Tropidia graminae 9 9 Tropidia effusa 12 Tropidia 7 62 14 Eulophia sp 15 Chysis bractescens 10 9 31 15 Isochilus amparoana 23 28 Leptotes bicolor 28 Coelia triptera 20 26 Calypso bulbosa 39 Ephippianthus schmidtii 15 19 Govenia sp 9 12 12 13 Corallorhiza trifida 5 Oreorchis patens

Figure 2.3: Strict consensus tree for trnL-F including gaps coded using simple gap method. Tree returned from 32 most parsimonious trees of length 1495 (CI=0.78, RI=0.714). Numbers indicate jackknife support values >50% for relevant clades.

Monadenia bracteata Brownleea coerulea Pterygodium catholicum Corycium carnosum Codonorchis lessonii Goodyera sp 66 Platylepis polyadenia Palmorchis Er211 cf trilobulata 100 Palmorchis sp. Palmorchis Palmorchis silvicola Cephalanthera damasonium Listera smallii Listera cordata Neottia nidus-avis 62 Neottia sp Neottieae Epipactis sp Epipactis Aphyllorchis pallida Aphyllorchis montana Limodorum spp Limodorum abortivum Tropidia effusa 100 Tropidia gramineae Tropidieae Xerorchis amazonica Xerorchis sp. Xerorchis Monophyllorchis maculata Monophyllorchis microstyloides Psilochilus macrophyllus 100 Psilochilus modestus Triphoreae Triphora gentianoides Triphora amazonica 55 Triphora trianthophora Coelia triptera 52 Chysis bractescens Calypso bulbosa Advanced Leptotes bicolor Eulophia sp Epidendroids Isochilus amparoanus Ponera striata Govenia liliacea Oreorchis patens Corallorhiza trifida Elleanthus lancifolius Elleanthus Sobralieae Corymborkis verticillata Epilyna jimenzii + Corymborkis Sertifera columbiana Sobralia crocea Sobralia mucronata Nervilia aragoana Nervilieae Nervilia shirenensis 99 Nervilia plicata Diceratostele gabonensis Diceratostele

Figure 2.3

Corymborkis Corymborkis verticillata

Nervilia aragoana Nervilieae Nervilia shirensis Diceratostele Nervilia plicata Diceratostele gabonensis Sobralia crocea Sobralia mucronata

Elleanthus lancifolius * 76 Sobralieae Elleanthus sp 374 * Epilyna jimenzii *

Sertifera columbiana

Figure 2.4: Adams consensus for the portion of the trnL-F strict consensus for which there was a lack of resolution. “*” indicates taxa in conflict in the 32 MPTs. Arrows indicate nodes which not recovered in the strict consensus. Number beneath branches are jackknife support values of > 50%.

Figure 2.5: Strict consensus tree for nad1, returned from 640 most parsimonious trees of length 3236 (CI=0.735, RI=0.536). Numbers indicate jackknife support > 50% .

Codonorchis lessonii Corycium nigrescens Brownleea caerulea Disperis lindleyana Habenaria repens Orchis quadripunctata Stenoglottis longifolia Goodyera pubescens Pachyplectron arifolium Altensteinia palacea Spiranthes cernua Palmorchis trilobulata Palmorchis 83 Palmorchis powellii Aphyllorchis montana Epipactis helleborine C. damasonium Limodorum abortivum Cephalanthera austiniae Neottieae Neottia nidus-avis Listera smallii Listera convol Listera cordata Ephippianthus schmidtii Calypso bulbosa 100 Aplectrum hyemale Advanced 50 Bletilla striata Epidendroids Isochilus amparoana Leptotes bicolor Chysis bractescens Coelia triptera Corymborkis vert Tropidia cuciculigoides Tropidieae 57 Tropidia Effusia Tropidia bambusifolia Monophyllorchis maculata Psilochilus macrophyllus 100 Psilochilus sp LJ6914 Triphoreae Triphora amazonica 94 Triphora trianthophora Triphora gentianoides Elleanthus sp Sobralia mucroanta Sobralia crocea Epilyna jemenzii Epilyna hirtzii Sobralieae Nervilia plicata Sertifera columbiana Sertifera sp N565 Xerorchis amazonica Diceratostele gabonensis Epipogium aphyllum 99 Nervilia shirensis Gastrodia sesamoides Gastrodia procera Gastrodia sp reunion Gastrodia confusa Gastrodieae Gastrodia zeylanica Didymoplexis pallens

Figure 2.5

Monophyllorchis maculata Psilochilus macrophyllus Psilochilus sp LJ6914 Triphoreae Triphora amazonica Triphora trianthophora Triphora gentianoides

* Xerorchis amazonica Diceratostele gabonensis

Epipogium aphyllum Nervilieae Nervilia shirensis Gastrodia sesamoides Gastrodia procera

Gastrodia sp reunion Gastrodieae Gastrodia confusa Gastrodia zeylanica Didymoplexis pallens

Figure 2.6: Portion of the nad1 Adams consensus tree; * indicates node not obtained in strict consensus.

Figure 2.7: Strict consensus tree returned from the parsimony analysis of the combined data from three loci: trnLF, trnLF gaps, ITS, and nad1, nad1 gaps (L= 5452, CI=0.666, RI=0.553).

Codonorchis lessonii Corycium sp. Brownleea coerulea Goodyera sp. Palmorchis sp. Palmorchis trilobulata Palmorchis 86 Gastrodia procera Aphyllorchis montana Epipactis sp. Limodorum abortivum C. damasonium Neottieae 97 Cephalanthera austiniae Listera smallii Listera cordata Neottia nidus-avis Epipogium aphyllum 100 Monophyllorchis maculata P. macrophyllus Psilochilus sp. LJ6914 Triphoreae Triphora amazonica T. trianthophora Triphora gentianoides Xerorchis amazonica Didymoplexis pallens 60 Diceratostele gabonensis 63 Nervilia plicata Nervilia shirensis Nervilieae Calypso bulbosa Chysis bractescens Advanced 100 Isochilus amparoana Epidendroids Corallorhiza trifida Oreorchis patens Tropidia effusa Corymborkis verticillata 100 Tropidia sp. Tropidieae Sobralia crocea

100 Sobralia mucronata Sertifera columbiana 100 100 Sertifera sp. Epilyna jimenzeii Sobralieae 72 100 Epilyna hirtzii 97 Elleanthus lancifolius 97 Elleanthus sp.

Figure 2.7

Figure 2.8: The strict consensus from calculated from 6 MPTs of length 5570 (CI=0.663, RI=0.546) returned from the combined analysis excluding Gastrodia procera & Triphora amazonica, but including all partial sequences of Wullschlaegelia, Epipogium and Gastrodia species. Numbers below branches indicate jackknife support >50%.

Codonorchis lessonii Corycium sp Brownleea coerulea Goodyera sp Palmorchis trilobulata 100 Palmorchis sp Aphyllorchis montana Palmorchis Cephalanthera damasonium 73 Cephalanthera austiniae Neottieae 97 Epipactis sp Limodorum abortivum Listera smallii Listera cordata Neottia nidus-avis Tropidia effusa Corymborkis verticillata 100 Tropidia sp Tropidieae Epipogium aphyllum 68 Epipogium roseum Monophyllorchis maculata Triphora trianthophora Triphoreae 71 Triphora gentianoides Psilochilus macrophyllus Psilochilus LJ6914 73 Sobralia crocea Sobralia mucronata Sertifera columbiana 96 Sertifera sp Sobralieae Epilyna jimenzeii Epilyna hirtzii Elleanthus lancifolius Elleanthus sp Wullschlaegelia aphylla Calypso bulbosa Chysis bractescens Advanced 99 Isochilus amparoana Corallorhiza trifida Epidendroids Oreorchis patens Diceratostele gabonensis Nervilieae Nervilia plicata 58 Nervilia shirensis Xerorchis amazonica Gastrodia sesamoides Didymoplexis pallens Gastrodieae Gastrodia zeylanica 66 Gastrodia sp reunion Gastrodia confusa

Figure 2.8

Figure 2.9: Topology from the Maximum likelihood combined analysis of the three data partitions, ITS, nad1, and trnL-F. Numbers indicate jackknife support > 50% for relevant nodes.

Palmorchis 94

100 Neottieae 100 Cephalanthera austiniae Neottia nidus-avis

Tropidieae 88 Corymborkis verticillata 100 Advanced Epidendroids 100 Corallorhiza trifida

82 Nervilieae 88 100

Monophyllorchis maculata 76 Triphoreae

Sobralieae 100

Figure 2.9

Figure 2.10: Maximum Likelihood topology returned from the combined analysis excluding Gastrodia procera and Triphora amazonica, but including all partial sequences of Wullschlaegelia, Epipogium and Gastrodia species.

Figure 2.10

CHAPTER 3

A PHYLOGENETIC HYPOTHESIS OF BASAL EPIDENDROIDEAE FROM

MORPHOLOGY AND MOLECULAR DATA: A TOTAL EVIDENCE APPROACH

INTRODUCTION

The use of morphological and anatomical characters has not, surprisingly,

decreased in the modern era of chemical and now molecular methods. The tactical

advantages of molecular data lie in the relative ease in which large quantities of data can

be gathered relatively rapidly (Soltis and Soltis 1998).

Many of the traditional orchid classifications were based exclusively on

morphology and anatomy, relying on a few key characteristics. Most of these characters

are related to the column, such as degree of fusion and anther number (3, 2, or 1) and

position (erect vs incumbent). One of the diagnostic characters of the Orchidaceae is the fusion of the androecium and gynoecium into a structure called the column. Many authors used these structures and degrees of fusion as a means to delimit relationships in the larger family (Schweinfurth 1959). At the subfamily level, two of the key characters

86 relied upon by most authors have been the number and position of anthers. However, with closer examination, as well as improved taxon sampling, many of these classifications have been subsequently modified. In light of recent findings (Kores et al.

1996, Cameron et al. 1999, Cameron and Chase 2000, and Freudenstein et al. 2002) the utility of key characters, such as anther number and incumbency, has been questioned.

Problems associated with the use of key characters are that many of these characters are of floral and reproductive structures, which are subject to selection. In orchid flowers and columns, character convergence is associated with specific pollinator interactions, which results in adaptations to the column and perianth reflecting this interaction. Plants with highly zygomorphic flowers often have very specific pollinator interactions (for example see Cubas 2004), which are suspected in enabling the radiation of many plant groups (Endress 1999, 2001a, 2001b). Interestingly, very little has been reported on the effects of the loss of pollinator specificity. At least among orchids this often results in an increased fusion of the perianth parts, reduction or loss of column characters such as rostellum and viscidium, soft mealy pollinia, and a decreased floral display (Catling 1990). In no anatomical or vegetative structures is convergence more obvious then the orchid gynostemium (anther, stigma and column regions. see Dressler

1993, Rasmussen 1982). The anthers and gynostemium of basal epidendroids have been studied in part by various researchers (Burns-Balogh and Bernhardt 1985, Freudenstein et al. 2002; Rasmussen 1982, Szlachetko and Rutkowski 2000). Until recently the importance of the single incumbent anther has not really been emphasized because the two groups which possess this condition, the vanilloids and the Epidendroideae, were thought to be related. Incumbency is defined as a change in anther position in which

87 during development the anther is bent forward (Dressler 1993), and was noted by

Bentham (1881). The incumbent anther has traditionally been considered a key

systematic feature of the Epidendroideae (Dressler 1981). However, Cameron et al.

(1999, 2000; but see also Kores et al. 1997) have sufficiently established that Vanilloids

are a distinct subfamily, considered either sister to the other monandrous orchids or the

first to branch off after core Orchidaceae diverged from the Apostasioideae (Chase et al.

2003).

MORPHOLOGICAL HYPOTHESES- The epidendroid subfamily includes

orchids with a single incumbent anther (Freudenstein and Rasmussen 1999; Pridgeon et

al. 1999), a type III stigma (Dannenbaum et al. 1989), and distinct hard or firm pollinia

(except some basal taxa). Burns-Balgoh and Funk (1986) utilized morphological and

vegetative characters in their phylogenetic reconstructions, however these trees were not

made using any explicit methodology, as a result it is not clear the significance of any findings. Dressler’s (1993) classification was based largely on the use of morphological

and vegetative characters, but was distinctly not cladistic, and for that reason any

phylogenetic relationships presented must be considered intuitive. The only cladistic

morphological study to include any significant numbers of Epidendroideae was

performed by Freudenstein and Rasmussen (1999). That study found that morphology

alone could not resolve relationships among the basal epidendroids. Epidendroid taxa, such as Triphora, grouped with the orchidoids sister to Caladenia, based on the

characters of seed striation, viscidium, and endothecial thickenings. The genus

88 Palmorchis is a difficult genus to place using morphology alone, and in the study of

Freudenstein and Rasmussen (1999) it united with vanilloids ([Vanilloideae] Cameron

and Chase 2000; Cameron et al. 1999) given characters of the seed and carinate parianth.

The basal epidendroid orchids have traditionally been difficult to place into a hierarchical grouping of relationships. Morphologically they are a mosaic of primitive and derived traits with few morphological synapomorphies. The purpose of this study is to examine morphological characters with a particular emphasis on the anther and column. The tribes of the basal Epidendroideae will be examined using a morphological dataset separately and in combination with the molecular dataset in a total evidence analysis (Kluge 1989, 1998, and 2004).

MATERIALS AND METHODS

The matrix of Freudenstein and Rasmussen (1999) is one of the most

comprehensive, both in terms of taxa and character sampling. The scope of the

Freudenstein and Rasmussen study was to address relationships at the level of the family

using a general representation of the diversity of taxa. As such the sampling of basal

epidendroids, while significant in the use of a number of tribal exemplars, excluded a

number of taxa that are important this study. For instance, Gastrodieae was particularly

poorly sampled, especially given its diversity and in light of the work of Chase et al.

(2003) which moved a number of these taxa tentatively into other tribes such as

Nervilieae (see Tables. 1.1 and 1.2 for a more complete listing) or Calyposeae

89 (Wullschlaegelia). In order to better understand the diversity and character distributions, sampling of the basal epidendroid taxa was increased in the current study to include an exemplar of each genus. Two taxa were excluded due to a lack of sufficient material; these were Neoclemensia and Silvorchis.

The character matrix of Freudenstein and Rasmussen (1999) was evaluated and characters that were uninformative for the present level were excluded. Given the prevalence of inaccurate or uncontested statements of homology for characters in the literature, characters were scored based on observations of fresh collected and alcohol preserved material or herbarium specimens (AMES, MO, MU, OS, K, US) whenever possible. However, given the rarity of some taxa in collections, additional character study was made using published illustrations and photos of dissected, sectioned or SEM images.

MICROMORPHOLOGY - Fresh or alcohol/FAA preserved material was used for sectioning of Paraplast embedded samples. Specimens were prepared for embedding by placing them in three changes of 70% EtOH, followed by standard dehydration series

(95%EtOH, TBA (tertiary butyl alcohol), dH20 in 50:35:15 ratio; 50:50 parts EtOH and

TBA; 25:75 parts EtOH and TBA). This was followed by three changes of 100% TBA.

The final TBA volume was reduced and Paraplast was added for a total of three changes; the final Paraplast change was placed in a vacuum oven at 58°C for 12-24 hours depending on the size of the specimen to help with infiltration and air removal from the specimen. Embedded samples were sectioned with a Microm HM340 microtome and mounted on slides using 1% gelatin and 2% phenol and stained.

90 The staining series consisted of two changes of 100% xylene for 5 min. each, 50% xylene: 50% EtOH for 2 min., followed by four steps of 100%-95%-70%- 50% EtOH for

2 min. each, 3% acetic acid for 2 min., 1% Alcian Blue in water for 20 min., water 3 min., 1% Safranin in 50% EtOH for 10 mins. and a final step of water for 3 min. This was followed by several dehydration washes of several dips in each 50%- 70%-95%-

100% EtOH, 50%EtOH and 50% xylene, and two changes of 100% xylene.

CHARACTER CODING - The use of characters of interest in phylogeny reconstruction is somewhat controversial due to issues of circularity and independence

(Deleporte 1993, de Queiroz 1996, Luckow and Bruneau 1997). However, it can be argued that since organisms are composed of characters, which are either functionally constrained or evolutionarily plastic, conditions not necessarily apparent a priori, the inclusion of all characters is preferred. Under a total evidence approach (Kluge 1989,

1998, 2004), the inclusion of these characters of special interest in phylogeny reconstruction allows them to contribute signal to the topology and is the approach used in this study.

Every effort was made to use a binary coding system when constructing the morphological matrix, however multistate character coding was necessary for a few of the characters; all multistate characters were treated as unordered.

OUTGROUP CHOICE - Based on previous studies of the Orchidaceae, the

Epidendroideae are monophyletic (Kores et al 1996, Cameron 1999, Freudenstein et al.

2004). The rbcL study of Cameron et al. (1999, but see also Kores et al.1996) clarified many of the more ambiguous relationships of the Orchidaceae, finding five subfamiles to the exclusion of the Neottioideae and Spiranthoideae of Dressler (1993). The

91 Neottioideae consisted of orchids with suberect to subincumbent anthers, mealy or

weakly sectile pollinia, while the Spiranthoideae contained those taxa with erect anthers,

Goodyera seed type, and a terminal viscidium. Taxa previously assigned to these

subfamlies were subsumed into either Orchidoideae or Epidendroideae. In Dressler’s

(1993) classification, the Spiranthoideae included three tribes: Diceratosteleae

(Diceratostele), Tropidieae (Corymborkis and Tropidia), and Cranichideae; the former two tribes were moved to the Epidendroideae based on the results of Cameron et al.

(1999). Furthermore, some of the Neottioideae are now considered members of a primitive grade of taxa at the base of the Epidendroideae. Cameron et al. (1999) found a lack of support for relationships among the basal epidendroid taxa, instead resolving a polytomy in the strict consensus.

Based on the findings of Kores et al. (1996) and Cameron et al. (1999), representatives from across the Orchidoideae were chosen to serve as outgroups; this provides the best method for establishing polarity and ancestor-descendant relationships

(Nixon and Carpenter 1993). Starting with the matrix of Freudenstein and Rasmussen

(1999), characters that were uninformative or invariant at this level were removed. To this new characters were added resulting in the construction of a matrix consisting of 40 taxa and 30 characters.

PHYLOGENETIC MORPHOLOGICAL ANALYSIS - Given the methodological and technical limitations of model based methods for use with morphology, cladistic analyses were performed on the dataset in a parsimony framework as implemented using the program PAUP* version 4.0b.10 (Swafford, 2002) using the heuristic search option.

Initially the analysis was run with all characters being treated as equally weighted, and

92 multistate characters were treated in all analyses as unordered. The following approach was taken for all searches: an initial heuristic search was performed on 1000 random taxon addition replicates using TBR, with settings to hold two trees per random addition sequence, saving only two trees, multrees in effect, and swapping on best trees only. The best trees from this search were used as starting trees for a second, more exhaustive heuristic search in order to search the tree space as thoroughly as possible.

A strict consensus tree was calculated. While it is not possible to determine which characters are homoplastic a priori, homoplasy nevertheless is a factor, therefore in order to more fully explore the data set it was determined to use an a posteriori differential weighting method. This was done using the successive approximation weighting method of Farris (1969, 1988) as implemented in the program PAUP* version 4.0b.10 (Swofford,

2002). This method uses a rescaled consistency measure to reweight characters.

Successive iterations were stopped when consistency values stabilized; this occurred in two iterations.

TOTAL EVIDENCE ANALYSIS- Using the molecular matrices of Chapter 2

(Appendix A.1-A-4) a combined morphological and molecular total evidence analysis

(TEA) was performed. This included a morphological matrix of 34 taxa coded for 30 characters, and molecular characters from the nuclear ITS, plastid trnL-F and mitochondrial nad1. In addition, sequence length variation was observed in nad1bc and trnL-F, therefore gaps were coded for these two loci using the simple gap coding method of Simmons and Ochoterena (2000) as implemented in SeqState (Müller 2005). Gaps were combined with both the sequence data and morphology (Appendix B.1) and analyzed using parsimony.

93 BRANCH SUPPORT- Branch support was evaluated on all trees using 5000 jackknife replicates as performed in PAUP*. In order to meet the criteria of Farris et al.

(1996), resampling was set to 37% character deletion corresponding to the probability of

1/e that a character will be deleted from the matrix; ‘‘emulate Jac’’ command was in effect. Two random addition sequences per replication were used, saving only two trees per random addition sequence, and TBR branch swapping was employed for all analyses with Multrees in effect, and swapping on best trees only.

RESULTS

CHARACTERS: Vegetative-

1. orchidoid root tubers 0=absent, 1=present

Most terrestrial species of orchids possess some form of root storage organ.

Within orchidoids, the entire root is often thickened forming a very distinct perennial structure from which new growth emerges. Orchidoid root tubers are considered

“polystelic”, in the sense that the roots are composed of multiple steles (i.e. vascular tissues an associated ground tissues [sensu Van Teighem and Douliot 1886]), however these steles are not derived through division of a monostele, but rather are an aggregation of roots (Pridgeon and Chase 1995). This distinguishes these root tuber structures from others seen in taxa such as Triphora, Gastrodia, and Epipogium among others.

94 Freudenstein and Rasmussen (1999) coded Triphora as possessing true root tubers,

however they do not possess this polystelic form observed in Orchidoideae, and as such

were recoded as absent for this character in the current study.

2. root epidermis 0= rhizodermis, 1= velamen, 2= root absent

3. spiranthosomes 0=absent, 1=present

4. leaf morphology 0=flat nonplicate, 1=plicate, 2=conduplicate, 3=

reduced/absent

5. leaf articulation 0=absent, 1=present

6. stegmata 0=conical, 1=spherical, 2= absent

7. leaf abaxial epidermal cells 0= straight, 1= wavy

8. subsidiary cells 0= present, 1=indistinguishable

9. inflorescence position 0= terminal, 1= lateral

Each of these vegetative characters was used by Freudenstein and Rasmussen

(1999) who discussed them in detail. Root epidermis was coded by these authors as unordered states, either rhizodermis or velaman; a third character state, root absent, was included for use in coding Epipogium (Groom 1894), Gastrodia and Stereosandra in the current study. This was done to account for the observation that these taxa tended to have

95 tuberous structures that lacked roots. While Triphora gentianoides and other species of

Triphora appeared to have similar types of tubers, Triphora trianthophora was coded here as having a rhizodermis on the basis of the observation made by Freudenstein and

Rasmussen (1999).

Spiranthosomes were initially reported in Cranchideae by Stern et al. (1993). At the time, this tribe was placed in the Spiranthoideae, hence the name. Given that this character has not been reported for any of the epidendroid taxa, Freudenstein and

Rasmussen (1999) coded this as an assumed absence for the basal epidendroids. Stern

(1999) reported on the presence of spiranthosomes in Wullschlaegelia and Uleiorchis, showing very detailed micrographs of the structures; these observations suggest a greater need for detailed morphological analysis of the basal epidendroid taxa. Given the results of this study and others it is clear that Wullschlaegelia is a member of the Epidendroideae and shares many features with the genus Uleiorchis (see Born et al. 1999 and Stern

1999).

Leaf morphology used by Freudenstein and Rasmussen (1999) was coded as a multistate character with three states. Many of the taxa in the current study had reduced or absent leaves. This state is often associated with a loss of chlorophyll, and an increased reliance upon fungal associates. Molvray et al. (2000) reported on the loss of chlorophyll and the associated reduction in leaf morphology. Among the basal epidendroid orchids there are a large number of taxa that have a reduced dependence on sunlight and chlorophyll for carbon fixation. Consequently, this condition was coded as having four multistate, unordered states.

96 Detailed studies of morphology are lacking for many of the rare taxa. Groom

(1894) performed detailed observations of the vegetative morphology of Aphyllorchis, including an illustration of the stomata in which no subsidiary cells were illustrated.

Based on these observations, for this study it was assumed that subsidiary cells were indistinguishable from other epidermal cells. In addition, Groom (1894) made observations of Epipogium finding that stomata were absent in the bracts; on this basis it was coded as absent, however there is definitely a need to perform additional observations of fresh material of each of these taxa, including vegetative morphology.

Dressler (1979) reported that both Psilochilus and Monophyllorchis had subsidiary cells with the implication that these were distinguishable from adjacent epidermal cells.

Stegmata were coded as absent in Didymoplexis on the basis of observations made by

Möller and Rasmussen (1984).

Gynostemium- Characters of the gynostemium have traditionally played a rather important role in orchid classifications. Anther position was considered to be erect, incumbent or recurved, and it has been used variously to delimit subfamilies by many authors. Generally, bending of the column and anther position is associated with positioning of the pollinium for pollen attachment and dispersal, therefore presumably under strong selective pressure. Freudenstein et al. (2002) showed that there is variation in the extent of incumbency among the epidendroid orchids resulting from both hetrochronic changes in the timing of anther bending and differential regional bending

97 within the anther. Given these results, anther bending in different regions may have

phylogenetic utility. Anther incumbency is essentially a complex character composed of

different levels bending within each of the zones of bending described in Freudenstein et

al. (2002).

10. sporogenous zone bending 0=absent, 1=present

11. basal zone bending 0=absent, 1=present

12. column zone bending 0=absent, 1=present

13. anther recurved 0=absent, 1=present

For this analysis, the composite character “anthers incumbent or erect” was

recoded as three binary characters in order to maximize the phylogenetic information

content. These are the column, basal and sporogenous zones (Fig 3.4) following the delimitations used by Freudenstein et al. (2002). Presence was coded based on the relative contribution each zone had in incumbency; erect anthers were coded as “0” for each character. Taxa such a Triphora and Tropidia are often reported as having more or less erect or recurved anthers, however it is unclear what the homology of these conditions is. Recurved anthers were seen only in a single tribe, Triphoreae (see Figs. 3.2

A -3.2D); observations of the anthers of Corymborkis veratrifolia and Tropidia curculigoides (Rasmussen 1982) show them having a clearly erect anther. Diceratostele gabonensis was coded based on photos of the column taken from the specimen ER44

(OS; Fig. 3.3); no microsections were prepared of this material.

14. endothecial thickenings 0 = other, 1 = intermediate, 2 = type II

15. endothecial thickenings II 0 = other, 1 = type III/IV

Coding for these characters was based on the published observations made by

Freudenstein (1991), no additional observations were made for these characters.

16. pollen unit 0 = monad 1= tetrad

17. massulae 0=absent, 1=singular regular, 2= multiple irregular, 3= hollow

18. pollen tectum 0= reticulate, 1= smooth, 3= perforated, 4= absent

19. pollen apertures 0=colpate/sulcate, 1=porate, 2= inaperturate

The evolution of pollinia and the pollinium is as diagnostic of the Orchidaceae as the fused gynostemium. Orchids typically pack their pollen grains into pollinia, which enable the pollen to be dispersed either as a unit or in parts. However the packaging itself is not the same in all orchids. In general, pollen grains can be packaged as monads (single units) or tetrads (in fours), weakly or strongly united under a single common exine, or into massule, a condition called sectile pollinia, in which subunits of monads or tetrads are separately packaged under a common exine. Pollinia therefore can appear mealy or granular, sectile or as a solid unit. The evolution of sectile pollinia has occurred in orchids least four times (Dressler 1993) but among the basal epidendroids the homology of this character proves easier to assess. Freudenstein and Rasmussen (1999) used four character states “absent, orchidoid, epidendroid, and arethusoid”. For ease, these are

99 renamed here to be more explicit, but refer to the same condition as those of the original

authors. The arethusoid type was observed in Arethusa and Calopogon in the analysis of

Freudenstein and Rasmussen (1999). The former is represented this study, and as such the condition is an autoapomorphy. The state “0” refers to otherwise solid pollinia such as those observed in Palmorchis and the more derived epidendroid taxa, or mealy/ granular pollinia such as that observed in Neottieae s.s.

Burns-Bologh and Funk (1986) produced two SEM images of pollen tetrads for a

Psilochilus species. Based on these images it was determined that Psilochilus was inaperturate and sectile with a reticulate tectum, and Psilochilus mollis (ER207) was prepared and sectioned (Fig. 3.2.A) which shows clearly the presence of sectile pollinia.

Freudenstein and Rasmussen (1999) coded Triphora trianthophora as lacking massulae, however dissections prepared for this study clearly show irregular massulae (Fig. 3.2.C inset). Sections were prepared for Monophyllorchis maculata (Fig. 3.2.D), showing a

nearly erect anther with some basal zone bending and irregular sectile pollinia.

Pollen morphology of Neottieae was characterized by Ackerman and Williams

(1980). Representatives from across the tribe included seven of 12 species of

Cephalanthera, Limodorum abortivum, 11 of 33 species of Epipactis, seven of 20 species

of Aphyllorchis, Neottia nidus-avis and Neottia listeroides, and three species of Listera.

These micrographs were the basis of character coding for Aphyllorchis, Neottia, and

Limodorum.

100 20. apical caudicle 0= absent, 1= present

21. basal caudicle 0=absent, 1=present

22. stipe 0=absent, 1=present

There are two types of pollinium stalks, caudicles and stipes, which are used for the attachment of pollinia to both the viscidium and pollinator. The former are derived from the anther, particularly the pollen itself, and the stipe is derived from the rostellum.

Caudicles are found in both Orchidoideae and Epidendroideae. In Freudenstein and

Rasmussen (1999) basal caudicles were observed primarily among the Orchidoideae and as a convergence in Epipogium. The derivation of the caudicle is most likely a product of anther position for pollen deposition, therefore the basal caudicule observed in orchidoids with erect anthers derives from the base of the anther; on the other hand, the epidendroid caudicle develops from the apical portion of the anther and is a result of incumbency.

Epipogium aphyllum is clearly incumbent (Rasmussen 1982, Fig. 28), whereas E. roseum is suberect (Rasmussen 1982, Fig. 30). For this character there is no apparent transformation, therefore they were coded as two unordered, binary characters.

Rasmussen (1982) distinguished between two types of stipes, the tegular and hamular stipes. The hamulus develops from the recurved apex of the rostellum, while the tegula is derived from the modified epidermis of the rostellum (Rasmussen 1982, 1986;

Dressler 1993). Both Tropidia and Corymborkis are reported to have a hamulus

(Rasmussen 1982, for Corymborkis see also Rasmussen 1977), while other taxa such as

Aplectrum, Calypso, and Govenia (each Calyposeae), have stipes to a varying degree;

101 Aplectrum has a hamulus, while Calypso and Govenia each possess a tegula.

Freudenstein and Rasmussen (1999) coded each as a separate binary character, however it was determined in the current study to code a single character, stipe as either present or absent.

23. pollinium number :2 0=absent, 1=present

24. pollinium number :8 0=absent, 1=present

Rasmussen (1986) stated that the plesiomorphic condition for the number of pollinia in orchids is four, which corresponds to the number of pollen sacs found in other lilioid monocots. In orchids, four pollinia are the predominant number and an apparent symplesiomorphy within orchids. This condition is most often observed in the

Epidendroideae among the basal members. Two pollinia are often the result of fusion of the four pollinia. Some authors (Freudenstein and Rasmussen 1999) suggested that bilobed or bi-partite pollinia were actually four pollinia. However from literature and observations of the published images used for this study it was concluded that bipartite/bilobed pollinia were actually two pollinia as was reported in Rasmussen (1982) for Stereosandra and Tropidia.

Freudenstein and Rasmussen (1996) report that there are two ways to obtain eight pollinia, either via transverse or longitudinal division of the pollen sacs. Based on this, the condition of eight pollinia was coded in Freudenstein and Rasmussen (1999) as three character states. Of the taxa observed in the current analysis the transverse condition is represented in Sobralia, as such the other genera in Sobralieae, which also have eight

102 pollinia, were assumed transverse as well. Xerorchis was also coded as having eight pollinia, however little is known about this neotropical genus, and since no fresh material of this was obtained, it was coded as present based on reports in the literature, not direct observations.

25. stigmatic cell shape 0=finger, 1=prosenchymatic

This character derives from the work of Dannenbaum, Wolter, and Schill (1989) who looked at orchid stigmas using scanning election microscopy. In that study they observed the shape of the stigma cells of receptive stigmatic surfaces. Freudenstein and

Rasmussen (1999) were the first to use the character in a systematic study in which they coded three conditions: various, finger, and prosenchymatic. In the current study, only two conditions of Freudenstein and Rasmussen (1999) were seen, finger and prosenchymatic. A comparison of stigmas from longitudinal column sections of Epipactis palustris (Schick 1989) with the SEM images of the same species made by Dannenbaum,

Wolter and Schill (1989), revealed that it was possible given well prepared microsections to identify the same condition of the underlying stigmatic surface cells observed using electron microscopy. With the exception of Cephalanthera, Neottieae are reported in the literature as having papillate stigmatic receptive surfaces, which is the result of the underlying cells’ shapes (Prutsch and Schill 2000), however based on the published images of Kurzweil (1988) which is the basis of these reports, it was not possible to establish this condition for all the taxa, therefore, Neottia and Limodorum were both coded as unknown for this character. For examples of the types, Triphora trianthophora

103 (Fig. 3.2.C), Psilochilus mollis (Fig. 3.2.A), Monophyllorchis macualta (3.2.D), Eulophia

(Freudenstein et al. 2002), Epipactis macrophylla (Bonatti et al. 2006) each show the condition of finger-like, while Gastrodia procera (Fig. 3.1.D), Palmorchis trilobulata

(Fig. 3.1.C; see also P. kuhlmannii in Szlachetko and Rutkowski [2000]), Epilyna hirtzii

(Fig. 3.2.A), and Didymoplexis pallens (Fig. 3.1.B) represent the prosenchymatic cells.

This character was coded as an unordered multistate character.

26. viscidium 0= none, 1= diffuse, 2=detachable

Orchid seeds- Orchid seeds are among the smallest seeds found in plants, and have often been described as “dust” seeds due to their extreme size reduction, which range in size from 0.05- 6 mm long and as little as five cells wide or 0.01mm (Arditti et al. 2000).

27. seed testa cell shape 0= isodiametric, 1=ends isodiametric w/ middle

elongate, 2=all elongate

28. seed striations 0=absent, 1=transverse or reticulate,

2=longitudinal

29. seed intercellular spaces 0=absent, 1= present

30. seed covered cell border 0=absent, 1=present

Orchid seeds, even with their small size and apparent reduction in morphology and anatomy have only recently been used in taxonomy of orchids. There is considerable

104 variation in the seed coat texture and decorations, size and shape of the seed, and distribution, size and shape of the testa cells, all of which may have phylogenetic utility.

The most comprehensive work on seed morphology was by Ziegler (1977) and summarized by Barthlott and Ziegler (1981), and Dressler (1993). These works each used a typological model where each seed type is a composite character. It is evident using this method that not all taxa that were described as particular type had all the characters that defined that type. As has been argued for amino acid coding, relying on a typological model fails to capture the underlying phylogenetic signal (Simmons 2000, Simmons and

Freudenstein 2002, and Simmons et al. 2002). For this study, the seed characters of

Freudenstein and Rasmussen were used. In order to complete the dataset, additional taxa were coded from the original work of Ziegler (1977), Barthlott and Ziegler (1981),

Dressler (1993), Arditti et al. (1980), and Tohda (1986).

EXCLUDED CHARACTERS- Freudenstein and Rasmussen (1999) included a number of characters that were informative at the level of their study but since many of these characters are not applicable at the level examined here, they were excluded.

Invariant or autapomorphic characters were excluded, as these provide nothing informative for phylogenetic inference. Additional characters not included in this study are discussed below.

Habit-All the orchids observed here were principally terrestrial or lithophytic, with only a single exception, Epilyna (Elleanthus; Sobralieae), which is typically epiphytic. There were observations made of Monophyllorchis maculata in which large numbers of individuals in one population along the Rio Pastaza, Ecuador were observed

105 epiphytic on trees; such observations from other taxa had been made by other authors, however, these are always considered rare, and not the typical habit.

Achlorophylly- While there are number of taxa in the basal Epidendroideae that lack chlorophyll, no study has ever included this character in the cladistic analysis. The switch from an autotrophic habit to achlorophylly and increased mycoheterotrophy however is associated with reductions in floral displays and vegetative morphology associated with leaves. As a character, the loss of chlorophyll has been discussed as being a convergent condition by a number of authors. Dressler (1993) reported that

“saprophytism” arose at a minimum of 10 times in the orchids. No doubt this is a conservative estimate given that Gastrodieae as circumscribed by most authors is a repository for achlorophyllous, leafless, mycoheterotrophic orchids with epidendroid affinities and as such may not be a natural group. Molvray et al. (2000) reported the high level of convergence this trait appeared to exhibit when it was mapped onto the tree produced using the 18S locus, but did not perform any cladistic analysis of the characters in part because it is difficult to homologize characters such as achlorophylly. While this is an important condition among these orchids, and originally was coded for this study, it was rejected because the character was observed to be non-independent, correlated with a reduced or absent leaf.

Leaf fiber bundles – This character was used by Freudenstein and Rasmussen

(1999), however it was observed to be uninformative here. This condition is typically observed in large leaves such as those of Palmorchis where it functions as structural

106 support, but given that many of these basal taxa have small non-plicate leaves or leaves

which are absent, this character would have to be coded as missing in many taxa,

therefore it was excluded.

Column foot- Freudenstein and Rasmussen (1999) decided not to include this

character stating that it was difficult assess homology without a better understanding of

its ontogeny. This character was again explored here for use, but rejected on grounds

similar to that of Freudenstein and Rasmussen (1999). A survey of the literature found

that this was a commonly applied term for any protuberance at the base of the column. A

closer look at the structures revealed that variation in size, location, attachment and

origin, existed. However, after a number of attempts to make homology statements it

was determined that without further detailed study of the origins of these various forms of

this character, especially at lower levels, it was not possible to determine homology.

Further investigation is suggested as this does have the potential to provide additional

phylogenetically informative characters.

Stigma shape- Freudenstein and Rasmussen (1999) included a number of

stigmatic characters not included in this study. Stigma shape has been reported (Dressler

1993) as being associated with the type of pollen produced such that “solid” pollinia

masses are seen with concave stigmas, the result being that there is a better “fit” between

the two. In this study, all the taxa except Sobralia (coded as protruded sensu Freudenstein

and Rasmussen [1999], it was observed that Sobralia lindleyana has a concave stigma)

were seen to possess a concave stigma, and no taxa studied possessed solid pollinia,

either being granular or sectile. It was therefore decided in this study to exclude the stigma condition.

107 TOPOLOGY- Morphology- using the above characters, a matrix of 40 taxa and

30 characters was prepared and submitted for phylogenetic analysis (Table 3.1). The morphological analysis of the equally weighted matrix returned four trees of equal length

(123 steps, CI= 0.333 RI= 0.657). Given the retention of multiple most parsimonious

trees, strict and Adams consensus trees were calculated in order to summarize the optimal

trees. The strict consensus topology had a considerable amount of structure considering

the size of the matrix and number of taxa (Fig. 3.5). Although much of the topology

failed to receive support greater than 50%, many of the traditionally recognized tribes of

Dressler (1993) were recovered, such as Nervilieae (Nervilia), Triphoreae, Tropidieae, and a good portion of Gastrodieae (subclade [SC] 1), as well as a clade of the derived

Epidendroid taxa. Three large, highly structured subclades were recovered, forming a polytomy. In SC 2, Nervilia and Triphoreae form a clade, sister to a weakly supported clade of a polyphyletic Sobralieae (Sobralia and Elleanthus) and the advanced

Epidendroideae. A large polytomy (SC 3) consisting of taxa from Neottieae, Epilyna

(Sobralieae), Xerorchis, Diceratostele gabonensis, Wullschlaegelia, Uleiorchis,

Stereosandra, and Aphyllorchis, as well as a very well supported Tropidieae (Tropidia and Corymborkis) and Limodorum sister to Cephalanthera and Palmorchis.

Since the strict consensus method only shows those clades observed in all MPTs, an Adams consensus was calculated in order to identify those taxa that were in conflicting positions. Most of the topology agreed with that of the strict consensus, with the exception of SC 3 (Fig. 3.6) in which Stereosandra came out in a polytomy at the base of the subclade; Listera formed a polytomy with Neottieae and the mixed clade of

Elleanthus, Epilyna, Diceratostele, Xerorchis and Tropidieae. There were two pairs of

108 identical topologies returned differing only in the placement of Listera and Stereosandra in SC 3 (Figs 3.7-3.8). In one topology, Listera forms a polytomy with Neottia at the base of a clade containing Limodorum, Cephalanthera, and Palmorchis (Fig. 3.7), or alternatively, Listera was sister to Epipactis (Fig. 3.8); Stereosandra was placed with

Uleiorchis and Wullschlaegelia sister to Aphyllorchis (Fig. 3.7) or Stereosandra sister to

Tropidieae (Fig. 3.8). The jackknife analysis found moderate support (70%) for the clade of Diceratostele, Xerorchis and Tropidieae, which was recovered with the Adams consensus (Fig. 3.6).

Goloboff (1994) argued that the only defensible reason to weight characters was to reduce the effect of homoplasy on tree construction. In order to more fully explore these data, a successively weighted analysis was performed. Consistency indices stabilized after two iterations and a single tree of length 27.65957 (CI=0.526, RI=0.805;

Fig. 3.9) was retained. The topology was consistent with that obtained from the unweighted analysis with a few exceptions, and provided resolution in SC 3. In one iteration, Epilyna united with Sobralieae sister to Elleanthus, a position consistent with previous analyses. Likewise, Listera came out with Neottia and Limodorum in a polytomy, this sister to a successively branching clade containing Epipactis sister to

Cephalanthera and Palmorchis, followed by a polytomy of Diceratostele and Xerorchis and Tropidieae. Stereosandra came out in a polytomy containing Uleiorchis and

Wullschlaegelia, this sister to Aphyllorchis.

TOTAL EVIDENCE- the Total Evidence Analysis was run using the combined matrices of morphology, ITS, trnL-F +gaps, nad1 +gaps (Appendix B.1). This matrix included 34 taxa coded for 4858 characters, in which 281 ITS characters were excluded.

109 Sequence characters were excluded based on the relative amount (i.e. >50%) of missing

data for the character position, or regions determined to be so variable that homology assessment was not possible. The resulting parsimony heuristic search returned a single

MPT of 4196 steps (Fig. 3.10; CI=0.712, RI= 0.461). The topology is highly structured, with resolution of many of the tribes with good support, however backbone and tribal level relationships failed to retrieve support (i.e. <50%). A clade of Palmorchis sister to

Neottieae is found at the base of the Epidendroideae, followed successively by

Triphoreae and Epipogium, then Sobralieae. The next to branch is a clade of Tropidieae sister to Stereosandra united with the advanced Epidendroideae and these sister to a successively branching clade containing Xerorchis, Diceratostele, Nervilieae, and

Gastrodieae.

Many of the morphological characters used in this study represent structures associated with leaves and the column. As many of the characters of interest were used in the construction of the morphological tree, evolution of morphological characters will be discussed mapped on the TEA topology (Figs. 3.12- 3.18). The use of multiple independent datasets in a TEA will better reflect the species tree (Kluge 1989, 1998,

2004), thus providing a better hypothesis of character evolution.

DISCUSSION

TOPOLOGY-Morphology- The morphology supports some tribal level compositions that were constructed using more intuitive models of relationships such as

Dressler (1993). In this work, many of these tribes were basal members of the

Cymbidioid Phylad (i.e., clade). Although relationships between the taxa were not

110 depicted, this basal group consisted of Palmorchis, followed successively by Triphoreae,

Gastrodieae, and Nervilieae. The remaining taxa were all basal members of the Reed

Stem Phylad, containing Neottieae, Pogoniinae, Xerorchis, and Sobralieae. Interestingly,

Dressler considered Neottieae and Palmorchis the most primitive members of each of these Phylads. This scheme however does not consider many of the taxa determined by

Dressler as belonging to Spiranthoideae, these being Tropidia, Corymborkis, and

Diceratostele; this was based on the presence of erect anthers.

Clades were obtained in this study that were supported by recent studies using molecular and morphological characters. The four most parsimonious trees returned from the analysis of the unweighted mrophological matrix contained clades of Gastrodieae,

Triphoreae, Nervilieae, and Tropidieae sensu Dressler (1993) with some exceptions. The results of the unweighted analyses were not surprising given the size of the matrix, and the number of characters. As was expected from analyses containing small numbers of characters and relatively few taxa, the topology was weakly supported with low consistency values. Most morphological characters that are informative in this study were also highly homoplasious, but provide a significant amount of the structure observed in

the tree. This results in topologies with low CI values and jackknife support, which is

typical of small datasets with relatively high number of taxa and low number of

characters; adding more characters is the only way to overcome this issue. In addition,

many of the characters used in this study could be considered symplesiomorphies such as

having pollen in tetrads and plicate leaf morphology. Among orchids, Dressler (1993)

111 argued that soft, herbaceous (e.g., flat nonplicate) and conduplicate leaves were derived

from plicate leaves, which is supported by the results of this study (Figs. 3.7 and 3.8).

The reduced or absent leaf morphology evolved a minimum of 5 times while flat

nonplicate and conduplicate leaves each evolved once.

The return of a largely monophyletic “Gastrodieae” sensu Dressler (1993) is not

unsurprising (Fig. 3.5 SC 1). Traditionally this tribe was the repository for epidendroid

orchids that lacked chlorophyll, had an increased reliance on mycoheterophy, and were

missing other derived features that supported other affinities. The absence of leaves and

roots, and possessing a detachable viscidium support the monophyly of this clade. All

taxa are lacking chlorophyll and share a reduced habit associated with this condition.

Epipogium has a basal caudicle, a characteristic of orchidoid orchids, and apparently

convergently evolved given the results of this study. One interesting hypothesis suggested

by this study is the relationship of Stereosandra, Wullschlaegelia, and Uleiorchis. Like

all members of Gastrodieae, these taxa are leafless achlorophyllous plants lacking roots

and have reduced perianth. Wullschlaegelia and Uleiorchis are often considered closely related, and are supported here by single regular massulae (#17). Both Rasmussen (1982) and Szalchetko and Rutkowski (2000) reported that Wullschlaegelia had thin plate-like or lamellate sectile anthers interpreted as the condition of single regular massulae in the current study. Uleiorchis has sectile pollinia, but as no fresh material was available, it was coded as single regular given its close association with Wullschlaegelia (Born et al.

1999), however new material is needed in order to confirm this. Stereosandra has porate pollen (#19) that supports its inclusion in SC3, whereas other Gastrodieae have aporate pollen and Uleiorchis and Wullschlaegelia were coded as missing data for pollen

112 aperatures. In two of the four MPTs obtained, these taxa were united by single regular

massulae, a characteristic not found among Neottieae, whereas other members of

Gastrodieae had irregular massulae. Aphyllorchis, Wullschlaegelia, Stereosandra and

Uleiorchis, which are related in two MPTs, all have two pollinia whereas other

Gastrodieae have four pollinia. With regard to pollinia number, the degree to which

pollinia are divided can be difficult to assess (Freudenstein and Rassmussen 1996), and it

is possible that some reported pollinia numbers in the literature are inaccurate. In

addition, the current study treated bilobed pollinia as being two, a condition observed in

Stereosandra, rather than four pollinia, as others have suggested. Freudenstein and

Rasmussen (1996) argued that bilobed pollina were unique, and should be coded as a

distinct character (referring to the Habenaria types specifically). There are two potential

developmental paths that could result in two bilobed pollinia in general, either incomplete

separation or partial fusion of the pollinia during development. As far as known, no one

has looked at development in theses taxa specifically.

Subclade 2 contains a number of interesting hypotheses. Nervilia sister to

Triphoreae is not a new hypothesis; previously these taxa were often associated based on

morphological similarities (Chapter 1). Morphological characters supporting this

relationship are multiple irregular massulae (#17), the presence of subsidiary cells, and

finger stigmatic cells; none of these is a unique synapomorphy for this group.

Freudenstein and Rassmussen (1999) found Triphora most closely related to diurid

orchids (Orchidoideae) based on the characters of intermediate Type I-II endothecial

thickenings, an “erect” anther, root tubers, fleshy leaves and the lack of subsidiary cells.

Nervilia was among a polytomy of Gastrodia species and Epipogium, sharing

113 epidendroid massulae (multiple irregular as per this study) and root tubers absent. The

anthers of Triphoreae (Fig. 3.2) and Nervilia (see Rasmussen 1982, Fig. 63) are very

similar in structure and morphology, but neither can be considered erect, with bending

being observed in at least one or two regions of the anther; the stigmatic surface cells are

also finger-like. In Dressler’s (1979) original proposal for the tribe Triphoreae, both

Monophyllorchis and Psilochilus were reported to have subsidiary cells, and were coded in this study as indistinguishable from other epidermal cells. Triphora, which has relatively small herbaceous leaves that may or may not have stomata and consequently may lack subsidiary cells. Some species (e.g., Triphora trianthophora, T. craigheadii, and T. ricketii) are green with relatively large, flat nonplicate leaves and others

(e.g., Triphora gentianoides) have reduced bract-like leaves; therefore stomata may be present but not observed.

The relationship of Nervilia and Triphoreae sister to the clade of Sobralieae and the higher Epidendroideae has not been suggested in previous studies. Three characters support this, which also received weak jackknife support (58%). The presence of a single uncontroverted synapomorphy, articulate leaf, supports the relationship between

Sobralieae and the advanced Epidendroideae, as well as two homoplasious characters of root with velamen, and smooth pollen tectum. The finding of Sobralieae most closely related to the advanced outgroups is suggested by other authors. Dressler (1993) placed

Sobralieae in the Reed-stem epidendroid Phylad; while not closely related based on

Dressler’s scheme, the Reed-stem Phylad also contained Arethuseae which was seen as an intermediate group between the Cymbidoid and the Reed-stem Phylads; Arethusa represents this group in this analysis as one of the advanced epidendroids. Freudenstein

114 and Rasmussen (1999) found Sobralia among a polytomy of advanced epidendroids in

the unweighted analysis, and in the PIWE weighted analysis, it was closely related to

Arethuseae. Sobralia has an operculate anther, a condition seen in more derived epidendroid taxa, but a character not included in this current study. With so many derived features, Sobralieae is frequently considered closely related to the advanced

Epidendroideae.

All molecular analyses of Sobralieae strongly support Epilyna sister to or imbedded within Elleanthus (Whitten et al. pers. com., and this study). The morphological analysis in the current study returned a polyphyletic Sobralieae (Fig. 3.5).

Looking at character distributions, it is clear that some characters that are optimized for

Epilyna are missing data. Such entries are suspected to cause Long Branch Attraction during individual character tree optimizations under certain instances; missing data produces effects similar to incomplete taxon sampling, which can cause spurious relationships and Long Branch Attraction (see Wiens 1998). Missing data accounts for

36% (11) of the characters coded for Epilyna and 19% of the matrix generally. One in particular, pollen aperture type (#19) is missing for 28% of the taxa including Epilyna. It is optimized in Epilyna as porate, a synapomorphy for the whole clade to which it is associated (Fig. 3.7-3.8), however, Sobralia, for which this is known, was coded as being inaperturate. All three taxa share the synapomorphy of eight pollina (#24). Based on previous results it is suspected that missing data may be contributing spurious associations to the topology based on optimizations considering only a few present

“weak” characters (see further discussion below EFFECTS OF WEIGHTING).

115 Subclade 3 is composed of members of Neottieae, Palmorchis, Tropidieae,

Gastrodieae and Nervilieae (sensu Chase et al 2003). The single uncontroverted synapomorphy subtending the clade is porate pollen, however it was not coded for six of the 15 taxa (40%). Several taxa in this subclade could be considered misplaced given the results of other studies (Kores et al 1997; Cameron et al 1999; Chase et al. 2003, this study) which support affinities elsewhere. For instance Epilyna is considered a member of Sobralieae, a position supported by the results of the molecular analysis (Chapter 2),

Xerorchis, Stereosandra and Diceratostele are found in Nervilieae (Chase et al 2003 and this study), and Uleiorchis and Wullschlaegelia (Gastrodieae sensu Dressler 1993, or

Arethuseae sensu Chase et al. 2003). The findings of this particular analysis may be the result of missing data (20-30% of matrix for these taxa).

All of the conflict among the four MPTs was the result of Listera and

Stereosandra moving between clades. The latter is missing about 23% of the characters used in this study, while the former was coded for all the characters. Experimental manipulations of the dataset by removing each of these taxa resulted in a topology consistent with that of the Adams consensus of the unaltered analysis. This suggests that missing data are not contributing as much to the associations observed within this clade as discussed previously with Epilyna.

Of the remaining relationships, Listera and Neottia form a polytomy with a clade of Limodorum sister to Cephalanthera and Palmorchis. This was supported by isodiametric seed testa cell shape, which is changed in Cephalanthera to ends isodiametric, middle elongate. A single homoplasious character, pollen unit, supports the clade of Limodorum sister to Cephalanthera and Palmorchis; Limodorum has condition

116 of tetrad, while other two taxa have monads. Palmorchis and Cephalanthera are united based on plicate leaf morphology and covered seed cell border. The results of the molecular analysis (Chapter 2, Figs. 2.7-2.8) place Palmorchis sister to the remaining

Neottieae, in which Aphyllorchis is basal to in polytomy with Cephalanthera, Neottia,

Listera, and Limodorum, and Epipactis in the strict consensus of the parsimony analysis.

Given the results of the morphological analysis alone, it is unclear what the relationships are among Neottieae.

The jackknife analysis strongly supported a clade of Aphyllorchis, Uleiorchis,

Stereosandra, and Wullschlaegelia, although it was not resolved in the strict consensus

(Fig. 3.5), and is unexpected based on current classifications. No study to date has included Stereosandra, given its rarity and difficulty to find. All of these taxa are achlorophyllous mycoheterotrophs, and therefore share a number of homoplasious features associated with this condition such as reduced or absent leaves. Uleiorchis and

Wullschlaegelia are each missing characters (43% and 2% respectively), mostly characters associated with the loss of leaves. The support for Diceratostele gabonensis and Xerorchis amazonica in a polytomy subtending Tropidieae is interesting. Xerorchis has been placed at least tentatively into Nervilieae (Chase et al 2003), and given the results of this study Diceratostele should be included in that tribe as well (Chapter 2).

Xerorchis is missing about 36% of the characters, while Diceratostele is missing only

2%. At least morphologically the placement of these taxa near Tropidieae is not surprising given similar vegetative and morphological features such as plicate leaves and erect anthers.

117 EFFECTS OF WEIGHTING- While weighting schemes are controversial, with the position taken by some authors that no weighting scheme [a priori, to a lesser extent a posteriori] is justifiable (Swofford and Olson 1990), others suggest weighting as a means to explore the data, especially a posteriori weighting (Goloboff 1993, but also see

Allard and Carpenter 1996, and Carpenter 1994). The arguments supporting a priori

weighting schemes are based on the notion that some characters inherently are worth

more than others (Bull et al. 1993; Swofford et al. 1996), however knowing the

importance of a character a priori is not possible in phylogenetics as character

distributions are a product of the evolutionary process and are only interpretable in the

context of a phylogenetic analysis. This is very much a problem for morphological

characters as selective processes influence these and convergences are common. A

posteriori successive weighting uses iterative heuristic searches whereby characters were

reweighted on the basis of their respective rescaled consistency indices (RCI). This

procedure will “downweight” characters with low consistency (i.e. favors characters that

are not homoplastic) in favor of characters that may have better phylogenetic signal.

Goloboff (1993) argues that this is the only defensible weighting scheme for phylogenetic

inference, as by definition, homoplasy is “discordance between the tree and the

character”; given that our goal is to provide a hypothesis of phylogenetic relationships,

characters that are homoplasious do not meet the expectation of a hierarchical

framework. The successively weighted analysis generally produces a more resolved

topology than a strict consensus topology, and provides a means to choose among

multiple most parsimonious topologies (Carpenter 1988, 1994, Goloboff 1993).

118 The weighted analysis returned a topology that was consistent with the

unweighted analysis. Based on the Adams consensus of the unweighted matrix, only

three taxa were problematic, and successive weighting suggests that character conflict

due to homoplasy was influencing patterns as the topologies of the unweighted and weighted analysis only differed in the placement of these three taxa (Carpenter 1988).

Epilyna moves back with the other Sobralieae, and Listera unites with Neottia and

Limodorum. Listera and Neottia are considered closely related, some authors arguing that

they are the same genus, therefore this position is consistent with previous observations.

Stereosandra was seen within the clade of Aphyllorchis, Uleiorchis and Wullschlaegelia,

in a polytomy with Uleiorchis and Wullschlaegelia. These taxa share a number of characteristics such as reduced or absent leaves, an achlorophyllous habit, a terminal inflorescence and two pollinia but no unique synapomorphies. The association of

Stereosandra, Uleiorchis and Wullschlaegelia had not previously been suggested, although Dressler (1993) had included them in Gastrodieae. Chase et al. (2003), based on molecular data, moved Wullschlaegelia to Arethuseae and Stereosandra to Nervilieae.

The results of the molecular analyses of Chapter 2 clearly support Aphyllorchis in

Neottieae, and Wullschlaegelia, which was included in the ITS analysis, was sister to a

clade containing Nervilieae, Tropidieae and the advanced Epidendroideae.

TOTAL EVIDENCE ANALYSIS- One of the stated applications of Freudenstein and Rassmussen (1999) was to provide a morphological dataset that could be used in

larger analyses. Morphology in orchids is strongly influenced by selection pressures

119 associated with pollination syndromes, the loss of chlorophyll, etc., which make

hypotheses regarding morphological character evolution difficult to evaluate. Adding

more characters, in particular those that are more or less independent of the characters of

interest could provide a better understanding of character evolution.

The fact that tribal level relationships are well resolved but not receiving

significant support continues to provide evidence supporting previous assertions that the

diversity of the Epidendroideae may be the result of a rapid evolutionary radiation

(Cameron et al. 1999, Chase et al. 2003). The TEA is the most comprehensive study to

date of the basal Epidendroideae, including five molecular datasets and morphology, and

provides the most resolved pattern of relationships among the tribes of the basal

Epidendroideae (Fig.3.10). This analysis returned many clades found in the molecular

study presented in Chapter 2, but differs in some significant respects, and with a few

exceptions is consistent with recently published molecular hypotheses of tribal

compositions (Chase et al. 2003). Here we find a basal clade of Neottieae and Palmorchis sister to the remaining Epidendroid orchids. Chase et al. (2003) tentatively placed

Palmorchis in Neottieae. Further study is necessary in order to confirm this, however at this time, both the morphological and TEA results provide evidence of a very close relationship between Neottieae and Palmorchis, and given the cumulative results of morphology and molecules, this group is sister to the rest of the Epidendroideae.

Bateman et al. (2006) presented two topologies for Neottieae with each of the genera represented (but excluding Aphyllorchis) using nuclear ITS alone and ITS combined with plastid markers. My findings of relationships within the tribe concur with their observations of Palmorchis sister to Neottieae s.s. followed by Cephalanthera.

120 Bateman et al. however found Neottia/Listera the next to branch off followed by

Limodorum, then Epipactis. In the current study, within Neottieae s.s., Cephalanthera is the first to branch off, followed by a clade of Aphyllorchis and Limodorum; this was sister to Epipactis, followed by Listera and Neottia. While Bateman et al. used more species within genera than the current study I used multiple independent loci representing each of the plant genomes as well as morphology, plus exemplars of all genera. This is the most complete sampling of generic level relationships of Neottieae to date and provides a unique alternative hypothesis of relationships within Neottieae.

There were two interesting hypotheses presented by this analysis. These are the overall position of Triphoreae and that Triphoreae is sister to Epipogium. This latter was an association also observed in the combined parsimony analysis presented in Chapter 2

(Fig. 2.7). Based on the findings of the molecular study it was concluded that Triphora amazonica might be contributing conflicting signal pulling Triphoreae down towards the base of the tree (see 2.8 and discussion of Chapter 2). However as T. amazonica was not represented in the analyses using morphology, the position of Triphoreae certainly cannot be due to the same reasons argued in Chapter 2 and requires further investigation. The rbcL study of Cameron et al. (1999) found Triphoreae and Nervilieae at the base of the epidendroid clade sister to the rest of the Epidendroideae. This was not strongly supported nor was it recovered in the strict consensus, but does provide evidence that a very basal position of the tribe is possible. Dressler (1993) stated that Triphoreae was superficially similar to Neottieae in the flower and Cephalanthera in particular resembled

Triphoreae in the column. While many of the characters thought to be used by Dressler in making this assertion are plesiomorphic, Cephalanthera (Rasmussen 1982: Fig. 5),

121 Triphora, and Psilochilus (see Fig. 3.2) have recurved anther locules and rather

prominent apical beaks. Member of Triphoreae have been associated with Nervilia at one

time or another based on morphology (see Chapter 1 for discussion), in particular the columns of Nervilia and Triphoreae are quite similar (Fig 3.2, see also Rasmussen 1982:

Fig. #63). A relationship between these taxa however is not supported by the TEA results. Within Triphoreae s.s., there is a clear and consistent pattern of relationships emerging. There is strong support for Monophyllorchis branching first, with Psilochilus sister to Triphora.

Nervilia, Xerorchis (both Nervilieae sensu Chase et al. 2003) and Diceratostele

(moved to Nervilieae, see Chapter 2) are found at the base of a clade with Gastrodieae

(sensu Dressler 1993). While there is structure within the clade, it is unclear what the

relationships are among Gastrodieae given the relatively short branches observed. The

observation that Nervilieae and Gastrodieae are in some way related, is similar to

findings of the nad1b-c analysis for which most of Gastrodia were sampled and the

combined molecular results. Morphology alone suggested a different pattern; following

the arguments made in Chapter 2, the results of the TEA may be due to a single locus

(nad1b-c) influencing the pattern. Further work is needed to assess this. Furthermore,

within Gastrodieae, the relationships of taxa such as Uleiorchis, Auxopus and

Didymoplexiella, which were not sequenced for any of the loci used in the study, remain to be clarified.

Sobralieae is seen branching after Triphoreae, followed by Tropidieae sister to the

advanced epidendroid outgroups and this sister to Nervilieae and Gastrodieae. This is the

first study to suggest these relationships. Sobralieae clearly forms a monophyletic group

122 with very good support. Within the tribe, Sobralia is the first to branch off, followed on successive branches by Sertifera, and a clade of Epilyna and Elleanthus. In their composite tree of orchid relationships, Chase et al. (2003) placed Sobralieae and

Tropidieae in a clade branching after Neottieae, sister to everything else. The morphological analysis performed as part of this study supports Sobralieae in a position near Triphoreae (Fig. 3.7) but the combined molecular analysis of this dataset finds

Sobralieae sister to Tropidieae (Chapter 2, Fig. 2.8). The Maximum Likelihood analysis of the combined dataset (Chapter 2, Figs. 2.9 and 2.12) resolves a well-supported relationship between Sobralieae and Triphoreae (including Epipogium).

While weakly supported, a clade of Stereosandra sister to Tropidia and

Corymborkis (Tropidieae) is obtained. Stereosandra was coded for only 23 morphological characters, and was not sampled for any of the molecular loci due to a lack of material. In recent classification schemes, this genus was considered to be a member of

Gastrodieae (Dressler 1993) or Nervilieae (Chase et al. 2003). Given the lack of any unique set of morphological characters supporting a relationship between Tropidieae and

Stereosandra, this must be considered a spurious association due to missing data. This being the case, the TEA results can neither support nor refute either of the hypotheses presented for Stereosandra.

CHARACTER EVOLUTION- Several morphological characters as well as suites of characters are diagnostic of monophyletic groups, however many of these are homoplastic (Fig. 3.11). This is not surprising given the effects of selection on orchids

123 generally, and in particular on characters associated with floral, habit, and vegetative

morphology. The TEA topology is used to discuss morphological character evolution as

this provides the best hypothesis of relationships using all the available data (Figs. 3.12-

3.18).

Spiranthosomes were assumed to be absent among the epidendroid orchids,

however Stern (1999) found spiranthosomes in both Wullschlaegelia and Uleiorchis.

Born et al. (1999) monographed these two genera, reporting on their close relationship.

All recent molecular studies, as well as the current morphological analysis, support

Wullschlaegelia in the Epidendroideae (Molvray 2000, this study). Wullschlaegelia and

Uleiorchis are nested within the Nervilieae/Gastrodieae grade (Fig. 3.10), as such it is clear that the presence of spiranthosomes in these orchids is an apparent case of convergence; this assumes that other taxa in the basal Epidendroideae also lack this trait, however vegetative morphological work is needed among the basal epidendroid taxa in order to evaluate this further.

Among the epidendroid taxa, plicate leaves are the primitive condition, with conduplicate leaves evolving once, in Epilyna (Sobralieae), and reduced or absent leaves five times (Fig. 3.12). Assuming that reduced or absent leaves is a condition associated with the loss of chlorophyll, this means that achlorophylly arose five times; the combined molecular study (Chapter 2) found that achlorophylly arose at least six times among the basal Epidendroideae. Given that the position of Stereosandra is likely due to missing data, it may be argued that when considered under either alternative placements for this genus, reduced or absent leaves have evolved a minimum of four times. Triphora was coded as having flat non-plicate leaves. This condition is a little difficult to determine in

124 plants with very small leaves, and may have been miscoded for this genus given that

Monophyllorchis and Psilochilus both have plicate leaves. Triphora trianthophora and

Triphora gentianoides both have reduced leaves, appearing conduplicate due to their

bract-like appearance, but in T. trianthophora which can have larger leaves, they are

clearly flat-non-plicate, while others such as T. ricketii and T. craigheadii appear to have

herbaceous plicate, cordate leaves similar to those of other taxa in the tribe. Given that

this was an autapomorphy for Triphora, it does not appear that recoding will change the

results of this study any.

Incumbency is a condition associated with epidendroid orchids, and as anther

position is related to pollinium deposition, it is very important to understand it in a

phylogenetic context. Freudenstein et al. (2002) reported that there is considerable

variation in how incumbency is achieved. Within epidendroids, anther bending can occur

late in development (non-vandoids) or early (vandoids), and can be attributed to one of the three regions of growth (Fig. 3.4). Freudenstein et al. (2002) found that the derived vandoid orchids and primitive non-vandoid taxa each express some level of elongation in the column zone contributing to anther bending, and point out that this must be considered the primitive condition in the Epidendroideae. The results of this study confirm this observation in a phylogenetic context. All of the orchids studied here are non-vandoid taxa and experience late stage anther bending (Figs. 3. 13-3.14). Among the taxa studied, it is apparent that column and basal (see Fig. 3.13) zone bending contribute the most to anther bending, with sporogenous zone bending contributing the least to

125 anther bending, showing up at least five times among the basal epidendroid orchids.

Sporogenous zone bending (Fig. 3.14) is found among taxa most considered fully

incumbent, such as Epipogium, Didymoplexis, Palmorchis and Gastrodia (Fig. 3.3 A-D).

Taxa considered erect or subincumbent, such as Triphoreae (Fig. 3.2 A-D),

Cephalanthera and other members of Neottieae (See Rasmussen 1982 and Szlachetko and Rutkowski 2000 for comparisons), tend to exhibit low-level basal zone bending, with

the majority of the bending attributed to the column zone. With the exception of

Palmorchis, which is fully incumbent (Fig. 3.1.C, also Szlachetko and Rutkowski 2000,

Fig 402), Neottieae s.s. is considered suberect to subincumbent (Dressler 1993, Pridgeon

et al 2005). Burns-Balogh and Bernhardt (1985), using a different classification scheme

and taxon sampling, concluded that the condition of suberect to subincumbent was the

primitive condition of the Epidendroideae (indicated by Gastrodieae and Triphoreae); the

significance of this is unclear given that the tree was not produced using any explicit

methodology. From the results of the current study, it is apparent that a suberect anther is

the primitive condition, with the incumbent anther evolving a minimum of five times

among the basal members of the Epidendroideae.

Anther position is associated with pollination syndromes as are pollen types. Taxa

that are pollinated by large insects or bees often have anthers that are fully incumbent and

hard or firm pollinia that are deposited as a single unit on the receptive stigma; suberect

or subincumbent anthers are often correlated with sectile or mealy pollinia (see below for

additional discussion), and large stigmatic receptive surfaces (Burns-Balogh and

Bernhardt 1985). Most of Neottieae are suberect to subincumbent and pollinated by small

flies and gnats, and have soft, mealy or sectile pollinia (Burns-Balogh et al 1987).

126 Palmorchis on the other hand is clearly incumbent having a firm granular pollen mass

(Fig. 3.1C). As such, Palmorchis may have evolved the incumbent anther in association with bee pollination. Like many terrestrial forest species, Palmorchis exhibits gregarious

blooming (Dressler 1984), which increases the probability of outcrossing, especially

when each flower lasts for short periods (Dressler 1981). Pollination has been observed in

two species of Palmorchis in Panama, with specific pollinators being identified for

Palmorchis nitida which was collected with Osiris melanothrix (Anthrophoridae; Shanks

1986) on the plant (Dressler 1984). Palmorchis powellii was reported to be pollinated by

Osiris mourei, however the relationship has never been reconfirmed (Shanks 1986).

Osiris is a group of neotropical parasitic bees.

The anthers of four taxa in this study can be considered erect, with a complete

absence of bending in all three zones; these are Diceratostele (Fig. 3.3), Xerorchis (see

Pridgeon et al. 2005), Tropidia and Corymborkis (see Rasmussen 1982 Fig. 35 and 37).

Given the results of this study, the first two may be considered closely related members

of Nervilieae, and the latter two belong to Tropidieae. The erect anther condition is

considered the primitive condition (Dressler 1993), found primarily outside of the

Epidendroideae; as a result, this condition among the primitive epidendroid orchids

evolved convergently at most three to four times. There is some possibility that

Stereosandra has an erect anther (Szlachetko and Rutkowski 2000) however fresh

material of this genus was not available. The specimen presented by Rasmussen (1982,

Figs. 32-33) was damaged during preparation, and interpretation of anther bending was

made using these figures. It is clearly not fully incumbent, but given the material, the

level of bending in the column zone is made more difficult to assess. New collections of

127 this genus are required in order to better understand the development and nature of anther

positioning. Given the position it has in the TEA tree, sister to Tropidieae, it possible that

it is erect as reported by some authors. This assumes that Stereosandra belongs here,

which as previously pointed out, may not be the case.

Pollen can be packaged into pollinia as either monads or tetrads. Among the taxa

sampled for this study, tetrads should be considered the primitive condition (Fig. 3.15),

and monads are found only in a subset of Neottieae (Palmorchis, Cephalanthera,

Aphyllorchis, and Limodorum). The hypothesis of relationships for Neottieae presented

by Burns-Balogh et al. (1987), who also included this character, suggests two parallel

evolutions of monads within the tribe and that the primitive condition is the tetrad.

However, they refer to the methods of Burns-Balogh and Funk (1986) for methods of tree

construction, which are not explicit. The work of Bateman et al. (in Pridgeon et al. 2005)

using a greater sampling of species within genera, did not include Aphyllorchis, and provides the first attempt to access relationships within the tribe using an explicit methodology; however given that not all genera were included, the origin of monads in

Neottieae cannot be conclusively answered. Therefore, of the studies using a significant sampling of Neottieae, the current study is the first to provide a complete genus level picture of relationships within the tribe. As both conditions, monads and tetrads are seen in the orchidoid outgroups, the primitive condition for the Epidendroideae is ambiguous

(Fig. 3. 15), therefore two alternative hypotheses might explain the origin of monads in

Neottieae. If tetrads are the primitive condition within the subfamily, monads evolved once in Neottieae with a reversal to tetrads in the clade of Epipactis, Listera, and Neottia.

On the other hand if you assume the monads is the primitive condition, tetrads would

128 have evolved independently twice. Both hypotheses require two steps and are equally

parsimonious, however, it is reported that tetrads are the primitive condition in the

subfamily, and therefore the former hypothesis is preferred.

Pollinia can be composed of either free pollen in monads or tetrads, or they can be aggregated into smaller packets of pollen; these pollinia are called sectile pollinia composed of individual units called massulae. Burns-Balogh and Funk (1986) reported

that sectile pollinia evolved five times in their study of the Orchidaceae. Furthermore,

other recent works (Dressler 1990a, b, c) indicate six independent derivations of sectile

pollinia. Freudenstein and Rasmussen (1997) recognized three types in their study of

orchid sectile pollinia. Among the orchids studied here, the primitive condition is free

tetrads or monads (Neottieae), in soft or mealy pollinia (Fig. 3.15). Within the

Epidendroideae, a single regularly arranged layer of uniform shape and size (“orchidoid”

of Freudenstein and Rasmussen 1997) in seen here in Tropidieae and Stereosandra,

Uleiorchis, Wullschlaegelia and Auxopus, which implies a minimum of three independent

derivations of this condition. At a minimum, multiple layers of irregular massulae

(“epidendroid” of Freudenstein and Rasmussen 1997) evolved twice in the Epipogium +

Triphoreae clade, and Gastrodieae and Nervilieae (Nervilia) clade. One thing that is apparent given these results is that there is a trend towards increasing cohesion of pollen grains from monads to tetrads, and increasing organization of the pollinium into larger, organized packets.

Pollinia may be attached either by caudicles, or caudicles and stipes to either a viscidium then a pollinator or directly onto an insect vector. Rasmussen (1986) reported on these stalks in detail. The caudicle is derived from pollen, and among epidendroid

129 orchids, caudicles can be seen as either attached to the apex or base of the pollinia.

Dressler (1993) reported that in orchids generally the presence of a caudicle is associated

with firm or hard pollinia and as the primitive condition for the pollinia is soft or mealy

in orchids, caudicles are derived multiple times. Based on this study (Fig. 3.16), the

primitive condition of the Epidendroideae is caudicles absent, with caudicles evolving

three times: in Sobralia (Sobralieae) and in the clade containing Tropidieae,

Stereosandra, and the advanced Epidendroid taxa, and basally attached pollinia

convergently evolving in Epipogium.

Among the epidendroid orchids, stipes may either be hamuluar or tegular. How

these were coded was discussed previously, however from these results, it is clear that the

stipe evolved a minimum of twice in Tropidieae and at least as far as sampling allows,

Calypso (Fig. 3.17). The stipe of Tropidieae is unique in that it contains a core of

scherenchyma tissues, and therefore may represent an independent derivation, or given

these results, it may be seen as the transitional or intermediate condition between taxa

lacking stipes and the tegular stipe that is observed some of the more derived taxa.

Dressler (1993) reported that stipes have evolved a number times; therefore the use of

this character in a broader analysis with greater sampling and more morphological/

developmental observations would help to address this question.

A recent study by Prutsch and Schill (2000) reported that Cephalanthera

(Neottieae) possesses a concave non-papillate stigma type (Type III; Calder and Slater

1985, Dannenbaum, et al. 1987) which is generally only found in the more derived members of the Epidendroideae (eg., Phaius tankervilliae). Papillate refers to the receptive surface of the stigma, however this is the result of the shape of underlying

130 receptive cells (finger vs prosenchymatic). Neottieae studied by Prutsch and Schill

(2000), with the exception of Cephalanthera, all had a Type II, or papillate stigma (i.e.

finger-like receptive cells). As a result they present a rather interesting hypothesis that

Cephalanthera is an intermediate between Neottieae and the more derived Epidendroid orchids. A number of molecular phylogenetic studies consistently place the genus

Cephalanthera within Neottieae (this study, Batemen et al. 2006). This study (Fig. 3.17) does not support the hypothesis of Prutsch and Schill (2000). Within the Epidendroideae, the primitive condition is clearly prosenchymatic with finger-like stigma receptive cells evolving independently four times, in the clades of Epipactis+ Neottia/Listera,

Triphoreae, Nervilia, and Gastrodia. There are a number of taxa in the

Nervilieae/Gastrodia clade for which this character is equivocal. Given the already stated questions surrounding this grouping, it not clear what the best optimization for this might be. The molecular partition analyses presented in Chapter 2 it can be stated that the nad1b-c partition is driving this association. In addition, Diceratostele and Xerorchis are

part of Nervilieae. Neither of these genera were coded for this character due to a lack of

material, but given their association with Nervilia, it is predicted that they would also

have finger-like stigmatic cells.

With the exception of Cephalanthera, Neottieae are reported in the literature as

having papillate stigmatic receptive surfaces (Prutsch and Schill 2000), however based on

the published images of Kurzweil (1988), it was not possible to establish this condition

for all the taxa, as a result Neottia and Limodorum were both coded as absent for this

131 character in this study. Given the results of the TEA, it can be predicted that Neottia should also possess a papillate stigma with finger stigma cells as previously reported, however, Limodorum is found in a clade with taxa possessing prosenchymatic stigmatic surface cells, therefore this needs to be investigated further.

Pollinium number has often been used to delimit groups of orchids at various levels. Rasmussen (1986) stated that the primitive number of pollinia in orchids is four, which corresponds to the number of pollen sacs found in other lilioid monocots. This study confirms that the primitive condition in the epidendroids is four, finding that among these orchids two and eight pollinia evolved four and two times respectively (Fig. 3.18).

Xerorchis, Sobralia, Epilyna and Elleanthus were coded as having eight pollina, however given the lack of material of Xerorchis it is not clear if the condition of eight pollinia in

Xerorchis and Sobralieae are the same, therefore further work is still needed in order to examine this more thoroughly.

CONCLUSION

It is becoming apparent that the diversity of the Epidendroideae is a result of a rapid evolutionary radiation. This was first pointed out by Cameron et al. (1999), and is indicated by the relatively short inferred branch lengths supporting the arrangement of the five basal tribes. The results of the current study are based on the most comprehensive sampling at the level of the genus performed to date, including characters from both morphology and molecules. The findings presented here are the first to provide a robust hypothesis of evolutionary relationships and a framework with which to address morphological evolution in these orchids. Although the topologies presented failed to

132 receive significant support for many tribal level relationships, the highly structured patterns indicate phylogenetic signal in molecular characters is present. The conflicting patterns seen using different methods (Chapter 2) are probably due more to the application and circularity of model-based methods compared to parsimony, and the technical limitations of likelihood methods. A significant amount of signal was from gap characters, which are excluded in likelihood analyses; the preferred phylogeny is that which minimizes ad hoc hypotheses of homoplasy and which utilizes all the available information.

Considering the significance of the basal Epidendroideae in understanding patterns of morphological evolution within the subfamily, it is surprising that a robust hypothesis of historical relationships had not been presented for these orchids previously.

This is the first study to improve both taxon and character sampling, and while these results provide the first look at a hypothesis of relationships among the basal

Epidendroideae, there are still a number of questions remaining. My findings indicate

Palmorchis is sister to Neottieae, and should be included in this tribe at the base of the

Epidendroideae. Following this clade, on successive branches we find Triphoreae sister to Epipogium, and this clade sister to Sobralieae. The finding of Epipogium sister to

Triphoreae is a new hypothesis, and while both tend to have reduced structures, there is no apparent morphological synapomorphies to confirm this association. Further work will be required with the addition the use of other loci and detailed morphology in order to confirm this. Branching after Sobralieae, Tropidieae form a clade with the advanced

Epidendroideae sister to a clade of Nervilieae and Gastrodieae; Diceratostele gabonensis groups within this clade. Freudenstein and Rasmussen (1999) reported a close

133 relationship between Nervilia and Gastrodieae, and given the results of the current study,

this is confirmed, however, the relationship between Gastrodieae and Nervilieae needs to

be investigated further as this appears to be the result of nad1+gaps partition; additional

locus sampling should help clarify this, as well as better sampling within the two tribes.

Furthermore, Gastrodieae sensu Dressler (1993) is polyphyletic (i.e., Epipogium grouping with Triphoreae) with most of Gastrodieae held together based on morphology and a single molecular marker, nad1+gaps. The Gastrodieae are all achlorophyllous, as such amplification of plastid is usually not possible; sequencing of additional loci representing the other plant genomes will provide more characters for phylogenetic study and could help to clarify relationships.

An objective of this study was to investigate anther evolution since anther position is important for pollination. Among the basal members we find anthers that are erect, or exhibit varying degrees of incumbency. It is clear from these results that the erect anthers of some these epidendroid orchids evolved independently from those observed in the Orchidoideae. The primitive condition among the basal Epidendroideae is suberect/subincumbent. Epidendroid incumbency is achieved via combinations of bending in different regions of the anther, with the primitive condition column zone bending and to a lesser extent, contributions from basal zone of the anther. The primitive condition for pollinia is free tetrads with monads evolving once in Neottieae, with a reversion to tetrads in Epipactis and Listera/Neottia; sectile pollinia have evolved four times. Some authors have suggested that the type III stigma of Cephalanthera, possessing other primitive features, was evidence that it was intermediate between Neottieae and advanced Epidendroideae. Given its position in this analysis, this is a case of

134 convergence. One thing that is apparent here is that there is a trend towards increasing cohesion of pollen grains from free monads or tetrads, into an organization of the pollinium into larger, more solid, organized packets.

Further work is need in vegetative and floral morphology in order to find new characters as well as to fill in some of the missing data and complete the matrix. New molecular loci in conjunction with these data should help to answer many of the outstanding issues of this study.

135

Table 3. 1. Morphological matrix consisting of 30 characters coded for 40 taxa. “?” indicates accessions for which data was lacking due to missing supporting structures or insufficient material. “-” indicates accessions which were not observed for the character and represent missing data.

136

1 2 3 123456789012345678901234567890

Codonorchis 11?00???0?110??000201010?01110 Goodyera 10100?000001001110201010022010 Chloraea 10000?010?11000100201010?12010 Caladenia 1 10000??10110001000201000111101 Caladenia 2 10000??10110001100201000111101 Spiranthes 11100?000000001100201010121100 Aphyllorchis 00-3???100110??000100010112000 Auxopus 0?-3????011?0??111-00000-2---- Cephalanthera 000100110011000000100000111001 Corymborkis 00010010100000011--10110-22010 Diceratostele 0101001010000??-0--00000-02000 Didymoplexis 02-3????01110?-103200000122200 Didymoplexiella 02-3?2??00110?-10--00000-2---- Elleanthus 01-112-1001100110--0000112---- Epilyna 0--202-100010?-10--0000112---- Epipactis 000102110011000100100000012000 Epipogium 0203?20?0111001120201000120000 Gastrodia elata 0203?2??0---001?21200000-?2101 Gastrodia siamensis 0203?2??01110--?2?-000000-0?00 Gastrodia sesamoides 0203?2??01110??12020000001???? Gastrodia procera 0203?2--01100--12?2000000----- Limodorum 00-3????0011000000100000-?0000 Listera 000002110011000100100000010000 Monophyllorchis 0--10--00?101--12020000011---- Neottia nidus-avis 00-3?21-0111000100100000-10000 Nervilia 000102000011001120200010012011 Palmorchis 000100100111000001?000001?0001 Psilochilus 0--10--00?1110012020000001---- Sobralia 010112000010001101210001112001 Stereosandra 02?3?---00010--114110010102001 Triphora 00000?000?01110124200000012101 Tropidia 010100100000000110?10110122011 Uleiorchis 0013????0???0---1-?00010-12200 Wullschlaegelia 0013?2??0?11001110?00010-22000 Xerorchis 00-10---00000------00001-22000 Arethusa 0101000?0111001131200000?12000 Bletilla 010110000111001101200000?12000 Calypso 01010?001111001101210100122101 Aplectrum 010110001111001101210100122101 Govenia 010110001111001101210100?22101

Table 3.1

137

Fig 3.1: A) Epilyna hirtzii (Sobralieae), B) Didymoplexis pallens bud just prior to opening showing granular pollinia, C) Palmorchis trilobulata, D) Gastrodia procera with distinctly sectile pollinia, inset showing stigmatic surface cells.

138

A B

C D

Fig. 3.1

139

Figure 3.2: The columns of Triphoreae. A) Psilochilus mollis (ER 207) with near erect anthers; parallel bars indicated location of B) showing close up of raphide cells. C) Triphora trianthophora from mature anther with inset of anther showing sectile pollinia and tetrads as observed in stage just prior to dehiscence. D) Monophyllorchis maculata (ER208) column damaged during preparation.

140 A B

Fig. 3.2

141

Figure 3.3: Column morphology of Diceratostele gabonensis (ER44) showing an erect anther with distinct staminoda and concave stigma. A) Lateral view, B) ventral view with inset of stigma and rosellum, C) dorsal view.

142

A B

Fig. 3.3

143

A B

Figure 3.4: Diagram of a longitudinal cross section of typical orchid column illustrating an epidendroid incumbent anther and delineating the three zones of bending as described and illustrated in Freudenstein et al. (2002). The zones of bending used in this study are the sporogenous zone (A), basal zone (B) and column zone (C)

144

Figure 3.5: Strict consensus tree of 4 MPTs (L= 123, CI= 0.333, RI= 0.657) returned from the analysis of the parsimony analysis of the morphological matrix. Numbers indicate jackknife support values >50%. SC refers to subclades discussed in text.

145 Codonorchis Spiranthes Goodyera Chloraea Caladenia 1 Caladenia 2 Didymoplexiella Didymoplexis Auxopus Gastrodia elata SC 1 Epipogium Gastrodieae Gastrodia siamensis Gastrodia sesamoides Gastrodia procera Nervilia Nervilia Monophyllorchis Psilochilus Triphoreae 100 Triphora Elleanthus Sobralieae SC 2 91 Sobralia Arethusa 58 Bletilla Calypso Advanced Aplectrum 100 epidendroids Govenia Aphyllorchis Diceratostele Epilyna Sobralieae Epipactis Listera Neottia nidus-avis Stereosandra Uleiorchis Wullschlaegelia SC 3 Xerorchis Corymborkis Tropidieae 100 Tropidia Limodorum Cephalanthera Palmorchis

Figure 3.5

146

Stereosandra Aphyllorchis Uleiorchis Wullschlaegelia Listera Neottia nidus-avis SC 3 Limodorum Cephalanthera Palmorchis Epipactis Epilyna Diceratostele Xerorchis 70 Corymborkis 100 Tropidia

Figure 3.6: Portion of the Adams consensus tree returned from the morphological analysis. Arrow indicates rest of tree that did not differ from the strict consensus topology. Numbers signify Jackknife support for clades not recovered in the strict consensus topology. “SC” refers to subclades discussed in text.

147

Figure 3.7: 1 of 4 MPTs obtained from the analysis of the morphological matrix with character distributions mapped. Black circles are synapomorphies, while unfilled circles are homoplasious characters.

148

Codonorchis 12 29 S piranthes 17 25 Goodyera 15 Chloraea 16 Caladenia 1 2 27 28 10 12 27 28 30 Caladen1 Caladenia 2 Caladen2 Didymoplexiella

3 8 26 2 26 18 28 Didymoplexis 17 10 18 Auxopus

Gastrodia elata SC1 17 21 E pipogium 27 23 29 Gastrodia siamensis 25 Gastrodia sesamoides 12 Gastrodia procera 23 29 Nervilia 17 12 Monophyllorchis 13

25 P silochilus 4 11 14 18 4 8 30 T riphora 8 26 1 4 21 24 E lleanthus 12 20 S obralia SC2 2 5 18 5 17 30 Arethusa

B letilla 6 10 5 Calypso 9 20 22 26 28 Aplectrum Govenia 16 Aphyllorchis 23 2 11 18 20 26 30 S terosandra 17 28 Uleiorchis 26 Wullschlaegelia 4 25 19 Listera 10 27 Neottia nidus avis Limodorum 16 27 Cephalanthera 15 4 30 8 10 18 SC3 P almorchis 25 E pipactis 4 4 24 E pilyna 2 9 26 11 26 Diceratostete 24 6 8 12 Xeorchis 9 17 20 22 23 29 Corymborkis 2 30 T ropidia

Figure 3.7

149

16 Aphyllorchis 23 Ap h y l l o r c h i s 28 17 UUleiorchisle i o r c h i s 26 wWullschlaegeliaul l s c l a e g e l i a 10 19 NNeottiaeottiean anidus-avisvis 27 Limodorum 16 Lim od o r u m 27 SC3 4 30 epCephalanthera h a l a n t h e r a 8 10 18 15 PaPalmorchis l m or c h i s 25 piEpipactis p a c t i s 4 27 Listera 4 Li s t e r a 4 24 Epilya E il na 11 26 2 9 26 DDiceratostelei c e r a t o s t e t e 24 6 8 12 Xerorchis XXerorchise o r c h i s 2 4 12 18 26 Stereosandra 17 20 23 Ste r o s a n d r a 9 22 29 CCorymborkisor y m bo r k i s 2 TTropidiar o p i d i a

Figure 3.8: A portion of 1of 4 MPTs derived from the analysis of the morphological matrix. Black circles are synapomorphies, while unfilled circles are homoplasious characters. “SC” refers to subclades discussed in text.

150

Codonorchis Spiranthes Goodyera Chloraea Caldenia 1 Caldenia 2 Didymoplexiella Didymoplexis Auxopus Gastrodia elata SC1 Epipogium Gastrodia siamensis Gastrodia sesamoides Gastrodia procera

Nervilia Monophyllorchis Psilochilus Triphora Sobralia SC2 Elleanthus Epilyna Arethusa Bletilla Calypso Aplectrum Govenia Aphyllorchis Stereosandra Uleiorchis Wullschlaegelia

Limodorum Listera SC3 Neottia navis Epipactis Cephalanthera Palmorchis Diceratostele Xerorchis Corymborkis Tropidia

Figure 3.9: Single most parsimonious tree obtained from the successively weighted analysis of 30 morphological characters.

151

Figure 3.10: The single most parsimonious tree of 4196 steps (CI= 0.712, RI= 0.461) returned from the parsimony analysis of the total evidence matrix including all Gastrodia species except Gastrodia procera. Numbers indicate jackknife support values.

152 TEA 1of 1 MPTs +gast -procera 30 morpho. L= 4196 ci=0.712 ri=0.461 1 Codonorchis Goodyera Palmorchis Cephalanthera

Aphyllorchis

69 Limodorum Epipactis Neottieae Listera Neottia 97 93 Epipogium Monophyllorchis Triphora Triphoreae 96 84 Psilochilus Sobralia Sertifera 97 Epilyna Sobralieae 89 96 Elleanthus Calypso Advanced 97 Chysis epidendroids SterosandraStereosandra 60 Corymborkis Tropidieae Tropidia Xerorchis Nervilia 95 Diceratostele Didymoplexiella Gastrodia sesamoides 534 gastrodiaGastrodia sp sp. reunion Reunion ER214 99 gastrodiaGastrodia confusa confusa 0801 O801 Gastrodia zeylanica gastrodia zyl 16313 Gastrodieae WullsclaegeliaWullschlaegelia Uleiorchis Auxopus Didymoplexis 50 changes

Figure 3.10

153

Codonorchis Goodyera Palmorchis Cephalanthera Aphyllorchis Limodorum Epipactis Listera Neottia Auxopus Didymoplexis Uleiorchis Wullschlaegelia Gastrodia zeylanica Gastrodia sp. Reunion confusa Gastrodia Gastrodia sesamoides Didymoplexiella Diceratostele Nervilia Xerorchis Corymborkis Tropidia Stereosandra Calypso Chysis Epilyna Elleanthus Sertifera Sobralia Epipogium Triphora Psilochilus Monophyllorchis 10 9 1 4 2 9 2 12 12 29 12 21 10 16 28 9 1 3 2 8 29 12 2 12 10

1 29211 21 29 Chars. that change Unambiguously on branch unique, uniform above changed above, not homoplasy above homoplasy outside homoplasy above an Figure 3.11: Single MPTs obtained using total evidence with unambiguious ambiguous change changes mapped onto branches. Numbers refer to character numbers. Symbolsderived state uncle used :“”synapomorphies, “” homoplasy above, “” homoplasy below, “” homoplasy above and below point on tree.

154

zeylanica Gastrodia

155

Figure 3.12: Distribution of leaf morphology mapped onto the single MPT obtained from total evidence

analysis of 4858 characters from ITS, nad1b-c+gaps, trnL-F +gaps and 30 morphological characters.

Gastrodia zeylanica zeylanica Gastrodia Gastrodia zeylanica zeylanica Gastrodia 156

Character # 10: Sporogenous zone Character # 11: Basal zone

Figure 3.13: Distribution of sporogenous and basal zone anther bending onto the single MPT obtained from total evidence

analysis of 4858 characters from ITS, nad1b-c+gaps, trnL-F +gaps and 30 morphological characters.

Gastrodia zeylanica zeylanica Gastrodia

157

Figure 3.14: Distribution of column zone bending mapped onto the single MPT obtained from total evidence analysis of 4858

ITS, nad1b-c+gaps, trnL-F +gaps and 30 morphological characters.

Gastrodia zeylanica zeylanica Gastrodia Gastrodia zeylanica zeylanica Gastrodia

158

Figure 3.15: Distribution of monads /tetrads and sectile pollinia mapped onto the single MPT obtained from total

evidence analysis of 4858 ITS, nad1b-c+gaps, trnL-F +gaps and 30 morphological characters

Gastrodia zeylanica zeylanica Gastrodia zeylanica Gastrodia 159

Figure 3.16: Distribution of caudices mapped onto the single MPT obtained from total evidence

analysis of 4858 ITS, nad1b-c+gaps, trnL-F +gaps and 30 morphological characters.

F Gastrodia zeylanica zeylanica Gastrodia Gastrodia zeylanica zeylanica Gastrodia i

u 160

3.17: Distribution of stipe and stigmatic cell shape mapped onto the single MPT obtained from

total evidence analysis of 4858 ITS, nad1b-c+gaps, trnL-F +gaps and 30 morphological characters.

Gastrodia zeylanica zeylanica Gastrodia Gastrodia zeylanica zeylanica Gastrodia 161

Figure 3.18: Distribution of pollinium number mapped onto the single MPT obtained from total

evidence analysis of 4858 ITS, nad1b-c +gaps, trnL-F +gaps and 30 morphological characters.

CHAPTER 4

A MONOGRAPH OF THE ORCHID GENUS PSILOCHILUS (TRIPHOREAE,

EPIDENDROIDEAE)

INTRODUCTION

The genus Psilochilus is composed of 7 species of neotropical orchids from south- central South America, north through Central America and the Caribbean (Fig. 4.1).

Tropical botanists, especially orchidologists, are most often interested in epiphytes consequently terrestrial species are often overlooked. This is especially a problem with

species having short-lived flowers and rather inconspicuous habits such as Psilochilus.

This genus is found in tropical rainforests of moderate to deep shade. It has been described as similar in appearance to Zebrina pendula (Commelinaceae), in reference to the green with silver striped leaf surface above and purple or magenta below seen in some populations. Morphologically, all species are similar in general appearance, with most of the variation found in the shape of the labellum (Fig. 4.2), and the shape of the leaf. This is the first monographic study of this genus.

162 GENERIC NOMENCLATURE AND HISTORY- The genus name derives from a description published by Barbosa Rodrigues (1882) in Genera et species orchidearum novarum with the description of Psilochilus modestus. Prior to this publication, many authors and subsequent authors (for examples see Reichenbach 1859, Cogniaux 1906,

Williams 1970) considered members of this genus as Pogonia or related taxa. The first reference to a species now considered Psilochilus is the publication of Pogonia macrophylla (=Psilochilus macrophyllus; Arethuseae, Euarethuseae) by Lindley (1858).

Bentham and Hooker (1893), while not specifically referring to any species, placed Pogonia and its relatives (Triphora, Cleistes, Nervilia and Eupogonia) into the tribe Neottieae. Pfitzer (1897) did not recognize Psilochilus at the level of the genus, instead regarding it as a section of Cleistes (Monandrae, Pogonieae, Neottiinae). In this work he made a reference to three species from Brazil, describing the leaves as sheathing and petiolate. Ames (1922), based on a discussion of Pogonia and Triphora by Holm

(1900), suggested that Psilochilus was distinct from Pogonia, Isotria and Cleistes in possessing an erect anther on an entire or simply lobed column, with pollen grains

“compound” (i.e. sectile) with a pitted or reticulate exine, the same as Triphora (but distinct from it on the basis of an “articulate anther”). Schlechter (1911-1914, 1926a) placed Triphora and Monophyllorchis, of which Triphora had also traditionally been regarded as Pogonia, into the subtribe Vanilleae (Monandreae, Acrotonae,

Polychondreae); Pogonia was also placed here. Schlechter did not specifically mention

Psilochilus by any reference to a species, but given that for the most part he used the works of Pfitzer as his basis, Psilochilus was most likely treated as by Pfitzer, in Cleistes.

Mansfeld (1937) using the classification system of Bentham and Hooker, but influenced

163 by Schlechter, combined the taxa of Vanilleae and Nervilieae into Vanillinae. Again it is not made clear exactly what taxa were included, as few specific references to species or genera were made. The first comprehensive work to go into intra-tribal composition of the Orchidaceae was Dressler and Dodson (1960). These authors included Psilochilus in

Pogoniinae (Vanillinae, Epidendreae, Orchidoideae). Concurrently, Garay (1960) also working on family level organization, mentioned Psilochilus in passing, referring it to the

Neottioideae. Brieger (1975), following the previous classification of Schlechter, treated

Psilochilus as a member of Pogoniinae. Dressler (1979) segregated three species from

Nerviliinae and Pogoniinae to make up the tribe Triphoreae; these included Triphora,

Psilochilus and Monophyllorchis. Psilochilus has remained in Triphoreae since this, with the most recent discussion in Pridgeon et al. (2005).

MATERIALS AND METHODS

MATERIALS- As previously stated this is not an often-collected genus, so in order to augment herbarium collections fresh materials were field collected in Panama,

Ecuador, Brazil and Puerto Rico. Specimens were prepared for study by pressing plants and preserving flowers and buds in FAA or 70% EtOH. For this project, specimens were obtained from A, AMES, BR, K, MO, MU, NY, S, SEL, and US, and other specimens were examined at QCA and QCNE. Spirit collections were borrowed from MSB and

SEL.

METHODS- The principle roles of systematics are to understand biological diversity, its evolution, and distribution. The most basic level of biological organization, in which there is still an apparent hierarchic order, is the species. The species is the

164 smallest most inclusive grouping that is diagnosable as being the same on the basis of

some criteria. Yet it is well known that there is considerable variation within groups of

similar organisms, and between populations of the same species. As a result, a number of

species concepts have been proposed to aid in the delimitation of species. For this study,

the morphological species concept will be used, as this is ideal for use with preserved materials and herbarium specimens.

Images of specimens were taken using a Nikon Coolpix 995 camera attached to a

Nikon SMZ1500 compound dissection light microscope with a HR plan APO 1x WD54

Nikon lens. Photos of plants in the field were taken with either a Nikon D50 or a Nikon

N60 SLR with an AF micro Nikkor 105mm lens using Fujichrome, Velvia 100 film. All illustrations were made from photos taken of fresh flowers or plants and herbarium sheets.

Distribution maps were made using planiglobe® beta (Körsgen, R. Kantz, and M.

Weineltk, k+w - digitale kartografie GmbH). Dots on the maps represent localities of

observed materials only.

TAXONOMY

Psilochilus Barbosa Rodrigues, Gen. Sp. Orchid. Nov., 2, 272 (1882).

Type species: Psilochilus modestus Barbosa Rodrigues.

Description: Habit terrestrial, generally solitary, herbaceous, decumbent and

sympodial. Stem erect, terate, smooth, purple or purple suffused with green, rhizomatous;

roots thick and fleshy, villose, unbranched, arising from basal nodes of the plant,

165 occasionally seen at other nodes. Leaves sheathing, petiolate or clasping, alternating, non- articulate, plicate, blade variously ovate, elliptic, lanceolate, acute or acuminate or obtuse at tip, upper surface light or dark green, may or may not possess markings of light green or white above, purple or purple-green below. Inflorescence a terminal raceme one to few flowered borne in succession, floral bracts ovate, acute, distichously arranged. Flowers erect. Sepals and petals free, green to purple, acute or blunt rounded. Sepals keeled, petals not. Labellum free, with claw, possessing one to three calli along upper surface; trilobed, mid-lobe fringed, crenulate, crisped or smooth, lateral lobes toothed or smooth, rounded or acute, may be hidden by mid-lobe in some cases. Column lobed at apex possessing a distinct rostellum; anther terminal and suberect or reflexed, pollinia four, soft, mealy pollen in tetrads (Fig. 3.2.A-B). Seed elongate, thicker in the middle, tapering towards ends, whitish-brown, testa cells distinctly elongate towards ends, less so towards the middle (Fig. 4.2).

Etymology: The name Psilochilus stems from the Greek, psilos, meaning bare, and cheilos, meaning lip, a reference to the glabrous lip of the type species.

Nomenclatural orthographic variants: Psylochyllus (Reis et al. 2004).

Distribution: Southern Brazil, north and central South America, Central America, southern Mexico and the Caribbean. (Fig. 4.1).

Ethnobotany: The only known medicinal or cultural uses of Psilochilus are from the Ecuadorian indigenous people, the Shuar. The name “kunsui” is used to refer to plants of this genus and are plants of medicinal use with reserved knowledge. What is known is that it is used in sacred rituals for the treatment of unspecified menstrual cycle conditions and in preparing the woman for pregnancy. It is an important component of establishing a

166 positive outlook for both the mother and baby during the pregnancy and for the baby after birth; the stripes of the leaves signify the pathway the child should follow in life, and indicate good intelligence. As with most cultures, this is particularly important for the first child. (pers. com., Sra. Teresa Dominga Shiki Masuink, President Omaere

Ethnobotanical Park, Puyo Ecaudor).

Cultivation: In general these plants are not cultivated widely as they possess neither showy nor persistent blooms. Cultivation however was needed in order to obtain information relevant to this study, therefore some basic observations are presented.

Psilochilus can be found under natural conditions growing from ca. 800 to 2500m in the

Ecuadorian Andes. Rains generally occurred daily in the area of Ecuador in which these plants are found. Plants in the wild would be running along the surface or just below leaf litter loosely attached to the substrate with new roots forming at the basal nodes. The author purchased plants from Ecuagenera Ltd. (Cuenca, Ecuador) as P. carinatus. Potting media used a combination of loose coarse bark, potting soil, sand, and sphagnum moss with Perlite added to improve drainage. Given the habit of the plants, roots were exposed but in loose association with the potting media. This plant was kept under fluorescent lights with lighting conditions as for Phalaenopsis (ca. 1000-1,500 foot candles), in controlled conditions for humidity and temperature. Average temperatures were 70ºF

(21ºC) during the day and 55ºF (12ºC) nights, consistent with cool to moderately warm conditions. Potting media was kept evenly moist but allowed to lightly dry out between watering so as to imitate conditions observed in the wild. Under artificial lights the plant survived well, set bud, but never flowered. Flowers matured and opened only under natural light conditions.

167 Phenology and pollination: This will be treated within the respective species accounts however some general observations will be reported here. Psilochilus blooms successively, from an indeterminate inflorescence. Flowers are open for up to four days, with plants considered to be gregarious or synchronous bloomers such that individuals in a population will all open at the same time. Reports exist which indicate that cleistogamy and autogamy are common (Ackerman 1995), referring to either the triandrous form of P.

physurifolius (Jost pers. com) or P. macrophyllus (Ames 1922), however in at least one

case (Psilochilus modestus) it is reported that while it is possible to self fertilize, it rarely

occurs.

ARTIFICIAL KEY TO THE SPECIES OF PSILOCHILUS

1. Claw of the labellum <5mm. 2. Petiole absent or extremely short, leaves clasping the stem; lacking a keel in the claw of the labellum .…………………………. 4. P. macrophyllus 2. Petiole distinct, sheathing the stem; with a distinct keel in the claw of the labellum. 3. Petiole < 0.5cm, lateral lobes of the labellum oblique triangular ………..…………………………………………….… 1. P. carinatus 3. Petiole >1cm, lateral lobes of the labellum acute equilateral triangular ……………………………………………...………… 5. P. modestus

1. Claw of the labellum >5mm. 4. Lateral lobes of the labellum acute; leaf blades elliptic to elliptic- lanceolate …………………………………………...... 7. P. physurifolius 4. Lateral lobes of the labellum blunt-rounded; leaf blades ovate. 5. Sinus between lateral lobes and midlobe of the labellum >4mm …………………………....……..………….……... 2. P. dusenianus 5. Sinus between the lateral lobes and midlobe of the labellum <1mm, lateral lobes. 6. Leaves narrowly ovate to ovate-lanceolate (8-9 x 3-5cm); midlobe suborbicular to subquadrate, margins crenulate-erose …………………………………………………… 6. P. mollis 6. Leaves broadly ovate (to 15 x 10cm); midlobe triangular, margins entire …………………….…..……. 3. P. ecuadoriensis

168

1. Psilochilus carinatus Garay. Botanical Museum Leaflets. 26(1): 2.1978.

TYPE: Colombia: Sierra Nevada de Santa Maria, Purdie s.n. (holotype: K!).

Description: Habit to 30 cm tall. Leaves green with or without stripes 7-7.5 x

2.5cm, ovate to ovate-elliptical, acute to sub-acuminate, leaf base rounded, possessing a short petiole (0.5-1cm). Inflorescence erect, bracts ovate, conduplicate. Sepals green, dorsal sepal sub-carinate linear-oblong to lanceolate, acute, to 20 x 3mm. Lateral sepals to 18-20 x 3.5 mm pale green falcate-linear, acute. Labellum green tinged with purple, with long claw (5mm) possessing a distinct keel extending from the base but tapering towards the tip, 15-17mm long. Lateral lobes oblique, triangular, medial lobe subquadrate

-round, margins erose-denticulate. Midlobe, 17 x 7 mm, possessing two calli. Column thin arching, subtruncate-denticulate, to 15mm long. (Fig. 4.3.G-H).

Etymology- refers to the carinate or keeled claw.

Distribution: Columbia, Costa Rica and Panama (Fig. 4.4).

Habitat: Lower montane rainforest (in Costa Rica) ca 800-1800m.

Blooming times: July – December.

Taxonomic notes: Dressler (2003) described an unidentified species based on the specimens Harrera 1484 and Grant et al. 90-00832. The description is consistent with that of P. carinatus and an examination of the specimens of Grant and Herrera confirms this. In Dressler’s description, he pointed out that the labellum of the Herrera specimen

169 possessed a single keel, an observation not confirmed by examination of the specimens,

however, additional material of these collections would help to clarify this.

Specimens examined: COLOMBIA. Fusagasugia, Holton 23-Dec-1852 (K).

PANAMA: Bocas del Torro, in vicinity of Fortuna Dam along Pipeline road to Chiriqui

Grande, at continental divide, 2.8 miles from divide, ca. 8˚45’N and 82˚15’W alt. 850-

950m, McPherson 9679 (MO). Chiriquí, vicinity of Fortuna Dam ca. 8˚45’N 82˚14’W forest above lake ca. 1100m, McPherson 9847 (MO). COSTA RICA. Limon, Guapiles,

Los Angeles, San Miguel, between the Rio Blanquito and the Rio Blanco 1300m, Grant et al. 90-00832 (SEL photos). Limon, Guapiles, Los Angeles, San Miguel, between the

Rio Blanquito and the Rio Blanco 1300m, Grant et al. 90-00832 (US). Guanacaste:

Parque Rincón dela la Vieja, Libreia. Cabeceras de Quebrada Rancho Grande, bosque circundante a Meseta Agracatales, 10˚ 46’N 85˚49’W 1300-1400m, Herrera 1484 (MO,

SEL). Alajuela: Upala, Bijagua El Pilon, ladera Atalantica del Volcan Tenerio, cuecna alta del Rio Celeste, 10˚43’30”N 85˚00’25”W 1500-1800m, Herrera 2144 (SEL).

Puntarenas on border with Alajuela in lower montane rainforest. Sendero brilliante at ca.

1600m, Atwood 89-282 (SEL).

2. Psilochilus dusenianus Kraenzl. ex Garay & Dunst. Venezuelan Orchids

Illustrated 3: 274. 1965. Type: Brazil, Panara Monte Alegra, Dusen 9022 (holotype: S, photo!).

Description: Habit to 30cm. Leaves to 10 x 4cm ovate to ovate-lanceolate, petiolate (1-1.5cm) with sheathing bases, blades with prominent nerves, green or dark

170 purple with or without silver/white stripes. Inflorescence with clasping, conduplicate bracts. Flowers few in succession. Sepals thick and fleshy, dorsally carinate. Dorsal sepal

30 x 5mm, linear-elliptic, acute. Lateral sepals falcate 28 x 5mm, acute. Petals shorter than sepals, 27 x 5mm. Labellum claw short (ca. 3mm), trilobed with deep wide (>4mm) sinus, lateral lobes 18 x 9mm, midlobe 5mm, with three prominent calli tapering to two.

Midlobe long narrow at base flaring near tip, orbicular or sub-globose, margins entire to weakly erose-crenulate. (Fig. 4.3.J).

Etymology: Kraenzlin named this species for Per Karl Hjalmar Dusén, the collector of the type material.

Distribution: Venezuela and Brazil (Fig. 4.5).

Habitat: In Venezuela it is collected in damp forests, or cloud forests (Carnevali et al. 2003) from 850-3500m.

Specimens examined: VENEZUELA. Boliviar, Uaipan-tepui, the summit of the west peak of Uaipan, 1980m, Agostini and Koyama 7488 (NYBG). Rio Negro, Cerro

Aracamuni summit, Proa. Camp, Liesner and Carnivali 22537 (MO).

3. Psilochilus ecuadoriensis ined. Rothacker and Jost. Type: Ecaudor,

Esmeraldas Reserva Canande Fundacion Jocotoco. Ca 500m Oct. 19, 2005, JOST

7955 (holotype QCA; OS [spirit]).

Description: Habit terrestrial, erect, to 30cm tall. Leaves petiolate (to 4cm) sheathing, green with 5 ribs broadly ovate (to 15 x 10cm), short acuminate. Inflorescence an erect raceme, with conduplicate acute bracts, with single flowers borne in succession.

171 Flower open, erect. Sepals green, strongly keeled, lateral sepals falcate, lanceolate, acute.

Dorsal sepal 25 x 5mm, acute. Petals similar to sepals, light green to white, 20 x 5mm, falcate, rounded, with a distinct keel. Labellum ca 22mm, white with purple along the margins, yellow with purple speckling in throat, with long connate claw (ca. 11mm), possessing two distinct calli extending as one to near the apex of midlobe. Lateral lobes rounded, falcate ca. 5 x 2-3mm extending behind the midlobe, midlobe triangular, (7 x

8mm) margins entire. Column ca. 20cm, with two broad wings, possessing a prominent apical beak, anther subincumbent to suberect, with locules recurved to suberect. (Figs.

4.6 -4.7).

Etymology: Named for the country in which the type material was collected.

Distribution: Ecuador and Panama (Fig. 4.8).

Habitat: Lowland tropical rainforest found in open, 500m (in Ecuador).

Blooming period: October.

Taxonomic notes: Collected in flower in October, the plant was described at the time of collection by the collector, Lou Jost, as being a robust plant for the genus and found in primary tropical rainforest growing in an open understory. Given the results of a phylogenetic analysis of the genus using the chloroplast trnL-F intergenic spacer

(Chapter 5), this species is most closely related to P. mollis. In Dressler (1981) there is an illustration of P. mollis made from a plant collected in Veraguas, Panama. The illustration of the flower is strikingly similar to the type specimen of this material and is clearly referable to this species. According to Dressler (pers. com.) this plant was identified by C. Dodson as P. mollis, however this is clearly a distinct species differing by the long cunate claw and triangular midlobe with entire margins.

172 Representative specimens: PANAMA. Veraguas, on the east ridge of Cerro

Arizona, above Santa Fe de Veraguas, 30 Oct. 1977, Dressler 5734 (FLAS).

4. Psilochilus macrophyllus (Lindl.) Ames. Orchidaceae. 7:45.1922. Pogonia

macrophylla Lindl. Annals and Magazine of Natural History, ser. 3 1: 335.1858.

Type: Cuba: in the east of Cuba, Wright 615 (holotype:K-L!, isotype: LE, PH).

Description: Habit fleshy up to ca. 40cm. Stems purple, ascending from creeping rhizome, erect to 31cm. Leaves, sheathing, sessile clasping to short petiolate, blades ovate acute to occasionally weakly acuminate, 5-10cm x 2.5-7cm, green with or without whitish longitudinal stripes above and with or without purple below. Inflorescence erect, flowering in succession, one to several flowered, floral bracts broad, conduplicate, less then 1cm long. Flowers erect, produced in succession. Sepals greenish yellow or red, linear-oblong, acute-acuminate, dorsal sepal 11-12 x 2mm, lateral sepals 11-12 x 2mm.

Petals linear falcate, 10-11 x 2mm. Labellum (Fig 4.3.D), cunate, ca. 12-15mm long with short claw, trilobed. Lateral lobes sharply acute to acute-obtuse, to 6 x 1-1.5mm, midlobe

4-6mm, suborbicular to subquadrate, crisp-erose, disk whitish with 2 longitudinal keels that extend to near the apex of the lip. Column, slender, nearly as long as the lip.

Etymology- Greek, “macro” meaning large, and Latin “folius” or leaves, referring to the large leaves of the plants.

Distribution: Central America, Mexico, Tropical South America and West Indies

(Fig. 4.9).

173 Habitat: The species is found in a diverse range of habitats from 200-1200m, typically a terrestrial of deep shade in leaf litter although occasionally found growing on rocks (i.e., Hamilton and Davidse 2625), tree falls, and as an epiphyte in Nicaragua (i.e.,

Rueda et al 15749, Heller 10463, and Heller 3756) and Saint Vincent (Judith and Judith

1951). In Nicaragua, Heller reported that he found #3756 a full 10 feet (ca. 3.3m) above ground attached to mossy branches, moreover he reported in a letter attached to the specimen he had never seen any plants in Nicaragua that were not epiphytes. Epiphytic habit is not common, however in rare cases when conditions are good, I have seen a closely related species, Monophyllorchis maculata, as an epiphyte on trees and tree trunks, along the river bank in the Rio Pastaza valley, Ecuador.

There are few cases where habitat and known associates are discussed. In Puerto

Rico, Ackerman (1995) reported that this species is found at 700-1100m, in terrestrial habitat, among a dense leaf litter or in clay soils of wet montane forests. Fawcet and

Randle (1910) reported that Psilochilus macrophyllus (as Pogonia) is a plant of moist shady habitats and can be seen in bloom year round. A Haitian specimen was collected in

Eugenia jamnbos (Myrtaceae) woods, and in Guatemala it was found in Liquidambar –

Pinus forest. In both Bolivia and Nicaragua (900-980m) specimens were collected in cloud forest. Hawkins collected specimens in Belize in a tropical moist hardwood forest composed of limestone soils. Dressler (#1501) collected a specimen in Chiapas, Mexico with detailed information regarding associates and habitat. He reported that the plants were found in moist cloud scrub and pine forest (Pinus, Hauya, and Saurauia), with tall evergreen Quercus, Talamuma and Cymbopetalum.

174 Phenology and pollination: Late spring to fall (March to December in Trinidad).

Ackerman (1995) reported self-pollination, with the occurrence of cleistogamy, and considerable seed set. Additionally he reported that the plants he observed lacked a

rostellum, however upon examination of material from Puerto Rico, there is a clear and

distinct rostellum on all material observed. It would be of interest to observe these plants

in vivo to see if the high seed set was due to selfing or cross-pollination. Fawcett and

Randle (1910) reported that flowers are found year round in Jamaica.

Specimens examined: BELIZE. Cayo: 0.2km W of Baldy Beacon UTM24-

102805, Catling and Brownell 55.1 (AMES). Toledo, Camp 3, SE Union camp, trail from

camp 3 toward Cabro on the Jimmy cut trail, 16˚23’14”N 89˚04’37”W 665-700m,

Hawkins 1463 (MO). BRAZIL. Municipo: Miguel Calmon near Jacobina in the north of

Chapada Diamantinia ca 1,000m R. M. Alves s.n. (illustration In Orchids from Chapada

Diamantina). BOLIVIA. Chochabamba , Cloud forest NE of Chochabamba towards

Villas Tunari, alt. 950m, Luer et al. 3570 (SEL). CUBA. Loma Gardero S. Maeitro, Roig et al. 6670 (NY). Oriente: Sierra Nipe, near Woodfred, 450-500m, Shafer 3150 (AMES).

Oriente: Vedado-Habana, Sierra Maestra, Loma del gato, Alain 366 (AMES). Oriente:

Sierra Maestra Pico de la Bayamesa, N. Slope, Alt. 4900-5200ft., Schultes et al. 605

(AMES). Crest of Sierra Maestra, Between Pico Turquino and La Bayamesa, alt. 1350m,

Morton and Acuna 3526 (AMES). Crest of Sierra Maestra, Between Pico Turquino and

La Bayamesa, alt. 1350m, Morton and Acuna 3526 (US). Slopes of La Bayamesa, crest

of Sierra Maestra near Serradero San Antonio de los Cumbres, alt. 1500-1800m, Morton

9226 (US). Southren Baracoa Region, Puerto del mate, Siera de Jamias, Leon 12283

(NY). Sierra Nipe, near woodfred, Oriente, Shafer 3150 (NY). COSTA RICA. La Palma

175 de San Ramon, Costa Rica, Alajuela 1113 (NY). Barring ’86 (F). La Palma, alt. 1250,

Brenes (116)480, (116)446, (244)1434 (AMES, F). La Palma de san Romón, Quirós

(238)220 (AMES). DOMINICA. NNE Roseau: Forêt dense entre Providence Estate et

Sylvania Estate 660m, Jérémie 1141 (A). Saint Paul, trail heading to Morne Trois Pitons

Rainforest, Wasshausen and Ayensu 389 (US). DOMINICAN REPUBLIC. “Las Abejas”,

wooded valley about 10 miles W of Aceitillar, Liogier 14199 (NY). Sobre la cima del

Pico Igau, Prov. De Santiago, 960m, Jimenez 1240 (US). Arroyo Jiconie’, District of San

Jose de Las Matas, Prov. Santiago, 750m, Valeur 723 (K, NY, US). Sierra de Baoruco,

Prov. Barahona: Loma “Pie Pol” [Pie de Palo en el mapa] de La Guasara de Barahona,

18˚10’N 21˚12’W, Zanoni et al. 38622 (NY). MT. Drablotum Llyod 909 (NY). MT.

Drablotum, Llyod 909 (K). Firme de Banilejo, Piedra Blanca, alt 800m, Liogier 19951

(NY). Arroyo del la Vieja, Loma la Vieja, An Juan, Prov. De Azusa, Ekmann H 13422

(AMES). Cordillera central, Prov. De Azusa, San Juan, Loma la Vieja, at Arroyo del la

Vieja in forest c 900m, Ekmann H 13422 (AMES, US). Prope Constansa 1250m in sylvis

umbrosis humidis, Turckheim 3134 (AMES, K, NY). Prov. Barahona at Paemingo in

sylvis 1400m, Fuertes # IV,1912 (AMES, NY). EL SALVADOR. San Salvador, Cerro

Montecristo, 2200m, Hamer 687 (SEL). GUADELOUPE. Rivere Noire, Anno 1093

(NY). Dugomier (Ténèbe) alt. 800m, Stehle 1304 (AMES, NY). Bains-Janis, 550m,

Questel 426, 4140, 4979 (US). Bains Chauds du Matouba, 1050m, Stele’ 2571, 1381

(NY). Terrestrial, plants on moss, [ca.16.25° -61.583333], Duss 3388 (NY).

GUATAMALA. Dept. Alta Verapaz: Mountains along road Tactic and divide on road to

Tamahú, alt. 1500-600m, Standly 91359 (F). Dept. San Marcos, above Finca el Porvenir,

Up Loma Bandera Shac lower S-face slope of Mabess River, 2000ft, Nichols 160

176 (AMES). alt. 1300-1500M, Steyermark 37344 (F). Dept. Huehuetenango: Cerro

Victoria, Sierra de los Cuchamatanes near Baraillas, alt. 1800-2000m, Steyermark 49721

(F). Dept. Huehuetenango: vicinity of Maxbal about 17 miles north of Barillas, Sierra de

los Cuchumatanes, alt. 1500m Steyermark 48897 (AMES). HAITI. Gros Chevel, Morne

des Commissaires, Holdridge 1951 (AMES). Rivere Glace, Elev. 2000’, 18˚15’N

73˚50’W, Curtis 16 (AMES). Massif de la Hotte, Western group Pestel, Mount Delecour,

Ekman 9000 (AMES, K, US) Gros Chevel, Morne des Commissaires, Holdridge 1951

(NY). Summit of Delcor, Eyerdam 348 (AMES, NY, US). JAMAICA. St. Andrew, Mt.

Horeb peak, 4750ft., Podzorski JA12 (K).Mabess River below Vinegar hill, 3000ft.,

Underwood 1349 (NY). Morris, JP2090 (NY). Jamaica, Purdie sn. (K). Below Vinegar

Hill, Botanical Departent 6462 (NY). Vinegar Hill, Harris 6252 (K). Ridge below

Vinegar Hill, Harris 10097 (AMES, K, NY). Mabess River, 2000ft, Nichols 160 (K).

Mabess River, 2000ft, Nichols 160 (AMES, NY). Jamaica, Morris XI 1885 (K). South eastern slopes of Stone Hole Bump, St. Thomas 600-800m, Maxon 9015 (NY, US).

Upper southern slopes and summit of Maccasucker Bump, St. Thomas, alt. 825-1025,

Maxon 9551 (US). MARTINIQUE. Camp Colson, Duss 4484 (NY). MEXICO. Chiapas:

Municipo de Ocosingo, near Laguna Octoal Grande, ca. 25-30km SE of Monte (Cerro)

Libano (45km E of Ocosingo) elev. 950m Dressler 1501 (AMES). Chiapas: Finca el

Suspiro,near Beriozabl, Dressler 2257 (US). MONTSERRAT. Upper W slopes Chances

Mt., Adams M17 (A). NICARAGUA. Near top of Mombacho volcano, 1300m, Heller

3756 (SEL). Zelaya: Cerro La Pimienta number 1, Summit and area adjacent to summit, ca. 13˚45’N84˚59’W, elev. 900-980m, Pipoly 5097 (MO). Madera Volcano, Ometepe

Island, Rives Prov. 4500ft, Heller 10436 (SEL). Municipo de Wiwili, Reserva Cerro

177 Kilambe, 13˚34’N 85˚42’W 1400-1750m, Rueda et al. 14958 (MO). Jinotega, Reserva

Kilambe, Municipo Bocay, Reuda et al. 15749 (MO). Jinotega, Reserva Kilambe,

Municipo Bocay, Comunidad Santa Teresa de Kilmabre, 13˚34’N 85˚39W, 900-1100m,

Reuda et al. 15550 (MO). Zelaya: Cerro La Pimienta number 1, Summit and area

adjacent to summit, ca. 13˚45’N84˚59’W, elev. 900-980m, Pipoly 5097 (SEL). Granada:

summit of extinct volcano Mombacho, Atwood et al. 7057 (MO). Granada: summit of

extinct volcano Mombacho, Atwood et al. 6737 (AMES). Dpto. de Matagalpa: Macizos

de Peñas Blancas, SE side drainage of Quebrada El Quebradon, Peak of WNW of Hda.

San Martín, ca. 13˚15’N 85˚39’W, elev. 1400-1600m, Moreno and Elmquist 21228

(MO). Dpto. Nueva Segovia, Las Planes, Moreno 26393 (MO). PANAMA. Panama:Area

surrounding Rancho Chorro, Mountians above Torti Arribam Canazas mountain chain,

400-700m, Folsom et al. 6692 (MO). Coclé: Carribean side of El Cope, 8˚45’N 80˚35W,

200-400M, Hamilton and Davidse 2625 (MO). Cerro Colorado, Top, 1500m , Bocas Rd.,

Folsom and Collins 1774 (MO). PUERTO RICO. Indera Fria, near Maricao 430-800m,

Britton et al. 4461 (NY). Maricao to Monte Alegrillo, mountain forest 900m, Mt.

Alegrillo Britton et al. 2603 (NY). Maricao: Maricao forest preserve, W end of Las Teta

de Cerro Gordo above Rd 120 elev. ca. 8390m, Rothacker and Ackerman ER02 (OS).

Maricao Insular forest, on top of moderate shade, Horn 5909 (AMES). Prope Adjuntas,

Urban 4246 (AMES, K). Prope Utuado, Urban 4479, 4474 (AMES, K). Maricao,

Sargent 719 (US). Utuado, Bo. Caonillas Ariba, Cero Morales, Upper NW slopes near summit area, Axelrod and Baymann 7038. Urban 74479 (NY). SAINT VINCENT. Judith

178 and Judith 1951 (K). VENEZUELA. Edo. Trujillo: Municipo Bocono. Parque Nacional

Guaramacal on road from Bocono to Guaramacal. SE of Guaramacal, N. slope of mountain, Dorr et al. 8126 (MO).

5. Psilochilus modestus Barb. Rodr. Genera et Species Orchidearum Novarum 2:

273. 1882. Pogonia modesta (Barb. Rodr.) Cogn. Flora Brasiliensis 3(4): 133.

1893. Type: specimen has been lost or destroyed.

Psilochilus maderoi (Schltr.) Schltr. Archivos de Botânica do São Paulo 1:180.

1926. Pogonia maderoi Schltr. Repertorium specierum novarum vegetabilis

7:41.1920. Type: Colombia, Rio Vangolis on the highlands from Papayan 1700-

2000m, Lehmann 10038 (Holotype: K!).

If a specimen is lost, damaged or one had not been designated as a

holotype for a species by the author, according to International Code of Botanical

Nomenclature, a Neotype must be designated (Articles 9.6 and 9.16, Saint Louis

Code 2000). Neotype remains to be chosen. For the purposes of identification the

illustration of Rodrigues (1877, 1996) can be used.

Description: Habit to 40cm tall; Leaves light green to purple, narrow 2-3.5cm wide and 5-8cm long, elliptic to oblong-lanceolate, acute or acuminate, tapering at base sheathing, short petiolate 1-1.5 cm. Inflorescence with conduplicate, acute bracts.

179

Flowers erect 1-2 open per inflorescence. Sepals green keeled linear- lanceolate 20 x

3mm, acute, tapering at base, lateral sepals falcate, dorsal sepal 25 x 3mm, petals 17 x

3mm acute tapering at base, petals similar to sepals, pale green or whitish. Labellum 12 x

5-6mm, magenta in throat and streaked with magenta on lip, short clawed (ca. 5mm), trilobed with deep narrow sinus, lateral lobes triangular, 6 x 3mm, midlobe rounded, orbicular to suborbicular, 4 x 4mm lobe crisped to crenulate undulating, with two thin calli. Column broadly winged, strongly curved. (Fig. 4.3.C and 4.10.A-B).

Etymology: Unknown.

Distribution: Brazil, Colombia, Ecuador, Nicaragua, and Venezuela (Fig. 4.11).

Pollination and blooming phenology: Pansarin (2000, also see Pridgeon et al.

2005), reported that while these plants are self-compatible, seed set in natural populations

was low, indicating that self-fertilization was not a common mechanism of pollination,

requiring a vector to transfer pollen from the anther to the stigmatic surface. This species

is visited primarily by social and solitary pollen collecting bees (Plebeia droryana and

Trigona spinipes). Psilochilus modestus provides pollen and nectar rewards. Nectar collecting bees, Melipona sp. and Halictid bees, were identified as pollinators. Psilochilus modestus (=P. maderoi) in Columbia was collected blooming in January 1897. Pansarin

(2000) reported that this species has a blooming phenology similar to that of the rest of the tribe. Typically blooming 3-4 times per blooming period, flowers open for a day or so at most and like other members of the tribe it exhibits gregarious blooming (E. Pansarin pers com.). Reise et al. (2004) reported that P. modestus releases a floral fragrance

180

composed of aromatic compounds like benzyl alcohol and benzyl tiglate (46%), as well as lesser amounts of isoprenoids like 6-methyl-5-hepten-2-one (an irregular isoprenoid), geranyl acetone (oxygenated terpene), -cadinene, -ylangene (sesquiterpenes) and nerolidol (oxygenated sesquiterpene), 6-methyl-5-hepten-2-one, geranyl acetone and benzyl alcohol.

Taxonomic notes: P. maderoi is known from a single collection in 1897. In

Schlechter’s description of the species from 1920, he differentiated P. maderoi from

P. macrophyllus and P. modestus by the longer “lippennagel” which probably refers to the claw of the lip. The type of P. modestus as illustrated shows a rather short claw, probably an artifact of preparation, as the illustration of this species (Fig. 4.3.C) from

Pansarin (2000) exhibits a longer claw. In principle the collection of P. maderoi agrees with P. modestus in all other aspects of vegetative morphology, with its longer narrow light green leaves. Given the variation observed in the specimens of P. modestus, and furthermore as there is no other diagnostic character that differentiates these collections, it was determined that P. maderoi and P. modestus were the same species.

Habitat: (Fig. 4.10). In Costa Rica it was collected on a mossy hummock at

1350m, and in Ecuador in a pluvial premontane rainforest at 1690m. Specimens from

Brazil are found in primary forest, from 3-1900m, and in Colombia at 1700-1900m.

Blooming time: December -March.

181 Notes regarding type specimen: It is unfortunate that no type specimen was designated for the epithet. Rodrigues was known to keep common gardens from which plant specimens were drawn and described, however collections, especially herbarium specimens are rare, of which many orchids described by B. Rodrigues are without herbarium collections (Rodrigues 1980).

There is an illustration made to accompany the original description, but not published by the author in his lifetime. Cogniaux (1893-1906) used the illustrations of

Rodrigues (1882) for his treatment of the Orchidaceae in Flora brasiliensis (Rodrigues

1970). It was not until 1996, when “Iconographie des orchidées du Brésil” (Friedrich

Reinhardt Verlag, Basle) was published as a two-volume set, which completed the work of B. Rodrigues by finally publishing all the text and accompanying illustrations together

(Cribb et al. 1996).

Speciemens examined: BRAZIL. Paraná, Tacarchy in siliva primaera ad terram sphagnosem reg. Lit, Dusen 170215. (AMES). Came from Brazil, Sanders and company sn (K). Sao Paulo, Angatuba, Fazenda do Servico Florestal Emmerich and Dressler

40919 (K, H). Serra do mar, Ypiranga in silvia primara ad terram, Dusen 14461 (AMES,

K, MBG, NYBG). Rio de Janerio. Matto vacintiy of Macieriras, Mt. Itatiaya Estacao biologica. alt. 1960m 22° 26’S 44° 40’ W, Smith 1770 (AMES). Sao Paluo, S. Fansicso dos Campos, Ex. Herv. Comm. Georg. E Geol. De S. S. P. 3592 (NY). Paraná, Morro Sae

Catira (mun. Quatro, Barrae). Paraná, Brejatuba, mun. Guaratuba, SILVA 5/2/1987

(MU). Paraná, Pontal do Poço, mun. Paranaguá, Hatschbach 43541 and Kummrow (MU,

DB). Parana, Morro Sae Catira, mun. Cuatro Barra, Hatschbach 15684 (US). COSTA

RICA. Cartago: Forested knoll just W of Quebrada Cas Blanca , Tapanti 9˚47’N 83˚48W 182 1350m, Grayum et al. 4652 (MO). ECAUDOR. Parque Nacional Sumaco Napo-Galeras

Cimbre de la Cordillera de Galeras, Bosque pluvial premontano 00˚59’09” S 077˚31’58”

W, 1600m, 11 March 2003, Farfin 523 (MO). Waechst am Boden in sehr feuchten, dichten Waeldern um Chinguinta Lehmann 1303 (K). NICARAGUA. Granada Summit of extinct volcano Mombacho, Atwood et al. 6737 (MO).

6. Psilochilus mollis Garay. Flora of Ecuador 9: 47. 1978. Type: Ecuador,

Morona-santiago, Río Chihuasi, 25 km SE of Logroño, Cordillera de Cutucú,

Madison & Coleman 2564 (Holotype: SEL, photo!; Isotype:AMES!).

Description: Habit up to 59 cm tall, stems green to purple, round. Leaves 8-9 x 3-

5cm, narrowly ovate to ovate-lanceolate, acuminate, green above with or without white

stripes to green or purple below, petiolate (0.5-1.5cm) encircling the stem. Inflorescence

a terminal nodding raceme with floral bracts conduplicate, ovate-lanceolate. Sepals and

petals light green, sepals sometimes suffused with purple; sepals keeled, 10-22 x 2-

3.5mm, linear to lanceolate, dorsal sepal 10-22 x 2-3.5mm linear to lanceolate, weakly

obtuse to acute, tapering at the base, lateral sepals wider than dorsal; Petals 12-21 x 2-

3.5mm, linear to lanceolate similar to sepals, weakly obtuse to acute. Labellum to 25 x

10mm with long cunate base, trilobed, white with two longitudinal purple stripes, with or

without yellow in the throat with or without violet spots, two distinct calli diminishing

toward the apex with a third smaller less distinct ridge obvious in some specimens; lateral

183

lobes falcate to triangular extending behind midlobe, blunt-rounded, medial lobe

suborbicular to subquadrate, margins crenulate-erose. Column 12-20mm, bent with a

distinct apical beak. (Fig. 4.12).

Etymology: Latin “mollis” meaning soft or pliable; refers to the soft texture of the dried leaves when compared to the leaves of P. physurifolius.

Distribution: Ecuador and Peru (Fig. 4.13).

Habitat: Found in dense moist tropical montane rainforest to lowland topical rainforest, from ca. 1700m-2400m.

Blooming phenology: Based on observations in the field and of specimens cultivated by Lou Jost and the author, it appears that this species blooms successively throughout the year, although there are apparent rest periods. All collections were made from October- March with a single specimen collected in flower in July. The plants do not go dormant, as in some species of the tribe (i.e. Triphora trianthophora and

T. gentianoides), and at least superficially the phenology appears similar to that of

P. modestus. A population was observed by L. Jost in the Tapachelach reserve in the Loja province of southern Ecuador; it was noted that some of the plants were triandrous and functionally selfing (Fig. 4.14.G-I) and others were outcrossing, monandrous plants

(Fig.4.14.J). Both types of plants were growing in sympatry. Other differences observed were that the triandrous forms possessed smaller, 3-veined leaves with green and silver stripes above, green below, and the outcrossing individuals had larger, 5-veined, green leaves above and below. The flowers were similar in shape, size and color.

184 Discussion: This species was originally described by Garay (1978) to refer to all collections of this genus in Ecuador. There is a considerable amount of variation in size, leaf color and variegation among the collections of Psilochilus from Ecuador. LØjtnant

(1977) referred at least some to P. physurifolius however Garay (1978) pointed out that

this was incorrect. Psilochilus mollis differs from P. physurifolius in the proportions of

the lip and the shape of the lateral lobes of the labellum. In P. mollis the lateral lobes are

rounded and extend well into the midlobe in the former, while in P. physurifolius, the

lateral lobes are acute and short (Fig. 4.3). Additionally they differ in the shape of the

leaf. Psilochilus mollis has leaves that are narrowly ovate to ovate-lanceolate, short

acuminate at the tip, and P. physurifolius has leaves that are elliptic to elliptic-lanceolate

and long acuminate.

It is unfortunate that the holotype specimen cannot be located, especially as the

only flower on the isotype is in poor condition (i.e, lacking a complete labellum). Equally

as disappointing is the illustration that accompanied the original description, however

after looking over Garay’s notes and other unpublished illustrations it is clear that he

viewed P. mollis as variable in size and shape of the flower (Garay pers. com.). Of the

paratypes discussed in the original publication, only a single collection had decent

flowers for observation. Of the populations observed in the field there is considerable

variation in flower color and size (Figs.12 and 14). A new collection will be needed from

Peru to help to confirm the identity, as I only had the flower on which to base my

decision.

Specimens examined: ECUADOR: Zamora Chinchipe, forest along Cordillera

del Condor near end of road to Los Encuentros 1700-1800m, Dalstrom 1901 (SEL).

185 Tungarahua, Rio Zunac near Rio Topo, 1400m, Jost LJ5902, LJ5903, LJ5904 (QCNE,

OS). Tungarahua, Rio Zunac near Rio Topo, 1400m, Rothacker ER207. Cordillera

Galaras, N. of Puyo, 1700m LJ5413. Cordillera Galaras, N. of Puyo, 1700m, Jost

LJ5381. Loja, Podocarpus National Park, Tapachulaca Reserve Yangana-Valladoloid Rd.

Jost LJ6852, LJ6853, LJ6913, LJ6914, LJ6914. PERU: Departamento Junin, Prov. Jauja,

Astilleros, near Monobamba, alt. 2020m, S11°23'51", W75°18'54", 10/9/2001, Weigend et al. 5683. Cusco, Sapan-sachayocc Vargas 2534 (NY photo of CUZ). CULTIVATED. specimen purchased from Ecuagenera, Cuenca, Ecuador, Rothacker ER220 (OS).

7. Psilochilus physurifolius (Rchb. f.) Løjtnant. Botaniska Notiser 130(2): 168.

1977. Pogonia physuraefolia Rchb. f. Nederlandsch Kruidkundig Archief. Verslangen en

Mededelingen der Nederlandsche Botanische Vereeniging 4: 324. 1859. Type: Guyana,

Schomurgk s.n. (K, photo!).

Description: Habit to 40 cm tall. Leaves distinctly petiolate 0.5-1cm, sheathing, green with or without white/silver stripes above 5-8 (rarely 10) x 2.5-3.6 (rarely 5)cm, elliptic to elliptic-lanceolate acuminate, leaf base rounded. Inflorescence erect or weakly nodding, short raceme with ovate acuminate bracts. Flowers one to few. Sepals green carinate, dorsal sepal 19-20mm x 3-3.4mm, lateral sepals falcate, 20-21 x 3-3.2mm.

Petals pale green/cream, similar to sepals, 18-19x 2-2.3mm. Labellum 15 -17 x 5mm, with long claw (8- 9mm), lateral lobes short, acute, midlobe ca. 4 x 3mm, suborbicular to round, margins crisped with magenta/purple, possesses two distinct calli. (Fig.3.E-F).

Etymology: refers to the Latin “ folius” or leaves which look like Physurus.

186 Distribution: Guyana, Panama,Venezuela, Costa Rica, and Granada. (Fig. 4.15)

Habitat: In Panama it was observed in premontane rainforest, while in Venezuela it was collected in Bamboo woods. Throughout most of its range it was collected along ridges or slopes from 1100-2255m.

Phenology and Pollination: This species has been collected in bud or flowering from March – October. At least two specimens determined are triandrous, and probably functionally autogamous.

Taxonomic notes: Often confused with P. macrophyllus, the description of P. physurifolius by Reichenbach (1859) is barely sufficient to differentiate them, and left the shape of the labellum (“labellum ligulatum?”) in question. In Lindley’s (1858) description of P. macrophyllus (as Pogonia macrophylla) he discussed a specimen in

Schomburgk’s collections which he stated was remarkably similar to the material for P. macrophylla but was in such bad condition it was not possible to identify; this being the same material which was the basis of the description of P. physurifolius by Reichenbach.

The type specimen was triandrous and dorsally carinate as noted by Garay. Both are conditions similar to one illustrated of P. marcrophyllus by Ames (1922). The Ames illustration of a specimen from Granada also has a long claw and is distinctly petiolate, similar to that of P. physurifolius, and probably refers to this species.

In the form of the lip, P. physurifolius is similar to P. macrophyllus, differing in the length of the claw. Løjtnant (1977), after observations of the type material for P. physurifolius, reported a series of vegetative characters that could be used to differentiate specimens of P. physurifolius from P. macrophyllus. He also included a single floral character, claw length of the labellum (long vs. short). Of the specimens examined,

187 Folsom 6115, Rothacker ER101 and Sheering 1890-91 all had flowers with long claws

and floral morphology similar to the type. Other specimens were diagnosed based on the

petiolate leaf morphology. From my observations, the characters of Løjtnant (1977) are

good for differentiating P. physurifolius from P. macrophyllus. Psilochilus physurifolius has leaves that are all petiolate, whereas P. macrophyllus has mostly amplexicant or clasping leaves with some of the lower leaves occasionally short petiolate. These taxa are clearly closely related based on similarities in the shape and proportions of the labellum.

Speciemens examined: COSTA RICA: Alajulea Upala, Biajaga el Pilón, Ladera

Atlántica del Volcan Tenorio, cuencea alta del Rio Celeste 10˚43’30” N 85˚00’25” W

1500-1800m, Herrera 2144 (F). GRANADA: Azimar Mountian woods, Broadway Nov.

18, 1905 (AMES). location unknown, Sherring s.n. October –May 1890-91 (K).

PANAMA: Darien: Ridgetop area north of Cerro Pirre, between Cerro Pirre and Rancho

Plastico 1200-1300m, Folsom et al. 6300 (MO). Hills N of El Valle, E slope and ridges leading to Cerro Gaital 8˚40’N 80˚07’W, Knapp 5778 (MO, SEL). Chiriquí, ca. 35km N-

NW from San Felix summit of Cerro Colorado, Rothacker ER101p (OS, PMA). Chiriqui

Fortuna Dam below road to STRI on Cable car trail, locally common 30 plants.

08˚43.119’N, 082˚13.965’W 1100-1205m, Rothacker ER92p (OS, PMA). Chiriquí,

Fortuna Dam top of mountain above camp to the south, 1700m, Folsom et al. 5409 (MO).

Cerro Colorado, border with of Chiriquí with Bocas del Toro along intersection of Bocas

Rd. with main ridge road, 11.8km from Chami along path heading into Bocas del Toro

1400-1700m, Folsom 6115 (MO). Veraguas: trail up Cerro Tute to 1200m, Witherspoon et al. 8843 (SEL). VENEZUELA: Merida, woods above Las Cuadras along Quebrada

188 Molino N of Torondoy alt. ca 1820-2255m., Steyermark 55780 (AMES). Merida, Trail between Las Cuadras and Timotes alt. ca 1820-2255m, Steyermark 55832 (NY).

SPECIMENS EXAMINED WITH UNCERTAIN PLACEMENT

1. Dressler 6030 (MO): Panama, Colcé, Los Pedregales, SSW Rio Blanco del Norte

(N of El. Copé, Caribbean slope. 22, Feb 1982. Terrestrial; sepals pale green,

petals cream, bordered pink above; Lip white with purple margins center yellow.

Dressler left this unnamed at the time of collection, and in 2000 again felt it was a unique plant, as yet unnamed. It is a plant with very large leaves (up to ca 14 x 6 cm), rather robust for the genus. It is unfortunate that the flower, which contained all the perianth parts, was either deformed/and or damaged. The labellum was clearly 20-22mm long with a very distinct midlobe. [However, another collection from this location is needed before a determination can be made.]

2. JOST 5414 (QCA). Ecuador, Napo, Cord. de Galaras.

This appears to be a distinct species given the material I have, however no other collections have been found to corroborate this. It is similar to P. macrophyllus in the shape of the lip (Fig. 4.3.I) but is considerably larger, and in vegetative appearance it has leaves that are petiolate, with a leaf blade that is ovate to ovate-laceolate, acuminate at the tip, similar to P. mollis. It however differs from all other Psilochilus species in that

189 the lip is papillate, with the two calli appearing as a single raised space (Fig 4. 15).

Further collections of this, and observations of it in vivo would help to determine if this form is stable.

UNCERTAIN NAMES

The name Psilochilus guatemalensis was discussed in Schlechter (1926b). In this publication he appears to reference a previous publication by use of his name after the species epithet, however upon examination of Schlechter’s works there are no descriptions or illustration of the species, and no additional references were found. With the exception of the country name, from the information given in Schlechter (1926b) it cannot be determined what this name may refer to. In Guatemala this could refer to

Psilochilus macrophyllus, but given the distributions of other taxa in Central America it is possible that this may refer to another species. At this time I believe this is not a valid name, and should be considered nomen nudem.

190

Figure 4.1: A generalized distribution map of Psilochilus.

191

Figure 4.2: Compound dissection light microscope images of Psilochilus macrophyllus seeds.

192

Figure 4.2

193

Figure 4.3: Species level variation in labellum morphology for Psilochilus. A. Psilochilus sp LJ7955 (P. ecuadoriensis ined.) B. Psilochilus mollis LJ5902. C. Psilochilus modestus (redrawn from illustration by Emerson R. Parinsin in Masters theisis.). D. Psilochilus macrophyllus ER02 from Puerto Rico. E. Psilochilus physuifiolis ER101 from Panama. F. Psilochilus physurifolius (Sherring 1890-91).G. Psilochilus carinatus redrawn from the type collection. H. Psilochilus dusenianus redrawn from type. I. Psilochilus sp. nov. LJ5414.

194

A B C D E

10mm

F G H I

194

Figure 4.3

Fig. 4.4: Distribution map of Psilochilus carinatus.

196

Fig. 4.5: Distribution map of Psilochilus dusenianus.

197

Fig. 4.6. Illustration of Psilochilus ecuadoriensis in ed. drawn from LJ7955. A. petals and labellum, B. characteristics of the column, C. Flower D. Habit.

198

Fig. 4.6

199

Fig. 4.7: Psilochilus ecuadoriensis sp. nov. showing flower. (Photos credits:Lou Jost.).

200

Fig. 4.8: Distribution map of Psilochilus ecuadoriensis.

201

Figure 4.9: Distribution map of Psilochilus macrophyllus.

202

Figure 4.10: Psilochilus modestus A. flower B. in habitat. (Photo credit. Emerson Pansarin)

203

Figure 4.10

204

Figure 4.11: Distribution map of Psilochilus modestus.

205

Figure 4.12: Variation in the labellum of Psilochilus mollis. Top row

shows variation in populations collected from direction fron east to west, Baños to

Puyo, Ecuador; second row are specimens collected arranged from north to south

along the eastern slope, from Cordillera del Galaras to Cord. del Condor south to

Junin, Peru. A. ER207, B. LJ5902, C. LJ5904 (A-C = Rio Topo); D. ER208 (N.

Shell Mera), E. LJ5381, F. LJ5413, G. ER220 (cultivated specimen from

Ecuagenera, Cuenca, Ecuador), H. SD1901 (Sel), I.Weigland et al. # 6853 (O-

15111, Junin, Peru).

206

A B C D

10mm

207

E F G H I

Figure 4. 12

Figure 4.13: Distribution map of Psilochilus mollis.

208

Figure 4.14: Variation in the flower color observed in Psilochilus mollis. A LJ5902 B. LJ5904 C. LJ8258 (ER208) D. LJ5413 E. ER220 F. LJ5381. G-I. LJ6852 (from triandrous anther), J.LJ6913 and K. SD1901. (Photo credits: “A-D” and “F-J” courtesy of Lou Jost and E. taken by the author and “K” by Stig Dalstrom E. taken by the author).

209 A B

D C

Figure 4.14

210

Figure 4.14 Continued

E F

Continued

211 Figure 4.14- continued

J K

212

Figure 4.15: Distribution of Psilochilus physurifolius.

213

5mm

Figure 4.16: Illustration of Psilochilus LJ5414. Collected in Cord. Galaras, Ecuador. Show cross section of a labellum at junction with lateral lobes, illustrating the papillate surface.

214

CHAPTER 5

PHYLOGENY OF PSILOCHILUS

(TRIPHOREAE, EPIDENDROIDEAE) USING THE PLASTID TRNL-F

INTERGENIC SPACER

INTRODUCTION

Psilochilus is a small neotropical genus consisting of 7 species, with a broad distribution ranging from Brazil, eastern and northern South America, north through

Central America to Chiapas, Mexico, and the Caribbean, from Cuba and Puerto Rico, through the Greater and Lesser Antilles to Trinidad and Tobago.

Treatment of the genus has often been problematic; originally Psilochilus was treated as a member of Pogonia or closely related taxa such as Cleistes. In 1979, Dressler

transferred Psilochilus from Pogoniinae to Triphoreae with Triphora and

Monophyllorchis. Triphoreae are all terrestrial orchids of deep to moderate shade, with thickened succulent stems. Psilochilus and Monophyllorchis each have thickened villous roots, while Triphora has reduced or absent roots with or without tuberous structures.

215 The leaves of Psilochilus are small and plicate, and can be easily distinguished from

Monophyllorchis, which has a single large plicate leaf, and from Triphora, which has multiple reduced bract-like or flat non-plicate leaves. In terms of other characteristics, all three genera possess erect, terminal racemes, and a clawed trilobed labellum, with 2-3 calli; Psilochilus differs in its distinctly triangular buds and well-defined keel on the sepals.

Previously, Psilochilus had not been included in molecular studies using exemplars of this tribe, and it was unclear what the relationships were within the tribe. In

Chapters 2 and 3, it was established that within Triphoreae s.s., Monophyllorchis was the first to branch off with Psilochilus and Triphora sisters; Epipogium is either sister to the tribe or sister to Monophyllorchis. This is the first study to use significant sampling within the genus Psilochilus.

MATERIALS AND METHODS

MATERIALS-Taxon sampling- Materials were collected in Panama and Ecuador, and provided from Brazil and Puerto Rico. Sampling within the genus is somewhat difficult owing to remoteness and rarity of some taxa such as P. dusenianus, which is located in the Tapui of southern Venezuela and Brazilian Amazonia, therefore DNA extractions of herbarium material were made in order to obtain sequences of P. carinatus,

P. dusenianus, and to improve the geographical sampling of the other species. The

216 resulting extractions were highly degraded and failed to yield usable sequences for the

trnL-F locus used in this study. Therefore, P. carinatus and P. dusenianus are not represented in the following analyses.

METHODS-DNA extraction and purification- Total DNA extraction from fresh, silica dried or herbarium material was performed using either the CTAB method of Doyle and Doyle (1987) or the DNeasy Plant Mini Kit (Qiagen, Valencia, California, USA) for very small quantities of tissue. All extractions were stored at –20°C. In some instances when weak amplifications were obtained further purification of the total DNA was performed using the Elu-Quik DNA purification kit (Schleicher and Schuell, Keene, New

Hampshire, USA).

Amplification and Sequencing- All amplifications were performed initially using standard PCR protocol methods as follows: 50 L reactions were prepared using 40L

HPLC water, 1 L of each of 10 M primer, 5 L buffer (100mM tris –HCL [pH 8.8], 35 mM MgCl2, and 250mM KCL), 0.5L of 0.20 M dNTPs, 0.5 L Taq polymerase, and

0.5L of 10 g/L of bovine serum albumen; to each reaction 1- 2.5L of template DNA

was added. For weak amplicons, a second round of amplification was performed in order

to increase overall yield.

The primers of Taberlet (1991) were used in the amplification and sequencing of

trnL-F. These primers were ”C” (5’ CGAAATCGGTAGACGCTACG 3’) and “F”

(5’ATTTGAACTGGTGACACGAG 3’); for difficult amplifications, the reverse primer

“D” (5’ GGGGATAGAGGGACTTGAAC 3’) and forward primer “E” (5’ GGTTCA

AGTCCCTCTATCCC 3’) were used to obtain smaller amplicons; amplification was

217 performed under the following PCR conditions: an initial denaturation step of 96°C for 3 min., followed by 29 cycles of 96°C for 45s, 64°C for 45s and 72°C for 2 min., with a final 5 min. extension at 72°C.

PCR products were quantified visually using an agarose gel. These products were cleaned using the Wizard PCR Prep DNA Purification system (Promega, Madison,

Wisconsin, USA), Ampure (Agencourt Bioscience, Beverly, Maine, USA), or 50 L of

20% polyethylene glycol–2.5 M NaCl and sequenced directly using the amplification primers. Sequencing reactions were performed using BigDye Terminator v3.1 chemistry

(Applied Biosystems, Foster City, California, USA) in 5 L reactions: 3.32L distilled water, 0.02L DMSO, 1L Big Dye, and 1L ABI buffer. These were combined into a master mix and aliquoted at 4.5 L to which 0.5L of the PCR product was added. The following cycle sequencing protocol was followed: initial denaturation step of 96°C for

1min, followed by 24 cycles of 96°C for 10s, 50°C for 5s and extension phase at 60°C for

4min. Sequences were cleaned using ethanol purification, Sephadex (Sigma-Aldrich, St.

Louis, MO USA.) spin columns or Cleanseq (Agencourt Bioscience, Beverly, Maine,

USA). All reactions were run on an ABI Prism 3100 automated sequencer (PE

Biosystems, Foster City, California, USA).

Alignment and phylogenetic analyses- Contiguous sequences were assembled using Sequencher 3.1.1 (Gene Codes, Ann Arbor, Michigan, USA) and aligned using

ClustalX (Thompson et al., 1994) with gap opening /extension costs of 6/4. It is well known that ClustalX does not perform well in regions possessing many gaps, so the

Clustal alignments were manually adjusted using Se-Al v. 2.0.11 (Rambaut, 1996).

218 Outgroup choice- Based on previous studies of the basal Epidendroideae it has

been established that Triphoreae are monophyletic (Chapters 2 and 3). To serve as

outgroups, representatives from Monophyllorchis and Triphora were used. While

Epipogium appears to be closely related to Triphoreae based on these studies, however sequences of this genus could not be amplified due to the difficulty in amplifying plastid loci in achlorophyllous taxa.

Gap coding- Gaps were coded using the simple gap coding method of Simmons and Ochoterena (2000) as implemented in SeqState (Müller 2005).

Parsimony- PAUP* version 4.0b.10 (Swofford, 2002) was used to run parsimony.

All analyses were performed with and without gaps coded. The following approach was taken for all searches: an initial heuristic search was performed on 1000 random taxon addition replicates using TBR, with settings to hold up to two trees per random addition sequence, saving only two trees, multrees in effect, and swapping on best trees only. The best trees from this search were used as starting trees for a second, exhaustive heuristic search in order to search the tree space as thoroughly as possible.

Maximum likelihood- Given the limitations of model-based methods (i.e., gaps characters cannot be included), sequence data alone were analyzed. Maximum likelihood analyses were performed in PAUP* using the following procedures: a parsimony heuristic search was used following the above methods to obtain the initial starting tree.

From this parsimony tree, likelihood parameters were estimated from the data in order to

determine the best substitution model for the analysis; a model of HKY85+G was

219 applied using this information. The estimated values were then applied, and a maximum

likelihood heuristic search was performed using the same search settings as in the

parsimony search.

Branch support- Support was evaluated using the jackknife search parameters

recommended by Freudenstein et al. (2003). Branch support was evaluated in PAUP* set to run 5000 jackknife replicate iterations and with one addition sequence replicate in each, saving only two trees per random addition sequence, and TBR branch swapping was employed on best trees only. PAUP* settings also included 37% deletion and the

‘‘emulate Jac’’ command; this is consistent with the sampling strategy of Farris et al.

(1996) in which each character has a probability of 1/e of deletion in the jackknife matrix.

RESULTS

PARSIMONY TOPOLOGY- A matrix of 18 taxa and 1255 sequence characters was constructed for analysis. Sites in which >50% of the data was missing were excluded leaving 997 in the matrix, of which 867 were parsimony uninformative and 131 (13%) were parsimony informative. Five most parsimonious trees (MPTs) were returned of 411 steps with a CI of 0.852 and an RI of 0.786 with very good support for most of the branches. The strict consensus was calculated (Fig. 5.1). Within Psilochilus, P. physurifolius (ER92) is at the base of the clade, followed by a clade of P. modestus

(ER65) sister to P. macrophyllus (ER02), this sister to a clade of P. mollis and P. ecuadoriensis. With this latter clade, an accession of Psilochilus mollis (LJ6860) subtends a polytomy of other accessions of P. mollis and P. ecuadoriensis (LJ7955). Four

220 of the five MPTs placed Psilochilus mollis (ER208) at the base of this clade, followed

successively by accessions of P. mollis (LJ8264 and LJ5381). In the one tree in which

this is not observed, LJ5381 formed a polytomy with ER208. Also in four of the five

trees, a clade of Psilochilus sp. (ER113) and P. mollis (015111) formed a polytomy with

P. mollis (ER207) sister to P. ecuadoriensis (LJ7955). Of the remaining accessions of

P. mollis, all subtended by short branches, terminals were observed in different positions

in each of the five topologies.

The inclusion of simple gap characters resulted in a matrix of 18 taxa and 1136

characters of which 178 (16%) were parsimony informative. The analysis of this dataset

returned seven MPTs of length 571 with a CI of 0.856 and an RI of 0.785. The inclusion

of gaps improved resolution of the strict consensus (Fig. 5.2). As with the sequence data

alone, P. physurifolius (ER92) is at the base of the genus followed on successive

branches by a clade of P. modestus (ER65) and P. macrophyllus (ER02), then P. mollis

(LJ6860), and a clade of P. mollis accessions LJ8264 and LJ6914. The remaining

accessions are part of a polytomy in which two clades are formed, Psilochilus sp. ER113 sister to P. mollis O15111, and a clade of P. mollis (ER207) sister to P. ecuadoriensis

(LJ7955).

Given the long branches beneath P. mollis (ER207) and P. ecuadoriensis, a test of long branch attraction was performed following the Siddall and Whiting (1999) method where taxa that are thought to be united by long branch attraction are alternately removed to see the effects of the removal on the other. The results from these manipulations reject

221 long branch attraction as an issue in this analysis. The topologies of both analyses were

the same as those of the unaltered analyses with the exception that the clade of P. mollis

(ER207) and P. ecuadoriensis is unresolved in a polytomy with the rest of P. mollis.

MAXIMUM LIKELIHOOD TOPOLOGY – Model-based ML methods prohibit the inclusion of gap characters, therefore only the sequence data were analyzed. From the parsimony topology the following parameters were estimated: nucleotide frequencies

(A=0.4=34752, G= 0.16282, C= 0.16881, and T= 0.32085), shape = 0.809847,

TI/TV= 0.637303, with 2 substitution types. These values correspond to an HKY85 + G model. The analysis resulted in a single tree (Fig. 5.3). In general the topology is the same as that produced using parsimony with the difference being in the positions of accessions of Psilochilus mollis. Within P. mollis, LJ6860 is found at the base but unlike the topology from parsimony, ER208 and LJ5881 formed a polytomy followed on successive branches by the remaining accessions of P. mollis (LJ8264, LJ6914, LJ 5413,) then a sister grouping of Psilochilus sp. (ER113) and P. mollis (O15111), this sister to P.

mollis (ER207) and P. ecuadoriensis (LJ7955).

DISCUSSION

TOPOLOGY- Regardless of the method used (i.e., gaps vs. non-gaps, parsimony

vs. ML), some consistent patterns of relationships are observed. Psilochilus physurifolius

is at the base of the genus, followed by clade of P. modestus and P. macrophyllus, this

sister to a larger clade containing P. mollis accessions and P. ecuadoriensis. The finding

that P. macrophyllus and P. physurifolius are not closely related is an unexpected

222 observation. Sometimes considered conspecifics, these results do not support this.

Morphologically, P. physurifolius can be distinguished as having distinctly petiolate

elliptic leaves and a long narrow claw of the labellum, while P. macrophyllus has

amplexicant or clasping ovate leaves and a labellum with a short broad claw. After

P. physurifolius, P. modestus and P. macrophyllus form a clade. While P. macrophyllus

overlaps in distribution with P. modestus, they are morphologically distinct. For the

purposes of further discussion, the parsimony topology using gaps will be used.

The trnL-F spacer region used in this study is reported to have phylogenetic

utility from the level of the family down to species, occasionally to the level of

populations (Solitis and Soltis 1998). Base substitutions alone were unable to completely

resolve relationships within the P. mollis clade, and while adding gaps improved resolution within the clade, it was unable to fully resolve relationships among populations within the species. Furthermore, the branches subtending many the accessions are short.

This suggests that this locus was not evolving fast enough to capture the diversification and variation at the population level, and a faster evolving locus is needed to clarify

patterns within the species.

Molecular evolutionary biologists generally assume a neutral model of evolution,

whereby sequences diverge in a clock-like manner. While this may not be true for all

sequences, it is unlikely that morphological evolution proceeds by the same mechanisms.

There is considerable variation in lip morphology in terms of shape and size within P.

mollis, (Chapter 4, Fig. 4.12) as well as the size and color of the leaves. Levin (2000)

stated that ecological, phenotypic, chromosomal, and genetic diversification need not

223 occur at the same time or at the same rate. Surprisingly, P. ecuadoriensis was part of the

larger clade of P. mollis and is probably very closely related to it. Morphologically,

Psilochilus ecuadoriensis is a very distinct species, differing from all other species by its

large broadly ovate leaves, long petiole (4cm), long clawed (11mm) labellum and

triangular midlobe with entire margins. In addition it is the only known species from dry

lowlands of Esmeraldas, Ecuador. Psilochlus mollis on the other hand has narrowly ovate

to ovate-lanceolate leaves with a short petiole (<1.5cm), while the labellum has a shorter

cuneate claw (<7mm) with subquadrate or suborbicular midlobe and crenulate-errose margins.

Some would argue that the use of a single organellar locus is itself problematic owing to issues of modes of inheritance and introgression. The use of a single locus for phylogenetic inference has been debated for some time, focusing on incongruence

between gene trees and species trees. This occurs when different genomes and individual

loci have different evolutionary rates or histories as consequences of lineage sorting, introgression or modes of inheritance (Wendel and Doyle 1998). The plastid genome is generally uniparentally inherited from the maternal side, thus providing a maternal history (Birky 1995, Chang et al. 2000), and is susceptible to the effects of introgression.

Orchid hybridizers are responsible for many interspecific and even intergeneric hybrids, leading to the characterization that orchids easily hybridize and that specific and even generic boundaries are not maintained (Arditti 1992). This may be true in the greenhouse, in which prezygotic barriers to hybridization can be easily overcome, however natural hybrids, while they can be found (e.g. Cypripedium, Case 1993; Epipactis, Harris &

224 Abbort 1997; Orchis, Catling and Brownell 1999; Ophrys, Nielsen & Siegismund 1999;

Platanthera, Soliva and Widmer 2003; Vanilla, Pellegrino et al. 2005), are not a common occurrence in the Orchidaceae, and when they do occur they often produce seeds with reduced viability (Arditii 1992). There are numerous prezygotic barriers to hybridization from different blooming phenologies to intricate and specific pollinator and plant interactions such as pseudocopulation and other forms of deception, pollinator entrapment, and pollinator incentives such oil collection by Euglossine bees (van der Pilj and Dodson 1996, Dressler 1982). Pollination and blooming phenology have not been significantly studied in Psilochilus. Psilochilus modestus has synchronous blooming like other members of the tribe, which improves the chances of outcrossing (Pansarin 2000).

With what little is known regarding blooming phenology and types of pollinators for the rest of the genus, it is unclear whether or not sympatric populations of species possess mechanisms to prevent hybridization. Further work on understanding these issues is needed, but given these barriers to hybridization generally, it is not a very likely argument against the use of plastid loci for phylogenetic inference among the

Orchidaceae.

BIOGEOGRAPHICAL IMPLICATIONS- The best geographical sampling of any species used in this study was that of Psilochilus mollis from Ecuador. Within the species, the accession LJ6860 from the southern region of Loja is sister to the rest, followed by LJ8264 from the Rio Cosnaga in Napo of northeastern Ecuador and LJ6914 again from Loja (LJ6860 and LJ6914 occur in the same site). The remaining accessions form a polytomy of collections from the Cordillera Galaras in Napo province (LJ5413

225 and LJ5381) and Shell-Mera in the Rio Pastaza water shed of the lower western

Amazonian foothills of the central cordillera (ER208). Within this polytomy there were

two clades: Psilochilus sp. (ER113) sister to a Peruvian collection of Weigend et al. 5683

(O-15111), and P. mollis (ER207) from the Rio Topo-Rio Zunac area of the Pastaza river valley sister to P. ecuadoriensis (LJ7955) from the northern pacific slope of the western

lowlands from Reserva Canande. Unfortunately the identity of the accession of

Psilochilus sp. (ER113), which was purchased from Ecuagenera (Cuenca, Ecuador) as a

live vegetative plant labeled P. carinatus, could not be verified as the plant was destroyed

in quarantine. Given the geographical distribution of the sampled specimens, there does not appear to be any pattern within P. mollis, and given the sampling within the genus,

the implications of geography remain unclear. Further sampling is needed to better

represent the geographical distribution of the genus.

MORPHOLOGICAL EVOLUTION – Conditions of the labellum and vegetative

leaf characters were mapped onto the strict consensus of the parsimony tree including

gaps (Figs. 5.4 -5.5). Both Monophyllorchis and Triphora have three calli or ridges on the

labellum, making the presence of two calli a synapomorphy for Psilochilus (Fig. 5.4). In

Psilochilus the primitive condition is to have acute lateral lobes, which are also found in

Triphora (e.g. T. trianthophora). Moreover, rounded lateral lobes evolved independently

in both Monophyllorchis and the clade of Psilochilus mollis and P. ecuadoriensis. Within

the tribe, the plesiomorphic condition for these characters is ambiguous. Epipogium,

which is most closely related to the tribe based on previous results (Chapter 3, Fig. 3.10),

lacks lateral lobes, and can have between 2-9 calli (Pridgeon et al. 2006). Vegetative

226 structures of the leaf such as clasping or apetiolate leaves are the primitive condition seen

in both of the outgroups, with petiolate leaves being a synapomorphy for Psilochilus (Fig.

5.5) and apetiolate or clasping leaves evolved independently in Psilochilus macrophyllus.

Psilochilus physurifolius is the only species to have elliptic to elliptic-lanceolate leaves

whereas the condition observed in the rest of Psilochilus is ovate to ovate-lanceolate with

ovate leaves found in both outgroups. The clade of Psilochilus modestus and P. macrophyllus is distinguished from the clade of P. mollis and P. ecuadoriensis by a labellum with acute lateral lobes and ovate leaves.

CONCLUSION

This is the first molecular analysis of Psilochilus representing any significant sampling. In this study, a phylogenetic analysis including five of the seven species was performed using the chloroplast trnL-F intergenic spacer. Results of both the ML and parsimony analyses were congruent with regards to species level relationships, but differ in the placement of accessions of P. mollis. Psilochilus physurifolius is found at the base of the clade followed by sister groupings of P. mollis and P. macrophyllus, sister to P. mollis sister to P. ecuadoriensis. Furthermore, on the basis of morphology Psilochilus is a

natural group based on the presence of petiolate leaves and two calli on the labellum.

227

Fig. 5.1: Strict consensus of 5MPTs of the matrix of nucleotide sequences. Number below branches indicate jackknife support values >50%.

228 Monophyllorchis maculata

Monophyllorchis microstyloides

Triphora amazonica

Triphora trianthophora 97 Triphora gentianoides

Psilochilus physurifolius 100 Psilochilus modestus 78 Psilochilus macrophyllus 71 Psilochilus mollis LJ6860

100 Psilochilus sp. ER113 Psilochilus mollis 015111

89 Psilochilus mollis LJ8264

Psilochilus mollis LJ5413

Psilochilus mollis ER208 69 Psilochilus mollis LJ5381

Psilochilus mollis LJ6914

Psilochilus mollis ER207

93 Psilochilus ecuadoriensis LJ7955

Figure 5.1

229

Figure. 5.2: Strict consensus topology of 7 MPTs returned from the analysis of nucleotide sequence data and gaps coded. Numbers below branches indicate jackknife support measures >50% and numbers above branches are branch lengths for only those nodes resolved in the strict consensus.

230 Monophyllorchis maculata M. microstyloides 27 Triphora amazonica 85 Triphora trianthophora Triphora gentianoides 47 65 100 Psilochilus physurifolius 26 9 Psilochilus modestus 93 98 Psilochilus macrophyllus 21 1 Psilochilus mollis LJ6860 100 3 Psilochilus mollis LJ8264 6 82 57 Psilochilus mollis LJ6914

4 Psilochilus mollis LJ5413

69 Psilochilus mollis ER208

Psilochilus mollis LJ5381 6 29 Psilochilus sp. ER113 Psilochilus mollis 015111 27 20 Psilochilus mollis ER207 59 95 P. ecuadoriensis LJ7955

Figure 5.2

231

Figure 5.3: Topology of the maximum likelihood analysis.

232

Monophyllorchis maculata

Monophyllorchis microstyloides

Triphora amazonica

Triphora trianthophora

Triphora gentianoides

Psilochilus physurifolius Psilochilus modestus

Psilochilus macrophyllus

Psilochilus mollis LJ6860

Psilochilus mollis ER208

Psilochilus mollis LJ5381

Psilochilus mollis LJ8264

Psilochilus mollis LJ6914

Psilochilus mollis LJ5413

Psilochilus sp. ER113

Psilochilus mollis 015111 Psilochilus mollis ER207

Psilochilus ecuadoriensis LJ7955

Figure 5.3

233

Figure 5.4: Labellum characters mapped on to simplified parsimony strict consensus tree. Thick bars indicate lateral lobe conditions and the thin bars mark the number of calli found on the lip. Solid boxes and lines are synapomorphies, unfilled boxes are homoplasies. At the tribal level, the plesiomorphic conditions for these characters are ambiguous.

234

Figure 5.5: Vegetative characters mapped on to simplified parsimony strict consensus tree. Thick bars indicate leaf shape conditions and the thin bars mark the petiole condition. Solid boxes and line are synapomorphies, and hollow lines are homoplasies.

235 APPENDIX A

NUCLEAR, CHLOROPLAST, MITOCHONDRIAL DNA SEQUENCES AND GAP

MATRICES USED IN CHAPTER 1, TOWARDS A PHYLOGENETIC HYPOTHESIS

OF THE BASAL EPIDENDROIDEAE (ORCHIDACEAE) INFERRED FROM 3 LOCI

AND 3 GENOMES.

236 DIMENSIONS NTAX=57 NCHAR=900; (281 w/ characters already excluded) FORMAT DATATYPE=DNA MISSING=? GAP=- ;

Palmorchis_trilobulata -C-AAACC---ATGAGATGGG-AGCGATTTTGCGAACTCGTGAACGAA-GTGATGGCAGTTGCTATCA-CGAAACAA--CCGTCC-A-GT Palmorchis_trilobulata_ER68 -C-AAACC---ATGAGATGGG-AGCGATTTTGCGAACTCGTGAACGAA-GTGATGGCAGTTGCTATCA-CGAAACAA--CCGTCC-A-GT V2115_PALMORCHIS_POWELII TCGAGACCAAAATGAG-TGGGGAGCGATTTTGTGAACCCGTGAACGAA-GTGATGGCAGTTGCTGTCA-CGGAACAA--CCATCC-A-GT Palmorchis_Sp_ER110 TCGAGACCAAAATGAGA-GGGGAGCGATTTTGCGAACTCGTGAACGAA-GTGATGGCAGTTGCTGTCA-CGGAACGA--CCATCC-A-GT Palmorchis_sp1_ER110E TCGAGACCAAAATGAGA-GGGGAGCGATTTTGCGAACTCGTGAACGAA-GTGATGGCAGTTGCTGTCA-CGGAACGA--CCATCC-A-GT Palmorchis_sp_ER129_selby TCGAGACCAAAATGAGATGGG-AGCGATTTTGCGAACTCGTGAACGAA-GTGATGGCAGTTGCTATCA-CGAAACAG--CCGTCC-A-GT Palmorchis_462 TCGAGACCAAAATGAGATGGG-AGCGATTTTGCGAACTCGTGAACGAA-GTGATGGCAGTTGCTATCA-CGAAACAA--CCGTCC-A-GT Gastrodia_procera_ER64 ------GTGAACGAA-GTGATGGCAGTTGCTATCA-CGGAACAA--CCGTCC-A-GT Cephalanthera_aus_Dat115 TCGAGACCAAAA-GAGATTGG-AG--ATTCTGAGAACTCATGAACCAA-GCGGTGGCAGTCACTGTCA-CGAAACAA--ACATTC-A-TT Cephalanthera_damasonium TCGAGACCAAAA-GAGATGGG-AG--ATTCAGAGAACTCATGAACTAA-GCGGTGACAGTCACTGTCA-CGAAACAA--ACATTC-A-GT CEPHALANTHERA_LONGIFOLIA_ay369 TCGAGACCAAAA-AAGATGGG-AG--ATTCAGAGAACTCATGAACCAA-GCGGTGGCAGTCACTGTCA-CGAAAAAA--ACATTC-G-GT Epipactis_helleborine TCGAGACCAAAA-GAAATGGGGAG--ATTTAGAGAACTCATGAACCAA-GTGGTGGCAGTCAATGCCA-CAAAACAT--ACGTCC-A-AC Epipactis_fageticola_AY351382 TCGAGACCAAAA-GAAATGGGGAG--ATTTAGAGAACTCATGAACCAA-GTGGTGGCAGTCAATGCCA-CAAAACAT--ACGTCC-A-AC Epipactis_lusitanica_AY351381 TCGAGACCAAAA-GAAATGGGGAG--ATTTAGAGAACTCATGAACCAA-TTGGTGGCAGTCAATGCCA-CAAAACAT--ACATCC-A-AC Limodorum_abortivum TCGAGACCAAAA-GAGATGGGGAG--ATCTAGAGAACTCACGAACCAA-GTGGTGGCAGTAACTGTCA-TGAAACAA--ACATCC-A-AC Listera_smallii TCGAGACCAAAA--AGATTGAGAG--ATTTAGAGAACTCATGAACCAA-GTGGTGGCAGACATTGTCA-CGGAACAA--TCATAC-A-AC Neottia_nidus_avis TCGAGACCAAAA-TTGATTGAGAG--ATTCAGATAACTCATGAACCAA-GTGGTGACAGTCACTGTCA-CACAATAA--ACATAC-A-GC Corymborkis_sp_0542 CCGAGACCGGAA-GATATT-A-AGCGATTCGGAGAACTCGTGAAATAA-GTGGCAGCA-TTGCTATCA-CGGAGCAA--CCATCCCA-GT Corymborkis_vert_ER66 ------GTGGCAG---TTGCTATCA-CGGAGCAA--CCAACCCA-GT

237 Tropidia_effusa_O211 TCGAG-CCGGAA-GATATTT--AGCGATTCGGAGAACTCGTGAAATAA-GTGGCAGCA-TTGCTATCA-CGGAGCAA--CCATCCCA-GT tropidia_gram T-GAG-CCGGAA-G-T-TTTA-AGG-ATTCGG-GAACTGG-GAAATAA-G-GGCAGCA-TTGGTGTCA-GGGAGAAA--CCTTCC-A-GT W2830_Tropidia_polystachya TCGAGACCGGAA-GATATTTA-AGCGATTCGGAGAACTCGTGAAATAA-GTGGCAGCA-TTGCTATCA-CGGAGCAA--CCATCCCA-GT Epilyna_jimenzeii_ER67 TCGAGACCCAGA-AAGA-GG------CAA-A-TCGCTG-CGGCGGAGCAG--CCATCCCA-AC Epilyna_hirtzii_n526 TCGAGACCGAGA-GAGA-GGG-AGAGATCTAGAGAACTCGT-AAAGAAAGCGGCAA---TCGCTG-CGGCGGAGCAG--CCATCCCA-AC Sertifera_columbiana_ER38 TCGAGACCGAAA-AAGA-GGG-AGTGATTTAGAGAACTCGT-AAAGAAAGTGACAACAGTTGCTG-CAGCAGTGCAG--ACATCCCA-AT Sertifera_n546 TCGAGACCGAAA-AAGA-GGG-AGTGATTTAGAGAACTCGT-AAAGAAAGTGACAACAGTTGCTG-CAGCAGTGCAG--ACATCCCA-AT Ellianthus_sp TCGAGACCAAAA-AAGT-GGG-AGCGATCTAGAGAACTCGT-AAAGAAAGCGG------G------AG--CCATCCCA-AC Elleanthus_lancifoliusER36 TCGAAGC-GAA--AAGC-CGG-A-CGATCTAT-GAACTCGT-AAAGAAAGCGG------G------AG--CCATCCCA-AC Elleanthus_cynarocephalus_g14 TCGAGACCGAAA-AAGCTGG--AGCGATCTAGAGAACTCGT-AAAGAAAGCGG------G------AG--CCATCCCA-AC Ellianthus_oliganthusER37 TCGAGACCAAAA-AAG-TGGG-AGCGATCTAGAGAACTCGT-AAAGAAAGCGG------G------AG--CCATCCCA-AC Elleanthus_tricallosus_n565 TCGAGACCGAAA-AAGA-GGG-AGCGATCTAGAGAACTCGT-AAAGAAAGCGGCAACAGTTGCTG------CG--GCA------GT Sobralia_amabilis_g18 TCGAGACCGAAA-GAGA-GGG-AGTGATTCAGAGAACTCGTAAAAGAA-GCGGCAACAGTTGCTG-CAGTGGAGCAG--GCATCCCA-AT Sobralia_fimbr_ER39 TCGAGACCGAAA-GAGA-GGG-AGTGATTCAGAGAACTCGTAAAAGAA-GCGGCAACAGTTGCTG-CAGTGGAGCAG--GCATCCCA-AT Sobralia_crocea_w533 TCGAGACCGAAA-GAGA-GGG-AGTGATTCAGCGAACCCGTAAAAGAA-GCGGTAACAGTTGCTG-CAGCGGAGCAG--GCATCCCA-AT Sobralia_mucronata_w535 TCGAGACCGAAA-GAGA-GGG-AGTGATTCAGCGAACCCGTAAAAGAA-GCGGTAACAGTTGCTG-CGGCGGAGCAG--GCATCCCA-AT Monophyllorchis_maculta TCGAGATC----T-----G-G-TTTGATTGTGCAAATTTGTGAAATAAG-TGGGT--A-TT------GG-TCCA--CC-TC------Triphora_trianth TC-AGATCG--AT----TGTG-AATGATTTAGAGAMCACGTCAAGTTCC-TG------TTGCC-TCCGT-AATC------TCC--GAT

Continued Table A.1. Primitive Epidendroideae analysis. ITS molecular matrix.

Table A.1 Continued

Triphora_genti_ER01 TCGAGAT-G--AT----TGTG-AATGATTTAGAGAACCCGTGAA-TT---TGA-GG---TTGCC-TCCGT-AATC------TCC--GAT Triphora_amazonica_ERP TCGAGACCNAAATGAGATGGG-AGCGATTTTGCGAACTCGTGAACG---GTGATGGCAGTTGCTATCA-CGAAACAA--CCGTCC-AG-T Diceratostele_gabonensis_ER44 ------GG------CGT----GA---CGG---CAGTCGCCGTCA-CGGCACAT--CCGTCCCCGAC Epipogium_aphyllum_O19248 ------GACCCCATAAAA-AAC---TGG-CAGTTGCTG-CC-T--AGCAA--CCTTCCT--TC epipogium_roseum ------AACATGTGGGCAAT-GCTGTCC-GAGAGCTGCACGCTCCTCTAC Nervilia_shirnensis_C280 TCGAGATCGAAA-GAGA-CGG-AGCGACTCGGAGAACGCGTGA--TG--GCCGCGGCGGTTACTG-CCGCGGAA--CTACCG-CCC-GAT Nervilia_plicata_AF324179 ------GAAA-GAGA-CGG-AGCGACTAGGAGAACGCGTGA--TG--GCCGTGGCAGTTGCTGTCA-CG-AA-ACTACCG-CCC-GAT Nervilia_holochila_AF324178 TCGAGATCGAAA-GAGA-CGG-CGCGACTCGGAGAACGCGTGA--TG--GCCGCGGCAGTCAATG-CAGCGGAA--TTACCGACC--GAT Wull_aphylla_er128 TCGAGACCGAAA-G-GAT-G------ATTCATTGAACTCGTGGGAATAAGCGGCGGCAATCGCTGTC-ATGGA-CAA--TAAGCCC--AT Xerorchis_amazonica_0799 ------AT------CA-----GC--CA-T------CG-AA--TT--CGTC---GCC Calypso_bulbosa TCGAGACCGAAGTTA--TG-G-AGTGATTCAGCGAACTCGTGAAATT--GCGATTGCAAT-GATGTT-GTGA-TTAG--CCGTCCCA-AT Ephi_schmidtii ------T---CA------Chysis_bractescens TCGAGACCCAAATTA--TCG--AGCGATTCGGAGAACCCGTGAA-TGA-GCGGCGGCAGT-GCCGTC-GCGAAATTG--CCGTCCCAGC- Coelia_triptera TCGAGACCGAAATTA--TCG--AGCGATTCGGAGAACTCGTGAAAT-AAGCGACGGTTGT-GCTGTT-GCGGAATAG--CCGTCCC-GGT C_trifida_2080 ------G--AGCGATTCGGAGAACATGTTAAAT-AAGCGGCAGCATT-GCTGTT-GCAAAAAAG--CCGTCCCT-AT Eulophia_sp TCGAGACCGAAATTGCACCG--AGTGACTCGGAGAACCCGTGGAACGACGTG-CGGCGTG-GCCGCC-GCGGAACGG--CCGTCC-AGGC Isochilus_amparoana TCGAGACCGAAAACA--TCG--AGCGATTCGGAGAAC-CGTGAA-TGA-GCGACGGCGGC-GTCGTC-GCGGAACAG--CCGTCCC-GGT Leptotes_bicolor TCGAGACCGGAATTA--TCG--AACGATTCGGAGAACCCGTGAA-TGT-CCGGCGGCGGT-GACGTC-GCGGAATGG--CCATCCC---- Oreorchis_patens TCGAGA-----A-TATATCG--AGCGATTCGGAGAACCTGTGAA-TTAAGCGGCGGCATT-GCTGTT-GCAAAAAAG--CCGTCCCAG-T 238 Govenia_sp TCGAGACCGAAATTA-AT-G--AGCGATTCGGTGAACCCGTGAAAT-AAGCGACGGCAAT-GCTGTT-GCATTATAG--CCACCCCAG-T

Palmorchis_trilobulata CTTTG--CCCCGCCTCC---AGGGTGAA---GGCTGGATGAG-A-CCCGAG-CAGGCACAGCTTCGTGCCAAGGCAAA-TGCGCAAA-CA Palmorchis_trilobulata_ER68 CTTTG--CCCCGCCTCC---AGGGTGAA---GGCTGGATGAG-A-CCCGAG-CAGGCACAGCTTCGTGCCAAGGCAAA-TGCGCAAA-CA V2115_PALMORCHIS_POWELII CGTTG--CCCCGCCTCC---AGGGTGAA---GGCTGGATGAG-A-CCTGAG-CTGGCACAGTTTCGTGCCAAGGGAAA-TGTCAAAA-CA Palmorchis_Sp_ER110 CGTTG--CCCCGCCTCC---AGGGTCAA---GGCTGGATGAG-A-CCCGAG-CTGGCACAGTTTCGTGCCAAGGGAAAATG--CAAA-GA Palmorchis_sp1_ER110E CGTTG--CCCCGCCTCC---AGGGTCAA---GGCTGGATGAG-A-CCCGAG-CTGGCACAGTTTCGTGCCAAGGGAAAATG--CAAA-GA Palmorchis_sp_ER129_selby CTTTG--CCCCGCCTCC---AGGGTGAA---GGCTGGAGGAG-A-CCCGAG-CAGGCACAGTTTCGTGCCAAGG-AAAATGCGCAAA-CA Palmorchis_462 CTTTG--CCCCGCCTCC---AGGGTGAA---GGCTGGATGAG-A-CCCGAG-CAGGCACAGCTTCGTGCCAAGGCAAA-TGCGCAAA-CA Gastrodia_procera_ER64 CTTTG--CCCCGCCTCC---TAGGTGAA---GGCTGGATGAG-A-CCCGAG-CAGGCACAGTTTCGTGCCAAGGGAAA-TGCGCAAA-CA Cephalanthera_aus_Dat115 CT-CG--CACGATCTCC---ACGGCGAA---GGCTGGATGAA-A-CCCGAA-CTAGCGCATTTTCGCGCCAA-GCAA--TGTGCAAAACA Cephalanthera_damasonium CT-CG--CACGATCTCC---ACGGCGAA---GGCTGGATGAA-A-CCCGAG-CTAGCGCATTTTCGCGCCAAGGCAA--TGTGCAAAACA CEPHALANTHERA_LONGIFOLIA_ay369 CT-CG--CACGATCTCC---ACGGCGAA---GGCCGGATGAA-A-CCCTAG-CTAGCGCATTTTCGCGCCAAGGCAA--TGTGCAAAACA Epipactis_helleborine CTTTG--CTTCAACTCC---GCGGTAAA---GGTTGGATGAATAACCCAAG-CTAGCGCATTATCGCGCCAAGGGAA--TGTGCAAAACA Epipactis_fageticola_AY351382 CTTTG--CTTCAACTCC---GCGGTAAA---GGTTGGATGAATAACCCAAG-CTAGCGCATTATCGCGCCAAGGGAA--TGTGCAAAACA Epipactis_lusitanica_AY351381 CTTTG--CTTCAACTCC---GCGGTAAA---GGTTGGATGAATAACCCAAG-CTAGCGCATTATCGCGCCAAGGGAA--TGTGCAAAACA Limodorum_abortivum -ATCG--CCTCTTCTCC---GCGGTGAA---GGTTGGATGA-TAACCCGAA-CCAGCGCAATTTCGCGCCAAGGGAA--TGTGCAAAACA Listera_smallii -TTAT--C-TTGTCTCC---AAGGTAAA---GGTTGGATGAA-AACTCGAG-CTAGCGCATTTTCGCGCCAAGGTAA--TGTGCAAAATA Neottia_nidus_avis CT-AG--CCTTGTATCC---ATGGTGAA---GGTTGTATGAA-AACCCGAG-CTAGCGCAATTTCGCGCCAAGGTAA--TGTGCAAAACA Corymborkis_sp_0542 CGTTG--CCTCATCTCCCC-ACGATGAAA--GGTCGGATGWA-AACTCGAG-CCGGCGCAGTTCCGCGCCAAGG-AAA-TGTGCAAA--A Corymborkis_vert_ER66 CGTTG--CCTCATCTCCCC-ACGATGAAA--GGTCGGATGAA-AACTCGAG-CCGGCGCAGTTCCGCGCCAAGG-AAA-TGTGCAAA--A Tropidia_effusa_O211 CGTTG--CCTCATCTCCC--ACGATGAA---GTTCGGATGAA-A-CTCGAG-CCGGCGCAGTTCCGCGCCAAGTGAA--TGTGCAAA--A

Continued

Table A.1 Continued

tropidia_gram CGTT---CCT-A-GTTCT--A-GA-GAA---GTTGGGATGAA-AACT-GAG---GGGGCAGT----CGCCAAGG-AA---G-GCAAA--A W2830_Tropidia_polystachya CGTTG--CCTCATCTCCC--ACGATGAA---GTTCGGATGA--AACTCGAG-CCGGCGCAGTTCCGCGCCAAGTGAA--TGTGCAAA--A Epilyna_jimenzeii_ER67 CATTG--TTGCGTCTCCCCCGCGATGAAAAAGGTTGGATAAA-AACTCAAAATCGGCGCAGTCTCGCGCCAAGGGAAAGTTTGCAAA-CA Epilyna_hirtzii_n526 CATTG--CTGCGTCTCCCCCGCGATGAAGGAGGTTGGATGAA-AACTCAAAATCGGCGCAGTCTCGCGCCAAGGGAAAATTCGCAAA-CA Sertifera_columbiana_ER38 TGTTG--CC--A-C------ACGATGACGAAGGTTGGATGAA-AACTCAAAATCGGCGCAGTCTCGCGCCAAGGGAAAATTTGCAAA-CG Sertifera_n546 TGTTG--CC--A-C------ACGATGACGAAGGTTGGATGAA-AACTCAAAATCGGCGCAGTCTCGCGCCAAGGGAAAATTTGCAAA-CG Ellianthus_sp TGTTG--TCGCATCTCCCCCGCGATGAAGAAGGTTGGATGAA-AACTCAAAACCGGCGCAGTCTCGCGCCAAGGGAAAATTTGCAAA-TG Elleanthus_lancifoliusER36 TGTTG--CCGCATCTCCCCCGCGGTGCAGAAGGTTGGATGAA-AACTCAAAACCGGCGCAGTCTCGCGCCAAGGGAAA-TTTGCAAA-CA Elleanthus_cynarocephalus_g14 TGTTG--CCGCATCTCCCCCGCGGCGAAGG-GGTTGGATGAA-AACTCAAAACCGGCGCAGTCTCGCGCCAAGGGAAAATTTGCAAA-CG Ellianthus_oliganthusER37 TGTTG--TCGCATCTCCCCCGCGATGAAGAAGGTTGGATGAA-AACTCAAAACCGGCGCAGTCTCGCGCCAAGGGAAAATTTGCAAA-TG Elleanthus_tricallosus_n565 TGTTG--CCGCATCTCCTCCGCGGTGAAGGAGGTCGGATGAA-AACTCAAAACCGGCGCAGTCTCGCGCCAAGGGAAAATTCGCAAA-CG Sobralia_amabilis_g18 TGTTG--CCACATCTCC---ACGATGACGAAGGTTGGATGAA-AACTCAAA-CCGGCGCAGTTTCGCGCCAAGGGAAAATATACAAA-CG Sobralia_fimbr_ER39 TGTTG--CCACATCTCC---GCGATGAAGAAGGTTGGATGAA-AACTCAAA-CCGGCGCAGTTTCGCGCCAAGGGAAAATATGTAAA-CG Sobralia_crocea_w533 TGTTG--CCACATCTCC---ACGATGAAGAAGGTTGGATGAA-AACTCAAA-CCGGCGCAGTTTCGCGCCAAGGGAAAATATGCAAA-CG Sobralia_mucronata_w535 TGTTG--CCACATGTCC---ACGATAAAGAAGGTTGGATGAA-AACTCAAA-CCGGCGCAGCTTCGCGCCAAGGGAAAATATGCAAA-CG Monophyllorchis_maculta ------TCAACACACC-CAACGATGAA---TGT-GG--GAA-AATCCTAAATGAGCGCAAGTAAGCGCCAAGTGAACAGACG-AAA--- Triphora_trianth -GCTG----AAC--ACC-----G-TGAAG--TGCCGGATGA----TACTAA-TTGGCGCAGCGCCGCGTCAAGTCAATCTA-G-AAA--T Triphora_genti_ER01 -GTTG--ATCGATC------GA-GAAA--TGTCGGATGA----TACTAA-TTGGCGCAGCATCGCGTCAAGTGAGTCCAT--AAA-TT Triphora_amazonica_ERP -CTTG--CCCCGCCTCC---TAGGTGAA---GGCTGGATGA-GA-CCCGAG-CAGGCACAGCTTCGTGCCAAGGCAAA-TGCGCAAA-CA 239 Diceratostele_gabonensis_ER44 -GT-G--TCCCCCCATC---ACGGGGGAGG-GGCCGGATGAA-A-CTCGAG-CCGGCGCAGATCTGCGCCAAGGGAA--TATGCAAA-CG Epipogium_aphyllum_O19248 TGTTG----AC--CTCC---ACGACGCG---GGTCGG-TGAA-A-CCCGAG-CCGGCGCAGCTTCGCGCCAAGG-AA--TTTGC----C- epipogium_roseum TTTTGCC-AGCA------GATT-----GGA------CATTAAG-CCGGCGCAGCACCGCGCCAAGGAAG--CGTGCG---TG Nervilia_shirnensis_C280 TGTCGCCGCGTCGCATC---GCGAAGGA---GGCAGGATGAA-AACTTGAG-CCGGCGCAGTTACGCGCCAAGGGAGA-TACGCGGA-CG Nervilia_plicata_AF324179 CGTCGCCGTGGTGCGTC---ACGGAGGA---GGTAGGATGAA-AACTCGAT-CCGGCGCAGCTACGCGCCAAGGGGAA-TATAAGAA-CG Nervilia_holochila_AF324178 TGTCGCCGCGTCGCATC---GCGAATGA---GGTGGGATGAA-AACTTGAG-CGGGCGCAGTTACGCGCCAAGGGAAA-CATTCAAA-CG Wull_aphylla_er128 C------CATCTCCTCGACG-TC-----GGGTCGACGAA-A-CACGAA-CTGACACAGGTTTGCGTCAAGGTAA--TATGCAGCCCA Xerorchis_amazonica_0799 CGT-G--TCACCAC------ACGATGGG---GGATGGATGAT-A-CTCAAG-CCGGCGCAATCCCGCGCCAAGTGAA--TTTGCAA--T- Calypso_bulbosa TGTTT--CCCCACGTT----GCGATGAA---GGATGGATTAA-AACTCAAA-CCGGCGCAGTTACGCGCCAAGGGAA--TACG-AAAGCA Ephi_schmidtii ---TG--TCTCATCTT----ATGATCAA---CGATGGTTGAA-AACTCAAA-TCGGCGCAGTTCCGCGCCAAGGGA---TTTG-AAAACA Chysis_bractescens CG-GG--CCTCGTC-A----ACGAGGAA---GGACGGATGAA-A-CTCAAA-CCGGCGCAGCTACGCGCCAAGGGAA--TACG-AAAACA Coelia_triptera CGTGT--ATC-ATCTCCG--ACGATGAA---GGACGGATGAA-AACTCAAA-CCGGCACAGTTTTGTGCCAAGGGAA--TATG-AAAACA C_trifida_2080 TGTCG--CCTCGGCTT-T-AACGATGAA---GGATGGATGAA-AATTCAAA-CCGGCGCAGTTCCGCGCCAAGGGAA--TACG-AAGACA Eulophia_sp CG-CG--CCCAATCTCCTC-GCGCGGC----GGACGGATGAA-AACACAAA-CCGGCGCAGCATCGCGCCAAGGGAAA-GC-G-AAAGCA Isochilus_amparoana CG-CG--CCTCGTCTCCCCGCCGTACAATA-GG-CGGTTGAA-AACTCAAA-CCGGCGCAGCCACGCGCCAAGGGAA--TACG-AATGCA Leptotes_bicolor -GAC---CCGGCCCTCTTCACCGGTGAAA--GGGCGGATCAA-AACTCAAA-CCGGCGCAGTTACGCGCCAAGGGAA--TACG-AAAACA Oreorchis_patens TGTCG--CCTCGGCTTA--AACGATGAA---GGATGGATGAA-AATTCAA--CCGGCGCAGTTTCGCGCCAAGGGAA--TACG-AAGACA Govenia_sp CGT----CCCCTCGCTT-CAGCGATGAA---GGATGGATGAA-AACACAAA-CCGGCGCAGTTCCGCGCCAAGGGAA--TACG-AAAACA

Palmorchis_trilobulata GGAGCCCTT--GCGGGTGCAGTAGCACGGAGCG--CTATT-CGC------TTATA---CGACTCTCGGCAACGGATATCTTGGCTCTCG Palmorchis_trilobulata_ER68 GGAGCCCTT--GCGGGTGCAGTAGCACGGAGCG--CTATT-CGC------TTATA---CGACTCTCGGCAACGGATATCTTGGCTCTCG V2115_PALMORCHIS_POWELII GGAGCCCTA--GCGGGTGCTGTAGCACGGAGCG--CTATT-CGC------TTATA---CGACTCTCGGCAACGGATATCTTGGCTCTCG Palmorchis_Sp_ER110 GGAGCCCTA--GCGGGTATAGTAGCACGGAGCG--CTACT-GGC------TTATA-TACGACTCTCGGCAACGGATATCTTGGCTCTCG

Continued

Table A.1 Continued

Palmorchis_sp1_ER110E GGAGCCCTA--GCGGGTATAGTAGCACGGAGCG--CTACT-GGC------TTATA-TACGACTCTCGGCAACGGATATCTTGGCTCTCG Palmorchis_sp_ER129_selby GGAGCCCTT--GCGGGTGCAGTAGCACGGAGCG--CTATT-CGC------TTGTA---CGACTCTCGGCAACGGATATCTTGGCTCTCG Palmorchis_462 GGAGCCCTT--GCGGGTGCAGTAGCACGGA------TT-CGC------TTATA---CGACTCTCGGCAACGGATATCTTGGCTCTCG Gastrodia_procera_ER64 GGAGCCCTT--GCGGGTGCAGTAGCACGGAGCG--CTATT-CGC------TTATA---CGACTCTCGGCAACGGATATCTTGGCTCTCG Cephalanthera_aus_Dat115 CGAGCCCCA--GCAGGTTTGGTGGCATTGA------TTATA---TGACTCTCGGCAACGGATATCTCGGCTCTCG Cephalanthera_damasonium CGAGCCCCA--ACAGGTTTGGTGGCATTGA------TTATA---TGACTCTCGGCAACGGATATCTCGGCTCTCG CEPHALANTHERA_LONGIFOLIA_ay369 CGAGCCCCA--ACAGGTTTGGCGGCATTGA------TTATA---TGACTCTCGGCAACGGATATCTCGGCTCTCG Epipactis_helleborine CGAGCCACA--TAAAGTTTGGTGGCATGTA------TA------TTATA---TGACTCTCGGCAACGGATATCTCGGCTCTCG Epipactis_fageticola_AY351382 CGAGCCACA--TAAAGTTTGGTGGCATGTA------TA------TTATA---TGACTCTCGGCAACGGATATCTCGGCTCTCG Epipactis_lusitanica_AY351381 CGAGCCACA--TAAAGTTTGGTGGCATGTA------TA------TTATA---TGACTCTCGGCAACGGATATCTCGGCTCTCG Limodorum_abortivum CGAGCCCCA--GCAGGTCTGGTGGCATGGA------TTATA---TGACTCTCGGCAACGGATATCTCGGCTCTCG Listera_smallii TGAGCCCCA--GCAAGTCTGGTGGCATGGA------TTATA---TGACTCTCGGCAACGGATATCTCGGCTCTCG Neottia_nidus_avis TGATTCCCA--GCATGTCTGGTGGCATGGA------TTATA---TGACTCTCGACAACGGATATCTCGGCTCTCG Corymborkis_sp_0542 TGAGCCCCGCAGCGGGCTTAGTAGCGTGGAGTG--CTGTTT-GCACGCCATTT--AACACGACTCTCGGCAATGGATATCTCGGCTCTCG Corymborkis_vert_ER66 TGAGCCCCGCAGCGGGCTTAGTAGCGTGGAGTG--CTGTTT-GCACGCCATTT--AACACGACTCTCGGCAATGGATATCTCGGCTCTCG Tropidia_effusa_O211 TGAGCCCTACACCGGGTTTAGTAGCGTGGGGTG--CTGT--CGCACACCACTT--AACACGACTCTCGGCAATGGATATCTCGGCTCTCG tropidia_gram TGA--CCT-CAGCGGGTTTAGTAGCGTGGAG------GCTCCCCATTT--AAC--GACT-TCGGCAATGGATAT--TGGCT--TG W2830_Tropidia_polystachya TGAGCCCTACACCGGGTTTAGTAGCGTGGGGTG--CTGT--CGCACACCACTT--AACACGACTCTCGGCAATGGATATCTCGGCTCTCG Epilyna_jimenzeii_ER67 TAAGCCCTACTGCGGGCTTAGCGGTGTGGAGTG--TT-----GC-CACCATTTATAACATGACTCTCGGCAATGGATATCTCGGCTCTCG Epilyna_hirtzii_n526 TGAGCCCTATTGCGGGCTTAGCGGTGTGGAGTG--TT-----GC-CAACATTTATAACATGACTCTCGGCAATGGATATCTCGGCTCTCG 240 Sertifera_columbiana_ER38 TAAGCCCTGTTGCGGGTTTAGCGGCGTGGAGTG--TTGTTACGCACACCATTTAAAATATGACTCTCGGCAATGGATATCTCGGCTCTCG Sertifera_n546 TAAGCCCTGTTGCGGGTTTAGCGGTGTGGAGTG--TTGTTACGCACACCATTTAAAATATGACTCTCGGCAATGGATATCTCGGCTCTCG Ellianthus_sp CAAGCCCTACAACGGGCTTAGCGGTGTGGAGTG--TTGTAACGCATACCATC-ATAACATGACTCTCGGCAATGGATATCTCGGCTCTCG Elleanthus_lancifoliusER36 TAAGCCCTGCAGCGGGCTTAGCGGTGTGGAGTG--CTGTTACGCATACCATC-ATAACATGACTCTCGGCAATGGATATCTCGGCTCTCG Elleanthus_cynarocephalus_g14 TAAGCCCCGCAATGGGCTTAGTGGTGTGGAGTG--TCGTTACGC--ACCATC-ATAACATGACTCTCGGCAATGGATATCTCGGCTCTCG Ellianthus_oliganthusER37 CAAGCCCTACAACGGGCTTAGCGGTGTGGAGTG--TTGTAACGC--ACCATC-ATAACATGACTCTCGGCAATGGATATCTCGGCTCTCG Elleanthus_tricallosus_n565 TAAGCCCCGCTGCGGGCTTAGCGGCGTGGAGCG--TTGTTACGC--ACCATTTATAACATGACTCTCGGCAATGGATATCTCGGCTCTCG Sobralia_amabilis_g18 TAAGCCCTGCTGTGGGTTTAGTGGTG------CTACGC--ACCATTTATAATATGACTCTCGGCAATGGATATCTCGGCTCTCG Sobralia_fimbr_ER39 TAAGCCCTGCTGCGGGTTTAGTGGTGCGGAGTG--TTGCTACGC--ACCATTTATAATATGACTCTCGGCAATGGATATCTCGGCTCTCG Sobralia_crocea_w533 TAAGCCCTGCTGCGGGTTTAGTGGTGCGGAGTG--TTGCTACGC--ACCATTTATAATATGACTCTCGGCAATGGATATCTCGGCTCTCG Sobralia_mucronata_w535 TAAGCCCTGCTGTGGGTTTAGTGGTGCGGAGTG--TTGCTACGC--ACCATTTATAATATGACTCTCGGCAATGGATATCTCGGCTCTCG Monophyllorchis_maculta --AG-CC-A--GCAA-TGTGGCGATGTGAA-T---CACTT-CTTA---CATTG-T-ACATGACCCTCGGCAATGGATATCTCAACTCTTG Triphora_trianth CTTCTCC-A--GCAAATTTATTGGATTGAAGCG--CACTC-C-C------TC--AACACGACTCTCGGCAATGGATATCTCGGCTCTCG Triphora_genti_ER01 CTTGTTC-A--ACAACTTTGGTGACTTGAAAAG--C-ATT------CATCC--AAAATGACTCTCAGCAATGGATATCTCGGCTCTCG Triphora_amazonica_ERP GGAGCCC----GCGGGTGCAGTAGCACGGAGCG--CTATT-CGC------TT---ATACGACTCTCGGCAACGGATATCTTGGCTCTCG Diceratostele_gabonensis_ER44 --AGCCCCGCAGCGGGCTTAGCGGCGTGGAGCG--CCGTC-CGCACAC---TT--AACACGACTCTCGGCAATGGATATCTCGGCTCTCG Epipogium_aphyllum_O19248 --AGCCC-GCAGCGGGCCA--CG---AGGAGTG--CTATT-CGC------CTA-AACATGACTCTCGGCAATGGATATCTCGGCTCCCG epipogium_roseum --AGCCCTACT--GGGT------GTCAGA---CATTTTCGC------TT--AACACGACTCTCGACAATGGATATCTCGGCTCTCG Nervilia_shirnensis_C280 --AGCCC-ACCGTGGGCCT--CGCCGAGCAGCGC---GCC-CGC----C-TTC--GACACGACTCTCGGCAATGGATATCTCGGCTCTCG Nervilia_plicata_AF324179 --AGCCC---GGCGGGCTG--CGCCGAGCAGCCC---GCT-CGT----C-TTT--GACACGACTCTCGGCAATGGATATCTCGGCTCTCG

Continued

Table A.1 Continued

Nervilia_holochila_AF324178 --GGCCC---AGCGGGCTG--CGCCGAGCAGCCC---GCG-CGT----C-TTC--GACACGACTCTCGGCAATGGATATCTCGGCTCTCG Wull_aphylla_er128 CGATCCC-A--GC------TG-A-----C-GTT-CGC--ACCGTTT--AAAATGACTCTCAGCAATGGATATCTCGGCTCTCG Xerorchis_amazonica_0799 T-AGCCCCA-AGCGGGTTTAGTGGAATGGG-CG--CCG---CGC--ACCATTT--GACACGACTCTCGGCAATGGATATCTCGGCTCTCG Calypso_bulbosa CGAGCCT--CATTGGGTTTAGTGTTGTGGAGTG--C-ATT--GCACACCATTT--GACATGACTCTCGGCAATGGATATCTCGGCTCTCG Ephi_schmidtii CTAGCC---T-TTGGCTTTAGTGGGATGGAGTG--CTAT---GCACACCATTTG-A-CATGACTCTCGGCAATGGATATCTCGGCTCTCG Chysis_bractescens CGAGCCC--TATCGGGTTTAGTGGCGTGGAGTG--C-GTC--GCACACCACTC--GACACGACTCTCGGCAATGGATATCTCGGCTCTCG Coelia_triptera TGAGCCC--CATTGGGTTTAGTGGCGTGGAGTG--CTGTT--GCACACCATTC--AACATGACTCTCGGCAATGGATATCTCGGCTCTCG C_trifida_2080 CGAGGCCC-TGTCGGGCTTAGTGGCGTGGAGTG-TCT-TT--GCACACCATTT--TACATGACTCTCGGCAATGGATATCTCGGCTCTCG Eulophia_sp CGAGCCCC-CGTCGGGCTCGGCGGCGTGGAGTG--CTATT--GCACGCCATTG--GACACGACTCTCGGCAATGGATATCTCGGCTCTCG Isochilus_amparoana CTACCCC--CATCGGGTTTCGTGGCGTGGGGTG--CTGTT--GCACACCATTC--CACACGACTCTCGGCAATGGATATCTCGGCTCTCG Leptotes_bicolor CGGGCCC--CATCGGGTTTTGTGGCATGGAGTG--CTGTT--GCACGCCATTC--GACACGACTCTCGGCAATGGATATCTCGGCTCTCG Oreorchis_patens CGAGCCC--CATCGGGCTTAGCGGCGTGGAGTG-TCT-TT--GCACACCATTT--AACATGACTCTCGGCAATGGATATCTCGGCTCTCG Govenia_sp CGAGCCC--CATCGGGTTTAGTGGCGTGGAGTG--CCGTT--GCACACCATTT--GACATGACTCTCGGCAATGGATATCTCGGCTCTCG

Palmorchis_trilobulata CATCGATGAAGAGCGCAGCGAAATGCGATACGTAGTGCGAATTGCAGAATCCCGTGAACCATCGAGTATTTGAACGCAAGTTGCGCCCGA Palmorchis_trilobulata_ER68 CATCGATGAAGAGCGCAGCGAAATGCGATACGTAGTGCGAATTGCAGAATCCCGTGAACCATCGAGTATTTGAACGCAAGTTGCGCCCGA V2115_PALMORCHIS_POWELII CATCGATGAAGAGCGCAGCGAAATGCGATACGTAGTGCGAATTGCAGAATCCCGTGAACCATCGAGTATTTGAACGCAAGTTGCGCCCGA Palmorchis_Sp_ER110 CATCGATGAAGAGCGCAGCGAAATGCGATACGTAGTGCGAATTGCAGAATCCCGTGAACCATCGAGTATTTGAACGCAAGTTGCGCCCGA 241 Palmorchis_sp1_ER110E CATCGATGAAGAGCGCAGCGAAATGCGATACGTAGTGCGAATTGCAGAATCCCGTGAACCATCGAGTATTTGAACGCAAGTTGCGCCCGA Palmorchis_sp_ER129_selby CATCGATGAAGAGCGCAGCGAAATGCGATACGTAGTGCGAATTGCAGAATCCCGTGAACCATCGAGTATTTGAACGCAAGTTGCGCCCGA Palmorchis_462 CATCGATGAAGAGCGCAGCGAAATGCGATACGTAGTGCGAATTGCAGAATCCCGTGAACCATCGAGTATTTGAACGCAAGTTGCGCCCGA Gastrodia_procera_ER64 CATCGATGAAGAGCGCAGCGAAATGCGATACGTAGTGCGAATTGCAGAATCCCGTGAACCATCGAGTATTTGAACGCAAGTTGCGCCCGA Cephalanthera_aus_Dat115 CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCAAGTCTTTGAACGCAAGTTGCGCCCGA Cephalanthera_damasonium CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCAAGTCTTTGAACGCAAGTTGCGCCCGA CEPHALANTHERA_LONGIFOLIA_ay369 CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCAAGTCTTTGAACGCAAGTTGCGCCCGA Epipactis_helleborine CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCAAGTCTTTGAACGCAAGTTGCGCCCGA Epipactis_fageticola_AY351382 CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCAAGTCTTTGAACGCAAGTTGCGCCCGA Epipactis_lusitanica_AY351381 CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCAAGTCTTTGAACGCAAGTTGCGCCCGA Limodorum_abortivum CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCAAGTCTTTGAACGCAAGTTGCGCCCGA Listera_smallii CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCAAGTCTTTGAACGCAAGTTGCGCCCGA Neottia_nidus_avis CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCAAGTCTTTGAACGCAAGTTGCGCCCGA Corymborkis_sp_0542 CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Corymborkis_vert_ER66 CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Tropidia_effusa_O211 CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGTGAATTGCAGAATCCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA tropidia_gram CATCGA-GAAGAG-GCAG-GAAAT-CGATACGTGG---GAATTGCAGAATCCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA W2830_Tropidia_polystachya CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGTGAATTGCAGAATCCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Epilyna_jimenzeii_ER67 CATCGATGAAGAGCGCAGCGAAATGCGATACATGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Epilyna_hirtzii_n526 CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Sertifera_columbiana_ER38 CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Sertifera_n546 CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA

Continued

Table A.1 Continued

Ellianthus_sp CATCGATGAAGAGCGCAGCGAAATGCGATACATGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Elleanthus_lancifoliusER36 CATCGATGAAGAGCGCAGCGAAATGCGATACATGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Elleanthus_cynarocephalus_g14 CATCGATGAAGAGCGCAGCGAAATGCGATACATGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Ellianthus_oliganthusER37 CATCGATGAAGAGCGCAGCGAAATGCGATACATGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Elleanthus_tricallosus_n565 CATCGATGAAGAGCGCAGCGAAATGCGATACATGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Sobralia_amabilis_g18 CATCGATGAAGAGCGCAGCGAAATGCGATACATGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Sobralia_fimbr_ER39 CATCGATGAAGAGCGCAGCGAAATGCGATACATGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Sobralia_crocea_w533 CATCGATGAAGAGCGCAGCGAAATGCGATACATGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Sobralia_mucronata_w535 CATCGATGAAGAGCGCAGCGAAATGCGATACATGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Monophyllorchis_maculta CTTCGATGAAGGACGCAGCAAAATGCGAGATTTGATGCGAATTGCAGAATCCCGTGAATCATCAAAAATTTGAACGCAAGTTGCGCTCGA Triphora_trianth CAACGATGAAGAGCGCAGCAAAATGCGACACATGGTGCGAATTGCAGAATCCCGCGAACCATCGAGTACTTGAACGCAAGTTGCGCCCAA Triphora_genti_ER01 CAACGATGAAGAGCGCAGCAAAATGTGACACATGGTGCGAATTGCAGAATCCCGTGAACCATCAAGTACTTGAACGCAAGTTGCGCCCAA Triphora_amazonica_ERP CATCGATGAAGAGCGCAGCGAAATGCGATACGTAGTGCGAATTGCAGAATCCCGTGAACCATCGAGTATTTGAACGCAAGTTGCGCCCGA Diceratostele_gabonensis_ER44 CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCTGA Epipogium_aphyllum_O19248 CATCGATGAAGAACGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCAA epipogium_roseum CATCGATGAAGAACGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCAA Nervilia_shirnensis_C280 CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Nervilia_plicata_AF324179 CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Nervilia_holochila_AF324178 CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Wull_aphylla_er128 CATCGATGAAGAGCACAACGAAATATGATACGTGGTGTGAATTACAGAATCCCACGAACCATCGAGTCTTTGAACGCAAGTTGCTCCCGA 242 Xerorchis_amazonica_0799 CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGTGAATTGCAGAATCCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Calypso_bulbosa CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGCGAACCATCGAGTTTTTGAACGCAAGTTGCGCCCGA Ephi_schmidtii CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTATTTGAACGCAAGTTGCGCCTAA Chysis_bractescens CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGCGAACCATCGAGAATTTGAACGCAAGTTGCGCCCGA Coelia_triptera CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCGAGAATTTGAACGCAAGTTGCGCCCGA C_trifida_2080 CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTTTTTGAACGCAAGTTGCGCCTGA Eulophia_sp CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCTGA Isochilus_amparoana CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGCGAACCATCGAGAATTTGAACGCAAGTTGCGCCCGA Leptotes_bicolor CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGCGAACCATCGAGAATTTGAACGCAAGTTGCGCCCGA Oreorchis_patens CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTTTTTGAACGCAAGTTGCGCCCGA Govenia_sp CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTTTTTGAACGCAAGTTGCGCCCGA

Palmorchis_trilobulata GGCCAGCCGGCCGAGGGCACGTCTGCTTGGGCGTGAAGCATTGCATCGCTCCGAGCCAGCGCCATCC-CCT---AATTTGGGTGCGTTGC Palmorchis_trilobulata_ER68 GGCCAGCCGGCCGAGGGCACGTCTGCTTGGGCGTGAAGCATTGCATCGCTCCGAGCCAGCGCCATCC-CCT---AATTTGGGTGCGTTGC V2115_PALMORCHIS_POWELII GGCCAGCCGGCCGAGGGCACGTCTGCTTGGGCGTGAAGCATTGCATCGCTCCGTGCCTGCGCCATCC-ACT---AATTTGGGTGTGTCGC Palmorchis_Sp_ER110 GGCCAGCCAGCCGAGGGCACGTCCGCTTGGGCGTCAAGCATTGCATCGCTCCGTGCCCGCGCCATCC-ACT---AATCTGTGGGTGTTGC Palmorchis_sp1_ER110E GGCCAGCCAGCCGAGGGCACGTCCGCTTGGGCGTCAAGCATTGCATCGCTCCGTGCCCGCGCCATCC-ACT---AATCTGTGGGTGTTGC Palmorchis_sp_ER129_selby GGCCAGCCGGCCGAGGGCACGTCTGCTTGGGCGTGAAGCATTGCATCGCTCCGTGCCAGCGCCATCC-CCT---AATTCGGGTGCGTTGC Palmorchis_462 GGCCAGCCGGCCGAGGGCACGTCTGCTTGGGCGTGAAGCATTGCATCGCTCCGAGCCAGCGCCATCC-CCT---AATTTGGGTGCGTTGC Gastrodia_procera_ER64 GGCCAGCCGGCCGAGGGCACGTCTGCCTGGGCGTGAAGCATTGCATCG-TCCGTGCCAGCGCCATCC-CCT---AATTTGGGTGCGTTGC Cephalanthera_aus_Dat115 GGCCAATCGGCTAAGGGCACGTCCGCCTGGGCGTCAAGCGTTGCTACGCTTCGTGCCATCACCACGC-GCC---AAT--GGGCGTGGTCG

Continued

Table A.1-Continued

Cephalanthera_damasonium GGCCAATCGGCTAAGGGCACGTCCGCCTGGGCGTCAAGCGTTGCATCGCTTCGTGCCGCCACCACAC-ACC---AAT--GTGCGTGGTCG CEPHALANTHERA_LONGIFOLIA_ay369 GGCCAATCGGCTAAGGGCACGTCCGCCTGGGCGTCAAGCGTTGCATCGCTTCGTGCCGTCACCACAC-ACC---AAT--GGGCGTTGTCG Epipactis_helleborine GGCCAATCGGCTAAGGGCACGTCTGCCTGGGCGTCAAGCGTTGCGTCACTTCGTACCATCACCACAC-ACT---AAT--GGGTGTGTTGC Epipactis_fageticola_AY351382 GGCCAATCGGCTAAGGGCACGTCTGCCTGGGCGTCAAGCGTTGCGTCACTTCGTACCATCACCACAC-ACT---AAT--GGGTGTGTTGC Epipactis_lusitanica_AY351381 GGCCAATCGGCTAAGGGCACGTCTGCCTGGGCGTCAAGCGTTGCGTCACTTCGTACCATCACCACAC-ACT---AAT--GGGTGTGTTGT Limodorum_abortivum GGCCAATCGGCCAAGGGCACGTCTGCCTGGGCGTCAAGCGTTGCGTCGCTTCGTGCCATCACCACCC-TCC----ATT-CGGTGTGTTGG Listera_smallii GGCCAATCGGCCAAGGGCACGTCTGCCTGGGCGTCAAGCGTTGCGTCGCTTCGTGCCATCACCACCC-ACC---GAT--AGGTGTGTTAG Neottia_nidus_avis GGCCAATCGGCCAAGGGCACGTCTGCCTGGGCGTCAAGCGTTGCGTCACTTCGTGTCATCACCACCC-ACC----ATT-GGGTGTGTTGG Corymborkis_sp_0542 GGCCAACCGGCCAAGGGCACGTCTGCCTGGGCGTCAAGCGCTGCGTCGCTCCGTGCCAACGTCATCCCACC---GAT--GGGTGGGTGGG Corymborkis_vert_ER66 GGCCAACCGGCCAAGGGCAAGTCTGCCTGGGCGTCAAGCGCTGCGTCGCTCCGTGCCAACGTCATCCCACC---GAT--GGGTGGGTGGG Tropidia_effusa_O211 GGCCAACCGGCCAAGGGCACGTCTGCCTGGGCGTCAAGCGCTGCGTCGCTCCGTGCCAACGCCATCCCGCC---AA---GGGTGTGTGGG tropidia_gram GGCCA-CCGGCCAAGGGCACGTCTGCCTGGGCGTCAAGCGCCG-GTCG-TCCGTGCCAA-GCCATCCCACC------GGTGGGTGGG W2830_Tropidia_polystachya GGCCAACCGGCCAAGGGCACGTCTGCCTGGGCGTCAAGCGCTGCGTCGCTCCGTGCCAACGCCATCCCGCC---AA---GGGTGTGTGGG Epilyna_jimenzeii_ER67 GGTCAATCGACCGAGGGCACGTCTGCCTGGGCGTCAAGCATCACATCGCTCCATGCCGACGCCATCCCACC---GA---GGGTGTGTCGG Epilyna_hirtzii_n526 GGCCAATCGACCGAGGGCACGTCTGCCTGGGCGTCAAGCATCACATCGCTCCACGCCGACGCCATCCCACC---GA---GGGTGTGCCGG Sertifera_columbiana_ER38 GGCCAATCGACCGAGGGCACGTCTGCCTGGGCGTCAAGCATTGCATCGCTCCATGCAGGCACCAACCCACC---TA---GGGTGAGCAGG Sertifera_n546 GGCCAATCGACCGAGGGCACGTCTGCCTGGGCGTCAAGCATTGCATCGCTCCATGCAGGCACCAACCCACC---TA---GGGTGAGCAGG Ellianthus_sp GGCCAATCGGCCGAGGGCACGTCCGCCTGGGCGTCAAGCATCGCATCGCTCCATGCCGACGCCATCCCACC---GA---GGGTGTGTTGG Elleanthus_lancifoliusER36 GGCCAATCGACCGAGGGCACGTCCGCCTGGGCGTCAAGCACCGCATCGCTCCATGCCGACGCCATCCCGCC---GA---GGGTGTGTTGG 243 Elleanthus_cynarocephalus_g14 GGCCAATCGACCGAGGGCACGCCCGCCTGGGCGTCAAGCACCGCATCGCTCCATGCCGACGCCATCCCACC---GA---GGGTGTGCTGG Ellianthus_oliganthusER37 GGCCAATCGGCCGAGGGCACGTCCGCCTGGGCGTCAAGCATCGCATCGCTCCATGCCGACGCCATCCCACC---GA---GGGTGTGTTGG Elleanthus_tricallosus_n565 GGCCAATCGACCGAGGGCACGTCCGCCTGGGCGTCAAGCATCGCATCGCTCCGTGCCGACGCCATCCCACC---GA---GGGTGTGTTGG Sobralia_amabilis_g18 GGCCAATCGGCCAAGGGCACGTCTGCCTGGGCGTCAAGCATTGCATCGCTCCATGCCAACACCATCCCACC---AA---GGGTGTGTCAG Sobralia_fimbr_ER39 GGCCAATCGGCCAAGGGCACGTCTGCCTGGGCGTCAAGCATTGCATCGCTCCATGCCAACACCATCCCACC---AA---GGGTGTGCCGG Sobralia_crocea_w533 GGCCAATCGGCCAAGGGCACGTCTGCCTGGGCGTCAAGCATTGCATCGCTCCATGCCAACACCATCCCACC---AA---GGGTGTGTTAG Sobralia_mucronata_w535 GGCCAATCGGCCAAGGGCACGTCTGCCTGGGCGTCAAGCATTGCATCGCTCCATGCCAACACTATCCCACC---AA---GGGTGTGTTAG Monophyllorchis_maculta GGCCATTAGGCCAAGGGCACGCCTGCTTGGGAGACATGCTTTGCTTTG-TCCGAACC-TCAC------TT----TGT----- Triphora_trianth GGCCAACATGCCGAGGGCACGTCCGCCTGGGGGTCCAGCACCA--TCCATCCGCCGCAGCCT---CCCACG---GATA----TGTGGGGA Triphora_genti_ER01 GGCCAGCATGCCGAGGGCACGTCTGCCTGGGGGTCCAACATCACTTCCATCCGTAGC------AA------GT-T--- Triphora_amazonica_ERP GGCCAGCCGGCCGAGGGCACGTCTGCTTGGGCGTGAAGCATTGCATCGCTCCGAGCCAGCGCCATCCC------TATTTGGGTGCGTTGC Diceratostele_gabonensis_ER44 GGCCAACCGGCCAAGGGCACGTCCGCCTGGGCGTCAAGCGCCGCATCGCTCCGTGCCAGCGCCATCCC-CG---GG---GGGWGTGCCGG Epipogium_aphyllum_O19248 GGCCCTTAGGCCAAGGGCACGCCTGCCTGGGCGTCATGCATTACGTCG-TCC-T---A-CCCTATCC------TGTGA-GG epipogium_roseum GGCCAGTAGGCCAAGGGCACGCCCGCTTGGGCGTCATGCATTGCATCTCTCCGAGCCATGGCCCTACAGGC----AG----ATTTGCCGG Nervilia_shirnensis_C280 GGCCCACCGGCCGAGGGCACGCCCGCCTGGGCGTCAAGCATCGCGTCG-TCCTTGCCAGGACCATCCCAC----GGC--GGATGCGTCGG Nervilia_plicata_AF324179 GGCCCACCGGCCGAGGGCACGCCCGCCTGGGCGTCAAGCATCACGTCA-TCCTCGCCAAGACCATCCCG------T-GG Nervilia_holochila_AF324178 GGCCCACCGGCCGAGGGCACGCCCGCCTGGGCGTCAAGCATCGCGTTG-TCCTTGCCAAGGCCATCCCA------C-GG Wull_aphylla_er128 AGCCAACCGGCCTAGGGCACATCCACCTGGGCGTTAGGCATTTTGTAGCTTCATGCTGACACTCGTGTGGC------G-GAGAG-CGG Xerorchis_amazonica_0799 GGCCAACCGGCCAAGG-CACGTCCGCCTGGGAGTCGAGCATTGCGTCGCTCCGTGCAGACACCGTCCCAC----TGA--GG-TGTGCGGG Calypso_bulbosa GGCCTGTCGGCCAAGGGCACGTCTGCCTGGGCGTCATGCGTTGCATCG-TCCGTGCCAACACCATCACACC---TAT--GAGTGT-TTGG Ephi_schmidtii GGCCAGCCGGCCAAGGGCACGTCCGCCTGGGTGTCAAGCGTTGCGTTGCTTCGTGCCAACTTCATCCCACC---GA---G-GTGTGTTGG Chysis_bractescens GGCCAGCCGGCCAAGGGCACGTCCGCCTGGGCGTCAAGCGTTGCGTCG-TCCGTGCCAACTCCATCCCATC---GAT--GGGTGTGTCGG Coelia_triptera GGCCAGCCGGCCAAGGGCACGTTCGCCTGGGCGTCAAGCATTACGTCGT-CCGTGCCAACTCCATCCTAC----GATT-GGGTGGGATGG C_trifida_2080 GGCCAGCCGGCCAAGGGCACGTCCGCCTGGGCGTCAAGCGTTGCGTCG-TCCGTGCCAACTCCATCACACC---TAT--GTGTGTGTCGG

Continued

Table A.1-Continued

Eulophia_sp GGCCAGCCGGCGGAGGGCACGTCCGCCTGGGCGTCAAGCTTCGCGTCG-TCCGTGCCAGCTCCGCTCCGCC---GAT--GGGTGTGAGGG Isochilus_amparoana GGCCAGCCGGCCAAGGGCACGTCCGCCTGGGCGTCAAGCGTTGCGTCG-TCCGTGCCAGCTCCATCCCACC---CAC--GGGGGTGTCGG Leptotes_bicolor GGCCAGCCGGCCAAGGGCACGTCCGCCTGGGCGTCAAGCGTTGCGTCG-TCCGTGCCAACTCCAGCCCCCC---AAC--GGGTGTGTCGG Oreorchis_patens GGCCAGCCGGCCAAGGGCACGTCCGCCTGGGCGTCAAGCGTTGCGCCG-TCCGTGCCAACTGCATCACACC---TAT--GGGTGTGTCGG Govenia_sp GGCCAGCCGGCCAAGGGCACGTCCGCCTGGGCGTCAAGCGTTGCGTTG-TCCGTGCCAACTCCGTCCCCCC----AT--GGGTGTGTCGG

Palmorchis_trilobulata TGC--A-AG-CTC-GGAT------GTGCAGAGTGGCTCGTCGTGCTTATTGGT----ACGGCGGGTTGAAGAGCGGGTTGTCGTCT Palmorchis_trilobulata_ER68 TGC--A-AG-CTC-GGAT------GTGCAGAGTGGCTCGTCGTGCTTATTGGT----ACGGCGGGTTGAAGAGCGGGTTGTCGTCT V2115_PALMORCHIS_POWELII TGC--A-TG-CTC-GGAT------GTGGAGAGTGGCTCGCCGCGCCGATTGGT----ACGGCGGGTTGAAGAGCGGGTTGTCGTCT Palmorchis_Sp_ER110 TGC--A-TG-CTC-GGAT------GTGGAGAGTGGCTCGCCGTGCTTATTGGT----GCGGCGGGGTGAAGAGCGGGCTGTCGTCT Palmorchis_sp1_ER110E TGC--A-TG-CTC-GGAT------GTGGAGAGTGGCTCGCCGTGCTTATTGGT----GCGGCGGGGTGAAGAGCGGGCTGTCGTCT Palmorchis_sp_ER129_selby TGC--A-TG-CTC-GGAT------GTGCAGAGTGGCTCCTCGTGCTTGTTGGT----ACGGCGGGTTGAAGTGCGGGTTGTCGTCT Palmorchis_462 TGC--A-AG-CTC-GGAT------GTGCAGAGTGGCTCGTCGTGCTTATTGGT----ACGGCGGGTTGAAGAGCGGGTTGTCGTCT Gastrodia_procera_ER64 TGC--AAG--CTC-GGAT------GTGCAGAGTGGCTCGTCGTGCTTATTGGT----ACGGCGGGTTGAAGAGCGGGTTGTCGTCT Cephalanthera_aus_Dat115 TGC--G-GG-CTC-GAAT------GCGAAGAGTGGTTCGCCGTGCTCATCGGT----GCGGCGGATTGAAGAACGGGTTGTCGTCT Cephalanthera_damasonium TGC--G-GG-CTC-GAAT------GCGAAGAGTGGTCCGCCGTGCTCATCGGT----GCGGCGGATTGAAGAGCGGGTTGTCGTCT CEPHALANTHERA_LONGIFOLIA_ay369 TGC--G-GG-CTC-GAAT------GCGGAGAGTGGTCCGCCGTGCTCATCGGT----GCGGCGGATTGAAGAGCGGGTTGTCGTCT Epipactis_helleborine TGT--A-GG-CTC-GAAT------GTGAAGAGTGGTTCGCCGTGCCCATTGGT----GCGACGGACTGAAGAGCGGGTTGTTGTCT Epipactis_fageticola_AY351382 TGT--A-GG-CTC-GAAT------GTGAAGAGTGGTTCGCCGTGCCCATTGGT----GCGACGGACTGAAGAGCGGGTTGTTGTCT 244 Epipactis_lusitanica_AY351381 TGT--A-GG-CTC-GAAT------GTGAAGAGTGGTTCGCCGTGCCCATTGGT----GCGACGGACTGAAGAGCGGGTTGTTGTCT Limodorum_abortivum TGC--A-GG-CTC-GAAT------GTGAAGAGTGGTTCGCCGTGCTAATTGGT----GCGACGGACTGAAGAGTGGGTTGTTGTCT Listera_smallii TGC--A-TG-CTC-GAAT------GTGAAGAGTGGTTCGCCGTGCCC-TTGGT----GCGGCGGATTGAAGAGCGGGT-GTTGTCT Neottia_nidus_avis TGC--A-TG-CTC-GAAT------GTGGAGAGTGGTTCTCCGTGTCC-TTGAT----GCGGCGGACTGAAGAACGGGTTGTTGTCT Corymborkis_sp_0542 -GC-GA-GG-CGC-GGAC------GTGAAGAGTGGCTCGCCGTACCAATTGGTGC--ACGGCGGGCTGAAGAGTGGGTTATCGTCT Corymborkis_vert_ER66 -GC-GA-GG-CGC-GGAC------GTGAAGAGTGGCTCGCCGTACCAATTGGTGC--ACGGCGGGCTGAAGAGTGGGTTATCGTCT Tropidia_effusa_O211 -GC-CAAGG-CTC-GGAT------GTGCAGAGTGGCTCGCCGTGCCGTTTGGTGC--GCGGCGGGCTGAAGAGCGGGTTACCGTCT tropidia_gram AGGGCA-GT-CT--GGAT------TGCAGAGTGCTGTTCCGCGG-GATTGG--C---TGGCGGG-T-AAGA-TGGGT--CCGT-T W2830_Tropidia_polystachya -GC-CAAGG-CTC-GGAT------GTGCAGAGTGGCTCGCCGTGCCGTTTGGTGC--GCGGCGGGCTGAAGAGCGGGTTACCGTCT Epilyna_jimenzeii_ER67 -G-G-AAGG-CCT-GGAT------GTGCAGAGTGGCCCGTCGTTCTCATCGGTGC-TGCGGCGGGCTAAAGAGCGGGCTTTT-TCT Epilyna_hirtzii_n526 -G-G-AAGG-CGT-GGAT------GTGTAGAGTGGCCCGTCGTTCTCATCGGTGC-TGCGGCGGGCTGAAGAGCGGGCTTTT-TCT Sertifera_columbiana_ER38 TGYG---GG-CAT-GGAT------GTGTAGAGTGGCTCGTCGTTCTCATTGGTGCGTGCGGCGGGCTAAAGAGCGGGCTTTCGTCT Sertifera_n546 TGCG---GG-CAT-GGAT------GTGTAGAGTGGCTCGTCGTTCTCATTGGTGCGTGCGGCGGGCTAAAGAGCGGGCTTTCGTCT Ellianthus_sp --CATAAGG-CCT-GGAT------GTGCAGAGTGGCCCGCCGTTCTCATCGGTGCGTGCGGCGGGTTGAAGAGCGGGCTTTTGTCT Elleanthus_lancifoliusER36 --CGCAAGG-CCT-GGAT------GTGCAGATTGGCCCGCCGTTCTCATCGGTGCGTGCGGCGGGCTAAAGAGCGGGCTTTCGTCT Elleanthus_cynarocephalus_g14 --CGCAAGG-CCT-GGAT------GTGCAGAGTGGCCCGCCGTTCTCATCGGTGCGTGCGGCGGGCTGAAGAGCGGGCTTTCGTCT Ellianthus_oliganthusER37 --CATAAGG-CCT-GGAT------GTGCAGAGTGGCCCGCCGTTCTCATCGGTGCGTGCGGCGGGTTGAAGAGCGGGCTTTTGTCT Elleanthus_tricallosus_n565 --CGCAAGG-CCY-GGAT------GTGCAGAGTGGCCCGCCGTTCTCATCGGTGCGTGCGGCGGGCTGAAGAGCGGGCTTTCGTCT Sobralia_amabilis_g18 TGCGCA-GG-CTT-GGAT------GTGTAGAGTGGCTCGTCGTTCTCATTGGTGCGGGCGGCGGGCTAAAGAGTGAGTTTTCGTCT Sobralia_fimbr_ER39 TGCGCA-GG-CTT-GGAT------GTGTAGAGTGGCTCGTCGTTCTCATTGGTGCGGGCGGCGGGCTAAAGAGTGAGTTTTCGTCT Sobralia_crocea_w533 TGCGCG-GG-CTT-GGAT------GTGTAGAGTGGCTCGTCGTTCTCATTGGTGCGGGCGGCGGGCTGAAGAGTGAGTTTTCGTCT Sobralia_mucronata_w535 TGCACA-GG-CTT-GGAT------GTGTAGAGTGGCTCGTCGTTCTCATTGGTGCG-GCGGCGGGCTGAAGAGTGAGTTTTCGTCT

Continued

Table A.1-Continued

Monophyllorchis_maculta ------CCT-GGAC------GTGGACATTGACTCGTCGTCCCCATCTA-----GCGGCGGGTTGAAGGTCAATTTTTTGTCT Triphora_trianth GAAAG--AT-CGC-GGAT------GACTTGATTGGCTCGCCGTGGTGTGTTAT----GCGGCGGGCTGAAGATCATTTTCTGGTTT Triphora_genti_ER01 ------AT-CTC-GGAT------GAAGAGATTGGCTCGCCGTGGTTATATAT----GCGGCGGGCTGAAAATTATTTTCAGGTTC Triphora_amazonica_ERP TGCA---AG-CTC-GGAT------GTGCAGAGTGGCTCGTCGTGCTTATTGGT----ACGGCGGGTTGAAGAGCGGGTTGTCGTCC Diceratostele_gabonensis_ER44 CGCA---GG-CAC-GGAT------GTGCAGAGTGGCCCGCCGTGCCCGTCGGC----GCGGCGGGCTGAAGAGCGGGTTATATTCT Epipogium_aphyllum_O19248 ---A-A-CT-CTT-GGAT------GCGGAAATTGGCCCTTCGTGCTC--CGGC----ATGGCGGGTTGAAGAGTGGGTTTTC---- epipogium_roseum ---AC------GTGGTTATTGGCCCATCGTGCT-ATTTGC----ATGGCGGGTTAAGAAGTGGGCTTTCGGC- Nervilia_shirnensis_C280 -GC----GG-----GGAT--GCGGGG------AGTGGCCCGCCGTGC-CGTCGGC----GCGGCGGGCTGAAGAGCGGGCGATCGTCT Nervilia_plicata_AF324179 ---AC------GGATGGGCGGGGACGTGCAGAGTGGCCCGCCGTGC-CGTCGGT----GCGGCGGGCTGAAGAGCGGGCGATCGTCT Nervilia_holochila_AF324178 ---AT------GGATGGGCGGGGACGTGCGTAGTGGCCCGCCGTGCCC-TCGGC----GCGGCGGGCTGAAGAGCGGGCGATCGTCT Wull_aphylla_er128 ACAAA--GG-CAC-GGAC------GTGTAGCGTGGCCCACTGCGTCCGACAAT----CTAGCGGGTTGAAGAGTAGGCACTGCACT Xerorchis_amazonica_0799 TGCG---GG-CTC-GGAT------GCGTAGAGTGACTCGCCGTGCCCATCCGC----ACGACGGTC-GAAGATTGGGTTGGCATGG Calypso_bulbosa GGAA---GG-CTC-GGAT------GTGCATATTGGCTCATCGTGCCCATTGGC----GCGGCGGGTTGAAGAGTGGGTTATCGCCT Ephi_schmidtii TGAA---GG-CTC-GGAT------GTGCATAAT--CTCATCGTGCCCTTTGGT----GCGGCGGGCTAAAGAGTGGGTTATTGTCT Chysis_bractescens TCGA---GG-CTC-GGAC------GTGCAGAGTGGCTCGTCGTGCCCGTCGGT----GCGGCGGGCTGAAGAGGGGGTCGTCGTCT Coelia_triptera TTGA---GG-CTC-GGAT------GTGCAGAGTGGCTCGTCGTGCCCGTCGGT----GCGGTGGGTTGAAGAGTGGTTAATCATCT C_trifida_2080 CCAA---GG-CTC-GGAC------GTGCAGAGTGGCTCATCGTGCCAATTGGT----GCGGCGGGTTGAAGAGCGGGTTATCGTCT Eulophia_sp CGT----GG-CTC-GGAC------GTGCAGAGTGGCCCGTCGCGCCGCTCGGT----GCGGCGGGCTGAAGAGCGGGCTA-CGTCT Isochilus_amparoana TCGA---GG-CCC-GGAC------GTGCAGAGTGGCCCGTCGTGCCCGTCGGT----GCGGCGGGCTGAAGAGTGGGTCGTCATCT 245 Leptotes_bicolor CCGA---GG-CCC-GGAT------GTGCAGAGTGGCCCGTCGTGCCAGTCGGT----GCGGCGGGCTGAAGAGTGGGTCATCGTCT Oreorchis_patens CCAA---GG-CCC-GGAC------GTGCAGAGTGGCTCATCGTGCCAATCGGT----GCGGCGGGTTGAAGAGCGGGTTATCGTCT Govenia_sp CCGA---GG-CCC-GGAC------GTGCAGAGTGGCTCATCGTGCCAATCGGT----GCGGCGGGCTGAAGAGCGGGTTATCGTCT

Palmorchis_trilobulata T--CG-GGCCATGCTGGACAAAGGGGTGGATGGAAGCCGTAAGCATG-C------TGTCTCATGCTGGCCAGATGAAA Palmorchis_trilobulata_ER68 T--CG-GGCCATGCTGGACAAAGGGGTGGATGGAAGCCGTAAGCATG-C------TGTCTCATGCTGGCCAGATGAAA V2115_PALMORCHIS_POWELII C--CG-GGCCATGCTGGACAAAGGGGTGGATGGAAGCCGTAAGCACG-C------TGTCTCATGCTGGCCAGAGGAAA Palmorchis_Sp_ER110 C--CG-GGCCATGCTGGACAAAGGGGTGGATGGAAGCCGTAAGCACG-C------TGTCTCATGCTGGCCCGATGAAG Palmorchis_sp1_ER110E C--CG-GGCCATGCTGGACAAAGGGGTGGATGGAAGCCGTAAGCACG-C------TGTCTCATGCTGGCCCGATGAAG Palmorchis_sp_ER129_selby T--CG-GGCCATGCTGGACATAGGGGTGGATGGAAGCCGTAAGCATG-C------CGTCTCATGCTGGCCAGATGAAA Palmorchis_462 T--CG-GGCCATGCTGGACAAAGGGGTGGATGGAAGCCGTAAGCATG-C------TGTCTCATGCTGGCCAGATGAAA Gastrodia_procera_ER64 T--CG-GGCCATGCTGGACAAAGGGGTGGATGGAAGCCGTAAGCATG-C------TGTCTCATGCTGGCCAGATGAAA Cephalanthera_aus_Dat115 C--AT-GGCCACGATCGAC-AAGGGGTGGACGGAAGCCACGAGCACGGCCAAACAGTGTCTCACGCTGGCCTGAGGAC- Cephalanthera_damasonium C--AT-GGCCACGATCGAC-AAGGGGTGGACGGAAGCCACGAGCACGGCCAAACAGTGTCTCACGCTGGCCTGAGGAC- CEPHALANTHERA_LONGIFOLIA_ay369 C--AT-GGCCACGATCGAC-AAGGGGTGGACGGAAGCCACGAGCACGGCCAAACAGTGTCTCACGCTGGCCTGAGGAC- Epipactis_helleborine C--AT-GGCCACGATTGACAAA-GGGTGGACGAAAGCCACGAGCACGACCAAACATTGTCTAATTCTGGCCTGAGGAA- Epipactis_fageticola_AY351382 C--AT-GGCCACGATTGACAAA-GGGTGGACGAAAGCCACGAGCACGACCAAACATTGTCTAATTCTGGCCTGAGGAA- Epipactis_lusitanica_AY351381 C--AT-GGCCACGATTGACAAA-GGGTGGACGAAAGCCACGAGCACGACCAAACATTGTCTAATTCTGGCCTGAGGAA- Limodorum_abortivum C--AT-GGCCACGATCGAC-AAGGGGTGGACGTATGCCACGAGCACGGCCAAACAATGTCCCATGGTGGCCTGAGGAA- Listera_smallii C--CT-GGCCACGATAGAC-AAGGGGTGGACGGAAGCCACGAGCACGGCCAAACAGTGTCTCATGCTGGTATGAGGAA- Neottia_nidus_avis C--CT-GGCCACGATAGAC-AAGGGGTGGACGGATGCCACGAGCACGGCCAAACAGTGTCTCATGTTGGCCTGAGGAA- Corymborkis_sp_0542 C--ATTGGCCACTATCGATAAAGGGGTGGATAAAAGCTGTGAGGAAGGCTTA-CGCTGTCTCATGCTGGCCTGA-GAAA Continued

Table A.1-Continued

Corymborkis_vert_ER66 C--ATTGGCCACTATCGATAAAGGGGTGGATAAAAGCTGTGAGGAAGGCTTA-CGCTGTCTCATGCTGGCCTGA-GAAA Tropidia_effusa_O211 C--ATTGGCCACGATCGATAAAGGGGTGGATAAAAGCTGTGAGCGAGGCTTA-CGTTGTCTCATGCTGGCCTGA-GAAG tropidia_gram C--AGTG-CCACG-T-GA-GAA----TGGA------G-GGAAA W2830_Tropidia_polystachya C--ATTGGCCACGATCGATAAAGGGGTGGATAAAAGCTGTGAGCGAGGCTTA-CGTTGTCTCATGCTGGCCTGA-GAAG Epilyna_jimenzeii_ER67 T--ATCAGCCACACTTGACGA-TGGGTGGATAAAAGCTGTGAGCATGACCTG-TGTCGCCTCGTGTTGGCCGGAGGAAA Epilyna_hirtzii_n526 T--ATCAGCCACACTTGACGA-TGGGTGGATAAAAGCTGCGAGCATGACCTA-TGTCGCCTCGTGTTGGCCGGAGGAAA Sertifera_columbiana_ER38 C--ATTAGCCACATCTGACGA-TGGGTGGATAAAAGCTATGAGCATGACCTA-CGTCGCCTCATGTTGGCTGGATGAAA Sertifera_n546 C--ATTAGCCACATCTGACGA-TGGGTGGATAAAAGCTATGAGCATGACCTA-CGTCGCCTCATGTTGGCTGGATGAAA Ellianthus_sp C--ATCGGCCACACTTGACGA-TGGGTGGAGAAAAGCTATGAGCACGACCTA-CGTCGCCTTGTGTTGGCCGGACGAAA Elleanthus_lancifoliusER36 C--ATCGGCCACACTTGACGA-TGGGTGGAGAAAAGCTATGAGCACGACCTA-TGTCGCCTCGTGCTGGCCGGAGGAAA Elleanthus_cynarocephalus_g14 C--ATCGGCCACACTTGACGA-TGGGTGGAGAAAAGCTATGAGCACGACCTA-TGTCGCCTCGTGCTGGCCGGAGGAAA Ellianthus_oliganthusER37 C--ATCGGCCACACTTGACGA-TGGGTGGAGAAAAGCTATGAGCACGACCTA-CGTCGCCTTGTGTTGGCCGGACGAAA Elleanthus_tricallosus_n565 T--ATCGGCCACGCTTGACGA-TGGGTGGATAATAGCTATGAGCACGACCTA-CGTCGCCTCGTGCTGGCCGGAGGAAA Sobralia_amabilis_g18 T--ATTAGCCACATTTGACGA-TGGGTGGATAAAAGCTATGAGCATGACCTA-CGTCGCCTCATGTTGGCTTGAGGAAA Sobralia_fimbr_ER39 T--ATTAGCCACGTTTGACGA-TGGGTGGATAAAAGCTATGAGCATGACCTA-CGTCGCCTCATGTTGGCTTGAGGAAA Sobralia_crocea_w533 T--ATTAGCCACGTTTGACGA-TGGGTGGATAAAAGCTATGAGCATGACCTA-CGTCGCCTCATGTTGGCTTGAGGAAA Sobralia_mucronata_w535 T--ATTAGCCATGTTTGACGA-TGGGTGGAAAAAAGCTATGAGCATGACCTA-CGTCGCCTCATGTTGGCTTGAGGAAA Monophyllorchis_maculta T--CCTGCCCCCAATCGA-GG-TGGGTGGATGGGCGCTTT--GCATGCCCTA-CAT-G-CTCATGATG-C-TGAAGAT- Triphora_trianth C--ATCTGTCATGAT-GA-TA-AGAGTGGATGA--GCA-----CACGTCCTGA-TTTG--TCCTGCTGAC---AAG-T- 246 Triphora_genti_ER01 T--ACTTGTCATGAT-GA-TA-AGGGTGGATGA--G-TT----CGCGTCCTAA-TTTA--TCGTGCTGGC---AA-TT- Triphora_amazonica_ERP T--TCGGGCCATGCTGGACAA-AGGGTGGATGGAAGCCGTAAGCATG--CT------GTCTCATGCTGGCC--A-GAT- Diceratostele_gabonensis_ER44 T--ATTGGCCACGATCG-CAA-GGGGTGGATA-AAGCCGCGGGCGCG---T--CGTTCGC--AT---GCCCCGAGGGAA Epipogium_aphyllum_O19248 TGCTGT-G--AC----G-TTA-TAGG-GGATTGGAGC-AT-AGCTTG------C-TTGGCCC-----GCCC-GCCGAA- epipogium_roseum TGCGT-----ACGAT--ATTA-GGGG---ATAGAAGC-AT-GTAGTG------C-TTGGCCCATGTTAAGC-TATGAAA Nervilia_shirnensis_C280 TGCTGCGGCCACGAATG-TGA-GGGGTGGATTGAAGCTATGAGCACGA--TGACGTCG------AACC------Nervilia_plicata_AF324179 TGCTGTGGCCACGAACA-TGA-GGGGTGGATAGAAGCTATGGGCACGG--TGACGTGGCATCG------Nervilia_holochila_AF324178 TGCTGCGGCCACGAACG-TGA-GGGGTGGATAGAAGCTATGGGCACGA--TGATGTCGCCTCGAG-GGGCC------Wull_aphylla_er128 TCTATCGACCATGAGCGAC-G--TTGTGG-TAAACGCCATGAGCTCGGCCT--GGTCGT-GCATGCTGGCC------Xerorchis_amazonica_0799 T--GTGGACCATGATA-AC-A-GGGGTGGATGAAATC--TGATCATGTCC-GAC-TC---TTAAA----CG---GG-A- Calypso_bulbosa C--ACTGGCCACGAACAAC-G-AGCGTGGATGAAAGCTGTGAGCAAGGCTTA-TGTTGTCTCGTTTTGGCTTGA-GAAA Ephi_schmidtii C--ATTGGCCACAAACAAC-A-AGGGTGTATGAAAGTTGCGAGTCGGGCCTA-TGTTGTCTTTGTTTTGCCTGA-GAAA Chysis_bractescens C--ATCGGCCACGAACAAC-A-AGGGTGGATGAGAGCTGTGAGCAAGGCCTA-CGTTGTCTCGTGCCGGCCTGA-GAAA Coelia_triptera C--ATTGGCCACGAACAAC-A-AGGGTGGATGAAAGCTGTGAGCAAGGTCTA-CGTTGTCTCGTGTTGGCTCGA-GAAA C_trifida_2080 C--ATTGGCCACGAACAAT-A-AGGGTGGATGAAATCTGTGAGCAAGGCCTA-CTTTGTCTCGTGTTGGCCAGA-GAAA Eulophia_sp C--GCCGGCCGCGAACAAC-A-AGGGTGGGTGAAGGCTGTGAACGCAGCCTG-TGTTGTCTCGTGGTGGCCAGA-GGGA Isochilus_amparoana C--ATCGGCCGCGAGCAAC-T-AGGGTGGAT----GCC--ATGCA-GAGCTG----TGCCTA--GTTGGCCTGA-GAAA Leptotes_bicolor C--ATCGGCCACGAACAGC-A-AGGGTGGATGAAAGTTGT--GCCTG---TG-C--TGCGTCGTGCCGGCCCGA-GAAA Oreorchis_patens C--ATTGGCCACGAACAAT-A-AGGGTGGATGAAATCTGTGAGCAAGGCCTA-CTTTGTCTCGTGTTGGCCAGA-GACA Govenia_sp C--ATTGGCCACGAACAAC-A-AGGGTGGATGAAAGCTGTGAGCAAGGCCTA-CGTTGTCTCGTGTTGGCCAGA-GAAA

DIMENSIONS ntax=53 NCHAR=1326;[344 indels coded] DATATYPE = standard GAP = - MISSING = ? symbols="0123456789A#C$EFG.IJ&L%>OPQ/'TU:*X

Monadenia_bracteata_AJ409430 TGGAAACTTGCTAAGTGTTAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTT------AAAAAAA Brownleea_coerulea_AF360512_AF360455 ------Codonorchis_lessonii_AJ409387 TGGAAACCTGCTAAGTGGTAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTTTTTT------Coelia_triptera_AF266972 TGGAAACCTGCTAAGTGGTAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAAAGGGCAATCCTGAGCCAAATCTTTGTTCTGAGAGAA Corycium_carnosum_AJ409391 TGGAAACCTGCTAAGTGTTAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTTTTTT------Goodyera_sp TGG-AACCTGCTAAGTGGTAACTTCCAAATTCAGAGAA-CCCTGGAACTAAAAATGGGCATCCCTGAGCCAAATYTTTTTTTTGAGAAAA Pterygodium_catholicum_AJ40944 TGG-AACCTACCAAGTGTTAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTTTTT----AAAA Platylepis_polyadenia_AJ544501 TGGAAACCTGCTAAGTGGTAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTTTTT-G-GAAAA Palmorchis_Er211_cf_trilobulat -GGAAACCTGCTAAGTGGTAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAAAA Palmorchis_AJ409435 TGGAAACCTGCTAAGTGGTAACTTCCAAATTCAGAGAAACCCTGGAACTAATAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAAAA palmorchis_silvicola_incomplete ------Cephalanthera_damasonium_AJ409 TGGAAACCTGCTAAGTGGTAACTTCCAAATTCAGAGAA-CCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAAAAAA Aphyllorchis_pall TGGAAACCTGCTAAGTGGTAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAAAA aphyllorchis_montana_mwc ?????????????????????????????????????????????????????????????????????????????????????????? Limodorum_spp TGGAAACCTGCTAAGTGGTAACTTCCAAATTCAGAGAAACCCTGGAACTAAGAATGGGCAATCCTGAGCCAAATCCTTCTTTTGAGAAAA

247 Limodorum_abortivum_0924 ------Epipactis_spp TGG-AA-CTGCTAAGTGGTA-CTTCCAAATTCAGAGAAACC-TGG-ACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAAAA Epipactis TGGAA--CTGCTAAGTGGTA-CTTCCAAATTCAGAGAAACC-TGG-ACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAAAA Listera_smalliigi_AJ409422 TGGAAACCTGCTAAGTGGTAACTTTCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTTTTTTGAGAAAA Listera_cordata_2580 ???????????????????????????????????GAAACCCTGGAA-TAAAAATGGGCAATCCTGAGCCAAATCTTTTTTTTAAGAAAA Neottia_nidus_avis_JVF_trnLF ?????????????????????????????????????????????????????????????????????CAAATCTTTTTT--AA----- Neottia_spp TGGAAACCTGCTAAGTGTTAACTTCAAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTTTT--AA----- Epilyna_jimenzii_ER67 -GGAAANNNGNTGAGNNNNNNCTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAGAA Ellenathus_lancifolius_ER36 -GGAAANNNGNTGAGNNNNNNCTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAGAA sertifera_columbiana_ER38 TGGAAACCTGCTCAGTGGTAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAGAA sobralia_crocea_W533 TGGAAACCTGCTAAGTGGTAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAGAA Sobralia_mucronata_W535 TGGAA-CCTGCTAAGTGGTAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAGAA Elleanthus_374_e&f ??????????????????????????????????????????????????????????????????????????????????????????

Continued

Table A.2. Primitive Epidendroideae analysis. trnL-F +gaps molecular matrix.

Table A.2 Continued

CORYMBORKIS_vert_partial ------ATCCTGAGCCAAATCTTTGTTTTGAGAGAA Tropidia_effusa_AJ409456 TGGAAACCTGCTAAGTGGTAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCCTTTTTTTG?????? Tropidia_gram_mwc21775_trnlf ?????????????????????????????????????????????????????????????????????????????????????????? Xerorchis_O799 TGGAAACCTGCTAAGTGGTAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCCTTATTTTGAGA-TA Xerorchis_sp_MWC12601 ????????????????????????????????????????????????????????????????TGAGCCAAATCCTTATTT-GAGA-TA Nervilia_aragoana_AJ409431 TGGAAACCTGCTAAGTGATAACTTCCAAATTCAGAGAAACCCCGGAACTAAAAAGGGGCAATCCTGAGCCAAATCTTTGTTTTTATAGAA nervilia_plicata_ER48_trnlf ???????????TGAGTGCTAACTTCCAAATTCAGAGAAACCCTGGAACTAAGAATGGGCAATCCTGAGCCAAATCCTTGTTTTGAGAGAA Nervilia_shirenensis_AF519945 -GGAAACCTGCTGAGTGCTAACTTCCAAATTCAGAGAAACCCTGGAACTAAGAATGGGCAATCCTGAGCCAAATCCTTGTTTTGAGAGAA Diceratostele_gabonensis_Er40 ?????????????????????????????????????????????????????????????????????????????????????????? Triphora_amazonica_Emerson_A06 TGGAAACCTGCTAAGTGGTAACTTCCAAATTCAGAGAAACCCTGGAACTAATAATGGGCAATCCTGAGCCAAATCTTTTTTTA-AGAAAA Triphora_trianthophora_ER19A TGGAA-CCTGGTAAGTGGTAACTTCCAAATTCAGAGANTTCATGGAACTAATAATGGGCAATCCTGAGCCAAATCCTTTTT-A-AGAAAG Triphora_gentianoides_ER01 TGGAA-CCTACCA-GTGGTAACTTCCAAATTCAGAGAAATCCTGGAACTAATAAAGGGCAATCCTGAGCCAAATCTTTTT--A-AGAAAA Monophyllorchis_sp TGGAAACCTGCTAAGTGGTAACTTCCAAATTCAGAGAAACCCTGGAACTAAGAAAGGGCAATCCTGAGCCAAATCTTTTTT-A-AGAAAA Monophyllorchis_micorstyloides ??????????????????????????????????????????????????????????????????????????CC------Psilochilus_macrophyllus_ER02 TGGAA-CCTT-TTAGTGATAACTTCCAAATTCAGAGAAATCCTGGAACTAAGAATGGGCAATCCTGAGCCAAATCTTTTTTTT-AGAAAA Psilochilus_modestus_ER65 ??????????????????????TTCC------TGGAACTAAGAATGGGCAATCCTGAGCCAAATCTTTTTTTT-AGAAAA Isochilus_amparoanus_AF266962 ---A--CCTCCTAAGTGGTTTCTTCCAAATTCCGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAGAA Chysis_bractescens_AF266971 TGGAAACCTGCTAAGTGGTAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCGAATCTTTGTTTTGAGAGAA Oreorchis_patens TGGAA-CCTGCTAAGTGATAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTTTTTTGAGAGAA Cor_trifida_2080 TGGAA-CCTGCTGAGCGATAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCCTTGTTTTGAGAGAA 248 Calypso_bulbosa_AF519960 TGGAAACCTGCTAAGTGGTAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAGAA Govenia_liliacea_AF519916 ------G-TAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAGAA Leptotes_bicolor_AF267014 -GGAAACCTGCTAAGTGGTAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAGAA Eulophia_sp_o403 TGGAAACCTGCTAACTGGTAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAGAA Ponera_striata_AF266965 TGGAAACCTGCTAAGTGGTAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAGAA

Monadenia_bracteata_AJ409430 AAAATGGAAAATGAGAATAAAAAGAGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTAGATTAGTAG Brownleea_coerulea_AF360512_AF360455 ------GTTCTAACGAATGAAA-TTGACTGCGTTAGATTAGTAG Codonorchis_lessonii_AJ409387 ------TTAGAA--AAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAAAGAATGAAA-TTTACTACGTTAGATTAGTAG Coelia_triptera_AF266972 AAAATGGAAAATGAGAAGAAAAAGGGATAGGTGCAGAGACTCAACGGAAGCTGTTCTAACGAATGAAA-TTGACTACGCTACGTTAGTAG Corycium_carnosum_AJ409391 ------TA---TAAAAA---A-A-----A-A-A---AATGAAA-CT---C-AA-GAATGAAA-TGGACTACGTAAGATTAGGAG Goodyera_sp AAAA--CAAAATGAGAATAAAAAGAGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTTACTACGTTAGATTAGTAG Pterygodium_catholicum_AJ40944 AA--TGGAAAATGAGAATAAAAAGAAATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTAGATTAGTAG Platylepis_polyadenia_AJ544501 AATA--CAAAATTAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTTACTACGTTAGATTAGTAG Palmorchis_Er211_cf_trilobulat AAAATGGAAAATGAAAATAAAAAGGGATAGGKGCAAAAACTCAAKGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACKTTAGTAG Palmorchis_AJ409435 GTAA-GGAAAATGAGAATAAAAAGGGATAGGTGCAGACACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAG palmorchis_silvicola_incomplete ------Cephalanthera_damasonium_AJ409 AAAATGGAAAATTAGAATAAAAAGGGATAGGTGCAAAAACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTA--A- Aphyllorchis_pall AAGATG-AAWATGAGAATAAAA-GGGATAGGTGCAGAGACTCGACGGAAGCTTTTCTAACAAATGAAA-TCGACTACGTTACGTTAGTAG aphyllorchis_montana_mwc ?????GGTGAATGAGAATAAAA-GGGATAGGTGCAGAGACTCAATGGAAGCTTTTCTAACANATGAAA-TTGACTACGTTACGTTAGTAG Limodorum_spp AGAGTGGAAAATGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACAAATGAAA-TTGACTACGTTACGTTAGTAG Limodorum_abortivum_0924 --AGTGGAAAATGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACAAATGAAA-TTGACTACGTTACGTTAGTAG

Continued

Table A.2 Continued

Epipactis_spp AAAATGGAAAATGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAG Epipactis AAAATGGAAAATGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAG Listera_smalliigi_AJ409422 AAA-TGGAAAATGAGAATAAAA-GGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGT------Listera_cordata_2580 AAA-TGGAAAATGAGAATAAAA-GGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTCCGTTACGT------Neottia_nidus_avis_JVF_trnLF ----TGTAAAATGATAATAAAAAGGGATAGGTGCAGAGACCCAATGGAAGCTATTCTAACAAATAAAAATTAAATTGACTACGTTAGTAG Neottia_spp ----TGTAAAATGATAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTATTCTAACAAATAAAAATTAAATTGACCACGTTAGTAG Epilyna_jimenzii_ER67 AAAAGGGCAAATGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAG Ellenathus_lancifolius_ER36 AAAATGGAAAATGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAG sertifera_columbiana_ER38 AAAATGGAAAATGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAG sobralia_crocea_W533 AAAATGGAAAATGAGAAGAAAAAGGGATAGGTGCAGAGACTCAATGGAAGTTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAG Sobralia_mucronata_W535 AAAATGGAAAATGAGAAGAAAAAGGGATAGGTGCAGAGACTCAATGGAAGTTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAG Elleanthus_374_e&f ?????????????????????????????????????????????????????????????????????????????????????????? CORYMBORKIS_vert_partial AAAATGGACAATGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAG Tropidia_effusa_AJ409456 ?????????????????????????????????????????????????????????????????????????????????????????? Tropidia_gram_mwc21775_trnlf ???????????????????????GG-CTAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAG Xerorchis_O799 A-GA-GGAAAATGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTTACTACGTTACATTAGGAG Xerorchis_sp_MWC12601 AAGA-GGAAAATGAGAATAGAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTTACTACGTTACATTAGGAG Nervilia_aragoana_AJ409431 AAAATGG------ATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACATGACGTTAGTAG nervilia_plicata_ER48_trnlf AAAATGG------ATAGGTGCAGAGACTCAATGGAAGATGTTCTAACGAATGAAA-TTGATTACGTGACGTTAGTAG Nervilia_shirenensis_AF519945 AAAATGG------ATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGATTACGTGACGCTAATAG 249 Diceratostele_gabonensis_Er40 ?????????????????????????????????????????????????????????????????????????????????????????? Triphora_amazonica_Emerson_A06 A---TG-AAAATGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTGCGTTA--A- Triphora_trianthophora_ER19A A---TGGAAAATGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTA--A- Triphora_gentianoides_ER01 A---TGGAAGATGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGATTACGTTACGTTA--A- Monophyllorchis_sp A---TGGAAAA---GAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTGCGCTACGTTAGTAG Monophyllorchis_micorstyloides ------TGAGAATAAAAACGGATAGGTGCAGAGACTCAAAGGAAGCTGTTCTAACGAATGAAA-TTGACTGCGCTACGTTAGTAG Psilochilus_macrophyllus_ER02 AA---GGAAAATGAGAATAAAAAGGGATAGGGGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTATGTTACGTTAGTAG Psilochilus_modestus_ER65 A---GGGAAA-TGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTATGTTACGTTAGTAG Isochilus_amparoanus_AF266962 AAAATATAAAATGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAG Chysis_bractescens_AF266971 AAAATGGAAAATGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAG Oreorchis_patens AAA-TGGAAAATGAGAAGAAAAAGGGATAGGTGCAGAGACTCGATGGAAGCTGTTCTAACGAATGAAA-TTGAATATGTTACGTTAGTAG Cor_trifida_2080 AAA-TRGAAAATGATAAKAAAAAGGGATAGGTGCAGAGACTCGATGGAAGCTGTTCTAACGAATGAAA-TTGAATATGTTACGTTAGTAG Calypso_bulbosa_AF519960 AAAATGGAAAATGAGAATAAAAAAGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACAAATGAAA-TTGACTACGTTACGTTAGTAG Govenia_liliacea_AF519916 AAAATGGAAA-TGAGAATAAAAAGGGATAGGTGCAGAGACTCGATGGAAGCTGTTCTAACGAATGAAA-TTGAATACGTTACCTTAGTAG Leptotes_bicolor_AF267014 AAAATGGAAAATGAGAAGAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACATTAGTAG Eulophia_sp_o403 AAAATGGAAAATGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGATTACGTTACATTAGTAG Ponera_striata_AF266965 AAAATATAAAATGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAG

Monadenia_bracteata_AJ409430 CTAAAATCCTTATATCAAAAGAAAAGATCGAAATGACAGAAAGGAGAATCTTATATACCTAATACGTACGTCTAGATACTGACATAGCAA Brownleea_coerulea_AF360512_AF360455 CTAAAATCCTTCTATCAAAAGAAAAGATCGAAATAACAGAAAGGATAATCTTATATACCTAATACGTACGTCTAGATACTTACATAGCAA Codonorchis_lessonii_AJ409387 CTAAAATCCTTCTATCAAAA------GAAATGACAGAAAGGATAACCTTATATATTTAATACGTACGTATACATACTTGCATAGCAA Coelia_triptera_AF266972 CTAAAATCCTTCTATC------GAAATGACAGAAAGGATAACCTTATATACCTAATACGTACGTATACATACTGACATAGCAA

Continued

Table A.2 Continued

Corycium_carnosum_AJ409391 CTAAAATCCTTATATCAAA-GGAAAGATTGGAATGATAGAAAGGTTAATCTTATAAACCTAATAAGTACGTTTAGATACTGACATAGCAA Goodyera_sp TTAAAATACTTCTATCAAGATAAAAGATTGAAATGACAGAAAGGATGACCTTATGTACCTAATAAATATGTATACATACTTACATAGCAA Pterygodium_catholicum_AJ40944 CTAAAATCCTTATATCAAAAGAAAAGATCAAAATGACAGAAAGGATAATATTATATACTTAATACGTACGTCTAGATACTGACATAGCAA Platylepis_polyadenia_AJ544501 CTAAAATACTTCTATCAAAATAAAAGATTGAAATGACAGAAAGGATGACCTTATATACTTAATACGTATGTATACATACTTACATAGCAA Palmorchis_Er211_cf_trilobulat CTAAAATCCTTCTATC------GAAATGACAAAAAGGAWAACCTTATATACCTAAWACGTACGTATACATACTGACATAGCAA Palmorchis_AJ409435 CTAAAATCCGTCTATC------GAAATGACAGAAAGGATAACCTTATATACCTAATACGTACGTATACATACTGACATAGCAA palmorchis_silvicola_incomplete ------Cephalanthera_damasonium_AJ409 ------GGATAACCTTATATACCTAATACGTACGTATACATACTGACATAGCAA Aphyllorchis_pall CTAAAATCCTTC------AAGGATAACCTTCTATTCCCAATACGTACGCATACATACTGACATAGCAA aphyllorchis_montana_mwc CTAAGATCCTTCTATC------GAAATGACAGAAAGGATAACCTTCTATACCTAATACGTACGTATACATACTGACATAGCAA Limodorum_spp CTAAAATCCTTCTATC------AAGATGACAGAACGGATAACCTTATATACCTAATACGTACGTATACATACTGACATAGCAA Limodorum_abortivum_0924 CTAAAATCCCCCCATC------AAGATGACAGAACGGATAACCTTATATACCTAATACGTACGTATACATACTGACATAGCAA Epipactis_spp CTAAAATCCTTC------CAGAAAGGATAACCTTATATACCTAATACATACGTATACATACTGACATAGCAA Epipactis CTAAAATCCTTC------CAGAAAGGATAACCTTATATACCTAATACATACGTATACATACTGACATAGCAA Listera_smalliigi_AJ409422 ------ATACATACTGATATAGCAA Listera_cordata_2580 ------ATACATACTGATATAGCAA Neottia_nidus_avis_JVF_trnLF ATAAAATCCTTCTATC------AAAAT------GG---ACCCCAGATAACTAATGAGTAC--ATACATACTGATATATAAA Neottia_spp ATAAAATCCTTCTATC------AAAATGACATAAAGG------ATAACTAATGAGTAC--ATACATACTGATATATAAA Epilyna_jimenzii_ER67 CTAAGATTCTTCTATC------GAAATGACAGAAAGGATAACCTTATATACCTAATACGTACGTATACATACTGACATAGCAA Ellenathus_lancifolius_ER36 CTAAAATTCTTCTATC------GAAATGACAGAAAGGATAACCTTATATACCTAATACGTACGTATACATACTGACATAGCAA 250 sertifera_columbiana_ER38 CTAAGATCCTTCTATC------GAAATGACAGAAAGGATAACCTTATATACCTAAGACGTACGTATACATACTGACATAGCAA sobralia_crocea_W533 CTAAAATTCTTCTATC------GAAATGACAGAAAGGATAACCTTATATACCTAATACGTACGTATACATACTGACATAGCAA Sobralia_mucronata_W535 CTAAAATTCTTCTATC------GAAATGACAGAAAGGATAACCTTATATACCTAATACGTACGTATACATACTGACATAGCAA Elleanthus_374_e&f ?????????????????????????????????????????????????????????????????????????????????????????? CORYMBORKIS_vert_partial CTAAAAT-CTTCTATC------GAAATGACAGAGAGG------TTATATACCTAATACGTACGTATACATACTGACATAGCAA Tropidia_effusa_AJ409456 ?????????????????????????????????????????????????????????????????????????????????????????? Tropidia_gram_mwc21775_trnlf CTAAAATCCTTCTACC------AAATGACAGAAAGGATAACCTTATATACCTAATACGTACGTATACATACTGACATAGCAA Xerorchis_O799 TTAAAATCCTTCTATT------GAAATGAAAGAAAGGATAACCTTATATACCTAATACGTACGTATACATACTGACATAGCAA Xerorchis_sp_MWC12601 TTAAAATCCTTCTAT------GAAATGAAAGAAAGGATAACCTTATATACCTAATACGTACGTATACATACTGACATAGCAA Nervilia_aragoana_AJ409431 CTAAAATATTTCTATC------GAAATGACAGAAAGGATAACCTTGTATACCTAATATGTACGTATACATACTGACATAGCAA nervilia_plicata_ER48_trnlf CTAAAATATTTCTATC------GAAATGACAGAAAGGATAACCTTATATACCTAATACGTACGTATACATACTGACATAGCAA Nervilia_shirenensis_AF519945 CTGAAATCTTTCTATC------GAAATGACAGAAAGGATAACCTTATATACCTAATACGTACGTATACATACTGACATAGCAA Diceratostele_gabonensis_Er40 ?????????????????????????????????????????????????????????????????????????????????????????? Triphora_amazonica_Emerson_A06 ATGA--TT-TTCT--C------TAAATGACATAC-GGATAACCTTATATACCTAATACCTACGTTTACATACTGACATAG--- Triphora_trianthophora_ER19A ATGA--TT-TTCT--C------TAAATGACATAA-GGATTACCTTATGTACCTAATACATACAT-TATACATTTACATAG--- Triphora_gentianoides_ER01 ATGA--TT-TTCTA------TAAATGACATAAAGGATAACCTTATATA--TAA-ACCT---TATATATA----TATA---- Monophyllorchis_sp ATAAAATCATT-TATC------TAAATGACATACA------AATACGTACGTATACATACTTACATAGCAA Monophyllorchis_micorstyloides ATAAAATCTCT-TATC------TAAATGACATACAG-ATAACCTTATAGACCTAATACGTACGTATACATACTTACATAGCAA Psilochilus_macrophyllus_ER02 CTAAAAT-TT-CTAAC------TAAATGACATATAGG------TA-TAAGTACATATACATACTGACATATCAA Psilochilus_modestus_ER65 CTAAAAT-AT-CTAAC------TAAATGACATTTAGG------A-TAAGT-C-----CATA-TT-CAT-TC-- Isochilus_amparoanus_AF266962 CTAAAATCCTTCTATC------GAAATGACAGAAAGGATAACCTTATATACCTAATACGTACGTATACATGCTGACATAGCAA Chysis_bractescens_AF266971 CTAAAATCCTTCTATC------GAAATGACAGAAAGGATAACCTTATATACCTAATACGTACGTATACATACTGACATAGCAA Oreorchis_patens CTAAAATCCTTCTATC------GAAATGACAGAAAGGATAACCTTATATATCTAATACGTACGTATACATACTGACATAGCAA

Continued

Table A.2 Continued

Cor_trifida_2080 CTAAAATCCTTCTATC------AAAATGACAGAAAGGATAACCTTATATATCTAATACGTACGCATACATACTGACATAGCAA Calypso_bulbosa_AF519960 CTAAAATCCTTCTAAC------GAAATGACAGAAAGGATAACCTTATATACCTAATACATACGTATACATACTGACATAGCAA Govenia_liliacea_AF519916 CTAAAATCCTTCTATC------GAAATGACAGAAAGGATAACCTTATATACCTAATACGTACGCATAAATACTGACATAGCAA Leptotes_bicolor_AF267014 CTAAAACCCTTCTATC------AAAATGACAGAAAGGATAACCTTATATACCTAATACGTACGTATACATACTGACATAGCAA Eulophia_sp_o403 CTAAAATCTTTCTATC------GAGATGACAGAAAGGATAACTTTATATACCTAATACGTACGTATACATACTGACATAGCAA Ponera_striata_AF266965 CTAAAACCCTTCTATC------GAAATGACAGAAAGGATAACCTTATATACCTAATACGTACGTATACATACTGACATAGCAA

Monadenia_bracteata_AJ409430 ATGATTCATCACAT------TCTT------CTATAAAAAATTGAAGAGTTATTGTGAATCAATTCTCATTGAAGTTGAAA Brownleea_coerulea_AF360512_AF360455 ATGATTCA------Codonorchis_lessonii_AJ409387 ACGATTAATCACAT------TCTTATATACA------GA------TTGAAGTTGAAA Coelia_triptera_AF266972 ACGATTAATCACAACACAAATCTTATAGAGATCAAAAAATATATGAAAAA------TTGAAGTTGAAA Corycium_carnosum_AJ409391 ATGATTCATCACAT------TCTTATATA------CTATGAAAAATTGAAGAGTTATTGTGAATCAATTCTCATTGAAGTTGAAA Goodyera_sp GCGATTAATCACAT------TCTTATAAA------CTATGAAAAGTT------AATTATAATTGAAGTTGAAA Pterygodium_catholicum_AJ40944 ATGATTCATCACAT------TCTTATATA------CTATAAAAAATTGAAGAGTTATTGTGAATCAATTCTCATTGAAGTTGAAA Platylepis_polyadenia_AJ544501 GCGATTAATCACAT------TCTTATAGA------CTATGAAAAGTTGAA------TTATAATTGAAGTTGAAA Palmorchis_Er211_cf_trilobulat ACGATTAATCACAACCCGAATCTTCTA-AGATCAAAAA-TCTATGAAAGATTGAAGAATTATTGTGAATCAATTCCAATTGAAGTTGAAA Palmorchis_AJ409435 ACGATTAA-----TCCCAA-----ATAGAGATCAAAAAATCTATGAAAGATT-AAGAATTATTGTGAATCAATTCCAATTGAAGT-GAAA palmorchis_silvicola_incomplete ------GAGATCAAAAAATCTTGGAAGGGTTTAAGAATTTTTGGGGATCCATTCCCATTGGAGGTGGAA 251 Cephalanthera_damasonium_AJ409 ACGATTAATCACAACCCAAATCTTATAGAGATCAAAAAATCTATGAAAAATTGAAGAATTATTGTGAATCAATTCCAATTGAAGTTGAAA Aphyllorchis_pall ACGATTAATCACAACCCGAATCCTATAGAGATCAAAGAATATATGAAGAATTGAAGAGTTATTGTGAATCAATTCCAATTGAA------aphyllorchis_montana_mwc ACGATTAATCACAACCCGAATCTTATAGAGATCAAAGAATCTATGAAAATTTGAAGAATTATTGTGAATCAATTCCAATTGAA------Limodorum_spp ACGATTAATCACAACCCGAATCTTATAGAGATCAAAAA-TATATGAAAAATTGAAGAATTATTGTGAATCAATTCCAAT--A------Limodorum_abortivum_0924 ACGATTAATCACAACCCGAATCTTATAGAGATCAAAAA-TATAGGAAAAATTGAAGAATTATTGTGAATCAATTCCAAT--A------Epipactis_spp ACGATTAATCACAACCCGAACCTTATAGAGATCAAAAAATCTATCAAAAATTGAAGAATTATTGTGAATCAATTCCAATTGAAGTTGAAA Epipactis ACGATTAATCACAACCCGAACCTTATAGAGATCAAAAAATCTATCAAAAATTGAAGAATTATTGTGAATCAATTCCAATTGAAGTTGAAA Listera_smalliigi_AJ409422 ACGATTAATCACAACCCAAATCTTATAGAGATCAAAAAATCTATGAAAAATTGAAGAATTATTTTGAATAAATTCCAATTGAAGTTGAAA Listera_cordata_2580 ATGATTAATCACAACCCAAAT---A-ATATTTCTATAAATCTATGAAAAATT------GAAGTTGGAA Neottia_nidus_avis_JVF_trnLF ATTATTAATCACAACCCAAATCTTATATATATCAAAAAATATATGAA-CATTTAAGAATTATTG-G------Neottia_spp ATTATTAATCACAACCCAAATCTTATATATATCAAAAAATATATGAA-CATTTAAGAATTATTGT------Epilyna_jimenzii_ER67 ACGATTAATCACAACCCGAATCTTATAGAGATCAAGAAATATATGAAAAATTGAAGAGTTATTGTCAATCAATTCCGATTGAAGG-GAAA Ellenathus_lancifolius_ER36 ACGATTAATCACAACCCGAATCTTATAGAGATCAAAAAATATATGAAAAATTGAAGAGTTATTGTCAATCAATTCCAATTGAAGTT-AAA sertifera_columbiana_ER38 ACGATTAATCACAACCCGAATCTTATAGAGATCAAAAA-TATATGAAAAATTGAAGAGTTATTGTCAATCAATTCCAATTGAAGTT-AAA sobralia_crocea_W533 ACGATTAATCACAACCCGAATCTTATAGAGATCAAAAAATYTWTGAAAAATTGAAGAGTTATTGTCAATCAWTTCCAATTGAAGTTCAAA Sobralia_mucronata_W535 ACGATTAATCACAACCCGAATCTTATAGAGATCAAAAAATCTATGAAAAATTGAAGAGTTATTGTCAATCAATTCCAATTGAAGTTCAAA Elleanthus_374_e&f ?????????????????????????????????????????????????????????????????????????????????????????? CORYMBORKIS_vert_partial ACGATTAATCACAATCCGAAT------Tropidia_effusa_AJ409456 ?????????????????????????????????????????????????????????????????????????????????????????? Tropidia_gram_mwc21775_trnlf ACGATTAATCACAACCCGAATCTTATAGATATCAAAAAATCTATGAAAAATT------TTATTGTGAATCAATTCCAATTGAAGTTGAAA Xerorchis_O799 ACGATTAATCAAAACCCAA------Xerorchis_sp_MWC12601 ACGATTAATCAAAACCCA------Nervilia_aragoana_AJ409431 ACGATTAATCACAACCC------ATAGAGATCAAAAAATATATGGAAATTTGAAG--TT------GAAA

Continued

Table A.2 Continued

nervilia_plicata_ER48_trnlf ACGATTAATCACAACCCGAATCTTATAGAGATCAAAAAATATATGAAAAATCGAAG--TT------GAAA Nervilia_shirenensis_AF519945 ACGATTAATCACAACCCGAATCTTATAGAGATCAAAAAATATATGAAAAATCGAAG--TT------GAAA Diceratostele_gabonensis_Er40 ?????????????????????????????????????????????????????????????????????????????????????????? Triphora_amazonica_Emerson_A06 -----TAA--ACAATTCGAATCTTAGAGAGATCAAAAAATCTATGAGAATTTGAAGAGTTATTGTGTTGTAAATCCA-TTGAAGTTGAAA Triphora_trianthophora_ER19A -----TAA--ACAATTCGAATCTTATAGAGATCAAAAAATCTATGGAGATTTGAAGAGTTATTGTGTTGTAAATCCA-TTGAAGTTGAAA Triphora_gentianoides_ER01 -----TAA------ATAGAGATCAAAAA-TATATGAAAAATTGAAGAGTTATTGTGTTGTAAATCCC-TTGAAGTTGAAA Monophyllorchis_sp ACAATTCATCACAATTCAAATCTTATAGAGATCAAAAAATATATGAAAAATGGAAGAGTTCTTGTTTTGTAAATCCA-TTGAAGTTGAAA Monophyllorchis_micorstyloides ACAATTCATCACAATTCAAATCTTATAGAGATCAAAAAATCTATGAAAAATGGAAGAGTTATTGTTTTGTAAATCCA-TTGAAGTTGAAA Psilochilus_macrophyllus_ER02 ACAATTAATCACAATTTGAATCTTATAGAGATCGAAAAATCTATGAAAAAATGAAGAGTTATTGTGTTGTAAATCCA-TTGAAGTTCAAA Psilochilus_modestus_ER65 -TGA--CATATCAA------ATAGAGATCGAAAAATCTATGAAAAAATGAAGAGTTATTGTGTTGTAAATCCA-TTGAAGTTCAAA Isochilus_amparoanus_AF266962 ACGATTAATCACAACCCAAATCTTATAGAGATCAAAAAAGATATGAAAAAT-GAAGAGTTATTGTGAATCAATTTCAATTGAAGTTGAAA Chysis_bractescens_AF266971 ACGATTAATCACAACCCAAATCTTATAGAGATAAAAAAATATATGAAAAATTGAAGAGTTATTGTGAATCAATTCCAATTGAAGTTGAAA Oreorchis_patens ACGATTAATCACAACCAAAATCTTATAGAGATCAAAAAGTATATGAAAAATTGAAGAGTTATTGTGAATCAATTCCTATTGAAGTTGACA Cor_trifida_2080 ATGATTAATCACAACCMAGATCTTATAGAAATCAAAAAGTATATGAAAAATTGAAGAGTTATTGTGAATCAATTCCTGTTGAAGTTGMCG Calypso_bulbosa_AF519960 ACGATTAATCACAACCCAAATTTTATAGGGATCAAAAAATATATGAAAAATTGAAGAGTTATTGTGAATCAATTCCAATTGAAGTTGAAA Govenia_liliacea_AF519916 ACGATTAATCACAAACCAGATCTTATAGAGATCAAAAAATATATGAAAAATTGAAGAGTTATTGTGAATCAATTCCTATTGAAGTTGACA Leptotes_bicolor_AF267014 ACGATTAATCACAACACAAATCTTATAGAGATCAAAAAATATATGAAAAATGGAAGAGTTATTGTGAATCAATTCCAATTGAAGTTGAAA Eulophia_sp_o403 ACGATTAATCACAACCCAAATCTTATAGAGATCAAAAAATATATGAAAAATCGAAGAGTTATTGTGAATCAATTCTAATTGAAGTTGAAA Ponera_striata_AF266965 ACGATTAATCACAACCCAAATCTTATAGAGATCAAAAAAGATATGAAAAATTGAAGAGTTATTGTGAATCAATTCCAATTGAAGTTGAAA 252

Monadenia_bracteata_AJ409430 AA-GAATTGAATTCTAA------TATTCAGT-GATCAAATTATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTAATCGGACGAGA Brownleea_coerulea_AF360512_AF360455 ------TTCCAGAGTTTGATGGATTTTTTGAAGATTAATCGGACGAGA Codonorchis_lessonii_AJ409387 AAAGAATCGAATTTGAA------TATTCAGT-GATCGAATGATTCATTCCAGAGTTTGATAAATCTTTTAAAGATTAATCGGACGAGA Coelia_triptera_AF266972 AAAGAATCGAATTCGAA------TATTCAGT-GATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTAATCGGACGAGA Corycium_carnosum_AJ409391 AAAGAATTGAATTCCAA------TATTCAGT-GATCAAATTATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTAATCGAACGAGA Goodyera_sp AAAGAATCGAATTCAAA------TATTCAGT-GATCAAATGAGTCATTCCAGAGTTTGATAGATTTTTTGAAGATAAATCGGACGAGA Pterygodium_catholicum_AJ40944 AAATAATTGAATTCC------AGAGTTTGATAGATCTTTTGAAGATTAATCGGACGAGA Platylepis_polyadenia_AJ544501 AAAGAATCGAATTCAAA------TATTCAGT-GATCAAATGAGTCATTCCAGAGTTTGATAAATTTTTTGAAGATGAATCGGACGAGA Palmorchis_Er211_cf_trilobulat AAAGAATTGAATTCGAA------TATTCAGG-GATCAAAAGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTAATCGGACGAGA Palmorchis_AJ409435 AAAGAATCGAATTCAAA------TATTCAGT-GATCAAAAGATTCATTCCAGAGTTGGATAGATCTTTTGAAGATTAATCGGACGAGA palmorchis_silvicola_incomplete AAAGAATCGA-TTCGAA------TATTCCGGGGGTCCAAAGATTCATTCCCGGGTTGGAAAGGTCTTTTGAAGATTAATCGGGCGGGG Cephalanthera_damasonium_AJ409 AAAGAATCGAATTCGAA------TATTCAGT-GATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTAATCGGACGAGA Aphyllorchis_pall ------GAAGATTAATCGGACGAGA aphyllorchis_montana_mwc ------GAAGATTAATCGGACGAGA Limodorum_spp ---GAA------GAAGATTAATCGGACGAGA Limodorum_abortivum_0924 ---GAA------GAAGATTAATCGGACGAGA Epipactis_spp AAAGAATCGAATTCAAA------TATTCAGT-GATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTAATTGGACGAGA Epipactis AAAGAATCGAATTCAAA------TATTCAGT-GATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTAATTGGACGAGA Listera_smalliigi_AJ409422 AAAGAATCGAATTTGAA------TATTCAGT-GATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTAATCGGACAAGA Listera_cordata_2580 AAAGAA------TCAAACCAGAGTTTGATAGATCTTTTGAAGATTAATTGGACAAGA Neottia_nidus_avis_JVF_trnLF ---GGATAAATTTTGAA------TAATCAGT-GATAAAATGATTCATT-GAGAGTTTGATAGATCTTTTGGAGATTAATTGGACGAGA

Continued

Table A.2 Continued

Neottia_spp ---GGATAAATTTTGAA------TAATCAGT-GATAAAATGATTCATT-GAGAGTTTGATAGATCTTTTGGAGATTAATTGGACGAGA Epilyna_jimenzii_ER67 AAAGAATCGAATTCGAA------TATTCAGG-GATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGRTTAATCGGACGRGA Ellenathus_lancifolius_ER36 AAAGAATCGAATTCGAA------TATTCAGT-GATCAAACGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTA-TCGGACGAGA sertifera_columbiana_ER38 AA-GAATCGAATTTTAA------TATT-AGT-GATCAAATGATTCCTTCCAGAGTTTGATAGATYTTTTGAAGATTAATCGGGCGAGA sobralia_crocea_W533 AA-GAATCGAATTCGAA------TATTCAGT-GATCAAATGATTCATT----AGTTTGATAGATCTTTTGAAGATTAATCGGACGAGA Sobralia_mucronata_W535 AA-GAATCGAATTCGAA------TATTCAGT-GATCAAATGATTCATT----AGTTTGATAGATCTTTTGAAGATTAATCGGACGAGA Elleanthus_374_e&f ?????????????????????????????????????????????????????????????????????????????????????????? CORYMBORKIS_vert_partial ------Tropidia_effusa_AJ409456 ?????????????????????????????????????????????????????????????????????????????????????????? Tropidia_gram_mwc21775_trnlf AAATAA-CGAATTCGAA------TATTCAGT-GATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTAATCGGACGAGA Xerorchis_O799 ------TCTT------ATT---CGGACGAGA Xerorchis_sp_MWC12601 ------ATCTT------ATT---CGGACGAGA Nervilia_aragoana_AJ409431 AAATA------TTAGAA------TATTCAGT-GATCAA------TAGATCTTTTGAAGATTAATCGGACGAGA nervilia_plicata_ER48_trnlf AAAGA------TTCGAA------TATTCAGT-GATAAAATGATTCATTCCAGAGTT-GATAGATCTTTTGAAGATTAATCGGACGAGA Nervilia_shirenensis_AF519945 AAAGA------TTCGAA------TATTCAGT-GATAAAATGATTCATTCCAGAGTT-GATAGATCTTTTGAAGATTAATCGGACGAGA Diceratostele_gabonensis_Er40 ????????????????????????????????????????????????????????????ATAGATCTTTTGAAGATTAATCGGACGAGA Triphora_amazonica_Emerson_A06 A-GGAATCAAATTCGAATAGTCAGTTATTCAGT-AATCAAATGATTCATTCCAGAGTTTGAAAGATCTTTTGAAGATTAATCAGACGAGA Triphora_trianthophora_ER19A AAGGAATCAAATTCGAATTTTCAGTTATTCAGT-AATCAAATGATTCATTCCAGAGTTTGAAAGATCTTTTGAAGATTAATCATACGAGA Triphora_gentianoides_ER01 AAGGAATCAAATTCGAATATTCAGTTATTCAGT-AATCAAATGATTCATTCCAAAGTTTGAAAGATCTTTTGAAGATTAATCGGACGAGA 253 Monophyllorchis_sp AAAGAATAGAATTCGAAT-----GTT---CAGT-AATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTAAAGATTAATCGAACGAGA Monophyllorchis_micorstyloides AA-GAATAGAATTCGAAT-----GTT---CAGT-AATCAAATGATTCATTCCAGAGTTTGATAGATCTTT-AAAGATGAATCGGACGAGA Psilochilus_macrophyllus_ER02 ---GAAAAGAAT-CGA-T---CAGTTATTCAGT-AATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTAATCGGACGAGA Psilochilus_modestus_ER65 ---GAAAAGAAT-CGA-T---CAGTTATTCAGT-AATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTAATCGGACGAGA Isochilus_amparoanus_AF266962 AAAGAATTGAATTCAAA------TATTCAGT-GATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTAATAGGACGAGA Chysis_bractescens_AF266971 AAAGAATCGAATTCGAA------TATTCAGT-GATCAAATGATTCA------TTTGATAGATCTTTTGAAGATTAATCGGACGAGA Oreorchis_patens AAAGAATCGAATTCAAA------TATTCAGT-GATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTAATCGGACGAGA Cor_trifida_2080 AAAGAATTGAATTCAGA------TATTCAGG-GATCAAANGATTCATTCCAGAGTTTGATAGATCTTTTGRAGATTTATCAGACGAGA Calypso_bulbosa_AF519960 AAAGAATCGAATTCAAA------TATTCAGT-GATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTAATTGGACGAGA Govenia_liliacea_AF519916 AAAGAATCGAATTCGAA------TATTCAGT-GATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATGAATCGGACGAGA Leptotes_bicolor_AF267014 AAAGAATCGAATTCAAA------TATTCAGTGGATCAAATGATTCATTCCAAAGTTTGATAGATCTTTTGAAGATTAATCGGACGAGA Eulophia_sp_o403 AAAGAATCGAATTCTAA------TATTCACT-GATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATGAATCGGACGAGA Ponera_striata_AF266965 AAAGAATTGAATTCGAA------TATTCAGT-GATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTAATAGGACGAGA

Monadenia_bracteata_AJ409430 ATAAAGAGAGAGTCCCATTTTACATGTCAATACCAACAACAATGAAATTTAGAGTAAGAGGAAAATCCGTCGAATTTTAAAATCGTGAGG Brownleea_coerulea_AF360512_AF360455 ATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTATAGTAATAGGAAAATCCGTCGAATTTTAAAATCGT---- Codonorchis_lessonii_AJ409387 ATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTG-AAAATCGTGAGG Coelia_triptera_AF266972 ATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTTAAA-TCGTGAGG Corycium_carnosum_AJ409391 ATAAAGAGAGAGTCCCATTTTACATGTCAATACCAACAACAATGAAATTTAGAGTAAGAGGAAAATCCGTCGAATTTTAAA-TCGTGAGG Goodyera_sp ATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTAGAGTAAGAGGAAAATCCGTCGAATTG-AAAATCGTGAGG Pterygodium_catholicum_AJ40944 ATAAAGAGAGAGTCCCATTTTACATGTAAATACCAACAACAATGAAATTTAGAGTAAGAGGAAAATCCGTCGAATTTTAAAATCGTGAGG Platylepis_polyadenia_AJ544501 ATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTAGAGTAAGAGGAAAATCCGTCGAATTG-AAAATCGTGAGG Palmorchis_Er211_cf_trilobulat ATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTT-AAAATCGTGAGG

Continued

Table A.2 Continued

Palmorchis_AJ409435 ATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTTAAAATCGTGAGG palmorchis_silvicola_incomplete ATAAAGAGAGAGTCCCATTTT-CATGTCAAT-CCGGCCCCA-TGAAATTTATAGTAAGGGGAAAATCCGTCGAATTTTAAAATCGGGAGG Cephalanthera_damasonium_AJ409 ATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATT-GAAAATCGTGAGG Aphyllorchis_pall ATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTGAAAATGGTGAGG aphyllorchis_montana_mwc ATAAAGAGAGAGTCCCGTTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTGAAAATCGTGAGG Limodorum_spp ATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTT-AAAATCGTGAGG Limodorum_abortivum_0924 ATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTT-AAAATCGTGAGG Epipactis_spp ATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGATATTTATAGTAAGAG---AATC-GTCGA-TT-GAAAATCGTGAGG Epipactis ATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGATATTTATAGTAAGAG---AATC-GTCGA-TT-GAAAATCGTGAGG Listera_smalliigi_AJ409422 ATAAAGAGAGAGTCCCGTTTAACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTGAAAATCGTGAGG Listera_cordata_2580 ATAAAGAGAGAGTCCCTTTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTGAAAATCGTGAGG Neottia_nidus_avis_JVF_trnLF ATAAAGATAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTATAGTAATAGGAAAATCCGTCGAATTTGAAAATCGTGAGG Neottia_spp ATAAAGATAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTATAGTAATAGGAAAATCCGTCGAATTTGAAAATCGTGAGG Epilyna_jimenzii_ER67 A-AAAGGGAGGGGCCCCTTTTACATGGCCAT-CCGACAACCATGGAATTTTTAGGAAG-GGAAAATCCGTCGAATTTTAAAATCGGGGGG Ellenathus_lancifolius_ER36 ATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAAGGAAATTTATGGTAAGAGGAAAATCCGTCGAATTTTAAAATCGTGAGG sertifera_columbiana_ER38 ATAAAGAGAGAGTCCCCTTTTTCATKTCAATWCCGGCAACAATGAAATTTTTAGTAAGAGGAAA-TCCGTTGAATTTTAAAATTGGGGGG sobralia_crocea_W533 ATAAAGAGAGAGTCCCCTTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTTGAATTTGAAAATTGTGAGG Sobralia_mucronata_W535 ATAAAGAGAGAGTCCCCTTTTACATGTCAAAACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTGAAAATCGTGAGG

254 Elleanthus_374_e&f ?????????????????????????????????????????????????????????????????????????????????????????G CORYMBORKIS_vert_partial ------Tropidia_effusa_AJ409456 ????????????????????????????????????????????????????????????????????????????????????????GG Tropidia_gram_mwc21775_trnlf ATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAA-TCCGTCGAATTTTAAA-TCGGGAGG Xerorchis_O799 ATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTTAAA-TCGTGAGG Xerorchis_sp_MWC12601 ATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTTAAA-TCGTGAGG Nervilia_aragoana_AJ409431 ATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTATAGTAATAGGAAAATCCGTCGAATTTTCAAATCGTGAGG nervilia_plicata_ER48_trnlf ATAAAGAGAGAGTCCCTTTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTTCAAATCGTGAGG Nervilia_shirenensis_AF519945 ATAAAGAGAGAGTCCCTTTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTTCAA-TCGTGAGG Diceratostele_gabonensis_Er40 ATAAAGAGAGAGTCC--TTTTACATGTNNATACCGNCAACAATGAAATTTNTAGTAAGAGGAAAATCCGTCGAATTTTCAAATCGTGAGG Triphora_amazonica_Emerson_A06 ATAAAGAGAGAGTCCCTTTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTTAAGATCGTGAGG Triphora_trianthophora_ER19A ATAAAGAGAGAGTCCCTTTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTTAAAATCGTGAGG Triphora_gentianoides_ER01 ATAAAGAGAGAGTCCCTTTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTTAAAATCGTGAGG Monophyllorchis_sp ATAAAGAGAGAGTCCCTTTT-ACATGTCAATACCGACAAAAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTCAAAATCGTGAGG Monophyllorchis_micorstyloides ATAAAGAGAGAGTCCCTTTTTACATGTCAATACCGACAAAAATGAAATTTATAGTTAGAGGAAAATCCGTCGAATTTCAAAATCGTGAGG Psilochilus_macrophyllus_ER02 ATAAAGAGAGAGTCCCTTTTTACATGTCAATACCGACAACAATGAAATTTCTAGTAAAAGGAAAATCCGTCGAATTTTAAAATCGTGAGG Psilochilus_modestus_ER65 ATAAAGAGAGAGTCCCTTTTTACATGTCAATACCGACAACAATGAAATTTCTAGTAAAAGGAAAATCCGTCGAATTTTAAAATCGTGAGG Isochilus_amparoanus_AF266962 ATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTTAAA-TCGTGAGG Chysis_bractescens_AF266971 ATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTTAA--TCGTGAGG Oreorchis_patens ATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAATAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTTAAA-TCGTGAGG Cor_trifida_2080 ATGAAGGGAGAGTCCCATTTTTCACGTYAATCCCGGCAATAATGRAAWTTATTGTAAGRGGAAAAWCCGKCGAATTTKAAA-TCATGAGG Calypso_bulbosa_AF519960 ATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTA--GTAT------Govenia_liliacea_AF519916 ATAAAGAGAGAGTCCCGTTTTACATGTCAATACCGACAA------

Continued

Table A.2 Continued

Leptotes_bicolor_AF267014 ATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAAAGGAAAATCCGTCGAATTTTAAA-TCGTGAGG Eulophia_sp_o403 ATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTATAGTAATAGGAAAATCCGTCGAATTTTAAA-TCGTGAGG Ponera_striata_AF266965 ATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTTAAA-TCGTGAGG

Monadenia_bracteata_AJ409430 GTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCATTTT-----ACTTC------Brownleea_coerulea_AF360512_AF360455 ------Codonorchis_lessonii_AJ409387 GTTCAAGTCCCTCTATCCCCAA--AAAAGCCCATTTT-----ACTTCC------TCATCCTATTTGTT--CAT---CAG Coelia_triptera_AF266972 GTTCAAGTCCCTCTATCCCCAATAAAAAGCCCATTTT-----ACTTCCTCGCTCTTTATTTATCCTCATCCTCTTTCTTTTCAT---CAG Corycium_carnosum_AJ409391 GTTCAAGTCCCTCTATCCCCAAGAAAAAGTCCATTTT-----ACCTCC------TCA--CTCT--GTTCT------Goodyera_sp GTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCATTTT-----AATTCCCCACTCTTTTTTTACTCTCATTCTCTTTTTTTT-AT---CAG Pterygodium_catholicum_AJ40944 GTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCATTT------Platylepis_polyadenia_AJ544501 GTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCATTTT-----AATTCCCCACTCTTTCTTTACTCTCATCCTCTTTTTTTT-AT---CAG Palmorchis_Er211_cf_trilobulat GTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCATTTT-----ACTTCCTCACTCTTTATTTATCCTCATCCTCTTTTTTTTCAT---CAG Palmorchis_AJ409435 GTTCAAGTCCTTCTATCCCCAAGAAAAAGCCCATTTT-----ACTTCCTCACTCTTTATTTATCCTCATCCTATTTTTTTTCAT---CAG palmorchis_silvicola_incomplete GTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCATTTT-----ACTTCCTCCCTCTTTATTTATCCTCATCCTATTTTTTTTCAT---CAG Cephalanthera_damasonium_AJ409 GTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCATTTT-----ACTTCCTCACTCTTTATTTATCCTCATCCTCTTTTT---CAT---CAG Aphyllorchis_pall GTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCATTTT-----ACTTCCTCAGTCYTTANWWATCCTCATCCTTTTYTTTT-CAT---CAG aphyllorchis_montana_mwc GTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCATTTT-----ACTTCCTCACTCTTTATTTATCCTCATCCTTTTTTT---CAT---CAG Limodorum_spp GTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCATTTT-----ACTTCCTC------255 Limodorum_abortivum_0924 GTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCATTTT-----ACTTCCTC------Epipactis_spp GTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCATTT------ACTTCCTCACTCTTTATTTATCCTCATCCTCTTTTTTTTAAT---CAG Epipactis GTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCATTT------ACTTCCTCACTCTTTATTTATCCTCATCCTCTTTTTTTTAAT---CAG Listera_smalliigi_AJ409422 GTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCATTTA-----ACTTCCTCACTCTTTATTTATCCTCATCCTCTTTTTTTTCAT---CAG Listera_cordata_2580 GTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCTTTTT-----A-TTCCTCACTCTTTATTTATCCTCATCCTCTTTTTTTTCAT---CTG Neottia_nidus_avis_JVF_trnLF GTTCAAGTCCCTCTATCCCCAATAAAAAGCCCATTTT-----ACTTCCTC------A--TA------CTTT-TTTTCAT---CTG Neottia_spp GTTCAAGTCCCTCTATCCCCAATAAAAAGCCCATTTT-----ACTTCCTC------A--TA------CTTT-TTTTCAT---CTG Epilyna_jimenzii_ER67 GTTCAAGGCCCCCCTTCCCCCAGAAAAACCCCATTTT-----CCT-CCCCGCCCTTTGTT-ATCCCCHACCCATTTCCTTTCATTTTCA- Ellenathus_lancifolius_ER36 GTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCATTTT-----ACTTCCTCGCTCTTTATTTATCCTCATCCTATTTCTTTTCATTTTCA- sertifera_columbiana_ER38 GTTCAAGTCCCTTTTTCCCCAAGAAAAAACCCCTTTT-----AWTTCCCCGCTCTTTATTTATCCTCATCCTCTTTTTTTTCATTTTCA- sobralia_crocea_W533 GTTCAAGTCCCTTTATCCCCAAGAAAAAGCCCCTTTT-----ACTTCCTCGCTCTTTATTTATCCTCATCCTCTTTTTTTTCATTTTCA- Sobralia_mucronata_W535 GTTCAAGTCCCTCTATCCCCCAGAAAAAGCCCCTTTT-----ACTTCCCCGCTCTTTATTTATCCTCATCCTCTTTCTTTTCATTTTCA- Elleanthus_374_e&f GTTCAAGTCCCTCTATCCCCAAGAAAAAGCGCATTTT-----ACTTCCCCGCTCTTTATTTATCCTCATCCTATTTCTTTTCATTTTCA- CORYMBORKIS_vert_partial ------Tropidia_effusa_AJ409456 GTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCATTTT-----ACTTCCTCGCTCTTTATTTATCCTCATCTTCTTTCTTTTCAT---CAG Tropidia_gram_mwc21775_trnlf GTTCAAGTCCCTCTATCCCCAATAAAAAGCCCCTTTT-----AAT-CCTCGCTCTTTATTTATCCTCATCTTCCTTCCTTTCAT---CAG Xerorchis_O799 GTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCATTTT-----AATTCCTCGTTCTTTATTTATCCTCATCCTTTTTTTTTTCAT---CAG Xerorchis_sp_MWC12601 GTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCATTTT-----AATTCCTCGTTCTTTATTTATCCTCATCCTTTTTTTTT-CAT---CAG Nervilia_aragoana_AJ409431 GTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCTTTTTATTCTATCTCCTCGCTCTTTATTTATCCTCATCCTATT-CTTTT-AT---CAG nervilia_plicata_ER48_trnlf GTTCAAGTCCCTCTATCCCCAAGAAGAAGCCCTTCTTCTTTTACTTTCTCTCTCTTTAATTATCCTCATCATAT--CTTTTCAT---TAG Nervilia_shirenensis_AF519945 GTTCAAGTCCCTCTATCCCCAAGAAGAAGCCCTTTTTCTTTTACTTTCTCTCTCTTTATTTATCCTCATCATAT--CTTTTCAT---CAG Diceratostele_gabonensis_Er40 GTTCAAGTCCCTCTATCCCCAAGAAGAAGCCCTTCTTCTTTTACTTTNTCTCTCTTTATTTATCCTCATCATAT--CTTTTCAT---TAG

Continued

Table A.2 Continued

Triphora_amazonica_Emerson_A06 GTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCATTTT-----ACTTCCTCG------Triphora_trianthophora_ER19A GTTCAAGTCCCTCTATCCCCAAGAAAA-GCCCATTTT-----ACTTCCTTG------Triphora_gentianoides_ER01 GTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCATTTT-----ACTTCCTCG------Monophyllorchis_sp GTTCAAGTCC-TCTATCCCCAATAAAAAGCCCATTTT-----ACTTCCTCGCTCTTTATTTATCCTCATCCTCTTTC----CAT---CAG Monophyllorchis_micorstyloides GTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCATTTT-----ACTTCCTCGCTCTTTATTTATCCTCATCCTCTTTC----CA----CAG Psilochilus_macrophyllus_ER02 GTTCAAGTCCCTCTATCCCCAAGAAAGAGCCCTTTTT-----ACTTCTTAAATCTTTTTTTATCCTCATCCTCTTTCTTTT------CAG Psilochilus_modestus_ER65 GTTCAAGTCCCTCTATCCCCAAGAAAGAGCCCTTTTT-----ACTTCTTCAATCTTTTTTTATCCTCATCCTCTTTCTTTT------CAG Isochilus_amparoanus_AF266962 GTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCATTTT-----ACTTCCTCGCTCTTTATTTATCCTCATCCTCTTTCTTTTCAT---CAG

Chysis_bractescens_AF266971 GTTCAAGTCCCTCTATCCCCAATAAAAAGCCCATTTT-----ACTTCCTCGCTCTTTATTTATCCTCATCCTCTTTCTTTTCAT---CAG Oreorchis_patens GTTCGAGTCCCTCTATCCCCAATAAAAAGCCCATTTT-----ACTTCCTCGCTCTTTATTTATCCTCATCCTCTTTCTTTTCAT---CGG Cor_trifida_2080 GTTCGAGTCCCTNTATCCCCAATAAAAAGCCCAWTTT-----ACTTCCTCGCTCTTTATTTATCCTCATCCTCTTTCTTTTCAT---CGG Calypso_bulbosa_AF519960 ------Govenia_liliacea_AF519916 ------Leptotes_bicolor_AF267014 GTTCAAGTCCCTCTATCCCCAATAAAAAGCCCATTTT-----ACTTCCTCGCTCTTTA-TTATCCTCATCCTCTTTCCTTTCAT---CAG Eulophia_sp_o403 GTTCAAGTCCCTCTATCCCCAATAAAAAGACCATTTT-----ACTTCCTCGCTTTTTATTTATCCTCATCCTCTTTATTTTCAT---CAG Ponera_striata_AF266965 GTTCAAGTCCCTCTATCCCCAATAAAAAGCCCATTTT-----ACTTCCTCGCTCTTTATTTATCCTCATCCTCTTTCTTTTCAT---CAG

256 Monadenia_bracteata_AJ409430 ------C-T-CACTCTGTTCTTTCACAAATGGATCTAAATATAAATTTTCGTATATTC Brownleea_coerulea_AF360512_AF360455 ------TC----C-T-CACTCTGTTCTTTCACA--CGAATC------TAAATTTTCGTATATTC Codonorchis_lessonii_AJ409387 TTGTTAAGTTCAAACAAAATTCAATATCTTTCTCATTTCATTCACTCTGTACTTTCACAAGTGGATCCGAATAGAAATTATCGTATCTTC Coelia_triptera_AF266972 TGGATCAGTTTAAACAAAATGAAATATCTTTCTCATTTCATTCACTCTGTTCTTTCACAAATGGATCCGAATAGAAATCCTCGTATCTTC Corycium_carnosum_AJ409391 -----CA---CAAA-TGGATCCAA-AT----CTAAATT--TTC------G------TAGATTC Goodyera_sp TTGTTCAGTTCAAACAAAATTAAATATCTTTCTAATTTCATTCACTCTGTTCTTTCACAAATGGATACGAATAGAAATTCTCGTATCTT- Pterygodium_catholicum_AJ40944 ------GA-----CTT------CC-TCACTCTGTTCTTTCACAAATGGATCCGAATATCCATTTTCGGATATTC Platylepis_polyadenia_AJ544501 TTGTTCAGTTCAAACAAAATGAAATATCTTTATAATTTCATTCACTCTGTTCTTTTACAAATGGATCCGAATAGAAATCCTCGTATCTTC Palmorchis_Er211_cf_trilobulat TGGTTCAGTTCAAACAA--TACAATATCTTTCTCATTTCATTCACCCTGTTCTTTCACAAATGGATCCGAATAGAAATCCTCGTATCTTC Palmorchis_AJ409435 TGGTTCAGTTCAAACAAAATTCAATATCTTTCTCATTTCATTCACTCTGTTCTTTCACAAATGGATCCGAATAGAAATCCTCGTATCTTC palmorchis_silvicola_incomplete TGGTTCAGTTCAAACAAAATTCAATATCTTTCTCATTTCATTCACTCTGTTCTTTCACAAATGGATCCGAATAGAAATCCTCGTATCTTC Cephalanthera_damasonium_AJ409 AGGTTCAGTTCAAACAAAATTAAATATCTTTCTCATTTCATTCACTCTGTTCTTTCACAAATGGATCCAAATAGAAATCCTCGTATCTTC Aphyllorchis_pall CGGTTTAGTTCAAACAAAATTCAATATCTTTCTCATTTCATTCACTCTGTTCTTTCACAACTGGATCCAAATAGAAATCCTCGTATCTTC aphyllorchis_montana_mwc TGGTTTAGTTCAAACAAAATTCAATATCTTTCTCATTTCATTCACTCTGTTCTTTCACAACTGGATCCAAATATAAATCCTCGTATCTTC Limodorum_spp ------CAAAATTCAATATTTTTCTCATTTCATTCACTCTGTTCTTTCACAACTGGATCCAAATGGAAATCCTCATATCTTC Limodorum_abortivum_0924 ------CAAAATTCAATATTTTTCTCATTTCATTCACTCTGTTCTTTCACAACTGGATCCAAATGGAAATCCTCATATCTTC Epipactis_spp TGGTTCAGTTCAAACAAAATTCAATATCTTTCTCATTTCATTCACTCTGTTCTTTTGCAACTGGATCCAAATAGAAATCCTCGTATCTTC Epipactis TGGTTCAGTTCAAACAAAATTCAATATCTTTCTCATTTCATTCACTCTGTTCTTTTGCAACTGGATCCAAATAGAAATCCTCGTATCTTC Listera_smalliigi_AJ409422 TGGTTCAGTTCAAACAAAATTCAAT------TTCATTTCATTCACTCTGTTCTTTCACAACTGGATCCAAATAGAAATCCTCGTATCTTC Listera_cordata_2580 TGGTTTAGTTCAAACAAAATGGAAT------TTCATTCCATTCACTCAGTTCTTTCACAACTGGATCAAAATAGAAATCCTCGTATCTTC Neottia_nidus_avis_JVF_trnLF TGGTTCAGTTCAACCAAAATT-AAG-T----TTCATTTCATTTACTCAGTTCTTTAATAACTAGATCCAAATATAAATCCTCATACATCC Neottia_spp TGGTTCAGTTCAACCAAAATT-AAG-T----TTAATTTCATTTACTCAGTTCTTTAATAACTAGATCCAAATATAAATCCTCATACATCC Epilyna_jimenzii_ER67 TAA-TAAGTTCAAAAAAGATTCAATATCTTTCTCATTTCATTCACTCTGTTCTTTCACAAATGGATCCGRATAGAAATCCTCGTATCTTA Ellenathus_lancifolius_ER36 TAA-TAAGTTCAAACAAAATTCAATATCTTTCTCATTTCATTCAGTGTGTTCTTTCACAAATGAATCCGAATAGAAATCCTCGTATCTTC

Continued

Table A.2 Continued

sertifera_columbiana_ER38 TAA-TCAGTTCAAACAAAATTCAATATATTTCTCATTTCATTCACTCTTTTCTTTCACAAATGGATCCGAATAGAAATCCTCGTATCTTC sobralia_crocea_W533 TAA-TCAGTTCAAACAAAATTCAATATATTTCTCATTTCATTCACTCTGTTCTTTCACAAATGGATCCGAATAGAAATCCTCGTATCTTC Sobralia_mucronata_W535 TAA-TCAGTTCAAACAAAATTCAATATATTTCTCATTTCATTCACTCTGTTCTTTCACAAATGGATCCGAATAGAAATCCTCGTATCTTC Elleanthus_374_e&f TAA-TAAGTTCAAACAAAATTCAATATCTTTCTCATTTCATTCACTCTGTTCTTTCACAAATGGATCCGAATAGAAATCCTCGTATCTTC CORYMBORKIS_vert_partial ------Tropidia_effusa_AJ409456 TGGCTCAGTTCAAACAAAATTCAATATCTTTCTCATTTCATTCACTCTGTTCTTTCACAAATGGATC------TCCTCGTATCTTC Tropidia_gram_mwc21775_trnlf TGGCTCAGTTCAAACAAAATTAAATATCTTTCTCATTTCATTCACTCTGTTCTTTCACAAATGGATC------TCCTCGTATCTTC Xerorchis_O799 TGGCTCAGTTCAAACAAAATTTAATATCCTTCTCATTTCATTCACTCTGTTCTTTCACAAATGGATCCGAATAAAAATCCTCGTAT---- Xerorchis_sp_MWC12601 TGGCTCAGTTCAAACAAAATTTAATATCCTTCTCATTTCATTCACTCTGTTCTTTCACAAATGGATCCGAATAAAAATCCTCGTAT---- Nervilia_aragoana_AJ409431 TGGCTCAGTTCAAACAAA------nervilia_plicata_ER48_trnlf TGGATCAGTTCAAACAAA------Nervilia_shirenensis_AF519945 TGGATCAGTTCAAACAAA------Diceratostele_gabonensis_Er40 TGGATCAGTTCAAA------Triphora_amazonica_Emerson_A06 ------TCCAATATCTTTCTCATTTCATTCACTCTGTTCTTTAACAGAAGGATTCGAATATAAATACTCATATCTTC Triphora_trianthophora_ER19A ------TCCAATATCTTTCTTATTTCATTCACTCTGTTCTTTAACAAAAGGATTCGAATATAAATCCTCACATCTTC Triphora_gentianoides_ER01 ------TCCAATATCTTTCTCATTTCATTCAATCTGTTCTTTAACAAAGGGATTCGAATATAAATCCTCATATCTTC Monophyllorchis_sp TGACTCGATTCAAACAAAATCCAATATTTTTCTCATTTCTTTCCCTCTTTTCTTTAACAAAAGGATCCGAATAGAAATCCTCATATCTTC Monophyllorchis_micorstyloides TGA------CAAACAAAATCCAATAATTTTCTCATTTCTTTCCCTCTTTTCTTTAACAAAAGGATCCGAATATAAATCCTCATATCTTC

257 Psilochilus_macrophyllus_ER02 TGGCTCGGTTCAAA-AAAATCCAATATCTTTCTCATTTCATTAACTCTGTTCTTTAACAAAAGGATCCGAATATAAATCCTCATATCTTC Psilochilus_modestus_ER65 TGGCTCGGTTCAAA-AAAATCCAATATCTTTCTCATTTCATTAACTCTGTTCTTTAACAAAAGGATCCG-ATATAAATCCTCATATCTTC Isochilus_amparoanus_AF266962 TGGCTCAGTTTAAACAAAATTAAATATTGTTCTAATTTCATTCACTCTGTTCTTTCACAAAAGGATCCGA------Chysis_bractescens_AF266971 TGGCTCAGTTTCAACAAAATGAAATATCTTTCTCATTTCATTCACTCTGTTCTTTCACAAATGGATCCGAATAGAAATCCTCGTATCTTC Oreorchis_patens CGGCTCAGTTTAAACAAAAWGAAATATCTTTCTCATTTCATTCACTCTGTTCTTTCACAAATGGATCCGAATAGAAATCCTCGTATCTTC Cor_trifida_2080 CGRCTCAGTTTAAACAAAATGTAATATCTTTTTCATTTCATTCACTCTGTTCTTTCACAAATGGATCCGAATAGRAATCCTCGTATCTTC Calypso_bulbosa_AF519960 ------Govenia_liliacea_AF519916 ------Leptotes_bicolor_AF267014 TAGCTCAGTTTAAACAAAATGAAATATCGTTCTAATTTCATTTACTCTGTTCTTTTACAAAAGGATCCAAATAGAAATCCTCATATCTTC Eulophia_sp_o403 TGGCTCAGTTTAAACAAGATGAAATATCTTTCTCGCTTCATTCACTCTGTTCTTTCACAAATGGATACGAATATAAATCCTCGTATCCTC Ponera_striata_AF266965 TGGCTCAGTTTAAACAAAATTAAATATTGTTCTAATTTCATTCACTCTGTTCTTTCACAAATGGATCC------

Monadenia_bracteata_AJ409430 -TTCCAATTCAATCCAATTTCATTTA-----TATAGATACGATACCTGCACAAATGAATATATATGTTCAAGGAATCTCCGTTATTTCAT Brownleea_coerulea_AF360512_AF360455 -TTCCAA------TTTCATTTT-----TATAGATACGATACCTGTACAAATGAACATAAATGTTCAAGGAATCTCCGTTATTTAAT Codonorchis_lessonii_AJ409387 -TTCCAATTTAATCCAATTTCATTTG----GTATAGATACGATACCTGCACAAATGAACATATATGTTCAAGGAATCTCCGTTATTTAAT Coelia_triptera_AF266972 -TTCCAATC-----CAATCTCATTTGTTTTGTATA-ATACGAT------ATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT Corycium_carnosum_AJ409391 -TTCCAATTCAATCCAATTTCATTT-----GTATAGATACAATACCTGAACAAATGAACATTTATGTTCAAGGAATTTCCGTTATCTAAT Goodyera_sp ATTCCAATT-A---CAATTTC-TTTGTTTTGTATAGATACGATACCTGCACAAATGAACATATATATTCAAGGAATCTCCCTTATTGAAT Pterygodium_catholicum_AJ40944 -TTCCAATTCAATCCAATTTCATTT-----GTATAGATACGATACCTGCACAAATGAGCATATATGTTCAAGAAATTTCCGTTATTTAAT Platylepis_polyadenia_AJ544501 -TTCCAATTCAATCCAATTTTCTTTGTTTTGTATAGATACGATACCTGCACAAATGAACATATATGTTCAAGGAATCTCCCTTATTTAAT Palmorchis_Er211_cf_trilobulat -TTCTAATC-----CAATTTCATTT-----GTATAG-TACGATACCTGTACAAATGAACWTATATGTTCAAGGAATCTCCGTTATTGAAT Palmorchis_AJ409435 -TTCTAATC-----CAATTTCATTT-----GTATAG-TACGATACCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT palmorchis_silvicola_incomplete -TTATAATC-----CAATTTCATTT-----GTATAG-TACGATACCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT Continued

Table A.2 Continued

Cephalanthera_damasonium_AJ409 -TTCCAATC-----AAATTTCATTT-----GTATAG-TACGATACCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT Aphyllorchis_pall -TTCCAATC-----CAATTTCATTT-----ATAGAG-TACGATATCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT aphyllorchis_montana_mwc -TTCCAATC-----CAATTTCATTT-----ATAGAG-TACGATATCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT Limodorum_spp -TTCCAATC-----CAATTTCATTT-----GTATAG-TACGATACCTGTACAAATGAACATA------GTTATTGAAT Limodorum_abortivum_0924 -TTCCAATC-----CAATTTCATTT-----GTATAG-TACGATACCTGTAC----G------Epipactis_spp -TTCCAATC------TT-----GTATAG-TACGATACCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT Epipactis -TTCCAATC------TT-----GTATAG-TACGATACCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT Listera_smalliigi_AJ409422 -TTCCAATC-----CAATTTCATTT-----GTATAG-TACGATACCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT Listera_cordata_2580 -TTCCAATA-----CAATTTCATTT-----GTATAG-TATGATACCTGTACAAATGAACATATATGTTCAAGA--TCTCCGTTATTGAAT Neottia_nidus_avis_JVF_trnLF -TTTCAATA-----CAATTTAATTT-----CTAT---TTTTTTACCTGTACAAAAGAACATATATGTTCAAGGAATTTCCGTTATTGAAT Neottia_spp -TTTCAATA-----CAATTTAATTT-----CTAG---TACGATACCTGTACAAAAGAACATATATGTTCAAGGAATTTCCGTTATTGAAT Epilyna_jimenzii_ER67 -TTCCAATC-----CMATTCCATTTGTTTTGTATAG-TACGATACCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT Ellenathus_lancifolius_ER36 -TTCCAATC-----CAATTTCATTTGTTTTGTATAG-TACGATACCTGTACAAATGA------sertifera_columbiana_ER38 -TTCCAATC-----CAATTTCATTTGTTTTTTATAG-TACGATACCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT sobralia_crocea_W533 -TTCCAATC-----CAATTTCATTTGTTTTGTATAG-TACGATACCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT Sobralia_mucronata_W535 -TTCCAATC-----CAATTTCATTTGTTTTGTATAG-TACGATACCTGTACAAATGAACATATATGTTAAAGGAATCTCCGTTATTGAAT Elleanthus_374_e&f -TTCCAATC-----CAATTTCATTTGTTTTGTATAG-TACGATACCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT CORYMBORKIS_vert_partial ------Tropidia_effusa_AJ409456 -TTCCAATC-----CAATTTCATTTGTTTTGTATAG-TACGATACCTGTAAAAATGAACATACATGTTCAAGGAATCTCCGTTATTGAAT 258 Tropidia_gram_mwc21775_trnlf -TTCCAATC-----CAATTTCATTTGTTTTGTATAG-TACGATACCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT Xerorchis_O799 ------ATA-----GAATTTCATTTGTTTTGTAGAG-TACGATGCCTGTACTAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT Xerorchis_sp_MWC12601 ------ATA-----GAATTTCATTTGGTTTGTAGAG-TACGATGCCTGTACTAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT Nervilia_aragoana_AJ409431 --TCCAATC------CATTTGTTTTGTATAG-TATGATGCCTTTACAAATAAACATATATGTTCAAAAATTCTCCGTTATTGAAT nervilia_plicata_ER48_trnlf ------TC-----CAATTTCATTTGTTTTGTATAG-CACAATGCCTGCACAAATG------TATGTTCAAGGAATCTCCGTTATTGAAC Nervilia_shirenensis_AF519945 --TCCAATC------TCATTTGTTTTGTATAG-CACAATGCCTGTACAAATGAACATATATGTTCAAGGAATCTCCGCTATTGAAC Diceratostele_gabonensis_Er40 ----CAATT-----CNATTTCATTTGTTTTGTATAG-CACAATGCCTGCACAAATGASCATATATGTTGGGGGAATCTCCGTTACTGAAC Triphora_amazonica_Emerson_A06 -TTCCAATC-----CAATTTCCTTTGTTTTTAATAG-TACAATACCTGTACAAAGGAACATATATGTTCAAGGAATCCGCCTTAT----- Triphora_trianthophora_ER19A -TTCCAATC-----CAATTTCCTTTGTT---AATAG-TACAATATCTGTACAAAGGAACATATATGTTAAAGGAATCCGCCTTAT----- Triphora_gentianoides_ER01 -TTCCAATC-----CAATTTCCTTTGTTTTTAATAG-TACAATACCTGTACAAAGGAACATATATGTTCAAGGAATCCGCATTATTGAAT Monophyllorchis_sp -TTCCAATC-----CAATTTCCTCTGTTTTTTCTAG-TACAATATCTGTACAAATGAACATATATGTTCAAGGAATCCGCGTTATTGAAT Monophyllorchis_micorstyloides -TTCCAATC-----CAATTTCCT--GGGGGTTCTAG-TACAATATCTGTACAAA------Psilochilus_macrophyllus_ER02 -TTCCAATC-----CAATTTCCTTTGTTTTTTATAG-TACGATACCTGTACAAAGGAACATCTATCTTCAAGGAATTCACATTCTTGAAT Psilochilus_modestus_ER65 -TTCCAATC-----CAATTTCCTTTGTTTTTTATA------GAATTCACATTCTTGAAT Isochilus_amparoanus_AF266962 ------TACGATA--TG------AACATATATGTTCAAAGAATCTCCGTTATTGAAT Chysis_bractescens_AF266971 -TTCCAATC-----CAATCTCATTTGTTTTGTATAA-TACGATA--TG------AACATATATGTTCAAGGAATCTCCGTTATGGAAT Oreorchis_patens -TTCCAATC-----CAATCTCATTTGTTCTGTATAA-TACGCTA--TG------AACATATATGTTCAAGGAATCTCCGTTATTGAAT Cor_trifida_2080 -TTCCAATC-----CAATCTCATTTGTTCTGTATAA-TAYGTTA--TG------AACATATATGCTCAAGGAATCTCCGTTATGGAAT Calypso_bulbosa_AF519960 ------Govenia_liliacea_AF519916 ------Leptotes_bicolor_AF267014 -TTCCAATC-----CAATCTCATTTGTTTTG-ATAA-TACGATA--TG------AACATATATGTTCAAGGAATCTCCGTTATTGAAT Eulophia_sp_o403 -TTCCAATC-----CAATCTCATTTTTTTTGTATAA-TACGATA--TG------AACATATATGTTCAAGGAATCTTCGTTATTGAAT Ponera_striata_AF266965 ------G----A-TACGATA--TG------AACATATATGTTCAAGGAATCTCCGTTATTGAAT

Continued

Table A.2 Continued

Monadenia_bracteata_AJ409430 AA--TTCACAGTCCATATCATTATCCTTACATTT-----ACAAAAAAAATCTTCTTTTTGAAGATCTAAGAAATTAAGGGGCTGGGTCCA Brownleea_coerulea_AF360512_AF360455 TA--T------CATATAATTATCTTTACATTG-----ACAAAGAAAGTCTTCTTTTTGAAAATCTAAGAAATTCAGGGGCTAGGTCCA Codonorchis_lessonii_AJ409387 --CATTCACAGTCCATATCATTCTCCTTTCATTT-----ACAAAGAAAAT------GAATATCTAA------Coelia_triptera_AF266972 AA--TTCATAGTCCATATCTTTTTCCTTACATTT-----ACAAAGAAAGTCTTCTTTTTGAAGATCTAAGAAATTCAGGAGCTAGGGCCA Corycium_carnosum_AJ409391 AA--TTCACAGTCCATA------TCCTTACATTT-----ACAAAGAAAGTCTTCGTTTTGAAGATCTAAGAAATTAAGGGGCTAGGTCCA Goodyera_sp AACATTCACAGTTCATATCATTATCTTTACATTT-----ACAAAGAAAGTTTT------Pterygodium_catholicum_AJ40944 AA--TTCACAGTCCATATCATTATCCTTACATTT-----ACAAA------A Platylepis_polyadenia_AJ544501 AACATTCACAGTTCATATCATTATCTTTACATTT-----ACAAAGAAAGTTTTATTTTTGAAGATCTAAGAAATTAAGGGGCTAGGTCCA Palmorchis_Er211_cf_trilobulat --CATTCACAGTCCATATCATT------TTT-----ACAAAGAAGGTCTTCTTTTTGAAGATCCAAGAAATTCAGGGGCTAGGTCCA Palmorchis_AJ409435 --CATTCACAGTCCATATCATT------TTT-----ACAAAGAAAGTCTTCTTTTTGAAGATTCAAGAAATTCAGGGGCTAGGTCCA palmorchis_silvicola_incomplete --CATTCACAGTCCATATCATT------TTG-----ACAAAGAAAGTCTTCTTTTTGAAGATCCAAGAAATTCAGGGGCTAGGTCCA Cephalanthera_damasonium_AJ409 --CATTCACAGTCCATATCATT------ATT------ACAAAGAAAGTCTTCTTTTTGAAGACCTAAGAAATTCAGGGGCTAGGTCCA Aphyllorchis_pall --CGTTCACAGTCCATATCACTATCCTTACATTT-----ACAAATAGAGTCTCCTTTTTGAAGACCTAAGGAATTCTGGGGCTAGGTCCT aphyllorchis_montana_mwc --CATTCACAGTCCATATCACTATCCTTACACTT-----AC------Limodorum_spp --CATTCACAGTCCATATCATTTTCTTTACATTT-----ACAAAGAAAGTCTTCTTTTTGAATACCTAAGAA-TTCAGGGGCTAGGTCCA Limodorum_abortivum_0924 ------Epipactis_spp --CATTCACAGTCCATAT------CATTA----TACAAAGAAAGTCTTCTTTTTGAAGACCTAAGAAATTCAGGGGCTAGGTCCA Epipactis --CATTCACAGTCCATATCATTAT------ACAAAGAAAGTCTTCTTTTTGAAGACCTAAGAAATTCAGGGGCTAGGTCCA 259 Listera_smalliigi_AJ409422 --CATTCACAGTCCATATCATTATCCTTACATA------AAAAAAAATCTTCTTTTTGAAGACCTAAGAAATTCGGGGGCTAGGTCCC Listera_cordata_2580 --CATTCACAGTCCATATCATTATCCTTGCATTT-----CCAAACAAAATCTTCTTTTTGAAGAACTAAGAAATTCGGGGGCTAGGTCCT Neottia_nidus_avis_JVF_trnLF ------CATTT------AAAGTTTTATTTTTGAAGACGTAATAAATTAAGG--CTAGGTCCA Neottia_spp ------CATTT------AAAGTTTTATTTTTGAAGACCTAATAAATTAAGG--CTAGGTCCA Epilyna_jimenzii_ER67 --CATTCACAGTCCAT------Ellenathus_lancifolius_ER36 ------sertifera_columbiana_ER38 --CATTCACAGTCCATAT----AT------sobralia_crocea_W533 --CATTCACAGTCCATAT----AT------Sobralia_mucronata_W535 --CATTCACAGTCCATAT----AT------Elleanthus_374_e&f --CATTCACAGTCCATAT----AT------CORYMBORKIS_vert_partial ------Tropidia_effusa_AJ409456 --CATTCACAGTCCATATCTTTTTCCTTACATTT-----ACAAAGAAAGTCTTCTTT------Tropidia_gram_mwc21775_trnlf --CATTCACAGTCCATATCTTTTTCCTTACATTT-----ACAAAGAAAG------Xerorchis_O799 --CATTCGCAGTCCATATCTCTATCCTTACATTT-----ACAAAGAAAGTCTTC------Xerorchis_sp_MWC12601 --CATTCGCAGTCCATATCTCTATCCTTACATTT-----ACAAAGAAAGKCTTC------Nervilia_aragoana_AJ409431 --CATTCACAGCCCATA-----ATCCTTACATTTAATTTACAAATAAAGTCTTCTTTTTGAAGATCTCAGAGATTCAGGGGCTAGGTCCA nervilia_plicata_ER48_trnlf --CATTCCCAGTCCATA-----ATCCTTACATTTCATTTACAAAGAAAGTCTTCTTTTTGAAGATCTAAGAGATTCAGGGTCTAGGTACA Nervilia_shirenensis_AF519945 --CATTCACAGTCCATA-----ATCCTTACATTTAATTTACAAAGAAAGTCTTCTTTTTGAAGATCTAAGAGATTCAGGGTCTAGATACA Diceratostele_gabonensis_Er40 --CATTCACAGTCCATA-----ATCCTTACATTTCATTTACAAAGAAAGTCTTCTTKTTGAAGNTCTNAGAGAGTCAGGGTCTAGGTACA Triphora_amazonica_Emerson_A06 ------CCTTA------CATTT-----A-AAAGGAAGCCTTC------Triphora_trianthophora_ER19A ------CA-TCCTTA-----ATCCTTACATTT-----A-AAA---ATACTT------Triphora_gentianoides_ER01 --CATTCACAGTCCTTATCTTTATCCTTACATTT-----A-AAAG-AAGACTTT------

Continued

Table A.2 Continued

Monophyllorchis_sp --CATTCACAGTCCTTATCTTTATCCTTACATTT-----A-AAA------TTTT----GAAGATCTAAGAAATTCAGGGGCTAGGTCCA Monophyllorchis_micorstyloides ------Psilochilus_macrophyllus_ER02 --CATTCACATTCCTTA------TCCTTACATTT-----A-AAAAGAAG------Psilochilus_modestus_ER65 --CATTCACATTCCTTA------TCCTTACATTT-----A-AAAAGAAG------Isochilus_amparoanus_AF266962 --CATTCATAGTCCATATATTTTTTCTTACATTT-----ACAAAGAAAGTCTTATTTTTTAAGATCTAAGAAATTCAGGGGCTAGGGCCA Chysis_bractescens_AF266971 --CATTCATAGTCCATATCTTTTTCCTTACATTG-----ACAAAGAAAGTCTTCTTTTAGAAGATCTAAGAAATTCAGGGGCTAGGGCCA Oreorchis_patens --CATTCATAGTCCATATCTTTTTCCTTTCATTT-----ACAAAGAAAGTCTTCTTTTTGAAGATCTAAAAGATTCAGGGGCTAGGGCCA Cor_trifida_2080 --CATTCATAGTCCATATCTTTTTTCTTTCATTT-----ACAAAGAAAGTCTTCTTTTTGAAGATCTAAAAGATTCAGGGGCTAGGGCCG Calypso_bulbosa_AF519960 ------Govenia_liliacea_AF519916 ------Leptotes_bicolor_AF267014 --CATTCATAGTCCATATCTTT-TCCTTACATTT-----ACAAAGAAAGTCTTCTTTTTGAAGATCTAATAAATTCAGGGGCTAGGGCCA Eulophia_sp_o403 --CATTCATAGTCCATATCTTT-TACTTACATTT-----ACAAAGAAAGTCTTCTTTTTGAAGATCTAAGAAATTCAGGGGCTAGGGCCA Ponera_striata_AF266965 --CATTCATAGTCCATATCTTT-TTCTTACATTT-----ACAAAAAAAATCTTCTTTTTGAAGATCTAAGAAATTCAGGGGTTAGGGCCC

Monadenia_bracteata_AJ409430 ATTTGTTAAGACTGCCTTTTT-AGTTCTTTTCATTGACA------TAAATACAAGTACTCTGCTAGGATGATGCACAGAAAA00000000 Brownleea_coerulea_AF360512_AF360455 ATTTGTTAAGACTTTCTTTTTTAGTTCTTTTCATTGACA------TAGATATAAGTACTCTGCTAGGATGATGCACAGAAAA???????? Codonorchis_lessonii_AJ409387 ------TTTAGTTTTTTTCATTGACA------TAGATACAAGTACTCTGCTAGGATAATGCACAGGAAA00000000 Coelia_triptera_AF266972 ATTTGTTAAGATTTTATTTTTTAGTTCTTTTCATTGACA------TAGATATAAGTACTCTGCTAGGATGATGCACGGGAAA00000000 260 Corycium_carnosum_AJ409391 ATTTGTTAAGACTGTCTTTTTTAGTTCTTTTCATTGACA------TAGATACAAGTATTCTGCTAGGATGATGCACGGAAAA00000000 Goodyera_sp ------ATTTTTTAGTTCTTTTCGTTTACA------TAGATACAAGTACTCTGCTAGGATTATGCA-GG-TAC10000000 Pterygodium_catholicum_AJ40944 AT------CTTTTTT----AGTTCTTTTCATTGATA------TAGATACAAGTACTCTGCTAGGATGATGCACGGAAAA10000000 Platylepis_polyadenia_AJ544501 ATTTGTTAATACTTTATTTTTTAGTTCTTTTCGTTTACA------TAGATACAAGTACTCTGCTAAAATGATGCA-GGGTAC00000000 Palmorchis_Er211_cf_trilobulat ATTTGTTAAGACTTTTTT----AGTTCTTTTCATTGACA------TAGATACAAGTCCTTTGCTAGGATGATGCACGAGAAA00000000 Palmorchis_AJ409435 ATTTGTTAAGACTTTTTT----AGTTCTTTTCATTGACA------TAGATACAAGTCCTCTGCTAGGATGATGCACGAGAAA00000000 palmorchis_silvicola_incomplete ATTTGTTAAGACTTTTTT----AGTTCTTTTCATT------???????? Cephalanthera_damasonium_AJ409 ATTTGTTAAGACTTTTTT----AGTTCTTTTCATTGACA------TAGATACAAGTACTTTGCTAGGATGATGCACGGGAAA00000000 Aphyllorchis_pall CTT-GTTAAGACTTTTTT----AGTTCTTTTCATTGACA------TAGATACAAGTACTTTGCTAGGATGATGCGCGGGAAA00000000 aphyllorchis_montana_mwc ------???????? Limodorum_spp ATTTCTTAAGACTTTTTT----AGTTCTTTTCATTGACA------TAGATACAAGTACTTTGCTAGGATGATGCACGGGAAA00000000 Limodorum_abortivum_0924 ------???????? Epipactis_spp ATTTGTTAAGACTTTTTT----AGTTCCTTTCATTGACA------TAGATACAAGTACTTTGCTAGGATGATGCACGGGAAA10001000 Epipactis ATTTGTTAAGACTTTTTT----AGTTCCTTTCATTGACA------TAGATACAAGTACTTTGCTAGGATGATGCACGGGAAA00?1?000 Listera_smalliigi_AJ409422 ATTTGTTAATACTTTTTT----AGTTTTTTTCATTGACA------TAGATAAAAGTACTTTGCTAGGATGATGCACGGGAAA00000000 Listera_cordata_2580 CTTTGTTAAGACNTTTTTT---AGTTCTTTTCATTGACA------TAGATAAAAGTACGGAACTAGGATGATGAACTTTAAA???????? Neottia_nidus_avis_JVF_trnLF ATTTGTTAAGACTTTTTT----AGTTCTTTTAATTAAAA------???????? Neottia_spp ATTTGTTAAGACTTTTTT----AGTTCTTTTAATTAAAA------TAGATACAAGTACTTTGCTAGGATGATGCAAGGGAA-00000000 Epilyna_jimenzii_ER67 ------00000000 Ellenathus_lancifolius_ER36 ------00000000 sertifera_columbiana_ER38 ------AAGTACTCTGCTAGGATGATTCACGGGAAA00000000 sobralia_crocea_W533 ------AAGTACTCTGCTAGGATGATTCACGGGAAA00000000

Continued

Table A.2 Continued

Sobralia_mucronata_W535 ------AAGTACTCTGCTAGGATGATTCACGGGAAA00100000 Elleanthus_374_e&f ------AAGTACTCTGCTAGGATGATTCACGGGAAA???????? CORYMBORKIS_vert_partial ------???????? Tropidia_effusa_AJ409456 ------AGTTATTTTCATTGACA------TAGATATAAGTACTCTGCTAGGATGATGCACGGGAAA00000000 Tropidia_gram_mwc21775_trnlf ------???????? Xerorchis_O799 ------CTTTTT-----AGTTCTTTTCATTGACA------TAGATAGAAGTGCTCTGCTAGGATGATGCAAGGGAAA00000000 Xerorchis_sp_MWC12601 ------CTTTTT-----AGTTCTTTTCATTGAC------???????? Nervilia_aragoana_AJ409431 ATTTGTTAAGACTTTATTTTT-AGTTCTTTTCATTGACT------TAGATATAAGTATTCGGCTAGGATGATGCACGGGAAA00000000 nervilia_plicata_ER48_trnlf ATTTGTTAAGACTCTCTTTTTTAGTTCTTTTCATTGAC??????????????AAGTACTCGGCTAGGATGAT------??????00 Nervilia_shirenensis_AF519945 ATTTGTTAAGACTCTCTTTTTTAGTTCTTTTCATTGACT------TAGATAGAAGTACTCGGATAGGATGATGCACGGGAAA00000000 Diceratostele_gabonensis_Er40 NTTTGTTAAGACTCTCTNGTNTAGCTCTCTTCATTGAGA------AGCTCGAAGTNCTCGGCNAGGATGATGCACGGGAAC???????? Triphora_amazonica_Emerson_A06 ------CCTTCTTAGTTCTTTTCATTGACATTG-AC-AGATAT-----CTCTGATAGGATGATGCAAGGGAAC00000000 Triphora_trianthophora_ER19A ------TTTATTTTTTAGTTCTTTTCATTGACATTG-AC-AGATATAAW------GATAGGATCAACTAAGGGAAC00100000 Triphora_gentianoides_ER01 ------ACTTTACTTTTTAGTTCTTTTCGTTGACA------AGATATAAA------GATAGGATGATGCAAGGGAA-00100010 Monophyllorchis_sp ATTWGTTAAGACGTTCTTTTTTAGTTCTTTTCATTGACA------AGATAT--GT------00000000 Monophyllorchis_micorstyloides ------???????? Psilochilus_macrophyllus_ER02 ------ACTTTATTTTTTAGTTCTTTTCATTGACATAGGAC-AGATATAAGTACT-TTATAGGATGATGCAAGGGAAA00100100 Psilochilus_modestus_ER65 ------ACTTTATTTTTTAGTTCTTTTCATTGACATAGGAC-AGATATAAGTGGGAATATAGGATGAT------???????? Isochilus_amparoanus_AF266962 ATTTGTTAATATTTTATTTTTTAGTTCTTTTCATTGACAT------AGATATAAGTCCTCTGCTAGGATGATGCACGGGAAA01?00000 Chysis_bractescens_AF266971 ATTTGTTAAGATTTTCTTTTTTAGTTCTTTTCATTGACAT------AGATA-AAGTACTCTGCTAGGATGATGCACGGGAAA00000000 261 Oreorchis_patens ATTTGTTAATATTTTATTTTTGAGTTCTTTTCATTGACAT------AGATA-AAGTACTCTGCTAGGATGATGCACAGGAAA00100000 Cor_trifida_2080 ATTTGTTAATATTTCATTTTTGAGWTCGTCWCAGAGACA------WRG-AWTMWGCTAGGATGATGCACAGGAAA00100000 Calypso_bulbosa_AF519960 ------00000000 Govenia_liliacea_AF519916 ------???????1 Leptotes_bicolor_AF267014 ATTTGTTAATATTTTCTTTTTTAGTTCTTTTCATTGACAT------AAATATAAGTACTTTGCTAGGATGATGCACAGGAAA00000000 Eulophia_sp_o403 ATTTTTTAAGATTTTATTTTTTAGTTCTTTTCATTGAAAG------AAATA-AAGTACTCTGCTAGGATGATGCACGCGAAA00000000 Ponera_striata_AF266965 ATTTGTTAATATTTTCTTTTTTAGTTCTTTTCATTGACAT------AGATCTAAGTCCTCTGCTAGGATGATGCACGGGAAA00000000

Monadenia_bracteata_AJ409430 000000001????00000000000000000000000000000000000100000000000000000000000000000000000000000 Brownleea_coerulea_AF360512_AF360455 ?????????????????????????????????????????????000100000000000000000000000000000000000000000 Codonorchis_lessonii_AJ409387 00000000000000??10???????????0?00010000000000000100000000000000000000100000000000000000000 Coelia_triptera_AF266972 00000000000000000000000000000000000000000000000010000000000000000010??00000000000000000000 Corycium_carnosum_AJ409391 00000000000000???1???????????0?001001?1111101111100000000000000000001000000000000000000000 Goodyera_sp 00010000000000000000000000?100000000000000000000100000000000000000000000000000000000000000 Pterygodium_catholicum_AJ40944 000000000000?1??00?000010?0000000000000000000000100000000000000000000000000000000000000000 Platylepis_polyadenia_AJ544501 00000000000010000010000000?100000000000000000000100000000000000000000000000000000000000000 Palmorchis_Er211_cf_trilobulat 00000000000000000000000000000000000000000000000010000000000000000010??00000000000000000000 Palmorchis_AJ409435 00000000000000000000000000100000000000000000000010000000000000000010??00000000000000000000 palmorchis_silvicola_incomplete ?????????????????????????????????????????????????????????????????????????????????????????? Cephalanthera_damasonium_AJ409 000100000000000000000000000000000000000000000000101?1????????????0?????0?00000000000000000 Aphyllorchis_pall 00000000000000000000000000001000000100000000000010000000000??1???0????00000000000000000000

Continued

Table A.2 Continued

aphyllorchis_montana_mwc ????????????????????????????0000000100000000000010000000000000000010??00000000000000000000 Limodorum_spp 00000000000000000000000000000000000000000000000010000000000000000010??00000000000000000000 Limodorum_abortivum_0924 ???????0????????00?0??0000000000000000000000000010000000000000000010??00000000000000000000 Epipactis_spp 10001100000000000000000000000000000000000000000010000000000?10???0????00000000000000000000 Epipactis 10001100000000000000000000000000000000000000000010000000000?10???0????00000000000000000000 Listera_smalliigi_AJ409422 00000000000000000000000001000000000100000000000011???????????????0??????????????????????0? Listera_cordata_2580 ???00010000000000000000001000000000100000000000011???????????????0??????????????????????0? Neottia_nidus_avis_JVF_trnLF ???????000?1?0000001????0?000000000000000000000000000000000000000010??10?00100000000000001 Neottia_spp 0000000000?1?0000001????0?000000000000000000000000000000000000000010??00000??1000000000001 Epilyna_jimenzii_ER67 00000000000000000000000000000000000000000000000010000000000000000010??00000000000000000000 Ellenathus_lancifolius_ER36 00000000000000000000000000000000000000000000000010000000000000000010??00000000000000000000 sertifera_columbiana_ER38 00000000000000000000000000000000000000000000000010000000000000000010??00000000000000000000 sobralia_crocea_W533 00000000000000000000000000000000000000000000000010000000000000000010??00000000000000000000 Sobralia_mucronata_W535 00000000000000000000000000000000000000000000000010000000000000000010??00000000000000000000 Elleanthus_374_e&f ?????????????????????????????????????????????????????????????????????????????????????????? CORYMBORKIS_vert_partial ???????0000000000000000000000000000000000000000010000010000000000010??00000?10000000000000 Tropidia_effusa_AJ409456 0000000?00000?0??????????????????????????????????????????????????????????????????????????? Tropidia_gram_mwc21775_trnlf ????????????????????????????????????010000000000100000000000000000?1??00000000000000000000 Xerorchis_O799 00000000000000000000110000100000000000000000000010000000000000000010??00000000000000000000 Xerorchis_sp_MWC12601 ???????00000100000001000001000000000000000000000100000000000000010?0??00000000000000000000 262 Nervilia_aragoana_AJ409431 000000000000000000000000000001????????000000000010000000000000000010??00000000000000000000 nervilia_plicata_ER48_trnlf 000000000000000000000000000001????????000000000010000000000000000010??00000000000000000000 Nervilia_shirenensis_AF519945 000000000000000000000000000001????????000000000010000000000000000010??00000000000000000000 Diceratostele_gabonensis_Er40 ?????????????????????????????????????????????????????????????????????????????????????????? Triphora_amazonica_Emerson_A06 000000000000001000000?1?0?001000000000000000000010110101000000100010??00100000000000000000 Triphora_trianthophora_ER19A 000000000010001000000?1?0?000000000000000000000010110101000000100010??00100000000000000000 Triphora_gentianoides_ER01 0000000001?0001000000?1?0?00000000000000000000001011010100000001?0?0??0000000000010010?100 Monophyllorchis_sp 000000000010001000000?1?0?000001000000000000000010000000001000000010??0001????????00000000 Monophyllorchis_micorstyloides ???????1?????????0???????????0?0000000000000000010000000001000000010??00001000000000000000 Psilochilus_macrophyllus_ER02 00000000000000100000000?1??00000000000000000000010000010010000000010??00000???10??01000000 Psilochilus_modestus_ER65 ?1???0000000001000000?1?0?000010000000000000000010000010010000000010??00000????1??0100100? Isochilus_amparoanus_AF266962 00000000000000000000000000000000000000000000000010000000000000000010??00000000000000000000 Chysis_bractescens_AF266971 00000000000000000000000000000000000000000000000010000000000000000010??00000000000000000000 Oreorchis_patens 00000000000000000000000001000000000000000000000010000000000000000010??00000000000000000000 Cor_trifida_2080 00000000000000000000000001000000000000000000000010000000000000000010??00000000000000000000 Calypso_bulbosa_AF519960 00000000000000000000000000000000000000000000000010000000000000000010??00000000000000000000 Govenia_liliacea_AF519916 00000000000000000000000000000010000000000000000010000000000000000010??00000000000000000000 Leptotes_bicolor_AF267014 00000000000000000000000000000000000000000000000010000000000000000010??00000000000000000000 Eulophia_sp_o403 00000000000000000000000000000000000000000000000010000000000000000010??00000000000000000000 Ponera_striata_AF266965 00000000000000000000000000000000000000000000000010000000000000000010??00000000000000000000

Continued

Table A.2 Continued

Monadenia_bracteata_AJ409430 0000000000000010000001?????000000000000000000000000100000000001??0010000000000000000000000 Brownleea_coerulea_AF360512_AF360455 0000000000???1???0?0??????????????????????????0?????????0???0???????0000000000000000000000 Codonorchis_lessonii_AJ409387 00000000000000100000000001?1???????0??0?00??0000000000000000001??0010000000000000000000000 Coelia_triptera_AF266972 0000000000000000000000000000001????0??0?00??0000000000000000001??0010000000000000000000000 Corycium_carnosum_AJ409391 0000000000000010000000001??000000000000000000000000000000000001??0010000000000000000000000 Goodyera_sp 0000000000000010000000001??00000??100?0?00?00000000000000000001??0010000000000000000000000 Pterygodium_catholicum_AJ40944 0000000000000010000000001??0000000000000000000000000000000001???????00?0000000000000000000 Platylepis_polyadenia_AJ544501 0000000000000010000000001??0000000001?0?00?00000000000000000001??0010000000000000000000000 Palmorchis_Er211_cf_trilobulat 000000000000000000000001001000000000000000000000000000000000001??0010000000000000000000000 Palmorchis_AJ409435 0000000000?100000010?000000000001000000000000001000000000000001??0010000000000000000000000 palmorchis_silvicola_incomplete ?????????????0???0?0?0?0000000000000000000000000000000000100001??0000000000000001110000000 Cephalanthera_damasonium_AJ409 000000000000000000000000000000000000000000000000000000000000001??0010000000000000000000000 Aphyllorchis_pall 00000000000000000000000000000000000000000000001??????????????????????????0?000000000000000 aphyllorchis_montana_mwc 00000000000000000000000000000000000000000000001??????????????????????????0?000000000000000 Limodorum_spp 00000000000000000000000000100000000000000000110?????0???1????????????????0?000000000000000 Limodorum_abortivum_0924 00000000000000000000000000100000000000000000110?????0???1????????????????0?000000000000000 Epipactis_spp 000000000000000000000000000000000000000000000000000000000000001??0010000000000000000001011 Epipactis 000000000000000000000000000000000000000000000000000000000000001??0010000000000000000001011 Listera_smalliigi_AJ409422 000000000000000000000000000000000000000000000000000000000000001??0010000000000000000000000 263 Listera_cordata_2580 00000000000000000000101000000000???1??0?00??000000000??10???0???????0000000000000000000000 Neottia_nidus_avis_JVF_trnLF 000000000000000000000000000001000000000101????0?????00000000001??0010010000000000000000000 Neottia_spp 00000000000000000000000000000100000000001?????0?????00000000001??0010010000000000000000000 Epilyna_jimenzii_ER67 000000000000000000000000000000000000000000000001000000000000001??0010000000001000100010000 Ellenathus_lancifolius_ER36 000000000000000000000000000000000000000000000000100000000000001??0010000000010000000000000 sertifera_columbiana_ER38 000000000000000000000000001000000000000000000000100100000000001??0110000000000000000000100 sobralia_crocea_W533 000000000000000000000000000000000000000000000000000100000000001??00100?1000000000000000000 Sobralia_mucronata_W535 000000000000000000000000000000000000000000000000000100000000001??00100?1000000000000000000 Elleanthus_374_e&f ?????????????????????????????????????????????????????????????????????????????????????????? CORYMBORKIS_vert_partial 00000000000000000000?????????????????????????????????????????????????????????????????????? Tropidia_effusa_AJ409456 ?????????????????????????????????????????????????????????????????????????????????????????? Tropidia_gram_mwc21775_trnlf 00000000000000000000000000000000?1000?0000000000000001000000001??0010000000000000000000100 Xerorchis_O799 000000000000000000?1??????????????????????????0?????????0????????????????1?1?0000000000000 Xerorchis_sp_MWC12601 000000000000000001?0??????????????????????????0?????????0????????????????1?1?0000000000000 Nervilia_aragoana_AJ409431 000000000000000010?0?000000000000000011?00???00?00001??00?00001??0011????00000000000000000 nervilia_plicata_ER48_trnlf 000000000000000000000000000000000000011?00???00?00001??00?00001??0010000100000000000000000 Nervilia_shirenensis_AF519945 000000000000000000000000000000000000011?00???00?00001??00?00001??0010000100000000000000000 Diceratostele_gabonensis_Er40 ?????????????????????????????????????????????????????????????????????????00000100000000000 Triphora_amazonica_Emerson_A06 00000001?010000000000000000000000000000000010000001000000000000000010000000000000000000000 Triphora_trianthophora_ER19A 01000001?010000000000000000000000000000000010000000000000000000000010000000000000000000000 Triphora_gentianoides_ER01 00?1?01??0??10???0?0?000001000000000000000010000000000000000000000010000000000000000000000 Monophyllorchis_sp 000000000000000000000000000000000000000000010000000000000000000?11010000000000010000000000 Monophyllorchis_micorstyloides 000000000000000000000000000000000000000000010000000100000000000?11010000001000000000000000

Continued

Table A.2 Continued

Psilochilus_macrophyllus_ER02 00000000000000000000000000000000000000000001000001??00000010010100010000000000000000000000 Psilochilus_modestus_ER65 1?101100110000?1?0?0?00000000000000000000001000001??00000010010100010000000000000000000000 Isochilus_amparoanus_AF266962 000000000000000000000000000000010000000000000000000000000000001??0010000000000000000000000 Chysis_bractescens_AF266971 000000000000000000000000000000000000000000000000000000000000001??00101??000000000000000000 Oreorchis_patens 000000000000000000000000000000000000000000000000000000000000001??0010000000000000000000000 Cor_trifida_2080 000000000000000000000000000000000000000000000000000000000000001??0010000000000000000000000 Calypso_bulbosa_AF519960 000000000000000000000000000000000000000000000000000000000000001??00100000000000000001????? Govenia_liliacea_AF519916 000000000000000000000000000000000000000000000000000000000000001??00100000000000000???????? Leptotes_bicolor_AF267014 000000000000000000000000000000000000000000000000000000000000001??0000000000000000000000000 Eulophia_sp_o403 000000000000000000000000000000000000000000000000000000000000001??0010000000000000000000000 Ponera_striata_AF266965 000000000000000000000000000000000000000000000000000000000000001??0010000000000000000000000 Monadenia_bracteata_AJ409430 000000000001001???????????????????????????0?00????????0101000000000010000000000?1?00000000 Brownleea_coerulea_AF360512_AF360455 00001?????????0???????????????????????????0?00??????01010101100?000011??000?000?1?00000000 Codonorchis_lessonii_AJ409387 010000010001000?1?00???00000001?0000100000000000000000000000000000001000000000010000000000 Coelia_triptera_AF266972 0001000000010000000000000000000000001000000000000000000000000000000010?1000?0000000001001? Corycium_carnosum_AJ409391 000100000001000?1?00???011?00000??1????0110000001001001?001??00?010010000000001?0000000000 Goodyera_sp 010000000001000000000000000000001000100000000000000000000000000000010010000110000000000000

264 Pterygodium_catholicum_AJ40944 000000000?1???0???????????????????????????0?0001??001?0010000000000010000000001?0000000000 Platylepis_polyadenia_AJ544501 010000000001000000000000000000001000100000000000000000000000000000001000000000000000000000 Palmorchis_Er211_cf_trilobulat 0100000000010000000000000000000000001000000100000000000000000000000010?1000?001?0000000100 Palmorchis_AJ409435 0000000000010000000000000000000000001000000000000000000000000000000010?1000?001?0000000100 palmorchis_silvicola_incomplete 0000000000010000000000000000000000001000000000000000000000000000000010?1000?001?0000000100 Cephalanthera_damasonium_AJ409 100000000001000000000000000001??00001000000000000000000000000000000010?1000?001?0000000100 Aphyllorchis_pall 0000000000010000000000000000000100001000000000000000000000000000000010?1000?001?0000000100 aphyllorchis_montana_mwc 000000000001000000000000000001??00001000000000000000000000000000000010?1000?001?0000000100 Limodorum_spp 01000000000100000?10?????????????????????00000000000000000000000000010?1000?001?0000000100 Limodorum_abortivum_0924 01000000000100000?10?????????????????????00000000000000000000000000010?1000?001?0000000100 Epipactis_spp 10000000010?0000000000000000000000001000000000000000000000000000000010????1??01?0000000100 Epipactis 10000000010?0000000000000000000000001000000000000000000000000000000010????1??01?0000000100 Listera_smalliigi_AJ409422 0000000000010000000000000000000000001000000000000?1?000000000000000010?1000?001?0000000100 Listera_cordata_2580 0000000000011000000000000000000000001000000000000?1?000000000000000010?1000?001?0000000100 Neottia_nidus_avis_JVF_trnLF 00000000000100000100?101?001000000001000000000100101000000000000000010?1000?001?00001?0?00 Neottia_spp 00000000000100000100?101?001000000001000000000100101000000000000000010?1000?001?00001?0?00 Epilyna_jimenzii_ER67 0000000000010100000000100000000000000110000000000000000000000000000010?1000?00000000000100 Ellenathus_lancifolius_ER36 0000000000010000000000000000000000000110000000000000000000000000000010?1000?00000000000100 sertifera_columbiana_ER38 0000000000010000000000000000000000000110000000000000000000000000000010?1000?00000000000100 sobralia_crocea_W533 0000000000010000000000000000000000000110000000000000000000000000000010?1000?00000000000100 Sobralia_mucronata_W535 0000000000010000000000000000000000000110000000000000000000000000000010?1000?00000000000100 Elleanthus_374_e&f ?????00000010000000000000000000000000110000000000000000000000000000010?1000?00000000000100 CORYMBORKIS_vert_partial ?????????????????????????????????????????????????????????????????????????????????????????? Tropidia_effusa_AJ409456 ?????0000001000000000000000000000000100000000000000000000000?10?000010?1000?00000000000100

Continued

Table A.2 Continued

Tropidia_gram_mwc21775_trnlf 000100000001010000000000000000000000100000000000000000000000?10?000010?1000?00000000000100 Xerorchis_O799 0001000000010000000000000000000000001000000000000000000000000000001??0?1000?00000000000100 Xerorchis_sp_MWC12601 0001000000010000000000000000000100001000000000000000000000000000001??0?1000?00000000000100 Nervilia_aragoana_AJ409431 0000000000000000000000000010000010001000000010????????????????0?0?0??0???10?00000000000100 nervilia_plicata_ER48_trnlf 00000000000000000000000001?00000000010000000?1????????????????0?0????0?1000?00000000000100 Nervilia_shirenensis_AF519945 00010000000000000000000001?0000000001000000010????????????????0?0?0??0??100?00000000000100 Diceratostele_gabonensis_Er40 00000000000000000000000001?00000000010000?1??0????????????????0?0?0??0?1000?00000000000100 Triphora_amazonica_Emerson_A06 00000000000100000001??????????????????????0?00000000000000000000000010?1000?00000000000100 Triphora_trianthophora_ER19A 00000000100100000001??????????????????????0?00000000000000000000000010?1000?00000100000100 Triphora_gentianoides_ER01 00000000000100000001??????????????????????0?00000000000000000000000010?1000?00000000000100 Monophyllorchis_sp 00000100000100000000000000001???00001000000000000000000000000000000010?1000?00000000000100 Monophyllorchis_micorstyloides 00000000000100000000000000001???0001?0?1?00000000000000000000000000010?1000?01000000000100 Psilochilus_macrophyllus_ER02 00000000000100000000000000000000?10??000010000000000000000000000000010?1000?00000000000100 Psilochilus_modestus_ER65 00000000000100000000000000000000?10??000010000000000000000000001000010?1000?000000000?1??? Isochilus_amparoanus_AF266962 00010000000100000000000000000000000010000000000000000000000000001?????????????????????0?01 Chysis_bractescens_AF266971 001?000000010000000000000000000000001000000000000000000000000000000010?1000?00000000000101 Oreorchis_patens 0001000000010000000000000000000000001000000000000000000000000000000010?1000?00000000000101 Cor_trifida_2080 0001000000010000000000000000000000001000000000000000000000000000000010?1000?00000000000101

265 Calypso_bulbosa_AF519960 ?????????????????????????????????????????????????????????????????????????????????????????? Govenia_liliacea_AF519916 ?????????????????????????????????????????????????????????????????????????????????????????? Leptotes_bicolor_AF267014 0001000000010000000010000000000000001000000000000000000000000000000010?1000?00000010000101 Eulophia_sp_o403 0001000000010000000000000000000000001000000000000000000000000000000010?1000?00000000000101 Ponera_striata_AF266965 000100000001000000000000000000000000100000000000000000000000001?0???????????????00?1000101

Monadenia_bracteata_AJ409430 000000000100000000000000?10000000000000000000000011000?00000000000 Brownleea_coerulea_AF360512_AF360455 00000000011?000000000000?10000000000000000000000001000?00000000000 Codonorchis_lessonii_AJ409387 000000010000000000000000?10000000100000?01????00001000?00000000000 Coelia_triptera_AF266972 000000000100000000000000?10000000000000000000000001000?00000000000 Corycium_carnosum_AJ409391 000000000100?10?0?000000?10000000000000000000000001000?00000000000 Goodyera_sp 000000000000000000000000?100000000?1????00????00001000?00000000011 Pterygodium_catholicum_AJ40944 000000000100000000000000?100??1?0?00000?00??1?01??1000?00000000000 Platylepis_polyadenia_AJ544501 000000000000000000000000?10000000000000000000000001000?00000000010 Palmorchis_Er211_cf_trilobulat 00000001000000000??10000?10000000000000000000001??1000?00000000000 Palmorchis_AJ409435 00000001000000000??10000?10000000000000000000001??1000?00000000000 palmorchis_silvicola_incomplete 00000001000000000??10000?10000000000000000000001?????????????????? Cephalanthera_damasonium_AJ409 00000001000000000?100010??0000000000000000000001??1000?00000000000 Aphyllorchis_pall 000000010000000000000000?10000000000000000000101??1000?00000000000 aphyllorchis_montana_mwc 000000010000000000000000?100?????????????????????????????????????? Limodorum_spp 0001?0010000000000000000?10000000000000000100001??1000?00000000000 Limodorum_abortivum_0924 01????????????????????????????????????????????????????????????????

Continued

Table A.2 Continued

Epipactis_spp 000000010000000?1?000000100000000000000000000001??1000?00000000000 Epipactis 0000000100000000000010?0??0000000000000000000001??1000?00000000000 Listera_smalliigi_AJ409422 0000000100000000000000?1??0?00000000000000000001??1000?00000000000 Listera_cordata_2580 000010010000000000000000?100000000000000000000001?1000?00000000000 Neottia_nidus_avis_JVF_trnLF 0000000?1?????????000000??1?00000000000000010001?????????????????? Neottia_spp 0000000?1?????????000000??1?00000000000000010001??1000?00000000000 Epilyna_jimenzii_ER67 000000010000?????????????????????????????????????????????????????? Ellenathus_lancifolius_ER36 000??????????????????????????????????????????????????????????????? sertifera_columbiana_ER38 00000001000000010000?1???????????????????????????????????000000000 sobralia_crocea_W533 00000001000000010000?1???????????????????????????????????000000000 Sobralia_mucronata_W535 00000001000000010000?1???????????????????????????????????000000000 Elleanthus_374_e&f 00000001000000010000?1???????????????????????????????????000000000 CORYMBORKIS_vert_partial ?????????????????????????????????????????????????????????????????? Tropidia_effusa_AJ409456 000000010000000000000000?1000000000000001?????????1000?00000000000 Tropidia_gram_mwc21775_trnlf 000000010000000000000000?1000000?????????????????????????????????? Xerorchis_O799 000000010000000000000000?10000000000?10?00????1???1000?00000000000 Xerorchis_sp_MWC12601 000000010000000000000000?10000000000?10?00????1??????????????????? Nervilia_aragoana_AJ409431 000000010000100?00000000000000000000000000000000011000?00000000000 nervilia_plicata_ER48_trnlf 001000010000100?00000?0000000000000000000000000000???????0000000?? 266 Nervilia_shirenensis_AF519945 000000010000100?00000000000000000000000000000000001000?00000000000 Diceratostele_gabonensis_Er40 000000010000100?0000000000000000000000000000000000?10???0000000000 Triphora_amazonica_Emerson_A06 00000?1?0?0???1???000000?10100000000??1?00????00000000110?1?000000 Triphora_trianthophora_ER19A 0000010?0?01100?00000000?101100?0010??0?00????0000000011000?1??000 Triphora_gentianoides_ER01 000000010000000000000000?10100010000100?00??0?0000?10???000?1??000 Monophyllorchis_sp 000000010000000000000000?101?10?000000010000000000?10???01000????? Monophyllorchis_micorstyloides 00???????????????????????????????????????????????????????????????? Psilochilus_macrophyllus_ER02 000000010000?10?0?000000?10100001?00?00?00??0?00000000010000010000 Psilochilus_modestus_ER65 ???000010000?10?0?000000?10100001?00?00?00??0?000000000100000000?? Isochilus_amparoanus_AF266962 1?0000010000000000000000?10000000000000000000000000001??0000000000 Chysis_bractescens_AF266971 1?0000010000000000000000?10000000000000000000000000001??1000000000 Oreorchis_patens 1?0000010000000000000000?10000000000000000000000000001??1000000000 Cor_trifida_2080 1?0000010000000000000000?1000000000000000000000000??1????001000000 Calypso_bulbosa_AF519960 ?????????????????????????????????????????????????????????????????? Govenia_liliacea_AF519916 ?????????????????????????????????????????????????????????????????? Leptotes_bicolor_AF267014 1?0000010000000001000000?10000000000000000000000000001??0000000000 Eulophia_sp_o403 1?0000010000000001000000?10000000000000000000000000001??1000000000 Ponera_striata_AF266965 1?0000010000000001000000?10000000000000000000000000001??0000000000

DIMENSIONS ntax=58 NCHAR=2602;[1122 indels coded] DATATYPE = standard GAP = - MISSING = ? symbols="0123456789A#C$EFG.IJ&L%>OPQ/'TU:*X

codonorchis_lessonii_01398 GCGAAGGCA-TCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA corycium_nigrescens_0695 GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA brownleea_caerulea_21870 GCGAAGGCAATCCCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA Altensteinia_palacea_535 GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA Disperis_lindleyana_696 -CGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA Goodyera_pubescens_212 GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA Habenaria_repens_381 GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA Orchis_quadripunctata_545 GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA Pachyplectron_arifolium_529 GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA Spiranthes_cernua_402 GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA Stenoglottis_longifolia_1136 GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA PLAMORCHIS_TRILOBULATA -CGAAGGCAATCTCTCGGATGTTCCCCTAACCCACCCCGGGAACGGACCGTATGGAACCGCATCATGAGGAATGTCCGCGTCTCGTCGCA PALMORCHIS_powellii ------GATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTC-CA Epipactis_helleborine_199 GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA Limodorum_abortivum_nadB CCGAAGGGAATCGGGCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGGCCGCGTCTCGTCGCA Cephalanthera_damasonium_575 GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGVANGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA

267 cepahalanthera_aust_dat115 CCGAAGGCA-TCG-TCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGG-AACCGCA-CATGAGGAATGWCCGCGTCTCGTCGCA Neottia_nidus_avis_JVF GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA Listera_smallii_486 GCGAAGGCAATCGCTCGGMTGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA listera_convol_2707 GCGAACGCCATAGCGCGGATGTTCCCCTA-CCCA-CCCGGGAACGGACCGGATGGAACCGCAACAAG-GGGATGTCCGCGTCTCGTCGCA listera_cordata_JVF2580 CCTCAGGCC-TCTCTCGGATGTTCCCCTAACCCATCCCTGGAACGGACCTCAGGGTACCCCCACAAGTTGAATGACCCCGTCTCCCCTCA aphyllorchis_montana ------CCG-AGCG-GAGGA-TGTCCGCGTCTCGTCGCA corymborkis_vert ------TCCCCTAACCCTACCCGGGAACGGACCGGAGGGAACCGCAGCTTGAGGAATGTCCGCGTCTCGGCGAA Tropidia_Effusia_211 G-GAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA tropidia_cuciculigoides_05560 GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA tropidia_bambusifolia_017721 G-GAAGGCAATCGCTCGGGTGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCA-CATGAGGAATGTCCGCGTCTCGTCGCA sertifera_columbiana TCGAAGGCA-TCGC--GGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA sertifera_sp_N565 TCGAAGGCA-TCGC--GGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA Elleanthus_sp_374_AF314871 GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA Epilyna_jemenzii_w2997 ------EPILYNA_HIRTZII TCTGAGACTCTTGCT---A-GTTCCCCTAACCCGACC-GGGATGGGACCCGATGTTTCCGCTTCATGACATGTGTCCGCGTCTCGTCGCG Sobralia_mucroanta_W535 ------sobralia_crocea GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA XEORCHIS_AMAZONICA_O799 GAGAA------GCTCATATGTTCCCCTGACCCAACCCGGGAAGGGACCGGAGGGAACCTCAGCATGGGGGATGTCCGCGTCTCGTCTCT

Continued

Table A.3. Primitive Epidendroideae analysis. nad1 +gaps molecular matrix.

Table A.3 Continued

Epipogium_aphyllum GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA Nervilia_plicata_ER48 TC-AAGGCA-TCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCATCCTGAGGAATGTCCGCGTCTCGTCGCA Nervilia_shirensis_c280 GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA Gastrodia_sesamoides_534 GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGTTA----CCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA Gastrodia_procera_PARTIAL CCGAATGCC-TCGCTCGCATGTTCCCCT--CCTGACCCGTTTA----CCCGACGGCACCGCCTCATGAGGAATGTCCCCGTCTCGTCGCA gastrodia_sp_reunion_ER214 ------CGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA gastrodia_confusa_0801 GCGAAGG------TCGGATGTTCCCCTAACCCAACCCGGT--C---CCGGAGGGGACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA gastrodia_zyl_16313 GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCC------GGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA diceratostele_gabonensis_ER GCTTAGGCGATCACGCTTATGTTCCCCTACCCCTTCCC-TTAAC---CCTTTAGTACCCTTATCTTGTGGTATGACCACGTCTGCTCTCA Didymoplexis_pallens GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCC------GGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA Psilochilus_macrophyllus_ER02 GCGAAGGCA-TCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAAT-TCCGCGTCTCGTCGCA Psilochilus_LJ6914 ----A------C-CT--GATCA------Triphora_trinathophora GCGAAGGCA-----TCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA Triphora_gentianoides_ER01 GCGAAGGCA-----TCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTACGCGTCTCGTCGCA triphora_amazonica_ER72 GCCAAG----TC-CTCC-ATTTCACCCTTATCCATCCG---AACTAACCGCTCC-ATCC--ACCTTGGGGGATGACCGCGTCTCGTCGCA Monophyllorchis_sp_435 GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA Aplectrum_hyemale_104 GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA Bletilla_striata_556 GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA Isochilus_amparoana_204 GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA 268 Calypso_bulbosa_JF GSGAAGGCAATCGCTCGGATGTTCCMCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA Leptotes_bicolor_1195 GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA ephi_schmidtii_JVF GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA Chysis_bractescens_436 GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCA Coelia_triptera_324 GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGGAACCGCAGCAT-AGGAATGTCCGCGTCTCGTCGCA

codonorchis_lessonii_01398 AGGCGCTTGCGTTTGAGTTTT------GGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGG corycium_nigrescens_0695 AGGCGCTTGCGTTTGAGTTTT------GGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGG brownleea_caerulea_21870 AGGCGCTTGCGTTTGAGTTTT------GGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGG Altensteinia_palacea_535 AGGCGCTTGCGTT-NNGTTTT------GGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGG Disperis_lindleyana_696 AGGCGCTTGCGTTTGAGTTTT------GGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGG Goodyera_pubescens_212 AGGCGCTTGCGTTTGAGTTTT------SGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGG Habenaria_repens_381 AGGCGCTTGCGTTTGAGTTTT------GGGCGGACAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGG Orchis_quadripunctata_545 AGGCGCTTGCGTTTGAGTTTT------GGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGG Pachyplectron_arifolium_529 AGGCGCTTGCGTTTGAGTTT??????????????????CGGGCAGTCCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGG Spiranthes_cernua_402 AGGCGCTTGCGTTTGAG------GCGNNCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGG Stenoglottis_longifolia_1136 AGGCGCTTGCGTTTGAGT------GGCAGTSCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGG PLAMORCHIS_TRILOBULATA AGGCGCTTGCGTTTGATTTTTGGGGGGCGAGCTTTGGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAAG PALMORCHIS_powellii AGGCGCTTGCGTTTGA-TTTTGGGGG-CGAGCTTTGGGCGGGCAGTGCACCCCGGGG------ACAAGGGTCC-TGGTACTACCCAGG Epipactis_helleborine_199 AGGCGCTTGCGTTTGAGTTTTGGG----GAGCTTTGGGCGGGCAGTGCAGTCCGGGGCGGGG--CACAAGGGTCC-TGGTACTACCCAGG

Continued

Table A.3 Continued

Limodorum_abortivum_nadB AGGCGCTTGCGTTTGAGTTTTGGGGGGCGAGCTTTGGGCGGGCAGTGCAGTCCGGGGCGGGG--CACAAGGGTCC-TGGTACTACCCAGG Cephalanthera_damasonium_575 AGGCGCTTGCGTTTGAGTTTTGGGGGNSSAGCTTTGGGCGGGCAGTGCAGTCCGGGGCGGGG--CACAAGGGTCC-TGGTACTACCCAGG cepahalanthera_aust_dat115 AGGCGCTTGCGTTTGAATTTTGGGTGGAGAGCTTTGGGCGGGCAGTGCAG----GGGCGGGG---ACAAGGGTCC-TGGTACTACCCAGG Neottia_nidus_avis_JVF AGGCGCTTGCGTTTGAGTTTTGGGGTCTGA-CTTA--GCG------GGGGCGGGG--CACAAGGGTCA-TGGTACTACCCAGG Listera_smallii_486 AGGCGCTTGCGTTTGAGTTTTGGGGGGCGAGCTTTGGGC----AGTGCAGTCCGGGGCGGGG--CACAAGGGTCC-TGGTACTACCCAGG listera_convol_2707 TGGCGCTTGTGTTTGTCTTTTGGGGGGCGAGCTTT------G---A-TC---GGCGGGGGGCGCAAGGGTCA-TGGTACTACAAAGG listera_cordata_JVF2580 AGGAACTTGCCTTTGAGTTTTGGCAGGCGAGCTTT------CA------CCGGGGCGGGG--CACCCGGGTCC-TGGTACTATCCAGG aphyllorchis_montana GGGCGC-TGCGTTTGAGTTTTGGGGGGCGA-CTTTGGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGG corymborkis_vert GGGCGCTTGCGTTTGAGTTTTGGGTGGTGAGCTTTGGGCGGGCAGTGCAATCC-GGGC------CCCAAGGGTCC-TGGTACTACCCAGG Tropidia_Effusia_211 AGGCGCTTGCGTTTGAGTTTTGGGGGGCGAGCTTTGGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGG tropidia_cuciculigoides_05560 AGGCGCTTGCGTTTGAGTTTTGGGGGGCGAGCTTTGGGCGGGCAGTGCAGTCCGGGG------ACAAGGGTCC-TGGTACTACCCAGG tropidia_bambusifolia_017721 AGGCGCTTGCGTTTGAGTTTTGGGGGGCGAGCTTTGGGCGGGCAGTGCCCTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGG sertifera_columbiana AGGCGCTTGCGTTTGAGTTATGGGGGGCGAGCTTTGGG----CAGTGCAGTCCGGGG------CAAAAGG-TCC-TGGTACTACCCAGG sertifera_sp_N565 AGGCGCTTGCGTTTGAGTTATGGGGGGCGAGCTTTGGG----CAGTGCAGTCCGGGG------CAAAAGG-TCC-TGGTACTACCCAGG Elleanthus_sp_374_AF314871 AGGCGCTTGCGTTTGAGTTTNSSGGGGCGAGCTTTGGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGG Epilyna_jemenzii_w2997 ------EPILYNA_HIRTZII CAGCGCTTGCTCT--AGCTCTGGGGGGCGAGCTTTGGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGG Sobralia_mucroanta_W535 ------sobralia_crocea AGGCGCTTGCGTTTGAGTTTTGGGGGGCGAGCTTTGGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGG XEORCHIS_AMAZONICA_O799 CGGCTCAT---TTT--GT--TGGGGGGC-AGCTTTGGG------CACAAGGGTCC-TGGWACAATCCAGG 269 Epipogium_aphyllum AGGCGCTTGCGTTTGAGTTTTTGGGGGCGAGCTTTGGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGG Nervilia_plicata_ER48 AGGCGCTTGCGTTTGAGTTTTGGGGGGCGAGCTTTGGGCGGGCAGTGCA-TCCGGGG------ACAAGGGTCC-TGGTACTACCCAGG Nervilia_shirensis_c280 AGGCGCTTGCGTTTGAGTTTTTGGGGGCGAGCTTTGGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGG Gastrodia_sesamoides_534 AGGCGCTTRCGTTTGAGTTBSGGGGGGCGAGCTTTGGGCGGGCAGTHCAGTCC------GGGTCC-TGGTACTACCCAGG Gastrodia_procera_PARTIAL AGGCGCTTGCGTTTGAGTTTTGGGTGGCGAGCTTTGGGCGGGAAATGAAGTCC------GGGCCC-TGGTACTACCCACG gastrodia_sp_reunion_ER214 AGGCGCTTGCGTTTGAGTTTTGGGGGGCGAGCTTTGGG------CCGGGGCGGGG--CACAAGGGTCC-TGGTACTATCCAGG gastrodia_confusa_0801 AGG---TTA--TTTGAGTTTTGGGGGGCGAGCTTTGGGCGGGCAGTGCAGTCC------GGGTCC-TGGTACTACCCAGG gastrodia_zyl_16313 AGGCGCTTGCGTTTGAGTTTTGGGGGGCGAGCTTTGGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGG diceratostele_gabonensis_ER CAGAACTTA--ATCGAGCTCTGGGGGGCGAGCTTTGGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGG Didymoplexis_pallens AGGCGCTTGCGTTTGAGTTTTGGGGGGCGAGCTTTGGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGG Psilochilus_macrophyllus_ER02 AGGCGCTTGCG------GG-GGGCGAGCTTTGGGCGGGC--TGAACTCCGGGG------CACAAGGG-----GGTACTACCCAGG Psilochilus_LJ6914 ------A--ATCGAGCTC------GAGCTTTGGGCGGGC--TGAACTCCGGGG------TACAACAC-CCCTGGTACTACCTTGG Triphora_trinathophora AGGCA----CGTTTGAG----GG--GGCGAGCTTTGGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGG Triphora_gentianoides_ER01 AGGCGCTTGCGTTTGAG----GG-GGGCGAGCTG-GAGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCCC-GGTACTACCCAGG triphora_amazonica_ER72 AGGCACTAGCGTTTGAG----GG-AGACGAGTTTT-----GGCA-TGTAGTACGGGG------AA---TAA--GG----ACCCTGG Monophyllorchis_sp_435 AGGCGCTTGCG???????TTTGGGGGGCGAGCTTTGGGCGGGCAGTGCAGTCCGGGG------CACAAGGSTCC-TGGTACTACCCAGG Aplectrum_hyemale_104 AGGCGCTTGCGTTTGASTTTT------GGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGG Bletilla_striata_556 AGGCGCTTGCGTTTGAGTTTTGGGGGGCGAGCTTTGGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGG Isochilus_amparoana_204 AGGCGCTTGCGTTTGAGTTTTGGGGGGCGAGCTTTGGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGG Calypso_bulbosa_JF AGGCGCTTGCGTTTGAGTTTNNGNGGG-GAGCTTTGGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGG Leptotes_bicolor_1195 AGGCGCTTGCGTTTGAGTTTTGGGGGGCGAGCTTTGGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGG ephi_schmidtii_JVF AGGCGCTTGCATTTGAGTTTTGGG------GGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGG Chysis_bractescens_436 AGGCGCTTGCGTTTGAGTTTTGGGGGGCGAGCTTTGGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGG Coelia_triptera_324 AGGCGCTTGCGTTTGAGTTTNSGGGGGCGAGCTTTGGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGG

Continued

Table A.3 Continued

codonorchis_lessonii_01398 TGCGAAGAACCCCGGAGGTGACTTCAATGAGATAAATTGAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT corycium_nigrescens_0695 TGCGAAGAACCCCGGAGGTTACTTCAATGAGATAAATTGAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT brownleea_caerulea_21870 TGCGAAGAACCCCGGAGGTTACTTCAATGAGATAAATTGAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT Altensteinia_palacea_535 TGTGAAGAACCCCGGAGGTTACTTCAATGAGAGAAATTGAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGASCAAGGGAT Disperis_lindleyana_696 TGCGAAGAACCCCGGAGGTTACTTCAATGAGATAAATTGAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT Goodyera_pubescens_212 TGCGAAGAACCCCGGAGGTTACTTCAATGAGAGAAATTGAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT Habenaria_repens_381 TGCGAAGAACCCCGGAGGTGACTTCAATGAGATAAATTGAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT Orchis_quadripunctata_545 TGCGAAGAACCCCGGAGGTTACTTCAATGAGATAAATTGAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTSAGAGCAAGGGAT Pachyplectron_arifolium_529 TGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAAATTGAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTKAGAGCAAGGGAT Spiranthes_cernua_402 TGCGAAGAACCCCGGAGGCGAGTTC--GGAGAGAAATTGAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT Stenoglottis_longifolia_1136 TGCGAAGAACCCCGGAGCTTACTTCAATGAGATAAATTGAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT PLAMORCHIS_TRILOBULATA TGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAAATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT PALMORCHIS_powellii TGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAAATTTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT Epipactis_helleborine_199 TGCGAAGAACCCCGGAGG-GACTTCAATGAGAGAAATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT Limodorum_abortivum_nadB TGCGAAGAACCCCGGAGGTGACTTC-ATGA-A-AAATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT Cephalanthera_damasonium_575 TGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAAATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT cepahalanthera_aust_dat115 TGCGAA-AACCCCGGAGGTGACTTCAATGAGAGAAATGTC-CTCACTGGCCTAAACGAC-AGCAAACACTC-AACGTGAGAGCAAGGGAT

270 Neottia_nidus_avis_JVF TGCGAAGAACCCCGGAGGTGACTGAAATTAGAGAAATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT Listera_smallii_486 TGCGAAGAACCCCGGAGGTGACTTAAATTAGAGAAATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT listera_convol_2707 TGTGAATATCCCC-TAGGTGACTTCTTTTAGAAAAATGTCACTCACTGGCCTATGCGACGAGCATG-ACTCGAACGTGA-ATCTAGGGAT listera_cordata_JVF2580 TGCCAAGAACCC-GGAGGTGACTTCAATTACAAAAATGTTTCTCACTGGCCTATACAACGAGCAAACACTCGAACGTGAGACCAAGGGAT aphyllorchis_montana TGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAAATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT corymborkis_vert TGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAAATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT Tropidia_Effusia_211 TGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAAATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT tropidia_cuciculigoides_05560 TGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAAATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT tropidia_bambusifolia_017721 TGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAAATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT sertifera_columbiana TGCGAAGAACCCCGGAGGTGACTTCAATGAGATAAATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT sertifera_sp_N565 TGCGAAGAACCCCGGAGGTGACTTCAATGAGATAAATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT Elleanthus_sp_374_AF314871 TGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAAATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT Epilyna_jemenzii_w2997 ------EPILYNA_HIRTZII TGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAAATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT Sobralia_mucroanta_W535 ------sobralia_crocea TGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAAATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT XEORCHIS_AMAZONICA_O799 TGCGAAGAACCCCGGAGGTGACTGCAATGAGAGAAATATAACTCACCGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT Epipogium_aphyllum TGCGAAGAACCCCGGAGG------ATTAGAGAAATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT Nervilia_plicata_ER48 TGCGAAGAACCCCGGAGGTGACTTCAATTAGAGAAATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT Nervilia_shirensis_c280 TGCGAAGAACCCCGGAGG------ATTAGAGAAATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT Gastrodia_sesamoides_534 TGCGAATAACCCCGGAGGCG----C--GGAGA----KGTAACTAACTGGCCTAAACGACGAAAAAACACTCGAACGTTAGACCAAGGGAT Gastrodia_procera_PARTIAL TGCCAATAACCCCGGTGGCG----C--GGAGA----TGTAACTAACTGGCCTAAACGACGAAAAAACACTCGAACGTGAGAGCAAGGGAT gastrodia_sp_reunion_ER214 TGCGAAGAACCCCGGAGGTGACTTCAATTAGAGAAATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT gastrodia_confusa_0801 TGCGAAGAACCCCGGAGGC------AATGTAACTCACTGGCCTAAACGACGAAAAAACACTCGAACGTGAGAGCAAGGGAT

Continued

Table A.3 Continued

gastrodia_zyl_16313 TGCGAATAACCC------AATGAGAGAAATGTAACTCACTGGCCTAAACGACGAACAAACACTCGAACGTGAGAGCAAGGGAT diceratostele_gabonensis_ER TGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAAATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT Didymoplexis_pallens TGCGAATAACCC------AATGAGAGAAATGTAACTCACTGGCCTAAACGACGAACAAACACTCGAACGTGAGAGCAAGGGAT Psilochilus_macrophyllus_ER02 TGCGAAGAATCCCGGTGGCGACTT------GAGAAATGTCACTCACTGGCCTAAACGACGAGCAAACATTCAAACGTGAGAGCAAGGGAT Psilochilus_LJ6914 TGCGAAGAATCCCGGTGGCGACTTCAA---GAGAAATGTCACTCACTGGCCTAAACGACCAACAAACATTCAAACGTGAGAGCAAGGGAT Triphora_trinathophora TGCGAATAACCCCGGAGGTGACTTCAATGAGAGAAATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT Triphora_gentianoides_ER01 TGCGAATAAACCCGGAGGTTACTTCAATGAGAGAAATGTCACTCACTGGCCTAAACGACGAG----CACTCGAACGTGAGAGCAAGGGAT triphora_amazonica_ER72 TGAGGCTGGACCCGGA------Monophyllorchis_sp_435 TGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAAATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTBAGAGCAAGGGAT Aplectrum_hyemale_104 TGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAAATGTAACTCACTGGCCTAAACGACGAACAAACACTCGAACGTGAGAGCAAGGGAT Bletilla_striata_556 TGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAAATTTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTNAGAGCAAGGGAT Isochilus_amparoana_204 TGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAAATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT Calypso_bulbosa_JF TGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAAATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT Leptotes_bicolor_1195 TGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAAATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTKAGAGCAAGGGAT ephi_schmidtii_JVF TGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAAATGTAACTCACTGGCCTAAACGACGAGCAAACACTCTAACGTGAGAGCAAGGGAT Chysis_bractescens_436 TGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAAATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT Coelia_triptera_324 TGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAAATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGAT

271 codonorchis_lessonii_01398 CACCAAACGAATGGACGAGCTCCAAGGAGGTAGGAGAAAGGGGGGC-AAGAACCATGCTTT----CATAGATGACATATTTTCACTCTGA corycium_nigrescens_0695 CACCAAACGAATGGACGAGCT--AATGAGGTAGGAGAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATGACATATTTTCACTCTGA brownleea_caerulea_21870 CACCAAACGAATGGACGAGCG--AATGAGGTAGGAGAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATTACATATTTTCACTCTGA Altensteinia_palacea_535 CACCAAACGAATGGACGAGCTCCAAGGAGGTAGGAGAAAGGGGGGC-AAGAACCATGCTTT----CATAGATGACATATTTGAACTCTTC Disperis_lindleyana_696 CACCAAACGAATGGACGAGCG--AAGGAGGTAGGAGAAAGGG------GAACCATGCTTT----CAGAGATGACATATTTTCACTCTGA Goodyera_pubescens_212 CACCAAACGAATGGACGAGCTCCAAGGAGGTAGGAGAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATGACATATTTBCACTCTGA Habenaria_repens_381 CACCAAA-GGA-----GAGCG--AAGGAGGTAGGAGAAAGGG------GAACCATGCTTT----CAGAGA----AGATTTGAACTCTGA Orchis_quadripunctata_545 CACCAAACGAATGGACGAGCG--AA---GGTAGGAGAAAGGSGGGC-AAGAACCATGCTTT----CAGAGATGACATATTTTCACTCTGA Pachyplectron_arifolium_529 CACCAAACGAATGGACGAGCTCCAAGGAGGTAGGAGAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATGACATATTTTCACTCTGA Spiranthes_cernua_402 CACCAAACGAATGGACGAGCTCCAAGGAGGTAGGAGAAAGGGGGGC-AAGAACCATGCTT------GAGATGACATATTTGAACTCTGA Stenoglottis_longifolia_1136 CACCAAACGAATGGACGAGCG--AAGGAGGTAGGAGAAAGGG------GAACCATGCTTT----CATAGATGACAGATTTTCAC----- PLAMORCHIS_TRILOBULATA CACCAAACGAATGGACGAGCTCCAAGGAGGGAGGAGAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATTACATATTTTCACTCTGA PALMORCHIS_powellii CACCAAAC-AATGGACGAGCTCCA-GGAGGGAGGAGAAAGGGGGGC-AAGAACCATGCTTT----CA-AGATTACATATTTTCACTCTGA Epipactis_helleborine_199 CACCAAACGAATGGCCGAGCTCCAAGGAGGGAGGAGAAAGGGGGGC-AATAACCATGCTTT----CAGAGATGACATATTTTCACTCTGA Limodorum_abortivum_nadB CACCAAAC-AATGGCC-AGCTCCAAGGAGG-AGGA-AAAGGGGGGC-AATAACCCTGCTTT----CAAA--TGAC-----TGAACTCTGA Cephalanthera_damasonium_575 CACCAAACGAATGGCCGAGCTCCAAGGAGGGAGGAGAAAGGGGGGC-AATAACCATGCTTT----CAGAGATGACATATCT-CACTCTGA cepahalanthera_aust_dat115 CACCAAACGAATGGC--AACTCC--GGAGGGAGGAGAAAGGGGGGC-AATAACCATGCTTT----CAAA--TGACAT-TTTTC-CTCTGA Neottia_nidus_avis_JVF CACCAAACGAATGGCCGAGCTCCAAGGAGGGAGGAGAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATGACAGATTTGAACTAGGA Listera_smallii_486 CACCAAACGAATGGACGAGCTCCAAGGAGGGAGGAGAAAGGGGGGC-AATAACCATGCTTT----CAGAGATTACCTATTTTAACTCTGA listera_convol_2707 CACCAAACGAATGGAATTCTTCCG-GGAGGCTAGAGAAAGGGGGGCCA-TAACCATGCTTT----CTAAAATTACATATTTTCACTCTGA listera_cordata_JVF2580 CACCCAACTTATGGAAAAACTCCAAGGAGGGAG------GCTTT----CCGAGATTACATATTTTCCCAATGA aphyllorchis_montana CACCAAACGAATGGACGAGCTCCAAGGAGGGAGGAGAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATTACATATTTTCACTCTGA corymborkis_vert CACCAAACGAATGGACGAGCTCCAAGGAGGGAGGAGAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATTACATATTTTCACTCTGA Continued

Table A.3 Continued

Tropidia_Effusia_211 CACCAAACGAATGGACGAGCTCCAAGGAGGGAGGAGAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATTACATATTTTCACTCTGA tropidia_cuciculigoides_05560 CACCAAACGAATGGACGAGCTCCAAGGAGGGAGGAGAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATTACATATTTTCACTCTGA tropidia_bambusifolia_017721 CACCAAACGAATGGACGAGCTCCAAGGAGGGAGGAGAAAGGGGGGC-AAGAACCATGCTTT----CA-AGATTACATATTTTCACTCTGA sertifera_columbiana CACCAAACGAATGGACGAGCTCCAAGGAGGGAGGAGAAAGGGGGGC-AAGAACCATGCTTG----AAGAGATTACAGATTTGAACTATGA sertifera_sp_N565 CACCAAACGAATGGACGAGCTCCAAGGAGGGAGGAGAAAGGGGGGC-AAGAACCATGCTTG----AAGAGATTACAGATTTGAACTATGA

Elleanthus_sp_374_AF314871 CACCAVACGAATGGACGAGCTCCAAGGAGGGAGGAGAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATTACATATTTTCACTCTGA Epilyna_jemenzii_w2997 ------EPILYNA_HIRTZII CACCAAACGAATGGACGAGCTCCAAGGAGGGAGGAGAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATTACATATTTTCACTCTGA Sobralia_mucroanta_W535 ------sobralia_crocea CACCAAACGAATGGACGAGCTCCAAGGAGGGAGGAGAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATTACATATTTTCACTCTGA XEORCHIS_AMAZONICA_O799 CACCCGACAAATGGACCAGTTCT--GAA------GA--GTG------AGAATCATGCTTT----CAAAGA---CAT---TTCGGTC-CT Epipogium_aphyllum CACCAAACGAATGGACGAGCTCCAAGGAGGGAGGAGAAAGG------CCATGCTTG-ATG------ACATCTTTTCACTCTGA Nervilia_plicata_ER48 CACCAAACGAATGGACGAGCTCCAAGGAGGGAGGAGAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATTACATCTTTTCACTCTGA Nervilia_shirensis_c280 CACCAAACGAATGGACGAGCTCCAAGGAGGGAGGAGAAAGG------CCATGCTTG-ATG------ACATCTTTTCACTCTGA Gastrodia_sesamoides_534 CACCAAACGAATGGACGAGCTCCAAGGA------GG----C------CCGTGC--GAATGCTAAG-GTCCATATTTGAACTCTGA Gastrodia_procera_PARTIAL CACCAAACGAATGGACGAGCTCCAAGGA------GG----C------CCGTGC--GAATGCTAAG-TTCCATATTTGAACTATTA gastrodia_sp_reunion_ER214 CACCCAACGAATGGTCGAGCACCGAGGAGGGAGGAGAAAGGGGGG--AA------TTCCATATTTGAACTCTGA gastrodia_confusa_0801 CACCAAACGAATG------CTCCAAGGAGGGAGGGGCTCTTGGAG---AGAG--ATG---GAA------TTCCATATTTGAACTCTGA 272 gastrodia_zyl_16313 CACCAAACGAATGGACGAGCTCCAA------GGGGGG---A---CCCTGCTGTAAT--AGA--TTACATA-TTGAACTTTGA diceratostele_gabonensis_ER CACCAAACGAATGGACGAGCTCCAAGGAGGGAGGAGAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATGACATATTTTCACTCTGA Didymoplexis_pallens CACCAAACGAATGGACGAGCTCCAA------GGGGGG------CC-TGCTGTAAT----AGATTACATA-TTGAACTTTGA Psilochilus_macrophyllus_ER02 CACCAAACGAATGG-CGAGCTCCAAGGAGGGAGGAGAAAGG----C-AAGAACCATGCTTT----CA-AGATGACGTATATGA--TTGGA Psilochilus_LJ6914 CACCAAACGAATGG-CGAGCTCCAAGGAGGGAGGAGAAAGG----C-AAGAACCATGCTTT----CAGAGATGACATATATGA--TTGGA Triphora_trinathophora CACCCAACGAATGGA--A---CC---GA---AGG-----GGT---CC--GAA---T-CGT-----C-----TT-CG------TGA Triphora_gentianoides_ER01 CACCCAACGAATGGACGAG------GGT---CCAA-A----T-CGT-----C-----TTGTCT-TCCTCA-TTTGA triphora_amazonica_ER72 ------Monophyllorchis_sp_435 CACCAAACGAATGGACGAGC-----GGAGGGAGGAGAAAGG----C-AAGA------TTT----CAGAGATTACATATTTTCAC----- Aplectrum_hyemale_104 CACCAAACGAATGGACGAGCTCCAAGGAGGGAGGAGAAAGGGGG-C-AAGAACCATGCTTT----CAGAGATTACATATTTTCACTCTGA Bletilla_striata_556 CACCAAACGAATGGACGAGCTCCAAGGAGGGAGGAGAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATTACATATTTGCACTCTGA Isochilus_amparoana_204 CACCAAACGAATGGACGAGCTCCAAGGAGGGAGGAGAAAGGGGG------Calypso_bulbosa_JF CACCAAACGAATGGACGAGCTCCAAGGAGGGAGGAGAAAGGGGG-C-AAGAACTATGCTTT----CAGAGATTACATATTTKCACTCTGA Leptotes_bicolor_1195 CACCAAACGAATGGACGRGCTCCAAGGAGGGAGGAGAAAGGGGG-C-AAGAACCATGCTTT----CAGAGATTACATATTTTCACTCTKA ephi_schmidtii_JVF CACCAAACGAATGGACGAGCTCCAAGGAGGGAGGAGAAAGGGGG-C-AAGAACCATGATTT----CAGAGATTACATATTTTCACTCTGA Chysis_bractescens_436 CACCAAACGAATGGACGAGCTCCAAGGAGGGAGGAGAAAGGGGG-C-AAGAACCATGCTTT----CAGAGATTACATATTTTCACTCTGA Coelia_triptera_324 CACCAAACGAATGGACGAGCTCCAAGGAGGGAGGAGAAAGGGGG-C-AAGAACCATGCTTT----CAGAGATTACATATTTTCACTCTGA

Continued

Table A.3 Continued

codonorchis_lessonii_01398 ACTGCGATAATAACTGACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGA corycium_nigrescens_0695 ACTGCGATAAGAACTTACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGG------GCCAAGCCCAGAATGTATGGGTGA brownleea_caerulea_21870 ACTGCGATAAGAACTTACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGA Altensteinia_palacea_535 ACTGCGATAATAACTGACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGG----A-----CCA-G-AAAGAATGTATGGGTGA Disperis_lindleyana_696 ACTGCGATAATAGCTGACT------CCTCCA----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGA Goodyera_pubescens_212 ACTGCGAGAAGAACTGACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGA Habenaria_repens_381 ACTGCGATAAGAACTGACTAAGCCGTGCCTCCA----GG-----TTCTCCACACGG------TAA-CCCA-----TATGGGTGA Orchis_quadripunctata_545 ACTGCGATAAGAACTGACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGG------TCA-CCCA-----TATGGGTGA Pachyplectron_arifolium_529 ACTGCGAGAAGAACTGACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGA Spiranthes_cernua_402 ACTGCGATAATAACTGACTCAGCCGTGCCTCCT----GGGGGCATTCTCCACACGGG----A-----CCA-G-AAAGAATGTATGGGTGA Stenoglottis_longifolia_1136 -----GRTAAGAACTGACTCAGCCGTGCCTACA----GGGGGCATTCTCCACAC------A--CCC----TG-ATGGGTGA PLAMORCHIS_TRILOBULATA ACTGCGATAATAACTGACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGATTGTATGGGTGA PALMORCHIS_powellii ACTGCGATAATAACTGACTCA-CCGTGCCTCCA----GGGGGCATTCTCCACACGGG----ACGGGGC-AA-CCCA-AATG-ATGGGTGA Epipactis_helleborine_199 ACTGCAAAAATCACTGACTCAGCCGTGCCTCCC----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGA Limodorum_abortivum_nadB AC------ACTGACTCAGCCG-GCCTCCA----GGGGGCATTC??????????????????????????????????????????? Cephalanthera_damasonium_575 AC-----TAATCACTGACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCAAGAATGTATGGGTGA cepahalanthera_aust_dat115 -C-----TAATCACTGACTCA-CCGTGC-TCC-----GGATGC-TTCTCCA-ACGGG----ACGGGGCCAA-CCAAAA-TGTA-GGGT-A Neottia_nidus_avis_JVF A-----A-AAGAACTGACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGGTGGGACGGGGCCAAGCC------GGGTGA Listera_smallii_486 ACTGCAAAAAGAACTGACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGGCGGGACGGGGCCAAGCC------GGGTGA 273 listera_convol_2707 ACT--GATAAAAACTGACTCAGCCGTGCCTC-A----GGGGGCATTCTCCA-ACGGGCGGGACGGGTCCAA-CC------GGTTGA listera_cordata_JVF2580 GCTGCAAAAAGAACTGACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGGCGGGACGGGGGCAAGCC------GGGTGA aphyllorchis_montana ACCGCGAGAATAACTTACTCAGCCGTGCCTCC-----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGA corymborkis_vert ACCGCGAGAATAACTTACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGA Tropidia_Effusia_211 ACTGCGAGAATAACTTACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGA tropidia_cuciculigoides_05560 ACCGCGAGAATAACTTACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCA-AATGTATGGGTGA tropidia_bambusifolia_017721 ACTGCGAGAATAACTTACTCA-CCGTGCCTCCA----GGAGGCATTCTCCACACGGG----ACGGGGCCAAGCCCA-AATGTATGGGTGA sertifera_columbiana ACTGCGAGAAGAACTTACTCAGCCGTGCCTCCA----GG-----TTCTCCACACGGG----ACGGGGCCAAGCCC--AATGTATGGGTGA sertifera_sp_N565 ACTGCGAGAAGAACTTACTCAGCCGTGCCTCCA----GG-----TTCTCCACACGGG----ACGGGGCCAAGCCC--AATGTATGGGTGA Elleanthus_sp_374_AF314871 ACTGCGAGAATAACTGACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGA Epilyna_jemenzii_w2997 ------EPILYNA_HIRTZII ACTGCGAGAATAACTGACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGA Sobralia_mucroanta_W535 ------GTATGGGTGA sobralia_crocea ACTGCGAGAATAACTGACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGA XEORCHIS_AMAZONICA_O799 A--GCGAAAAAGACTGACTC-GCCGCTATAACA------C-T-----A-A------ACGGG---AAAC--AGTTTGT-TGGGTGA Epipogium_aphyllum AC-----GAAGAA------CC-GGGCGGGGGCATTCTCCACAC------ACGG------CCAGAATGTATGGGTGA Nervilia_plicata_ER48 ACTGCGAGAATAACTGACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGA Nervilia_shirensis_c280 AC-----GAAGAA------CC-GGGCGGGGGCATTCTCCACAC------ACGG------CCAGAATGTATGGGTGA Gastrodia_sesamoides_534 ACTGCGAGAATAACTGACTAAGCCGTGCCTCCA----GGGGG------ACGGG------AATGTCTGGGTGA Gastrodia_procera_PARTIAL ACTGCGAGAATAACTGACTAAGCCGTGCCTCCA----GGGGG------ACGGG------AATGTCTGGGTGA gastrodia_sp_reunion_ER214 ACTGCGAGAATAACTGA-TAAGCCGTGCCTCCAGGGCGG------ACGGGG------AATGTATGGGTGA gastrodia_confusa_0801 ACTGCGAGAATAACTGACTAAGCCGTGCCTCCAGGGCGG------ACGGGG------AATGTATGGGTGA gastrodia_zyl_16313 ACTGCGAGAATAACTGACTAAGCCGTGCCTCCA---CGGGG-AATTCTCCACACGGG------CC--GCCCAGAATGTATGGGTGA

Continued

Table A.3 Continued

diceratostele_gabonensis_ER AC-----GAATAACTTACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCA-AATGTATGGGTGA Didymoplexis_pallens ACTGCGAGAATAACTGACTAAGCCGTGCCTCCA---CGGGG-CATTCTCCACACGGG------CC--GCCCAGAATGTATGGGTGA Psilochilus_macrophyllus_ER02 AC---GAGAATCACTGACTAAGCCGTGCCTCC-----GGGGGCATTCTCCCCACGGG----ACGGGGCCAAGCCC-AAATGTATGGGTGA Psilochilus_LJ6914 AC---GAGAATCACTGACTAAGCCGTGCCTCCA----GGGGG-ATTCTCCCCACGGG----ACGGGGCCAAGCCCATAATGTATGGGTGA Triphora_trinathophora AC---GAG------GACTAAGCC---CC------GGT--CATTCTC-----G------ACGGGGCC------GA-TGT-TGGGTGA Triphora_gentianoides_ER01 AC---GAG------GACTAAGCC---C------GGTC-CATTCTCCA---GGG----ACGACGGCGGGCC--GA-TGT-TGGGTGA triphora_amazonica_ER72 ------Monophyllorchis_sp_435 -----GAGAATAACTKACTCAGACGT---TCC-----GGGG-CATTCTCCACACGGG----ACGGGGGCAAGCCCAGAATGTATCGGTSA Aplectrum_hyemale_104 ACTGCGAGAATAACTGACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGA Bletilla_striata_556 ACTGCGAGAATAACTGACTCAGCCGTGCCTCCA----GGGGGCATTCTCCAAACGGG------CCAAGCC-----TGTATGGGTGA Isochilus_amparoana_204 ------CATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGA Calypso_bulbosa_JF ACTGCGATAATAACTGACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGA Leptotes_bicolor_1195 ACTKCGAGAATAACTGACTYAGCCGTGC-TCCA----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGA ephi_schmidtii_JVF ACTGCGAGAATAACTGACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGA Chysis_bractescens_436 ACTGCGAGAATAACTGACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGG----RCGGGGCCAAGCCCAGANTGTATGGGTGA Coelia_triptera_324 ACTGCGAGAATAACTGACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGA

codonorchis_lessonii_01398 CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAG

274 corycium_nigrescens_0695 CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAG brownleea_caerulea_21870 CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAG Altensteinia_palacea_535 CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGGAG Disperis_lindleyana_696 CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAG Goodyera_pubescens_212 CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAG Habenaria_repens_381 CAGATCGGCCATAGGGATACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAG Orchis_quadripunctata_545 CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAG Pachyplectron_arifolium_529 CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAG Spiranthes_cernua_402 CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAG Stenoglottis_longifolia_1136 CAGATCGGSCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCCTTTTCATTTCGTGGAAG PLAMORCHIS_TRILOBULATA CAGATCGGCTATACGGGTACTACGGGGTATACACCAGGGCAC-GCA-TGTCGAGCATACGACGATGCCGCCCGTGTTCTTTTCCTGGAAG PALMORCHIS_powellii CAGATC-GCCATAGGG-TACTCCGGGATA--CACCAG--CAA-CAA-TGTC-AGC--ATCACGATGCC-CCCGTTTTCATTTC--GGAAA Epipactis_helleborine_199 CAGATCGGCCATAGGGGTACTCCGGGGTATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAG Limodorum_abortivum_nadB ????????????????????????????????????????????????????????????????TGCCGCCCGTTTTCATCTCACG-AAG Cephalanthera_damasonium_575 CAGATCGGCCATAGGGGTACTCCGGGGTATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAG cepahalanthera_aust_dat115 CA-ATCG-CC-TAGGG--AC-CCGGG-TTT---CC------CMYACGACGATGCCGCCCGTTTTCATTTCGTGGAAG Neottia_nidus_avis_JVF CAGATCAGCCATAGGGGTACTCCGGGGTATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAG Listera_smallii_486 CAGATCGGCCATAGGGGTACTCCGGGGTATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAG listera_convol_2707 CA-ATCAGACATAAGG-TACTCCGGGGTATACACCAGGTAAA-CGATTGTCAAGAATACCTCTATGCTTCCAGTTTTCATTTCGTG-AAG listera_cordata_JVF2580 CACATCGGCCATTGGGGTGCTCCGGGGTATACACCCGGGCAA-CAAATGTCGAGAATGC-ATCACATCCGCCGTTTTCATTTCGTGTAAG aphyllorchis_montana CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATAC-ACGATCCCGCCCGTTTTCATTTCGTG-AAG corymborkis_vert CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAA-TGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAG Tropidia_Effusia_211 CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAG

Continued

Table A.3 Continued

tropidia_cuciculigoides_05560 CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACAACGATGCCGCCCGTTTTCATTTCGTGGAAA tropidia_bambusifolia_017721 CA-ATCGGCCATAGGG-TACTCCGGGATATACACCAGGGCAA-CAAATGTC-AACATACGACGATACCGCCCGTTTTCATTTCG-GGAAT sertifera_columbiana CAGATCGGCCATAGGG-TACTCCGGGATATAC-CCAG--CAA-CAAATGTC-AGC-TACGA---TGCCGCCCGTTTTCATTT----GAAG sertifera_sp_N565 CAGATCGGCCATAGGG-TACTCCGGGATATAC-CCAG--CAA-CAAATGTC-AGC-TACGA---TGCCGCCCGTTTTCATTT----GAAG Elleanthus_sp_374_AF314871 CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAG Epilyna_jemenzii_w2997 ------EPILYNA_HIRTZII CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCAAACAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAG Sobralia_mucroanta_W535 CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAG sobralia_crocea CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAG XEORCHIS_AMAZONICA_O799 CATATCGGCCATATGATTACTCCGGGATATA-----GGGCAA-CCA--GTTGAGCATACGACAATGCCCCCCGTTTTCATTTCATGGAA- Epipogium_aphyllum CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAG Nervilia_plicata_ER48 CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAG Nervilia_shirensis_c280 CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCA------Gastrodia_sesamoides_534 CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-AAAAGGTCGAGCATATGACGATGCCGCCCGTTTTCCTTTCGTGGAAG Gastrodia_procera_PARTIAL CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-AAAAGGTCGAGCATATGACGATGCCGCCCGTTTTCCTTTCGTG-ACK gastrodia_sp_reunion_ER214 CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-AAAATGTCGAGCATATGACGATGCCGCCCGTTTTCCTTTCGTGGAAG gastrodia_confusa_0801 CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-AAAATGTCGAGCATATGACGATGCCGCCCGTTTTCCTTTCGTGGAAG gastrodia_zyl_16313 CAGATCGGCCATAGGGGTACTCCGGGA------CCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAA-

275 diceratostele_gabonensis_ER CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTC--GGAAT Didymoplexis_pallens CAGATCGGCCATAGGGGTACTCCGGG------ACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAA- Psilochilus_macrophyllus_ER02 CAGATCGGCCATAAGGGTACTCCGGGATATACACCAGGGCA--CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAG Psilochilus_LJ6914 CA-ATCGGCCATAGGGGTACTCCGGGATATAC-CCAGG-CA--CAA-TGTCGAGCAT-CGACGATGCCGCCCGTTTTCATTTCGTGGAAG Triphora_trinathophora CAGATCGGCCATACCAG-ACTCCGGGATAGACACCAGGGCAA-CAAATGTCGAGCATAC-ACGATGCCGCCCGTTTTCATTTCGTGGAAG Triphora_gentianoides_ER01 CAGATCGGCCATAGGAGTACTCCGGGATA-ACACCAGG-CAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTC-TTTC-TGGAA- triphora_amazonica_ER72 ------Monophyllorchis_sp_435 CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAG Aplectrum_hyemale_104 CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAG Bletilla_striata_556 CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAG Isochilus_amparoana_204 CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAG Calypso_bulbosa_JF CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAG Leptotes_bicolor_1195 CAGATCGGCCATAGGGGTACTCCGGGGTATACATCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAG ephi_schmidtii_JVF CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAG Chysis_bractescens_436 CAGATCGGCCATAGGGGTMCTCCGGGWTATHCACCAGGGCAV-CAAATGTCGAGCATACGACGATGCCGBCCGTTTTCATTTCGTGGAAG Coelia_triptera_324 CAGATCGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAG

codonorchis_lessonii_01398 TCCCCGGCAGAGGAAAGGGCTGTAGGTGA----GCGTTCTGCTTCTTAGGGCGCA-AA--ATCGTGACTCTGGGG----TCGTGCGTGGC corycium_nigrescens_0695 TCCCCGGCAGAGGAAAGGGCTGTAGGTGA----GCGTTYTGCTTCTTAGGGCGCATAA--AT-GTGACTCTGGGG----TCGTGCGTGGC brownleea_caerulea_21870 TCCCCGGCAGAGGAAAGGGCTGTAGGTGA----GCGTTCTGCTTCTTAGGGCGCATAA--ATCGTGACTCTGGGG----TCGTGCGTGGC Altensteinia_palacea_535 TCCCCGGCAGAGGAAAGGGCTGTAGGTGA----GCGTTCTGCTTATTAGGGCGCATAA--ATCGTGACTCTGGGG----TCGTGCGTGGC Disperis_lindleyana_696 TCCCCGGCAGAGGAAAGGGCTGTAGGTGA----GCGTTCTGCTTCTTAGGGCGCAGAA--ATCATGACTCTGG------Goodyera_pubescens_212 TCCCCGGCAGAGGAAAGGGCTGTAGGTGA----GCCTTCTGCTTATTAGGGCGCATAA--ATCGTGACTCTGGGG----TCGTGCGTGGC

Continued

Table A.3 Continued

Habenaria_repens_381 TCCCCGGCAGAGGAAAGGGCTGTAGGTGA----GCGTTCTGCTTCTTAGGGCGCATAA--ATCGTGACTCTGGGG----TCGT-----GC Orchis_quadripunctata_545 TCCCCGGCAGAGGAAAGGGCTGTAGGTGA----GCGTTCTGCTTCTTAGGGCGCATAA--ATCGTGACTCTGGGG----TCGTGCGTGGC Pachyplectron_arifolium_529 TCCCCGGCAGAGGAAAGGGCTGTAGGTGA----GCGTTCTGCTTATTAGGGCGCATAA--ATCGTGACTCTGGGG----TCGTGCGTGGC Spiranthes_cernua_402 TCCCCGGCAGAGGAAAGGGCTGTAGGTGA----GCGTTCTGCTTATG-GGGCGCATAA--ATCGTGACTCTGGGG----TCGTGCGTGGC Stenoglottis_longifolia_1136 TCCCCGGCAGAGGAAAGGGCTGTAGGTGA----GCGTTCTGCTTCTTAGGG-----AA--ATCGTGACTCTGGGG----TCGTGCGTGGC PLAMORCHIS_TRILOBULATA TCCCCGGGGGAGGAATGGGCTGTATGTGA-GGTGCGTTCTGCTTCTTAGG-CGCAGA----TTGTTCCTAT------TC-T--G---C PALMORCHIS_powellii T-CCCGGCA-AG-AAAGGGCTGAAGG-GATGGCGCGTTCTGCTTCTTAGG-CGCAGAA--ATCGTTCCTATGGGG----TCGTGCGTGGC Epipactis_helleborine_199 TCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCTTAGGGCGCAGAA--A------GGGG----TCGTGCG--GC Limodorum_abortivum_nadB TCCCCG------GGGCGG--AA---TCGGCTGTAT------GTGCGTGGG Cephalanthera_damasonium_575 TCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCT-GGGGCGCAGAA--ATCGTTCCTATGGGTGGGGTCGTGCGTGGC cepahalanthera_aust_dat115 TCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCTTAGGGCGCAGAA--ATCGTTCCTATGGGTGGGGTCGTGCGTGGC Neottia_nidus_avis_JVF TCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTT-TGCTTCTTAGGGCGCATAA--ATCGTTCC-----G-GGGGTCGTGCGTGGC Listera_smallii_486 TCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCTTAGGGCGCAGAA--ATCGTACCTCTGGGTGGGGTCGTGCGTGGC listera_convol_2707 TGCCCTCTAAAAGAAAGGACTG-AAGTGATGGCCCTTTCTGCTTCTT------TCGT---TGGC listera_cordata_JVF2580 TCCCCAGCACAGGAAAGGGCTGGACGTGATGGGACGTTCTGCTTCTTATGGCRCTCAA--ATCGTA-CTC------TC-T-C-TGGC aphyllorchis_montana TCCCCGGCCGAG-AAAGAGATGTAGGTGATGGATCGTTCTGCTTCTTACGGAGGAAAA---TCGTTCCTTTCG-G----TCGTGCGTGGG corymborkis_vert TCCCCGGCAGAGGAAAGGGCTGTAG-TGATGGCGCGTTCTGCTTCTTAGGGAGCAAAA---TCRTTCCTT-GG-G----TCGTGCGTGGC Tropidia_Effusia_211 TACCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCTTAGGGCGCATAA--ATCGTTCCTATGG-G----TCGTGCGTAGC tropidia_cuciculigoides_05560 TCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGC-CGTTCTGCTTCTTAGGGCGCATAA--ATCGTTCCTATGG-G----TCGTGCGTGGC tropidia_bambusifolia_017721 TCCCCGGCAAAGGAAAGGGCTGTAG-TGATGGGGT-TTCTGCTTCTTAGG-CGCAAAA--ATCGTTCCC--GG-A----TC-TGCGTGGC 276 sertifera_columbiana TCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCGCAGGGCGCATAA--ATCGTTCCTATGG-G----TCGTGCG---- sertifera_sp_N565 TCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCGCAGGGCGCATAA--ATCGTTCCTATGG-G----TCGTGCG---- Elleanthus_sp_374_AF314871 TCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCTTAGGGCGCAGAA--ATCGTTCCTATGG-G----TCGTGCG---- Epilyna_jemenzii_w2997 ------EPILYNA_HIRTZII TCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCTTAGG-CGCAGAA--ATCGTTCCTATGG-G----TCGTGCG---- Sobralia_mucroanta_W535 TCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCTTAGGGCGCATAA--ATCGTTCCTATGG-G----TCGTGCG---- sobralia_crocea TCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCTTAGGGCGCATAA--ATCGTTCCTATGG-G----TCGTGCG---- XEORCHIS_AMAZONICA_O799 TCCCAGGCAGAG-A--GGGCTGTAGATGATGGCGCGTTCATCTTCTT------G----TCGTGAGGA-- Epipogium_aphyllum TCCCCGGCAGAGGAAAGGGCTGTAGG--A-----CGTTC-GG-TCT------TTCCTA-GG-G------Nervilia_plicata_ER48 TCCCCGGCAGAGGAAAGGGCTGTATGTGATGGCGCGTTCTGCTTCTTAGGG------TCGTTCCTAT------Nervilia_shirensis_c280 ------Gastrodia_sesamoides_534 TCCCCGGCAGAGGAAAGGGCTGTAGGTGAT----CGTTCTGC---TTAGGGCGCATAAGCATAAT-CCTATGG-G----TCGTGCGTGGC Gastrodia_procera_PARTIAL TCCCCGGCGGAGGAAAGG-CTGTATGTCATG-C---T-CGAC--CTT-TG-CGCATAAGCATA-TC--AAT-G------TC-T--G---C gastrodia_sp_reunion_ER214 TCCCCGGCAGAGGAAAGGGCTGTAGGTTTT-----GTTCTTCTTCTTATA-T---TAAGCTTA-T---TAAGG-G------GC gastrodia_confusa_0801 TCCCCGGCAGAGGAAAGGGCTGTAGGTTTT------TTCTTT--CT-ATA-TAGA-AA---TCGTTCCTATGG-G----TCGTGCGTGGC gastrodia_zyl_16313 TCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGTGTTCTACTTCTGAT--T-GA-AA---TCGTTCCTATGG-G----TCGT--GTGGC diceratostele_gabonensis_ER TCCCCGGCA-AG-AAAGGGCTG-AGGGGATGGCCCGT-CTGCTTCTTAGG-CGCA-AA--ATCGT-CCTAT-G-G----TCGG--G-GGC Didymoplexis_pallens TCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGTGTTCTACTTCT--GATTG-A-AA---TCGTTCCTATGG-G----TCGT--GTGGC Psilochilus_macrophyllus_ER02 TCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCTTAGGGCGCAGAA--ATTGTTCC----G-G----TCGTGCGTGGC Psilochilus_LJ6914 TCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCTTAGGGCGCAGAA--ATTGTTCC----G-G----TCGTGCGTGGC Triphora_trinathophora TCCCCGGCGGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTATAA------AAAA--AT-G----TATGG-G----TCCT------Triphora_gentianoides_ER01 -CCCCGGCA-AGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCTTA------TCT---CTA-GG-G----TCCTGCGCGGG

Continued

Table A.3 Continued

triphora_amazonica_ER72 ------GG-G------Monophyllorchis_sp_435 TTCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCTTAGGGCGCATAA--ATCGTTCC---GG-G----TCGTGCGTGGC Aplectrum_hyemale_104 TCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCTTAGGGCGCAGAA--ATCGTTCCTATGG-G----TCGTGCGTGGC Bletilla_striata_556 TCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCTTAGGGCGCAGAA--ATCGTTCCTATGG-G----TCGTGCGTBGC Isochilus_amparoana_204 TCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCTTAGGGCGCAGAA--ATCGTTCCTATGG-G----TCGTGCGTCGC Calypso_bulbosa_JF TCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCTGAGGGCGCATAA--ATCGTTCCTATGG-G----TCGTGCGTGGC Leptotes_bicolor_1195 TCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCTTAGGGCGCAGAA--ATTGTTCCTATGG-G----TCGTAGTCGGC ephi_schmidtii_JVF TCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTATTAGGGCGCATAA--ATCGTTCCTATGG-G----TCGTGCGTGGC Chysis_bractescens_436 TCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCTTAGGGCGCAGAA--ATCGTACCTCTGG-AGGGGTCGTGCGTGGC Coelia_triptera_324 TCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCTTAGGGCGCAGAA--ATCGTTCCTATGG-G----TCGTGCGTGGC

codonorchis_lessonii_01398 ACTGGTATAGATGATGAAAGGCGG------CCGGGACCTC-T-C--T-TGAAGAGGCGGCAAGCAAGAAGAGGAAAGGG------TTAT corycium_nigrescens_0695 ACTGGTATAGATGATGAAAGGCTTACTTGAGCCGGGACCTATT-T--T-TGAAGAGGCGGCAAGCAAGAAGAGGAAAGGG------TGAT brownleea_caerulea_21870 ACTGGTATATATGATGAAAGGCGGGCTTGAGCCGGGACCTCTT-C--T-TG----GCCGGCA-GCAAGAA-A------GGCTGAT Altensteinia_palacea_535 ACTGGTATAGATGAGGAAAGGCGGGCTTGA-CCGGGTACTCTT-TG-TGTGAAGA---GGCAAGCAAGAATAGGAAAGGGGGCGGCTGAT Disperis_lindleyana_696 ----GTATAGATGATGAAAGGCGGGCTTGA-CCGGGACCTCTT-CT---TGAAGAGGCGGCAAGCAAGAAGAGGAAAGGCG------Goodyera_pubescens_212 ACTGGTATAGATGATGAAAGGCGGGCTTGA-CCGGGACCTCTT-CT---TGAATAGGCGGCAAGCAAGAATAGGAAAGGGGGCGGCTGAT Habenaria_repens_381 ACTGGTATAGATGATGAAA-----GCTTGA-CCGGGACCTCTT-CA---AGAAGAGGCAGCAAGCAAGAAGAGG------CGGCTGAG Orchis_quadripunctata_545 ACTGGTATAGATGATGAAAGGCGGGCTTGA-CCGGGACCTCTT-CT---TGAAGAGGCGGCAAGCAAGAAGAGGAAAGGC------TGAT Pachyplectron_arifolium_529 ACTGGTATAGATGATGAAAGGCGGGCTTGA-CCGGGACCTATT-CT---TGAATAGGCGGCAAGCAAGAATAGGAAAGGGGGCGGCTGAT 277 Spiranthes_cernua_402 ATTGGTATAGATGATGAAAGGCGGGCTTGA-CCGGGACCTCTT-CT---TGAATAGGCGGCAAGCAAGAAT------GGGCGGCTGAT Stenoglottis_longifolia_1136 ACTGGTATAGATGATGAAAGGCGGGCTTGA-CCGG-ACCTCTT-CT---TG-AGAGGCGGCAAGCAAGAAGAG------PLAMORCHIS_TRILOBULATA ACTGGTATAGATGATGAAAGGCGGGCTTGAACC---ACCTATT-CTCTT--AATAG-CCACA--CAAGAATAGGAAAGGGGGCGGCTGAT PALMORCHIS_powellii ACTGGTATAGATGATGAAAGGCGGGCTTGAACCGGGACCTATT-CTCTT--AATAGGCGGCAAGCAAGAATAGGAAAGGGGGCGGCTGAT Epipactis_helleborine_199 ACTGGTATAGATGATGAAAGGCGGG------GGACCTATT-CTCTT--AATAGGCGGCAAGCAATAATAGGAAAGGGGGCGGCTGAT Limodorum_abortivum_nadB GCTGG-ATAGATGATGAAAGG-GGGCTTGAACCGGGACCTATT-CTC--A-AA-AGGCGG-AAGCAATAATAGGAAAGGG--CGGGCG-- Cephalanthera_damasonium_575 ACTGGTATAGATGATGAAAGGCGGGCTTGAACCGGGACCTATT-CTCTTATAATAGGCGGCAAGCAATAATAGGAAAGGGGGCGGG---- cepahalanthera_aust_dat115 ACTGGTATAGATGATGAAAGGCGGGCTTGAACCGGGACCTATT-CTCTTATAATAGGCGGCAAGCAATAATAGGAAAGGGGGCGGCTGAT Neottia_nidus_avis_JVF ACTGGTATAGAT------GGG------GGGACCTATT-CTATTATAATAGGCGGCAAGCAAGAATAGGAAAGGTTACGAA-G-T Listera_smallii_486 ACTGGTATAGATGATGAAAGGCGGGCTTGAACCGGGACCTATT-CTCTT--AATAGGCGGCAAGCAATAATAGGAAAGGGGGCGGCTGAT listera_convol_2707 ACTGGTTTAAATGATGAAAGGCGGGCTGGAACCAGGATCTATT-CTCTTATAA--G----TTTTTAATAGWAGRAAWKGRGGCRGKTGAT listera_cordata_JVF2580 ACTGGCCGAGATG--GAA---CGGGCTTT--CCGGG----CTT-GCCTT--AATAGGC--TAAACAA----AGGAGA-----C------aphyllorchis_montana ACTGGT-GAGATGATGAA-GGGGGGCTTGAACAGGC-CCCCTT-TT-TT-TAATAGGCAGCAAA-AA-----GGAAAGGGGG-GGGTGAT corymborkis_vert ACTGGTATA-ATGATGAATGGCGGGCTTGAACCGGGACT-ATT-CTCTTATAAAAGGCGGCAAGCAAGAATAGGAAAGGGG-CGGYTGAT Tropidia_Effusia_211 ACTGGTATAGATGATGAAAGGCGGGTTTGAACCGGGACCTATT-CTCTTATAAGAGGCGGCAAGCAAGAATAGGAAAGGGGGCGGCTGAT tropidia_cuciculigoides_05560 ACTGGTATAGATGATGAAAGG-GGGCTTGA-CCGGGACCTATTTCTCTT-TAAGA-GCGGCAAGCAAGAATAGGAAAGGGG-CGGGTGAT tropidia_bambusifolia_017721 ACTGGTATAGATGATGAAAGGCGGGCTTGAACCCGGACTC-TT-CTCTTATAAGAGGCGGCAAGCAAGAAGAGGAAAAGGGGCGGCTGAT sertifera_columbiana ACTGGTATAGATGATGAAAGGCGGGCTTGAACCGGGACCTATT-CTCTTATAAAAAGCGGCAAGCAAG------sertifera_sp_N565 ACTGGTATAGATGATGAAAGGCGGGCTTGAACCGGGACCTATT-CTCTTATAAAAAGCGGCAAGCAAGAAT------Elleanthus_sp_374_AF314871 ACTGGTATAGATGATGAAAGGCGGGCTTGAACCGGGACCTATT-CTCTTATAATAGGCGGCAAGCAAGAATAGGAAAGGGGGCGGCTGAT Epilyna_jemenzii_w2997 ------

Continued

Table A.3 Continued

EPILYNA_HIRTZII ACTGGTATAGATGATGAAAGGCGGGCTTGAACCGGGACCTATT-CTCTTAT-ATAGGCGGCAAGCAAGATTAGGAAAGGGGGCGGCTGA- Sobralia_mucroanta_W535 ACTGGTATAGATGATGAAAGGCGGGCTTGAACCGGGACCTATT-CTCTTATAATAGGCGGCAAGCAAGAATAGGAAAGGGGGCGGCTGAT sobralia_crocea ACTGGTATAGATGATGAAAGGCGGGCTTGAACCGGGACCTATT-CTCTTATAATAGGCGGCAAGCAAGAATAGGAAAGGGGGCGGCTGAT XEORCHIS_AMAZONICA_O799 -A------T----AT------G--CCG-TATCTAAT-CTTTTATA-AAGGG--CAAGCATGAGTGGGAAAACGCATTTCT-CC Epipogium_aphyllum -TTGGTCTAG------CTTGAA--GGGGCCTATT-CTCTGAT------Nervilia_plicata_ER48 -CTGGTATAAAT-ATGAAA---GGG-TTGAAC-GGGAC-TATT---TTTATAATA-GCGG-AAGCA--AA--G-AA-GGGG-TGG-TGAT Nervilia_shirensis_c280 ------Gastrodia_sesamoides_534 ACTGGTATAGATGATGAAAGGCG---T----C-GGGACCTATT-CT--GAT------GGCAAGCAAGAATA------Gastrodia_procera_PARTIAL ACTGGTATAGATGATGAAAGGCG---T----C-GGGACCTATT-CT--GAT------GGAAAGCAAGAATAG------CTTCTG-- gastrodia_sp_reunion_ER214 ACTGGT-T-GA--ATGA-----G--CTT-AA--CTCACCT----CT--TC-AAAA-----CCTAC------gastrodia_confusa_0801 ACTGGTATAGATGATGAAA------TT-AA-----TTCTAT--CT-TTCTAAATGGAGGCAAGCAAGAATAG------gastrodia_zyl_16313 ACTGGTATAGATGATGAA-GG-T------AAAGGGCTTCTA---CTCTTCT-ATTGGCGGCAAGCAAGAATAGGAAATGGAA------diceratostele_gabonensis_ER ACTGGT-TA-ATGATGAAAGG--GGCTTGA-C-GG-ACTTATT--T---AT-ATA--AGGAAAG---G-CTAAGAAA------Didymoplexis_pallens ACTGGTATAGATGATGAA----GGGAATGTACCGG------TT-CT---ACA-TAGGCGGCAAGCAAGAATAGGAAA------TG-- Psilochilus_macrophyllus_ER02 ACTGGTATAGATGA-GAAAGGCAGGCTTGAAC-GGGACCTATT-CTCTTATAATAGGCGGCAAGCAAGAATAGGAAAGGGGGCGACTGAT Psilochilus_LJ6914 ACTGGTATAGATGA-GAAAGGCAGGCTTGAAC-GGGACCTATT-CTATTATAATAGGCGG-AAGCAAGAATAGGAAAGGGGGCGACTGAT Triphora_trinathophora ------AT------TGGG--TG--C-GGGACCTA-T-CTATTATAATAG-CGT----C-AGA------Triphora_gentianoides_ER01 A--GGT-T--ATGATGAAR--TGGG--TG------GGYGSMAARCAAGAAWAGGAA-GG---CGA----- triphora_amazonica_ER72 ------Monophyllorchis_sp_435 ACTGGTATAGATGATGAAAGACAGG----A-CCGGGACCTATT-CTCTTATAATAGGCGGCAAGCAAGAATAGGAAAGGGGGCGACTGAT 278 Aplectrum_hyemale_104 ACTGGTATAGATGATGAAAGGCGGGCTTGAACCGAGACCTATT-CTCTTAT-A-AGGCGGCAAGCAAGAATAGGAAAGGGGGCGGCTGAT Bletilla_striata_556 ACTGGTATAGATGATGAAAGGCGGGCTTTAACCGGGACCTATT-CTCTTATAA-AGGCGGCAAGCAATAATAGGAAAGGGGGCGGCTGAT Isochilus_amparoana_204 ACTGGTATAGATGATGAAAGGTGGGCTTGAACCGGGACCTATT-CTCTTCTAA-AGGCGGCAAGCAAGAATAGGAAAGGGGGCGGCTGAT Calypso_bulbosa_JF ACTGGTATAGATGATGAGAGGCGGGCTTGAACCGGGACCTATT-CTGTTATAA-AGGCGGCAAGCAAGAGTAGGAAAGGGGGCGGCTGAT Leptotes_bicolor_1195 A------AA----C--C---C-----TA------ephi_schmidtii_JVF ACTGGTATA-ATGATGAAAGGCGGGCTTGAACC-GGACCTATT-CTCTTATAATAAGCGGCAAGCAAGAATAAGAAAGGGGGCGGCCTAT Chysis_bractescens_436 ACTGGTATAGATGATGAAAGGCGGGCTTGAACCGGGACCTATT-CTCTT--AA-AGGCGGCAAGCAATAATAGGAAAGGGGGCGGCTGAT Coelia_triptera_324 ACTGGTATATATGATGAAAGGCGGGCTTGAACCGGGACCTATT-CTCTTATAA-AGGCGGCAAGCAAGAATAGGAAAGGGGGCGGCTGAT

codonorchis_lessonii_01398 GAGTGCCTTTTTAG--AAAAA------GGGTGGAATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGA----CGGGACGGA corycium_nigrescens_0695 GAGTGCCTTT--AG--AAAAA------GGGTTGG-TTTT------C------GCC------CGCC----- brownleea_caerulea_21870 GAGTGCCTTTT-AG--AAAAA------GGGTTTAATGTGGAGCTAACCTGGCTACAAGTCTAGCCAAAGAAAGA----CGGGACGGA Altensteinia_palacea_535 GAGTGGCTT------CT--CTA------Disperis_lindleyana_696 GA----CTTT--AG--AAAAA------GGGTTGAATGTGGAGCTAACCTGGCTACAAGTCTAGCCAAAGAAAGA----CGGGACGGA Goodyera_pubescens_212 GAGTGCCTTTTTAG--AAAAA------GGGTTGAATGTCGAGCTAACCTGGCTACAAGTCTAGC-AAAGAAAGA----CGGGACGGA Habenaria_repens_381 GAGTGCCSSCBTAG--AAAAA------GGGTTG------Orchis_quadripunctata_545 GAGTGCCTTTTTAG--AAAAA------GGGTTG------Pachyplectron_arifolium_529 GAGTGCCTTTTTAT--AAAAA------GGGTTGAATGTGGAGCTAACCTGGCTACAAGTCTAGCCAAAGCAAGA----CGGGACGGA Spiranthes_cernua_402 GAGTGGCTTCTTAG------GAATGTGGA-CTTTTC-----ATAAGTCTAGCCAAAGAAAGA------A--GA Stenoglottis_longifolia_1136 ------PLAMORCHIS_TRILOBULATA GA-TGCCTTTTTA--CATAAA-TAGAAAAAGGGTTGAATGTGGAGCTAACCTGGCTACAA?????????????????????????????? PALMORCHIS_powellii GAGTGCCTTTTTAGTCATAAA-TAGAAAAAGGGTTGAATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGA

Continued

Table A.3 Continued

Epipactis_helleborine_199 GAGTGCCTTTTTAGTCAGAAA-TAGAAAAAGGGTGGAATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGA Limodorum_abortivum_nadB -----CC------GAAAA--GGCTATGGGTG-AATGT----C-AA-ATCACTTGGTCTCGACTGAAAG-----GAGAGGTGA---- Cephalanthera_damasonium_575 -AGTGCCTTTTTAGTCATAAA-TAGAAAAAGGGTGGAATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGA cepahalanthera_aust_dat115 GAGTGCCTTTTTAGTCCTAAA-TAGAAAAAGGGTGGAATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGA Neottia_nidus_avis_JVF GAGTGCCC------GAAAA-GG----A------Listera_smallii_486 GAGTGCCTTTTTAGTCCTAAA-TAGAAAAAGGGTGGAATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGA listera_convol_2707 KWASTSCTTTTTMGTC-RTAW-WTGGWAAAGGGTGGAATGGGWGMTWTACCTGG-TACAAGTATAGGCAAAGAAAGCGAAA------listera_cordata_JVF2580 ----GCCTTTT----C-GAA----GAAA-----TTGA-TGT------CCTG-CTACAA-TAATGCCAT-GACACC-AAA-G------aphyllorchis_montana G------TTTTTA-TCAGAAA--A-AAAAAGG-T--AATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGA corymborkis_vert GRA----TTTTTA-TCAAAAA-TAAAAAAAGGGTTGAATGKGGAG-TAACCTGGCTMCAA------AAAGAAAGAGAGATGGGACGGA Tropidia_Effusia_211 GAGTGCCTTTTTAGTCAGAAA-GAGAAAAAGGGTTGAATGT----CTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGA tropidia_cuciculigoides_05560 GAGT---TTT--AATCAGAAA-TAGAAAAAGGGTTGAATGTGGAGCTAACCTGGT-AC------AAAGAAAGAGAGATGGGACGGA tropidia_bambusifolia_017721 GAGTGCCTTTT-AGTCAGAAA-GAGAAAAAGGGTTGAATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGA sertifera_columbiana ------sertifera_sp_N565 ------TT------Elleanthus_sp_374_AF314871 GAGTGCCTTTTTAGTAAGAAA-TAGAAAAAGGGTTGAATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGA Epilyna_jemenzii_w2997 ------EPILYNA_HIRTZII GAGTGCCTTTTTA-T-AGAAA-TAAAAAA-GGGTTTAATGTGGAG-TCACCTGG-TACCAGTAT-GCCAA-GAAAGAGAGACGGGACGGA Sobralia_mucroanta_W535 GAGTGCCTTTTTAGTAAGAAA-GAGAAAAAGGGTTGAATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGA sobralia_crocea GAGTGCCTTTTTAGTAAGAAA-GAGAAAAAGGGTTGAATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGA 279 XEORCHIS_AMAZONICA_O799 -AATGCGTTAGCAGT---AAA-TCGAACTCGG---GAA--TGGAGTT-----GGCTTC--GT------GAAAAACACAA-GG- Epipogium_aphyllum ------GGT------TGGC-ACA------Nervilia_plicata_ER48 GA-TGC-TTTTTA-TA-TAAA-TAAAAAA-GGGTTGAATGTG-A--TAA--TGGT------Nervilia_shirensis_c280 ------Gastrodia_sesamoides_534 ----GC-TTCTGAGTCA------TGGTTGAATGTGGAGCTAACCTGGCTACTTGTA--GCCAAAGAAAGG------Gastrodia_procera_PARTIAL ------AGTCA------TGGTTTAATGTGGAGCTAACCTGGCTACTTGTA--GCCAAAGAAAGG------gastrodia_sp_reunion_ER214 ------GGTGGAT-TAACCTGGA-GCCA-TCTAGCCAAAGAAAGAGAGACGG------gastrodia_confusa_0801 -----C-TTCT-AGTCA------TGGTTGAATGTGGAGCTAACCTGGA-GCCA-TCTAGCCAAAGAAAGAGAGACGG------gastrodia_zyl_16313 ------TCAAAAA------GGGTGGAA------TGGCTACAAGTATAGCCAA-GAAAGA-AGACGGGAC--- diceratostele_gabonensis_ER ----GCCTTTTTAGTCATAAAATAGAAAAAGGGTTGAATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGA Didymoplexis_pallens ------GTC------GAAAAAGGGTGGAA------TGGCTACAAGTATAGCCAAAGAAAGAGA------Psilochilus_macrophyllus_ER02 GAGTGCG-----AGTCAGAAA-GAGAAAAAGG--CGAA-GTGG-----ACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGA Psilochilus_LJ6914 GAGTGCG-----AGTCAGAAA-GAGAAAAAGG--CGAA-GTGG-----ACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGA Triphora_trinathophora --GTGC-T----AGTCATAAA-GAGAAAAAGGGTGG--TGTGGAGCTCACCTGG-TACAAGTATA-CCA------GAGACGGGACGGA Triphora_gentianoides_ER01 RAR----TGTTTA-TCAMAAA-G------GTTGAATGTGGARCTCMCCTGGCTTCAAGTATAGCCAAAGAAAGAGAGAGGGGACGGA triphora_amazonica_ER72 ------A-AAGTA------Monophyllorchis_sp_435 GAGTGCCTTTTTAGTCAGAAA-GAGAAAAAGGGTTGAATGTGGAGCTCACCTGGCTACAAGTATAGCAAAAGAAAGAGAGACGGGACGGA Aplectrum_hyemale_104 GAGTGCCTTTTTAGTCAGAAA-TAGAAAAAGGGTTGAATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGA Bletilla_striata_556 GAGTGCCTTTTTAGTCATAAA-TATAAAAAGGGTTTAATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGA Isochilus_amparoana_204 GAGTGCCTTTTTAGTCAGAAA-TAGRAAAAGGGTTGAATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGA Calypso_bulbosa_JF GAGTGCCTTTKTAGTCATAAA-TAGAAAAAGGGTTGAATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGA Leptotes_bicolor_1195 ----GCCTTTTT------AGAAAAAGGGTTGAATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGA

Continued

Table A.3 Continued

ephi_schmidtii_JVF RAGTGCCTTTTT-GTWRTMAWAWAKAAAAAGGKTG-AATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGA Chysis_bractescens_436 GAGTGCCTTTTTAGTCCTAAA-TAGRAAAAGGGTGGAATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGA Coelia_triptera_324 GAGTGCCTTTTTAGTCATAAA-TAGAAAAAGGGTTGAATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGA

codonorchis_lessonii_01398 CTGTAAGAGGCCGCAGCGGGACGACCAGAGGAAAGCCCGCCCCCGCTAGCTAACATAGTATTCTCGGTGCGCATATTCTAGATTGAGAAT corycium_nigrescens_0695 ------brownleea_caerulea_21870 CTGTAAGAGGCCGCAGCGGGACGACCAGAGGAAAGCCCGCCCCCGCTAGCTAACATA-TATTCTCGGTGCGCATATTATCTATTTAGAAG Altensteinia_palacea_535 ------GGGGCAA-GGG------Disperis_lindleyana_696 CTGTAAGAGGCCGCAGCGGGACGACCAGAGGAAAGCCCGCCCCCGCTAGCTAACATAGTATTCTCGGTGCGCATATTCTCTATTTAGAAG Goodyera_pubescens_212 CTGTAAGACGCCGCAGCGGGACGACCAGAGGAAA----GCCCCCGCTAGCTAACATAGTATTCTCGGTGCGCATATTCTCTCTGTAGAAT Habenaria_repens_381 ------Orchis_quadripunctata_545 ------Pachyplectron_arifolium_529 CTGTAAGAGGCCGCAGCGGGACGACCAGAGGAAAGCCCGCCCCCGCTAGCTCACATAGTATTCTCGGTGCGCATATTCTCTCTTTAGAAT Spiranthes_cernua_402 CTGTAAGAGGCCGCAGCGGGACGACCAGAGG----C--GCCCCCGTTAGCTCACATAGTATTCTCGGTGCGCATATTCTCTATTGCGAAG Stenoglottis_longifolia_1136 ------PLAMORCHIS_TRILOBULATA ?????????????????????????????????????????????????????????????????????????????????????????? PALMORCHIS_powellii CTGTCAGAGGCCGCAGCGGGACGACCAGAGGAAAGCCCGCCCCCGCTAGCTAACATAGTATTCTCGGTGCGCATATTCTCTCTTTATAAT Epipactis_helleborine_199 CTTTCAGAGGCCGCAGCGGGACGACCAGAGGAAAGCCCGCCCCCGCTAGC------AG-ATTCTCGGTGCGCATATTCTCTCTTTAGAAT Limodorum_abortivum_nadB -T------GAAAG------A------Cephalanthera_damasonium_575 CTTTCAGAGGCCGCAGCGGGACGACCAGAGGAAAGCCCGCCCCCGCTAGCTAACATATTATTCTCGGTGCGCATATTCTCTCTTTAGAAT 280 cepahalanthera_aust_dat115 CTTTCAGAGGCCGCAGCGGGACGACCAGAGGAAAGCCCGCCCCCGCTAGCTAACATATTATTCTCGGTGCGCATATTCTCTCTTTAGAAT Neottia_nidus_avis_JVF ------Listera_smallii_486 CTTTCAGAGGCCGCAGCGGGACGACCAGAGGAAAGCCCGCCCCCGCTAGCTCACATATTATTCTCGGTGCGCATATTCTCTCTTTAGAAT listera_convol_2707 -TTT-AGAGACAGCAAAGGGATGACTAGAGGAAAACCCGCCCCCGCTAGCTAACAAATTATTTTCGTTGCGCGAATTCTCTCTTTGTAAT listera_cordata_JVF2580 -TTT------aphyllorchis_montana CTTTCAGAGGCCGCAGCGGGACGACCAGAGGAAAGCCCGCCCCCGCTAGCTAACATATTATTCTCGGTGCGCATATTCTCTCTTTAGAAT corymborkis_vert CTGTCAGAGGCCGCAGCGGGACGACCA------Tropidia_Effusia_211 CTGTCAGAGGCCGCAGCGAGACGACCA------tropidia_cuciculigoides_05560 CTGTCAGAGGCCGCAGCGGGACGACCA------tropidia_bambusifolia_017721 CTGTCAGAGGCCGCAGCGGGACGACCA------sertifera_columbiana ------sertifera_sp_N565 ------Elleanthus_sp_374_AF314871 CTGTCAGAGGCCGCAGCGGGACGACCAGAGGAAAGCCCGCCCCCCCTAGCTAACATAGTATTCTCGG----CATATTCTCTCTTTAGAAT Epilyna_jemenzii_w2997 ------EPILYNA_HIRTZII CTTTCAGAG-CCGCAGCGGGACGACCAGAGGAAAGCCCGCCCCCGCTAGCTAACATAGTATTCTCGG---GCATATTCTCTCTT-AGCAT Sobralia_mucroanta_W535 CTGTCAGAGGCCGCAGCGGGACGACCAGAGGAAAGCCCGCCCCCGCTAGCTAACATAGGATTCTCGG----CATATTCTCTCTTTAGAAT sobralia_crocea CTGTCAGAGGCCGCAGCGGGACGACCAGAGGAAAGCCCGCCCCCGCTAGCTAACATAGGATTCTCGG----CATATTCTCTCTTTAGAAT XEORCHIS_AMAZONICA_O799 -TTT------CCG-AGC---A-GACCACAGCGAGA------CTA-CT------G----CTCCG------CT--CTTT----- Epipogium_aphyllum ------GC-A-CAT--G-TT--CGG------Nervilia_plicata_ER48 ------Nervilia_shirensis_c280 ------

Continued

Table A.3 Continued

Gastrodia_sesamoides_534 -TGTTATAGGCCGCAGCGGCACGACCAGAGGA--GCCCGCTC-----A-CTCACATAGGATTCTCGG----CATATTCTCTCTTTAGAAT Gastrodia_procera_PARTIAL -TGTTATAG------gastrodia_sp_reunion_ER214 ------gastrodia_confusa_0801 ------CTAAC------GAAC gastrodia_zyl_16313 ------GACCA------CTCACAT-GGATTCTCGG----CATATTCTCTATTT----- diceratostele_gabonensis_ER CTGTCAGAGGCCGCAGCGGGACGACCAGAGGAAAGCCCGCCCCCGCTAGCTAACATAG--TTCTCGGTGCGCATATTCTCTCTTAAGAAT Didymoplexis_pallens ------CGGGACGACC------C-AGCTCACATAGGATTCTCGG----CATATTCTCTATTTCGAAT Psilochilus_macrophyllus_ER02 ----AAGAGGCT--AGTGGC-CGACCATAGGAAAGCCCGCCCCCGCTAGCTAACATATGATTCTCGG----CAGATTCTCTATTCAGAA- Psilochilus_LJ6914 ----AAGAGGCT--AGTGGC-CGACCATA-AAAAGCCCGCCCCC-CTAGCTAACATATGATTCTCGG-----AGATTCTCTATTCAAAA- Triphora_trinathophora C-----GAGGCC-----GGGACGACCAGAGGAAAGCCCGCCCCCGCTATCTAACATAGGA------GTGCGC---TT-TCT-----GAA- Triphora_gentianoides_ER01 CTGTCAGAGGCCGCAGCGGGAC----AGAGGAA---CCGCCCGCGCTAGCTAACATAGGATTCTTGGTGCGCATCTT-T-TCTTTA-TAT triphora_amazonica_ER72 ------C-CAA----TGGCTAACACAG----CTC-GTGAGAGC--GGGATC---AGAAT Monophyllorchis_sp_435 CTGTCAGAGGCCGCAGCGGGACGACCAGAGGAAAGCCCGCCCCCGYTAGCTAACATAGGATTCTCGGTGCGCATATTCTCTATTTAGAAT Aplectrum_hyemale_104 C-G-GACAGGCCGCAGCGGG------Bletilla_striata_556 CTGTCAGAGGCCGCAGCGGGACGACCAGAGGAAAGCCCGCCCCCGCTAGCTAACATAG--TTCTCGGTGCGCATATTCTCTCTTTAGAAT Isochilus_amparoana_204 CTGTCAGAGGCCACAGCGGGACGACCAGAGGAAAGCCCGCCCCCGCTAGCTAACATAG--TT-TTGGTGC---TATTCTCTATTTAGAAT Calypso_bulbosa_JF CTGTGAGAGGCCGCAGCGGGACGACCAGAGGAAAGCCCGCCCCCGCTAGCTAACATAG--TTCTCGGTGCGCATATTCTCTCTTTAGAAT Leptotes_bicolor_1195 CTKT--GAG------CAG------ephi_schmidtii_JVF CTGTCAGAGGCCGCAGCGGGACGACCAGAGGAA--C---CCCCCGCTAGCTAACATAG--TTCTCGG----CATATTCTCTCTTTAGAAT Chysis_bractescens_436 CTTTCAGAGGCCGCAGCGGGACGACCAGAGGRAAGCCCGCCMCCGATAGCTYACATAT--TTCTCGGTGCGCATWTT-TCTCTTTAGA-T 281 Coelia_triptera_324 CTGTCACAG------

codonorchis_lessonii_01398 AGATTACCGACCAGGCCAGGCCGAATCGGGCCACCACTTGGGATGGGAATGGCTCAGCCCACATGCATCATTTGATGAAAGCATTCCAGT corycium_nigrescens_0695 ------brownleea_caerulea_21870 AGATTCCCGACCAGGCCAGGCCGAATCGGGCCACCACTTGGGATGGGAATGGCTCAGCCCACATGCATCATTTGATGAAAGCATTCCAGT Altensteinia_palacea_535 ------Disperis_lindleyana_696 AGATTCCCGACCAGGCCAGGCCGAATCGG-----CACTTGGGA------ACATGCATCATTTGATGAAAG------T Goodyera_pubescens_212 CTATTCCCGACCAGGCCAGGCCGAATCGGGCCACCACTTGGGATGGGAATGGCTCAGCCCACATGCATCATTTGATGRAAGCATTCCAGT Habenaria_repens_381 ------Orchis_quadripunctata_545 ------Pachyplectron_arifolium_529 CTATTCCCGACCAGGCCAGGCCGAATCGGGCCACCACTTGGGATGGGAATGGCTCAGCCCACATGCATCATTTGATGAAAGCATTCCAGT Spiranthes_cernua_402 AGAHTCCCGAC------GCCGAATCGGGC------GG-ATGGGAATGGCTCAGCCCACATGCATAATTTGA-----GCATTCAAGT Stenoglottis_longifolia_1136 ------PLAMORCHIS_TRILOBULATA ??????????????????????????????????????????ATGGGAAGGGTCCAGCCCCCCTGCCTCATTTGCGGAAA-CTTTCCAGT PALMORCHIS_powellii CTATTCCCGACCAGGCCAGGCCGAATCGGGCCACCACTTGGGATGGGAATGGCTCA-CCCACATGCATCATTTGATGAAAGCATTCCAGT Epipactis_helleborine_199 CTATTCCCGACCAGACCAGGCCGAATCGGGCCACCACTTGGGATGGGAATGGCTCAGCCCACATGCATCATTTGAGGAAAGCATTCCAGT Limodorum_abortivum_nadB ------TGCT--CACTATAGA-GAGATG-ATC-TTTCTT-AAAGGA------Cephalanthera_damasonium_575 CTATTCCCGACCAGACCAGGCCGAATCGG-CCACCACTTGGGATGGGAATGGCTCAGCCCACATGCATCATTTGAGGAAAGCATTCCAGT cepahalanthera_aust_dat115 CTATTCCCGACCAGACCAGGCCGAATCGGGCCACCACTTGGGATGGGAGTGGCTCAGCCCACATGCATCATTTGAGGAAAGCATTCCAGT Neottia_nidus_avis_JVF ------Listera_smallii_486 CTATTCCCGACCAGACCAGGCCGAATCGGGCCAC-----GG-ATGGGAATGGCTCAGCCCACATGCATCATTTGAGGAAAGCATTCCAGT

Continued

Table A.3 Continued

listera_convol_2707 AAATCCCCGACCAGACCAGGTAGAATCGGGCCCCCGCTTGGGATGGGTATGGGTCAGCCCACATGCATCATAAGCGGACAGCATTCCAGT listera_cordata_JVF2580 ------aphyllorchis_montana CTATTCCCGACCAGACCAGGCCGAATCGGGCCACCACTTGGGATGGGAATGGCTCAGCCCACATGCATCATTTGAGGAAAGCATTCCAGT corymborkis_vert ------CTTGGGATGGGGATGGCTCAGCTCACATGCATCATTTGATGAAAGCATTCCAGT Tropidia_Effusia_211 ------CTTGGGATGGGGATGGCTCAGCCCACATGCATCATTTGATGAAAGCATTCCAGT tropidia_cuciculigoides_05560 ------CTTGGGATGGGGATGGCTCAGCCCACATGCATCATTTGATGAAAGCATTCCAGT tropidia_bambusifolia_017721 ------CTTGGGATGGGGATGGCTCAGCCTACATGCATCATTTGATGAAAGCATTCCAGT sertifera_columbiana ------AATTTGATGAAAGCATTCCAGT sertifera_sp_N565 ------GATGAAAGCATTCCAGT Elleanthus_sp_374_AF314871 CTATTCCCGACCAGGCCAGGCCGAATCGGGCCACCACTTGGGATGGGGATGGCTCA-----CATGCATCATTTGATGAAAGCATTCCAGT Epilyna_jemenzii_w2997 ------GA-GG-TC------CATGCATCATT--A-GAAA-C-TTTCAGT EPILYNA_HIRTZII CTATTCCCGACCAGGCCAGGCCGAATCGGGCCACCACTTGGGATGGGGATGGCTCA-----CATGCATCATTTGATGAAAGCATTCCAGT Sobralia_mucroanta_W535 CTATTCCCGACCAGGCCAGGCCGAATCGGGCCACCACTTGGGATGGGGATGGCTCA-----CATGCATCATTTGATGAAAGCATTCCAGT sobralia_crocea CTATTCCCGACCAGGCCAGGCCGAATCGGGCCACCACTTGGGATGGGGATGGCTCA-----CATGCATCATTTGATGAAAGCATTCCAGT XEORCHIS_AMAZONICA_O799 ------Epipogium_aphyllum ------ACCA------CA-CCCACA-GGATC-GA-GATGG------AG- Nervilia_plicata_ER48 ------Nervilia_shirensis_c280 ------Gastrodia_sesamoides_534 AGATTACCGACCAGGCCAGGCCGAATC-----ACCACTTGGG------GCTCAGCCCACATGCATCATTT------T-CC-AGT Gastrodia_procera_PARTIAL ------282 gastrodia_sp_reunion_ER214 ------CCGAC------gastrodia_confusa_0801 C------GG--A---CGA------gastrodia_zyl_16313 ------diceratostele_gabonensis_ER AGATTCCCGACCAGGCCAGGCCGAATCGGGCCACCACTTGGGATGGGGATGGCTCAGCCCACATGCATCATTTGATGAAAGCATTCCAGT Didymoplexis_pallens AGATTCCCGACCAGGCCAGGC------GG-CCGCCACTTGGGATGGGGATGGCTCAGCCCACATGCATCATTTGATGAT-G-AATCCA-- Psilochilus_macrophyllus_ER02 -GA------GGCCAGGCCGAATCGGGCCACCGCTTGGGATGGGGATGGCTCAGCCCACATGCATCATTTGATGAAATCATTCCA-- Psilochilus_LJ6914 --A------GGCCAGGC-GAATCGGGCCACCGCTTGG-ATGGGGATGG-TCN-CCCAC-TSC-TCATT--ATGAAT-CATTCC--- Triphora_trinathophora -GA------CAGGCCGAATCGGGTCAC-----AG-ATCGG-ATT------CCCACATGCATCATTTGATGAAAGCATTCCAGT Triphora_gentianoides_ER01 -GATT------CAGGCCGAATCGGGTCAC-----GG-ATCGG-ATT------CCCACATGCATCATTTGATGAAAGCACTCAAGT triphora_amazonica_ER72 GGATT------GG--AAATGGGGTC-C-----AA-ATCGC--TT-C------G---CATTTAATAAAAGCATCCAAGT Monophyllorchis_sp_435 ------CAGGCCAGGCCGAATCGGGCCACCACTTGGGATGGGGATGGCTCAGCCCACATGCATCATTTGATTCAAGCATTCCAGT Aplectrum_hyemale_104 ------CCACCACTTGGGATGGGGATGGCTCAGCCCACATGCATCATTTGATGAAAGCATTCCAGT Bletilla_striata_556 AGATTCCCGACCAGGCCAGGCCGAATCGGGCCACCACTTGGGATGGGGATGGCTCAGCCCACATGCATCATTTGATGAAAGCATTCCAGT Isochilus_amparoana_204 CTATTCCCGACCAGGCCAGGCCGAATCGGGCCACCACTTGGGATGGGG------Calypso_bulbosa_JF CTATTCCCGACCAGGCCAGGCCGAATCGGGCCACCACTTGG-ATGGGGATGGCTCAGCCCACATGCATCATTTGATGAAAGCATTCCAGT Leptotes_bicolor_1195 ------AGGCCGAATCGGGCCACCACTTGGG------ephi_schmidtii_JVF CTATTCCCGACCAGGCAAGGCCGAATCGGGCCACCACTTGGGATGGGGATGGCTCAGCCCACATGCATCATTTGATGAAAGCATTCCAGT Chysis_bractescens_436 CTATTCCCGACCAGGCCAGGCCGAATCGGGCCACCACCT?GGATGGGGATGGCTCAGCCCACATGCATCATTTGATGAAAGCATTCCAGT Coelia_triptera_324 ------

Continued

Table A.3 Continued

codonorchis_lessonii_01398 CGCCTCCGATCAGTGGCTTGTCAACCACCGGACCGTAGCTC------GG------AAACACAGCGCAT-----GAGTAG corycium_nigrescens_0695 ------TTAG brownleea_caerulea_21870 CGCCTCCGATCAGTGGCTTGTCAACCACCGGACCGTAGCTCCTCAAAAAATGACCTTGGGTTGGGGAAACACAGCGCAT-----GAGTAG Altensteinia_palacea_535 ------Disperis_lindleyana_696 CGCCTCCGATCAGTGGCTTGT------ACCGTAGCTCCTCAAAAAATGACCTTG------CACAGCGCAT-----GAGTAG Goodyera_pubescens_212 CGCCTCCGATCAGTGGCTTGTCAACCACCGGACCGTAGCTCCTCACAAAATGCCC--GG------AAACACAGCGCAT-----GAGTAG Habenaria_repens_381 ------T-----GAGTAG Orchis_quadripunctata_545 ------T-----GAGTAG Pachyplectron_arifolium_529 CGCCTCCGATCAGTGGCTTGTCAACCACCGGACCGTAGCTCCTCACAAAATGCCC--GG------AAACACAGCGCAT-----GAGTAG Spiranthes_cernua_402 CGCCTCCGATCAGTGGCTTGTCAACCACCGGACCGTAGCT-----CAAA-TGCCC--GG------AAACACAGCGCAT-----GAGTAG Stenoglottis_longifolia_1136 ------GGGTTG------T-----GAGTAG PLAMORCHIS_TRILOBULATA -GC-TTCGATCAGT-GCTTGTCAAACACCGGATGGTAGCTCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACAT-----GAGTAG PALMORCHIS_powellii CGCCTCCGATCA-TGGCTTGTCAACCACCGGACCGAA-CTCCTCACCAAATGCCCTTGGGTTGGGGAAAC-CAGCACAT-----GAGTAG Epipactis_helleborine_199 CGCCTCCGATCAGTGGCTTGTCAACCACCGGACCGTAGCTCCTCACCAAATGCCC--GGG------AAACACAGCAC-T-----GAATAG Limodorum_abortivum_nadB ------AGCGTGAAGCACTTGATATCATA------TATCA-AGG-CGT-----GA-TTC Cephalanthera_damasonium_575 CGCCTCCGATCAGTGGCTTGTCAACCACCGGACCGTAGCTCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACATCACATGAATAG cepahalanthera_aust_dat115 CGCCTCCGATCAGTGGCTTGTCAACCCCCGGACCGTAGCTCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACATCACATGAATAG Neottia_nidus_avis_JVF ------Listera_smallii_486 CGCCTCCGATCAGTGTCTTGTCAACCACCGGACCGTAGCTCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACATCACATGRATAG listera_convol_2707 TGCCATCGATCAGTGGCTTGTCAACCACCGGAACGTAGCTCCTCAACAAATGCCTTTTGGTTGGGGAAACACAGCACATCACATGAATAG 283 listera_cordata_JVF2580 ------aphyllorchis_montana CGCCTCCGATCAGTGGCTTGTCAACCACCGGACCGTAGCTCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACATCACATGAATAG corymborkis_vert CGCCTCCGATCAGTGGCTTGTCAACCACCGGACGGTAGCTCCTCACCAAATGCGCTTGGGTTGGGGAAACACACCACAT-----GAGTAG Tropidia_Effusia_211 CGCCTCCGATCAGTGGCTTGTCAACCACCGGACCGTAGCTCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACAT-----GAGTAG tropidia_cuciculigoides_05560 CGCCTCCGATCAGTGGCTTGTCAACCACCGGACCGTAGCTCCTCACCAAATGCGCTTGGGTTGGGGAAACACAGCACAT-----GAGTAG tropidia_bambusifolia_017721 CGCCTCCGATCAGTGGCTTGTCAACCACCGGACCGTAGCTCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACAT-----GAGTAG sertifera_columbiana CGCCTCCGATCAGTGGCTTGTAAACCACCGGACCGTAGCTACTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACAT-----GAGTAG sertifera_sp_N565 CGCCTCCGATCAGTGGCTTGTAAACCACCGGACCGTAGCTACTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACAT-----GAGTAG Elleanthus_sp_374_AF314871 CGCCTCCGATCAGTGGCTTGTCAACCACCGGACCGTAGCTCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACAT-----GAGTAG Epilyna_jemenzii_w2997 -G-CT--GATCAG-GG-TT-TC-ACCA-CGG---GTAG-T-CTC-CCAA-T-CC--TGGG---GGGAACCACA-C------G-GT-G EPILYNA_HIRTZII CGCCTCCGATCAGTGGCTTGTCAACCACCGGACCGTAGCTCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACAT-----GAGTAG Sobralia_mucroanta_W535 CCCCTCCGATCAGTGGCTTGTCAACC------sobralia_crocea CCCCTCCGATCAGTGGCTTGTCAACC------XEORCHIS_AMAZONICA_O799 CGCG------C--GTC------GGG------CAT------Epipogium_aphyllum C------AACC------TAG------ACC------Nervilia_plicata_ER48 ------Nervilia_shirensis_c280 ------Gastrodia_sesamoides_534 C------GATCAGTGGCTTGTAAACC-----ACCGTAGCTCCTCACCAAAAGCCC----G-TAGG------CAGCACAT-----GAGTAG Gastrodia_procera_PARTIAL ------gastrodia_sp_reunion_ER214 ------gastrodia_confusa_0801 ------gastrodia_zyl_16313 ------

Continued

Table A.3 Continued

diceratostele_gabonensis_ER CGCCTCCGATCAGTGGCTTGTCAACCACCGGACCGTAGCTCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACAT-----GAGTAG Didymoplexis_pallens -GC--CC------GCTTGTCAACCACCGGAC------GGTTGGGGAAACACAGCGCAT-----GAGTAG Psilochilus_macrophyllus_ER02 CGTCTCCGATCAGTGGCTTGTCAACCACCGGACCGTAGCTCCTCACCAAATGCGCTTGGGTTGGGGAAAGACAGCACAT-----GAGTAG Psilochilus_LJ6914 CCTTTTCGATCAGTGGCTTGTCAACCCCCG-ACCG-AGCTCTTC-TCGAATGCG-TTCGGTTGGGGAAAGGCAGCCCTT-----GAGTAT Triphora_trinathophora CGCCTCTGATCAGTGGCTTGTCAACCACCGGACGG-ACCGCCTCACCAAATGCC----GGTTGG------AC----CAT-----GAGTAG Triphora_gentianoides_ER01 CGCCTCTGATCGGTGGCTTGTCTCTCACCGGACG-TACCTCCTCACCAAATGCC----GGTTGG------ACAGCGCAT-----GAGTAG triphora_amazonica_ER72 CGC-T-TGATCAGTGGTTTATTCCCGAC-GGACCATAGCTTCTCACCAAATGCCC-TGGG-TGG------ATAGC-CAT-----GAGTAG Monophyllorchis_sp_435 CGCCTCCGG--AGTGGTTTA-CAAA--CC--ACG-CCGCTCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCGCAT-----GAGTAG Aplectrum_hyemale_104 CGC-TCCGATCAGTGGCTTGTCAACCACCGGACAGTAGCTCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCA------G Bletilla_striata_556 CGCCTCCGATCAGTGGCTTGTCAACCACCGGACCGTAGCTCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACAT-----GAGTAG Isochilus_amparoana_204 ------AAACACAGCACAT-----GAGTAG Calypso_bulbosa_JF CGCCTCCGATCAGTGGCTTGTCAACCACCGGACCGTAGCTCCTCACAAAATGCCCTTGGGTTGGGGAAACACAGCACAT-----GAGTAG Leptotes_bicolor_1195 ------TTGGGGAAACACAGCACAT-----GAGTAG ephi_schmidtii_JVF CGCCTCCGATAAGTGGCTTGTAAACCACCGGACCGTAGCTCCTCACCAAATGCCTTTGGGTTGGGGAAACACAGCACAT-----GAGTAG Chysis_bractescens_436 CGCCTCCGATCAGTGGCTTGTCAACCACSGGACCGTAGCCCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACAT-----GAGTAG Coelia_triptera_324 ------CACAT-----GAGTAG

codonorchis_lessonii_01398 TTCGTTCAAGGACCACACCCTTTC---GAGAGCAGGATGCTGGCCGAGATGGAGCTGGGATAAAA------CGCGCCTT-GG-TT----- corycium_nigrescens_0695 TTCGTTCAAGGACCACACCC------AGAGCAGGATGCTGGCCGAGATGGAGCTGGGATAAA--CT---CTCGCCTTGGGCTTGCCTC 284 brownleea_caerulea_21870 TTCGTTCAAGGACCACACCC------AGAGCAGGATGCTGGCCGAGATGGAGCTGGGATAAA--CT---CTCGCCTTGGGCTT----- Altensteinia_palacea_535 ------Disperis_lindleyana_696 TTCGTTCAAGGACCACACCC------AGAGCAGGATGCTGGCCGAGATGGAGCTGGGATAAA--CTAT-C------GCCTT Goodyera_pubescens_212 ------GACCACAACC------AGAGCAGGATGCTGGCCGAGATGGAGC-GGGATAAAA-CG---CGCGCCTTGCGCTTGCCTT Habenaria_repens_381 TTCGTTCAAGGACCACACCC------AGAGCAGGATGCTGGCCGAGATGGA------CT---CTCGCCTTGGGCTTGCCTT Orchis_quadripunctata_545 TTCGTTCAAGGACCACACCC------AGAGCAGAATGCTGGCCGAGATGGAGCTGG------CT---CTCGCCTTGGGCTTGCCTC Pachyplectron_arifolium_529 TTCGTTCAAGGACCACACCC------AGAGCAGGATGCTGGCCGAGATGGAGCTGGGATAAAA-CT----TCGCCTTGGGCTTGCCTT Spiranthes_cernua_402 TTCGTTCAAGGACCACACC------AGGATGCTGGCCGAGATGGA------CGA--C------GGCTTGCCTT Stenoglottis_longifolia_1136 TTCGTTCAAGGACCACACCC------AGAGCAGGATGCTGGCCGAGATGGAGCTGGGATAGA--CT---C------GCTTGCCTC PLAMORCHIS_TRILOBULATA TTCGTTCAAGGACCACACCCTCTC---GAGAGCAGGATGCTGGCCGAGATGGAGCTGGGAGTCAACCTATACTTTCCTTGGGCTTGCCTT PALMORCHIS_powellii TTCGTTCAAGGACCACACCCTCT----SAGAGCAGGATGCTGGCC-AGATGGAGCTGGGAGCCAACCTATACTTTCCTTGGGCTTGCCTT Epipactis_helleborine_199 TTCGTTCAAGGACCACACCCTCCC---GAGAGCAGGATGCTGGCCGAGATGGAGCTGGGAGCCAACCTAGACTTTCCTTGGGCTTGCCTT

Continued

Table A.3 Continued

Limodorum_abortivum_nadB TTC-TTAAAGGA------AGG------CG---TG------AA---A------CTT------CT Cephalanthera_damasonium_575 TTCGTTCAAGGACCACACCCTCTC---GAGAGCAGGATGCTGGCCGAGATGGAGCTGGGAGCCAACCTAGACTTTCCTTGGGCTTGCCTT cepahalanthera_aust_dat115 TTCGTTCAAGGACCACACCCTCTC---GAGAGCAGGATGCTGGCCGAGATGGAGCTGGGAGCCAACCTAGACTTTCCTTGGGCTTGCCTT Neottia_nidus_avis_JVF ------Listera_smallii_486 TTCGTTCA??????????CCYCYC---GAGAGCAGGATGCTGGCCGAGATGGAGCTGGGAGCCAACCTAGACTTTCCTTGGGCTTGCCTT listera_convol_2707 TTTGTTCAAGGACCACACCCTATC---GAGAGCAGGATTCTGGCCGAGAGGGAGATGGGAGCCAACCTAGAATTTCCTTGGGCTTGCCTT listera_cordata_JVF2580 ------aphyllorchis_montana TTCGTTCAAGGACCACACCCTCTC---GAGAGCAGGATGCTGGCCGAGATGGAGCTGGGAGCCAACCTATACTTTCCTTGGGCTTGCCTT corymborkis_vert TTCGTTCAAGGACCACACCCTCTC---GAGAGCAGGATGCTGGCCGAGATGGAGCTGGAAGCCAACCTAGACTTTCCTTGGGCTTGCCTT Tropidia_Effusia_211 TTCGTTCAAGGACCACACCCTCTC---GAGAGCAGGATGCTGGCCGAGATGGAGCTGGGAGCCAACCTAGACTTTCCTTGGGCTTGCCTT tropidia_cuciculigoides_05560 TTCGTTCAAGGACCACACCCTCTC---GAGAGCAGGATGCTGGCCGAGATGGAGCTGGAAGCCAACCTAGACTTTCCTTGGGCTTGCCTT tropidia_bambusifolia_017721 TTCGTTCAAGGACCACACCCTCTC---GAGAGCAGGATGCTGGCCGAGATGGAGCTGGGAGCCAACCTAGACTTTCCTTGGGCTTGCCTT sertifera_columbiana TTCGTTCAAGGACCACACCCA--C---GA-AGCAGGATGCTGGCCGAGATGGAGCTGGGAGCCAACCTA-ACTTTCCTT-CGCT------sertifera_sp_N565 TTCGTTCAAGGACCACACCCA--C---GA-AGCAGGATGCTGGCCGAGATGGAGCTGGGAGCCAACCTA-ACTTTCCTT-CGCT------Elleanthus_sp_374_AF314871 TTCGTTCAAGGACCACACCCTCTC---GAGAGCAGGATGCTGGCCGAGATGGAGCTGGGAGCCAACCTAGACTTTCCTT------GCCTT Epilyna_jemenzii_w2997 T---TTCA-GG-CC----CCTTT----GAGA-C--GAT--T-GC-GAGA--GAG-TGGGA-CCA--CTAGACTTT-CTT-CG-TCGCCT- EPILYNA_HIRTZII TTCGTTCAAGGACCACACCCTCTC---GAGAGCAGGATGCTGGCCGAGATGGAGCTGGGAGCCAACCTAGACTTTCCTT-CGCTCGCCTT Sobralia_mucroanta_W535 ------sobralia_crocea ------XEORCHIS_AMAZONICA_O799 --C--TCCACGTGAATA---TTTG---TGGCACCGCATCATA-CC------AG-T--GA-CAAA--T------285 Epipogium_aphyllum ------CC-- Nervilia_plicata_ER48 ------Nervilia_shirensis_c280 ------Gastrodia_sesamoides_534 TTCGTGAAAG------CCTCTC---GAAA------TGCTGGCCGAGATGGAGCTGGGAGCCAACCTATACTT-CCTTGGGCTTGCCTT Gastrodia_procera_PARTIAL ------gastrodia_sp_reunion_ER214 ------gastrodia_confusa_0801 ------gastrodia_zyl_16313 ------diceratostele_gabonensis_ER TTCGTTCAAGGACCACACCCTCTC---GAGAGCAGGATGCTGGCCGAGATGGAGCTGGGAGCCAACCTAGACTTTCCTTGGGCTTGCCTT Didymoplexis_pallens TTCGTGAAAGGACCACACCCTCTC---GAGAGCAGGATGCTGGCCGAGATGGAGCTGGGAGCCAACCTATACTTTCCTT------Psilochilus_macrophyllus_ER02 TTCGTTCAAGGACCACACC------GCA-GATGCTGGCCGAGATGGAGCTGGGAGCCCA-CTAGACTTTC---GG-CTTGCCTT Psilochilus_LJ6914 TT-GTTCAAGGACCACACCGCCTC------C----TGCTTGCCGAGATGGAGCTGTGAGCCCA-CTAGACTTTC---GG-CTTGCCTT Triphora_trinathophora TTCGTTCAAGGACCACACC------GCAGGATGCTGGCCGAGA------TGAGCCAACCTAGAATT-----GGGC-----TT Triphora_gentianoides_ER01 TTC------GGACCACACCGCAGG------GCAGGATGCTGGCCGAGA------GGGAGCCAACCTATAATT-----GGGC--GGCTT triphora_amazonica_ER72 TTCGTTCAAGGACCACTCC------GCAGGATGCTGGCCGTGATGGAG-TGGGAGCCAACTTAGAATT-----GGGCTTGCCTT Monophyllorchis_sp_435 TTCGTTCAAGGACCACACC------GCAGGATG----CCGAGATGGAGCTGGGAGCCCAC-TAGACTTTCCTTGGGCTTGCCTT Aplectrum_hyemale_104 TTCGTTC------Bletilla_striata_556 TTCGTTCAAGGACCACACCCTCTCGAGGAGAGCAAGATGCTGGCCGAGATGGAGCTGGGAGCCAACCTATACTTTCCTTGGGCTTGCCTT Isochilus_amparoana_204 TTCGTTCAAGGACCACACCCTCTCGAGGAGAGCAGGATGCTGGCCGAGATGGAGCTGGGAGCCAACCTAGACTTTCCTTGGGCTTGCCTT Calypso_bulbosa_JF TTCGTTCAAGGACCACACCCTCTCGA---GAGCAGGATGCTGGCCGAGATGGAGCTGGGAGCCAACCTAGACTTTCCTTGGGCTTGCCTT Leptotes_bicolor_1195 TTCGTTCAAGGACCACACCCTYTCGA---GAGCAGGATGCTGGCCGAGATGGAGCTGGGAGCCAACCTATACTTTCCTTGGGCTTGCCTT

Continued

Table A.3 Continued

ephi_schmidtii_JVF TTCGTTCAAGGACCACACCCTCTCGA-GAGAGCAGGATGCTGGCCGAGATGGAGCTGGGAGCCAACCTATACTTTCCTTGGGCTTGCCTT Chysis_bractescens_436 TYCGTTCAAGGACCACACCCTCTCGAGGAGAGCAGGATGCTGGCCGAGATGGAGCTGGGAGCCAACCTATACTTSCCTTGGGCTTGCCTT Coelia_triptera_324 TTCGTTCAAGGACCACACCCTCTCGAGGAGAGCAGGATGCTGGCCGAGATGGAGCTGGGAGCCAACCTATACTTTCCTTGGGCTTGCCTT codonorchis_lessonii_01398 GCCCCACCATCTA-ATCAAGGGCGGGCGCCGAAAAGGAAAGGAACCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTT corycium_nigrescens_0695 GCCCCACCAT-TA-ATAAAGGGCGGGCGCCGAAAA-----GGAACCAGTGACGCCTTTT----GAAAGCTTAGCTTGGTAGGCGCTGCTT brownleea_caerulea_21870 GCCCCACCATCTA-ATAAAGGGCGGGCGCCGAAAAGGAAAGGAACCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTT Altensteinia_palacea_535 ------TT------GAAA-----GCTTGGTAGGCGCTGCTT Disperis_lindleyana_696 GCCCCACCATCTA-ATCAA------G-CGAAAAGGAAAGGAA------CCTTTTCGACGAAAGCTGAGCTTGGTAGGCGCTGCTT Goodyera_pubescens_212 GCCCCACCATCAA-ATCAA------GGAA------CCATTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTT Habenaria_repens_381 GCCCCVCSVBVTA-ATAAA------GA---GGAAAGG--CSCGT-A-GCGATTT----GAAA------TTGGTAGGCGCTGTTT Orchis_quadripunctata_545 GCCCCACCATAGA-ATAAA------CGCCGAAAAGGAAAGGAA----TGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTT Pachyplectron_arifolium_529 GCCCCACCATCGA-ATAAA----GGGCGCCGAAAAGGAAAGGA------GACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTT Spiranthes_cernua_402 GCCCCACCATCGCCATAAAGGGCGGG--T-GAAA-GG---G----CA------CC----CGACGAAAGCGACGCTTGGTAGGCGCTGCTT Stenoglottis_longifolia_1136 GCCCCACCATAGA-ATAAAGGGCGGGCGCCGAAAAGGAAAGGAACCAGTGACGCCTTTTCGAC------GCTTGGTAGGCGCTGCTT PLAMORCHIS_TRILOBULATA GCCCCCCCATCTAAATAAAGGGCGGGTGCCGAAAAGGAA-----CCAGTGACGCCTTTTCAACGAAAGCTTAGCTTGGTAGGCGCTGCTT PALMORCHIS_powellii GCCCCCCCAT-TAAATAAAGGGCGGGCGCCGAAAAGGCA-----CCAGTGACGCCTTTTCAACGAAAGCTTAGCTTGGTAGGCGCTGCTT Epipactis_helleborine_199 GCCCCAC------AAAGGGCGGGCGCCGAAAAGGAA-----CCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTT Limodorum_abortivum_nadB G------CTAAGTAA---G-TT------AAGGAAAGGAACCAGTGACGCCTTTTCGACGAAAGCTTAGCTTG-TAGGCGCTGCTT Cephalanthera_damasonium_575 GCCCCACCATCTAAATAAAGGGCTTA-GCCGAAAAGGAA-----CCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTT cepahalanthera_aust_dat115 GCCCCACCATT-AAATAAAGGGCTAA-GCCGAAAAGGAA-----CCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTT 286 Neottia_nidus_avis_JVF ------GAC---T---CGACGAAAGCTTAGCTTGGTAGGCGCTGCTT Listera_smallii_486 GCCCCACCATCTAAATAAAGGGCTAA-GSCGAAAAGGA------GACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTT listera_convol_2707 GCCCCACCATTTAAAGAAAGGGGTAA-GCCGAAAAGGA------GACGCCTTTTCGAAGAAAGCCAAGGTTGGTTCGCGCTGATT listera_cordata_JVF2580 ------aphyllorchis_montana GCCCCACCATCTAAAGAAA-----GG-GCCGAAAAGGAA-----CCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTT corymborkis_vert GCCCCACCATATAAATA------G-CT--AAAAAAAGGAACCA------CTTGGTAGGCGCTGCTT Tropidia_Effusia_211 GCCCCACCATCTAAATAAAGGGCGGG---CGAAAAGGAA-----CCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTT tropidia_cuciculigoides_05560 GCCCCACCATCTAAATAAAGGGCGGG---CTAAAAAAAA-GGAACCA------CCTTTT----GAA----TAGCTTGGTAGGCGCTGCTT tropidia_bambusifolia_017721 GCCCCACCATCTAAAGAAAGGGCGGG---CGAAAAGG-----AACCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTT sertifera_columbiana ------CCGCGG---CCAAAAAGGAAAGGAACC------TTTTC-AC-AA-GCTTA-CTTGGTAG-CGCTGCTT sertifera_sp_N565 ------CCGCGG---CCAAAAAGGAAAGGAACC------TTTTC-AC-AA-GCTTA-CTTGGTAG-CGCTGCTT Elleanthus_sp_374_AF314871 GCCCCACCATCTAAAGAAAGGGCGGGCGCCGAAAAGGAAAGGWVCCAGTGACGCCTTTTCGWCGAAAGCTTAGCTTGGTAGTCGCTGCTT Epilyna_jemenzii_w2997 -CCCC-C-AT-TAAAGAAAGGGCGGGCGC-GAAAAGGAAAGGAACCAGTGACGCCTTTTCGACGAAAG-TTAGCT-GGTAGGCG--GCTT EPILYNA_HIRTZII GCCCCACCATCTAAAGAAAGGGCGGGCGCCGAAAAGGAAAGGAACCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTT Sobralia_mucroanta_W535 ------sobralia_crocea ------XEORCHIS_AMAZONICA_O799 ------Epipogium_aphyllum -CCACACCATCTCAAGAAAGG------GTT-CGCCTTTT------Nervilia_plicata_ER48 ------Nervilia_shirensis_c280 ------Gastrodia_sesamoides_534 GCCCCAC----T-AAGAAAGGGCGGGCTC-AA---GGAA------CCCTTTTCGACTGGGCTTGGTATTGGTAGGCGCTGCTT Gastrodia_procera_PARTIAL ------gastrodia_sp_reunion_ER214 ------TGG----CGCT----

Continued

Table A.3 Continued

gastrodia_confusa_0801 ------TGG----CGC----- gastrodia_zyl_16313 ------diceratostele_gabonensis_ER GCCCCACCATCTAAAGAAAGGGCGGGCT--GAAAAGGAA-CGAACCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTT Didymoplexis_pallens GCCCCACCA-CT---GAAAGGG------CAAA-GGA------TT--CGACG------TTGGTAGGCGCTGCTT Psilochilus_macrophyllus_ER02 GCCCCACCATCTCAAGATA------GAAAA------CC-----CGCCTTTT----GAAAGCTTAGCT-GGTAGGCGCTGCTG Psilochilus_LJ6914 GCCCCACCATTTCAAGATT------GAAAA------CC-----CGCCTTTT----GAAAGCTAAGCTTGGTAGGCGCTGTTG Triphora_trinathophora GCCCCACC------GAA------GAAAA------AACCATTGA----TT------A----TTAGCTTGGTAGGCGCT---- Triphora_gentianoides_ER01 GCCCCACC------A------GAAAA------AACCATT------CGACGA----TTAGCTTGGTAGGCGGCGCTG triphora_amazonica_ER72 GCCCCACCATCTAAAGAAA------GAAAAGGAG-GGAACCAT------CGAGGATTAGCT-GGTAGTCG---CTG Monophyllorchis_sp_435 GCCCCACCATCTAAAGAAA------GCCGAAAA-----GAAACCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTT Aplectrum_hyemale_104 ------Bletilla_striata_556 GCCCCACCATCTAAATAAAGGGCGGGC---GAAAA-----GGAACCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAG------Isochilus_amparoana_204 GCCCCACCATATAAAGAAAGGGCGGGCGCCGAAAA-----GGAACCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTT Calypso_bulbosa_JF GCCCCACCATCTAAATAAAGGGCGGGCGCCGAAAA-----GGAACCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTT Leptotes_bicolor_1195 GCCCCACCATATAAAGAAAGGGCGGGCGCCGAAAA-----GGAACCAGTGACGSCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTT ephi_schmidtii_JVF GCCCCACCATCTAA-TAAAGGGCGGGCGCCAAAAAGGAA-----CCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTT Chysis_bractescens_436 GCCCCACCATATAAATAAAGGGCGGGCGCCGAAAA-----GGAACCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTT Coelia_triptera_324 GCCCCACCATCTAAATAAAGGGCGGGCGCCGAAAA-----GGAACCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTT

287

codonorchis_lessonii_01398 ACTCACCCTATTCCCTCATACAATGCCCTGAA--CACTCAA------TT-----CCATTTTCCCAT------GCCTC corycium_nigrescens_0695 ACTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAA------TT-----CCCTTTTGCCATGCGGAGTCACAGGCAGCGCCTC brownleea_caerulea_21870 ACTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAA------TGAATCCCCCTTTTCCCATGCG------CCTC Altensteinia_palacea_535 ACTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAA------TGAATCCCCCTTTTCCCATGCGGAGTCACAGGCAGCGCCTC Disperis_lindleyana_696 ACTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAA------TTA-----CCTTTTCCCATGCGGAGTCACAGGCAGCGCCTC Goodyera_pubescens_212 ACTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAA------TGAATCCCCCTTTTCCCATGCGGAGTCACAGGCAGCGCCTC Habenaria_repens_381 ACTCACCCTATTCCCTCAGAAAATGCCCTTCA--CACGAAA------TTAATCCCCCTTTTCCCAT----AGTCACAGGCAGCGCCTC Orchis_quadripunctata_545 ACTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAA------TTCAT-CCCCTTTTCCCATGCGGAGTCACAGGCAGCGCCTC Pachyplectron_arifolium_529 ACTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAA------TGAATCCCCCTTTTCCCATGCGGAGTCACAGGCAGCGCCTC Spiranthes_cernua_402 ACTCACCCTATTCCCTAATAAAATGTCCTGCCA-CACGAAA------TGAATCCCCCTTTCCCVATGCGGAGTCACAGGCAGCGCCTC Stenoglottis_longifolia_1136 ACTCACCCTATTCCCTCAGATAATGCCCTGAA--CACTCAA------TTCATCCCCCTTTTCCCATGCTAAGTCACAGGCAGCGCCTC PLAMORCHIS_TRILOBULATA ACTCACC------TCAGACAATGCCCTGAA--CACGAAAGTTTGCAGTTCAGCCCCCTTTTCCCATGCGGAGTCACAGGCAGCGCCTC PALMORCHIS_powellii ACTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAAGTTTGCAGTTCAGCCCCCTTTTCCCATGCGGAGTCACAGGCAGCGCCTC Epipactis_helleborine_199 ACTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAA------TTTCCCCATGCGGAGTCACAGGCAGCGCCTC Limodorum_abortivum_nadB ACTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAAGTTTGCAGTTAAGCCCCCTTTTCCCATGCGGAGTCACATGCAGCGCCTC Cephalanthera_damasonium_575 ACTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAAGTTTGCAGTTCAGCCCCCTTTTCCCATGCGGAGTCACAGGNAGCGCCTC cepahalanthera_aust_dat115 ACTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAAGTTTGCAGTTCAGCCCCCTTTTCCCATGCGGAGTCACAGGCAGCGCCTC Neottia_nidus_avis_JVF ACTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAAGTTTGCAGTTCAGCCCGCTTTTCCCATGCGGAGTCACAGGCAGCGCCTC Listera_smallii_486 ACTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAAGTTTGCAGTTCAGCCCCCTTTTCCCATGCGGAGTCACAGGCAGCGCCTC listera_convol_2707 ACTCACCCTATTCCCTCCAACAATGCCATCAA--CACGAAAGTCATCAGCTCAGCCCCCTTTTCCCATGCGGTGTCACAGGCAGCGCCTC

Continued

Table A.3 Continued

listera_cordata_JVF2580 ------aphyllorchis_montana ACTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAAGTTTGCAGTTCAGCCCCCTTTTCCCATGCGGAGTCACAGGCAGCGCCTC corymborkis_vert ACTCACCCTATTCCTTCAGACAATGCCCT------CGAAAGTTTGCTGTTCCGCCCCCTTTTCCCATGCGGAGTCCCAGGCAGCGCCTC Tropidia_Effusia_211 ACTGACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAAGTTTGCAGTTCCGCCCCCTTTTCCCATGCGGAGTSACAGGCAGCGCCTC tropidia_cuciculigoides_05560 ACTCACCCTATTCCCTCAGACAATGCCCT------CGAAAGTTTGCAGTTCCGCCCCCTTTTCCCATGCGGAGGCACAGGCAGCGCCTC tropidia_bambusifolia_017721 ACTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAAGTTTGCAGTTCCGCCCCCTTTTCCCATGCGGAGTCACAGGCAGCGCCTC sertifera_columbiana ACTC-CCCTATTCCCTCA-ACAATGCCCTGAA--CAC--AAGTGT----TTCC-CCCCCTTTTCC-ATGCAGAG------Sertifera_sp_N565 ACTC-CCCTATTCCCTCA-ACAATGCCCTGAA--CAC--AAGTGT----TTCC-CCCCCTTTTCC-ATGCAGAG-C------Elleanthus_sp_374_AF314871 ACTCACCCTATTCCCTCAGACAATGCCCTGAA--CTCGAAAGTTTGCTGTTCYGCCCCCTTTTCCCATGCGGAGTCACAGGCAGCGCCTC Epilyna_jemenzii_w2997 ACTCACCCTATTCCCT--GACAATGCCCTGAA--CA-GAAAGTTTGCAGTTCTGCCCCCTTTTCCCATGCGGAGTCACAGGCAGCGCCTC EPILYNA_HIRTZII ACTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAAGTTTGCAGTTCCGCCCCCTTTTCCCATGCGGAGTCACAGGCAGCGCCTC Sobralia_mucroanta_W535 ------sobralia_crocea ------XEORCHIS_AMAZONICA_O799 ------TTT-CC------TTGT--CA-----GCCAK Epipogium_aphyllum ------GAC------GAAA------GTTCACTCACCTATTCCA------CCTC Nervilia_plicata_ER48 ------Nervilia_shirensis_c280 ------Gastrodia_sesamoides_534 ACTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAAGTGTGAAG-TCTCTC------GCKTTCGCCTC Gastrodia_procera_PARTIAL ------gastrodia_sp_reunion_ER214 ------GGC-----GAAAA-----AGAA--CAAGAG------TT-CGC-CCC------G------288 gastrodia_confusa_0801 ------GGCC-TC--AAAA-----AGAA--CAAGAG------TT-CGC-CCCCCCT------CGGA------GCCTC gastrodia_zyl_16313 ------diceratostele_gabonensis_ER ACTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAAGTTTGCAGTTCCGCCCCCTTTTCCCATGCGGAGTCACAGG----GCCTC Didymoplexis_pallens TGTCACCCC-GGCC---ATACAATGCCCC-AA---A-GAA-GTT-G-A------CCTTTTCCCATGCGGAGTGACAG-----GCCTC Psilochilus_macrophyllus_ER02 ACTCACC-TATTCC-TCAGACAATGCCCTGAA--CACGAAAGTTTGCAGTTCCGC-CCCTTT-CCCATGCGGAGTCACAG-CAGCGC--- Psilochilus_LJ6914 ACTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGTAA-TTTGCAGTTCCGCCCCCTTTTCCCATGAGGACTCTCAGGCAGCGA--- Triphora_trinathophora -CTCACCCTATTCCCTCAGAGAATGCCCTGAA--CACGAGACT----AGTTTCG------GGCAGCGC--- Triphora_gentianoides_ER01 --TCACCCTATTCCCTCAGAGAATGCCCTGAA--CACG-GAGT------TTCC-C-CCCTTTTCCCATGCGGAGTAACAGGCAGCGC--- triphora_amazonica_ER72 --TCGCCCTATTCC-TCTTAAAAAACCCTGAA--CAGGAAA-TATGCGG--CC---CCCTTTTCCCATGCGGAGTCACATGCACCGC--- Monophyllorchis_sp_435 ACTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAAGTTTGCAGTTCCGC-CCCT---CC-ATGCGGAGTCACAGGCAGCGCCTC Aplectrum_hyemale_104 ------Bletilla_striata_556 -CTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAAGTTTGCAGTTCCGCCCCCTTTTCCCATGCGGAGTCACAGGCAGCGCCTC Isochilus_amparoana_204 ACTCACCCTATTCCCTCAGACAATGCCCTGAACTCACGAAAGTTTGCAGTTCCGCCCCCTTTTCCCATGCGGAGTCACAGGCAGCGCCTC Calypso_bulbosa_JF ACTCACCCTATTCCCTCAGACAATGCCCTGAACTCACGAAAGTTTGCAGTTCCGCCCCCTTTTCCCATGCGGAGTCAAAGGCAGCGCCTC Leptotes_bicolor_1195 ACTCACCCTATTCCCTCAGACAATGCCCTGAACTCACGAAAGTTTGCAGTTCCGCCCCCTTTTCCCATGCGGAGTCACAGGCAGCGCCTA ephi_schmidtii_JVF ACTCACCCTATTCCCTCAGACAATGCCCTGAACT---GAAAGTTTGCAGTTCCGCCCCCTTTTCCCATGCGGAGTCACAGGCAGCGCCTC Chysis_bractescens_436 ACTCACCCTATTCCCTCAGACAATGCCCTGAACTCACGAAAGTTTGCAGTTCCGCCCCCTTTTCCCATGCGGAGTCACAGGCAGCGCCTC Coelia_triptera_324 ACTCACCCTATTCCCTCAGACAATGCCCTGAACTCACGAAAGTTTGCAGTTCCGCCCCCTTTTCCCATGCGGAGTCACAGGCAGCGCCTC

codonorchis_lessonii_01398 GGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGT corycium_nigrescens_0695 GGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGT brownleea_caerulea_21870 GGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGT

Continued

Table A.3 Continued

Altensteinia_palacea_535 GGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTCTACTGTACTAATATGTGTAGGT Disperis_lindleyana_696 GGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGT Goodyera_pubescens_212 GGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGT Habenaria_repens_381 GTAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGT Orchis_quadripunctata_545 GGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGT Pachyplectron_arifolium_529 GGAAAAAAVMTCGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGT Spiranthes_cernua_402 GGAAAAAAKNWNGGACGAGCCACRNGCAGGGAAACTTGCACGTGTGGTTCCGGCCGGGGACVCCGGTATACTGTACTAATATGTGTAGGTStenoglottis_longifolia_1136 GGAAAAAAGCACGGACGAGCCACATGCGGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGT PLAMORCHIS_TRILOBULATA GGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCATGGGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATAT------PALMORCHIS_powellii GGAAAAAAGCACGGACGAGCCACATTCAGGGAAACTTGCA------Epipactis_helleborine_199 GGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCSGGGCACCCSGGTATACTGTACTAATATGTGTAGGT Limodorum_abortivum_nadB GG-AAAAAGCACGGACGAGCCACATGCAGG-TGTGGAGCCTGTGTGTTTCTGGCCGGGGAC-CCGGCAGGA--TCCGAATAGGGGTAGG- Cephalanthera_damasonium_575 GGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGT cepahalanthera_aust_dat115 GGAAAAAAGCACGGACGAGCCACAGGCAGGGAGACCAGCACGGGTGGTTCTGGCCGGGGACCCCGGTATTCTGTCCTAATATGTGTAGGT Neottia_nidus_avis_JVF GGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTCTACTGTACTAATATGTGTAGGT Listera_smallii_486 GGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGT listera_convol_2707 GGAAAAAAGCACAGACGAGCCACAGGCAGGGAAAATTGCACGGGTGGTTATGCCCGGGGACTCCGGTATACTGTAATAATATGCGTAGGT listera_cordata_JVF2580 ------aphyllorchis_montana GGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGT 289 corymborkis_vert GGAAAAAAGCACGGACGACCCACATGCAGGGAAACTTGCACGGGTGGTTCTGGCCGG-----CCGGTATACTGTACTAATATGTGTAGGT Tropidia_Effusia_211 GGAAAAA-GCAYGGACGAGCGACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTCTACTGTACTAATATGTGTAGGT tropidia_cuciculigoides_05560 GGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGT tropidia_bambusifolia_017721 GGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTCTACTGTAATAATATGTGTAGGT sertifera_columbiana ------sertifera_sp_N565 ------Elleanthus_sp_374_AF314871 GGAAAASAGCVCGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGT Epilyna_jemenzii_w2997 GGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCGGGGGTGGTT-TGGCCGGGGACCCCGGTATACTGTA-TAATATGTGTAGGT EPILYNA_HIRTZII GGAAAAAAGTA-GGATCA-CCAGTCAAAAGG--T-TT-CA--TATAGTTTTGGCCGGGGACCCCGGTATACGATT-TA-TATGGGTAGGT Sobralia_mucroanta_W535 ------sobralia_crocea ------XEORCHIS_AMAZONICA_O799 GCTGTAAAGCACGGACGAGCCACATGCAGGGAAACTCGCACGTGTGGTTCTGGCTGGGGACCCCGGTATACTGTACTAATATGTGTAGGT Epipogium_aphyllum AGAAAAT-GCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGT Nervilia_plicata_ER48 ------Nervilia_shirensis_c280 ------Gastrodia_sesamoides_534 GTCAAAAAB-ACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGT Gastrodia_procera_PARTIAL ------gastrodia_sp_reunion_ER214 --AAAAAAGCACGGACGAGCCACATGCGGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGT gastrodia_confusa_0801 GGAAAAA-GCACGGACGAGCCACATGCGGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGT gastrodia_zyl_16313 ------diceratostele_gabonensis_ER GGAAAG--GCA-TTACGATC-ACA-GCAGGGAATGATTT-CTTATAG-TAACAATCAGTACCCCGGATTACTG-A-TAA--TTAACAGGA Didymoplexis_pallens GTAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGT

Continued

Table A.3 Continued

Psilochilus_macrophyllus_ER02 -GAAAGAA-CACGG-CGA-CCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGT-TACTGTA-TAATATG-GTAGGT Psilochilus_LJ6914 -GAAAGAAGCA-TTACGATC----TGCAGCTCAGATGGTTCGTGTGGTGTTTATTGGGGTAACAG--TTATCGGTGGAATATGTGTAGGC Triphora_trinathophora -GAA----GCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTCTACTGTACTAATATGTGTAGGT Triphora_gentianoides_ER01 -GAA----GCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTCTACTGTACTAATATGTGTAGGT triphora_amazonica_ER72 -TAAAAAAACACGGACGAGCCACATGCAGGGAAACTTGCACGGGTGGTTCTGGCCGGGGA-----GAAT-CTGCA-TAAC--G-ATA--- Monophyllorchis_sp_435 GGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGT Aplectrum_hyemale_104 ------GACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGT Bletilla_striata_556 GGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGT Isochilus_amparoana_204 GGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGT Calypso_bulbosa_JF GGAAANNNN-ACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACSCCGGTATACTGTACTAATATGTGTAGGT Leptotes_bicolor_1195 GGAAARAGGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGT ephi_schmidtii_JVF GGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGAACCCCGGTATACTGTACTAATATGTGTAGGT Chysis_bractescens_436 GGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGT Coelia_triptera_324 GGAAAAA-GCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGT

codonorchis_lessonii_01398 CCCTGTAATTCGAG-GAGATTGTCATGGCGCAAAAGCAGA00000010000000000000000000000000000000000000000000 corycium_nigrescens_0695 CCCTGTAATTCGAGCTAGATTGTCATGGCGCAAAAGCAGA00000000000000000000000000000000000000000000000000 brownleea_caerulea_21870 CCCTGTAATTCGAG-GAGATTGTCATGGCGCAAAAGCAGA00000000000000000000000000000000000000000000000000 Altensteinia_palacea_535 CCCTGTAATTCGAG-GAGATTGTCATGGCGCAAAAGCAGA00000000000000000000000000000000000000000010000000 290 Disperis_lindleyana_696 CCCTGTAATTCGAG-GAGATTGTCATGGCGCAAAAGCAGA00000000000000000000000000000000000000000000000000 Goodyera_pubescens_212 CCCTGTAATTCGAG-GAGATTGTCATGGCGCAAAAGCAGA00000000000000000000000000000000000000000000000000 Habenaria_repens_381 CCCTGTAATTCGAG-GAGATTGTCATGGCGCAAAAGCAGA00000000000000000000000000000000000000000000000000 Orchis_quadripunctata_545 CCCTGTAATTCGAG-GAGATTGTCATGGCGCAAAAGCAGW00000000000000000000000000000000000000000000000000 Pachyplectron_arifolium_529 CCCTGTAATTCGAG-GAGATTGTCATGGCGCAAAAGCAGA00000000000000000000000000000000000000000?0000??0? Spiranthes_cernua_402 CCCTGTAATTCGAG-GAGATTGTCATGGCGCAAAAGCAGA0000000000000000000000000000000000000000000000?1?0 Stenoglottis_longifolia_1136 CCCTGTAATTCGAG-GAGATTGTCATGGCGCAAAAGCAGA000000000000000000000000000000000000000000000000?1 PLAMORCHIS_TRILOBULATA ------00000000000000000000000000000000000000000000000000 PALMORCHIS_powellii ------????????????00000000000000000000000100000000010000 Epipactis_helleborine_199 CCCTGTAATTCGAGTGAGATTGTCATGGCGCRCAAGCAGA00000000000000000000000000000000000000000000000000 Limodorum_abortivum_nadB ------A---GA-TG---TTG-CATGCCACAAAAGCAGA00000000000000000000000000000000000000000000000000 Cephalanthera_damasonium_575 CCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAAGCAGA00000000000000000000000000000000000000000000000000 cepahalanthera_aust_dat115 CCCAGTAATTCGAGTCAGATTGTCATGGCGCAAAAGCAGA00000010010000000000000000100100000000000000000000 Neottia_nidus_avis_JVF CCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAAGCAGA00000000000000000000000000000000000000000000000000 Listera_smallii_486 CCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAAGCAGA00000000000000000000000000000000000000000000000000 listera_convol_2707 CCCTGTAATTCGAGTCAGAT-GTCAAGGCGCAAAAGCAGA00000000000000000110000000000000100000000000000000 listera_cordata_JVF2580 ------00000010000000000000000000000000000000000000000000 aphyllorchis_montana CCCAGTAATTCGAGC-AGATTGTCATGGCGCAAAAGCAGA???????????????0???????????01010010000100000000000 corymborkis_vert CCCTGTAATTCGAGTCTGATTGTCATGGCG------???????????????00000000000000000000000000000000000 Tropidia_Effusia_211 CCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAAGCAGA10000000000000000000000000000000000000000000000000 tropidia_cuciculigoides_05560 CCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAAGCAGA00000000000000000000000000000000000000000000000000

Continued

Table A.3 Continued

tropidia_bambusifolia_017721 CCCTGTAATTCGAGTGAGATTGTAATGGCGCAAAAGCAGA10000000000000000000000000000100000000000000000000 sertifera_columbiana ------00000010001000000000000000000000000000000000000000 sertifera_sp_N565 ------00000010001000000000000000000000000000000000000000 Elleanthus_sp_374_AF314871 CCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAAGCAGA00000000000000000000000000000000000000000000000000 Epilyna_jemenzii_w2997 CCCTGTAATTCGAGCATGATTG-CA-GGCGCAAAAGCAGA?????????????????????????????????????????????????? EPILYNA_HIRTZII TC-TGTAAATCGACCA-GAAT-----GGCCCCAAAGCAGA00000000000?1?1000010000000000000000000000?1000000 Sobralia_mucroanta_W535 ------?????????????????????????????????????????????????? sobralia_crocea ------00000000000000000000000000000000000000000000000000 XEORCHIS_AMAZONICA_O799 CCCCGTAATTCGAGTGGGATTGTCATGGCGCAAAAGCAGA00?1?0?000000000000000000000000000000001?000100010 Epipogium_aphyllum CCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAAGCAGA00000000000000000000000000000000000000000000000000 Nervilia_plicata_ER48 ------01000010000000000000000000000000000000000000000000 Nervilia_shirensis_c280 ------00000000000000000000000000000000000000000000000000 Gastrodia_sesamoides_534 CCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAAGCAGA0000000000000000000000001?000000000000000000000000 Gastrodia_procera_PARTIAL ------00000010000000001?0000001?000000000000000000000000 gastrodia_sp_reunion_ER214 CCCTGTAATTCGAGTGAAA-TGTCATGGCGCAAAAGCAGA??????????0000000000000000000000000000000000000000 gastrodia_confusa_0801 CCCTGTAATTCGAGTGAAATTGTCATGGCGCAAAAGCAGA000001????0000000000000101000000000010001000000000 gastrodia_zyl_16313 ------00000000000000000000??1???000000000000000000000000 diceratostele_gabonensis_ER ACCTGTAATATGAGTGAGAT-GTCATAGCACAAA-GCACA00000000000000000000100001000000000000001000000000 Didymoplexis_pallens CCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAAGCAGA00000000000000000000??1???000000000000000000000000 Psilochilus_macrophyllus_ER02 CCCTGTAA------000000100000000000000000000000000010000001?????0?0 291 Psilochilus_LJ6914 TCGT-TAATTTGA-CGAGATA-TCATGGAACAAA-G-AGA??10?0?010010001?????????????????????0?01000000000 Triphora_trinathophora CCCTGTAATTCGA-TGAGATTGTCATGGCGCAAAAGCAGA000000?1??0000000000000000000000000001?000000010?0 Triphora_gentianoides_ER01 CCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAAGCAGA000000?1??00000000000000000000000000000000000010?0 triphora_amazonica_ER72 -----TAAG-CG--T-A-TTTGT-A-----CAAA------000010?0100001000000?1000011?0000000000000000010?0 Monophyllorchis_sp_435 CCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAAGCAGA00000000000000000000000000000000000000000???????00 Aplectrum_hyemale_104 CCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAAGCAGA00000000000000000000000000000000000000000000000000 Bletilla_striata_556 CCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAAGCAGA00000000000000000000000000000000000000000000000000 Isochilus_amparoana_204 CCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAAGCAGA00000000000000000000000000000000000000000000000000 Calypso_bulbosa_JF CCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAAGCAGA00000000000000000000000000000000000000000000000000 Leptotes_bicolor_1195 CCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAAGCAGA00000000000000000000000000000000000000000000000000 ephi_schmidtii_JVF CCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAAGCAGA00000000000000000000000000000000000000000000000000 Chysis_bractescens_436 CCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAAGCAGA00000000000000000000000000000000000000000000000000 Coelia_triptera_324 CCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAAGCAGA00000000000000000000000000000001000000000000000000

codonorchis_lessonii_01398 01???0?????000000000000000000100??00000100000000000000000000000000000000000000000000000000 corycium_nigrescens_0695 01???0?????000000000000000000100??00000100000000000000000000000000000000000100000000000000 brownleea_caerulea_21870 01???0?????000000000000000000100??00000100000000000000000000000000000000000100000000000000 Altensteinia_palacea_535 01???0?????000000000000000000100??00000100000000000000000000000000000000000000000000000000 Disperis_lindleyana_696 01???0?????000000000000000000100??00000100000000000000000000000000000000000100000000000000 Goodyera_pubescens_212 01???0?????000000000000000000100??00000100000000000000000000000000000000000000000000000000 Habenaria_repens_381 01???0?????000000000000000000100??00000100000000000000000000000001010?00000100000000000000

Continued

Table A.3 Continued

Orchis_quadripunctata_545 01???0?????000000000000000000100??00000100000000000000000000000000000000000100010000000000 Pachyplectron_arifolium_529 ???????????????00000000000000100??00000100000000000000000000000000000000000000000000000000 Spiranthes_cernua_402 ?????0??????00000000000000000100??0000010000000000000?100000000000000000000000000000000000 Stenoglottis_longifolia_1136 ?????????????0000000000000000100??00000100000000000000000000000000000000000100000000000000 PLAMORCHIS_TRILOBULATA 00000000000000000000000000000100??00000100000000000000000000000000000000000000000000000000 PALMORCHIS_powellii 00000010000000000000000000000?10???0000100000000000000000000000000100000000000100000000000 Epipactis_helleborine_199 000010??0000000000000000000000000100000100000000100000000000000000000000000000000000000000 Limodorum_abortivum_nadB 00000000000000000000000000000000010000010000000?000001001100000000100001000000000000100100 Cephalanthera_damasonium_575 000000000000000000000000000000000100000100000000000000000000000000000000000000000000000000 cepahalanthera_aust_dat115 000000000000000000000000010?00000?1000010001000000000000000110010000001?000010?00000000000 Neottia_nidus_avis_JVF 00000000010100000001?????00000000100000100000000000000000000000000000000000000000000000000 Listera_smallii_486 000000000000000000100000000000000100000100000000000000000000000000000000000000000000000000 listera_convol_2707 00000000000???1?00?00001101?00000000000100000010000000000000001010000000000000100000000000 listera_cordata_JVF2580 00000000000??10?00000?1??0000000010000010000100000000000000000000000000000000000000001???? aphyllorchis_montana 00000000010000000000000000000100??00000100000000000000000000000000000000000000000000000000 corymborkis_vert 000000000000000000000000000100001?00000100000000000000000000000000000000000000000000000000 Tropidia_Effusia_211 00000000000000000000000000000100??00000100000000000000000000000000000000000000000000000000 tropidia_cuciculigoides_05560 00000000000000000000000000000?10???0000100000000000000000000000000000000000000000000000000 tropidia_bambusifolia_017721 00000000000000000000000000000100??00000100000000000000000000000000000000000000000000000000 sertifera_columbiana 00000000000000010000000000000100??00100100000000000000000000000000000000000000000000000000 292 sertifera_sp_N565 00000000000000010000000000000100??00100100000000000000000000000000000000000000000000000000 Elleanthus_sp_374_AF314871 00000000000000000000000000000100??00000100000000000000000000000000000000000000000000000000 Epilyna_jemenzii_w2997 ?????????????????????????????????????????????????????????????????????????????????????????? EPILYNA_HIRTZII 00000000000000000000000000000100??00000100000000000000000000000000000000000000000000000000 Sobralia_mucroanta_W535 ???????????????????????????????????????????????0?????????????????????????????????????????? sobralia_crocea 00000000000000000000000000000100??00000100000000000000000000000000000000000000000000000000 XEORCHIS_AMAZONICA_O799 000000001000000??1??????????0?00??00000100000000000000000000000000000000000010?00?10?00010 Epipogium_aphyllum 00000000000000000000000000000100??00000100000000?10?0?00000000000000000000000000000000000? Nervilia_plicata_ER48 00000000000000000000000010000?10???0000100000000000000000000000000000000000000000000000000 Nervilia_shirensis_c280 00000000000000000000000000000100??00000100000000?10?0?00000000000000000000000000000000000? Gastrodia_sesamoides_534 000000000000000000000000000?1??????000010000000000010?100?10000000000000000000000??1?0???1 Gastrodia_procera_PARTIAL 000000000000000000000000000?1??????000010000000000010?100?10000000000000000000000??1?0???1 gastrodia_sp_reunion_ER214 000000000000000?10?0?????00000000100000100000000000000000000000000000000000000000000000000 gastrodia_confusa_0801 000000000000000000000000000?1??????0000100000000001???????00000000001???000000000000000000 gastrodia_zyl_16313 00000000000000000000000000000100??0000010000?1?0?00?000000000000000000000000000?1????0???0 diceratostele_gabonensis_ER 00000000000000000000000000000100??00000100000000000000000000000000000000000000000000000000 Didymoplexis_pallens 00000000000000000000000000000100??0000010000?1?0?00?000000000000000000000000000?1????0???0 Psilochilus_macrophyllus_ER02 001000000000000000001?0000000100??000?1???00000000001???0000000000000100000000000000000001 Psilochilus_LJ6914 10???0??0000000000001?0000000100??00010000000000000000010000000000000100000000000000000001 Triphora_trinathophora 00?10000000000000000000000000100??0000010000000000000000000000000000001?1000?1?00100?01??0 Triphora_gentianoides_ER01 00100000001000000000000000000100??0000000100000000000000000001000000000001???????????0???0 triphora_amazonica_ER72 00100000000?10000000010000000??1???1?00?1?100001??????????????????????????????????????????

Continued

Table A.3 Continued

Monophyllorchis_sp_435 00000000000000000000000000000100??00000100000000000000000000000000000000001??0?00000000001 Aplectrum_hyemale_104 01???0?????000000000000000000100??00000100000000000000000000000000000000000000000000000000 Bletilla_striata_556 00000000000000000000000000000100??00000100000000000000000000000000000000000000000000000000 Isochilus_amparoana_204 00000000000000000000000000000100??00000100000000000000000000000000000000000000000000000000 Calypso_bulbosa_JF 00000001000000000000000000000100??00000100000000000000000000000000000000000000000000000000 Leptotes_bicolor_1195 00000000000000000000000000000100??00000100000000000000000000000000000000000000000000000000 ephi_schmidtii_JVF 0000?1??????00000000000000000100??00000100000000000000000000000000000000000000000000000000 Chysis_bractescens_436 00000000000000000000000000000100??00000100000000000000000000000000000000000000000000000000 Coelia_triptera_324 00000000000000000000000000000100??00000100000000000000000000000000000000000000000000000000

codonorchis_lessonii_01398 00000000010000000000000000?1000000000000000000000000000000000000000000000?1000000000000000 corycium_nigrescens_0695 00000000010000000000000000?1000000000000000000000000000000000000000000000?1000000000000000 brownleea_caerulea_21870 00000000010000000000000000?1000000000000000000000000000000000000000000000?1000000000000000 Altensteinia_palacea_535 00000000010000000000000000?1000000000000000000000000000000000000000000000?1000000000000000 Disperis_lindleyana_696 0??1?0??0?0??0000000000000?10000000000000000000000000000000001????0000000?1000000000000000 Goodyera_pubescens_212 00000000010000000000000000?1000000000000000000000000000000000000000000000?1000000000000000 Habenaria_repens_381 0??1?0??0?0??0000000000000?100000000?1?0000000000000000000000000000000000?1010???0?0000000 Orchis_quadripunctata_545 00000000010000000000000000?1000000000000000000000000000000000000000000000?1000000000000000 Pachyplectron_arifolium_529 00000000010000000000000000?1000000000000000000000000000000000000000000000?1000000000000000 293 Spiranthes_cernua_402 000000000100000000000000?1??0?0000000000000000000000000000000000000000000?1000000000000000 Stenoglottis_longifolia_1136 0??1?0??0?0??0000000000000?1000000000000000000001???0?00?0000000000000000?10000000000000?1 PLAMORCHIS_TRILOBULATA 00000000010000000000000000?1000000000000000000000000000000000000000000000?1000000000000000 PALMORCHIS_powellii 00000000010000000000000000?1000001000000000000000000000000000001000000000?1000000000000000 Epipactis_helleborine_199 00000000010000000000000000?1000000000000000000000000000000000000000000000?1000000000000000 Limodorum_abortivum_nadB 00000000010000000000000000?10000001?00010???000000000??1??000000010000000?100?000?0??????? Cephalanthera_damasonium_575 00000000010000000000000000?10000000000000000100000000?10?0000000000000000?1000000000000000 cepahalanthera_aust_dat115 00000000010000000000000000?10000001?00000100010000100?10?00000010001000?1??000000010010000 Neottia_nidus_avis_JVF 00000000010000000000000000?100000000000000000000000?1?00?1000000000000000?1000000000000000 Listera_smallii_486 00000000010000000000000000?1000000000000000000000000000000000000000000000?1000000000000000 listera_convol_2707 00000000000010000000000000?1000000000000000000000000000010000000000000100?1000000000010000 listera_cordata_JVF2580 ?????0?????????0?0???00000?1000000000000000000000000000000000000000000000?1000000000000000 aphyllorchis_montana 00000000010000000000000000?10000000000000000000000000000000000000000000?1??000000000000000 corymborkis_vert 00000000010000000000000000?1000000000000000000000000000000000000000000000?1000000000000000 Tropidia_Effusia_211 00000000010000000000000000?1000000000000000000000000000000000000000000000?1000000000000000 tropidia_cuciculigoides_05560 00000000010000000000000000?1000000000000000000000000000000000000000000000?1000000000000000 tropidia_bambusifolia_017721 00000000010000000000000000?1000001000000000000000000000000000001000000000?1000000000000000 sertifera_columbiana 00000000010000000000000000?1000000000000000000000000000000000000000000000?1010???0?0000000 sertifera_sp_N565 00000000010000000000000000?1000000000000000000000000000000000000000000000?1010???0?0000000 Elleanthus_sp_374_AF314871 00000000010000000000000000?1000000000000000000000000000000000000000000000?1000000000000000 Epilyna_jemenzii_w2997 ?????????????????????????????????????????????????????????????????????????????????????????? EPILYNA_HIRTZII 00000000010000000000000000?1000000000000000000000000000000000000000000000?1000000000000000

Continued

Table A.3 Continued

Sobralia_mucroanta_W535 ?????????????????????????????????????????????????????????????????????????????????????????? sobralia_crocea 00000000010000000000000000?1000000000000000000000000000000000000000000000?1000000000000000 XEORCHIS_AMAZONICA_O799 0?10?0??0?0000000000000000?10000000010?00?1?00000101000000000010000000000??100??00110101?0 Epipogium_aphyllum 1????0?????????00000000000100001????00000000000000000?10?001????????0001000000000000000010 Nervilia_plicata_ER48 00000000010000000000000000?1000000000000000000000000000000000000000000000?1000000000000000 Nervilia_shirensis_c280 1????0?????????00000000000100001????00000000000000000?10?001????????0001000000000000000010 Gastrodia_sesamoides_534 0?00?0000?1????0000000010000000000010000000000000000000000000000000000000?100000?1???????0 Gastrodia_procera_PARTIAL 0?00?0000?1????0000000010000000000010000000000000000000000000000000000000?100000?1???????0 gastrodia_sp_reunion_ER214 000000100?000??1???????????????0????0000000000000000000000001000000000000000?1???????????0 gastrodia_confusa_0801 000000?10?0000000010001?00001??0????0000000000000000000000000000000000000000?1???????????0 gastrodia_zyl_16313 000000?10?000?100000000000000100001?000000010000000000000000000000000000010000010000000000 diceratostele_gabonensis_ER 00000000010000000000000000?10000000000000000000000000?10?0000000000000000?1000000000000000 Didymoplexis_pallens 000000??1??????00000100000000?100?00000000010000000000000000000000000000010000010000000000 Psilochilus_macrophyllus_ER02 0?00?000010000000000000000?100000100000000000?1?00000100?00000000000000?1??000000000000000 Psilochilus_LJ6914 0?00?000010000000000000000?100000000000000000?1?00000100?0000000000000000?1000001000000000 Triphora_trinathophora 0100?0000001?00000?1?10010??00001???00101???????00000100?01000001?0001?????0001?00001??000 Triphora_gentianoides_ER01 0100?0000000010010???10010??00001???00000100000100000100?01000001?0?1??????0000100000?1000 triphora_amazonica_ER72 ?????????????????????????????????????????????????????????????????????????????????????????? Monophyllorchis_sp_435 0?00?00001000000?1????0000?1000000000000000000001???0?00?0000000001?000?1??000010000000000 Aplectrum_hyemale_104 00001000010000000000000000?1000000000000000000000000000000000000000000000?1000000000000000 294 Bletilla_striata_556 00000000010000000000000000?1000000000000000000000000000000000000000000000?1000000000000000 Isochilus_amparoana_204 0000?1??????????????????????????????????????????????????????????????????????00??0000000000 Calypso_bulbosa_JF 00001000010000000000000000?1000000000000000000000000000000000000000000000?1000000000000000 Leptotes_bicolor_1195 00001000010000000000000000?1000000000000000000000000000000000000000100000?1000000000000000 ephi_schmidtii_JVF 00001000010000000000000000?1000000000000000000000000000000000000000000000?1000000000000000 Chysis_bractescens_436 00001000010000000000000000?1000000000000000000000000000000000000000000000?1000000000000000 Coelia_triptera_324 00001000010000000000000000?1000000000000000000000000000000000000000000000?1000000000000000

codonorchis_lessonii_01398 0010000000000000000000000000000000000000000000000001000000000000000000000000000?10000?0000 corycium_nigrescens_0695 00?1000000000000000000000000000000000000000000000001000000000000000000000000000?10000?0000 brownleea_caerulea_21870 0010000000000000000000000000000000000000000000000001000000000000000000000000000?10000?0000 Altensteinia_palacea_535 0010010000000100100000000000000000000000000000000001000000000000000000000000000?10000?0000 Disperis_lindleyana_696 0010000000000000000000000000000000000000000000000001000000000000000000000000000?10000?0000 Goodyera_pubescens_212 0010000000000000000000000000000000000000000000000001000000000000000000000000000?10000?0000 Habenaria_repens_381 01????000000000100000000?1?0000000000000000000000001000000000000000000000000000?10000?0000 Orchis_quadripunctata_545 01????000000000100000000?1?0000000000000000000000001000000000000000000000000000?10000?0000 Pachyplectron_arifolium_529 0010000000000000000000000000000000000000000000000001000000000000000000000000000?10000?0000 Spiranthes_cernua_402 0010010000000100100000000000000000000000000000000001000000000000000000000000000?10000?0000 Stenoglottis_longifolia_1136 ??????0?00?00?1?00000??1?0?1000000000000000000000001000000000000000000000000000?10000?0000 PLAMORCHIS_TRILOBULATA 001000000000000000000000000000000000000000000000000110000000000000000000000000010000000000 PALMORCHIS_powellii 001000000010000100000000100100001001000000?100001?01101?1000100?1?000101100001000000000000 Epipactis_helleborine_199 001000000000000000000000000000000000000000000000000100000000000000000000000000000000000000

Continued

Table A.3 Continued

Limodorum_abortivum_nadB ????????????????????????????????????????????????????????????00000010001??????????????????? Cephalanthera_damasonium_575 001000000000000000000000000000000000000000000000000100000000000000000000000000000000000000 cepahalanthera_aust_dat115 00100000000000010000000000100111011?1?11000010?1???????00000000000000000000000000000000000 Neottia_nidus_avis_JVF 000000000000000000??1?????????000000000000000000000100000000000000000000000000000000000000 Listera_smallii_486 000000000000000000??1?????????000000000000000000000100000000000000000000000000000000000000 listera_convol_2707 000000000000000100??1?????????010001000000000000000100000000000000100000000100000000000000 listera_cordata_JVF2580 000000000000000000??1?????????000000000000000000000100000010000000000000000000000000000000 aphyllorchis_montana 001000000000000000000000000000000000000000000000000100000010000000100000100000000000000000 corymborkis_vert 001000000000000000000000000000000000000000000000000110000000000000000000000010000000000000 Tropidia_Effusia_211 001000000000000000000000000000000000000000000000000100000000000000000000000000000000000000 tropidia_cuciculigoides_05560 001000000000000000000000100000000000000000000000000100000000000000000000000000000000001000 tropidia_bambusifolia_017721 001000000000000000000000100000010001000000000000000100100000000001000000000010000000000010 sertifera_columbiana 001000000000000000000?10?000000000010000000000101?0100110001001???000000000000000000000000 sertifera_sp_N565 001000000000000000000?10?000000000010000000000101?0100110001001???000000000000000000000000 Elleanthus_sp_374_AF314871 001000000000000000000000000000000000000000000000000100000000000000000000000000000000000000 Epilyna_jemenzii_w2997 ?????????????????????????????????????????????????????????????????????????????????????????? EPILYNA_HIRTZII 001000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Sobralia_mucroanta_W535 ????????????????????0????0?000000000000000000000000100000000000000000000000000000000000000 sobralia_crocea 001000000000000000000000000000000000000000000000000100000000000000000000000000000000000000 XEORCHIS_AMAZONICA_O799 ?0?0000100?00000010000000000100000000000000001?00001?1000000000000010000110000000000000000 295 Epipogium_aphyllum ?0?0001?00??0????000000000000000000000000000000000010000000000000000000000000?1??1?00??000 Nervilia_plicata_ER48 001000000000000000000000000000000000000000000000000100000000000000000000000000000000000000 Nervilia_shirensis_c280 ?0?0001?00??0????000000000000000000000000000000000???????????????????????????????????????? Gastrodia_sesamoides_534 ?0?0000?1??????????00??0?000000000000000000000000001000000000000000000000000000000100??000 Gastrodia_procera_PARTIAL ?0?0000?1??????????00??0?0000000000000000000000000010000000000000010000000100000000001?1?1 gastrodia_sp_reunion_ER214 ?0?0000001?????????00??0?000000000000000000000000001000000000000000000000000000000?10??000 gastrodia_confusa_0801 ?0?0000001?????????00??0?000000000000000000000000001000000000000000000000000000000??1????0 gastrodia_zyl_16313 00??1?0000010?0000000000000000000000000001???0?0000100000000000000010000000000000000000000 diceratostele_gabonensis_ER 001000000000000000000000100000000000000000000000000100000000000?1?000001100100000000000001 Didymoplexis_pallens 00??1?0000010?0000000000000000000000000?10??0000000100000000000000010000000000000000000000 Psilochilus_macrophyllus_ER02 001000000000000000000100000000000000000000000000001?00000000000000000000000000000000000000 Psilochilus_LJ6914 001000000000000000000000000000010000000000000010011?10000100000000000000000000000000000000 Triphora_trinathophora 10?00000000?1??????00?00001010000000010000000000000100000010000000000000000000000000000000 Triphora_gentianoides_ER01 001000000000000000100?000010100000000000001000000101000000000101000?1001000000000000000000 triphora_amazonica_ER72 ?????????????????????????????????????????????????????????????????????????????????????????? Monophyllorchis_sp_435 001000000000000000000000000000000000000000000000000100000000000000000000000000000000000000 Aplectrum_hyemale_104 001000000000000000000000000000000000000000000000000100000000000000000000000000000000000000 Bletilla_striata_556 00??1?000000000000?10????0?000000000000000000000000100000000000000000000000000000000000000 Isochilus_amparoana_204 001000000000000000000000000000000000000000000000000100000000000000000000000000000000000000 Calypso_bulbosa_JF 001000000000000000000000000000000000000000000000000100000000000000000000000000000000000000 Leptotes_bicolor_1195 001000000000000000000000000000000000000000000000000100000000000000000000000000000000000000

Continued

Table A.3 Continued

ephi_schmidtii_JVF 001000000000000000000000000000000000000000000000000100000000000000000000000000000000000000 Chysis_bractescens_436 001000000000000000000000000000000000000000000000000100000000000000000000000000000000000000 Coelia_triptera_324 001000000000000000000000000000000000000000000000000100000000000000000000000000000000000000

codonorchis_lessonii_01398 000000000000000000000101000000000000000000000000100000000000000000000000000000000000000000 corycium_nigrescens_0695 000000000000000000000001001000000000000000000000100000000000000000000000000000000000000000 brownleea_caerulea_21870 000000000000000000000001000000000000000000000000100000000000000000000000000000000000000000 Altensteinia_palacea_535 000000000000000000000001000000000000000000000000100000000000000000000000000000000000000000 Disperis_lindleyana_696 00000000000000000000000100000000000000000000??1????0?????0???????0000000000000000000000000 Goodyera_pubescens_212 000000000000000000000001000000000000000000000000100000000000000000000000000000000000000000 Habenaria_repens_381 00000000000000000000000100000000000000000000000010000???10???00000000000000000000000??10?? Orchis_quadripunctata_545 000000000000000000000001000000000000000000000000100000000000000000000000000000000000000000 Pachyplectron_arifolium_529 000000000000000000000001000000000000000000000000100000000000000000000000000000000000000000 Spiranthes_cernua_402 000000001000000000000001000000000000000000000000100000000000000000000000000000000000000000 Stenoglottis_longifolia_1136 00000000000000010?????01000000000000000000000000100000000000000000000000000000000000000000 PLAMORCHIS_TRILOBULATA 00000000000000100000001??000000000000000?100??0??0001?10000??10000000000000000000000000000 PALMORCHIS_powellii 000000000000001000000001000000000000000000000000100000000000000000000000000000000000000000 Epipactis_helleborine_199 00000000000000000000000101?????????00??00000000010000000000?100000000000000000000000000000 Limodorum_abortivum_nadB ???????0?000000000001?0?1000000000000000??10??0??00000000000000000010000000000000000000010 Cephalanthera_damasonium_575 000001000000000000000001000000000000000000000000000000000000000000000000000000000000000000 296 cepahalanthera_aust_dat115 000000000000000000000001000000000000000000000000000000000000000000000000000000000000000000 Neottia_nidus_avis_JVF 1000000000000000000000010000000000??1??0?0000001000000000000000000000000000?1?????????00?0 Listera_smallii_486 000000000000000000000001000000000000000000000000000000000000000000000000000000000000000000 listera_convol_2707 00000000??1???????????????????????????????00??0??0000??100?0000000000000000000000000000000 listera_cordata_JVF2580 00000000000000000000000100000000100000?1??00??0??00011000010000000000000000001?00?10?00000 aphyllorchis_montana 00000000000000000000000?100000000000000000001000100000000000000000001000000000000100000000 corymborkis_vert 00000000000000000000000?100000000000001000001000100000000000000000000000100000000000000000 Tropidia_Effusia_211 000000000000000000000001000000000000000000001000100000000000000000000000000000000000000000 tropidia_cuciculigoides_05560 000000000000000000000001000000000000000000001000100000000000000000000000000000000000000010 tropidia_bambusifolia_017721 00000000000000100000000100000000000001?000001000100010000000000000000000000000000000000000 sertifera_columbiana 00000000000000000000000100000000000000000000100010000000000???1000000000000000000000000000 sertifera_sp_N565 00000000000000000000000100000000000000000000100010000000000???1000000000000000000000000000 Elleanthus_sp_374_AF314871 00000000000000000000000100000000000000000000100010000000000???1000000000000000000000000000 Epilyna_jemenzii_w2997 ?????????????????????????????????????????????????????????????????????????????????????????? EPILYNA_HIRTZII 00000000000000100000000100000000000000000000100010000000000???1000000000000000000000000000 Sobralia_mucroanta_W535 00000000000000000000000100000000000000000000100010000000000???1000000000000000000000000000 sobralia_crocea 00000000000000000000000100000000000000000000100010000000000???1000000000000000000000000000 XEORCHIS_AMAZONICA_O799 00000000?10????????????????????????????0?000?0001000000000000001001????0?0??00010?000000?? Epipogium_aphyllum 01100??1?00??????????????0??00000000001000001000??10?????0??????0000000001?????????????0?? Nervilia_plicata_ER48 000000000000000?1????????000000000000000???1??0????0?????0??????00000000000100000000?100?0 Nervilia_shirensis_c280 ?????????????????????????????????????????????????????????????????????????????????????????? Gastrodia_sesamoides_534 00??10000000000000000000000000100000000000001000100000000000000000000000000000000000000000

Continued

Table A.3 Continued

Gastrodia_procera_PARTIAL 00?10000100000100000000000010000?10000001000?10??0001?10000??10000000000000000000000000000 gastrodia_sp_reunion_ER214 00000000000000100?1?0000000100?1??00000000001000?100?????0???00000001100001?00001?????00?0 gastrodia_confusa_0801 00?10100000000100000010?100000000000000000001000100000000000000000000000000000000000???1?? gastrodia_zyl_16313 00000000000001?00100010?10000000000000000000100010000?100000000000000000000000000100000010 diceratostele_gabonensis_ER 00000000000000100000010100000010000000001000100010000?1000010000000010001000000000000000?1 Didymoplexis_pallens 00000?10?00000000001010?10000000000000000000100010000?100000000000000000000000000??1??00?0 Psilochilus_macrophyllus_ER02 0000000000000000000000010000000000?10??0?0001000100000000000000000000000000000100000000000 Psilochilus_LJ6914 0000000000000000000000010000000000?10??0?0001000100000000000000000000000000000100000000000 Triphora_trinathophora 0000000000010??00?0?00010010?1????0000000000100010000????1???????00?0??1?0??0???0??0?00000 Triphora_gentianoides_ER01 00000000000?1????????????00010?0?000001000001000100000000000000010001?10?00000000000100000 triphora_amazonica_ER72 ?????????00????????????????????????00??000001000???1?????????????????????????????????????? Monophyllorchis_sp_435 0000000000000000000000010000000000100??000001000100000000000000000000000000000000000000000 Aplectrum_hyemale_104 000000000000000000000001000000000000000000001000100000000000000000000000000000000000000000 Bletilla_striata_556 000000000000000000000001000000000000000000001000100000000000000000000000000000000000000000 Isochilus_amparoana_204 000000000000000000000001000000000000000000001000100000000000000000000000000000000000000000 Calypso_bulbosa_JF 000000000000000000000001000000000000000000001000100000000000000000000000000000000000000000 Leptotes_bicolor_1195 0000000000000000000000010000000000000000000010001000000000000000?1???????????????????????? ephi_schmidtii_JVF 000000000000000000000001000000000000000000001000100000000000000000000000100000000000000000 Chysis_bractescens_436 000000000000000000000001000000000000000000001000000000000000000000000000000000000000000000 Coelia_triptera_324 000000000000000000000001000000000000000000001000100000000000000000000000000000000000000000 297

codonorchis_lessonii_01398 00001???00???0?000000000000001001001?00010000000000000000000000000000000000000000000000000 corycium_nigrescens_0695 000000000000000000000000000000001001?00010000000000000000000000000000000000000000000000000 brownleea_caerulea_21870 000000000000000000000000000000001001?0001000?100???000000000001000000000000100010??00???00 Altensteinia_palacea_535 0000000000000010000000000000000010001000000000000000??10?000000000000000000000000000000000 Disperis_lindleyana_696 000000000000001000000000000000001000??1??0000000000000000000000000000000000000000000000000 Goodyera_pubescens_212 000000000000001000000000000000001000??1??0000000000000000000000000000000000000000000000000 Habenaria_repens_381 000000000000001000000000000000001000??1??000000000000000000000000000000000000000000001??00 Orchis_quadripunctata_545 000000000000001000000000000000001000??1??0000000000000000000000000000000000000000000000000 Pachyplectron_arifolium_529 000000000000001000000000000000001000??1??0000000000000000000000000000000000000000000000000 Spiranthes_cernua_402 000000000000001000000000000000001000??1??0000000000000000000000000000000000001000?0000?000 Stenoglottis_longifolia_1136 000000000000001000000100000000001000??1??0001000000000000000000000000000000000000???1????? PLAMORCHIS_TRILOBULATA 000000000000000000?1??0000000000100000000?1?000000000000100000?1000000000?0000000000?00000 PALMORCHIS_powellii 00000000000000000000000000000000100000000?1?0000000000000000000000000000000000000000000000 Epipactis_helleborine_199 00000????1???0??0??0000000000000100000000?1?0000000000000000000000000000000000000000000000 Limodorum_abortivum_nadB 0000000000000000000000000000000010000001?0010000010000000001000000000000000000000000000000 Cephalanthera_damasonium_575 000000000000000000000000000000001000000000000000000000000000000000000000000000000000000000 cepahalanthera_aust_dat115 000000000000000000000000000000001000000000000000000000000000000000000000000000000000000000 Neottia_nidus_avis_JVF 00000???10???0??0?000000000000001000000000000000000000000000000000000000000000000000000000 Listera_smallii_486 00000000000000000000000000000000100000000?1?0000000000000000000000000000000000000000000000 listera_convol_2707 0000000000000000000000000000000010000000000000000?100000?1?0000000000000000000000000000000

Continued

Table A.3 Continued

listera_cordata_JVF2580 00000000000010?00000000?1??00000100000000?1?0000000000000010000000000010?00?00000000000100 aphyllorchis_montana 0000000000000000000000010000000010001000010000000000000000000000100000?1?00??0000000000000 corymborkis_vert 000000000000000000000000001000001000000000000000000000000000000000000000000000000000000000 Tropidia_Effusia_211 000000000000000000000000000000001000000000000000000000000000000000000000000000000000000000 tropidia_cuciculigoides_05560 000000000000001000000000000000000000000001000000000010000000000000000000000000000000000000 tropidia_bambusifolia_017721 000000000000000000000000000100001000000000000000000000000000000000000000000000000000000000 sertifera_columbiana 000000000000000000000000000000001000000000000000000000000000000000000000?1??????????0????? sertifera_sp_N565 00000000000000000000000000000000100000000000000000000000000000000000000000000?1?????0????? Elleanthus_sp_374_AF314871 000000000000000000000000000000001000000000000000000000000000000000000000000000000000000000 Epilyna_jemenzii_w2997 ?????????????????????????????????????????????????????????????????????????0??????????0????? EPILYNA_HIRTZII 000000000000000000000000000000001000000000001000000000000000000000000000000000000000000000 Sobralia_mucroanta_W535 000000000000000000000000000000001000000000000000000000000000000000000000000000000000000000 sobralia_crocea 000000000000000000000000000000001000000000000000000000000000000000000000000000000000000000 XEORCHIS_AMAZONICA_O799 1??00??0000010?000001000000000001000000000000000100000000010000000000000000000000000000000 Epipogium_aphyllum 0?000000000000010?00000000000000100000000000???1????????????????????0????0??????????0????? Nervilia_plicata_ER48 00000100000000000100000001000000??10000000000000000010000001000000000100000?10000100001000 Nervilia_shirensis_c280 ?????????????????????????????????????????????????????????????????????????????????????????? Gastrodia_sesamoides_534 0?100?00001??0?001000000000000001000?1000000??10???????0?0000000000000000000000?1??00????? Gastrodia_procera_PARTIAL 0?100?00001??0?001000000000000001000?1000000??10???????0?000000000000000000000000?100???00 gastrodia_sp_reunion_ER214 01000000000100010?000000000?1????000?100000100000000???1???0000000??1????0??????????0????? 298 gastrodia_confusa_0801 0??00?000001000?1?????0000000001?000100000000000000000000000000000000000000000000??10????? gastrodia_zyl_16313 0??10???000?00000000000000000?1??000000000001000000000000000000000000000000000000000000000 diceratostele_gabonensis_ER 00000000000000100100010000000000?100??1??00010000000?100?0000000?1?00000100000000000000??1 Didymoplexis_pallens 000000000000000000000?1?????00001000??1??0000000100000000000000000000000000000000000000?10 Psilochilus_macrophyllus_ER02 000000000000000001000000000000001000000000000000000000000000000000000000000000000000000000 Psilochilus_LJ6914 000000000000000001000000000000001000000000000000000000000001000000000000000000000000000000 Triphora_trinathophora 00000?10000010?00100000000000100100000000000000000000000100?1???00100000001???0?0??00????0 Triphora_gentianoides_ER01 00000?100000?1????????????????????????????????00???000000000000000000000000000000000001000 triphora_amazonica_ER72 ?????????????????????????????????????????????????????????????????????????0??????????0????? Monophyllorchis_sp_435 00000??1000?001000000000000000001000000000000000000000000000000000000000000000000000000000 Aplectrum_hyemale_104 000000000000000000000000000000001000000000001000010000000000000000000000000000000000000000 Bletilla_striata_556 000000000000000000000000000000001000000000000000010000000000000000000000000000000000000000 Isochilus_amparoana_204 000000000000000000000000000000001000000000000000010000000000000000000000000000000000000000 Calypso_bulbosa_JF 000000000000000000000000000000001000000000000000010000000000000000000000000000000000000000 Leptotes_bicolor_1195 ?????????????0??????????????????????????????00000??1??00?01001??00?10?00?000000?1??00????? ephi_schmidtii_JVF 000000000000000000100000000000001000000000000000000000000000000000000000000000000000000000 Chysis_bractescens_436 00000000000000000000000000000000100000000?1?00000100000000000000000000000?0000000000?00000 Coelia_triptera_324 000000000000000000000000000000001000000000000000010000000000000000000000000000000000000000

Continued

Table A.3 Continued

codonorchis_lessonii_01398 0?1?0?00?0000000000000000000000000000010?00000??1?0?0?000000000000000000000000000000000000 corycium_nigrescens_0695 0?1?0?00?00000000000000000000001?0000010?00000??1?0?0?0000000001000000?1?????0?0?1?????0?0 brownleea_caerulea_21870 ??0?0?0000000000000000000000000010000010?00000??1?0?0?000000000000000000000000000000000000 Altensteinia_palacea_535 0000000000000000000000000000010????????????????????????????0??0?0??0?????????0?0001?00?1?? Disperis_lindleyana_696 000?1?00???0??000?00?10000000001?0000010?00000??1?0?0?000000000000000000000000000000000000 Goodyera_pubescens_212 0000000000000000000000000000000000000010?00000??1?0?0?000000000000000000000000000000000000 Habenaria_repens_381 ??0?000000000000000000000000000000000010?00000??1?0?0?0000000?1?0????????????????????????? Orchis_quadripunctata_545 0?1?0?00?0000000000000000000000000000010?00000??1?0?0?0000000?1?0????????????????????????? Pachyplectron_arifolium_529 0000000000000000000000000000000000000010?00000??1?0?0?000000000000000000000000000000000000 Spiranthes_cernua_402 00000000000000000000000000000000000000?1?????????????????0000000000000000100000010????0000 Stenoglottis_longifolia_1136 ??????????????????????????????????????????????????????????????0?0????????????????????????? PLAMORCHIS_TRILOBULATA 000000000000000000001000000000?00000?1000000001000000000000000?0?0000000000000000?00000?0? PALMORCHIS_powellii 000000000000000000000000000000000000000000000010000000000000000000000000000000000000000000 Epipactis_helleborine_199 000000000000000000000000000000000000000000000010000000000000000000000000000000000000000000 Limodorum_abortivum_nadB 010?000000000?100??0?0000?1?000????0???0?0?000000100000000001000000010?00?0010100000000000 Cephalanthera_damasonium_575 0000000000?1??000??00000000000000000000000000010000000000000000000000000000000000000000000 cepahalanthera_aust_dat115 000000000000000000000000000000000000000000000010000000000000000000000000000000000000000000 Neottia_nidus_avis_JVF 000000000010010000000000000?100????????0????0???0?0001???1?0?00?1????????????????????????? Listera_smallii_486 0000000000000000000000000000000000000000000000100000000000000000?0000000000000000000000000 listera_convol_2707 000000000000000000000000000000000000000000100010000000000000000000000000000000000000100000 299 listera_cordata_JVF2580 ??0?0001??????000??0?00000000000?1?0??00001001??0?001??0000000010000?1?0?????0000001000000 aphyllorchis_montana 00000100000000000001?????000000000001000000000?1000100100010?00000000000000000000000000000 corymborkis_vert 00010000000000000000001??00000000000100000000010000000000000000000000000000100000000000000 Tropidia_Effusia_211 0000000000000000000000000000000000000000000000100000000000000000000010?00?0000000000000000 tropidia_cuciculigoides_05560 000100000000000000000001?0000001?0000000000000100000000000000000000000000000000000000100?1 tropidia_bambusifolia_017721 000000000000000000000000000000001000000000000010000000000000000000000000000000000000000000 sertifera_columbiana ??????????????????????????????0???????????????????????????????0?0????????????????????????? sertifera_sp_N565 ??????0????????00????????0000?1???????????????????????????????0?0????????????????????????? Elleanthus_sp_374_AF314871 000000000000000000000000000000000000000000000010000000000000000000000000000000000000000000 Epilyna_jemenzii_w2997 ??????????????????????????????0???????????????????????????????0?0????????????????????????? EPILYNA_HIRTZII 000000000000000001000000000000000000100010000010000001000000000000000000000100000000100000 Sobralia_mucroanta_W535 000000000000000000000000000000000000000000000010000000000000000000000000000000000000000000 sobralia_crocea 000000000000000000000000000000000000000000000010000000000000000000000000000000000000000000 XEORCHIS_AMAZONICA_O799 0000000000001000001000000000000000000000?1?00010000000??100000000?100000000001??0000000010 Epipogium_aphyllum ?????????????????????????????00????????0??????????0?0?0000?1??0?0????????????0??0000010000 Nervilia_plicata_ER48 0001000010000000000010001000000000001000001000100000010000000000000000100?1?00?100000????? Nervilia_shirensis_c280 ?????????????????????????????????????????????????????????????????????????????????????????? Gastrodia_sesamoides_534 ??????0???????000??0?000100000000000000000001?????0?0?000000000000000000000000000000000000 Gastrodia_procera_PARTIAL ??0?000000000??10?????????0?000??000000000001?????0?0?000000000000000000000000000000000000 gastrodia_sp_reunion_ER214 ?????????????????????????????00????????????????????????????0??0?00000000000100000000010000 gastrodia_confusa_0801 ??????0????????00??0?000100000001000000000001?????0?0?000000000000000000000000000000010000

Continued

Table A.3 Continued

gastrodia_zyl_16313 00000?1???????????????????0?000??0?0?000000000??1?0?0?00000000000??1?????????0??0000000000 diceratostele_gabonensis_ER ??????0???????000??0?000000000000000000000000000000000000000000000000000000000000000000000 Didymoplexis_pallens ????0?00?0000???1?????????0?000??0?0000000?10???0?000000000000000??1?????????0??0000000000 Psilochilus_macrophyllus_ER02 000000000000000000000000010?000??000000000000010000000?100000000010000001????0000000000000 Psilochilus_LJ6914 000000000000000000000000010?000??000000000000010000000?100000000010000001????0000000000000 Triphora_trinathophora ??????00??????000??000001001000??000000000000010000000000000010?00000000000000000000100000 Triphora_gentianoides_ER01 1?0?0000?1?0??000?00001??00000000000100000000010001?0?000000000000000000000000000000000000 triphora_amazonica_ER72 ??????????????????????????????0???????????????????????????????0?0????????????????0????1000 Monophyllorchis_sp_435 000000000000000000000000000000000000000000000010000000000000000000000000000000000000000000 Aplectrum_hyemale_104 000000000000000000000000000000000000000000000010000000000000000000000000000000000000000000 Bletilla_striata_556 000000000000000000000000000000000000000000000010000000000000000000000000000000000000000000 Isochilus_amparoana_204 000000000000000000000000000000000000000000000010000000000000000000000000000000000000000000 Calypso_bulbosa_JF 000000000000000000000000000000000000000000000010000000000000000000000000000000000000000000 Leptotes_bicolor_1195 ??????0???????000??0?0000000000000?1???0???000??000000000000000000000000000000000000000000 ephi_schmidtii_JVF 000000000000000000000000000000000010000000000000000000000000100000000000000000000000000000 Chysis_bractescens_436 000000000000000000000000000000?0000000000000001000000000000000?0?0000000000000000000000000 Coelia_triptera_324 000000000000000000000000000000000000000000000010000000000000000000000000000000000000000000

300 codonorchis_lessonii_01398 0000000000000?1000000000000000000000000000000000000000000000000000000000000000000000000000 corycium_nigrescens_0695 0?00?0?001?????000000001???????????????????????0?????????????????????????????????????????? brownleea_caerulea_21870 0000000000000?1000000000000000000000000000000000000000000000000000000000000000100000000000 Altensteinia_palacea_535 0????0???????????0???000???0????0???000000010??1?????????????????????????????????????????? Disperis_lindleyana_696 0000000000000?1000000000000000000000000000000000000000000000000000000000000000000000000000 Goodyera_pubescens_212 0000000010000?100000000000000000000000000000000000000000000100?000000000000000000000000000 Habenaria_repens_381 ???????????????????????0???????????????????????0?????????????????????????????????????????? Orchis_quadripunctata_545 ???????????????????????0???????????????????????0?????????????????????????????????????????? Pachyplectron_arifolium_529 0000000000000?1000000000000000000000000000000000000000000000000000000000000000000000000000 Spiranthes_cernua_402 0000000000000??100?00000?1000000000000000000000000000001??00001000000000000000000000000000 Stenoglottis_longifolia_1136 ???????????????????????0???????????????0???????0?????????????????????????????????????????? PLAMORCHIS_TRILOBULATA ?????????????????????????????????????????????????????????????????????????????????????????? PALMORCHIS_powellii 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Epipactis_helleborine_199 00000000000000000000000000000000000000000000000000000000000000000000000?10?000010000000000 Limodorum_abortivum_nadB 000000000000100000000000??10?0001??????0??????00??0000?00000?1????????1??????????????????? Cephalanthera_damasonium_575 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 cepahalanthera_aust_dat115 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Neottia_nidus_avis_JVF ???????????????????????????????????????????????0?????????????????????????????????????????? Listera_smallii_486 00000000000000000000000000000000000000000000000?000000000000000000000000000000000000000000 listera_convol_2707 000000000000000000?1?000???0?0000010000000000000000000000000000000000000000000000000000000 listera_cordata_JVF2580 010000000001010000101000???0?00000????????????????????????????????????????????????????????

Continued

Table A.3 Continued

aphyllorchis_montana 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 corymborkis_vert 0?10?0???000000000000000000000000000000000000000000?1?????????????????0??????????????????? Tropidia_Effusia_211 000000000000000000000000000000000000000000000000000?1?????????????????0??????????????????? tropidia_cuciculigoides_05560 0??0?0???000000000000000000000000000000000000000000?1?????????????????0??????????????????? tropidia_bambusifolia_017721 000000000000000000000000000000000000000000000000000?1?????????????????0??????????????????? sertifera_columbiana ???????????????????????0???????????????0???????0?????????????????????????????????????????? sertifera_sp_N565 ???????????????????????0???????????????0???????0?????????????????????????????????????????? Elleanthus_sp_374_AF314871 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000?10 Epilyna_jemenzii_w2997 ???????????????????????0???????????????0???????0?????????????????????????????????????????? EPILYNA_HIRTZII 000000100001000000000000000000000000010000000000000000000000000000000000000000000000000100 Sobralia_mucroanta_W535 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000?10 sobralia_crocea 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000?10 XEORCHIS_AMAZONICA_O799 0001?0???00?0000000000001000100000??1?000010100010000000000010???00?010001?0?00??1?0000??? Epipogium_aphyllum 1????????????????????000???????????????0??????00???000???????????????0010010?1?00010?10??? Nervilia_plicata_ER48 ?????????????????????????????????????????????????????????????????????????????????????????? Nervilia_shirensis_c280 ?????????????????????????????????????????????????????????????????????????????????????????? Gastrodia_sesamoides_534 000010?000000???10???000???0?000000000000000000000000000100000000?1??100000000000000000?10 Gastrodia_procera_PARTIAL 000010?000000???10???000???0?00000000????????????????????????????????????????????????????? gastrodia_sp_reunion_ER214 010000000000000000000?10???????????????0??????00????00????????????????0??????????????????? gastrodia_confusa_0801 010000000000000000000100???????????????0??????00????00????????????????000001?????????????? 301 gastrodia_zyl_16313 0000000000010100000000000001????0?????00??????00?00100????????????????00000010000000000?10 diceratostele_gabonensis_ER 0000000000000000000000000000000000000000000000000000000000000000000000000000000?10?0000000 Didymoplexis_pallens 000000000000000001???000???0????0?????00?0?00000001000???????0???00?1000000000000000000?10 Psilochilus_macrophyllus_ER02 000000000000000000000000000001?00?00000010?00100000000000000000000000000000000000000000?10 Psilochilus_LJ6914 000000000000000000000000000001?00?00000010?00100000000100000000000010000000000000000000??1 Triphora_trinathophora 00000001001??00000000000000000?10???0000?1??0000000000000000000000000000000000000001???000 Triphora_gentianoides_ER01 000000000000000000000000000000000000000000000000010000000?10000000000000000000000000000000 triphora_amazonica_ER72 0000?1???????????????000???????????????0??????00??0000?????00000110?00000000000??1?0001000 Monophyllorchis_sp_435 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Aplectrum_hyemale_104 000000000000000000000000000000100100000000000?10????0?????????????????0??????????????????? Bletilla_striata_556 0000000000000000000000000000000000000000000000000000000000000000000000000000000?10?0000000 Isochilus_amparoana_204 0000000000000000000000000000000000000000000000000000000000000000000000000000000?10?0100000 Calypso_bulbosa_JF 0000000000000000000000000000000000000000000000000000000000000000000000000000000?10?0000000 Leptotes_bicolor_1195 0000000000000000000000000000000000?10?10??????00?00001????????????????0??????????????????? ephi_schmidtii_JVF 00000000000000000000000000000000000000000000000000000000010000?1?00000000000000?10?0000?10 Chysis_bractescens_436 00000000000000000000000?000000000000000?0000000?0000000000000000000000?00000000?10?0000000 Coelia_triptera_324 0000000000000000000000000000000000000??1???????0??????????????????????????????????????????

codonorchis_lessonii_01398 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 corycium_nigrescens_0695 ????????????????????????0?????0??????????????????????????????????????????????????????????? brownleea_caerulea_21870 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Altensteinia_palacea_535 ????????????????????????0?????0???????????????????????????????????????????????????????????

Continued

Table A.3 Continued

Disperis_lindleyana_696 00000000000000000000000000000000?10?000001??0????00?0?000000000000000?1??0?000000000000000 Goodyera_pubescens_212 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Habenaria_repens_381 ????????????????????????0?????0??????????????????????????????????????????????????????????? Orchis_quadripunctata_545 ????????????????????????0?????0??????????????????????????????????????????????????????????? Pachyplectron_arifolium_529 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Spiranthes_cernua_402 0000000000000000000000010?000000001??01000000000000000000000000?1?0?0000000000000000000000 Stenoglottis_longifolia_1136 ????????????????????????0?????0?????????0???0????????????????????????????????????????????? PLAMORCHIS_TRILOBULATA ???????????????????????????????????????000000000000000000000000000001000000000010001000000 PALMORCHIS_powellii 000000000000000000000000000000000000000000000000000100000000000000000000000000000000000000 Epipactis_helleborine_199 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Limodorum_abortivum_nadB ???????????0????????????0?????0??????0?000?10000000001001001000001000000?1???????????????? Cephalanthera_damasonium_575 000000000000000000000000000000001000000000000000000000000000000000000000000000000000000000 cepahalanthera_aust_dat115 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Neottia_nidus_avis_JVF ????????????????????????0?????0??????????????????????????????????????????????????????????? Listera_smallii_486 000000000000000000000000?00000?00000101000000000000000000000000000000000000000000000000000 listera_convol_2707 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 listera_cordata_JVF2580 ?????????????????????????????????????????????????????????????????????????????????????????? aphyllorchis_montana 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 corymborkis_vert ???????????0????????????0?????0???0?000000000000000000000000000000000000000000000000000000 Tropidia_Effusia_211 ???????????0????????????0?????0???0?000000000000000000000000000000000000000000000000000000 302 tropidia_cuciculigoides_05560 ???????????0????????????0?????0???0?000000000000000000000000000000000000000000000000000000 tropidia_bambusifolia_017721 ???????????0????????????0?????0???0?000000000000000000000000000000000000000000000000000000 sertifera_columbiana ???????????0????????????0?????0?????????0???0??????????????0000000000000000000000000000000 sertifera_sp_N565 ???????????0????????????0?????0?????????0???0????????????????00000000000000000000000000000 Elleanthus_sp_374_AF314871 000000000000000000000000000000000000000000000000000?1?000000000000000000000000000000000000 Epilyna_jemenzii_w2997 ???????????0????????????0?????0??????0?000000100101???000000?1010000100100000001001000?100 EPILYNA_HIRTZII 000000000010000000000000000000000000000000000000000?1?000000000000000000000000000000000000 Sobralia_mucroanta_W535 000000000000000000000000000000000000000000000000000?1?000000000000000000000000000000000000 sobralia_crocea 000000000000000000000000000000000000000000000000000?1?000000000000000000000000000000000000 XEORCHIS_AMAZONICA_O799 10???0?10001????????????0?????0?????????0???0????????????????????????????0???0?0000001???? Epipogium_aphyllum ?1?????????0????????????0?????0??00001??00??0??0?001000100011000001???0??0?00010?1???????? Nervilia_plicata_ER48 ?????????????????????????????????????????????????????????????????????????????????????????? Nervilia_shirensis_c280 ?????????????????????????????????????????????????????????????????????????????????????????? Gastrodia_sesamoides_534 00000000000000000000000000000001?000000100??0?00000000000000001???0???001010000010???0??00 Gastrodia_procera_PARTIAL ?????????????????????????????????????????????????????????????????????????????????????????? gastrodia_sp_reunion_ER214 ?0?????????0?????000000?1????????????????????????????????????????????????????????????????? gastrodia_confusa_0801 ?0?????????00000001?00000110001??????????????????????????????????????????????????????????? gastrodia_zyl_16313 00000000000??????????????????????????????????????????????????????????????????????????????? diceratostele_gabonensis_ER 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Didymoplexis_pallens 0000000000000000000000000000?10010000000000000000000000000000000000101000000?1??000?10001? Psilochilus_macrophyllus_ER02 0000000000000010?0010000000000000000000000000000000000000000000000000000000010?00000000000

Continued

Table A.3 Continued

Psilochilus_LJ6914 00000000000000?1?0010000000010000000001000000000100100100010?100000010000001?0?00000000000 Triphora_trinathophora 000101001??00010?00?1?000000000000001010001000?1?00?00000000000000000000000000000000000000 Triphora_gentianoides_ER01 0000011000001000100001000000000000001010001000?1?00?00000000000000000000000000000000000000 triphora_amazonica_ER72 0000100001?0000000000?100?01?0000001101000?1001001???????1?0000000000000000000000001001000 Monophyllorchis_sp_435 0000000000000000?1000000000000000000000000000000000000000000000000000000000000000000000001 Aplectrum_hyemale_104 ?0?????????0????????????0?????00?000000000000000000000000000000000000000000000000001000000 Bletilla_striata_556 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Isochilus_amparoana_204 001000000000000000000000000000000000000000001????????????????????????????????????????????? Calypso_bulbosa_JF 000000000000000000000000000000000000001000000000000000000000000000000000000000000000000000 Leptotes_bicolor_1195 ?0?????????0??????????000?0000000000000?1???0????????????????????????????????????????????? ephi_schmidtii_JVF 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Chysis_bractescens_436 00000100000?010000000000?00000?000000?0000000000000000000000000000000000000000000000000000 Coelia_triptera_324 ????????????????????????0?????0???????????????????????????????????????????????????????????

codonorchis_lessonii_01398 000000000000000000000000001?0????00??001???00000000000010000000000000000000000100?00000000 corycium_nigrescens_0695 ????????????????????????????0????????????????????????0??0?000000000000000001???00?00000000 brownleea_caerulea_21870 0000000000000000000000000000000000000000000000000000000100000000000000000001???00?00000000 Altensteinia_palacea_535 ??????????????????????????????????????????????????????????????????0??????????????????????? Disperis_lindleyana_696 00000001?0??0????0000000000000000000001????000000000000100000000000000000001???00?00000000 303 Goodyera_pubescens_212 00000000000000000000000000000000000?1001???000000000000100001?????0?00000001???00?00000000 Habenaria_repens_381 ????????????????????????????0???????????????????????00?100000000000000000001???00?00000000 Orchis_quadripunctata_545 ????????????????????????????0???????????????????????00?100000000000000000001???00?00000000 Pachyplectron_arifolium_529 00000000000000000000000000000000000?1001???000000000000100000000000000000001???00?00000000 Spiranthes_cernua_402 000000000000000000000000?10?0100000?1001???000000000000100000000000000000?1??????????00000 Stenoglottis_longifolia_1136 ?????????0????????0?????????0????00??0000001????????00?100000000000000000001???00?00000000 PLAMORCHIS_TRILOBULATA 001000000000000000000000000000000000000000000000000000010000000000000000000000100?00000000 PALMORCHIS_powellii 100000000000000000000100000000000000000000000001000000010000000000000000000001?00?00000000 Epipactis_helleborine_199 00000000000000000000000000000000000?1000??100000000000110000000000000000000000100?00000000 Limodorum_abortivum_nadB ?????????0??0????00000000000000???1???0????0000010010001001000010000001??????????????00001 Cephalanthera_damasonium_575 000000000000000000000000000000000000000000000000000000000000000000000000000000100?00000000 cepahalanthera_aust_dat115 000000000000000000000000000000000000000000000000000000000000000000000000000000100?00000000 Neottia_nidus_avis_JVF ??????????????????????????????????????????????????????????????????0??????????????????????? Listera_smallii_486 0000000000000000000000000000?0000000000000000000000000000000?0000????????00000100?00000000 listera_convol_2707 000000000000000000000000000000000000000000000000000000000000000000000000000000100?00000000 listera_cordata_JVF2580 ?????????????????????????????????????????????????????????????????????????????????????????? aphyllorchis_montana 000000000000000000000000000000000000000000000000000000000000000000000000000000100?00000000 corymborkis_vert 000000000000000000000000000000000000000000000000000000010000000000000000000000100?00000000 Tropidia_Effusia_211 000000000000000000000000000000000000000000000000000000010000000000000000000000100?00000000 tropidia_cuciculigoides_05560 000000000000000000000000000000000000000000000000000000010000000000000000000000100?00000000 tropidia_bambusifolia_017721 000000000000000000000000000000000000000000000000000000010000000000000000000000100?00000000 sertifera_columbiana 000000000000000000000000000000000000000000000000000000010000000000000000000010100?01000000 sertifera_sp_N565 000000000000000000000000000000000000000000000000000000010000000000000000000010100?01000000

Continued

Table A.3 Continued

Elleanthus_sp_374_AF314871 000000000000000000000000000000000000000000000000000000010000000000000000000000100?00000000 Epilyna_jemenzii_w2997 0101010010000100010000101001011?100?0000?1000000001?10??010101??00010101000001?00?001010?0 EPILYNA_HIRTZII 000000000000000000000000000000000000000000000000000000010000000000000000000000100?00000000 Sobralia_mucroanta_W535 00000000000??????????????????????????????????????????????????????????????????????????????? sobralia_crocea 00000000000??????????????????????????????????????????????????????????????????????????????? XEORCHIS_AMAZONICA_O799 ???01000?1??????????????????0?????0???00??00001?????000?1???000?10000000100000100?00000000 Epipogium_aphyllum ???????0000?1?????0?00?1?0001?????????????????????????????????????0??????????????????????? Nervilia_plicata_ER48 ?????????????????????????????????????????????????????????????????????????????????????????? Nervilia_shirensis_c280 ?????????????????????????????????????????????????????????????????????????????????????????? Gastrodia_sesamoides_534 0000000000010????000000000000000000??1001000010?000000010000000000001?0?000000100?00?1???0 Gastrodia_procera_PARTIAL ?????????????????????????????????????????????????????????????????????????????????????????? gastrodia_sp_reunion_ER214 ??????????????????????????????????????????????????????????????????0??????????????????????? gastrodia_confusa_0801 ??????????????????????????????????????????????????????????????????0??????????????????????? gastrodia_zyl_16313 ?????????????????????????????????????????????????????????????????????????????????????????? diceratostele_gabonensis_ER 000000000000000000000000000000000000000000000000000000010000000000000000000000100?00000000 Didymoplexis_pallens ???0000000000000001?????????0?????0??00000000000000000010000000000000000000000100?00000000 Psilochilus_macrophyllus_ER02 000000000000000000000000000000000000000000000000000000010000000000000000010?????0???000010 Psilochilus_LJ6914 000000000000000010001000000100010000000000000000000000010000001000000000000000??1????0?1?0 Triphora_trinathophora 0000000000000000000010000000000??10??0000000100001??00010000000000000000010?????0???000000 Triphora_gentianoides_ER01 0000000000000000000100000000000??10??00000001000000000010000000??10?0000000000?10???000000 304 triphora_amazonica_ER72 000000000000001000000000000000000001000010001000000100010000000000000000010?????0???000000 Monophyllorchis_sp_435 0000001000100001?0010000000000000000000000000000000000010000000000000000010?????0???000000 Aplectrum_hyemale_104 000000000000000000000000000000000000000000000000000001??0???0000001??????????????????????? Bletilla_striata_556 000000000000000000000000000000000000000000000000000000010000000000000000000000000000000000 Isochilus_amparoana_204 ????????????????????????????0?????????0????00000000000010000000000000000000000000000000000 Calypso_bulbosa_JF 000000000000000000000000000000000000000000000000000000010000000000000000000000000?10000000 Leptotes_bicolor_1195 ?????????0??????????????????0?????0???0000000000000000010000000000000000000000000?10000000 ephi_schmidtii_JVF 000000000000000000000000000000000000000000000000000000010000000000000000000000000100000000 Chysis_bractescens_436 000000000000000000000000000000000000000000000000000000010000000000000000000000000000000000 Coelia_triptera_324 ????????????????????????????0??????????????0??0??0?000010000000000000000000000000000000000

codonorchis_lessonii_01398 0000000000000000000???1??00??0?00000001000010001000000000000001000000000000000000000000000 corycium_nigrescens_0695 0000000000000000001?0000100??0?00000000000000000000000000010001000000000000000000000000010 brownleea_caerulea_21870 0000000000000000001?0000100??0?00000000000000001000000000000001000000000000000000000000000 Altensteinia_palacea_535 ??????????????????????????0???????????????????????????????????????????????????????????????

Continued

Table A.3 Continued

Disperis_lindleyana_696 0000000000000000001?00000000001??1??????00???0000000000000000010000???1000?000?00010000000 Goodyera_pubescens_212 000000000000001000010000100??0?000000000000000000000000000000010000?????10??????????????00 Habenaria_repens_381 0000000000001???????0000100??0?000000000000000000000000000000010000????100???0???????01?00 Orchis_quadripunctata_545 00000000000000001???0000100??0?000000000000000000000000000000010000??10000?000000000000000 Pachyplectron_arifolium_529 000000000000000000010000?10??0?0000000000000000000000000000000100001000000?000000000000000 Spiranthes_cernua_402 0000000000001???????0000000?10?100?????000000000000000000000000000000000000000?10000100100 Stenoglottis_longifolia_1136 0000000000000000001?0000100??0??10?????000000000000000000000001000000000000000000000000000 PLAMORCHIS_TRILOBULATA 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 PALMORCHIS_powellii 000001000000000000000000000000000000000000000000000000000010000000000000000000000000000000 Epipactis_helleborine_199 0000000000000000000000000000000000000000000000000000??1?0???????00000000000000000000000000 Limodorum_abortivum_nadB ????000100010???0?0??10?000??1?000?0?0??10????00001??0000?000000010000000010?1????????0000 Cephalanthera_damasonium_575 000000000000000000000000000000000000000000000000000000000000000000000000000000100000000000 cepahalanthera_aust_dat115 000000000000000000000000000000000000000000000000000000000001000000000000000000100000000000 Neottia_nidus_avis_JVF ??????????????????????????0??????????????????????????????????????????????????????????????? Listera_smallii_486 000000000000000000000000000000000000000000000000000000000000000000000000000000100000000000 listera_convol_2707 000000000000000000000000000000000000000000000000000000000000000000000000000000100000000000 listera_cordata_JVF2580 ?????????????????????????????????????????????????????????????????????????????????????????? aphyllorchis_montana 0000000000000000000000000000000000000000000000000000000000000000000?100000?000100000000000 corymborkis_vert 00000000000000000000000000000000000000000000000000000000000000001?0????000?000?00010010000 Tropidia_Effusia_211 000000000000000000000000000000000000000000000000000000000000000000000000000000??10?0000000 305 tropidia_cuciculigoides_05560 000000000000000000000000000000000000000000000000000000000000000000000000000000??10?0000000 tropidia_bambusifolia_017721 000000000000000000000000000000000000000000000000000000000000000000000000000000??10?0000000 sertifera_columbiana 00000000000000000000000000010000000000100000001?????????????????00000000000010??0000000000 sertifera_sp_N565 00000000000000000000000000010000000000100000001?????????????????00000000000010??0000000000 Elleanthus_sp_374_AF314871 00000000000000000000000000000000000000?100???000000000000000000000000000000000000000000000 Epilyna_jemenzii_w2997 1010100010000100011?0000000000000000101000010000010110000010000000000000000000000000100000 EPILYNA_HIRTZII 000000000000000000000000000000000000001000000000000000000000000000000000000000000000000000 Sobralia_mucroanta_W535 ?????????????????????????????????????????????????????????????????????????????????????????? sobralia_crocea ?????????????????????????????????????????????????????????????????????????????????????????? XEORCHIS_AMAZONICA_O799 00010?1??0000101010?100???1??????????????????????????????????????????????????????????????? Epipogium_aphyllum ??????????????????????????0?????????????00???0001?000000000000000000000001???????????????? Nervilia_plicata_ER48 ?????????????????????????????????????????????????????????????????????????????????????????? Nervilia_shirensis_c280 ?????????????????????????????????????????????????????????????????????????????????????????? Gastrodia_sesamoides_534 0000000000000000000000000000000000100000000000000000?1000??0100000000000000000000000101?00 Gastrodia_procera_PARTIAL ?????????????????????????????????????????????????????????????????????????????????????????? gastrodia_sp_reunion_ER214 ??????????????????????????0??????????????????????????????????????????????????????????????? gastrodia_confusa_0801 ??????????????????????????0??????????????????????????????????????????????????????????????? gastrodia_zyl_16313 ?????????????????????????????????????????????????????????????????????????????????????????? diceratostele_gabonensis_ER 0000000000000000000000000000000000000000000000000000000000000000000000000000000000?1?00000 Didymoplexis_pallens 00000000000000000000000000000000000000???1????0?000000000100?1??0000000000?1?0???????00100 Psilochilus_macrophyllus_ER02 0000000000000000000100000000000000000100001000000000000000000000000????100???0???????000?? Psilochilus_LJ6914 0000000000000000000100000000000000000100001000000000000000000000000????100???0???????000??

Continued

Table A.3 Continued

Triphora_trinathophora 00000000??100??0000000000000000000?1??000000?100000000010???????0?1?????00???0???????000?1 Triphora_gentianoides_ER01 00000000?1000??0000000000000000000?1??00000010000000000?1???????0?1?????00???0???????000?1 triphora_amazonica_ER72 0000000000000100000000000000000000?1??00000000000000000000000000000????100???0???????00000 Monophyllorchis_sp_435 01??000000000000000000010000000000000000000000000000000000000000000???1000?000?00000000010 Aplectrum_hyemale_104 ?????????????????????????????????????????????????????????????????????????????????????????? Bletilla_striata_556 0000000000000000000000000000000000000000000000000000000000000000000000000000000001???00010 Isochilus_amparoana_204 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000010 Calypso_bulbosa_JF 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000010 Leptotes_bicolor_1195 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000010 ephi_schmidtii_JVF 000000000000000000000000000000000000000000000000000000000000000100000000000000000000000000 Chysis_bractescens_436 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000010 Coelia_triptera_324 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000010

codonorchis_lessonii_01398 0000000000000000000000000000000000000000000000000000000000000000000010?000000??10?????000? corycium_nigrescens_0695 0?000?00000000000000000000000010?0000000000000000000000000000000000010?000000??10?????000? brownleea_caerulea_21870 0000000000000000000000000000000000000000000000000000000000000000000010?000000??10?????0000 Altensteinia_palacea_535 ?????????????????00?0????00?10?0?00000010?0000000000000000000000000010?000000??10?????0000 Disperis_lindleyana_696 000000000000?1?0?00?0??00000000000000000000000000000000000000000000010?000000??10?????0000 Goodyera_pubescens_212 00000???1??????0?00?0??00000000000000000000000000000000000000000000010?000000??10?????0000 306 Habenaria_repens_381 00000000001000000001001000000010?000000?1??000000000000000000000000010?000000??10?????0000 Orchis_quadripunctata_545 0000000000001000000000000000000000000000000000000000000000000000000010?000000??10?????0000 Pachyplectron_arifolium_529 000000000001?000000000000000000000000000000000000000000000000000000010?000000??10?????0000 Spiranthes_cernua_402 01000?0001?00000100?0??001??0000000000000000000000000000000000000000001000000??10?????0000 Stenoglottis_longifolia_1136 000000000000000000000000000000000?10????0?0000000000000000000000000010?000000??10?????0000 PLAMORCHIS_TRILOBULATA 00000?1000?00000000000000000000000000000000000000000000?1?0?0000000010?0000000000000000000 PALMORCHIS_powellii 00000?1000?00000000000000000000000000000000000000000000000000000000010?0000000000000000000 Epipactis_helleborine_199 00000?1000?00000000000000000000000000000000000000000000000000000000010?000000???1????????? Limodorum_abortivum_nadB 0000000000000000000000000000000000000000000010000000000000000000000010?0000000000000000000 Cephalanthera_damasonium_575 00000?1000?00000000000000000000000000000000000000000000000000000000010?0000000000000000000 cepahalanthera_aust_dat115 00000?1000?00000000000000000000000000000000000000000000000000000000010?0000000000000000000 Neottia_nidus_avis_JVF ????0??00????00000000000101?000000000000000000000000000000000000000010?0000000000000000000 Listera_smallii_486 00010??00????000000000000000000000000000000000000000000000000000000010?0000000000000000000 listera_convol_2707 00010??00????000000000000000000000000000000000000000000000000000000010?0000000000000000000 listera_cordata_JVF2580 ?????????????????????????????????????????????????????????????????????????????????????????? aphyllorchis_montana 00000?1000?00000000000000000000000000000000000000000000000000000000010?0000000000000000000 corymborkis_vert 0000000000000000?1?????????????0???0????0??00000000000000000000000?1???0000000000000000000 Tropidia_Effusia_211 00000?1000?00000000000000000000000000000000000000000000000000000000010?0000000000000000000 tropidia_cuciculigoides_05560 0000010000000000100?0??000000010?0000?100?000000000000000000000000?1???0000000000000000000 tropidia_bambusifolia_017721 0?100?0000000000000000000000000000000000000000000000000000000000000010?0000000000000000000 sertifera_columbiana 00000000000000?1?00?0????000000011000100001000100000001000000001000010?001?0000000001?0000 sertifera_sp_N565 00000000000000?1?00?0????000000011000100001000100000001000000001000010?001?0000000001?0000

Continued

Table A.3 Continued

Elleanthus_sp_374_AF314871 0000000000000000000000000000000000000000000000000000000000000000000010?0000000000000000000 Epilyna_jemenzii_w2997 0000000000000000000000000000000000000000010100001000000000000100000010?0100000000000000000 EPILYNA_HIRTZII 0000000000000000000000000000000000000000000000000000000000000000000010?0000000000000000000 Sobralia_mucroanta_W535 ?????????????????????????????????????????????????????????????????????????????????????????? sobralia_crocea ?????????????????????????????????????????????????????????????????????????????????????????? XEORCHIS_AMAZONICA_O799 ?????????????????????????????????????????????????????????????????????????????????????????? Epipogium_aphyllum ???00??00??0000000000100000000?1??????????????????????????????001????????0000?100?0?0?0000 Nervilia_plicata_ER48 ?????????????????????????????????????????????????????????????????????????????????????????? Nervilia_shirensis_c280 ?????????????????????????????????????????????????????????????????????????????????????????? Gastrodia_sesamoides_534 00000??10????0?0000?0??00000000000000000000000000000000000000000000010?0000000000000000100 Gastrodia_procera_PARTIAL ?????????????????????????????????????????????????????????????????????????????????????????? gastrodia_sp_reunion_ER214 ???????????????????????????????0???????????001?0000?1???0?1???00010010?0000?1???0?????0001 gastrodia_confusa_0801 ???????????????????????????????0???????????001?0001?????0?01001?010010?0000?1???0?????0001 gastrodia_zyl_16313 ?????????????????????????????????????????????????????????????????????????????????????????? diceratostele_gabonensis_ER 0000010000000000000000000000000000000000000000000000000000000000000010?0000000000000000000 Didymoplexis_pallens 000?1????????????00?0????00100000001???????0000000000000010?10000010?1?0100100000001011??? Psilochilus_macrophyllus_ER02 1??00??000?00010000?0?0000000010?0000000000100000000000100010000000010?0000000000000000000 Psilochilus_LJ6914 1??00??000?00010000?0?0000000010?0000000000000000000000000000000000010?0000001000000000000 Triphora_trinathophora 0??00?0000000000000000?1?00??1?0??001?000?0000000001000000000000000010?000000000010?0?0000 Triphora_gentianoides_ER01 0??00?0000000000000?1???????000000001?000?0000000000010000000000000010?0001000000?1???0000 307 triphora_amazonica_ER72 0000010000000000001??????????0?0?000000000010000?100010000010000000010?0000001000000000?10 Monophyllorchis_sp_435 0?000?0000000000000000000000000000000000000000000000000000000000000010?0000000000000000000 Aplectrum_hyemale_104 ?????????????????????????????????????????????????????????????????????????????????????????? Bletilla_striata_556 0?000?0000000000000000000000000000000000000000?1??0?000000000000000010?0000000000000000000 Isochilus_amparoana_204 0?000?000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Calypso_bulbosa_JF 0?000?000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Leptotes_bicolor_1195 0?000?000000000000000000000000000000000000000000000000000000000000000000000000000000000000 ephi_schmidtii_JVF 00000?1000?0000000000000000000000000000000000000000000000000000000000001?00000000000000000 Chysis_bractescens_436 0?000?000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Coelia_triptera_324 0?000?000000000000000000000000000000000000000000000000000000000000000000000000000000000000

codonorchis_lessonii_01398 10???0?00000000?100??????000000000000000000000000000000000000000000100000000000000 corycium_nigrescens_0695 10???0?000000000000000000000000000000000000000000000000000000000000000000000000000 brownleea_caerulea_21870 0000000000000000010??????000000000000000000000000000000000000000000100000000000000 Altensteinia_palacea_535 0000000000000000000000000000000000000000000000000000000000000000000100000000000000 Disperis_lindleyana_696 01???0?000000000000000000000000000000000000000000000000000000000000100000000000000 Goodyera_pubescens_212 0000000000000000000000000000000000000000000000000000000000000000000100000000000000 Habenaria_repens_381 0000000000000001000000000000000000000000000000000000000000000000000100000000000000 Orchis_quadripunctata_545 0000100000000000000000000000000000000000000000000000000000000000000100000000000000 Pachyplectron_arifolium_529 0000000000000000000000000000000000000000000000000000000000000000000100000000000000

Continued

Table A.3 Continued

Spiranthes_cernua_402 0000000000000000000000000000000000000000000000000000000000000000000100000000000000 Stenoglottis_longifolia_1136 0000000000000000000000000000000000000000000000000000000000000000000100000000000000 PLAMORCHIS_TRILOBULATA 0000000000000000000000000000000000000000000000000000000000???????????????????????? PALMORCHIS_powellii 0000000000000000000000000000000000000000000??????????????????????????????????????? Epipactis_helleborine_199 ?????0?000000000000000000000000000000000000000000000000000000000000000000000000000 Limodorum_abortivum_nadB 0000000000000000000000000010000000000010000000001000100000001??1?0100?1?0000100000 Cephalanthera_damasonium_575 0000000000000000000000000000000000000000000000000000000000000000000000000000000000 cepahalanthera_aust_dat115 0000000000000000000000000000000000000000000000000000000000000000000000000000000000 Neottia_nidus_avis_JVF 0000000000000000000000000000000000000000000000000000000000000000000000000000000000 Listera_smallii_486 0000000000000000000000000000000000000000000000000000000000000000000000000000000000 listera_convol_2707 0000000000000000000000000000000000000000000000000000000000000000000000000100000000 listera_cordata_JVF2580 ?????????????????????????????????????????????????????????????????????????????????? aphyllorchis_montana 0000000000000000000000000000000000000000000000000000000000000000000010000000000000 corymborkis_vert 000000000000000000000000000000000000000000000010?0000000000000000000000000000000?? Tropidia_Effusia_211 0000000000000000000000000000010000000000000000000000000000000000000000000000000000 tropidia_cuciculigoides_05560 0000000000000000000000000000000000000000000000000000000000000000000000000000000000 tropidia_bambusifolia_017721 0000000000000000000000000000000000000000000000000000000000000000000000000000000000 sertifera_columbiana 00100000000010000000?????????????????????????????????????????????????????????????? sertifera_sp_N565 001000000000100000001????????????????????????????????????????????????????????????? Elleanthus_sp_374_AF314871 0000000000000000000000000000000000000000000000000000000000000000000000000000000000 308 Epilyna_jemenzii_w2997 0000000000000000000000000000000000000000000001000000001000000000000000000000101000 EPILYNA_HIRTZII 00000000000000000000000000000000101000011101000000000011000001000000010000?1???000 Sobralia_mucroanta_W535 ?????????????????????????????????????????????????????????????????????????????????? sobralia_crocea ?????????????????????????????????????????????????????????????????????????????????? XEORCHIS_AMAZONICA_O799 ?????0?00010?10?000001?1?000000000000000000000000000000000000000000000000000000000 Epipogium_aphyllum 000000000000001???0??????000010000000000000000000000000000000000000000000000000000 Nervilia_plicata_ER48 ?????????????????????????????????????????????????????????????????????????????????? Nervilia_shirensis_c280 ?????????????????????????????????????????????????????????????????????????????????? Gastrodia_sesamoides_534 00000001??????0?0000??000000000100000000000000000000000000000000000000000000000000 Gastrodia_procera_PARTIAL ?????????????????????????????????????????????????????????????????????????????????? gastrodia_sp_reunion_ER214 000000101????000001???????00000000000000000000000000000000000000000000001000000000 gastrodia_confusa_0801 000000100001?0000001?????000010000000000000000000000000000000000000000000000000000 gastrodia_zyl_16313 ?????????????????????????????????????????????????????????????????????????????????? diceratostele_gabonensis_ER 00000000000000000000000010001?0010010100001010000000011010000000000000000100000010 Didymoplexis_pallens ?????0?000000000000000?1?000000000000000000000000000000000000000000000000000000000 Psilochilus_macrophyllus_ER02 000000100010000000000010010000100110000000000000001000100010000??????????????????? Psilochilus_LJ6914 00000000000000000000000001000000100?1000000000000100000000000010001000000010000011 Triphora_trinathophora 0000?1????????0?0000??000101??0000000000000000000000000000000000001000000000000000 Triphora_gentianoides_ER01 0010001000000000000000000101??0000000000000000000000000000000000000000000000000000 triphora_amazonica_ER72 00?1?0?00000000000000000010000000000000000000001?001001001110??011?01001000001?1?? Monophyllorchis_sp_435 0000001001?01000000000000000000000000000000000000000000000000000000000000000000000 Aplectrum_hyemale_104 ?????????????????????????????????0000000000000000000000000000000000000000000000000

Continued

Table A.3 Continued

Bletilla_striata_556 0000000000000000000000000000000000000000000000000000000000000000000000000000000000 Isochilus_amparoana_204 0000000000000000000000000000000000000000000000000000000000000000000000000000000000 Calypso_bulbosa_JF 0000000000000000000000000000000100000000000000000000000000000000000000000000000000 Leptotes_bicolor_1195 0000000000000000000000000000000000000000000000000000000000000000000000000000000000 ephi_schmidtii_JVF 0000000000000000000000000000000000000000000000000000000000000000000000000000000000 Chysis_bractescens_436 0000000000000000000000000000000000000000000000000000000000000000000000000000000000 Coelia_triptera_324 0000000000000000000000000000010000000000000000000000000000000000000000000000000000

309

BEGIN DATA; DIMENSIONS NTAX=43 NCHAR=4828; FORMAT DATATYPE=DNA MISSING=? INTERLEAVE GAP=- symbols="0123456789A#C$EFG.IJ&L%>OPQ/'TU:*X

Codonorchis_lessonii TCGAGACCCGGA-GAGACCG--AGCGATCCTG-GAACCCATGA-TTAA--AATTGGCCGC----GGCG-CGCCGC------GTCC-A-GC Corycium_sp TCGAGACCGAAATACGACCG--TRYGATTC-GA-AACATGTGAATGAAT-ATATGGCAGCT------CCC-A--- Goodyera_sp ------A------Brownleea_coerulea ------TGA-GCACCCG---T Palmorchis_trilobulata -C-AAACC---ATGAGATGGG-AGCGATTTTGCGAACTCGTGAACGAA-GTGATGGCAGTTGCTATCA-CGAAACAA--CCGTCC-A-GT Palmorchis_sp TCGAGACCAAAATGAG-TGGGGAGCGATTTTGTGAACCCGTGAACGAA-GTGATGGCAGTTGCTGTCA-CGGAACAA--CCATCC-A-GT Cephalanthera_damasonium TCGAGACCAAAA-GAGATGGG-AG--ATTCAGAGAACTCATGAACTAA-GCGGTGACAGTCACTGTCA-CGAAACAA--ACATTC-A-GT Cephalanthera_aus TCGAGACCAAAA-GAGATTGG-AG--ATTCTGAGAACTCATGAACCAA-GCGGTGGCAGTCACTGTCA-CGAAACAA--ACATTC-A-TT Aphyllorchis_montana ?????????????????????????????????????????????????????????????????????????????????????????? Epipactis_sp TCGAGACCAAAA-GAAATGGGGAG--ATTTAGAGAACTCATGAACCAA-GTGGTGGCAGTCAATGCCA-CAAAACAT--ACGTCC-A-AC Limodorum_abortivum TCGAGACCAAAA-GAGATGGGGAG--ATCTAGAGAACTCACGAACCAA-GTGGTGGCAGTAACTGTCA-TGAAACAA--ACATCC-A-AC Listera_smallii TCGAGACCAAAA--AGATTGAGAG--ATTTAGAGAACTCATGAACCAA-GTGGTGGCAGACATTGTCA-CGGAACAA--TCATAC-A-AC Listera_cordata ?????????????????????????????????????????????????????????????????????????????????????????? Neottia_nidus_avis TCGAGACCAAAA-TTGATTGAGAG--ATTCAGATAACTCATGAACCAA-GTGGTGACAGTCACTGTCA-CACAATAA--ACATAC-A-GC Corymborkis_vert_ER66 ------GTGGCAG---TTGCTATCA-CGGAGCAA--CCAACCCA-GT Tropidia_effusa TCGAG-CCGGAA-GATATTT--AGCGATTCGGAGAACTCGTGAAATAA-GTGGCAGCA-TTGCTATCA-CGGAGCAA--CCATCCCA-GT Tropidia_sp T-GAG-CCGGAA-G-T-TTTA-AGG-ATTCGG-GAACTGG-GAAATAA-G-GGCAGCA-TTGGTGTCA-GGGAGAAA--CCTTCC-A-GT Epilyna_jimenzeii TCGAGACCCAGA-AAGA-GG------CAA-A-TCGCTG-CGGCGGAGCAG--CCATCCCA-AC

310 Epilyna_hirtzii TCGAGACCGAGA-GAGA-GGG-AGAGATCTAGAGAACTCGT-AAAGAAAGCGGCAA---TCGCTG-CGGCGGAGCAG--CCATCCCA-AC Sertifera_columbiana_ER38 TCGAGACCGAAA-AAGA-GGG-AGTGATTTAGAGAACTCGT-AAAGAAAGTGACAACAGTTGCTG-CAGCAGTGCAG--ACATCCCA-AT Sertifera_sp TCGAGACCGAAA-AAGA-GGG-AGTGATTTAGAGAACTCGT-AAAGAAAGTGACAACAGTTGCTG-CAGCAGTGCAG--ACATCCCA-AT Elleanthus_lancifolius_ER36 TCGAAGC-GAA--AAGC-CGG-A-CGATCTAT-GAACTCGT-AAAGAAAGCGG------G------AG--CCATCCCA-AC Elleanthus_sp TCGAGACCAAAA-AAGT-GGG-AGCGATCTAGAGAACTCGT-AAAGAAAGCGG------G------AG--CCATCCCA-AC Sobralia_crocea_w533 TCGAGACCGAAA-GAGA-GGG-AGTGATTCAGCGAACCCGTAAAAGAA-GCGGTAACAGTTGCTG-CAGCGGAGCAG--GCATCCCA-AT Sobralia_mucronata_w535 TCGAGACCGAAA-GAGA-GGG-AGTGATTCAGCGAACCCGTAAAAGAA-GCGGTAACAGTTGCTG-CGGCGGAGCAG--GCATCCCA-AT Diceratostele_gabonensis_ER44 ------GG------CGT----GA---CGG---CAGTCGCCGTCA-CGGCACAT--CCGTCCCCGAC Epipogium_aphyllum ------GACCCCATAAAA-AAC---TGG-CAGTTGCTG-CC-T--AGCAA--CCTTCCT--TC Gastrodia_procera_ER64 ------GTGAACGAA-GTGATGGCAGTTGCTATCA-CGGAACAA--CCGTCC-A-GT Xerorchis_amazonica_0799 ------AT------CA-----GC--CA-T------CG-AA--TT--CGTC---GCC Nervilia_plicata ------GAAA-GAGA-CGG-AGCGACTAGGAGAACGCGTGA--TG--GCCGTGGCAGTTGCTGTCA-CG-AA-ACTACCG-CCC-GAT Nervilia_shirensis TCGAGATCGAAA-GAGA-CGG-AGCGACTCGGAGAACGCGTGA--TG--GCCGCGGCGGTTACTG-CCGCGGAA--CTACCG-CCC-GAT Triphora_amazonica_ERP TCGAGACCNAAATGAGATGGG-AGCGATTTTGCGAACTCGTGAACG---GTGATGGCAGTTGCTATCA-CGAAACAA--CCGTCC-AG-T Triphora_trianthophora TC-AGATCG--AT----TGTG-AATGATTTAGAGAMCACGTCAAGTTCC-TG------TTGCC-TCCGT-AATC------TCC--GAT Triphora_gentianoides_ER01 TCGAGAT-G--AT----TGTG-AATGATTTAGAGAACCCGTGAA-TT---TGA-GG---TTGCC-TCCGT-AATC------TCC--GAT Monophyllorchis_maculta TCGAGATC----T-----G-G-TTTGATTGTGCAAATTTGTGAAATAAG-TGGGT--A-TT------GG-TCCA--CC-TC------Psilochilus_macrophyllus_ER02 ??????????????????????????????????????????????????????????????????????????????????????????

Continued

Table A.4 Primitive Epidendroideae analysis. Combined molecular matrix for ITS (281 characters already excluded), trnL-F +gaps, nad1 +gaps.

Table A.4 Continued

Psilochilus_LJ6914 ?????????????????????????????????????????????????????????????????????????????????????????? Didymoplexis_pallens TC-A-A-CGA-A--A-ATG-G-ATCGAGCCACCAAACCCGYGAAACA-G-CGGC--CA-CCGC-G--ACCG---CATTCTGCTCC---AT Calypso_bulbosa TCGAGACCGAAGTTA--TG-G-AGTGATTCAGCGAACTCGTGAAATT--GCGATTGCAAT-GATGTT-GTGA-TTAG--CCGTCCCA-AT Chysis_bractescens TCGAGACCCAAATTA--TCG--AGCGATTCGGAGAACCCGTGAA-TGA-GCGGCGGCAGT-GCCGTC-GCGAAATTG--CCGTCCCAGC- Isochilus_amparoana TCGAGACCGAAAACA--TCG--AGCGATTCGGAGAAC-CGTGAA-TGA-GCGACGGCGGC-GTCGTC-GCGGAACAG--CCGTCCC-GGT C_trifida ------G--AGCGATTCGGAGAACATGTTAAAT-AAGCGGCAGCATT-GCTGTT-GCAAAAAAG--CCGTCCCT-AT Oreorchis_patens TCGAGA-----A-TATATCG--AGCGATTCGGAGAACCTGTGAA-TTAAGCGGCGGCATT-GCTGTT-GCAAAAAAG--CCGTCCCAG-T

Codonorchis_lessonii TTCTG--TCCTGCCTCC---TGA-CGGA---GGATG-GAAAA-ATC--AAA-CCAGCATAGCC-CGCGCCAAGCGAGA-TGTACAGA-TG Corycium_sp ---TG--CCCRTCCATCTGTTCATATACA--GG--GAGGGAG-ATC--AAA-CGGGCGCARCTTTGCGCCAAGGAAAA-TATGCAG--CA Goodyera_sp ------Brownleea_coerulea CA-TG-----T-AATC----AAGATGAA------TGGA-T---ACTCCAAA-CCGGCACAGCTTTGTGCCAAGGGAAA-TGCGCGG--CG Palmorchis_trilobulata CTTTG--CCCCGCCTCC---AGGGTGAA---GGCTGGATGAG-A-CCCGAG-CAGGCACAGCTTCGTGCCAAGGCAAA-TGCGCAAA-CA Palmorchis_sp CGTTG--CCCCGCCTCC---AGGGTGAA---GGCTGGATGAG-A-CCTGAG-CTGGCACAGTTTCGTGCCAAGGGAAA-TGTCAAAA-CA Cephalanthera_damasonium CT-CG--CACGATCTCC---ACGGCGAA---GGCTGGATGAA-A-CCCGAG-CTAGCGCATTTTCGCGCCAAGGCAA--TGTGCAAAACA Cephalanthera_aus CT-CG--CACGATCTCC---ACGGCGAA---GGCTGGATGAA-A-CCCGAA-CTAGCGCATTTTCGCGCCAA-GCAA--TGTGCAAAACA Aphyllorchis_montana ?????????????????????????????????????????????????????????????????????????????????????????? Epipactis_sp CTTTG--CTTCAACTCC---GCGGTAAA---GGTTGGATGAATAACCCAAG-CTAGCGCATTATCGCGCCAAGGGAA--TGTGCAAAACA Limodorum_abortivum -ATCG--CCTCTTCTCC---GCGGTGAA---GGTTGGATGA-TAACCCGAA-CCAGCGCAATTTCGCGCCAAGGGAA--TGTGCAAAACA 311 Listera_smallii -TTAT--C-TTGTCTCC---AAGGTAAA---GGTTGGATGAA-AACTCGAG-CTAGCGCATTTTCGCGCCAAGGTAA--TGTGCAAAATA Listera_cordata ?????????????????????????????????????????????????????????????????????????????????????????? Neottia_nidus_avis CT-AG--CCTTGTATCC---ATGGTGAA---GGTTGTATGAA-AACCCGAG-CTAGCGCAATTTCGCGCCAAGGTAA--TGTGCAAAACA Corymborkis_vert_ER66 CGTTG--CCTCATCTCCCC-ACGATGAAA--GGTCGGATGAA-AACTCGAG-CCGGCGCAGTTCCGCGCCAAGG-AAA-TGTGCAAA--A Tropidia_effusa CGTTG--CCTCATCTCCC--ACGATGAA---GTTCGGATGAA-A-CTCGAG-CCGGCGCAGTTCCGCGCCAAGTGAA--TGTGCAAA--A Tropidia_sp CGTT---CCT-A-GTTCT--A-GA-GAA---GTTGGGATGAA-AACT-GAG---GGGGCAGT----CGCCAAGG-AA---G-GCAAA--A Epilyna_jimenzeii CATTG--TTGCGTCTCCCCCGCGATGAAAAAGGTTGGATAAA-AACTCAAAATCGGCGCAGTCTCGCGCCAAGGGAAAGTTTGCAAA-CA Epilyna_hirtzii CATTG--CTGCGTCTCCCCCGCGATGAAGGAGGTTGGATGAA-AACTCAAAATCGGCGCAGTCTCGCGCCAAGGGAAAATTCGCAAA-CA Sertifera_columbiana_ER38 TGTTG--CC--A-C------ACGATGACGAAGGTTGGATGAA-AACTCAAAATCGGCGCAGTCTCGCGCCAAGGGAAAATTTGCAAA-CG Sertifera_sp TGTTG--CC--A-C------ACGATGACGAAGGTTGGATGAA-AACTCAAAATCGGCGCAGTCTCGCGCCAAGGGAAAATTTGCAAA-CG Elleanthus_lancifolius_ER36 TGTTG--CCGCATCTCCCCCGCGGTGCAGAAGGTTGGATGAA-AACTCAAAACCGGCGCAGTCTCGCGCCAAGGGAAA-TTTGCAAA-CA Elleanthus_sp TGTTG--TCGCATCTCCCCCGCGATGAAGAAGGTTGGATGAA-AACTCAAAACCGGCGCAGTCTCGCGCCAAGGGAAAATTTGCAAA-TG Sobralia_crocea_w533 TGTTG--CCACATCTCC---ACGATGAAGAAGGTTGGATGAA-AACTCAAA-CCGGCGCAGTTTCGCGCCAAGGGAAAATATGCAAA-CG Sobralia_mucronata_w535 TGTTG--CCACATGTCC---ACGATAAAGAAGGTTGGATGAA-AACTCAAA-CCGGCGCAGCTTCGCGCCAAGGGAAAATATGCAAA-CG Diceratostele_gabonensis_ER44 -GT-G--TCCCCCCATC---ACGGGGGAGG-GGCCGGATGAA-A-CTCGAG-CCGGCGCAGATCTGCGCCAAGGGAA--TATGCAAA-CG Epipogium_aphyllum TGTTG----AC--CTCC---ACGACGCG---GGTCGG-TGAA-A-CCCGAG-CCGGCGCAGCTTCGCGCCAAGG-AA--TTTGC----C- Gastrodia_procera_ER64 CTTTG--CCCCGCCTCC---TAGGTGAA---GGCTGGATGAG-A-CCCGAG-CAGGCACAGTTTCGTGCCAAGGGAAA-TGCGCAAA-CA Xerorchis_amazonica_0799 CGT-G--TCACCAC------ACGATGGG---GGATGGATGAT-A-CTCAAG-CCGGCGCAATCCCGCGCCAAGTGAA--TTTGCAA--T- Nervilia_plicata CGTCGCCGTGGTGCGTC---ACGGAGGA---GGTAGGATGAA-AACTCGAT-CCGGCGCAGCTACGCGCCAAGGGGAA-TATAAGAA-CG Nervilia_shirensis TGTCGCCGCGTCGCATC---GCGAAGGA---GGCAGGATGAA-AACTTGAG-CCGGCGCAGTTACGCGCCAAGGGAGA-TACGCGGA-CG Triphora_amazonica_ERP -CTTG--CCCCGCCTCC---TAGGTGAA---GGCTGGATGA-GA-CCCGAG-CAGGCACAGCTTCGTGCCAAGGCAAA-TGCGCAAA-CA Triphora_trianthophora -GCTG----AAC--ACC-----G-TGAAG--TGCCGGATGA----TACTAA-TTGGCGCAGCGCCGCGTCAAGTCAATCTA-G-AAA--T Triphora_gentianoides_ER01 -GTTG--ATCGATC------GA-GAAA--TGTCGGATGA----TACTAA-TTGGCGCAGCATCGCGTCAAGTGAGTCCAT--AAA-TT

Continued

Table A.4 Continued

Monophyllorchis_maculta ------TCAACACACC-CAACGATGAA---TGT-GG--GAA-AATCCTAAATGAGCGCAAGTAAGCGCCAAGTGAACAGACG-AAA--- Psilochilus_macrophyllus_ER02 ?????????????????????????????????????????????????????????????????????????????????????????? Psilochilus_LJ6914 ?????????????????????????????????????????????????????????????????????????????????????????? Didymoplexis_pallens C-TCGCCTCCCCAGTGGCGCGCGGTGCC---GGCCGGATGAA---TTTGAAAGGGGCG--GA-CTGGGCCAAGGGAA----CGCGA--TG Calypso_bulbosa TGTTT--CCCCACGTT----GCGATGAA---GGATGGATTAA-AACTCAAA-CCGGCGCAGTTACGCGCCAAGGGAA--TACG-AAAGCA Chysis_bractescens CG-GG--CCTCGTC-A----ACGAGGAA---GGACGGATGAA-A-CTCAAA-CCGGCGCAGCTACGCGCCAAGGGAA--TACG-AAAACA Isochilus_amparoana CG-CG--CCTCGTCTCCCCGCCGTACAATA-GG-CGGTTGAA-AACTCAAA-CCGGCGCAGCCACGCGCCAAGGGAA--TACG-AATGCA C_trifida TGTCG--CCTCGGCTT-T-AACGATGAA---GGATGGATGAA-AATTCAAA-CCGGCGCAGTTCCGCGCCAAGGGAA--TACG-AAGACA Oreorchis_patens TGTCG--CCTCGGCTTA--AACGATGAA---GGATGGATGAA-AATTCAA--CCGGCGCAGTTTCGCGCCAAGGGAA--TACG-AAGACA

Codonorchis_lessonii TGATCGGCG--TGGCGTATCCTCGGACGTCGGG---GAT--CGC------TTATA--GAGATTCTCGGTAATGGATATCTTGGTTCTCG Corycium_sp TGAGCGTTG--TGGCAACTCCTAAAACWTAGGC--GGAT--T------TTGTA---TGACTCTCGACAATGGATATCTTGGCTCCCG Goodyera_sp ------AAG------T---TT----AGCGGAATG------TTGTA---TGACTCTCGGCAATGGATATCTTGGCTCTTG Brownleea_coerulea ACAAATCTC--AGCCATT------CC--GTG---GATTATGC------ATGTA---TGACTCTCGACAATGGATATCTCGGCTCTTG Palmorchis_trilobulata GGAGCCCTT--GCGGGTGCAGTAGCACGGAGCG--CTATT-CGC------TTATA---CGACTCTCGGCAACGGATATCTTGGCTCTCG Palmorchis_sp GGAGCCCTA--GCGGGTGCTGTAGCACGGAGCG--CTATT-CGC------TTATA---CGACTCTCGGCAACGGATATCTTGGCTCTCG Cephalanthera_damasonium CGAGCCCCA--ACAGGTTTGGTGGCATTGA------TTATA---TGACTCTCGGCAACGGATATCTCGGCTCTCG Cephalanthera_aus CGAGCCCCA--GCAGGTTTGGTGGCATTGA------TTATA---TGACTCTCGGCAACGGATATCTCGGCTCTCG 312 Aphyllorchis_montana ?????????????????????????????????????????????????????????????????????????????????????????? Epipactis_sp CGAGCCACA--TAAAGTTTGGTGGCATGTA------TA------TTATA---TGACTCTCGGCAACGGATATCTCGGCTCTCG Limodorum_abortivum CGAGCCCCA--GCAGGTCTGGTGGCATGGA------TTATA---TGACTCTCGGCAACGGATATCTCGGCTCTCG Listera_smallii TGAGCCCCA--GCAAGTCTGGTGGCATGGA------TTATA---TGACTCTCGGCAACGGATATCTCGGCTCTCG Listera_cordata ?????????????????????????????????????????????????????????????????????????????????????????? Neottia_nidus_avis TGATTCCCA--GCATGTCTGGTGGCATGGA------TTATA---TGACTCTCGACAACGGATATCTCGGCTCTCG Corymborkis_vert_ER66 TGAGCCCCGCAGCGGGCTTAGTAGCGTGGAGTG--CTGTTT-GCACGCCATTT--AACACGACTCTCGGCAATGGATATCTCGGCTCTCG Tropidia_effusa TGAGCCCTACACCGGGTTTAGTAGCGTGGGGTG--CTGT--CGCACACCACTT--AACACGACTCTCGGCAATGGATATCTCGGCTCTCG Tropidia_sp TGA--CCT-CAGCGGGTTTAGTAGCGTGGAG------GCTCCCCATTT--AAC--GACT-TCGGCAATGGATAT--TGGCT--TG Epilyna_jimenzeii TAAGCCCTACTGCGGGCTTAGCGGTGTGGAGTG--TT-----GC-CACCATTTATAACATGACTCTCGGCAATGGATATCTCGGCTCTCG Epilyna_hirtzii TGAGCCCTATTGCGGGCTTAGCGGTGTGGAGTG--TT-----GC-CAACATTTATAACATGACTCTCGGCAATGGATATCTCGGCTCTCG Sertifera_columbiana_ER38 TAAGCCCTGTTGCGGGTTTAGCGGCGTGGAGTG--TTGTTACGCACACCATTTAAAATATGACTCTCGGCAATGGATATCTCGGCTCTCG Sertifera_sp TAAGCCCTGTTGCGGGTTTAGCGGTGTGGAGTG--TTGTTACGCACACCATTTAAAATATGACTCTCGGCAATGGATATCTCGGCTCTCG Elleanthus_lancifolius_ER36 TAAGCCCTGCAGCGGGCTTAGCGGTGTGGAGTG--CTGTTACGCATACCATC-ATAACATGACTCTCGGCAATGGATATCTCGGCTCTCG Elleanthus_sp CAAGCCCTACAACGGGCTTAGCGGTGTGGAGTG--TTGTAACGCATACCATC-ATAACATGACTCTCGGCAATGGATATCTCGGCTCTCG Sobralia_crocea_w533 TAAGCCCTGCTGCGGGTTTAGTGGTGCGGAGTG--TTGCTACGC--ACCATTTATAATATGACTCTCGGCAATGGATATCTCGGCTCTCG Sobralia_mucronata_w535 TAAGCCCTGCTGTGGGTTTAGTGGTGCGGAGTG--TTGCTACGC--ACCATTTATAATATGACTCTCGGCAATGGATATCTCGGCTCTCG Diceratostele_gabonensis_ER44 --AGCCCCGCAGCGGGCTTAGCGGCGTGGAGCG--CCGTC-CGCACAC---TT--AACACGACTCTCGGCAATGGATATCTCGGCTCTCG Epipogium_aphyllum --AGCCC-GCAGCGGGCCA--CG---AGGAGTG--CTATT-CGC------CTA-AACATGACTCTCGGCAATGGATATCTCGGCTCCCG Gastrodia_procera_ER64 GGAGCCCTT--GCGGGTGCAGTAGCACGGAGCG--CTATT-CGC------TTATA---CGACTCTCGGCAACGGATATCTTGGCTCTCG

Continued

Table A.4 Continued

Xerorchis_amazonica_0799 T-AGCCCCA-AGCGGGTTTAGTGGAATGGG-CG--CCG---CGC--ACCATTT--GACACGACTCTCGGCAATGGATATCTCGGCTCTCG Nervilia_plicata --AGCCC---GGCGGGCTG--CGCCGAGCAGCCC---GCT-CGT----C-TTT--GACACGACTCTCGGCAATGGATATCTCGGCTCTCG Nervilia_shirensis --AGCCC-ACCGTGGGCCT--CGCCGAGCAGCGC---GCC-CGC----C-TTC--GACACGACTCTCGGCAATGGATATCTCGGCTCTCG Triphora_amazonica_ERP GGAGCCC----GCGGGTGCAGTAGCACGGAGCG--CTATT-CGC------TT---ATACGACTCTCGGCAACGGATATCTTGGCTCTCG Triphora_trianthophora CTTCTCC-A--GCAAATTTATTGGATTGAAGCG--CACTC-C-C------TC--AACACGACTCTCGGCAATGGATATCTCGGCTCTCG Triphora_gentianoides_ER01 CTTGTTC-A--ACAACTTTGGTGACTTGAAAAG--C-ATT------CATCC--AAAATGACTCTCAGCAATGGATATCTCGGCTCTCG Monophyllorchis_maculta --AG-CC-A--GCAA-TGTGGCGATGTGAA-T---CACTT-CTTA---CATTG-T-ACATGACCCTCGGCAATGGATATCTCAACTCTTG Psilochilus_macrophyllus_ER02 ?????????????????????????????????????????????????????????????????????????????????????????? Psilochilus_LJ6914 ?????????????????????????????????????????????????????????????????????????????????????????? Didymoplexis_pallens -GA-CCC-G---TGGAA--CAAGGGCCGGA-CG--CCGTT-C--TCA-CATTT---ACACGACTCTTGGCAATGGATATCTCGGTTCTCG Calypso_bulbosa CGAGCCT--CATTGGGTTTAGTGTTGTGGAGTG--C-ATT--GCACACCATTT--GACATGACTCTCGGCAATGGATATCTCGGCTCTCG Chysis_bractescens CGAGCCC--TATCGGGTTTAGTGGCGTGGAGTG--C-GTC--GCACACCACTC--GACACGACTCTCGGCAATGGATATCTCGGCTCTCG Isochilus_amparoana CTACCCC--CATCGGGTTTCGTGGCGTGGGGTG--CTGTT--GCACACCATTC--CACACGACTCTCGGCAATGGATATCTCGGCTCTCG C_trifida CGAGGCCC-TGTCGGGCTTAGTGGCGTGGAGTG-TCT-TT--GCACACCATTT--TACATGACTCTCGGCAATGGATATCTCGGCTCTCG Oreorchis_patens CGAGCCC--CATCGGGCTTAGCGGCGTGGAGTG-TCT-TT--GCACACCATTT--AACATGACTCTCGGCAATGGATATCTCGGCTCTCG

313 Codonorchis_lessonii CATCGATGAAGAGCACAGTGAAATGCGATACGTGGTGCGAATTGCAGAATCCCTTGAACCATCAAATTTTTGAACGCAAGTTGCGTCGGA Corycium_sp CATCGATGAAGAGCGCAGCGAAATGYGATACGTGGTGCGAATTGCARAATCCCATGAACCATCGAGTTTTTGAAAGCAAGTTGCGCCCGA Goodyera_sp CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTTTTTGAACGCAAGTTGCGCCTGA Brownleea_coerulea CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGTGAATTGCAGAATCCCGTGAACCATCGAATTTTTGAACGCAAGTTGCGCCTGA Palmorchis_trilobulata CATCGATGAAGAGCGCAGCGAAATGCGATACGTAGTGCGAATTGCAGAATCCCGTGAACCATCGAGTATTTGAACGCAAGTTGCGCCCGA Palmorchis_sp CATCGATGAAGAGCGCAGCGAAATGCGATACGTAGTGCGAATTGCAGAATCCCGTGAACCATCGAGTATTTGAACGCAAGTTGCGCCCGA Cephalanthera_damasonium CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCAAGTCTTTGAACGCAAGTTGCGCCCGA Cephalanthera_aus CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCAAGTCTTTGAACGCAAGTTGCGCCCGA Aphyllorchis_montana ?????????????????????????????????????????????????????????????????????????????????????????? Epipactis_sp CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCAAGTCTTTGAACGCAAGTTGCGCCCGA Limodorum_abortivum CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCAAGTCTTTGAACGCAAGTTGCGCCCGA Listera_smallii CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCAAGTCTTTGAACGCAAGTTGCGCCCGA Listera_cordata ?????????????????????????????????????????????????????????????????????????????????????????? Neottia_nidus_avis CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCAAGTCTTTGAACGCAAGTTGCGCCCGA Corymborkis_vert_ER66 CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Tropidia_effusa CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGTGAATTGCAGAATCCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Tropidia_sp CATCGA-GAAGAG-GCAG-GAAAT-CGATACGTGG---GAATTGCAGAATCCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Epilyna_jimenzeii CATCGATGAAGAGCGCAGCGAAATGCGATACATGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Epilyna_hirtzii CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Sertifera_columbiana_ER38 CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Sertifera_sp CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Elleanthus_lancifolius_ER36 CATCGATGAAGAGCGCAGCGAAATGCGATACATGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA

Continued

Table A.4 Continued

Elleanthus_sp CATCGATGAAGAGCGCAGCGAAATGCGATACATGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Sobralia_crocea_w533 CATCGATGAAGAGCGCAGCGAAATGCGATACATGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Sobralia_mucronata_w535 CATCGATGAAGAGCGCAGCGAAATGCGATACATGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Diceratostele_gabonensis_ER44 CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCTGA Epipogium_aphyllum CATCGATGAAGAACGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCAA Gastrodia_procera_ER64 CATCGATGAAGAGCGCAGCGAAATGCGATACGTAGTGCGAATTGCAGAATCCCGTGAACCATCGAGTATTTGAACGCAAGTTGCGCCCGA Xerorchis_amazonica_0799 CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGTGAATTGCAGAATCCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Nervilia_plicata CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Nervilia_shirensis CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGA Triphora_amazonica_ERP CATCGATGAAGAGCGCAGCGAAATGCGATACGTAGTGCGAATTGCAGAATCCCGTGAACCATCGAGTATTTGAACGCAAGTTGCGCCCGA Triphora_trianthophora CAACGATGAAGAGCGCAGCAAAATGCGACACATGGTGCGAATTGCAGAATCCCGCGAACCATCGAGTACTTGAACGCAAGTTGCGCCCAA Triphora_gentianoides_ER01 CAACGATGAAGAGCGCAGCAAAATGTGACACATGGTGCGAATTGCAGAATCCCGTGAACCATCAAGTACTTGAACGCAAGTTGCGCCCAA Monophyllorchis_maculta CTTCGATGAAGGACGCAGCAAAATGCGAGATTTGATGCGAATTGCAGAATCCCGTGAATCATCAAAAATTTGAACGCAAGTTGCGCTCGA Psilochilus_macrophyllus_ER02 ?????????????????????????????????????????????????????????????????????????????????????????? Psilochilus_LJ6914 ?????????????????????????????????????????????????????????????????????????????????????????? Didymoplexis_pallens CATCGATGAAGATCATAGTGAAATGAAATACGTGGTGTAAATTGCAGAATCCTGCGAACCATCTAGTCTATGAATGCAAGTTGCGCCTGA Calypso_bulbosa CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGCGAACCATCGAGTTTTTGAACGCAAGTTGCGCCCGA Chysis_bractescens CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGCGAACCATCGAGAATTTGAACGCAAGTTGCGCCCGA Isochilus_amparoana CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGCGAACCATCGAGAATTTGAACGCAAGTTGCGCCCGA 314 C_trifida CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTTTTTGAACGCAAGTTGCGCCTGA Oreorchis_patens CATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAATCCCGTGAACCATCGAGTTTTTGAACGCAAGTTGCGCCCGA

Codonorchis_lessonii GGCCTGCTGACCGAGGGCACGTCCGCCTGGGCGTCTAGCACCGCCTCGCTCCGT--C-GG--CACGA-GCCTC-GA-TA-GATGCGTTGG Corycium_sp GGCCACCTGGCCAAGGGCACGTCYGCCTGGGCATCAAGCATTAGCACGCTCCAC--TTAA--CACCC-ACCTCGGAA-TGGGTGGTTT-- Goodyera_sp GGCCAATTGGCTAAGGGCACGTCCGCCTGGGCGTCAAGCATTACGTCGCTTCAA-TC-GT--CACCAAGCC---AA-TA---TTGTTGCG Brownleea_coerulea AGCCAACTGGCCAAGGGCACGTCCGCCTGGGGGTCAAGCATTGGATCGCTCCGT--CTGT--CATCG-ACC---AAGTAGGATGTGTCG- Palmorchis_trilobulata GGCCAGCCGGCCGAGGGCACGTCTGCTTGGGCGTGAAGCATTGCATCGCTCCGAGCCAGCGCCATCC-CCT---AATTTGGGTGCGTTGC Palmorchis_sp GGCCAGCCGGCCGAGGGCACGTCTGCTTGGGCGTGAAGCATTGCATCGCTCCGTGCCTGCGCCATCC-ACT---AATTTGGGTGTGTCGC Cephalanthera_damasonium GGCCAATCGGCTAAGGGCACGTCCGCCTGGGCGTCAAGCGTTGCATCGCTTCGTGCCGCCACCACAC-ACC---AAT--GTGCGTGGTCG Cephalanthera_aus GGCCAATCGGCTAAGGGCACGTCCGCCTGGGCGTCAAGCGTTGCTACGCTTCGTGCCATCACCACGC-GCC---AAT--GGGCGTGGTCG Aphyllorchis_montana ?????????????????????????????????????????????????????????????????????????????????????????? Epipactis_sp GGCCAATCGGCTAAGGGCACGTCTGCCTGGGCGTCAAGCGTTGCGTCACTTCGTACCATCACCACAC-ACT---AAT--GGGTGTGTTGC Limodorum_abortivum GGCCAATCGGCCAAGGGCACGTCTGCCTGGGCGTCAAGCGTTGCGTCGCTTCGTGCCATCACCACCC-TCC----ATT-CGGTGTGTTGG Listera_smallii GGCCAATCGGCCAAGGGCACGTCTGCCTGGGCGTCAAGCGTTGCGTCGCTTCGTGCCATCACCACCC-ACC---GAT--AGGTGTGTTAG Listera_cordata ?????????????????????????????????????????????????????????????????????????????????????????? Neottia_nidus_avis GGCCAATCGGCCAAGGGCACGTCTGCCTGGGCGTCAAGCGTTGCGTCACTTCGTGTCATCACCACCC-ACC----ATT-GGGTGTGTTGG Corymborkis_vert_ER66 GGCCAACCGGCCAAGGGCAAGTCTGCCTGGGCGTCAAGCGCTGCGTCGCTCCGTGCCAACGTCATCCCACC---GAT--GGGTGGGTGGG Tropidia_effusa GGCCAACCGGCCAAGGGCACGTCTGCCTGGGCGTCAAGCGCTGCGTCGCTCCGTGCCAACGCCATCCCGCC---AA---GGGTGTGTGGG Tropidia_sp GGCCA-CCGGCCAAGGGCACGTCTGCCTGGGCGTCAAGCGCCG-GTCG-TCCGTGCCAA-GCCATCCCACC------GGTGGGTGGG Epilyna_jimenzeii GGTCAATCGACCGAGGGCACGTCTGCCTGGGCGTCAAGCATCACATCGCTCCATGCCGACGCCATCCCACC---GA---GGGTGTGTCGG Epilyna_hirtzii GGCCAATCGACCGAGGGCACGTCTGCCTGGGCGTCAAGCATCACATCGCTCCACGCCGACGCCATCCCACC---GA---GGGTGTGCCGG

Continued

Table A.4 Continued

Sertifera_columbiana_ER38 GGCCAATCGACCGAGGGCACGTCTGCCTGGGCGTCAAGCATTGCATCGCTCCATGCAGGCACCAACCCACC---TA---GGGTGAGCAGG Sertifera_sp GGCCAATCGACCGAGGGCACGTCTGCCTGGGCGTCAAGCATTGCATCGCTCCATGCAGGCACCAACCCACC---TA---GGGTGAGCAGG Elleanthus_lancifolius_ER36 GGCCAATCGACCGAGGGCACGTCCGCCTGGGCGTCAAGCACCGCATCGCTCCATGCCGACGCCATCCCGCC---GA---GGGTGTGTTGG Elleanthus_sp GGCCAATCGGCCGAGGGCACGTCCGCCTGGGCGTCAAGCATCGCATCGCTCCATGCCGACGCCATCCCACC---GA---GGGTGTGTTGG Sobralia_crocea_w533 GGCCAATCGGCCAAGGGCACGTCTGCCTGGGCGTCAAGCATTGCATCGCTCCATGCCAACACCATCCCACC---AA---GGGTGTGTTAG Sobralia_mucronata_w535 GGCCAATCGGCCAAGGGCACGTCTGCCTGGGCGTCAAGCATTGCATCGCTCCATGCCAACACTATCCCACC---AA---GGGTGTGTTAG Diceratostele_gabonensis_ER44 GGCCAACCGGCCAAGGGCACGTCCGCCTGGGCGTCAAGCGCCGCATCGCTCCGTGCCAGCGCCATCCC-CG---GG---GGGWGTGCCGG Epipogium_aphyllum GGCCCTTAGGCCAAGGGCACGCCTGCCTGGGCGTCATGCATTACGTCG-TCC-T---A-CCCTATCC------TGTGA-GG Gastrodia_procera_ER64 GGCCAGCCGGCCGAGGGCACGTCTGCCTGGGCGTGAAGCATTGCATCG-TCCGTGCCAGCGCCATCC-CCT---AATTTGGGTGCGTTGC Xerorchis_amazonica_0799 GGCCAACCGGCCAAGG-CACGTCCGCCTGGGAGTCGAGCATTGCGTCGCTCCGTGCAGACACCGTCCCAC----TGA--GG-TGTGCGGG Nervilia_plicata GGCCCACCGGCCGAGGGCACGCCCGCCTGGGCGTCAAGCATCACGTCA-TCCTCGCCAAGACCATCCCG------T-GG Nervilia_shirensis GGCCCACCGGCCGAGGGCACGCCCGCCTGGGCGTCAAGCATCGCGTCG-TCCTTGCCAGGACCATCCCAC----GGC--GGATGCGTCGG Triphora_amazonica_ERP GGCCAGCCGGCCGAGGGCACGTCTGCTTGGGCGTGAAGCATTGCATCGCTCCGAGCCAGCGCCATCCC------TATTTGGGTGCGTTGC Triphora_trianthophora GGCCAACATGCCGAGGGCACGTCCGCCTGGGGGTCCAGCACCA--TCCATCCGCCGCAGCCT---CCCACG---GATA----TGTGGGGA Triphora_gentianoides_ER01 GGCCAGCATGCCGAGGGCACGTCTGCCTGGGGGTCCAACATCACTTCCATCCGTAGC------AA------GT-T--- Monophyllorchis_maculta GGCCATTAGGCCAAGGGCACGCCTGCTTGGGAGACATGCTTTGCTTTG-TCCGAACC-TCAC------TT----TGT----- Psilochilus_macrophyllus_ER02 ??????????????????????????????????????????????????????????????????????????????????????????

315 Psilochilus_LJ6914 ?????????????????????????????????????????????????????????????????????????????????????????? Didymoplexis_pallens GGCTAATCGGCTGAGGGCACGCCCGCCTGG------CATTGCGTCR-TCCGCGTCGG-GCCA------GC-TTCC Calypso_bulbosa GGCCTGTCGGCCAAGGGCACGTCTGCCTGGGCGTCATGCGTTGCATCG-TCCGTGCCAACACCATCACACC---TAT--GAGTGT-TTGG Chysis_bractescens GGCCAGCCGGCCAAGGGCACGTCCGCCTGGGCGTCAAGCGTTGCGTCG-TCCGTGCCAACTCCATCCCATC---GAT--GGGTGTGTCGG Isochilus_amparoana GGCCAGCCGGCCAAGGGCACGTCCGCCTGGGCGTCAAGCGTTGCGTCG-TCCGTGCCAGCTCCATCCCACC---CAC--GGGGGTGTCGG C_trifida GGCCAGCCGGCCAAGGGCACGTCCGCCTGGGCGTCAAGCGTTGCGTCG-TCCGTGCCAACTCCATCACACC---TAT--GTGTGTGTCGG Oreorchis_patens GGCCAGCCGGCCAAGGGCACGTCCGCCTGGGCGTCAAGCGTTGCGCCG-TCCGTGCCAACTGCATCACACC---TAT--GGGTGTGTCGG

Codonorchis_lessonii T------GG-CCC---AT------CGCGT-GTGCT-A--GC-----GCAGTGGGCTGAAGAGCGGCTGCCCTCCT Corycium_sp -----A-T--CTC-GGAA------GCRGA-AATGGCCCATCGTGTGGC--GC-----GCGGCGGGTTGAAGAAAGGGTGATT-TCT Goodyera_sp GGCC---GG--TTTGAAT------GCGGAGAGTGGCCCTTCGCGCA-ATTGT-----GCGACGGGTTGAAGAACAGTTTGCTTCC- Brownleea_coerulea TGCC---GT-GTC-GGAT------GCGCAGAATGGCTCGTCGTGTATAT------GCGGCGGGTTGAAGAGTTGGTTGATTTCT Palmorchis_trilobulata TGC--A-AG-CTC-GGAT------GTGCAGAGTGGCTCGTCGTGCTTATTGGT----ACGGCGGGTTGAAGAGCGGGTTGTCGTCT Palmorchis_sp TGC--A-TG-CTC-GGAT------GTGGAGAGTGGCTCGCCGCGCCGATTGGT----ACGGCGGGTTGAAGAGCGGGTTGTCGTCT Cephalanthera_damasonium TGC--G-GG-CTC-GAAT------GCGAAGAGTGGTCCGCCGTGCTCATCGGT----GCGGCGGATTGAAGAGCGGGTTGTCGTCT Cephalanthera_aus TGC--G-GG-CTC-GAAT------GCGAAGAGTGGTTCGCCGTGCTCATCGGT----GCGGCGGATTGAAGAACGGGTTGTCGTCT Aphyllorchis_montana ?????????????????????????????????????????????????????????????????????????????????????????? Epipactis_sp TGT--A-GG-CTC-GAAT------GTGAAGAGTGGTTCGCCGTGCCCATTGGT----GCGACGGACTGAAGAGCGGGTTGTTGTCT Limodorum_abortivum TGC--A-GG-CTC-GAAT------GTGAAGAGTGGTTCGCCGTGCTAATTGGT----GCGACGGACTGAAGAGTGGGTTGTTGTCT Listera_smallii TGC--A-TG-CTC-GAAT------GTGAAGAGTGGTTCGCCGTGCCC-TTGGT----GCGGCGGATTGAAGAGCGGGT-GTTGTCT Listera_cordata ?????????????????????????????????????????????????????????????????????????????????????????? Neottia_nidus_avis TGC--A-TG-CTC-GAAT------GTGGAGAGTGGTTCTCCGTGTCC-TTGAT----GCGGCGGACTGAAGAACGGGTTGTTGTCT Corymborkis_vert_ER66 -GC-GA-GG-CGC-GGAC------GTGAAGAGTGGCTCGCCGTACCAATTGGTGC--ACGGCGGGCTGAAGAGTGGGTTATCGTCT

Continued

Table A.4 Continued

Tropidia_effusa -GC-CAAGG-CTC-GGAT------GTGCAGAGTGGCTCGCCGTGCCGTTTGGTGC--GCGGCGGGCTGAAGAGCGGGTTACCGTCT Tropidia_sp AGGGCA-GT-CT--GGAT------TGCAGAGTGCTGTTCCGCGG-GATTGG--C---TGGCGGG-T-AAGA-TGGGT--CCGT-T Epilyna_jimenzeii -G-G-AAGG-CCT-GGAT------GTGCAGAGTGGCCCGTCGTTCTCATCGGTGC-TGCGGCGGGCTAAAGAGCGGGCTTTT-TCT Epilyna_hirtzii -G-G-AAGG-CGT-GGAT------GTGTAGAGTGGCCCGTCGTTCTCATCGGTGC-TGCGGCGGGCTGAAGAGCGGGCTTTT-TCT Sertifera_columbiana_ER38 TGYG---GG-CAT-GGAT------GTGTAGAGTGGCTCGTCGTTCTCATTGGTGCGTGCGGCGGGCTAAAGAGCGGGCTTTCGTCT Sertifera_sp TGCG---GG-CAT-GGAT------GTGTAGAGTGGCTCGTCGTTCTCATTGGTGCGTGCGGCGGGCTAAAGAGCGGGCTTTCGTCT Elleanthus_lancifolius_ER36 --CGCAAGG-CCT-GGAT------GTGCAGATTGGCCCGCCGTTCTCATCGGTGCGTGCGGCGGGCTAAAGAGCGGGCTTTCGTCT Elleanthus_sp --CATAAGG-CCT-GGAT------GTGCAGAGTGGCCCGCCGTTCTCATCGGTGCGTGCGGCGGGTTGAAGAGCGGGCTTTTGTCT Sobralia_crocea_w533 TGCGCG-GG-CTT-GGAT------GTGTAGAGTGGCTCGTCGTTCTCATTGGTGCGGGCGGCGGGCTGAAGAGTGAGTTTTCGTCT Sobralia_mucronata_w535 TGCACA-GG-CTT-GGAT------GTGTAGAGTGGCTCGTCGTTCTCATTGGTGCG-GCGGCGGGCTGAAGAGTGAGTTTTCGTCT Diceratostele_gabonensis_ER44 CGCA---GG-CAC-GGAT------GTGCAGAGTGGCCCGCCGTGCCCGTCGGC----GCGGCGGGCTGAAGAGCGGGTTATATTCT Epipogium_aphyllum ---A-A-CT-CTT-GGAT------GCGGAAATTGGCCCTTCGTGCTC--CGGC----ATGGCGGGTTGAAGAGTGGGTTTTC---- Gastrodia_procera_ER64 TGC--AAG--CTC-GGAT------GTGCAGAGTGGCTCGTCGTGCTTATTGGT----ACGGCGGGTTGAAGAGCGGGTTGTCGTCT Xerorchis_amazonica_0799 TGCG---GG-CTC-GGAT------GCGTAGAGTGACTCGCCGTGCCCATCCGC----ACGACGGTC-GAAGATTGGGTTGGCATGG Nervilia_plicata ---AC------GGATGGGCGGGGACGTGCAGAGTGGCCCGCCGTGC-CGTCGGT----GCGGCGGGCTGAAGAGCGGGCGATCGTCT Nervilia_shirensis -GC----GG-----GGAT--GCGGGG------AGTGGCCCGCCGTGC-CGTCGGC----GCGGCGGGCTGAAGAGCGGGCGATCGTCT

316 Triphora_amazonica_ERP TGCA---AG-CTC-GGAT------GTGCAGAGTGGCTCGTCGTGCTTATTGGT----ACGGCGGGTTGAAGAGCGGGTTGTCGTCC Triphora_trianthophora GAAAG--AT-CGC-GGAT------GACTTGATTGGCTCGCCGTGGTGTGTTAT----GCGGCGGGCTGAAGATCATTTTCTGGTTT Triphora_gentianoides_ER01 ------AT-CTC-GGAT------GAAGAGATTGGCTCGCCGTGGTTATATAT----GCGGCGGGCTGAAAATTATTTTCAGGTTC Monophyllorchis_maculta ------CCT-GGAC------GTGGACATTGACTCGTCGTCCCCATCTA-----GCGGCGGGTTGAAGGTCAATTTTTTGTCT Psilochilus_macrophyllus_ER02 ?????????????????????????????????????????????????????????????????????????????????????????? Psilochilus_LJ6914 ?????????????????????????????????????????????????????????????????????????????????????????? Didymoplexis_pallens TG-----GG-G-C-AAAT------GCGCATGATGAGCCGCTGTTCCAAAGGGC------GGTAGTTCGAAGGGTGCGACGGCGCCT Calypso_bulbosa GGAA---GG-CTC-GGAT------GTGCATATTGGCTCATCGTGCCCATTGGC----GCGGCGGGTTGAAGAGTGGGTTATCGCCT Chysis_bractescens TCGA---GG-CTC-GGAC------GTGCAGAGTGGCTCGTCGTGCCCGTCGGT----GCGGCGGGCTGAAGAGGGGGTCGTCGTCT Isochilus_amparoana TCGA---GG-CCC-GGAC------GTGCAGAGTGGCCCGTCGTGCCCGTCGGT----GCGGCGGGCTGAAGAGTGGGTCGTCATCT C_trifida CCAA---GG-CTC-GGAC------GTGCAGAGTGGCTCATCGTGCCAATTGGT----GCGGCGGGTTGAAGAGCGGGTTATCGTCT Oreorchis_patens CCAA---GG-CCC-GGAC------GTGCAGAGTGGCTCATCGTGCCAATCGGT----GCGGCGGGTTGAAGAGCGGGTTATCGTCT

Codonorchis_lessonii ------GGCCCTG----ACGACTGG??????????????????????????????????????????????????????TGGAAACCTGC Corycium_sp ------GGCGACG----ATGATTGGGTGGATGAA?????????????????????????????????????????????TGGAAACCTGC Goodyera_sp ------GGCAATG----TTTGAGGGGTGGATGTA?????????????????????????????????????????????TGG-AACCTGC Brownleea_coerulea T-----GGCAGTA----GTGATTGGGTGGATGGAA????????????????????????????????????????????------Palmorchis_trilobulata T--CG-GGCCATGCTGGACAAAGGGGTGGATGGAAGCCGTAAGCATG-C------TGTCTCATGCTGGCCAGATGAAATGGAAACCTGC Palmorchis_sp C--CG-GGCCATGCTGGACAAAGGGGTGGATGGAAGCCGTAAGCACG-C------TGTCTCATGCTGGCCAGAGGAAA------Cephalanthera_damasonium C--AT-GGCCACGATCGAC-AAGGGGTGGACGGAAGCCACGAGCACGGCCAAACAGTGTCTCACGCTGGCCTGAGGAC-TGGAAACCTGC Cephalanthera_aus C--AT-GGCCACGATCGAC-AAGGGGTGGACGGAAGCCACGAGCACGGCCAAACAGTGTCTCACGCTGGCCTGAGGAC-??????????? Aphyllorchis_montana ?????????????????????????????????????????????????????????????????????????????????????????? Epipactis_sp C--AT-GGCCACGATTGACAAA-GGGTGGACGAAAGCCACGAGCACGACCAAACATTGTCTAATTCTGGCCTGAGGAA-TGGAA--CTGC

Continued

Table A.4 Continued

Limodorum_abortivum C--AT-GGCCACGATCGAC-AAGGGGTGGACGTATGCCACGAGCACGGCCAAACAATGTCCCATGGTGGCCTGAGGAA------Listera_smallii C--CT-GGCCACGATAGAC-AAGGGGTGGACGGAAGCCACGAGCACGGCCAAACAGTGTCTCATGCTGGTATGAGGAA-TGGAAACCTGC Listera_cordata ?????????????????????????????????????????????????????????????????????????????????????????? Neottia_nidus_avis C--CT-GGCCACGATAGAC-AAGGGGTGGACGGATGCCACGAGCACGGCCAAACAGTGTCTCATGTTGGCCTGAGGAA-??????????? Corymborkis_vert_ER66 C--ATTGGCCACTATCGATAAAGGGGTGGATAAAAGCTGTGAGGAAGGCTTA-CGCTGTCTCATGCTGGCCTGA-GAAA------Tropidia_effusa C--ATTGGCCACGATCGATAAAGGGGTGGATAAAAGCTGTGAGCGAGGCTTA-CGTTGTCTCATGCTGGCCTGA-GAAGTGGAAACCTGC Tropidia_sp C--AGTG-CCACG-T-GA-GAA----TGGA------G-GGAAA??????????? Epilyna_jimenzeii T--ATCAGCCACACTTGACGA-TGGGTGGATAAAAGCTGTGAGCATGACCTG-TGTCGCCTCGTGTTGGCCGGAGGAAA-GGAAANNNGN Epilyna_hirtzii T--ATCAGCCACACTTGACGA-TGGGTGGATAAAAGCTGCGAGCATGACCTA-TGTCGCCTCGTGTTGGCCGGAGGAAA??????????? Sertifera_columbiana_ER38 C--ATTAGCCACATCTGACGA-TGGGTGGATAAAAGCTATGAGCATGACCTA-CGTCGCCTCATGTTGGCTGGATGAAATGGAAACCTGC Sertifera_sp C--ATTAGCCACATCTGACGA-TGGGTGGATAAAAGCTATGAGCATGACCTA-CGTCGCCTCATGTTGGCTGGATGAAA??????????? Elleanthus_lancifolius_ER36 C--ATCGGCCACACTTGACGA-TGGGTGGAGAAAAGCTATGAGCACGACCTA-TGTCGCCTCGTGCTGGCCGGAGGAAA-GGAAANNNGN Elleanthus_sp C--ATCGGCCACACTTGACGA-TGGGTGGAGAAAAGCTATGAGCACGACCTA-CGTCGCCTTGTGTTGGCCGGACGAAA??????????? Sobralia_crocea_w533 T--ATTAGCCACGTTTGACGA-TGGGTGGATAAAAGCTATGAGCATGACCTA-CGTCGCCTCATGTTGGCTTGAGGAAATGGAAACCTGC Sobralia_mucronata_w535 T--ATTAGCCATGTTTGACGA-TGGGTGGAAAAAAGCTATGAGCATGACCTA-CGTCGCCTCATGTTGGCTTGAGGAAATGGAA-CCTGC Diceratostele_gabonensis_ER44 T--ATTGGCCACGATCG-CAA-GGGGTGGATA-AAGCCGCGGGCGCG---T--CGTTCGC--AT---GCCCCGAGGGAA???????????

317 Epipogium_aphyllum TGCTGT-G--AC----G-TTA-TAGG-GGATTGGAGC-AT-AGCTTG------C-TTGGCCC-----GCCC-GCCGAA-??????????? Gastrodia_procera_ER64 T--CG-GGCCATGCTGGACAAAGGGGTGGATGGAAGCCGTAAGCATG-C------TGTCTCATGCTGGCCAGATGAAA??????????? Xerorchis_amazonica_0799 T--GTGGACCATGATA-AC-A-GGGGTGGATGAAATC--TGATCATGTCC-GAC-TC---TTAAA----CG---GG-A-TGGAAACCTGC Nervilia_plicata TGCTGTGGCCACGAACA-TGA-GGGGTGGATAGAAGCTATGGGCACGG--TGACGTGGCATCG------??????????? Nervilia_shirensis TGCTGCGGCCACGAATG-TGA-GGGGTGGATTGAAGCTATGAGCACGA--TGACGTCG------AACC------GGAAACCTGC Triphora_amazonica_ERP T--TCGGGCCATGCTGGACAA-AGGGTGGATGGAAGCCGTAAGCATG--CT------GTCTCATGCTGGCC--A-GAT-TGGAAACCTGC Triphora_trianthophora C--ATCTGTCATGAT-GA-TA-AGAGTGGATGA--GCA-----CACGTCCTGA-TTTG--TCCTGCTGAC---AAG-T-TGGAA-CCTGG Triphora_gentianoides_ER01 T--ACTTGTCATGAT-GA-TA-AGGGTGGATGA--G-TT----CGCGTCCTAA-TTTA--TCGTGCTGGC---AA-TT-TGGAA-CCTAC Monophyllorchis_maculta T--CCTGCCCCCAATCGA-GG-TGGGTGGATGGGCGCTTT--GCATGCCCTA-CAT-G-CTCATGATG-C-TGAAGAT-TGGAAACCTGC Psilochilus_macrophyllus_ER02 ???????????????????????????????????????????????????????????????????????????????TGGAA-CCTT- Psilochilus_LJ6914 ?????????????????????????????????????????????????????????????????????????????????????????? Didymoplexis_pallens C--GTCGACCGCGGTCG-C-A-CARGTGGGTTGT-GCCGACTGCAT---CAG-TGCTGACTCGTC--GGC-TGAGGCAG??????????? Calypso_bulbosa C--ACTGGCCACGAACAAC-G-AGCGTGGATGAAAGCTGTGAGCAAGGCTTA-TGTTGTCTCGTTTTGGCTTGA-GAAATGGAAACCTGC Chysis_bractescens C--ATCGGCCACGAACAAC-A-AGGGTGGATGAGAGCTGTGAGCAAGGCCTA-CGTTGTCTCGTGCCGGCCTGA-GAAATGGAAACCTGC Isochilus_amparoana C--ATCGGCCGCGAGCAAC-T-AGGGTGGAT----GCC--ATGCA-GAGCTG----TGCCTA--GTTGGCCTGA-GAAA---A--CCTCC C_trifida C--ATTGGCCACGAACAAT-A-AGGGTGGATGAAATCTGTGAGCAAGGCCTA-CTTTGTCTCGTGTTGGCCAGA-GAAATGGAA-CCTGC Oreorchis_patens C--ATTGGCCACGAACAAT-A-AGGGTGGATGAAATCTGTGAGCAAGGCCTA-CTTTGTCTCGTGTTGGCCAGA-GACATGGAA-CCTGC

Codonorchis_lessonii TAAGTGGTAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTTTTTT------Corycium_sp TAAGTGTTAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTTTTTT------Goodyera_sp TAAGTGGTAACTTCCAAATTCAGAGAA-CCCTGGAACTAAAAATGGGCATCCCTGAGCCAAATYTTTTTTTTGAGAAAAAAAA--CAAAA Brownleea_coerulea ------Palmorchis_trilobulata TAAGTGGTAACTTCCAAATTCAGAGAAACCCTGGAACTAATAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAAAAGTAA-GGAAAA

Continued

Table A.4 Continued

Palmorchis_sp ------Cephalanthera_damasonium TAAGTGGTAACTTCCAAATTCAGAGAA-CCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAAAAAAAAAATGGAAAA Cephalanthera_aus ?????????????????????????????????????????????????????????????????????????????????????????? Aphyllorchis_montana ????????????????????????????????????????????????????????????????????????????????????GGTGAA Epipactis_sp TAAGTGGTA-CTTCCAAATTCAGAGAAACC-TGG-ACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAAAAAAAATGGAAAA Limodorum_abortivum ------AGTGGAAAA Listera_smallii TAAGTGGTAACTTTCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTTTTTTGAGAAAAAAA-TGGAAAA Listera_cordata ????????????????????????GAAACCCTGGAA-TAAAAATGGGCAATCCTGAGCCAAATCTTTTTTTTAAGAAAAAAA-TGGAAAA Neottia_nidus_avis ??????????????????????????????????????????????????????????CAAATCTTTTTT--AA------TGTAAAA Corymborkis_vert_ER66 ------ATCCTGAGCCAAATCTTTGTTTTGAGAGAAAAAATGGACAA Tropidia_effusa TAAGTGGTAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCCTTTTTTTG????????????????? Tropidia_sp ?????????????????????????????????????????????????????????????????????????????????????????? Epilyna_jimenzeii TGAGNNNNNNCTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAGAAAAAAGGGCAAA Epilyna_hirtzii ?????????????????????????????????????????????????????????????????????????????????????????? Sertifera_columbiana_ER38 TCAGTGGTAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAGAAAAAATGGAAAA Sertifera_sp ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_lancifolius_ER36 TGAGNNNNNNCTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAGAAAAAATGGAAAA

318 Elleanthus_sp ?????????????????????????????????????????????????????????????????????????????????????????? Sobralia_crocea_w533 TAAGTGGTAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAGAAAAAATGGAAAA Sobralia_mucronata_w535 TAAGTGGTAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAGAAAAAATGGAAAA Diceratostele_gabonensis_ER44 ?????????????????????????????????????????????????????????????????????????????????????????? Epipogium_aphyllum ?????????????????????????????????????????????????????????????????????????????????????????? Gastrodia_procera_ER64 ?????????????????????????????????????????????????????????????????????????????????????????? Xerorchis_amazonica_0799 TAAGTGGTAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCCTTATTTTGAGA-TAA-GA-GGAAAA Nervilia_plicata TGAGTGCTAACTTCCAAATTCAGAGAAACCCTGGAACTAAGAATGGGCAATCCTGAGCCAAATCCTTGTTTTGAGAGAAAAAATGG---- Nervilia_shirensis TGAGTGCTAACTTCCAAATTCAGAGAAACCCTGGAACTAAGAATGGGCAATCCTGAGCCAAATCCTTGTTTTGAGAGAAAAAATGG---- Triphora_amazonica_ERP TAAGTGGTAACTTCCAAATTCAGAGAAACCCTGGAACTAATAATGGGCAATCCTGAGCCAAATCTTTTTTTA-AGAAAAA---TG-AAAA Triphora_trianthophora TAAGTGGTAACTTCCAAATTCAGAGANTTCATGGAACTAATAATGGGCAATCCTGAGCCAAATCCTTTTT-A-AGAAAGA---TGGAAAA Triphora_gentianoides_ER01 CA-GTGGTAACTTCCAAATTCAGAGAAATCCTGGAACTAATAAAGGGCAATCCTGAGCCAAATCTTTTT--A-AGAAAAA---TGGAAGA Monophyllorchis_maculta TAAGTGGTAACTTCCAAATTCAGAGAAACCCTGGAACTAAGAAAGGGCAATCCTGAGCCAAATCTTTTTT-A-AGAAAAA---TGGAAAA Psilochilus_macrophyllus_ER02 TTAGTGATAACTTCCAAATTCAGAGAAATCCTGGAACTAAGAATGGGCAATCCTGAGCCAAATCTTTTTTTT-AGAAAAAA---GGAAAA Psilochilus_LJ6914 ?????????????????????????????????????????????????------Didymoplexis_pallens ?????????????????????????????????????????????????????????????????????????????????????????? Calypso_bulbosa TAAGTGGTAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAGAAAAAATGGAAAA Chysis_bractescens TAAGTGGTAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCGAATCTTTGTTTTGAGAGAAAAAATGGAAAA Isochilus_amparoana TAAGTGGTTTCTTCCAAATTCCGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAGAAAAAATATAAAA C_trifida TGAGCGATAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCCTTGTTTTGAGAGAAAAA-TRGAAAA Oreorchis_patens TAAGTGATAACTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTTTTTTGAGAGAAAAA-TGGAAAA

Continued

Table A.4 Continued

Codonorchis_lessonii TTAGAA--AAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAAAGAATGAAA-TTTACTACGTTAGATTAGTAGCTAAAATCCTT Corycium_sp -TA---TAAAAA---A-A-----A-A-A---AATGAAA-CT---C-AA-GAATGAAA-TGGACTACGTAAGATTAGGAGCTAAAATCCTT Goodyera_sp TGAGAATAAAAAGAGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTTACTACGTTAGATTAGTAGTTAAAATACTT Brownleea_coerulea ------GTTCTAACGAATGAAA-TTGACTGCGTTAGATTAGTAGCTAAAATCCTT Palmorchis_trilobulata TGAGAATAAAAAGGGATAGGTGCAGACACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAGCTAAAATCCGT Palmorchis_sp ------Cephalanthera_damasonium TTAGAATAAAAAGGGATAGGTGCAAAAACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTA--A------Cephalanthera_aus ?????????????????????????????????????????????????????????????????????????????????????????? Aphyllorchis_montana TGAGAATAAAA-GGGATAGGTGCAGAGACTCAATGGAAGCTTTTCTAACANATGAAA-TTGACTACGTTACGTTAGTAGCTAAGATCCTT Epipactis_sp TGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAGCTAAAATCCTT Limodorum_abortivum TGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACAAATGAAA-TTGACTACGTTACGTTAGTAGCTAAAATCCCC Listera_smallii TGAGAATAAAA-GGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGT------Listera_cordata TGAGAATAAAA-GGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTCCGTTACGT------Neottia_nidus_avis TGATAATAAAAAGGGATAGGTGCAGAGACCCAATGGAAGCTATTCTAACAAATAAAAATTAAATTGACTACGTTAGTAGATAAAATCCTT Corymborkis_vert_ER66 TGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAGCTAAAAT-CTT Tropidia_effusa ?????????????????????????????????????????????????????????????????????????????????????????? Tropidia_sp ????????????GG-CTAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAGCTAAAATCCTT Epilyna_jimenzeii TGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAGCTAAGATTCTT Epilyna_hirtzii ?????????????????????????????????????????????????????????????????????????????????????????? 319 Sertifera_columbiana_ER38 TGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAGCTAAGATCCTT Sertifera_sp ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_lancifolius_ER36 TGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAGCTAAAATTCTT Elleanthus_sp ?????????????????????????????????????????????????????????????????????????????????????????? Sobralia_crocea_w533 TGAGAAGAAAAAGGGATAGGTGCAGAGACTCAATGGAAGTTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAGCTAAAATTCTT Sobralia_mucronata_w535 TGAGAAGAAAAAGGGATAGGTGCAGAGACTCAATGGAAGTTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAGCTAAAATTCTT Diceratostele_gabonensis_ER44 ?????????????????????????????????????????????????????????????????????????????????????????? Epipogium_aphyllum ?????????????????????????????????????????????????????????????????????????????????????????? Gastrodia_procera_ER64 ?????????????????????????????????????????????????????????????????????????????????????????? Xerorchis_amazonica_0799 TGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTTACTACGTTACATTAGGAGTTAAAATCCTT Nervilia_plicata ------ATAGGTGCAGAGACTCAATGGAAGATGTTCTAACGAATGAAA-TTGATTACGTGACGTTAGTAGCTAAAATATTT Nervilia_shirensis ------ATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGATTACGTGACGCTAATAGCTGAAATCTTT Triphora_amazonica_ERP TGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTGCGTTA--A-ATGA--TT-TT Triphora_trianthophora TGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTA--A-ATGA--TT-TT Triphora_gentianoides_ER01 TGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGATTACGTTACGTTA--A-ATGA--TT-TT Monophyllorchis_maculta ---GAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTGCGCTACGTTAGTAGATAAAATCATT Psilochilus_macrophyllus_ER02 TGAGAATAAAAAGGGATAGGGGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTATGTTACGTTAGTAGCTAAAAT-TT- Psilochilus_LJ6914 ------Didymoplexis_pallens ?????????????????????????????????????????????????????????????????????????????????????????? Calypso_bulbosa TGAGAATAAAAAAGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACAAATGAAA-TTGACTACGTTACGTTAGTAGCTAAAATCCTT

Continued

Table A.4 Continued

Chysis_bractescens TGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAGCTAAAATCCTT Isochilus_amparoana TGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAGCTAAAATCCTT C_trifida TGATAAKAAAAAGGGATAGGTGCAGAGACTCGATGGAAGCTGTTCTAACGAATGAAA-TTGAATATGTTACGTTAGTAGCTAAAATCCTT Oreorchis_patens TGAGAAGAAAAAGGGATAGGTGCAGAGACTCGATGGAAGCTGTTCTAACGAATGAAA-TTGAATATGTTACGTTAGTAGCTAAAATCCTT

Codonorchis_lessonii CTATCAAAA------GAAATGACAGAAAGGATAACCTTATATATTTAATACGTACGTATACATACTTGCATAGCAAACGATTAATCA Corycium_sp ATATCAAA-GGAAAGATTGGAATGATAGAAAGGTTAATCTTATAAACCTAATAAGTACGTTTAGATACTGACATAGCAAATGATTCATCA Goodyera_sp CTATCAAGATAAAAGATTGAAATGACAGAAAGGATGACCTTATGTACCTAATAAATATGTATACATACTTACATAGCAAGCGATTAATCA Brownleea_coerulea CTATCAAAAGAAAAGATCGAAATAACAGAAAGGATAATCTTATATACCTAATACGTACGTCTAGATACTTACATAGCAAATGATTCA--- Palmorchis_trilobulata CTATC------GAAATGACAGAAAGGATAACCTTATATACCTAATACGTACGTATACATACTGACATAGCAAACGATTAA--- Palmorchis_sp ------Cephalanthera_damasonium ------GGATAACCTTATATACCTAATACGTACGTATACATACTGACATAGCAAACGATTAATCA Cephalanthera_aus ?????????????????????????????????????????????????????????????????????????????????????????? Aphyllorchis_montana CTATC------GAAATGACAGAAAGGATAACCTTCTATACCTAATACGTACGTATACATACTGACATAGCAAACGATTAATCA Epipactis_sp C------CAGAAAGGATAACCTTATATACCTAATACATACGTATACATACTGACATAGCAAACGATTAATCA Limodorum_abortivum CCATC------AAGATGACAGAACGGATAACCTTATATACCTAATACGTACGTATACATACTGACATAGCAAACGATTAATCA Listera_smallii ------ATACATACTGATATAGCAAACGATTAATCA 320 Listera_cordata ------ATACATACTGATATAGCAAATGATTAATCA Neottia_nidus_avis CTATC------AAAAT------GG---ACCCCAGATAACTAATGAGTAC--ATACATACTGATATATAAAATTATTAATCA Corymborkis_vert_ER66 CTATC------GAAATGACAGAGAGG------TTATATACCTAATACGTACGTATACATACTGACATAGCAAACGATTAATCA Tropidia_effusa ?????????????????????????????????????????????????????????????????????????????????????????? Tropidia_sp CTACC------AAATGACAGAAAGGATAACCTTATATACCTAATACGTACGTATACATACTGACATAGCAAACGATTAATCA Epilyna_jimenzeii CTATC------GAAATGACAGAAAGGATAACCTTATATACCTAATACGTACGTATACATACTGACATAGCAAACGATTAATCA Epilyna_hirtzii ?????????????????????????????????????????????????????????????????????????????????????????? Sertifera_columbiana_ER38 CTATC------GAAATGACAGAAAGGATAACCTTATATACCTAAGACGTACGTATACATACTGACATAGCAAACGATTAATCA Sertifera_sp ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_lancifolius_ER36 CTATC------GAAATGACAGAAAGGATAACCTTATATACCTAATACGTACGTATACATACTGACATAGCAAACGATTAATCA Elleanthus_sp ?????????????????????????????????????????????????????????????????????????????????????????? Sobralia_crocea_w533 CTATC------GAAATGACAGAAAGGATAACCTTATATACCTAATACGTACGTATACATACTGACATAGCAAACGATTAATCA Sobralia_mucronata_w535 CTATC------GAAATGACAGAAAGGATAACCTTATATACCTAATACGTACGTATACATACTGACATAGCAAACGATTAATCA Diceratostele_gabonensis_ER44 ?????????????????????????????????????????????????????????????????????????????????????????? Epipogium_aphyllum ?????????????????????????????????????????????????????????????????????????????????????????? Gastrodia_procera_ER64 ?????????????????????????????????????????????????????????????????????????????????????????? Xerorchis_amazonica_0799 CTATT------GAAATGAAAGAAAGGATAACCTTATATACCTAATACGTACGTATACATACTGACATAGCAAACGATTAATCA Nervilia_plicata CTATC------GAAATGACAGAAAGGATAACCTTATATACCTAATACGTACGTATACATACTGACATAGCAAACGATTAATCA Nervilia_shirensis CTATC------GAAATGACAGAAAGGATAACCTTATATACCTAATACGTACGTATACATACTGACATAGCAAACGATTAATCA Triphora_amazonica_ERP CT--C------TAAATGACATAC-GGATAACCTTATATACCTAATACCTACGTTTACATACTGACATAG------TAA--A Triphora_trianthophora CT--C------TAAATGACATAA-GGATTACCTTATGTACCTAATACATACAT-TATACATTTACATAG------TAA--A Triphora_gentianoides_ER01 CTA------TAAATGACATAAAGGATAACCTTATATA--TAA-ACCT---TATATATA----TATA------TAA--- Monophyllorchis_maculta -TATC------TAAATGACATACA------AATACGTACGTATACATACTTACATAGCAAACAATTCATCA

Continued

Table A.4 Continued

Psilochilus_macrophyllus_ER02 CTAAC------TAAATGACATATAGG------TA-TAAGTACATATACATACTGACATATCAAACAATTAATCA Psilochilus_LJ6914 ------Didymoplexis_pallens ?????????????????????????????????????????????????????????????????????????????????????????? Calypso_bulbosa CTAAC------GAAATGACAGAAAGGATAACCTTATATACCTAATACATACGTATACATACTGACATAGCAAACGATTAATCA Chysis_bractescens CTATC------GAAATGACAGAAAGGATAACCTTATATACCTAATACGTACGTATACATACTGACATAGCAAACGATTAATCA Isochilus_amparoana CTATC------GAAATGACAGAAAGGATAACCTTATATACCTAATACGTACGTATACATGCTGACATAGCAAACGATTAATCA C_trifida CTATC------AAAATGACAGAAAGGATAACCTTATATATCTAATACGTACGCATACATACTGACATAGCAAATGATTAATCA Oreorchis_patens CTATC------GAAATGACAGAAAGGATAACCTTATATATCTAATACGTACGTATACATACTGACATAGCAAACGATTAATCA

Codonorchis_lessonii CAT------TCTTATATACA------GA------TTGAAGTTGAAAAAAGAATCGAA Corycium_sp CAT------TCTTATATA------CTATGAAAAATTGAAGAGTTATTGTGAATCAATTCTCATTGAAGTTGAAAAAAGAATTGAA Goodyera_sp CAT------TCTTATAAA------CTATGAAAAGTT------AATTATAATTGAAGTTGAAAAAAGAATCGAA Brownleea_coerulea ------Palmorchis_trilobulata --TCCCAA-----ATAGAGATCAAAAAATCTATGAAAGATT-AAGAATTATTGTGAATCAATTCCAATTGAAGT-GAAAAAAGAATCGAA Palmorchis_sp ------GAGATCAAAAAATCTTGGAAGGGTTTAAGAATTTTTGGGGATCCATTCCCATTGGAGGTGGAAAAAGAATCGA- Cephalanthera_damasonium CAACCCAAATCTTATAGAGATCAAAAAATCTATGAAAAATTGAAGAATTATTGTGAATCAATTCCAATTGAAGTTGAAAAAAGAATCGAA Cephalanthera_aus ?????????????????????????????????????????????????????????????????????????????????????????? Aphyllorchis_montana CAACCCGAATCTTATAGAGATCAAAGAATCTATGAAAATTTGAAGAATTATTGTGAATCAATTCCAATTGAA------321 Epipactis_sp CAACCCGAACCTTATAGAGATCAAAAAATCTATCAAAAATTGAAGAATTATTGTGAATCAATTCCAATTGAAGTTGAAAAAAGAATCGAA Limodorum_abortivum CAACCCGAATCTTATAGAGATCAAAAA-TATAGGAAAAATTGAAGAATTATTGTGAATCAATTCCAAT--A------GAA----- Listera_smallii CAACCCAAATCTTATAGAGATCAAAAAATCTATGAAAAATTGAAGAATTATTTTGAATAAATTCCAATTGAAGTTGAAAAAAGAATCGAA Listera_cordata CAACCCAAAT---A-ATATTTCTATAAATCTATGAAAAATT------GAAGTTGGAAAAAGAA----- Neottia_nidus_avis CAACCCAAATCTTATATATATCAAAAAATATATGAA-CATTTAAGAATTATTG-G------GGATAAAT Corymborkis_vert_ER66 CAATCCGAAT------Tropidia_effusa ?????????????????????????????????????????????????????????????????????????????????????????? Tropidia_sp CAACCCGAATCTTATAGATATCAAAAAATCTATGAAAAATT------TTATTGTGAATCAATTCCAATTGAAGTTGAAAAAATAA-CGAA Epilyna_jimenzeii CAACCCGAATCTTATAGAGATCAAGAAATATATGAAAAATTGAAGAGTTATTGTCAATCAATTCCGATTGAAGG-GAAAAAAGAATCGAA Epilyna_hirtzii ?????????????????????????????????????????????????????????????????????????????????????????? Sertifera_columbiana_ER38 CAACCCGAATCTTATAGAGATCAAAAA-TATATGAAAAATTGAAGAGTTATTGTCAATCAATTCCAATTGAAGTT-AAAAA-GAATCGAA Sertifera_sp ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_lancifolius_ER36 CAACCCGAATCTTATAGAGATCAAAAAATATATGAAAAATTGAAGAGTTATTGTCAATCAATTCCAATTGAAGTT-AAAAAAGAATCGAA Elleanthus_sp ?????????????????????????????????????????????????????????????????????????????????????????? Sobralia_crocea_w533 CAACCCGAATCTTATAGAGATCAAAAAATYTWTGAAAAATTGAAGAGTTATTGTCAATCAWTTCCAATTGAAGTTCAAAAA-GAATCGAA Sobralia_mucronata_w535 CAACCCGAATCTTATAGAGATCAAAAAATCTATGAAAAATTGAAGAGTTATTGTCAATCAATTCCAATTGAAGTTCAAAAA-GAATCGAA Diceratostele_gabonensis_ER44 ?????????????????????????????????????????????????????????????????????????????????????????? Epipogium_aphyllum ?????????????????????????????????????????????????????????????????????????????????????????? Gastrodia_procera_ER64 ?????????????????????????????????????????????????????????????????????????????????????????? Xerorchis_amazonica_0799 AAACCCAA------Nervilia_plicata CAACCCGAATCTTATAGAGATCAAAAAATATATGAAAAATCGAAG--TT------GAAAAAAGA------Nervilia_shirensis CAACCCGAATCTTATAGAGATCAAAAAATATATGAAAAATCGAAG--TT------GAAAAAAGA------

Continued

Table A.4 Continued

Triphora_amazonica_ERP CAATTCGAATCTTAGAGAGATCAAAAAATCTATGAGAATTTGAAGAGTTATTGTGTTGTAAATCCA-TTGAAGTTGAAAA-GGAATCAAA Triphora_trianthophora CAATTCGAATCTTATAGAGATCAAAAAATCTATGGAGATTTGAAGAGTTATTGTGTTGTAAATCCA-TTGAAGTTGAAAAAGGAATCAAA Triphora_gentianoides_ER01 ------ATAGAGATCAAAAA-TATATGAAAAATTGAAGAGTTATTGTGTTGTAAATCCC-TTGAAGTTGAAAAAGGAATCAAA Monophyllorchis_maculta CAATTCAAATCTTATAGAGATCAAAAAATATATGAAAAATGGAAGAGTTCTTGTTTTGTAAATCCA-TTGAAGTTGAAAAAAGAATAGAA Psilochilus_macrophyllus_ER02 CAATTTGAATCTTATAGAGATCGAAAAATCTATGAAAAAATGAAGAGTTATTGTGTTGTAAATCCA-TTGAAGTTCAAA---GAAAAGAA Psilochilus_LJ6914 ------ATAGAGATCGAAAAATCT-TGAAAAATTGAAGAGTTTTTGGGTTGTAAATCCA-TTGAAGTTCAAA---GAAAAGAA Didymoplexis_pallens ?????????????????????????????????????????????????????????????????????????????????????????? Calypso_bulbosa CAACCCAAATTTTATAGGGATCAAAAAATATATGAAAAATTGAAGAGTTATTGTGAATCAATTCCAATTGAAGTTGAAAAAAGAATCGAA Chysis_bractescens CAACCCAAATCTTATAGAGATAAAAAAATATATGAAAAATTGAAGAGTTATTGTGAATCAATTCCAATTGAAGTTGAAAAAAGAATCGAA Isochilus_amparoana CAACCCAAATCTTATAGAGATCAAAAAAGATATGAAAAAT-GAAGAGTTATTGTGAATCAATTTCAATTGAAGTTGAAAAAAGAATTGAA C_trifida CAACCMAGATCTTATAGAAATCAAAAAGTATATGAAAAATTGAAGAGTTATTGTGAATCAATTCCTGTTGAAGTTGMCGAAAGAATTGAA Oreorchis_patens CAACCAAAATCTTATAGAGATCAAAAAGTATATGAAAAATTGAAGAGTTATTGTGAATCAATTCCTATTGAAGTTGACAAAAGAATCGAA

Codonorchis_lessonii TTTGAA------TATTCAGT-GATCGAATGATTCATTCCAGAGTTTGATAAATCTTTTAAAGATTAATCGGACGAGAATAAAGAGAGA Corycium_sp TTCCAA------TATTCAGT-GATCAAATTATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTAATCGAACGAGAATAAAGAGAGA 322 Goodyera_sp TTCAAA------TATTCAGT-GATCAAATGAGTCATTCCAGAGTTTGATAGATTTTTTGAAGATAAATCGGACGAGAATAAAGAGAGA Brownleea_coerulea ------TTCCAGAGTTTGATGGATTTTTTGAAGATTAATCGGACGAGAATAAAGAGAGA Palmorchis_trilobulata TTCAAA------TATTCAGT-GATCAAAAGATTCATTCCAGAGTTGGATAGATCTTTTGAAGATTAATCGGACGAGAATAAAGAGAGA Palmorchis_sp TTCGAA------TATTCCGGGGGTCCAAAGATTCATTCCCGGGTTGGAAAGGTCTTTTGAAGATTAATCGGGCGGGGATAAAGAGAGA Cephalanthera_damasonium TTCGAA------TATTCAGT-GATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTAATCGGACGAGAATAAAGAGAGA Cephalanthera_aus ?????????????????????????????????????????????????????????????????????????????????????????? Aphyllorchis_montana ------GAAGATTAATCGGACGAGAATAAAGAGAGA Epipactis_sp TTCAAA------TATTCAGT-GATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTAATTGGACGAGAATAAAGAGAGA Limodorum_abortivum ------GAAGATTAATCGGACGAGAATAAAGAGAGA Listera_smallii TTTGAA------TATTCAGT-GATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTAATCGGACAAGAATAAAGAGAGA Listera_cordata ------TCAAACCAGAGTTTGATAGATCTTTTGAAGATTAATTGGACAAGAATAAAGAGAGA Neottia_nidus_avis TTTGAA------TAATCAGT-GATAAAATGATTCATT-GAGAGTTTGATAGATCTTTTGGAGATTAATTGGACGAGAATAAAGATAGA Corymborkis_vert_ER66 ------Tropidia_effusa ?????????????????????????????????????????????????????????????????????????????????????????? Tropidia_sp TTCGAA------TATTCAGT-GATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTAATCGGACGAGAATAAAGAGAGA Epilyna_jimenzeii TTCGAA------TATTCAGG-GATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGRTTAATCGGACGRGAA-AAAGGGAGG Epilyna_hirtzii ?????????????????????????????????????????????????????????????????????????????????????????? Sertifera_columbiana_ER38 TTTTAA------TATT-AGT-GATCAAATGATTCCTTCCAGAGTTTGATAGATYTTTTGAAGATTAATCGGGCGAGAATAAAGAGAGA Sertifera_sp ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_lancifolius_ER36 TTCGAA------TATTCAGT-GATCAAACGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTA-TCGGACGAGAATAAAGAGAGA Elleanthus_sp ??????????????????????????????????????????????????????????????????????????????????????????

Continued

Table A.4 Continued

Sobralia_crocea_w533 TTCGAA------TATTCAGT-GATCAAATGATTCATT----AGTTTGATAGATCTTTTGAAGATTAATCGGACGAGAATAAAGAGAGA Sobralia_mucronata_w535 TTCGAA------TATTCAGT-GATCAAATGATTCATT----AGTTTGATAGATCTTTTGAAGATTAATCGGACGAGAATAAAGAGAGA Diceratostele_gabonensis_ER44 ?????????????????????????????????????????????????ATAGATCTTTTGAAGATTAATCGGACGAGAATAAAGAGAGA Epipogium_aphyllum ?????????????????????????????????????????????????????????????????????????????????????????? Gastrodia_procera_ER64 ?????????????????????????????????????????????????????????????????????????????????????????? Xerorchis_amazonica_0799 ------TCTT------ATT---CGGACGAGAATAAAGAGAGA Nervilia_plicata TTCGAA------TATTCAGT-GATAAAATGATTCATTCCAGAGTT-GATAGATCTTTTGAAGATTAATCGGACGAGAATAAAGAGAGA Nervilia_shirensis TTCGAA------TATTCAGT-GATAAAATGATTCATTCCAGAGTT-GATAGATCTTTTGAAGATTAATCGGACGAGAATAAAGAGAGA Triphora_amazonica_ERP TTCGAATAGTCAGTTATTCAGT-AATCAAATGATTCATTCCAGAGTTTGAAAGATCTTTTGAAGATTAATCAGACGAGAATAAAGAGAGA Triphora_trianthophora TTCGAATTTTCAGTTATTCAGT-AATCAAATGATTCATTCCAGAGTTTGAAAGATCTTTTGAAGATTAATCATACGAGAATAAAGAGAGA Triphora_gentianoides_ER01 TTCGAATATTCAGTTATTCAGT-AATCAAATGATTCATTCCAAAGTTTGAAAGATCTTTTGAAGATTAATCGGACGAGAATAAAGAGAGA Monophyllorchis_maculta TTCGAAT-----GTT---CAGT-AATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTAAAGATTAATCGAACGAGAATAAAGAGAGA Psilochilus_macrophyllus_ER02 T-CGA-T---CAGTTATTCAGT-AATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTAATCGGACGAGAATAAAGAGAGA Psilochilus_LJ6914 T-C-AAT---CAGTTATTCAGT-AATCAAATGATTCATTCCAGAGTTTGATAGATCTTT-GAAGATTCATCGGACGAGAATAAAGAGAGA Didymoplexis_pallens ?????????????????????????????????????????????????????????????????????????????????????????? Calypso_bulbosa TTCAAA------TATTCAGT-GATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTAATTGGACGAGAATAAAGAGAGA Chysis_bractescens TTCGAA------TATTCAGT-GATCAAATGATTCA------TTTGATAGATCTTTTGAAGATTAATCGGACGAGAATAAAGAGAGA Isochilus_amparoana TTCAAA------TATTCAGT-GATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTAATAGGACGAGAATAAAGAGAGA C_trifida TTCAGA------TATTCAGG-GATCAAANGATTCATTCCAGAGTTTGATAGATCTTTTGRAGATTTATCAGACGAGAATGAAGGGAGA 323 Oreorchis_patens TTCAAA------TATTCAGT-GATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTAATCGGACGAGAATAAAGAGAGA

Codonorchis_lessonii GTCCCATTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTG-AAAATCGTGAGGGTTCAAGTCCC Corycium_sp GTCCCATTTTACATGTCAATACCAACAACAATGAAATTTAGAGTAAGAGGAAAATCCGTCGAATTTTAAA-TCGTGAGGGTTCAAGTCCC Goodyera_sp GTCCCATTTTACATGTCAATACCGACAACAATGAAATTTAGAGTAAGAGGAAAATCCGTCGAATTG-AAAATCGTGAGGGTTCAAGTCCC Brownleea_coerulea GTCCCATTTTACATGTCAATACCGACAACAATGAAATTTATAGTAATAGGAAAATCCGTCGAATTTTAAAATCGT------Palmorchis_trilobulata GTCCCATTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTTAAAATCGTGAGGGTTCAAGTCCT Palmorchis_sp GTCCCATTTT-CATGTCAAT-CCGGCCCCA-TGAAATTTATAGTAAGGGGAAAATCCGTCGAATTTTAAAATCGGGAGGGTTCAAGTCCC Cephalanthera_damasonium GTCCCATTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATT-GAAAATCGTGAGGGTTCAAGTCCC Cephalanthera_aus ?????????????????????????????????????????????????????????????????????????????????????????? Aphyllorchis_montana GTCCCGTTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTGAAAATCGTGAGGGTTCAAGTCCC Epipactis_sp GTCCCATTTTACATGTCAATACCGACAACAATGATATTTATAGTAAGAG---AATC-GTCGA-TT-GAAAATCGTGAGGGTTCAAGTCCC Limodorum_abortivum GTCCCATTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTT-AAAATCGTGAGGGTTCAAGTCCC Listera_smallii GTCCCGTTTAACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTGAAAATCGTGAGGGTTCAAGTCCC Listera_cordata GTCCCTTTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTGAAAATCGTGAGGGTTCAAGTCCC Neottia_nidus_avis GTCCCATTTTACATGTCAATACCGACAACAATGAAATTTATAGTAATAGGAAAATCCGTCGAATTTGAAAATCGTGAGGGTTCAAGTCCC Corymborkis_vert_ER66 ------Tropidia_effusa ?????????????????????????????????????????????????????????????????????????????GGGTTCAAGTCCC Tropidia_sp GTCCCATTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAA-TCCGTCGAATTTTAAA-TCGGGAGGGTTCAAGTCCC Epilyna_jimenzeii GGCCCCTTTTACATGGCCAT-CCGACAACCATGGAATTTTTAGGAAG-GGAAAATCCGTCGAATTTTAAAATCGGGGGGGTTCAAGGCCC Epilyna_hirtzii ??????????????????????????????????????????????????????????????????????????????????????????

Continued

Table A.4 Continued

Sertifera_columbiana_ER38 GTCCCCTTTTTCATKTCAATWCCGGCAACAATGAAATTTTTAGTAAGAGGAAA-TCCGTTGAATTTTAAAATTGGGGGGGTTCAAGTCCC Sertifera_sp ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_lancifolius_ER36 GTCCCATTTTACATGTCAATACCGACAACAAGGAAATTTATGGTAAGAGGAAAATCCGTCGAATTTTAAAATCGTGAGGGTTCAAGTCCC Elleanthus_sp ??????????????????????????????????????????????????????????????????????????????GGTTCAAGTCCC Sobralia_crocea_w533 GTCCCCTTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTTGAATTTGAAAATTGTGAGGGTTCAAGTCCC Sobralia_mucronata_w535 GTCCCCTTTTACATGTCAAAACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTGAAAATCGTGAGGGTTCAAGTCCC Diceratostele_gabonensis_ER44 GTCC--TTTTACATGTNNATACCGNCAACAATGAAATTTNTAGTAAGAGGAAAATCCGTCGAATTTTCAAATCGTGAGGGTTCAAGTCCC Epipogium_aphyllum ?????????????????????????????????????????????????????????????????????????????????????????? Gastrodia_procera_ER64 ?????????????????????????????????????????????????????????????????????????????????????????? Xerorchis_amazonica_0799 GTCCCATTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTTAAA-TCGTGAGGGTTCAAGTCCC Nervilia_plicata GTCCCTTTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTTCAAATCGTGAGGGTTCAAGTCCC Nervilia_shirensis GTCCCTTTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTTCAA-TCGTGAGGGTTCAAGTCCC Triphora_amazonica_ERP GTCCCTTTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTTAAGATCGTGAGGGTTCAAGTCCC Triphora_trianthophora GTCCCTTTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTTAAAATCGTGAGGGTTCAAGTCCC Triphora_gentianoides_ER01 GTCCCTTTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTTAAAATCGTGAGGGTTCAAGTCCC Monophyllorchis_maculta GTCCCTTTT-ACATGTCAATACCGACAAAAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTCAAAATCGTGAGGGTTCAAGTCC- Psilochilus_macrophyllus_ER02 GTCCCTTTTTACATGTCAATACCGACAACAATGAAATTTCTAGTAAAAGGAAAATCCGTCGAATTTTAAAATCGTGAGGGTTCAAGTCCC Psilochilus_LJ6914 GTCCCTTTTTCCATGTCAAT-CCGACAACAATGAAATTT-TAGTAAAAGGAAAATCCGTCGAATTTTAAAATCGTGAGGGTTCAAGTCCC Didymoplexis_pallens ?????????????????????????????????????????????????????????????????????????????????????????? 324 Calypso_bulbosa GTCCCATTTTACATGTCAATACCGACAACAATGAAATTTA--GTAT------Chysis_bractescens GTCCCATTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTTAA--TCGTGAGGGTTCAAGTCCC Isochilus_amparoana GTCCCATTTTACATGTCAATACCGACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTTAAA-TCGTGAGGGTTCAAGTCCC C_trifida GTCCCATTTTTCACGTYAATCCCGGCAATAATGRAAWTTATTGTAAGRGGAAAAWCCGKCGAATTTKAAA-TCATGAGGGTTCGAGTCCC Oreorchis_patens GTCCCATTTTACATGTCAATACCGACAATAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTTAAA-TCGTGAGGGTTCGAGTCCC

Codonorchis_lessonii TCTATCCCCAA--AAAAGCCCATTTT-----ACTTCC------TCATCCTATTTGTT--CAT---CAGTTGTTAAGTTC Corycium_sp TCTATCCCCAAGAAAAAGTCCATTTT-----ACCTCC------TCA--CTCT--GTTCT------CA---C Goodyera_sp TCTATCCCCAAGAAAAAGCCCATTTT-----AATTCCCCACTCTTTTTTTACTCTCATTCTCTTTTTTTT-AT---CAGTTGTTCAGTTC Brownleea_coerulea ------Palmorchis_trilobulata TCTATCCCCAAGAAAAAGCCCATTTT-----ACTTCCTCACTCTTTATTTATCCTCATCCTATTTTTTTTCAT---CAGTGGTTCAGTTC Palmorchis_sp TCTATCCCCAAGAAAAAGCCCATTTT-----ACTTCCTCCCTCTTTATTTATCCTCATCCTATTTTTTTTCAT---CAGTGGTTCAGTTC Cephalanthera_damasonium TCTATCCCCAAGAAAAAGCCCATTTT-----ACTTCCTCACTCTTTATTTATCCTCATCCTCTTTTT---CAT---CAGAGGTTCAGTTC Cephalanthera_aus ?????????????????????????????????????????????????????????????????????????????????????????? Aphyllorchis_montana TCTATCCCCAAGAAAAAGCCCATTTT-----ACTTCCTCACTCTTTATTTATCCTCATCCTTTTTTT---CAT---CAGTGGTTTAGTTC Epipactis_sp TCTATCCCCAAGAAAAAGCCCATTT------ACTTCCTCACTCTTTATTTATCCTCATCCTCTTTTTTTTAAT---CAGTGGTTCAGTTC Limodorum_abortivum TCTATCCCCAAGAAAAAGCCCATTTT-----ACTTCCTC------Listera_smallii TCTATCCCCAAGAAAAAGCCCATTTA-----ACTTCCTCACTCTTTATTTATCCTCATCCTCTTTTTTTTCAT---CAGTGGTTCAGTTC Listera_cordata TCTATCCCCAAGAAAAAGCCCTTTTT-----A-TTCCTCACTCTTTATTTATCCTCATCCTCTTTTTTTTCAT---CTGTGGTTTAGTTC Neottia_nidus_avis TCTATCCCCAATAAAAAGCCCATTTT-----ACTTCCTC------A--TA------CTTT-TTTTCAT---CTGTGGTTCAGTTC Corymborkis_vert_ER66 ------

Continued

Table A.4 Continued

Tropidia_effusa TCTATCCCCAAGAAAAAGCCCATTTT-----ACTTCCTCGCTCTTTATTTATCCTCATCTTCTTTCTTTTCAT---CAGTGGCTCAGTTC Tropidia_sp TCTATCCCCAATAAAAAGCCCCTTTT-----AAT-CCTCGCTCTTTATTTATCCTCATCTTCCTTCCTTTCAT---CAGTGGCTCAGTTC Epilyna_jimenzeii CCCTTCCCCCAGAAAAACCCCATTTT-----CCT-CCCCGCCCTTTGTT-ATCCCCHACCCATTTCCTTTCATTTTCA-TAA-TAAGTTC Epilyna_hirtzii ?????????????????????????????????????????????????????????????????????????????????????????? Sertifera_columbiana_ER38 TTTTTCCCCAAGAAAAAACCCCTTTT-----AWTTCCCCGCTCTTTATTTATCCTCATCCTCTTTTTTTTCATTTTCA-TAA-TCAGTTC Sertifera_sp ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_lancifolius_ER36 TCTATCCCCAAGAAAAAGCCCATTTT-----ACTTCCTCGCTCTTTATTTATCCTCATCCTATTTCTTTTCATTTTCA-TAA-TAAGTTC Elleanthus_sp TCTATCCCCAAGAAAAAGCGCATTTT-----ACTTCCCCGCTCTTTATTTATCCTCATCCTATTTCTTTTCATTTTCA-TAA-TAAGTTC Sobralia_crocea_w533 TTTATCCCCAAGAAAAAGCCCCTTTT-----ACTTCCTCGCTCTTTATTTATCCTCATCCTCTTTTTTTTCATTTTCA-TAA-TCAGTTC Sobralia_mucronata_w535 TCTATCCCCCAGAAAAAGCCCCTTTT-----ACTTCCCCGCTCTTTATTTATCCTCATCCTCTTTCTTTTCATTTTCA-TAA-TCAGTTC Diceratostele_gabonensis_ER44 TCTATCCCCAAGAAGAAGCCCTTCTTCTTTTACTTTNTCTCTCTTTATTTATCCTCATCATAT--CTTTTCAT---TAGTGGATCAGTTC Epipogium_aphyllum ?????????????????????????????????????????????????????????????????????????????????????????? Gastrodia_procera_ER64 ?????????????????????????????????????????????????????????????????????????????????????????? Xerorchis_amazonica_0799 TCTATCCCCAAGAAAAAGCCCATTTT-----AATTCCTCGTTCTTTATTTATCCTCATCCTTTTTTTTTTCAT---CAGTGGCTCAGTTC Nervilia_plicata TCTATCCCCAAGAAGAAGCCCTTCTTCTTTTACTTTCTCTCTCTTTAATTATCCTCATCATAT--CTTTTCAT---TAGTGGATCAGTTC Nervilia_shirensis TCTATCCCCAAGAAGAAGCCCTTTTTCTTTTACTTTCTCTCTCTTTATTTATCCTCATCATAT--CTTTTCAT---CAGTGGATCAGTTC Triphora_amazonica_ERP TCTATCCCCAAGAAAAAGCCCATTTT-----ACTTCCTCG------Triphora_trianthophora TCTATCCCCAAGAAAA-GCCCATTTT-----ACTTCCTTG------Triphora_gentianoides_ER01 TCTATCCCCAAGAAAAAGCCCATTTT-----ACTTCCTCG------325 Monophyllorchis_maculta TCTATCCCCAATAAAAAGCCCATTTT-----ACTTCCTCGCTCTTTATTTATCCTCATCCTCTTTC----CAT---CAGTGACTCGATTC Psilochilus_macrophyllus_ER02 TCTATCCCCAAGAAAGAGCCCTTTTT-----ACTTCTTAAATCTTTTTTTATCCTCATCCTCTTTCTTTT------CAGTGGCTCGGTTC Psilochilus_LJ6914 TCTATCCCCAAGAAAGAGCCCTTTTT-----ACTTCTTCAATCTTTTTTTATCCTCATCCTCTTTCTTTT------CAGTGGCTCGGTTC Didymoplexis_pallens ?????????????????????????????????????????????????????????????????????????????????????????? Calypso_bulbosa ------Chysis_bractescens TCTATCCCCAATAAAAAGCCCATTTT-----ACTTCCTCGCTCTTTATTTATCCTCATCCTCTTTCTTTTCAT---CAGTGGCTCAGTTT Isochilus_amparoana TCTATCCCCAAGAAAAAGCCCATTTT-----ACTTCCTCGCTCTTTATTTATCCTCATCCTCTTTCTTTTCAT---CAGTGGCTCAGTTT C_trifida TNTATCCCCAATAAAAAGCCCAWTTT-----ACTTCCTCGCTCTTTATTTATCCTCATCCTCTTTCTTTTCAT---CGGCGRCTCAGTTT Oreorchis_patens TCTATCCCCAATAAAAAGCCCATTTT-----ACTTCCTCGCTCTTTATTTATCCTCATCCTCTTTCTTTTCAT---CGGCGGCTCAGTTT

Codonorchis_lessonii AAACAAAATTCAATATCTTTCTCATTTCATTCACTCTGTACTTTCACAAGTGGATCCGAATAGAAATTATCGTATCTTC-TTCCAATTTA Corycium_sp AAA-TGGATCCAA-AT----CTAAATT--TTC------G------TAGATTC-TTCCAATTCA Goodyera_sp AAACAAAATTAAATATCTTTCTAATTTCATTCACTCTGTTCTTTCACAAATGGATACGAATAGAAATTCTCGTATCTT-ATTCCAATT-A Brownleea_coerulea ------TC----C-T-CACTCTGTTCTTTCACA--CGAATC------TAAATTTTCGTATATTC-TTCCAA---- Palmorchis_trilobulata AAACAAAATTCAATATCTTTCTCATTTCATTCACTCTGTTCTTTCACAAATGGATCCGAATAGAAATCCTCGTATCTTC-TTCTAATC-- Palmorchis_sp AAACAAAATTCAATATCTTTCTCATTTCATTCACTCTGTTCTTTCACAAATGGATCCGAATAGAAATCCTCGTATCTTC-TTATAATC-- Cephalanthera_damasonium AAACAAAATTAAATATCTTTCTCATTTCATTCACTCTGTTCTTTCACAAATGGATCCAAATAGAAATCCTCGTATCTTC-TTCCAATC-- Cephalanthera_aus ?????????????????????????????????????????????????????????????????????????????????????????? Aphyllorchis_montana AAACAAAATTCAATATCTTTCTCATTTCATTCACTCTGTTCTTTCACAACTGGATCCAAATATAAATCCTCGTATCTTC-TTCCAATC-- Epipactis_sp AAACAAAATTCAATATCTTTCTCATTTCATTCACTCTGTTCTTTTGCAACTGGATCCAAATAGAAATCCTCGTATCTTC-TTCCAATC-- Limodorum_abortivum ---CAAAATTCAATATTTTTCTCATTTCATTCACTCTGTTCTTTCACAACTGGATCCAAATGGAAATCCTCATATCTTC-TTCCAATC--

Continued

Table A.4 Continued

Listera_smallii AAACAAAATTCAAT------TTCATTTCATTCACTCTGTTCTTTCACAACTGGATCCAAATAGAAATCCTCGTATCTTC-TTCCAATC-- Listera_cordata AAACAAAATGGAAT------TTCATTCCATTCACTCAGTTCTTTCACAACTGGATCAAAATAGAAATCCTCGTATCTTC-TTCCAATA-- Neottia_nidus_avis AACCAAAATT-AAG-T----TTCATTTCATTTACTCAGTTCTTTAATAACTAGATCCAAATATAAATCCTCATACATCC-TTTCAATA-- Corymborkis_vert_ER66 ------Tropidia_effusa AAACAAAATTCAATATCTTTCTCATTTCATTCACTCTGTTCTTTCACAAATGGATC------TCCTCGTATCTTC-TTCCAATC-- Tropidia_sp AAACAAAATTAAATATCTTTCTCATTTCATTCACTCTGTTCTTTCACAAATGGATC------TCCTCGTATCTTC-TTCCAATC-- Epilyna_jimenzeii AAAAAAGATTCAATATCTTTCTCATTTCATTCACTCTGTTCTTTCACAAATGGATCCGRATAGAAATCCTCGTATCTTA-TTCCAATC-- Epilyna_hirtzii ?????????????????????????????????????????????????????????????????????????????????????????? Sertifera_columbiana_ER38 AAACAAAATTCAATATATTTCTCATTTCATTCACTCTTTTCTTTCACAAATGGATCCGAATAGAAATCCTCGTATCTTC-TTCCAATC-- Sertifera_sp ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_lancifolius_ER36 AAACAAAATTCAATATCTTTCTCATTTCATTCAGTGTGTTCTTTCACAAATGAATCCGAATAGAAATCCTCGTATCTTC-TTCCAATC-- Elleanthus_sp AAACAAAATTCAATATCTTTCTCATTTCATTCACTCTGTTCTTTCACAAATGGATCCGAATAGAAATCCTCGTATCTTC-TTCCAATC-- Sobralia_crocea_w533 AAACAAAATTCAATATATTTCTCATTTCATTCACTCTGTTCTTTCACAAATGGATCCGAATAGAAATCCTCGTATCTTC-TTCCAATC-- Sobralia_mucronata_w535 AAACAAAATTCAATATATTTCTCATTTCATTCACTCTGTTCTTTCACAAATGGATCCGAATAGAAATCCTCGTATCTTC-TTCCAATC-- Diceratostele_gabonensis_ER44 AAA------CAATT-- Epipogium_aphyllum ?????????????????????????????????????????????????????????????????????????????????????????? Gastrodia_procera_ER64 ?????????????????????????????????????????????????????????????????????????????????????????? Xerorchis_amazonica_0799 AAACAAAATTTAATATCCTTCTCATTTCATTCACTCTGTTCTTTCACAAATGGATCCGAATAAAAATCCTCGTAT------ATA-- Nervilia_plicata AAACAAA------TC-- 326 Nervilia_shirensis AAACAAA------TCCAATC-- Triphora_amazonica_ERP ------TCCAATATCTTTCTCATTTCATTCACTCTGTTCTTTAACAGAAGGATTCGAATATAAATACTCATATCTTC-TTCCAATC-- Triphora_trianthophora ------TCCAATATCTTTCTTATTTCATTCACTCTGTTCTTTAACAAAAGGATTCGAATATAAATCCTCACATCTTC-TTCCAATC-- Triphora_gentianoides_ER01 ------TCCAATATCTTTCTCATTTCATTCAATCTGTTCTTTAACAAAGGGATTCGAATATAAATCCTCATATCTTC-TTCCAATC-- Monophyllorchis_maculta AAACAAAATCCAATATTTTTCTCATTTCTTTCCCTCTTTTCTTTAACAAAAGGATCCGAATAGAAATCCTCATATCTTC-TTCCAATC-- Psilochilus_macrophyllus_ER02 AAA-AAAATCCAATATCTTTCTCATTTCATTAACTCTGTTCTTTAACAAAAGGATCCGAATATAAATCCTCATATCTTC-TTCCAATC-- Psilochilus_LJ6914 AAA-AAAATCCAATATCTTTCTCATTTCATTAACTCTGTTCTTTAACAAAAGGATCCGAATAGAAATCCTCATATCTTC-TCCCAATC-- Didymoplexis_pallens ?????????????????????????????????????????????????????????????????????????????????????????? Calypso_bulbosa ------Chysis_bractescens CAACAAAATGAAATATCTTTCTCATTTCATTCACTCTGTTCTTTCACAAATGGATCCGAATAGAAATCCTCGTATCTTC-TTCCAATC-- Isochilus_amparoana AAACAAAATTAAATATTGTTCTAATTTCATTCACTCTGTTCTTTCACAAAAGGATCCGA------C_trifida AAACAAAATGTAATATCTTTTTCATTTCATTCACTCTGTTCTTTCACAAATGGATCCGAATAGRAATCCTCGTATCTTC-TTCCAATC-- Oreorchis_patens AAACAAAAWGAAATATCTTTCTCATTTCATTCACTCTGTTCTTTCACAAATGGATCCGAATAGAAATCCTCGTATCTTC-TTCCAATC--

Codonorchis_lessonii ATCCAATTTCATTTG----GTATAGATACGATACCTGCACAAATGAACATATATGTTCAAGGAATCTCCGTTATTTAAT--CATTCACAG Corycium_sp ATCCAATTTCATTT-----GTATAGATACAATACCTGAACAAATGAACATTTATGTTCAAGGAATTTCCGTTATCTAATAA--TTCACAG Goodyera_sp ---CAATTTC-TTTGTTTTGTATAGATACGATACCTGCACAAATGAACATATATATTCAAGGAATCTCCCTTATTGAATAACATTCACAG Brownleea_coerulea ------TTTCATTTT-----TATAGATACGATACCTGTACAAATGAACATAAATGTTCAAGGAATCTCCGTTATTTAATTA--T------Palmorchis_trilobulata ---CAATTTCATTT-----GTATAG-TACGATACCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT--CATTCACAG Palmorchis_sp ---CAATTTCATTT-----GTATAG-TACGATACCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT--CATTCACAG Cephalanthera_damasonium ---AAATTTCATTT-----GTATAG-TACGATACCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT--CATTCACAG

Continued

Table A.4 Continued

Cephalanthera_aus ?????????????????????????????????????????????????????????????????????????????????????????? Aphyllorchis_montana ---CAATTTCATTT-----ATAGAG-TACGATATCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT--CATTCACAG Epipactis_sp ------TT-----GTATAG-TACGATACCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT--CATTCACAG Limodorum_abortivum ---CAATTTCATTT-----GTATAG-TACGATACCTGTAC----G------Listera_smallii ---CAATTTCATTT-----GTATAG-TACGATACCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT--CATTCACAG Listera_cordata ---CAATTTCATTT-----GTATAG-TATGATACCTGTACAAATGAACATATATGTTCAAGA--TCTCCGTTATTGAAT--CATTCACAG Neottia_nidus_avis ---CAATTTAATTT-----CTAT---TTTTTTACCTGTACAAAAGAACATATATGTTCAAGGAATTTCCGTTATTGAAT------Corymborkis_vert_ER66 ------Tropidia_effusa ---CAATTTCATTTGTTTTGTATAG-TACGATACCTGTAAAAATGAACATACATGTTCAAGGAATCTCCGTTATTGAAT--CATTCACAG Tropidia_sp ---CAATTTCATTTGTTTTGTATAG-TACGATACCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT--CATTCACAG Epilyna_jimenzeii ---CMATTCCATTTGTTTTGTATAG-TACGATACCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT--CATTCACAG Epilyna_hirtzii ?????????????????????????????????????????????????????????????????????????????????????????? Sertifera_columbiana_ER38 ---CAATTTCATTTGTTTTTTATAG-TACGATACCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT--CATTCACAG Sertifera_sp ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_lancifolius_ER36 ---CAATTTCATTTGTTTTGTATAG-TACGATACCTGTACAAATGA------Elleanthus_sp ---CAATTTCATTTGTTTTGTATAG-TACGATACCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT--CATTCACAG Sobralia_crocea_w533 ---CAATTTCATTTGTTTTGTATAG-TACGATACCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT--CATTCACAG Sobralia_mucronata_w535 ---CAATTTCATTTGTTTTGTATAG-TACGATACCTGTACAAATGAACATATATGTTAAAGGAATCTCCGTTATTGAAT--CATTCACAG Diceratostele_gabonensis_ER44 ---CNATTTCATTTGTTTTGTATAG-CACAATGCCTGCACAAATGASCATATATGTTGGGGGAATCTCCGTTACTGAAC--CATTCACAG 327 Epipogium_aphyllum ?????????????????????????????????????????????????????????????????????????????????????????? Gastrodia_procera_ER64 ?????????????????????????????????????????????????????????????????????????????????????????? Xerorchis_amazonica_0799 ---GAATTTCATTTGTTTTGTAGAG-TACGATGCCTGTACTAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT--CATTCGCAG Nervilia_plicata ---CAATTTCATTTGTTTTGTATAG-CACAATGCCTGCACAAATG------TATGTTCAAGGAATCTCCGTTATTGAAC--CATTCCCAG Nervilia_shirensis ------TCATTTGTTTTGTATAG-CACAATGCCTGTACAAATGAACATATATGTTCAAGGAATCTCCGCTATTGAAC--CATTCACAG Triphora_amazonica_ERP ---CAATTTCCTTTGTTTTTAATAG-TACAATACCTGTACAAAGGAACATATATGTTCAAGGAATCCGCCTTAT------Triphora_trianthophora ---CAATTTCCTTTGTT---AATAG-TACAATATCTGTACAAAGGAACATATATGTTAAAGGAATCCGCCTTAT------CA- Triphora_gentianoides_ER01 ---CAATTTCCTTTGTTTTTAATAG-TACAATACCTGTACAAAGGAACATATATGTTCAAGGAATCCGCATTATTGAAT--CATTCACAG Monophyllorchis_maculta ---CAATTTCCTCTGTTTTTTCTAG-TACAATATCTGTACAAATGAACATATATGTTCAAGGAATCCGCGTTATTGAAT--CATTCACAG Psilochilus_macrophyllus_ER02 ---CAATTTCCTTTGTTTTTTATAG-TACGATACCTGTACAAAGGAACATCTATCTTCAAGGAATTCACATTCTTGAAT--CATTCACAT Psilochilus_LJ6914 ---CAATTTCCTTTTTTTTTTATAG-TACGATACCTGTACAAAGGAACATCTATCTTCAAGGAATTCAAATTCTTGAAT--CATTCACAT Didymoplexis_pallens ?????????????????????????????????????????????????????????????????????????????????????????? Calypso_bulbosa ------Chysis_bractescens ---CAATCTCATTTGTTTTGTATAA-TACGATA--TG------AACATATATGTTCAAGGAATCTCCGTTATGGAAT--CATTCATAG Isochilus_amparoana ------TACGATA--TG------AACATATATGTTCAAAGAATCTCCGTTATTGAAT--CATTCATAG C_trifida ---CAATCTCATTTGTTCTGTATAA-TAYGTTA--TG------AACATATATGCTCAAGGAATCTCCGTTATGGAAT--CATTCATAG Oreorchis_patens ---CAATCTCATTTGTTCTGTATAA-TACGCTA--TG------AACATATATGTTCAAGGAATCTCCGTTATTGAAT--CATTCATAG

Continued

Table A.4 Continued

Codonorchis_lessonii TCCATATCATTCTCCTTTCATTT-----ACAAAGAAAAT------GAATATCTAA------Corycium_sp TCCATA------TCCTTACATTT-----ACAAAGAAAGTCTTCGTTTTGAAGATCTAAGAAATTAAGGGGCTAGGTCCAATTTGTTAAGA Goodyera_sp TTCATATCATTATCTTTACATTT-----ACAAAGAAAGTTTT------Brownleea_coerulea --CATATAATTATCTTTACATTG-----ACAAAGAAAGTCTTCTTTTTGAAAATCTAAGAAATTCAGGGGCTAGGTCCAATTTGTTAAGA Palmorchis_trilobulata TCCATATCATT------TTT-----ACAAAGAAAGTCTTCTTTTTGAAGATTCAAGAAATTCAGGGGCTAGGTCCAATTTGTTAAGA Palmorchis_sp TCCATATCATT------TTG-----ACAAAGAAAGTCTTCTTTTTGAAGATCCAAGAAATTCAGGGGCTAGGTCCAATTTGTTAAGA Cephalanthera_damasonium TCCATATCATT------ATT------ACAAAGAAAGTCTTCTTTTTGAAGACCTAAGAAATTCAGGGGCTAGGTCCAATTTGTTAAGA Cephalanthera_aus ?????????????????????????????????????????????????????????????????????????????????????????? Aphyllorchis_montana TCCATATCACTATCCTTACACTT-----AC------Epipactis_sp TCCATAT------CATTA----TACAAAGAAAGTCTTCTTTTTGAAGACCTAAGAAATTCAGGGGCTAGGTCCAATTTGTTAAGA Limodorum_abortivum ------Listera_smallii TCCATATCATTATCCTTACATA------AAAAAAAATCTTCTTTTTGAAGACCTAAGAAATTCGGGGGCTAGGTCCCATTTGTTAATA Listera_cordata TCCATATCATTATCCTTGCATTT-----CCAAACAAAATCTTCTTTTTGAAGAACTAAGAAATTCGGGGGCTAGGTCCTCTTTGTTAAGA Neottia_nidus_avis ------CATTT------AAAGTTTTATTTTTGAAGACGTAATAAATTAAGG--CTAGGTCCAATTTGTTAAGA Corymborkis_vert_ER66 ------Tropidia_effusa TCCATATCTTTTTCCTTACATTT-----ACAAAGAAAGTCTTCTTT------Tropidia_sp TCCATATCTTTTTCCTTACATTT-----ACAAAGAAAG------Epilyna_jimenzeii TCCAT------Epilyna_hirtzii ?????????????????????????????????????????????????????????????????????????????????????????? 328 Sertifera_columbiana_ER38 TCCATAT----AT------Sertifera_sp ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_lancifolius_ER36 ------Elleanthus_sp TCCATAT----AT------Sobralia_crocea_w533 TCCATAT----AT------Sobralia_mucronata_w535 TCCATAT----AT------Diceratostele_gabonensis_ER44 TCCATA-----ATCCTTACATTTCATTTACAAAGAAAGTCTTCTTKTTGAAGNTCTNAGAGAGTCAGGGTCTAGGTACANTTTGTTAAGA Epipogium_aphyllum ?????????????????????????????????????????????????????????????????????????????????????????? Gastrodia_procera_ER64 ?????????????????????????????????????????????????????????????????????????????????????????? Xerorchis_amazonica_0799 TCCATATCTCTATCCTTACATTT-----ACAAAGAAAGTCTTC------Nervilia_plicata TCCATA-----ATCCTTACATTTCATTTACAAAGAAAGTCTTCTTTTTGAAGATCTAAGAGATTCAGGGTCTAGGTACAATTTGTTAAGA Nervilia_shirensis TCCATA-----ATCCTTACATTTAATTTACAAAGAAAGTCTTCTTTTTGAAGATCTAAGAGATTCAGGGTCTAGATACAATTTGTTAAGA Triphora_amazonica_ERP -CCTTA------CATTT-----A-AAAGGAAGCCTTC------Triphora_trianthophora TCCTTA-----ATCCTTACATTT-----A-AAA---ATACTT------Triphora_gentianoides_ER01 TCCTTATCTTTATCCTTACATTT-----A-AAAG-AAGACTTT------A Monophyllorchis_maculta TCCTTATCTTTATCCTTACATTT-----A-AAA------TTTT----GAAGATCTAAGAAATTCAGGGGCTAGGTCCAATTWGTTAAGA Psilochilus_macrophyllus_ER02 TCCTTA------TCCTTACATTT-----A-AAAAGAAG------A Psilochilus_LJ6914 TCCTTATCTTTATCCTTACATTT-----A-AAAGGAAG------A Didymoplexis_pallens ?????????????????????????????????????????????????????????????????????????????????????????? Calypso_bulbosa ------Chysis_bractescens TCCATATCTTTTTCCTTACATTG-----ACAAAGAAAGTCTTCTTTTAGAAGATCTAAGAAATTCAGGGGCTAGGGCCAATTTGTTAAGA Isochilus_amparoana TCCATATATTTTTTCTTACATTT-----ACAAAGAAAGTCTTATTTTTTAAGATCTAAGAAATTCAGGGGCTAGGGCCAATTTGTTAATA C_trifida TCCATATCTTTTTTCTTTCATTT-----ACAAAGAAAGTCTTCTTTTTGAAGATCTAAAAGATTCAGGGGCTAGGGCCGATTTGTTAATA Oreorchis_patens TCCATATCTTTTTCCTTTCATTT-----ACAAAGAAAGTCTTCTTTTTGAAGATCTAAAAGATTCAGGGGCTAGGGCCAATTTGTTAATA Continued

Table A.4 Continued

Codonorchis_lessonii ------TTTAGTTTTTTTCATTGACA------TAGATACAAGTACTCTGCTAGGATAATGCACAGGAAA0000000000000000000 Corycium_sp CTGTCTTTTTTAGTTCTTTTCATTGACA------TAGATACAAGTATTCTGCTAGGATGATGCACGGAAAA0000000000000000000 Goodyera_sp ----ATTTTTTAGTTCTTTTCGTTTACA------TAGATACAAGTACTCTGCTAGGATTATGCA-GG-TAC1000000000010000000 Brownleea_coerulea CTTTCTTTTTTAGTTCTTTTCATTGACA------TAGATATAAGTACTCTGCTAGGATGATGCACAGAAAA??????????????????? Palmorchis_trilobulata CTTTTTT----AGTTCTTTTCATTGACA------TAGATACAAGTCCTCTGCTAGGATGATGCACGAGAAA0000000000000000000 Palmorchis_sp CTTTTTT----AGTTCTTTTCATT------??????????????????? Cephalanthera_damasonium CTTTTTT----AGTTCTTTTCATTGACA------TAGATACAAGTACTTTGCTAGGATGATGCACGGGAAA0000000000010000000 Cephalanthera_aus ?????????????????????????????????????????????????????????????????????????????????????????? Aphyllorchis_montana ------??????????????????? Epipactis_sp CTTTTTT----AGTTCCTTTCATTGACA------TAGATACAAGTACTTTGCTAGGATGATGCACGGGAAA1000100010001100000 Limodorum_abortivum ------???????????????0??? Listera_smallii CTTTTTT----AGTTTTTTTCATTGACA------TAGATAAAAGTACTTTGCTAGGATGATGCACGGGAAA0000000000000000000 Listera_cordata CNTTTTTT---AGTTCTTTTCATTGACA------TAGATAAAAGTACGGAACTAGGATGATGAACTTTAAA???????????00010000 Neottia_nidus_avis CTTTTTT----AGTTCTTTTAATTAAAA------???????????????000? Corymborkis_vert_ER66 ------???????????????0000 Tropidia_effusa ------AGTTATTTTCATTGACA------TAGATATAAGTACTCTGCTAGGATGATGCACGGGAAA000000000000000?000 Tropidia_sp ------??????????????????? Epilyna_jimenzeii ------0000000000000000000 Epilyna_hirtzii ?????????????????????????????????????????????????????????????????????????????????????????? 329 Sertifera_columbiana_ER38 ------AAGTACTCTGCTAGGATGATTCACGGGAAA0000000000000000000 Sertifera_sp ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_lancifolius_ER36 ------0000000000000000000 Elleanthus_sp ------AAGTACTCTGCTAGGATGATTCACGGGAAA??????????????????? Sobralia_crocea_w533 ------AAGTACTCTGCTAGGATGATTCACGGGAAA0000000000000000000 Sobralia_mucronata_w535 ------AAGTACTCTGCTAGGATGATTCACGGGAAA0010000000000000000 Diceratostele_gabonensis_ER44 CTCTCTNGTNTAGCTCTCTTCATTGAGA------AGCTCGAAGTNCTCGGCNAGGATGATGCACGGGAAC??????????????????? Epipogium_aphyllum ?????????????????????????????????????????????????????????????????????????????????????????? Gastrodia_procera_ER64 ?????????????????????????????????????????????????????????????????????????????????????????? Xerorchis_amazonica_0799 CTTTTT-----AGTTCTTTTCATTGACA------TAGATAGAAGTGCTCTGCTAGGATGATGCAAGGGAAA0000000000000000000 Nervilia_plicata CTCTCTTTTTTAGTTCTTTTCATTGAC??????????????AAGTACTCGGCTAGGATGAT------??????0000000000000 Nervilia_shirensis CTCTCTTTTTTAGTTCTTTTCATTGACT------TAGATAGAAGTACTCGGATAGGATGATGCACGGGAAA0000000000000000000 Triphora_amazonica_ERP ----CCTTCTTAGTTCTTTTCATTGACATTG-AC-AGATAT-----CTCTGATAGGATGATGCAAGGGAAC0000000000000000000 Triphora_trianthophora -TTTATTTTTTAGTTCTTTTCATTGACATTG-AC-AGATATAAW------GATAGGATCAACTAAGGGAAC0010000000000000001 Triphora_gentianoides_ER01 CTTTACTTTTTAGTTCTTTTCGTTGACA------AGATATAAA------GATAGGATGATGCAAGGGAA-001000100000000001? Monophyllorchis_maculta CGTTCTTTTTTAGTTCTTTTCATTGACA------AGATAT--GT------0000000000000000001 Psilochilus_macrophyllus_ER02 CTTTATTTTTTAGTTCTTTTCATTGACATAGGAC-AGATATAAGTACT-TTATAGGATGATGCAAGGGAAA0010010000000000000 Psilochilus_LJ6914 CTTTCTTTTTTAGTTCTTTTCATTGACATAGGAC-AGATATAAGTACTCTTATAGGAT-ATGCAAGGGAAA??????????????????? Didymoplexis_pallens ?????????????????????????????????????????????????????????????????????????????????????????? Calypso_bulbosa ------0000000000000000000 Chysis_bractescens TTTTCTTTTTTAGTTCTTTTCATTGACAT------AGATA-AAGTACTCTGCTAGGATGATGCACGGGAAA0000000000000000000

Continued

Table A.4 Continued

Isochilus_amparoana TTTTATTTTTTAGTTCTTTTCATTGACAT------AGATATAAGTCCTCTGCTAGGATGATGCACGGGAAA01?0000000000000000 C_trifida TTTCATTTTTGAGWTCGTCWCAGAGACA------WRG-AWTMWGCTAGGATGATGCACAGGAAA0010000000000000000 Oreorchis_patens TTTTATTTTTGAGTTCTTTTCATTGACAT------AGATA-AAGTACTCTGCTAGGATGATGCACAGGAAA0010000000000000000

Codonorchis_lessonii 000??10???????????0?0001000000000000010000000000000000000010000000000000000000000000000000 Corycium_sp 000???1???????????0?001001?111110111110000000000000000000100000000000000000000000000000000 Goodyera_sp 000000000000000?10000000000000000000010000000000000000000000000000000000000000000000000000 Brownleea_coerulea ??????????????????????????????????0001000000000000000000000000000000000000000000000000000? Palmorchis_trilobulata 000000000000000100000000000000000000010000000000000000010??000000000000000000000000000000? Palmorchis_sp ?????????????????????????????????????????????????????????????????????????????????????????? Cephalanthera_damasonium 0000000000000000000000000000000000000101?1????????????0?????0?0000000000000000000000000000 Cephalanthera_aus ?????????????????????????????????????????????????????????????????????????????????????????? Aphyllorchis_montana ?????????????????0000000100000000000010000000000000000010??0000000000000000000000000000000 Epipactis_sp 000000000000000000000000000000000000010000000000?10???0????0000000000000000000000000000000 Limodorum_abortivum ?????00?0??0000000000000000000000000010000000000000000010??0000000000000000000000000000000 Listera_smallii 000000000000001000000000100000000000011???????????????0??????????????????????0?00000000000 Listera_cordata 000000000000001000000000100000000000011???????????????0??????????????????????0?00000000000 Neottia_nidus_avis 1?0000001????0?000000000000000000000000000000000000000010??10?0010000000000000100000000000 330 Corymborkis_vert_ER66 000000000000000000000000000000000000010000010000000000010??00000?1000000000000000000000000 Tropidia_effusa 00?0?????????????????????????????????????????????????????????????????????????????????????? Tropidia_sp ?????????????????????????010000000000100000000000000000?1??0000000000000000000000000000000 Epilyna_jimenzeii 000000000000000000000000000000000000010000000000000000010??0000000000000000000000000000000 Epilyna_hirtzii ?????????????????????????????????????????????????????????????????????????????????????????? Sertifera_columbiana_ER38 000000000000000000000000000000000000010000000000000000010??0000000000000000000000000000000 Sertifera_sp ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_lancifolius_ER36 000000000000000000000000000000000000010000000000000000010??0000000000000000000000000000000 Elleanthus_sp ?????????????????????????????????????????????????????????????????????????????????????????? Sobralia_crocea_w533 000000000000000000000000000000000000010000000000000000010??0000000000000000000000000000000 Sobralia_mucronata_w535 000000000000000000000000000000000000010000000000000000010??0000000000000000000000000000000 Diceratostele_gabonensis_ER44 ?????????????????????????????????????????????????????????????????????????????????????????? Epipogium_aphyllum ?????????????????????????????????????????????????????????????????????????????????????????? Gastrodia_procera_ER64 ?????????????????????????????????????????????????????????????????????????????????????????? Xerorchis_amazonica_0799 000000000110000100000000000000000000010000000000000000010??0000000000000000000000000000000 Nervilia_plicata 0000000000000000001????????000000000010000000000000000010??0000000000000000000000000000000 Nervilia_shirensis 0000000000000000001????????000000000010000000000000000010??0000000000000000000000000000000 Triphora_amazonica_ERP 0001000000?1?0?001000000000000000000010110101000000100010??0010000000000000000000000001?01 Triphora_trianthophora 0001000000?1?0?000000000000000000000010110101000000100010??0010000000000000000001000001?01 Triphora_gentianoides_ER01 0001000000?1?0?00000000000000000000001011010100000001?0?0??0000000000010010?10000?1?01??0? Monophyllorchis_maculta 0001000000?1?0?000001000000000000000010000000001000000010??0001????????0000000000000000000

Continued

Table A.4 Continued

Psilochilus_macrophyllus_ER02 000100000000?1??00000000000000000000010000010010000000010??00000???10??0100000000000000000 Psilochilus_LJ6914 ?????????????????????????????????????????????????????????????????????????????????????????? Didymoplexis_pallens ?????????????????????????????????????????????????????????????????????????????????????????? Calypso_bulbosa 000000000000000000000000000000000000010000000000000000010??0000000000000000000000000000000 Chysis_bractescens 000000000000000000000000000000000000010000000000000000010??0000000000000000000000000000000 Isochilus_amparoana 000000000000000000000000000000000000010000000000000000010??0000000000000000000000000000000 C_trifida 000000000000001000000000000000000000010000000000000000010??0000000000000000000000000000000 Oreorchis_patens 000000000000001000000000000000000000010000000000000000010??0000000000000000000000000000000

Codonorchis_lessonii 000100000000001?1???????0??0?00??0000000000000000001??001000000000000000000000001000001000 Corycium_sp 00010000000001??000000000000000000000000000000000001??001000000000000000000000000010000000 Goodyera_sp 00010000000001??00000??100?0?00?00000000000000000001??001000000000000000000000001000000000 Brownleea_coerulea ??1???0?0??????????????????????????0?????????0???0???????000000000000000000000000001?????? Palmorchis_trilobulata 100000010?000000000001000000000000001000000000000001??001000000000000000000000000000000000 Palmorchis_sp ??0???0?0?0?0000000000000000000000000000000000100001??000000000000000111000000000000000000 Cephalanthera_damasonium 0000000000000000000000000000000000000000000000000001??001000000000000000000000010000000000 Cephalanthera_aus ?????????????????????????????????????????????????????????????????????????????????????????? 331 Aphyllorchis_montana 000000000000000000000000000000000001??????????????????????????0?00000000000000000000000000 Epipactis_sp 0000000000000000000000000000000000000000000000000001??001000000000000000000101110000000010 Limodorum_abortivum 000000000000000100000000000000000110?????0???1????????????????0?00000000000000001000000000 Listera_smallii 0000000000000000000000000000000000000000000000000001??001000000000000000000000000000000000 Listera_cordata 000000000101000000000???1??0?00??000000000??10???0???????000000000000000000000000000000000 Neottia_nidus_avis 0000000000000000001000000000101????0?????00000000001??001001000000000000000000000000000000 Corymborkis_vert_ER66 000000000????????????????????????????????????????????????????????????????????????????????? Tropidia_effusa ????????????????????????????????????????????????????????????????????????????????????000000 Tropidia_sp 000000000000000000000?1000?0000000000000001000000001??001000000000000000000010000010000000 Epilyna_jimenzeii 0000000000000000000000000000000000001000000000000001??001000000000100010001000000000000000 Epilyna_hirtzii ?????????????????????????????????????????????????????????????????????????????????????????? Sertifera_columbiana_ER38 0000000000000001000000000000000000000100100000000001??011000000000000000000010000000000000 Sertifera_sp ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_lancifolius_ER36 0000000000000000000000000000000000000100000000000001??001000000001000000000000000000000000 Elleanthus_sp ????????????????????????????????????????????????????????????????????????????????????000000 Sobralia_crocea_w533 0000000000000000000000000000000000000000100000000001??00100?100000000000000000000000000000 Sobralia_mucronata_w535 0000000000000000000000000000000000000000100000000001??00100?100000000000000000000000000000 Diceratostele_gabonensis_ER44 ??????????????????????????????????????????????????????????????0000010000000000000000000000 Epipogium_aphyllum ?????????????????????????????????????????????????????????????????????????????????????????? Gastrodia_procera_ER64 ?????????????????????????????????????????????????????????????????????????????????????????? Xerorchis_amazonica_0799 0000000?1??????????????????????????0?????????0????????????????1?1?000000000000000010000000

Continued

Table A.4 Continued

Nervilia_plicata 0000000000000000000000000011?00???00?00001??00?00001??001000010000000000000000000000000000 Nervilia_shirensis 0000000000000000000000000011?00???00?00001??00?00001??001000010000000000000000000010000000 Triphora_amazonica_ERP 000000000000000000000000000000001000000100000000000000001000000000000000000000000000000000 Triphora_trianthophora 000000000000000000000000000000001000000000000000000000001000000000000000000000000000000100 Triphora_gentianoides_ER01 ?10???0?0?00000100000000000000001000000000000000000000001000000000000000000000000000000000 Monophyllorchis_maculta 0000000000000000000000000000000010000000000000000000?1101000000000001000000000000000100000 Psilochilus_macrophyllus_ER02 000000000000000000000000000000001000001??0000001001010001000000000000000000000000000000000 Psilochilus_LJ6914 ??0???0?0?00000001000000000000001000001??0000001100010001000000100000010100000000000000000 Didymoplexis_pallens ?????????????????????????????????????????????????????????????????????????????????????????? Calypso_bulbosa 0000000000000000000000000000000000000000000000000001??00100000000000000001???????????????? Chysis_bractescens 0000000000000000000000000000000000000000000000000001??00101??000000000000000000001?0000000 Isochilus_amparoana 0000000000000000000010000000000000000000000000000001??001000000000000000000000000010000000 C_trifida 0000000000000000000000000000000000000000000000000001??001000000000000000000000000010000000 Oreorchis_patens 0000000000000000000000000000000000000000000000000001??001000000000000000000000000010000000

Codonorchis_lessonii 1000?1?00???00000001?000010000000000000000000000000000000100000000001000000000000000001000 Corycium_sp 1000?1?00???011?00000??1????0110000001001001?001??00?010010000000001?000000000000000000010 Goodyera_sp 100000000000000000000100010000000000000000000000000000001001000011000000000000000000000000 332 Brownleea_coerulea ???0???????????????????????????0?00??????01010101100?000011??000?000?1?0000000000000000011 Palmorchis_trilobulata 10000000000000000000000001000000000000000000000000000000010?1000?001?000000010000000001000 Palmorchis_sp 10000000000000000000000001000000000000000000000000000000010?1000?001?000000010000000001000 Cephalanthera_damasonium 1000000000000000001??00001000000000000000000000000000000010?1000?001?000000010000000001000 Cephalanthera_aus ?????????????????????????????????????????????????????????????????????????????????????????? Aphyllorchis_montana 1000000000000000001??00001000000000000000000000000000000010?1000?001?000000010000000001000 Epipactis_sp ?0000000000000000000000001000000000000000000000000000000010????1??01?000000010000000001000 Limodorum_abortivum 100000?10?????????????????????00000000000000000000000000010?1000?001?000000010001????????? Listera_smallii 10000000000000000000000001000000000000?1?000000000000000010?1000?001?000000010000000001000 Listera_cordata 11000000000000000000000001000000000000?1?000000000000000010?1000?001?000000010000001001000 Neottia_nidus_avis 100000100?101?001000000001000000000100101000000000000000010?1000?001?00001?0?000000000?1?? Corymborkis_vert_ER66 ?????????????????????????????????????????????????????????????????????????????????????????? Tropidia_effusa 1000000000000000000000000100000000000000000000000?10?000010?1000?0000000000010000000001000 Tropidia_sp 1010000000000000000000000100000000000000000000000?10?000010?1000?0000000000010000000001000 Epilyna_jimenzeii 10100000000100000000000000110000000000000000000000000000010?1000?0000000000010000000001000 Epilyna_hirtzii ?????????????????????????????????????????????????????????????????????????????????????????? Sertifera_columbiana_ER38 10000000000000000000000000110000000000000000000000000000010?1000?0000000000010000000001000 Sertifera_sp ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_lancifolius_ER36 10000000000000000000000000110000000000000000000000000000010?1000?00000000000100000???????? Elleanthus_sp 10000000000000000000000000110000000000000000000000000000010?1000?0000000000010000000001000 Sobralia_crocea_w533 10000000000000000000000000110000000000000000000000000000010?1000?0000000000010000000001000 Sobralia_mucronata_w535 10000000000000000000000000110000000000000000000000000000010?1000?0000000000010000000001000

Continued

Table A.4 Continued

Diceratostele_gabonensis_ER44 000000000000001?00000000010000?1??0????????????????0?0?0??0?1000?0000000000010000000001000 Epipogium_aphyllum ?????????????????????????????????????????????????????????????????????????????????????????? Gastrodia_procera_ER64 ?????????????????????????????????????????????????????????????????????????????????????????? Xerorchis_amazonica_0799 10000000000000000000000001000000000000000000000000000001??0?1000?0000000000010000000001000 Nervilia_plicata 000000000000001?00000000010000000?1????????????????0?0????0?1000?0000000000010000100001000 Nervilia_shirensis 000000000000001?0000000001000000010????????????????0?0?0??0??100?0000000000010000000001000 Triphora_amazonica_ERP 100000001??????????????????????0?00000000000000000000000010?1000?0000000000010000000?1?0?0 Triphora_trianthophora 100000001??????????????????????0?00000000000000000000000010?1000?000001000001000000010?0?0 Triphora_gentianoides_ER01 100000001??????????????????????0?00000000000000000000000010?1000?0000000000010000000001000 Monophyllorchis_maculta 100000000000000001???00001000000000000000000000000000000010?1000?0000000000010000000001000 Psilochilus_macrophyllus_ER02 100000000000000000000?10??000010000000000000000000000000010?1000?0000000000010000000001000 Psilochilus_LJ6914 100000000000000000000?10??000010000000000000000000000000010?1000?0000000000010000000001000 Didymoplexis_pallens ?????????????????????????????????????????????????????????????????????????????????????????? Calypso_bulbosa ?????????????????????????????????????????????????????????????????????????????????????????? Chysis_bractescens 10000000000000000000000001000000000000000000000000000000010?1000?000000000001011?000001000 Isochilus_amparoana 100000000000000000000000010000000000000000000000000001?????????????????????0?011?000001000 C_trifida 10000000000000000000000001000000000000000000000000000000010?1000?000000000001011?000001000 Oreorchis_patens 10000000000000000000000001000000000000000000000000000000010?1000?000000000001011?000001000

333 codonorchis_lessonii 0000000000000?10000000100000?01????00001000?00000000000GCGAAGGCA-TCGCTCGGATGTTCCCCTAACCCAA Corycium_sp 0?10?0?000000?10000000000000000000000001000?00000000000GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAA Goodyera_sp 0000000000000?100000000?1????00????00001000?00000000011GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAA Brownleea_coerulea ?000000000000?10000000000000000000000001000?00000000000GCGAAGGCAATCCCTCGGATGTTCCCCTAACCCAA Palmorchis_trilobulata 000000??10000?10000000000000000000001??1000?00000000000-CGAAGGCAATCTCTCGGATGTTCCCCTAACCCAC Palmorchis_sp 000000??10000?10000000000000000000001??????????????????------GATGTTCCCCTAACCCAA Cephalanthera_damasonium 000000?100010??0000000000000000000001??1000?00000000000GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAA Cephalanthera_aus ???????????????????????????????????????????????????????CCGAAGGCA-TCG-TCGGATGTTCCCCTAACCCAA Aphyllorchis_montana 0000000000000?100??????????????????????????????????????------Epipactis_sp 0000?1?000000100000000000000000000001??1000?00000000000GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAA Limodorum_abortivum ???????????????????????????????????????????????????????CCGAAGGGAATCGGGCGGATGTTCCCCTAACCCAA Listera_smallii 00000000000?1??0?00000000000000000001??1000?00000000000GCGAAGGCAATCGCTCGGMTGTTCCCCTAACCCAA Listera_cordata 0000000000000?100000000000000000000001?1000?00000000000CCTCAGGCC-TCTCTCGGATGTTCCCCTAACCCAT Neottia_nidus_avis ???????000000??1?00000000000000010001??????????????????GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAA Corymborkis_vert_ER66 ???????????????????????????????????????????????????????------TCCCCTAACCCTA Tropidia_effusa 0000000000000?1000000000000001?????????1000?00000000000G-GAAGGCAATCGCTCGGATGTTCCCCTAACCCAA Tropidia_sp 0000000000000?1000000??????????????????????????????????GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAA Epilyna_jimenzeii 0??????????????????????????????????????????????????????------Epilyna_hirtzii ???????????????????????????????????????????????????????TCTGAGACTCTTGCT---A-GTTCCCCTAACCCGA Sertifera_columbiana_ER38 000010000?1???????????????????????????????????000000000TCGAAGGCA-TCGC--GGATGTTCCCCTAACCCAA Sertifera_sp ???????????????????????????????????????????????????????TCGAAGGCA-TCGC--GGATGTTCCCCTAACCCAA Elleanthus_lancifolius_ER36 ??????????????????????????????????????????????????????????????????????????????????????????

Continued

Table A.4 Continued

Elleanthus_sp 000010000?1???????????????????????????????????000000000GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAA Sobralia_crocea_w533 000010000?1???????????????????????????????????000000000GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAA Sobralia_mucronata_w535 000010000?1???????????????????????????????????000000000------Diceratostele_gabonensis_ER44 0100?0000000000000000000000000000000000?10???0000000000GCTTAGGCGATCACGCTTATGTTCCCCTACCCCTT Epipogium_aphyllum ???????????????????????????????????????????????????????GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAA Gastrodia_procera_ER64 ???????????????????????????????????????????????????????CCGAATGCC-TCGCTCGCATGTTCCCCT--CCTGA Xerorchis_amazonica_0799 0000000000000?10000000000?10?00????1???1000?00000000000GAGAA------GCTCATATGTTCCCCTGACCCAA Nervilia_plicata 0100?00000?0000000000000000000000000000???????0000000??TC-AAGGCA-TCGCTCGGATGTTCCCCTAACCCAA Nervilia_shirensis 0100?00000000000000000000000000000000001000?00000000000GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAA Triphora_amazonica_ERP ???1???000000?10100000000??1?00????00000000110?1?000000GCCAAG----TC-CTCC-ATTTCACCCTTATCCAT Triphora_trianthophora 1100?00000000?101100?0010??0?00????0000000011000?1??000GCGAAGGCA-----TCGGATGTTCCCCTAACCCAA Triphora_gentianoides_ER01 0000000000000?10100010000100?00??0?0000?10???000?1??000GCGAAGGCA-----TCGGATGTTCCCCTAACCCAA Monophyllorchis_maculta 0000000000000?101?10?000000010000000000?10???01000?????GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAA Psilochilus_macrophyllus_ER02 0?10?0?000000?10100001?00?00?00??0?00000000010000010000GCGAAGGCA-TCGCTCGGATGTTCCCCTAACCCAA Psilochilus_LJ6914 0000000000000?10100001?00?00?00??0?00000000010000000100----A------C-CT--GATCA------Didymoplexis_pallens ???????????????????????????????????????????????????????GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAA Calypso_bulbosa ???????????????????????????????????????????????????????GSGAAGGCAATCGCTCGGATGTTCCMCTAACCCAA Chysis_bractescens 0000000000000?10000000000000000000000000001??1000000000GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAA Isochilus_amparoana 0000000000000?10000000000000000000000000001??0000000000GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAA 334 C_trifida 0000000000000?1000000000000000000000000??1????001000000??????????????????????????????????? Oreorchis_patens 0000000000000?10000000000000000000000000001??1000000000???????????????????????????????????

Codonorchis_lessonii CCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTT------Corycium_sp CCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTT------Goodyera_sp CCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTT------Brownleea_coerulea CCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTT------Palmorchis_trilobulata CCCGGGAACGGACCGTATGGAACCGCATCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGATTTTTGGGGGGCGAGCTTT Palmorchis_sp CCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTC-CAAGGCGCTTGCGTTTGA-TTTTGGGGG-CGAGCTTT Cephalanthera_damasonium CCCGGGAACGGACCGVANGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTTGGGGGNSSAGCTTT Cephalanthera_aus CCCGGGAACGGACCGGAGG-AACCGCA-CATGAGGAATGWCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAATTTTGGGTGGAGAGCTTT Aphyllorchis_montana ------CCG-AGCG-GAGGA-TGTCCGCGTCTCGTCGCAGGGCGC-TGCGTTTGAGTTTTGGGGGGCGA-CTTT Epipactis_sp CCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTTGGG----GAGCTTT Limodorum_abortivum CCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGGCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTTGGGGGGCGAGCTTT Listera_smallii CCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTTGGGGGGCGAGCTTT Listera_cordata CCCTGGAACGGACCTCAGGGTACCCCCACAAGTTGAATGACCCCGTCTCCCCTCAAGGAACTTGCCTTTGAGTTTTGGCAGGCGAGCTTT Neottia_nidus_avis CCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTTGGGGTCTGA-CTTA Corymborkis_vert_ER66 CCCGGGAACGGACCGGAGGGAACCGCAGCTTGAGGAATGTCCGCGTCTCGGCGAAGGGCGCTTGCGTTTGAGTTTTGGGTGGTGAGCTTT Tropidia_effusa CCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTTGGGGGGCGAGCTTT Tropidia_sp CCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTTGGGGGGCGAGCTTT

Continued

Table A.4 Continued

Epilyna_jimenzeii ------Epilyna_hirtzii CC-GGGATGGGACCCGATGTTTCCGCTTCATGACATGTGTCCGCGTCTCGTCGCGCAGCGCTTGCTCT--AGCTCTGGGGGGCGAGCTTT Sertifera_columbiana_ER38 CCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTATGGGGGGCGAGCTTT Sertifera_sp CCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTATGGGGGGCGAGCTTT Elleanthus_lancifolius_ER36 ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_sp CCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTNSSGGGGCGAGCTTT Sobralia_crocea_w533 CCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTTGGGGGGCGAGCTTT Sobralia_mucronata_w535 ------Diceratostele_gabonensis_ER44 CCC-TTAAC---CCTTTAGTACCCTTATCTTGTGGTATGACCACGTCTGCTCTCACAGAACTTA--ATCGAGCTCTGGGGGGCGAGCTTT Epipogium_aphyllum CCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTTTGGGGGCGAGCTTT Gastrodia_procera_ER64 CCCGTTTA----CCCGACGGCACCGCCTCATGAGGAATGTCCCCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTTGGGTGGCGAGCTTT Xerorchis_amazonica_0799 CCCGGGAAGGGACCGGAGGGAACCTCAGCATGGGGGATGTCCGCGTCTCGTCTCTCGGCTCAT---TTT--GT--TGGGGGGC-AGCTTT Nervilia_plicata CCCGGGAACGGACCGGAGGGAACCGCATCCTGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTTGGGGGGCGAGCTTT Nervilia_shirensis CCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTTTGGGGGCGAGCTTT Triphora_amazonica_ERP CCG---AACTAACCGCTCC-ATCC--ACCTTGGGGGATGACCGCGTCTCGTCGCAAGGCACTAGCGTTTGAG----GG-AGACGAGTTTT Triphora_trianthophora CCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCA----CGTTTGAG----GG--GGCGAGCTTT Triphora_gentianoides_ER01 CCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTACGCGTCTCGTCGCAAGGCGCTTGCGTTTGAG----GG-GGGCGAGCTG- Monophyllorchis_maculta CCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCG???????TTTGGGGGGCGAGCTTT Psilochilus_macrophyllus_ER02 CCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAAT-TCCGCGTCTCGTCGCAAGGCGCTTGCG------GG-GGGCGAGCTTT 335 Psilochilus_LJ6914 ------A--ATCGAGCTC------GAGCTTT Didymoplexis_pallens CCC------GGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTTGGGGGGCGAGCTTT Calypso_bulbosa CCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTNNGNGGG-GAGCTTT Chysis_bractescens CCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTTGGGGGGCGAGCTTT Isochilus_amparoana CCCGGGAACGGACCGGAGGGAACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTTGGGGGGCGAGCTTT C_trifida ?????????????????????????????????????????????????????????????????????????????????????????? Oreorchis_patens ??????????????????????????????????????????????????????????????????????????????????????????

Codonorchis_lessonii GGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTCAATGAGATAA Corycium_sp GGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTTACTTCAATGAGATAA Goodyera_sp SGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTTACTTCAATGAGAGAA Brownleea_coerulea GGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTTACTTCAATGAGATAA Palmorchis_trilobulata GGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAAGTGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAA Palmorchis_sp GGGCGGGCAGTGCACCCCGGGG------ACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAA Cephalanthera_damasonium GGGCGGGCAGTGCAGTCCGGGGCGGGG--CACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAA Cephalanthera_aus GGGCGGGCAGTGCAG----GGGCGGGG---ACAAGGGTCC-TGGTACTACCCAGGTGCGAA-AACCCCGGAGGTGACTTCAATGAGAGAA Aphyllorchis_montana GGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAA Epipactis_sp GGGCGGGCAGTGCAGTCCGGGGCGGGG--CACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGG-GACTTCAATGAGAGAA Limodorum_abortivum GGGCGGGCAGTGCAGTCCGGGGCGGGG--CACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTC-ATGA-A-AA Listera_smallii GGGC----AGTGCAGTCCGGGGCGGGG--CACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTAAATTAGAGAA

Continued

Table A.4 Continued

Listera_cordata ------CA------CCGGGGCGGGG--CACCCGGGTCC-TGGTACTATCCAGGTGCCAAGAACCC-GGAGGTGACTTCAATTACAAAA Neottia_nidus_avis --GCG------GGGGCGGGG--CACAAGGGTCA-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTGAAATTAGAGAA Corymborkis_vert_ER66 GGGCGGGCAGTGCAATCC-GGGC------CCCAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAA Tropidia_effusa GGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAA Tropidia_sp GGGCGGGCAGTGCAGTCCGGGG------ACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAA Epilyna_jimenzeii ------Epilyna_hirtzii GGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAA Sertifera_columbiana_ER38 GGG----CAGTGCAGTCCGGGG------CAAAAGG-TCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTCAATGAGATAA Sertifera_sp GGG----CAGTGCAGTCCGGGG------CAAAAGG-TCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTCAATGAGATAA Elleanthus_lancifolius_ER36 ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_sp GGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAA Sobralia_crocea_w533 GGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAA Sobralia_mucronata_w535 ------Diceratostele_gabonensis_ER44 GGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAA Epipogium_aphyllum GGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGG------ATTAGAGAA Gastrodia_procera_ER64 GGGCGGGAAATGAAGTCC------GGGCCC-TGGTACTACCCACGTGCCAATAACCCCGGTGGCG----C--GGAGA--- Xerorchis_amazonica_0799 GGG------CACAAGGGTCC-TGGWACAATCCAGGTGCGAAGAACCCCGGAGGTGACTGCAATGAGAGAA Nervilia_plicata GGGCGGGCAGTGCA-TCCGGGG------ACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTCAATTAGAGAA Nervilia_shirensis GGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGG------ATTAGAGAA 336 Triphora_amazonica_ERP -----GGCA-TGTAGTACGGGG------AA---TAA--GG----ACCCTGGTGAGGCTGGACCCGGA------Triphora_trianthophora GGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGGTGCGAATAACCCCGGAGGTGACTTCAATGAGAGAA Triphora_gentianoides_ER01 GAGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCCC-GGTACTACCCAGGTGCGAATAAACCCGGAGGTTACTTCAATGAGAGAA Monophyllorchis_maculta GGGCGGGCAGTGCAGTCCGGGG------CACAAGGSTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAA Psilochilus_macrophyllus_ER02 GGGCGGGC--TGAACTCCGGGG------CACAAGGG-----GGTACTACCCAGGTGCGAAGAATCCCGGTGGCGACTT------GAGAA Psilochilus_LJ6914 GGGCGGGC--TGAACTCCGGGG------TACAACAC-CCCTGGTACTACCTTGGTGCGAAGAATCCCGGTGGCGACTTCAA---GAGAA Didymoplexis_pallens GGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGGTGCGAATAACCC------AATGAGAGAA Calypso_bulbosa GGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAA Chysis_bractescens GGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAA Isochilus_amparoana GGGCGGGCAGTGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAA C_trifida ?????????????????????????????????????????????????????????????????????????????????????????? Oreorchis_patens ??????????????????????????????????????????????????????????????????????????????????????????

Codonorchis_lessonii ATTGAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAAGGAGGTAGGA Corycium_sp ATTGAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCT--AATGAGGTAGGA Goodyera_sp ATTGAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAAGGAGGTAGGA Brownleea_coerulea ATTGAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCG--AATGAGGTAGGA Palmorchis_trilobulata ATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAAGGAGGGAGGA Palmorchis_sp ATTTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAAC-AATGGACGAGCTCCA-GGAGGGAGGA Cephalanthera_damasonium ATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGCCGAGCTCCAAGGAGGGAGGA

Continued

Table A.4 Continued

Cephalanthera_aus ATGTC-CTCACTGGCCTAAACGAC-AGCAAACACTC-AACGTGAGAGCAAGGGATCACCAAACGAATGGC--AACTCC--GGAGGGAGGA Aphyllorchis_montana ATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAAGGAGGGAGGA Epipactis_sp ATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGCCGAGCTCCAAGGAGGGAGGA Limodorum_abortivum ATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAAC-AATGGCC-AGCTCCAAGGAGG-AGGA Listera_smallii ATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAAGGAGGGAGGA Listera_cordata ATGTTTCTCACTGGCCTATACAACGAGCAAACACTCGAACGTGAGACCAAGGGATCACCCAACTTATGGAAAAACTCCAAGGAGGGAG-- Neottia_nidus_avis ATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGCCGAGCTCCAAGGAGGGAGGA Corymborkis_vert_ER66 ATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAAGGAGGGAGGA Tropidia_effusa ATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAAGGAGGGAGGA Tropidia_sp ATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAAGGAGGGAGGA Epilyna_jimenzeii ------Epilyna_hirtzii ATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAAGGAGGGAGGA Sertifera_columbiana_ER38 ATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAAGGAGGGAGGA Sertifera_sp ATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAAGGAGGGAGGA Elleanthus_lancifolius_ER36 ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_sp ATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAVACGAATGGACGAGCTCCAAGGAGGGAGGA Sobralia_crocea_w533 ATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAAGGAGGGAGGA Sobralia_mucronata_w535 ------Diceratostele_gabonensis_ER44 ATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAAGGAGGGAGGA 337 Epipogium_aphyllum ATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAAGGAGGGAGGA Gastrodia_procera_ER64 -TGTAACTAACTGGCCTAAACGACGAAAAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAAGGA------Xerorchis_amazonica_0799 ATATAACTCACCGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCCGACAAATGGACCAGTTCT--GAA------Nervilia_plicata ATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAAGGAGGGAGGA Nervilia_shirensis ATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAAGGAGGGAGGA Triphora_amazonica_ERP ------Triphora_trianthophora ATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCCAACGAATGGA--A---CC---GA---AGG- Triphora_gentianoides_ER01 ATGTCACTCACTGGCCTAAACGACGAG----CACTCGAACGTGAGAGCAAGGGATCACCCAACGAATGGACGAG------Monophyllorchis_maculta ATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTBAGAGCAAGGGATCACCAAACGAATGGACGAGC-----GGAGGGAGGA Psilochilus_macrophyllus_ER02 ATGTCACTCACTGGCCTAAACGACGAGCAAACATTCAAACGTGAGAGCAAGGGATCACCAAACGAATGG-CGAGCTCCAAGGAGGGAGGA Psilochilus_LJ6914 ATGTCACTCACTGGCCTAAACGACCAACAAACATTCAAACGTGAGAGCAAGGGATCACCAAACGAATGG-CGAGCTCCAAGGAGGGAGGA Didymoplexis_pallens ATGTAACTCACTGGCCTAAACGACGAACAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAA------Calypso_bulbosa ATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAAGGAGGGAGGA Chysis_bractescens ATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAAGGAGGGAGGA Isochilus_amparoana ATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAAGGAGGGAGGA C_trifida ?????????????????????????????????????????????????????????????????????????????????????????? Oreorchis_patens ??????????????????????????????????????????????????????????????????????????????????????????

Codonorchis_lessonii GAAAGGGGGGC-AAGAACCATGCTTT----CATAGATGACATATTTTCACTCTGAACTGCGATAATAACTGACTCAGCCGTGCCTCCA-- Corycium_sp GAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATGACATATTTTCACTCTGAACTGCGATAAGAACTTACTCAGCCGTGCCTCCA-- Goodyera_sp GAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATGACATATTTBCACTCTGAACTGCGAGAAGAACTGACTCAGCCGTGCCTCCA--

Continued

Table A.4 Continued

Brownleea_coerulea GAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATTACATATTTTCACTCTGAACTGCGATAAGAACTTACTCAGCCGTGCCTCCA-- Palmorchis_trilobulata GAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATTACATATTTTCACTCTGAACTGCGATAATAACTGACTCAGCCGTGCCTCCA-- Palmorchis_sp GAAAGGGGGGC-AAGAACCATGCTTT----CA-AGATTACATATTTTCACTCTGAACTGCGATAATAACTGACTCA-CCGTGCCTCCA-- Cephalanthera_damasonium GAAAGGGGGGC-AATAACCATGCTTT----CAGAGATGACATATCT-CACTCTGAAC-----TAATCACTGACTCAGCCGTGCCTCCA-- Cephalanthera_aus GAAAGGGGGGC-AATAACCATGCTTT----CAAA--TGACAT-TTTTC-CTCTGA-C-----TAATCACTGACTCA-CCGTGC-TCC--- Aphyllorchis_montana GAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATTACATATTTTCACTCTGAACCGCGAGAATAACTTACTCAGCCGTGCCTCC--- Epipactis_sp GAAAGGGGGGC-AATAACCATGCTTT----CAGAGATGACATATTTTCACTCTGAACTGCAAAAATCACTGACTCAGCCGTGCCTCCC-- Limodorum_abortivum -AAAGGGGGGC-AATAACCCTGCTTT----CAAA--TGAC-----TGAACTCTGAAC------ACTGACTCAGCCG-GCCTCCA-- Listera_smallii GAAAGGGGGGC-AATAACCATGCTTT----CAGAGATTACCTATTTTAACTCTGAACTGCAAAAAGAACTGACTCAGCCGTGCCTCCA-- Listera_cordata ------GCTTT----CCGAGATTACATATTTTCCCAATGAGCTGCAAAAAGAACTGACTCAGCCGTGCCTCCA-- Neottia_nidus_avis GAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATGACAGATTTGAACTAGGAA-----A-AAGAACTGACTCAGCCGTGCCTCCA-- Corymborkis_vert_ER66 GAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATTACATATTTTCACTCTGAACCGCGAGAATAACTTACTCAGCCGTGCCTCCA-- Tropidia_effusa GAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATTACATATTTTCACTCTGAACTGCGAGAATAACTTACTCAGCCGTGCCTCCA-- Tropidia_sp GAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATTACATATTTTCACTCTGAACCGCGAGAATAACTTACTCAGCCGTGCCTCCA-- Epilyna_jimenzeii ------Epilyna_hirtzii GAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATTACATATTTTCACTCTGAACTGCGAGAATAACTGACTCAGCCGTGCCTCCA-- Sertifera_columbiana_ER38 GAAAGGGGGGC-AAGAACCATGCTTG----AAGAGATTACAGATTTGAACTATGAACTGCGAGAAGAACTTACTCAGCCGTGCCTCCA-- Sertifera_sp GAAAGGGGGGC-AAGAACCATGCTTG----AAGAGATTACAGATTTGAACTATGAACTGCGAGAAGAACTTACTCAGCCGTGCCTCCA-- Elleanthus_lancifolius_ER36 ?????????????????????????????????????????????????????????????????????????????????????????? 338 Elleanthus_sp GAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATTACATATTTTCACTCTGAACTGCGAGAATAACTGACTCAGCCGTGCCTCCA-- Sobralia_crocea_w533 GAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATTACATATTTTCACTCTGAACTGCGAGAATAACTGACTCAGCCGTGCCTCCA-- Sobralia_mucronata_w535 ------Diceratostele_gabonensis_ER44 GAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATGACATATTTTCACTCTGAAC-----GAATAACTTACTCAGCCGTGCCTCCA-- Epipogium_aphyllum GAAAGG------CCATGCTTG-ATG------ACATCTTTTCACTCTGAAC-----GAAGAA------CC-GG Gastrodia_procera_ER64 ----GG----C------CCGTGC--GAATGCTAAG-TTCCATATTTGAACTATTAACTGCGAGAATAACTGACTAAGCCGTGCCTCCA-- Xerorchis_amazonica_0799 GA--GTG------AGAATCATGCTTT----CAAAGA---CAT---TTCGGTC-CTA--GCGAAAAAGACTGACTC-GCCGCTATAACA-- Nervilia_plicata GAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATTACATCTTTTCACTCTGAACTGCGAGAATAACTGACTCAGCCGTGCCTCCA-- Nervilia_shirensis GAAAGG------CCATGCTTG-ATG------ACATCTTTTCACTCTGAAC-----GAAGAA------CC-GG Triphora_amazonica_ERP ------Triphora_trianthophora ----GGT---CC--GAA---T-CGT-----C-----TT-CG------TGAAC---GAG------GACTAAGCC---CC------Triphora_gentianoides_ER01 ----GGT---CCAA-A----T-CGT-----C-----TTGTCT-TCCTCA-TTTGAAC---GAG------GACTAAGCC---C------Monophyllorchis_maculta GAAAGG----C-AAGA------TTT----CAGAGATTACATATTTTCAC------GAGAATAACTKACTCAGACGT---TCC--- Psilochilus_macrophyllus_ER02 GAAAGG----C-AAGAACCATGCTTT----CA-AGATGACGTATATGA--TTGGAAC---GAGAATCACTGACTAAGCCGTGCCTCC--- Psilochilus_LJ6914 GAAAGG----C-AAGAACCATGCTTT----CAGAGATGACATATATGA--TTGGAAC---GAGAATCACTGACTAAGCCGTGCCTCCA-- Didymoplexis_pallens ----GGGGGG------CC-TGCTGTAAT----AGATTACATA-TTGAACTTTGAACTGCGAGAATAACTGACTAAGCCGTGCCTCCA-- Calypso_bulbosa GAAAGGGGG-C-AAGAACTATGCTTT----CAGAGATTACATATTTKCACTCTGAACTGCGATAATAACTGACTCAGCCGTGCCTCCA-- Chysis_bractescens GAAAGGGGG-C-AAGAACCATGCTTT----CAGAGATTACATATTTTCACTCTGAACTGCGAGAATAACTGACTCAGCCGTGCCTCCA-- Isochilus_amparoana GAAAGGGGG------C_trifida ?????????????????????????????????????????????????????????????????????????????????????????? Oreorchis_patens ??????????????????????????????????????????????????????????????????????????????????????????

Continued

Table A.4 Continued

Codonorchis_lessonii --GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGACAGATCGGCCATAGGGGTACTCCGGGATATACACC Corycium_sp --GGGGGCATTCTCCACACGGG------GCCAAGCCCAGAATGTATGGGTGACAGATCGGCCATAGGGGTACTCCGGGATATACACC Goodyera_sp --GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGACAGATCGGCCATAGGGGTACTCCGGGATATACACC Brownleea_coerulea --GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGACAGATCGGCCATAGGGGTACTCCGGGATATACACC Palmorchis_trilobulata --GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGATTGTATGGGTGACAGATCGGCTATACGGGTACTACGGGGTATACACC Palmorchis_sp --GGGGGCATTCTCCACACGGG----ACGGGGC-AA-CCCA-AATG-ATGGGTGACAGATC-GCCATAGGG-TACTCCGGGATA--CACC Cephalanthera_damasonium --GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCAAGAATGTATGGGTGACAGATCGGCCATAGGGGTACTCCGGGGTATACACC Cephalanthera_aus --GGATGC-TTCTCCA-ACGGG----ACGGGGCCAA-CCAAAA-TGTA-GGGT-ACA-ATCG-CC-TAGGG--AC-CCGGG-TTT---CC Aphyllorchis_montana --GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGACAGATCGGCCATAGGGGTACTCCGGGATATACACC Epipactis_sp --GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGACAGATCGGCCATAGGGGTACTCCGGGGTATACACC Limodorum_abortivum --GGGGGCATTC?????????????????????????????????????????????????????????????????????????????? Listera_smallii --GGGGGCATTCTCCACACGGGCGGGACGGGGCCAAGCC------GGGTGACAGATCGGCCATAGGGGTACTCCGGGGTATACACC Listera_cordata --GGGGGCATTCTCCACACGGGCGGGACGGGGGCAAGCC------GGGTGACACATCGGCCATTGGGGTGCTCCGGGGTATACACC Neottia_nidus_avis --GGGGGCATTCTCCACACGGGTGGGACGGGGCCAAGCC------GGGTGACAGATCAGCCATAGGGGTACTCCGGGGTATACACC Corymborkis_vert_ER66 --GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGACAGATCGGCCATAGGGGTACTCCGGGATATACACC Tropidia_effusa --GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGACAGATCGGCCATAGGGGTACTCCGGGATATACACC Tropidia_sp --GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCA-AATGTATGGGTGACAGATCGGCCATAGGGGTACTCCGGGATATACACC Epilyna_jimenzeii ------Epilyna_hirtzii --GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGACAGATCGGCCATAGGGGTACTCCGGGATATACACC 339 Sertifera_columbiana_ER38 --GG-----TTCTCCACACGGG----ACGGGGCCAAGCCC--AATGTATGGGTGACAGATCGGCCATAGGG-TACTCCGGGATATAC-CC Sertifera_sp --GG-----TTCTCCACACGGG----ACGGGGCCAAGCCC--AATGTATGGGTGACAGATCGGCCATAGGG-TACTCCGGGATATAC-CC Elleanthus_lancifolius_ER36 ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_sp --GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGACAGATCGGCCATAGGGGTACTCCGGGATATACACC Sobralia_crocea_w533 --GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGACAGATCGGCCATAGGGGTACTCCGGGATATACACC Sobralia_mucronata_w535 ------GTATGGGTGACAGATCGGCCATAGGGGTACTCCGGGATATACACC Diceratostele_gabonensis_ER44 --GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCA-AATGTATGGGTGACAGATCGGCCATAGGGGTACTCCGGGATATACACC Epipogium_aphyllum GCGGGGGCATTCTCCACAC------ACGG------CCAGAATGTATGGGTGACAGATCGGCCATAGGGGTACTCCGGGATATACACC Gastrodia_procera_ER64 --GGGGG------ACGGG------AATGTCTGGGTGACAGATCGGCCATAGGGGTACTCCGGGATATACACC Xerorchis_amazonica_0799 ------C-T-----A-A------ACGGG---AAAC--AGTTTGT-TGGGTGACATATCGGCCATATGATTACTCCGGGATATA---- Nervilia_plicata --GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGACAGATCGGCCATAGGGGTACTCCGGGATATACACC Nervilia_shirensis GCGGGGGCATTCTCCACAC------ACGG------CCAGAATGTATGGGTGACAGATCGGCCATAGGGGTACTCCGGGATATACACC Triphora_amazonica_ERP ------Triphora_trianthophora --GGT--CATTCTC-----G------ACGGGGCC------GA-TGT-TGGGTGACAGATCGGCCATACCAG-ACTCCGGGATAGACACC Triphora_gentianoides_ER01 --GGTC-CATTCTCCA---GGG----ACGACGGCGGGCC--GA-TGT-TGGGTGACAGATCGGCCATAGGAGTACTCCGGGATA-ACACC Monophyllorchis_maculta --GGGG-CATTCTCCACACGGG----ACGGGGGCAAGCCCAGAATGTATCGGTSACAGATCGGCCATAGGGGTACTCCGGGATATACACC Psilochilus_macrophyllus_ER02 --GGGGGCATTCTCCCCACGGG----ACGGGGCCAAGCCC-AAATGTATGGGTGACAGATCGGCCATAAGGGTACTCCGGGATATACACC Psilochilus_LJ6914 --GGGGG-ATTCTCCCCACGGG----ACGGGGCCAAGCCCATAATGTATGGGTGACA-ATCGGCCATAGGGGTACTCCGGGATATAC-CC Didymoplexis_pallens -CGGGG-CATTCTCCACACGGG------CC--GCCCAGAATGTATGGGTGACAGATCGGCCATAGGGGTACTCCGGG------ACC Calypso_bulbosa --GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGACAGATCGGCCATAGGGGTACTCCGGGATATACACC Chysis_bractescens --GGGGGCATTCTCCACACGGG----RCGGGGCCAAGCCCAGANTGTATGGGTGACAGATCGGCCATAGGGGTMCTCCGGGWTATHCACC Isochilus_amparoana ------CATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGACAGATCGGCCATAGGGGTACTCCGGGATATACACC

Continued

Table A.4 Continued

C_trifida ?????????????????????????????????????????????????????????????????????????????????????????? Oreorchis_patens ??????????????????????????????????????????????????????????????????????????????????????????

Codonorchis_lessonii AGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGA----GC Corycium_sp AGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGA----GC Goodyera_sp AGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGA----GC Brownleea_coerulea AGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGA----GC Palmorchis_trilobulata AGGGCAC-GCA-TGTCGAGCATACGACGATGCCGCCCGTGTTCTTTTCCTGGAAGTCCCCGGGGGAGGAATGGGCTGTATGTGA-GGTGC Palmorchis_sp AG--CAA-CAA-TGTC-AGC--ATCACGATGCC-CCCGTTTTCATTTC--GGAAAT-CCCGGCA-AG-AAAGGGCTGAAGG-GATGGCGC Cephalanthera_damasonium AGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGC Cephalanthera_aus ------CMYACGACGATGCCGCCCGTTTTCATTTCGTGGAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGC Aphyllorchis_montana AGGGCAA-CAAATGTCGAGCATAC-ACGATCCCGCCCGTTTTCATTTCGTG-AAGTCCCCGGCCGAG-AAAGAGATGTAGGTGATGGATC Epipactis_sp AGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGC Limodorum_abortivum ?????????????????????????????TGCCGCCCGTTTTCATCTCACG-AAGTCCCCG------Listera_smallii AGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGC Listera_cordata CGGGCAA-CAAATGTCGAGAATGC-ATCACATCCGCCGTTTTCATTTCGTGTAAGTCCCCAGCACAGGAAAGGGCTGGACGTGATGGGAC Neottia_nidus_avis AGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGC Corymborkis_vert_ER66 AGGGCAA-CAA-TGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAGTCCCCGGCAGAGGAAAGGGCTGTAG-TGATGGCGC 340 Tropidia_effusa AGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAGTACCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGC Tropidia_sp AGGGCAA-CAAATGTCGAGCATACAACGATGCCGCCCGTTTTCATTTCGTGGAAATCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGC-C Epilyna_jimenzeii ------Epilyna_hirtzii AGGGCAAACAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGC Sertifera_columbiana_ER38 AG--CAA-CAAATGTC-AGC-TACGA---TGCCGCCCGTTTTCATTT----GAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGC Sertifera_sp AG--CAA-CAAATGTC-AGC-TACGA---TGCCGCCCGTTTTCATTT----GAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGC Elleanthus_lancifolius_ER36 ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_sp AGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGC Sobralia_crocea_w533 AGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGC Sobralia_mucronata_w535 AGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGC Diceratostele_gabonensis_ER44 AGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTC--GGAATTCCCCGGCA-AG-AAAGGGCTG-AGGGGATGGCCC Epipogium_aphyllum AGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAGTCCCCGGCAGAGGAAAGGGCTGTAGG--A-----C Gastrodia_procera_ER64 AGGGCAA-AAAAGGTCGAGCATATGACGATGCCGCCCGTTTTCCTTTCGTG-ACKTCCCCGGCGGAGGAAAGG-CTGTATGTCATG-C-- Xerorchis_amazonica_0799 -GGGCAA-CCA--GTTGAGCATACGACAATGCCCCCCGTTTTCATTTCATGGAA-TCCCAGGCAGAG-A--GGGCTGTAGATGATGGCGC Nervilia_plicata AGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAGTCCCCGGCAGAGGAAAGGGCTGTATGTGATGGCGC Nervilia_shirensis AGGGCA------Triphora_amazonica_ERP ------Triphora_trianthophora AGGGCAA-CAAATGTCGAGCATAC-ACGATGCCGCCCGTTTTCATTTCGTGGAAGTCCCCGGCGGAGGAAAGGGCTGTAGGTGATGGCGC Triphora_gentianoides_ER01 AGG-CAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTC-TTTC-TGGAA--CCCCGGCA-AGGAAAGGGCTGTAGGTGATGGCGC Monophyllorchis_maculta AGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAGTTCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGC Psilochilus_macrophyllus_ER02 AGGGCA--CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGC Psilochilus_LJ6914 AGG-CA--CAA-TGTCGAGCAT-CGACGATGCCGCCCGTTTTCATTTCGTGGAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGC

Continued

Table A.4 Continued

Didymoplexis_pallens AGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAA-TCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGT Calypso_bulbosa AGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGC Chysis_bractescens AGGGCAV-CAAATGTCGAGCATACGACGATGCCGBCCGTTTTCATTTCGTGGAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGC Isochilus_amparoana AGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGTGGAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGC C_trifida ?????????????????????????????????????????????????????????????????????????????????????????? Oreorchis_patens ??????????????????????????????????????????????????????????????????????????????????????????

Codonorchis_lessonii GTTCTGCTTCTTAGGGCGCA-AA--ATCGTGACTCTGGGG----TCGTGCGTGGCACTGGTATAGATGATGAAAGGCGG------CCGG Corycium_sp GTTYTGCTTCTTAGGGCGCATAA--AT-GTGACTCTGGGG----TCGTGCGTGGCACTGGTATAGATGATGAAAGGCTTACTTGAGCCGG Goodyera_sp CTTCTGCTTATTAGGGCGCATAA--ATCGTGACTCTGGGG----TCGTGCGTGGCACTGGTATAGATGATGAAAGGCGGGCTTGA-CCGG Brownleea_coerulea GTTCTGCTTCTTAGGGCGCATAA--ATCGTGACTCTGGGG----TCGTGCGTGGCACTGGTATATATGATGAAAGGCGGGCTTGAGCCGG Palmorchis_trilobulata GTTCTGCTTCTTAGG-CGCAGA----TTGTTCCTAT------TC-T--G---CACTGGTATAGATGATGAAAGGCGGGCTTGAACC-- Palmorchis_sp GTTCTGCTTCTTAGG-CGCAGAA--ATCGTTCCTATGGGG----TCGTGCGTGGCACTGGTATAGATGATGAAAGGCGGGCTTGAACCGG Cephalanthera_damasonium GTTCTGCTTCT-GGGGCGCAGAA--ATCGTTCCTATGGGTGGGGTCGTGCGTGGCACTGGTATAGATGATGAAAGGCGGGCTTGAACCGG Cephalanthera_aus GTTCTGCTTCTTAGGGCGCAGAA--ATCGTTCCTATGGGTGGGGTCGTGCGTGGCACTGGTATAGATGATGAAAGGCGGGCTTGAACCGG Aphyllorchis_montana GTTCTGCTTCTTACGGAGGAAAA---TCGTTCCTTTCG-G----TCGTGCGTGGGACTGGT-GAGATGATGAA-GGGGGGCTTGAACAGG Epipactis_sp GTTCTGCTTCTTAGGGCGCAGAA--A------GGGG----TCGTGCG--GCACTGGTATAGATGATGAAAGGCGGG------G 341 Limodorum_abortivum ------GGGCGG--AA---TCGGCTGTAT------GTGCGTGGGGCTGG-ATAGATGATGAAAGG-GGGCTTGAACCGG Listera_smallii GTTCTGCTTCTTAGGGCGCAGAA--ATCGTACCTCTGGGTGGGGTCGTGCGTGGCACTGGTATAGATGATGAAAGGCGGGCTTGAACCGG Listera_cordata GTTCTGCTTCTTATGGCRCTCAA--ATCGTA-CTC------TC-T-C-TGGCACTGGCCGAGATG--GAA---CGGGCTTT--CCGG Neottia_nidus_avis GTT-TGCTTCTTAGGGCGCATAA--ATCGTTCC-----G-GGGGTCGTGCGTGGCACTGGTATAGAT------GGG------GG Corymborkis_vert_ER66 GTTCTGCTTCTTAGGGAGCAAAA---TCRTTCCTT-GG-G----TCGTGCGTGGCACTGGTATA-ATGATGAATGGCGGGCTTGAACCGG Tropidia_effusa GTTCTGCTTCTTAGGGCGCATAA--ATCGTTCCTATGG-G----TCGTGCGTAGCACTGGTATAGATGATGAAAGGCGGGTTTGAACCGG Tropidia_sp GTTCTGCTTCTTAGGGCGCATAA--ATCGTTCCTATGG-G----TCGTGCGTGGCACTGGTATAGATGATGAAAGG-GGGCTTGA-CCGG Epilyna_jimenzeii ------Epilyna_hirtzii GTTCTGCTTCTTAGG-CGCAGAA--ATCGTTCCTATGG-G----TCGTGCG----ACTGGTATAGATGATGAAAGGCGGGCTTGAACCGG Sertifera_columbiana_ER38 GTTCTGCTTCGCAGGGCGCATAA--ATCGTTCCTATGG-G----TCGTGCG----ACTGGTATAGATGATGAAAGGCGGGCTTGAACCGG Sertifera_sp GTTCTGCTTCGCAGGGCGCATAA--ATCGTTCCTATGG-G----TCGTGCG----ACTGGTATAGATGATGAAAGGCGGGCTTGAACCGG Elleanthus_lancifolius_ER36 ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_sp GTTCTGCTTCTTAGGGCGCAGAA--ATCGTTCCTATGG-G----TCGTGCG----ACTGGTATAGATGATGAAAGGCGGGCTTGAACCGG Sobralia_crocea_w533 GTTCTGCTTCTTAGGGCGCATAA--ATCGTTCCTATGG-G----TCGTGCG----ACTGGTATAGATGATGAAAGGCGGGCTTGAACCGG Sobralia_mucronata_w535 GTTCTGCTTCTTAGGGCGCATAA--ATCGTTCCTATGG-G----TCGTGCG----ACTGGTATAGATGATGAAAGGCGGGCTTGAACCGG Diceratostele_gabonensis_ER44 GT-CTGCTTCTTAGG-CGCA-AA--ATCGT-CCTAT-G-G----TCGG--G-GGCACTGGT-TA-ATGATGAAAGG--GGCTTGA-C-GG Epipogium_aphyllum GTTC-GG-TCT------TTCCTA-GG-G------TTGGTCTAG------CTTGAA--GG Gastrodia_procera_ER64 -T-CGAC--CTT-TG-CGCATAAGCATA-TC--AAT-G------TC-T--G---CACTGGTATAGATGATGAAAGGCG---T----C-GG Xerorchis_amazonica_0799 GTTCATCTTCTT------G----TCGTGAGGA---A------T----AT------G--CCG- Nervilia_plicata GTTCTGCTTCTTAGGG------TCGTTCCTAT------CTGGTATAAAT-ATGAAA---GGG-TTGAAC-GG Nervilia_shirensis ------Triphora_amazonica_ERP ------GG-G------

Continued

Table A.4 Continued

Triphora_trianthophora GTTCTGCTTATAA------AAAA--AT-G----TATGG-G----TCCT------AT------TGGG--TG--C-GG Triphora_gentianoides_ER01 GTTCTGCTTCTTA------TCT---CTA-GG-G----TCCTGCGCGGGA--GGT-T--ATGATGAAR--TGGG--TG------Monophyllorchis_maculta GTTCTGCTTCTTAGGGCGCATAA--ATCGTTCC---GG-G----TCGTGCGTGGCACTGGTATAGATGATGAAAGACAGG----A-CCGG Psilochilus_macrophyllus_ER02 GTTCTGCTTCTTAGGGCGCAGAA--ATTGTTCC----G-G----TCGTGCGTGGCACTGGTATAGATGA-GAAAGGCAGGCTTGAAC-GG Psilochilus_LJ6914 GTTCTGCTTCTTAGGGCGCAGAA--ATTGTTCC----G-G----TCGTGCGTGGCACTGGTATAGATGA-GAAAGGCAGGCTTGAAC-GG Didymoplexis_pallens GTTCTACTTCT--GATTG-A-AA---TCGTTCCTATGG-G----TCGT--GTGGCACTGGTATAGATGATGAA----GGGAATGTACCGG Calypso_bulbosa GTTCTGCTTCTGAGGGCGCATAA--ATCGTTCCTATGG-G----TCGTGCGTGGCACTGGTATAGATGATGAGAGGCGGGCTTGAACCGG Chysis_bractescens GTTCTGCTTCTTAGGGCGCAGAA--ATCGTACCTCTGG-AGGGGTCGTGCGTGGCACTGGTATAGATGATGAAAGGCGGGCTTGAACCGG Isochilus_amparoana GTTCTGCTTCTTAGGGCGCAGAA--ATCGTTCCTATGG-G----TCGTGCGTCGCACTGGTATAGATGATGAAAGGTGGGCTTGAACCGG C_trifida ?????????????????????????????????????????????????????????????????????????????????????????? Oreorchis_patens ??????????????????????????????????????????????????????????????????????????????????????????

Codonorchis_lessonii GACCTC-T-C--T-TGAAGAGGCGGCAAGCAAGAAGAGGAAAGGG------TTATGAGTGCCTTTTTAG--AAAAA------GGGTG Corycium_sp GACCTATT-T--T-TGAAGAGGCGGCAAGCAAGAAGAGGAAAGGG------TGATGAGTGCCTTT--AG--AAAAA------GGGTT Goodyera_sp GACCTCTT-CT---TGAATAGGCGGCAAGCAAGAATAGGAAAGGGGGCGGCTGATGAGTGCCTTTTTAG--AAAAA------GGGTT Brownleea_coerulea GACCTCTT-C--T-TG----GCCGGCA-GCAAGAA-A------GGCTGATGAGTGCCTTTT-AG--AAAAA------GGGTT Palmorchis_trilobulata -ACCTATT-CTCTT--AATAG-CCACA--CAAGAATAGGAAAGGGGGCGGCTGATGA-TGCCTTTTTA--CATAAA-TAGAAAAAGGGTT 342 Palmorchis_sp GACCTATT-CTCTT--AATAGGCGGCAAGCAAGAATAGGAAAGGGGGCGGCTGATGAGTGCCTTTTTAGTCATAAA-TAGAAAAAGGGTT Cephalanthera_damasonium GACCTATT-CTCTTATAATAGGCGGCAAGCAATAATAGGAAAGGGGGCGGG-----AGTGCCTTTTTAGTCATAAA-TAGAAAAAGGGTG Cephalanthera_aus GACCTATT-CTCTTATAATAGGCGGCAAGCAATAATAGGAAAGGGGGCGGCTGATGAGTGCCTTTTTAGTCCTAAA-TAGAAAAAGGGTG Aphyllorchis_montana C-CCCCTT-TT-TT-TAATAGGCAGCAAA-AA-----GGAAAGGGGG-GGGTGATG------TTTTTA-TCAGAAA--A-AAAAAGG-T- Epipactis_sp GACCTATT-CTCTT--AATAGGCGGCAAGCAATAATAGGAAAGGGGGCGGCTGATGAGTGCCTTTTTAGTCAGAAA-TAGAAAAAGGGTG Limodorum_abortivum GACCTATT-CTC--A-AA-AGGCGG-AAGCAATAATAGGAAAGGG--CGGGCG------CC------GAAAA--GGCTATGGGTG Listera_smallii GACCTATT-CTCTT--AATAGGCGGCAAGCAATAATAGGAAAGGGGGCGGCTGATGAGTGCCTTTTTAGTCCTAAA-TAGAAAAAGGGTG Listera_cordata G----CTT-GCCTT--AATAGGC--TAAACAA----AGGAGA-----C------GCCTTTT----C-GAA----GAAA-----TT Neottia_nidus_avis GACCTATT-CTATTATAATAGGCGGCAAGCAAGAATAGGAAAGGTTACGAA-G-TGAGTGCCC------GAAAA-GG--- Corymborkis_vert_ER66 GACT-ATT-CTCTTATAAAAGGCGGCAAGCAAGAATAGGAAAGGGG-CGGYTGATGRA----TTTTTA-TCAAAAA-TAAAAAAAGGGTT Tropidia_effusa GACCTATT-CTCTTATAAGAGGCGGCAAGCAAGAATAGGAAAGGGGGCGGCTGATGAGTGCCTTTTTAGTCAGAAA-GAGAAAAAGGGTT Tropidia_sp GACCTATTTCTCTT-TAAGA-GCGGCAAGCAAGAATAGGAAAGGGG-CGGGTGATGAGT---TTT--AATCAGAAA-TAGAAAAAGGGTT Epilyna_jimenzeii ------Epilyna_hirtzii GACCTATT-CTCTTAT-ATAGGCGGCAAGCAAGATTAGGAAAGGGGGCGGCTGA-GAGTGCCTTTTTA-T-AGAAA-TAAAAAA-GGGTT Sertifera_columbiana_ER38 GACCTATT-CTCTTATAAAAAGCGGCAAGCAAG------Sertifera_sp GACCTATT-CTCTTATAAAAAGCGGCAAGCAAGAAT------TT------Elleanthus_lancifolius_ER36 ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_sp GACCTATT-CTCTTATAATAGGCGGCAAGCAAGAATAGGAAAGGGGGCGGCTGATGAGTGCCTTTTTAGTAAGAAA-TAGAAAAAGGGTT Sobralia_crocea_w533 GACCTATT-CTCTTATAATAGGCGGCAAGCAAGAATAGGAAAGGGGGCGGCTGATGAGTGCCTTTTTAGTAAGAAA-GAGAAAAAGGGTT Sobralia_mucronata_w535 GACCTATT-CTCTTATAATAGGCGGCAAGCAAGAATAGGAAAGGGGGCGGCTGATGAGTGCCTTTTTAGTAAGAAA-GAGAAAAAGGGTT

Continued

Table A.4 Continued

Diceratostele_gabonensis_ER44 -ACTTATT--T---AT-ATA--AGGAAAG---G-CTAAGAAA------GCCTTTTTAGTCATAAAATAGAAAAAGGGTT Epipogium_aphyllum GGCCTATT-CTCTGAT------GGT- Gastrodia_procera_ER64 GACCTATT-CT--GAT------GGAAAGCAAGAATAG------CTTCTG------AGTCA------TGGTT Xerorchis_amazonica_0799 TATCTAAT-CTTTTATA-AAGGG--CAAGCATGAGTGGGAAAACGCATTTCT-CC-AATGCGTTAGCAGT---AAA-TCGAACTCGG--- Nervilia_plicata GAC-TATT---TTTATAATA-GCGG-AAGCA--AA--G-AA-GGGG-TGG-TGATGA-TGC-TTTTTA-TA-TAAA-TAAAAAA-GGGTT Nervilia_shirensis ------Triphora_amazonica_ERP ------Triphora_trianthophora GACCTA-T-CTATTATAATAG-CGT----C-AGA------GTGC-T----AGTCATAAA-GAGAAAAAGGGTG Triphora_gentianoides_ER01 ------GGYGSMAARCAAGAAWAGGAA-GG---CGA-----RAR----TGTTTA-TCAMAAA-G------GTT Monophyllorchis_maculta GACCTATT-CTCTTATAATAGGCGGCAAGCAAGAATAGGAAAGGGGGCGACTGATGAGTGCCTTTTTAGTCAGAAA-GAGAAAAAGGGTT Psilochilus_macrophyllus_ER02 GACCTATT-CTCTTATAATAGGCGGCAAGCAAGAATAGGAAAGGGGGCGACTGATGAGTGCG-----AGTCAGAAA-GAGAAAAAGG--C Psilochilus_LJ6914 GACCTATT-CTATTATAATAGGCGG-AAGCAAGAATAGGAAAGGGGGCGACTGATGAGTGCG-----AGTCAGAAA-GAGAAAAAGG--C Didymoplexis_pallens ------TT-CT---ACA-TAGGCGGCAAGCAAGAATAGGAAA------TG------GTC------GAAAAAGGGTG Calypso_bulbosa GACCTATT-CTGTTATAA-AGGCGGCAAGCAAGAGTAGGAAAGGGGGCGGCTGATGAGTGCCTTTKTAGTCATAAA-TAGAAAAAGGGTT Chysis_bractescens GACCTATT-CTCTT--AA-AGGCGGCAAGCAATAATAGGAAAGGGGGCGGCTGATGAGTGCCTTTTTAGTCCTAAA-TAGRAAAAGGGTG Isochilus_amparoana GACCTATT-CTCTTCTAA-AGGCGGCAAGCAAGAATAGGAAAGGGGGCGGCTGATGAGTGCCTTTTTAGTCAGAAA-TAGRAAAAGGGTT C_trifida ?????????????????????????????????????????????????????????????????????????????????????????? Oreorchis_patens ??????????????????????????????????????????????????????????????????????????????????????????

343

Codonorchis_lessonii GAATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGA----CGGGACGGACTGTAAGAGGCCGCAGCGGGACGACCAGAGGAAAG Corycium_sp GG-TTTT------C------GCC------CGCC------Goodyera_sp GAATGTCGAGCTAACCTGGCTACAAGTCTAGC-AAAGAAAGA----CGGGACGGACTGTAAGACGCCGCAGCGGGACGACCAGAGGAAA- Brownleea_coerulea TAATGTGGAGCTAACCTGGCTACAAGTCTAGCCAAAGAAAGA----CGGGACGGACTGTAAGAGGCCGCAGCGGGACGACCAGAGGAAAG Palmorchis_trilobulata GAATGTGGAGCTAACCTGGCTACAA????????????????????????????????????????????????????????????????? Palmorchis_sp GAATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGACTGTCAGAGGCCGCAGCGGGACGACCAGAGGAAAG Cephalanthera_damasonium GAATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGACTTTCAGAGGCCGCAGCGGGACGACCAGAGGAAAG Cephalanthera_aus GAATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGACTTTCAGAGGCCGCAGCGGGACGACCAGAGGAAAG Aphyllorchis_montana -AATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGACTTTCAGAGGCCGCAGCGGGACGACCAGAGGAAAG Epipactis_sp GAATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGACTTTCAGAGGCCGCAGCGGGACGACCAGAGGAAAG Limodorum_abortivum -AATGT----C-AA-ATCACTTGGTCTCGACTGAAAG-----GAGAGGTGA-----T------GAAAG Listera_smallii GAATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGACTTTCAGAGGCCGCAGCGGGACGACCAGAGGAAAG Listera_cordata GA-TGT------CCTG-CTACAA-TAATGCCAT-GACACC-AAA-G------TTT------Neottia_nidus_avis -A------Corymborkis_vert_ER66 GAATGKGGAG-TAACCTGGCTMCAA------AAAGAAAGAGAGATGGGACGGACTGTCAGAGGCCGCAGCGGGACGACCA------Tropidia_effusa GAATGT----CTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGACTGTCAGAGGCCGCAGCGAGACGACCA------Tropidia_sp GAATGTGGAGCTAACCTGGT-AC------AAAGAAAGAGAGATGGGACGGACTGTCAGAGGCCGCAGCGGGACGACCA------Epilyna_jimenzeii ------Epilyna_hirtzii TAATGTGGAG-TCACCTGG-TACCAGTAT-GCCAA-GAAAGAGAGACGGGACGGACTTTCAGAG-CCGCAGCGGGACGACCAGAGGAAAG Sertifera_columbiana_ER38 ------

Continued

Table A.4 Continued

Sertifera_sp ------Elleanthus_lancifolius_ER36 ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_sp GAATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGACTGTCAGAGGCCGCAGCGGGACGACCAGAGGAAAG Sobralia_crocea_w533 GAATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGACTGTCAGAGGCCGCAGCGGGACGACCAGAGGAAAG Sobralia_mucronata_w535 GAATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGACTGTCAGAGGCCGCAGCGGGACGACCAGAGGAAAG Diceratostele_gabonensis_ER44 GAATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGACTGTCAGAGGCCGCAGCGGGACGACCAGAGGAAAG Epipogium_aphyllum ------TGGC-ACA------Gastrodia_procera_ER64 TAATGTGGAGCTAACCTGGCTACTTGTA--GCCAAAGAAAGG------TGTTATAG------Xerorchis_amazonica_0799 GAA--TGGAGTT-----GGCTTC--GT------GAAAAACACAA-GG--TTT------CCG-AGC---A-GACCACAGCGAGA Nervilia_plicata GAATGTG-A--TAA--TGGT------Nervilia_shirensis ------Triphora_amazonica_ERP ------A-AAGTA------Triphora_trianthophora G--TGTGGAGCTCACCTGG-TACAAGTATA-CCA------GAGACGGGACGGAC-----GAGGCC-----GGGACGACCAGAGGAAAG Triphora_gentianoides_ER01 GAATGTGGARCTCMCCTGGCTTCAAGTATAGCCAAAGAAAGAGAGAGGGGACGGACTGTCAGAGGCCGCAGCGGGAC----AGAGGAA-- Monophyllorchis_maculta GAATGTGGAGCTCACCTGGCTACAAGTATAGCAAAAGAAAGAGAGACGGGACGGACTGTCAGAGGCCGCAGCGGGACGACCAGAGGAAAG Psilochilus_macrophyllus_ER02 GAA-GTGG-----ACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGA----AAGAGGCT--AGTGGC-CGACCATAGGAAAG Psilochilus_LJ6914 GAA-GTGG-----ACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGA----AAGAGGCT--AGTGGC-CGACCATA-AAAAG Didymoplexis_pallens GAA------TGGCTACAAGTATAGCCAAAGAAAGAGA------CGGGACGACC------Calypso_bulbosa GAATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGACTGTGAGAGGCCGCAGCGGGACGACCAGAGGAAAG 344 Chysis_bractescens GAATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGACTTTCAGAGGCCGCAGCGGGACGACCAGAGGRAAG Isochilus_amparoana GAATGTGGAGCTAACCTGGCTACAAGTATAGCCAAAGAAAGAGAGACGGGACGGACTGTCAGAGGCCACAGCGGGACGACCAGAGGAAAG C_trifida ?????????????????????????????????????????????????????????????????????????????????????????? Oreorchis_patens ??????????????????????????????????????????????????????????????????????????????????????????

Codonorchis_lessonii CCCGCCCCCGCTAGCTAACATAGTATTCTCGGTGCGCATATTCTAGATTGAGAATAGATTACCGACCAGGCCAGGCCGAATCGGGCCACC Corycium_sp ------Goodyera_sp ---GCCCCCGCTAGCTAACATAGTATTCTCGGTGCGCATATTCTCTCTGTAGAATCTATTCCCGACCAGGCCAGGCCGAATCGGGCCACC Brownleea_coerulea CCCGCCCCCGCTAGCTAACATA-TATTCTCGGTGCGCATATTATCTATTTAGAAGAGATTCCCGACCAGGCCAGGCCGAATCGGGCCACC Palmorchis_trilobulata ?????????????????????????????????????????????????????????????????????????????????????????? Palmorchis_sp CCCGCCCCCGCTAGCTAACATAGTATTCTCGGTGCGCATATTCTCTCTTTATAATCTATTCCCGACCAGGCCAGGCCGAATCGGGCCACC Cephalanthera_damasonium CCCGCCCCCGCTAGCTAACATATTATTCTCGGTGCGCATATTCTCTCTTTAGAATCTATTCCCGACCAGACCAGGCCGAATCGG-CCACC Cephalanthera_aus CCCGCCCCCGCTAGCTAACATATTATTCTCGGTGCGCATATTCTCTCTTTAGAATCTATTCCCGACCAGACCAGGCCGAATCGGGCCACC Aphyllorchis_montana CCCGCCCCCGCTAGCTAACATATTATTCTCGGTGCGCATATTCTCTCTTTAGAATCTATTCCCGACCAGACCAGGCCGAATCGGGCCACC Epipactis_sp CCCGCCCCCGCTAGC------AG-ATTCTCGGTGCGCATATTCTCTCTTTAGAATCTATTCCCGACCAGACCAGGCCGAATCGGGCCACC Limodorum_abortivum ------A------Listera_smallii CCCGCCCCCGCTAGCTCACATATTATTCTCGGTGCGCATATTCTCTCTTTAGAATCTATTCCCGACCAGACCAGGCCGAATCGGGCCAC- Listera_cordata ------Neottia_nidus_avis ------Corymborkis_vert_ER66 ------

Continued

Table A.4 Continued

Tropidia_effusa ------Tropidia_sp ------Epilyna_jimenzeii ------Epilyna_hirtzii CCCGCCCCCGCTAGCTAACATAGTATTCTCGG---GCATATTCTCTCTT-AGCATCTATTCCCGACCAGGCCAGGCCGAATCGGGCCACC Sertifera_columbiana_ER38 ------Sertifera_sp ------Elleanthus_lancifolius_ER36 ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_sp CCCGCCCCCCCTAGCTAACATAGTATTCTCGG----CATATTCTCTCTTTAGAATCTATTCCCGACCAGGCCAGGCCGAATCGGGCCACC Sobralia_crocea_w533 CCCGCCCCCGCTAGCTAACATAGGATTCTCGG----CATATTCTCTCTTTAGAATCTATTCCCGACCAGGCCAGGCCGAATCGGGCCACC Sobralia_mucronata_w535 CCCGCCCCCGCTAGCTAACATAGGATTCTCGG----CATATTCTCTCTTTAGAATCTATTCCCGACCAGGCCAGGCCGAATCGGGCCACC Diceratostele_gabonensis_ER44 CCCGCCCCCGCTAGCTAACATAG--TTCTCGGTGCGCATATTCTCTCTTAAGAATAGATTCCCGACCAGGCCAGGCCGAATCGGGCCACC Epipogium_aphyllum ------GC-A-CAT--G-TT--CGG------ACC Gastrodia_procera_ER64 ------Xerorchis_amazonica_0799 ------CTA-CT------G----CTCCG------CT--CTTT------Nervilia_plicata ------Nervilia_shirensis ------Triphora_amazonica_ERP --C-CAA----TGGCTAACACAG----CTC-GTGAGAGC--GGGATC---AGAATGGATT------GG--AAATGGGGTC-C- Triphora_trianthophora CCCGCCCCCGCTATCTAACATAGGA------GTGCGC---TT-TCT-----GAA--GA------CAGGCCGAATCGGGTCAC- Triphora_gentianoides_ER01 -CCGCCCGCGCTAGCTAACATAGGATTCTTGGTGCGCATCTT-T-TCTTTA-TAT-GATT------CAGGCCGAATCGGGTCAC- 345 Monophyllorchis_maculta CCCGCCCCCGYTAGCTAACATAGGATTCTCGGTGCGCATATTCTCTATTTAGAAT------CAGGCCAGGCCGAATCGGGCCACC Psilochilus_macrophyllus_ER02 CCCGCCCCCGCTAGCTAACATATGATTCTCGG----CAGATTCTCTATTCAGAA--GA------GGCCAGGCCGAATCGGGCCACC Psilochilus_LJ6914 CCCGCCCCC-CTAGCTAACATATGATTCTCGG-----AGATTCTCTATTCAAAA---A------GGCCAGGC-GAATCGGGCCACC Didymoplexis_pallens ------C-AGCTCACATAGGATTCTCGG----CATATTCTCTATTTCGAATAGATTCCCGACCAGGCCAGGC------GG-CCGCC Calypso_bulbosa CCCGCCCCCGCTAGCTAACATAG--TTCTCGGTGCGCATATTCTCTCTTTAGAATCTATTCCCGACCAGGCCAGGCCGAATCGGGCCACC Chysis_bractescens CCCGCCMCCGATAGCTYACATAT--TTCTCGGTGCGCATWTT-TCTCTTTAGA-TCTATTCCCGACCAGGCCAGGCCGAATCGGGCCACC Isochilus_amparoana CCCGCCCCCGCTAGCTAACATAG--TT-TTGGTGC---TATTCTCTATTTAGAATCTATTCCCGACCAGGCCAGGCCGAATCGGGCCACC C_trifida ?????????????????????????????????????????????????????????????????????????????????????????? Oreorchis_patens ??????????????????????????????????????????????????????????????????????????????????????????

Codonorchis_lessonii ACTTGGGATGGGAATGGCTCAGCCCACATGCATCATTTGATGAAAGCATTCCAGTCGCCTCCGATCAGTGGCTTGTCAACCACCGGACCG Corycium_sp ------Goodyera_sp ACTTGGGATGGGAATGGCTCAGCCCACATGCATCATTTGATGRAAGCATTCCAGTCGCCTCCGATCAGTGGCTTGTCAACCACCGGACCG Brownleea_coerulea ACTTGGGATGGGAATGGCTCAGCCCACATGCATCATTTGATGAAAGCATTCCAGTCGCCTCCGATCAGTGGCTTGTCAACCACCGGACCG Palmorchis_trilobulata ???????ATGGGAAGGGTCCAGCCCCCCTGCCTCATTTGCGGAAA-CTTTCCAGT-GC-TTCGATCAGT-GCTTGTCAAACACCGGATGG Palmorchis_sp ACTTGGGATGGGAATGGCTCA-CCCACATGCATCATTTGATGAAAGCATTCCAGTCGCCTCCGATCA-TGGCTTGTCAACCACCGGACCG Cephalanthera_damasonium ACTTGGGATGGGAATGGCTCAGCCCACATGCATCATTTGAGGAAAGCATTCCAGTCGCCTCCGATCAGTGGCTTGTCAACCACCGGACCG Cephalanthera_aus ACTTGGGATGGGAGTGGCTCAGCCCACATGCATCATTTGAGGAAAGCATTCCAGTCGCCTCCGATCAGTGGCTTGTCAACCCCCGGACCG Aphyllorchis_montana ACTTGGGATGGGAATGGCTCAGCCCACATGCATCATTTGAGGAAAGCATTCCAGTCGCCTCCGATCAGTGGCTTGTCAACCACCGGACCG Epipactis_sp ACTTGGGATGGGAATGGCTCAGCCCACATGCATCATTTGAGGAAAGCATTCCAGTCGCCTCCGATCAGTGGCTTGTCAACCACCGGACCG Limodorum_abortivum ------TGCT--CACTATAGA-GAGATG-ATC-TTTCTT-AAAGGA------AGCG Listera_smallii ----GG-ATGGGAATGGCTCAGCCCACATGCATCATTTGAGGAAAGCATTCCAGTCGCCTCCGATCAGTGTCTTGTCAACCACCGGACCG

Continued

Table A.4 Continued

Listera_cordata ------Neottia_nidus_avis ------Corymborkis_vert_ER66 -CTTGGGATGGGGATGGCTCAGCTCACATGCATCATTTGATGAAAGCATTCCAGTCGCCTCCGATCAGTGGCTTGTCAACCACCGGACGG Tropidia_effusa -CTTGGGATGGGGATGGCTCAGCCCACATGCATCATTTGATGAAAGCATTCCAGTCGCCTCCGATCAGTGGCTTGTCAACCACCGGACCG Tropidia_sp -CTTGGGATGGGGATGGCTCAGCCCACATGCATCATTTGATGAAAGCATTCCAGTCGCCTCCGATCAGTGGCTTGTCAACCACCGGACCG Epilyna_jimenzeii ------GA-GG-TC------CATGCATCATT--A-GAAA-C-TTTCAGT-G-CT--GATCAG-GG-TT-TC-ACCA-CGG---G Epilyna_hirtzii ACTTGGGATGGGGATGGCTCA-----CATGCATCATTTGATGAAAGCATTCCAGTCGCCTCCGATCAGTGGCTTGTCAACCACCGGACCG Sertifera_columbiana_ER38 ------AATTTGATGAAAGCATTCCAGTCGCCTCCGATCAGTGGCTTGTAAACCACCGGACCG Sertifera_sp ------GATGAAAGCATTCCAGTCGCCTCCGATCAGTGGCTTGTAAACCACCGGACCG Elleanthus_lancifolius_ER36 ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_sp ACTTGGGATGGGGATGGCTCA-----CATGCATCATTTGATGAAAGCATTCCAGTCGCCTCCGATCAGTGGCTTGTCAACCACCGGACCG Sobralia_crocea_w533 ACTTGGGATGGGGATGGCTCA-----CATGCATCATTTGATGAAAGCATTCCAGTCCCCTCCGATCAGTGGCTTGTCAACC------Sobralia_mucronata_w535 ACTTGGGATGGGGATGGCTCA-----CATGCATCATTTGATGAAAGCATTCCAGTCCCCTCCGATCAGTGGCTTGTCAACC------Diceratostele_gabonensis_ER44 ACTTGGGATGGGGATGGCTCAGCCCACATGCATCATTTGATGAAAGCATTCCAGTCGCCTCCGATCAGTGGCTTGTCAACCACCGGACCG Epipogium_aphyllum A------CA-CCCACA-GGATC-GA-GATGG------AG-C------AACC------Gastrodia_procera_ER64 ------Xerorchis_amazonica_0799 ------CGCG------C--GTC------

346 Nervilia_plicata ------Nervilia_shirensis ------Triphora_amazonica_ERP ----AA-ATCGC--TT-C------G---CATTTAATAAAAGCATCCAAGTCGC-T-TGATCAGTGGTTTATTCCCGAC-GGACCA Triphora_trianthophora ----AG-ATCGG-ATT------CCCACATGCATCATTTGATGAAAGCATTCCAGTCGCCTCTGATCAGTGGCTTGTCAACCACCGGACGG Triphora_gentianoides_ER01 ----GG-ATCGG-ATT------CCCACATGCATCATTTGATGAAAGCACTCAAGTCGCCTCTGATCGGTGGCTTGTCTCTCACCGGACG- Monophyllorchis_maculta ACTTGGGATGGGGATGGCTCAGCCCACATGCATCATTTGATTCAAGCATTCCAGTCGCCTCCGG--AGTGGTTTA-CAAA--CC--ACG- Psilochilus_macrophyllus_ER02 GCTTGGGATGGGGATGGCTCAGCCCACATGCATCATTTGATGAAATCATTCCA--CGTCTCCGATCAGTGGCTTGTCAACCACCGGACCG Psilochilus_LJ6914 GCTTGG-ATGGGGATGG-TCN-CCCAC-TSC-TCATT--ATGAAT-CATTCC---CCTTTTCGATCAGTGGCTTGTCAACCCCCG-ACCG Didymoplexis_pallens ACTTGGGATGGGGATGGCTCAGCCCACATGCATCATTTGATGAT-G-AATCCA---GC--CC------GCTTGTCAACCACCGGAC-- Calypso_bulbosa ACTTGG-ATGGGGATGGCTCAGCCCACATGCATCATTTGATGAAAGCATTCCAGTCGCCTCCGATCAGTGGCTTGTCAACCACCGGACCG Chysis_bractescens ACCT?GGATGGGGATGGCTCAGCCCACATGCATCATTTGATGAAAGCATTCCAGTCGCCTCCGATCAGTGGCTTGTCAACCACSGGACCG Isochilus_amparoana ACTTGGGATGGGG------C_trifida ?????????????????????????????????????????????????????????????????????????????????????????? Oreorchis_patens ??????????????????????????????????????????????????????????????????????????????????????????

Codonorchis_lessonii TAGCTC------GG------AAACACAGCGCAT-----GAGTAGTTCGTTCAAGGACCACACCCTTTC---GAGAGCAG Corycium_sp ------TTAGTTCGTTCAAGGACCACACCC------AGAGCAG Goodyera_sp TAGCTCCTCACAAAATGCCC--GG------AAACACAGCGCAT-----GAGTAG------GACCACAACC------AGAGCAG Brownleea_coerulea TAGCTCCTCAAAAAATGACCTTGGGTTGGGGAAACACAGCGCAT-----GAGTAGTTCGTTCAAGGACCACACCC------AGAGCAG Palmorchis_trilobulata TAGCTCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACAT-----GAGTAGTTCGTTCAAGGACCACACCCTCTC---GAGAGCAG Palmorchis_sp AA-CTCCTCACCAAATGCCCTTGGGTTGGGGAAAC-CAGCACAT-----GAGTAGTTCGTTCAAGGACCACACCCTCT----SAGAGCAG Cephalanthera_damasonium TAGCTCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACATCACATGAATAGTTCGTTCAAGGACCACACCCTCTC---GAGAGCAG Cephalanthera_aus TAGCTCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACATCACATGAATAGTTCGTTCAAGGACCACACCCTCTC---GAGAGCAG

Continued

Table A.4 Continued

Aphyllorchis_montana TAGCTCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACATCACATGAATAGTTCGTTCAAGGACCACACCCTCTC---GAGAGCAG Epipactis_sp TAGCTCCTCACCAAATGCCC--GGG------AAACACAGCAC-T-----GAATAGTTCGTTCAAGGACCACACCCTCCC---GAGAGCAG Limodorum_abortivum TGAAGCACTTGATATCATA------TATCA-AGG-CGT-----GA-TTCTTC-TTAAAGGA------AG Listera_smallii TAGCTCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACATCACATGRATAGTTCGTTCA??????????CCYCYC---GAGAGCAG Listera_cordata ------Neottia_nidus_avis ------Corymborkis_vert_ER66 TAGCTCCTCACCAAATGCGCTTGGGTTGGGGAAACACACCACAT-----GAGTAGTTCGTTCAAGGACCACACCCTCTC---GAGAGCAG Tropidia_effusa TAGCTCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACAT-----GAGTAGTTCGTTCAAGGACCACACCCTCTC---GAGAGCAG Tropidia_sp TAGCTCCTCACCAAATGCGCTTGGGTTGGGGAAACACAGCACAT-----GAGTAGTTCGTTCAAGGACCACACCCTCTC---GAGAGCAG Epilyna_jimenzeii TAG-T-CTC-CCAA-T-CC--TGGG---GGGAACCACA-C------G-GT-GT---TTCA-GG-CC----CCTTT----GAGA-C-- Epilyna_hirtzii TAGCTCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACAT-----GAGTAGTTCGTTCAAGGACCACACCCTCTC---GAGAGCAG Sertifera_columbiana_ER38 TAGCTACTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACAT-----GAGTAGTTCGTTCAAGGACCACACCCA--C---GA-AGCAG Sertifera_sp TAGCTACTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACAT-----GAGTAGTTCGTTCAAGGACCACACCCA--C---GA-AGCAG Elleanthus_lancifolius_ER36 ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_sp TAGCTCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACAT-----GAGTAGTTCGTTCAAGGACCACACCCTCTC---GAGAGCAG Sobralia_crocea_w533 ------Sobralia_mucronata_w535 ------

347 Diceratostele_gabonensis_ER44 TAGCTCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACAT-----GAGTAGTTCGTTCAAGGACCACACCCTCTC---GAGAGCAG Epipogium_aphyllum TAG------ACC------Gastrodia_procera_ER64 ------Xerorchis_amazonica_0799 ------GGG------CAT------C--TCCACGTGAATA---TTTG---TGGCACCG Nervilia_plicata ------Nervilia_shirensis ------Triphora_amazonica_ERP TAGCTTCTCACCAAATGCCC-TGGG-TGG------ATAGC-CAT-----GAGTAGTTCGTTCAAGGACCACTCC------GCAG Triphora_trianthophora -ACCGCCTCACCAAATGCC----GGTTGG------AC----CAT-----GAGTAGTTCGTTCAAGGACCACACC------GCAG Triphora_gentianoides_ER01 TACCTCCTCACCAAATGCC----GGTTGG------ACAGCGCAT-----GAGTAGTTC------GGACCACACCGCAGG------GCAG Monophyllorchis_maculta CCGCTCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCGCAT-----GAGTAGTTCGTTCAAGGACCACACC------GCAG Psilochilus_macrophyllus_ER02 TAGCTCCTCACCAAATGCGCTTGGGTTGGGGAAAGACAGCACAT-----GAGTAGTTCGTTCAAGGACCACACC------GCA- Psilochilus_LJ6914 -AGCTCTTC-TCGAATGCG-TTCGGTTGGGGAAAGGCAGCCCTT-----GAGTATTT-GTTCAAGGACCACACCGCCTC------C-- Didymoplexis_pallens ------GGTTGGGGAAACACAGCGCAT-----GAGTAGTTCGTGAAAGGACCACACCCTCTC---GAGAGCAG Calypso_bulbosa TAGCTCCTCACAAAATGCCCTTGGGTTGGGGAAACACAGCACAT-----GAGTAGTTCGTTCAAGGACCACACCCTCTCGA---GAGCAG Chysis_bractescens TAGCCCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACAT-----GAGTAGTYCGTTCAAGGACCACACCCTCTCGAGGAGAGCAG Isochilus_amparoana ------AAACACAGCACAT-----GAGTAGTTCGTTCAAGGACCACACCCTCTCGAGGAGAGCAG C_trifida ?????????????????????????????????????????????????????????????????????????????????????????? Oreorchis_patens ??????????????????????????????????????????????????????????????????????????????????????????

Codonorchis_lessonii GATGCTGGCCGAGATGGAGCTGGGATAAAA------CGCGCCTT-GG-TT-----GCCCCACCATCTA-ATCAAGGGCGGGCGCCGAAAA Corycium_sp GATGCTGGCCGAGATGGAGCTGGGATAAA--CT---CTCGCCTTGGGCTTGCCTCGCCCCACCAT-TA-ATAAAGGGCGGGCGCCGAAAA Goodyera_sp GATGCTGGCCGAGATGGAGC-GGGATAAAA-CG---CGCGCCTTGCGCTTGCCTTGCCCCACCATCAA-ATCAA------Brownleea_coerulea GATGCTGGCCGAGATGGAGCTGGGATAAA--CT---CTCGCCTTGGGCTT-----GCCCCACCATCTA-ATAAAGGGCGGGCGCCGAAAA

Continued

Table A.4 Continued

Palmorchis_trilobulata GATGCTGGCCGAGATGGAGCTGGGAGTCAACCTATACTTTCCTTGGGCTTGCCTTGCCCCCCCATCTAAATAAAGGGCGGGTGCCGAAAA Palmorchis_sp GATGCTGGCC-AGATGGAGCTGGGAGCCAACCTATACTTTCCTTGGGCTTGCCTTGCCCCCCCAT-TAAATAAAGGGCGGGCGCCGAAAA Cephalanthera_damasonium GATGCTGGCCGAGATGGAGCTGGGAGCCAACCTAGACTTTCCTTGGGCTTGCCTTGCCCCACCATCTAAATAAAGGGCTTA-GCCGAAAA Cephalanthera_aus GATGCTGGCCGAGATGGAGCTGGGAGCCAACCTAGACTTTCCTTGGGCTTGCCTTGCCCCACCATT-AAATAAAGGGCTAA-GCCGAAAA Aphyllorchis_montana GATGCTGGCCGAGATGGAGCTGGGAGCCAACCTATACTTTCCTTGGGCTTGCCTTGCCCCACCATCTAAAGAAA-----GG-GCCGAAAA Epipactis_sp GATGCTGGCCGAGATGGAGCTGGGAGCCAACCTAGACTTTCCTTGGGCTTGCCTTGCCCCAC------AAAGGGCGGGCGCCGAAAA Limodorum_abortivum G------CG---TG------AA---A------CTT------CTG------CTAAGTAA---G-TT------AA Listera_smallii GATGCTGGCCGAGATGGAGCTGGGAGCCAACCTAGACTTTCCTTGGGCTTGCCTTGCCCCACCATCTAAATAAAGGGCTAA-GSCGAAAA Listera_cordata ------Neottia_nidus_avis ------Corymborkis_vert_ER66 GATGCTGGCCGAGATGGAGCTGGAAGCCAACCTAGACTTTCCTTGGGCTTGCCTTGCCCCACCATATAAATA------G-CT--AA Tropidia_effusa GATGCTGGCCGAGATGGAGCTGGGAGCCAACCTAGACTTTCCTTGGGCTTGCCTTGCCCCACCATCTAAATAAAGGGCGGG---CGAAAA Tropidia_sp GATGCTGGCCGAGATGGAGCTGGAAGCCAACCTAGACTTTCCTTGGGCTTGCCTTGCCCCACCATCTAAATAAAGGGCGGG---CTAAAA Epilyna_jimenzeii GAT--T-GC-GAGA--GAG-TGGGA-CCA--CTAGACTTT-CTT-CG-TCGCCT--CCCC-C-AT-TAAAGAAAGGGCGGGCGC-GAAAA Epilyna_hirtzii GATGCTGGCCGAGATGGAGCTGGGAGCCAACCTAGACTTTCCTT-CGCTCGCCTTGCCCCACCATCTAAAGAAAGGGCGGGCGCCGAAAA Sertifera_columbiana_ER38 GATGCTGGCCGAGATGGAGCTGGGAGCCAACCTA-ACTTTCCTT-CGCT------CCGCGG---CCAAAAA Sertifera_sp GATGCTGGCCGAGATGGAGCTGGGAGCCAACCTA-ACTTTCCTT-CGCT------CCGCGG---CCAAAAA

348 Elleanthus_lancifolius_ER36 ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_sp GATGCTGGCCGAGATGGAGCTGGGAGCCAACCTAGACTTTCCTT------GCCTTGCCCCACCATCTAAAGAAAGGGCGGGCGCCGAAAA Sobralia_crocea_w533 ------Sobralia_mucronata_w535 ------Diceratostele_gabonensis_ER44 GATGCTGGCCGAGATGGAGCTGGGAGCCAACCTAGACTTTCCTTGGGCTTGCCTTGCCCCACCATCTAAAGAAAGGGCGGGCT--GAAAA Epipogium_aphyllum ------CC---CCACACCATCTCAAGAAAGG------Gastrodia_procera_ER64 ------Xerorchis_amazonica_0799 CATCATA-CC------AG-T--GA-CAAA--T------Nervilia_plicata ------Nervilia_shirensis ------Triphora_amazonica_ERP GATGCTGGCCGTGATGGAG-TGGGAGCCAACTTAGAATT-----GGGCTTGCCTTGCCCCACCATCTAAAGAAA------GAAAA Triphora_trianthophora GATGCTGGCCGAGA------TGAGCCAACCTAGAATT-----GGGC-----TTGCCCCACC------GAA------GAAAA Triphora_gentianoides_ER01 GATGCTGGCCGAGA------GGGAGCCAACCTATAATT-----GGGC--GGCTTGCCCCACC------A------GAAAA Monophyllorchis_maculta GATG----CCGAGATGGAGCTGGGAGCCCAC-TAGACTTTCCTTGGGCTTGCCTTGCCCCACCATCTAAAGAAA------GCCGAAAA Psilochilus_macrophyllus_ER02 GATGCTGGCCGAGATGGAGCTGGGAGCCCA-CTAGACTTTC---GG-CTTGCCTTGCCCCACCATCTCAAGATA------GAAAA Psilochilus_LJ6914 --TGCTTGCCGAGATGGAGCTGTGAGCCCA-CTAGACTTTC---GG-CTTGCCTTGCCCCACCATTTCAAGATT------GAAAA Didymoplexis_pallens GATGCTGGCCGAGATGGAGCTGGGAGCCAACCTATACTTTCCTT------GCCCCACCA-CT---GAAAGGG------CAAA- Calypso_bulbosa GATGCTGGCCGAGATGGAGCTGGGAGCCAACCTAGACTTTCCTTGGGCTTGCCTTGCCCCACCATCTAAATAAAGGGCGGGCGCCGAAAA

Continued

Table A.4 Continued

Chysis_bractescens GATGCTGGCCGAGATGGAGCTGGGAGCCAACCTATACTTSCCTTGGGCTTGCCTTGCCCCACCATATAAATAAAGGGCGGGCGCCGAAAA Isochilus_amparoana GATGCTGGCCGAGATGGAGCTGGGAGCCAACCTAGACTTTCCTTGGGCTTGCCTTGCCCCACCATATAAAGAAAGGGCGGGCGCCGAAAA C_trifida ?????????????????????????????????????????????????????????????????????????????????????????? Oreorchis_patens ??????????????????????????????????????????????????????????????????????????????????????????

Codonorchis_lessonii GGAAAGGAACCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTTACTCACCCTATTCCCTCATACAATGCCCTGAA--C Corycium_sp -----GGAACCAGTGACGCCTTTT----GAAAGCTTAGCTTGGTAGGCGCTGCTTACTCACCCTATTCCCTCAGACAATGCCCTGAA--C Goodyera_sp GGAA------CCATTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTTACTCACCCTATTCCCTCAGACAATGCCCTGAA--C Brownleea_coerulea GGAAAGGAACCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTTACTCACCCTATTCCCTCAGACAATGCCCTGAA--C Palmorchis_trilobulata GGAA-----CCAGTGACGCCTTTTCAACGAAAGCTTAGCTTGGTAGGCGCTGCTTACTCACC------TCAGACAATGCCCTGAA--C Palmorchis_sp GGCA-----CCAGTGACGCCTTTTCAACGAAAGCTTAGCTTGGTAGGCGCTGCTTACTCACCCTATTCCCTCAGACAATGCCCTGAA--C Cephalanthera_damasonium GGAA-----CCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTTACTCACCCTATTCCCTCAGACAATGCCCTGAA--C Cephalanthera_aus GGAA-----CCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTTACTCACCCTATTCCCTCAGACAATGCCCTGAA--C Aphyllorchis_montana GGAA-----CCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTTACTCACCCTATTCCCTCAGACAATGCCCTGAA--C Epipactis_sp GGAA-----CCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTTACTCACCCTATTCCCTCAGACAATGCCCTGAA--C Limodorum_abortivum GGAAAGGAACCAGTGACGCCTTTTCGACGAAAGCTTAGCTTG-TAGGCGCTGCTTACTCACCCTATTCCCTCAGACAATGCCCTGAA--C Listera_smallii GGA------GACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTTACTCACCCTATTCCCTCAGACAATGCCCTGAA--C 349 Listera_cordata ------Neottia_nidus_avis ------GAC---T---CGACGAAAGCTTAGCTTGGTAGGCGCTGCTTACTCACCCTATTCCCTCAGACAATGCCCTGAA--C Corymborkis_vert_ER66 AAAAAGGAACCA------CTTGGTAGGCGCTGCTTACTCACCCTATTCCTTCAGACAATGCCCT------Tropidia_effusa GGAA-----CCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTTACTGACCCTATTCCCTCAGACAATGCCCTGAA--C Tropidia_sp AAAA-GGAACCA------CCTTTT----GAA----TAGCTTGGTAGGCGCTGCTTACTCACCCTATTCCCTCAGACAATGCCCT------Epilyna_jimenzeii GGAAAGGAACCAGTGACGCCTTTTCGACGAAAG-TTAGCT-GGTAGGCG--GCTTACTCACCCTATTCCCT--GACAATGCCCTGAA--C Epilyna_hirtzii GGAAAGGAACCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTTACTCACCCTATTCCCTCAGACAATGCCCTGAA--C Sertifera_columbiana_ER38 GGAAAGGAACC------TTTTC-AC-AA-GCTTA-CTTGGTAG-CGCTGCTTACTC-CCCTATTCCCTCA-ACAATGCCCTGAA--C Sertifera_sp GGAAAGGAACC------TTTTC-AC-AA-GCTTA-CTTGGTAG-CGCTGCTTACTC-CCCTATTCCCTCA-ACAATGCCCTGAA--C Elleanthus_lancifolius_ER36 ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_sp GGAAAGGWVCCAGTGACGCCTTTTCGWCGAAAGCTTAGCTTGGTAGTCGCTGCTTACTCACCCTATTCCCTCAGACAATGCCCTGAA--C Sobralia_crocea_w533 ------Sobralia_mucronata_w535 ------Diceratostele_gabonensis_ER44 GGAA-CGAACCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTTACTCACCCTATTCCCTCAGACAATGCCCTGAA--C Epipogium_aphyllum ------GTT-CGCCTTTT------GAC------Gastrodia_procera_ER64 ------Xerorchis_amazonica_0799 ------Nervilia_plicata ------Nervilia_shirensis ------Triphora_amazonica_ERP GGAG-GGAACCAT------CGAGGATTAGCT-GGTAGTCG---CTG--TCGCCCTATTCC-TCTTAAAAAACCCTGAA--C Triphora_trianthophora ------AACCATTGA----TT------A----TTAGCTTGGTAGGCGCT-----CTCACCCTATTCCCTCAGAGAATGCCCTGAA--C Triphora_gentianoides_ER01 ------AACCATT------CGACGA----TTAGCTTGGTAGGCGGCGCTG--TCACCCTATTCCCTCAGAGAATGCCCTGAA--C

Continued

Table A.4 Continued

Monophyllorchis_maculta -----GAAACCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTTACTCACCCTATTCCCTCAGACAATGCCCTGAA--C Psilochilus_macrophyllus_ER02 ------CC-----CGCCTTTT----GAAAGCTTAGCT-GGTAGGCGCTGCTGACTCACC-TATTCC-TCAGACAATGCCCTGAA--C Psilochilus_LJ6914 ------CC-----CGCCTTTT----GAAAGCTAAGCTTGGTAGGCGCTGTTGACTCACCCTATTCCCTCAGACAATGCCCTGAA--C Didymoplexis_pallens GGA------TT--CGACG------TTGGTAGGCGCTGCTTTGTCACCCC-GGCC---ATACAATGCCCC-AA--- Calypso_bulbosa -----GGAACCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTTACTCACCCTATTCCCTCAGACAATGCCCTGAACTC Chysis_bractescens -----GGAACCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTTACTCACCCTATTCCCTCAGACAATGCCCTGAACTC Isochilus_amparoana -----GGAACCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGCTGCTTACTCACCCTATTCCCTCAGACAATGCCCTGAACTC C_trifida ?????????????????????????????????????????????????????????????????????????????????????????? Oreorchis_patens ??????????????????????????????????????????????????????????????????????????????????????????

Codonorchis_lessonii ACTCAA------TT-----CCATTTTCCCAT------GCCTCGGAAAAAAGCACGGACGAGCCACATGCAGGGAAAC Corycium_sp ACGAAA------TT-----CCCTTTTGCCATGCGGAGTCACAGGCAGCGCCTCGGAAAAAAGCACGGACGAGCCACATGCAGGGAAAC Goodyera_sp ACGAAA------TGAATCCCCCTTTTCCCATGCGGAGTCACAGGCAGCGCCTCGGAAAAAAGCACGGACGAGCCACATGCAGGGAAAC Brownleea_coerulea ACGAAA------TGAATCCCCCTTTTCCCATGCG------CCTCGGAAAAAAGCACGGACGAGCCACATGCAGGGAAAC Palmorchis_trilobulata ACGAAAGTTTGCAGTTCAGCCCCCTTTTCCCATGCGGAGTCACAGGCAGCGCCTCGGAAAAAAGCACGGACGAGCCACATGCAGGGAAAC Palmorchis_sp ACGAAAGTTTGCAGTTCAGCCCCCTTTTCCCATGCGGAGTCACAGGCAGCGCCTCGGAAAAAAGCACGGACGAGCCACATTCAGGGAAAC Cephalanthera_damasonium ACGAAAGTTTGCAGTTCAGCCCCCTTTTCCCATGCGGAGTCACAGGNAGCGCCTCGGAAAAAAGCACGGACGAGCCACATGCAGGGAAAC 350 Cephalanthera_aus ACGAAAGTTTGCAGTTCAGCCCCCTTTTCCCATGCGGAGTCACAGGCAGCGCCTCGGAAAAAAGCACGGACGAGCCACAGGCAGGGAGAC Aphyllorchis_montana ACGAAAGTTTGCAGTTCAGCCCCCTTTTCCCATGCGGAGTCACAGGCAGCGCCTCGGAAAAAAGCACGGACGAGCCACATGCAGGGAAAC Epipactis_sp ACGAAA------TTTCCCCATGCGGAGTCACAGGCAGCGCCTCGGAAAAAAGCACGGACGAGCCACATGCAGGGAAAC Limodorum_abortivum ACGAAAGTTTGCAGTTAAGCCCCCTTTTCCCATGCGGAGTCACATGCAGCGCCTCGG-AAAAAGCACGGACGAGCCACATGCAGG-TGTG Listera_smallii ACGAAAGTTTGCAGTTCAGCCCCCTTTTCCCATGCGGAGTCACAGGCAGCGCCTCGGAAAAAAGCACGGACGAGCCACATGCAGGGAAAC Listera_cordata ------Neottia_nidus_avis ACGAAAGTTTGCAGTTCAGCCCGCTTTTCCCATGCGGAGTCACAGGCAGCGCCTCGGAAAAAAGCACGGACGAGCCACATGCAGGGAAAC Corymborkis_vert_ER66 -CGAAAGTTTGCTGTTCCGCCCCCTTTTCCCATGCGGAGTCCCAGGCAGCGCCTCGGAAAAAAGCACGGACGACCCACATGCAGGGAAAC Tropidia_effusa ACGAAAGTTTGCAGTTCCGCCCCCTTTTCCCATGCGGAGTSACAGGCAGCGCCTCGGAAAAA-GCAYGGACGAGCGACATGCAGGGAAAC Tropidia_sp -CGAAAGTTTGCAGTTCCGCCCCCTTTTCCCATGCGGAGGCACAGGCAGCGCCTCGGAAAAAAGCACGGACGAGCCACATGCAGGGAAAC Epilyna_jimenzeii A-GAAAGTTTGCAGTTCTGCCCCCTTTTCCCATGCGGAGTCACAGGCAGCGCCTCGGAAAAAAGCACGGACGAGCCACATGCAGGGAAAC Epilyna_hirtzii ACGAAAGTTTGCAGTTCCGCCCCCTTTTCCCATGCGGAGTCACAGGCAGCGCCTCGGAAAAAAGTA-GGATCA-CCAGTCAAAAGG--T- Sertifera_columbiana_ER38 AC--AAGTGT----TTCC-CCCCCTTTTCC-ATGCAGAG------Sertifera_sp AC--AAGTGT----TTCC-CCCCCTTTTCC-ATGCAGAG-C------Elleanthus_lancifolius_ER36 ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_sp TCGAAAGTTTGCTGTTCYGCCCCCTTTTCCCATGCGGAGTCACAGGCAGCGCCTCGGAAAASAGCVCGGACGAGCCACATGCAGGGAAAC Sobralia_crocea_w533 ------Sobralia_mucronata_w535 ------Diceratostele_gabonensis_ER44 ACGAAAGTTTGCAGTTCCGCCCCCTTTTCCCATGCGGAGTCACAGG----GCCTCGGAAAG--GCA-TTACGATC-ACA-GCAGGGAATG Epipogium_aphyllum --GAAA------GTTCACTCACCTATTCCA------CCTCAGAAAAT-GCACGGACGAGCCACATGCAGGGAAAC Gastrodia_procera_ER64 ------

Continued

Table A.4 Continued

Xerorchis_amazonica_0799 ------TTT-CC------TTGT--CA-----GCCAKGCTGTAAAGCACGGACGAGCCACATGCAGGGAAAC Nervilia_plicata ------Nervilia_shirensis ------Triphora_amazonica_ERP AGGAAA-TATGCGG--CC---CCCTTTTCCCATGCGGAGTCACATGCACCGC----TAAAAAAACACGGACGAGCCACATGCAGGGAAAC Triphora_trianthophora ACGAGACT----AGTTTCG------GGCAGCGC----GAA----GCACGGACGAGCCACATGCAGGGAAAC Triphora_gentianoides_ER01 ACG-GAGT------TTCC-C-CCCTTTTCCCATGCGGAGTAACAGGCAGCGC----GAA----GCACGGACGAGCCACATGCAGGGAAAC Monophyllorchis_maculta ACGAAAGTTTGCAGTTCCGC-CCCT---CC-ATGCGGAGTCACAGGCAGCGCCTCGGAAAAAAGCACGGACGAGCCACATGCAGGGAAAC Psilochilus_macrophyllus_ER02 ACGAAAGTTTGCAGTTCCGC-CCCTTT-CCCATGCGGAGTCACAG-CAGCGC----GAAAGAA-CACGG-CGA-CCACATGCAGGGAAAC Psilochilus_LJ6914 ACGTAA-TTTGCAGTTCCGCCCCCTTTTCCCATGAGGACTCTCAGGCAGCGA----GAAAGAAGCA-TTACGATC----TGCAGCTCAGA Didymoplexis_pallens A-GAA-GTT-G-A------CCTTTTCCCATGCGGAGTGACAG-----GCCTCGTAAAAAAGCACGGACGAGCCACATGCAGGGAAAC Calypso_bulbosa ACGAAAGTTTGCAGTTCCGCCCCCTTTTCCCATGCGGAGTCAAAGGCAGCGCCTCGGAAANNNN-ACGGACGAGCCACATGCAGGGAAAC Chysis_bractescens ACGAAAGTTTGCAGTTCCGCCCCCTTTTCCCATGCGGAGTCACAGGCAGCGCCTCGGAAAAAAGCACGGACGAGCCACATGCAGGGAAAC Isochilus_amparoana ACGAAAGTTTGCAGTTCCGCCCCCTTTTCCCATGCGGAGTCACAGGCAGCGCCTCGGAAAAAAGCACGGACGAGCCACATGCAGGGAAAC C_trifida ?????????????????????????????????????????????????????????????????????????????????????????? Oreorchis_patens ??????????????????????????????????????????????????????????????????????????????????????????

Codonorchis_lessonii TTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGTCCCTGTAATTCGAG-GAGATTGTCATGGCGCAAAA 351 Corycium_sp TTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGTCCCTGTAATTCGAGCTAGATTGTCATGGCGCAAAA Goodyera_sp TTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGTCCCTGTAATTCGAG-GAGATTGTCATGGCGCAAAA Brownleea_coerulea TTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGTCCCTGTAATTCGAG-GAGATTGTCATGGCGCAAAA Palmorchis_trilobulata TTGCATGGGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATAT------Palmorchis_sp TTGCA------Cephalanthera_damasonium TTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGTCCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAA Cephalanthera_aus CAGCACGGGTGGTTCTGGCCGGGGACCCCGGTATTCTGTCCTAATATGTGTAGGTCCCAGTAATTCGAGTCAGATTGTCATGGCGCAAAA Aphyllorchis_montana TTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGTCCCAGTAATTCGAGC-AGATTGTCATGGCGCAAAA Epipactis_sp TTGCACGTGTGGTTCTGGCSGGGCACCCSGGTATACTGTACTAATATGTGTAGGTCCCTGTAATTCGAGTGAGATTGTCATGGCGCRCAA Limodorum_abortivum GAGCCTGTGTGTTTCTGGCCGGGGAC-CCGGCAGGA--TCCGAATAGGGGTAGG------A---GA-TG---TTG-CATGCCACAAAA Listera_smallii TTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGTCCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAA Listera_cordata ------Neottia_nidus_avis TTGCACGTGTGGTTCTGGCCGGGGACCCCGGTCTACTGTACTAATATGTGTAGGTCCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAA Corymborkis_vert_ER66 TTGCACGGGTGGTTCTGGCCGG-----CCGGTATACTGTACTAATATGTGTAGGTCCCTGTAATTCGAGTCTGATTGTCATGGCG----- Tropidia_effusa TTGCACGTGTGGTTCTGGCCGGGGACCCCGGTCTACTGTACTAATATGTGTAGGTCCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAA Tropidia_sp TTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGTCCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAA Epilyna_jimenzeii TTGCGGGGGTGGTT-TGGCCGGGGACCCCGGTATACTGTA-TAATATGTGTAGGTCCCTGTAATTCGAGCATGATTG-CA-GGCGCAAAA Epilyna_hirtzii TT-CA--TATAGTTTTGGCCGGGGACCCCGGTATACGATT-TA-TATGGGTAGGTTC-TGTAAATCGACCA-GAAT-----GGCCCCAAA Sertifera_columbiana_ER38 ------Sertifera_sp ------Elleanthus_lancifolius_ER36 ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_sp TTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGTCCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAA

Continued

Table A.4 Continued

Sobralia_crocea_w533 ------Sobralia_mucronata_w535 ------Diceratostele_gabonensis_ER44 ATTT-CTTATAG-TAACAATCAGTACCCCGGATTACTG-A-TAA--TTAACAGGAACCTGTAATATGAGTGAGAT-GTCATAGCACAAA- Epipogium_aphyllum TTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGTCCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAA Gastrodia_procera_ER64 ------Xerorchis_amazonica_0799 TCGCACGTGTGGTTCTGGCTGGGGACCCCGGTATACTGTACTAATATGTGTAGGTCCCCGTAATTCGAGTGGGATTGTCATGGCGCAAAA Nervilia_plicata ------Nervilia_shirensis ------Triphora_amazonica_ERP TTGCACGGGTGGTTCTGGCCGGGGA-----GAAT-CTGCA-TAAC--G-ATA------TAAG-CG--T-A-TTTGT-A-----CAAA- Triphora_trianthophora TTGCACGTGTGGTTCTGGCCGGGGACCCCGGTCTACTGTACTAATATGTGTAGGTCCCTGTAATTCGA-TGAGATTGTCATGGCGCAAAA Triphora_gentianoides_ER01 TTGCACGTGTGGTTCTGGCCGGGGACCCCGGTCTACTGTACTAATATGTGTAGGTCCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAA Monophyllorchis_maculta TTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGTCCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAA Psilochilus_macrophyllus_ER02 TTGCACGTGTGGTTCTGGCCGGGGACCCCGGT-TACTGTA-TAATATG-GTAGGTCCCTGTAA------Psilochilus_LJ6914 TGGTTCGTGTGGTGTTTATTGGGGTAACAG--TTATCGGTGGAATATGTGTAGGCTCGT-TAATTTGA-CGAGATA-TCATGGAACAAA- Didymoplexis_pallens TTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGTCCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAA Calypso_bulbosa TTGCACGTGTGGTTCTGGCCGGGGACSCCGGTATACTGTACTAATATGTGTAGGTCCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAA Chysis_bractescens TTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGTCCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAA Isochilus_amparoana TTGCACGTGTGGTTCTGGCCGGGGACCCCGGTATACTGTACTAATATGTGTAGGTCCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAA C_trifida ?????????????????????????????????????????????????????????????????????????????????????????? 352 Oreorchis_patens ??????????????????????????????????????????????????????????????????????????????????????????

Codonorchis_lessonii GCAGA0000001000000000000000000000000000000000000000000001???0?????000000000000000000100??0 Corycium_sp GCAGA0000000000000000000000000000000000000000000000000001???0?????000000000000000000100??0 Goodyera_sp GCAGA0000000000000000000000000000000000000000000000000001???0?????000000000000000000100??0 Brownleea_coerulea GCAGA0000000000000000000000000000000000000000000000000001???0?????000000000000000000100??0 Palmorchis_trilobulata -----0000000000000000000000000000000000000000000000000000000000000000000000000000000100??0 Palmorchis_sp -----????????????0000000000000000000000010000000001000000000010000000000000000000000?10??? Cephalanthera_damasonium GCAGA0000000000000000000000000000000000000000000000000000000000000000000000000000000000010 Cephalanthera_aus GCAGA00000010010000000000000000100100000000000000000000000000000000000000000000010?00000?1 Aphyllorchis_montana GCAGA???????????????0???????????0101001000010000000000000000000010000000000000000000100??0 Epipactis_sp GCAGA00000000000000000000000000000000000000000000000000000010??000000000000000000000000010 Limodorum_abortivum GCAGA0000000000000000000000000000000000000000000000000000000000000000000000000000000000010 Listera_smallii GCAGA0000000000000000000000000000000000000000000000000000000000000000000010000000000000010 Listera_cordata -----0000001000000000000000000000000000000000000000000000000000000??10?00000?1??0000000010 Neottia_nidus_avis GCAGA0000000000000000000000000000000000000000000000000000000000010100000001?????0000000010 Corymborkis_vert_ER66 -----???????????????00000000000000000000000000000000000000000000000000000000000000100001?0 Tropidia_effusa GCAGA1000000000000000000000000000000000000000000000000000000000000000000000000000000100??0 Tropidia_sp GCAGA0000000000000000000000000000000000000000000000000000000000000000000000000000000?10??? Epilyna_jimenzeii GCAGA????????????????????????????????????????????????????????????????????????????????????? Epilyna_hirtzii GCAGA00000000000?1?1000010000000000000000000000?100000000000000000000000000000000000100??0

Continued

Table A.4 Continued

Sertifera_columbiana_ER38 -----0000001000100000000000000000000000000000000000000000000000000000010000000000000100??0 Sertifera_sp -----0000001000100000000000000000000000000000000000000000000000000000010000000000000100??0 Elleanthus_lancifolius_ER36 ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_sp GCAGA0000000000000000000000000000000000000000000000000000000000000000000000000000000100??0 Sobralia_crocea_w533 -----0000000000000000000000000000000000000000000000000000000000000000000000000000000100??0 Sobralia_mucronata_w535 -----????????????????????????????????????????????????????????????????????????????????????? Diceratostele_gabonensis_ER44 GCACA0000000000000000000010000100000000000000100000000000000000000000000000000000000100??0 Epipogium_aphyllum GCAGA0000000000000000000000000000000000000000000000000000000000000000000000000000000100??0 Gastrodia_procera_ER64 -----00000010000000001?0000001?000000000000000000000000000000000000000000000000000?1?????? Xerorchis_amazonica_0799 GCAGA00?1?0?000000000000000000000000000000001?000100010000000001000000??1??????????0?00??0 Nervilia_plicata -----0100001000000000000000000000000000000000000000000000000000000000000000000010000?10??? Nervilia_shirensis -----0000000000000000000000000000000000000000000000000000000000000000000000000000000100??0 Triphora_amazonica_ERP -----000010?0100001000000?1000011?0000000000000000010?000100000000?10000000010000000??1??? Triphora_trianthophora GCAGA000000?1??0000000000000000000000000001?000000010?000?10000000000000000000000000100??0 Triphora_gentianoides_ER01 GCAGA000000?1??00000000000000000000000000000000000010?000100000001000000000000000000100??0 Monophyllorchis_maculta GCAGA00000000000000000000000000000000000000000???????0000000000000000000000000000000100??0 Psilochilus_macrophyllus_ER02 -----000000100000000000000000000000000010000001?????0?0001000000000000000001?0000000100??0

353 Psilochilus_LJ6914 G-AGA??10?0?010010001?????????????????????0?0100000000010???0??0000000000001?0000000100??0 Didymoplexis_pallens GCAGA00000000000000000000??1???00000000000000000000000000000000000000000000000000000100??0 Calypso_bulbosa GCAGA0000000000000000000000000000000000000000000000000000000001000000000000000000000100??0 Chysis_bractescens GCAGA0000000000000000000000000000000000000000000000000000000000000000000000000000000100??0 Isochilus_amparoana GCAGA0000000000000000000000000000000000000000000000000000000000000000000000000000000100??0 C_trifida ?????????????????????????????????????????????????????????????????????????????????????????? Oreorchis_patens ??????????????????????????????????????????????????????????????????????????????????????????

Codonorchis_lessonii 000010000000000000000000000000000000000000000000000000000000000010000000000000000?10000000 Corycium_sp 000010000000000000000000000000000000000010000000000000000000000010000000000000000?10000000 Goodyera_sp 000010000000000000000000000000000000000000000000000000000000000010000000000000000?10000000 Brownleea_coerulea 000010000000000000000000000000000000000010000000000000000000000010000000000000000?10000000 Palmorchis_trilobulata 000010000000000000000000000000000000000000000000000000000000000010000000000000000?10000000 Palmorchis_sp 000010000000000000000000000000010000000000010000000000000000000010000000000000000?10000010 Cephalanthera_damasonium 000010000000000000000000000000000000000000000000000000000000000010000000000000000?10000000 Cephalanthera_aus 000010001000000000000000110010000001?000010?0000000000000000000010000000000000000?10000001 Aphyllorchis_montana 000010000000000000000000000000000000000000000000000000000000000010000000000000000?10000000 Epipactis_sp 000010000000010000000000000000000000000000000000000000000000000010000000000000000?10000000 Limodorum_abortivum 000010000000?00000100110000000010000100000000000010010000000000010000000000000000?10000001 Listera_smallii 000010000000000000000000000000000000000000000000000000000000000010000000000000000?10000000 Listera_cordata 000010000100000000000000000000000000000000000000001?????????0?????????0?0???00000?10000000 Neottia_nidus_avis 000010000000000000000000000000000000000000000000000000000000000010000000000000000?10000000 Corymborkis_vert_ER66 000010000000000000000000000000000000000000000000000000000000000010000000000000000?10000000

Continued

Table A.4 Continued

Tropidia_effusa 000010000000000000000000000000000000000000000000000000000000000010000000000000000?10000000 Tropidia_sp 000010000000000000000000000000000000000000000000000000000000000010000000000000000?10000000 Epilyna_jimenzeii ?????????????????????????????????????????????????????????????????????????????????????????? Epilyna_hirtzii 000010000000000000000000000000000000000000000000000000000000000010000000000000000?10000000 Sertifera_columbiana_ER38 010010000000000000000000000000000000000000000000000000000000000010000000000000000?10000000 Sertifera_sp 010010000000000000000000000000000000000000000000000000000000000010000000000000000?10000000 Elleanthus_lancifolius_ER36 ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_sp 000010000000000000000000000000000000000000000000000000000000000010000000000000000?10000000 Sobralia_crocea_w533 000010000000000000000000000000000000000000000000000000000000000010000000000000000?10000000 Sobralia_mucronata_w535 ????????????0????????????????????????????????????????????????????????????????????????????? Diceratostele_gabonensis_ER44 000010000000000000000000000000000000000000000000000000000000000010000000000000000?10000000 Epipogium_aphyllum 0000100000000?10?0?00000000000000000000000000000000000?1????0?????????00000000000100001??? Gastrodia_procera_ER64 000010000000000010?100?10000000000000000000000??1?0???10?00?0000?1????00000000100000000000 Xerorchis_amazonica_0799 0000100000000000000000000000000000000000010?00?10?000100?10?0??0?0000000000000000?10000000 Nervilia_plicata 000010000000000000000000000000000000000000000000000000000000000010000000000000000?10000000 Nervilia_shirensis 0000100000000?10?0?00000000000000000000000000000000000?1????0?????????00000000000100001??? Triphora_amazonica_ERP 1?00?1?100001?????????????????????????????????????????????????????????????????????????????

354 Triphora_trianthophora 000010000000000000000000000000000001?1000?1?00100?01??00100?0000001?00000?1?10010??00001?? Triphora_gentianoides_ER01 000000100000000000000000001000000000001???????????0???00100?0000000010010???10010??00001?? Monophyllorchis_maculta 0000100000000000000000000000000000000001??0?000000000010?00?00001000000?1????0000?10000000 Psilochilus_macrophyllus_ER02 00?1???00000000001???00000000000001000000000000000000010?00?000010000000000000000?10000010 Psilochilus_LJ6914 00100000000000000000100000000000001000000000000000000010?00?000010000000000000000?10000000 Didymoplexis_pallens 000010000?1?0?00?000000000000000000000000000?1????0???0000000??1??????00000100000000?100?0 Calypso_bulbosa 000010000000000000000000000000000000000000000000000000000001000010000000000000000?10000000 Chysis_bractescens 000010000000000000000000000000000000000000000000000000000001000010000000000000000?10000000 Isochilus_amparoana 00001000000000000000000000000000000000000000000000000000000?1????????????????????????????? C_trifida ?????????????????????????????????????????????????????????????????????????????????????????? Oreorchis_patens ??????????????????????????????????????????????????????????????????????????????????????????

Codonorchis_lessonii 00000000000000000000000000000000000000?100000000000000000100000000000000000000000000000000 Corycium_sp 00000000000000000000000000000000000000?100000000000000000?10000000000000000000000000000000 Goodyera_sp 00000000000000000000000000000000000000?100000000000000000100000000000000000000000000000000 Brownleea_coerulea 00000000000000000000000000000000000000?100000000000000000100000000000000000000000000000000 Palmorchis_trilobulata 00000000000000000000000000000000000000?100000000000000000100000000000000000000000000000000 Palmorchis_sp 00000000000000000000000000001000000000?100000000000000000100000001000010000000010010000100 Cephalanthera_damasonium 000000000100000000?10?0000000000000000?100000000000000000100000000000000000000000000000000 Cephalanthera_aus ?00000100010000100?10?00000010001000?1??00000001001000000100000000000010000000000100111011 Aphyllorchis_montana 000000000000000000000000000000000000?1??00000000000000000100000000000000000000000000000000 Epipactis_sp 00000000000000000000000000000000000000?100000000000000000100000000000000000000000000000000

Continued

Table A.4 Continued

Limodorum_abortivum ?00010???000000000??1??000000010000000?100?000?0?????????????????????????????????????????? Listera_smallii 00000000000000000000000000000000000000?1000000000000000000000000000000000??1?????????00000 Listera_cordata 00000000000000000000000000000000000000?1000000000000000000000000000000000??1?????????00000 Neottia_nidus_avis 0000000000000000?1?00?1000000000000000?1000000000000000000000000000000000??1?????????00000 Corymborkis_vert_ER66 00000000000000000000000000000000000000?100000000000000000100000000000000000000000000000000 Tropidia_effusa 00000000000000000000000000000000000000?100000000000000000100000000000000000000000000000000 Tropidia_sp 00000000000000000000000000000000000000?100000000000000000100000000000000000000010000000000 Epilyna_jimenzeii ?????????????????????????????????????????????????????????????????????????????????????????? Epilyna_hirtzii 00000000000000000000000000000000000000?100000000000000000100000000000000000000000000000000 Sertifera_columbiana_ER38 00000000000000000000000000000000000000?1010???0?0000000001000000000000000000?10?0000000000 Sertifera_sp 00000000000000000000000000000000000000?1010???0?0000000001000000000000000000?10?0000000000 Elleanthus_lancifolius_ER36 ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_sp 00000000000000000000000000000000000000?100000000000000000100000000000000000000000000000000 Sobralia_crocea_w533 00000000000000000000000000000000000000?100000000000000000100000000000000000000000000000000 Sobralia_mucronata_w535 ???????????????????????????????????????????????????????????????????????????0????0?00000000 Diceratostele_gabonensis_ER44 000000000000000000?10?0000000000000000?100000000000000000100000000000000000000010000000000 Epipogium_aphyllum ?00000000000000000?10?001????????0001000000000000000010?0?0001?00??0????000000000000000000

355 Gastrodia_procera_ER64 10000000000000000000000000000000000000?100000?1???????0?0?0000?1??????????00??0?0000000000 Xerorchis_amazonica_0799 010?00?1?00000101000000000010000000000??100??00110101?0?0?0000100?000000100000000001000000 Nervilia_plicata 00000000000000000000000000000000000000?100000000000000000100000000000000000000000000000000 Nervilia_shirensis ?00000000000000000?10?001????????0001000000000000000010?0?0001?00??0????000000000000000000 Triphora_amazonica_ERP ?????????????????????????????????????????????????????????????????????????????????????????? Triphora_trianthophora ?00101???????00000100?01000001?0001?????0001?00001??00010?00000000?1??????00?0000101000000 Triphora_gentianoides_ER01 ?00000100000100000100?01000001?0?1??????0000100000?1000001000000000000000100?0000101000000 Monophyllorchis_maculta 00000000000001???0?00?0000000001?000?1??00001000000000000100000000000000000000000000000000 Psilochilus_macrophyllus_ER02 0000000000?1?00000100?00000000000000?1??00000000000000000100000000000000000010000000000000 Psilochilus_LJ6914 0000000000?1?00000100?0000000000000000?100000100000000000100000000000000000000000000001000 Didymoplexis_pallens 000000001000000000000000000000000000001000001000000000000??1?0000010?000000000000000000000 Calypso_bulbosa 00000000000000000000000000000000000000?100000000000000000100000000000000000000000000000000 Chysis_bractescens 00000000000000000000000000000000000000?100000000000000000100000000000000000000000000000000 Isochilus_amparoana ?????????????????????????????????????????00??000000000000100000000000000000000000000000000 C_trifida ?????????????????????????????????????????????????????????????????????????????????????????? Oreorchis_patens ??????????????????????????????????????????????????????????????????????????????????????????

Codonorchis_lessonii 00000000000000001000000000000000000000000000?10000?000000000000000000000000010100000000000 Corycium_sp 00000000000000001000000000000000000000000000?10000?000000000000000000000000000100100000000 Goodyera_sp 00000000000000001000000000000000000000000000?10000?000000000000000000000000000100000000000 Brownleea_coerulea 00000000000000001000000000000000000000000000?10000?000000000000000000000000000100000000000 Palmorchis_trilobulata 000000000000000011000000000000000000000000001000000000000000000000000100000001??0000000000 Palmorchis_sp 1000000?100001?01101?1000100?1?00010110000100000000000000000000000000100000000100000000000

Continued

Table A.4 Continued

Cephalanthera_damasonium 000000000000000010000000000000000000000000000000000000000000100000000000000000100000000000 Cephalanthera_aus ?1?11000010?1???????0000000000000000000000000000000000000000000000000000000000100000000000 Aphyllorchis_montana 000000000000000010000001000000010000010000000000000000000000000000000000000000?10000000000 Epipactis_sp 000000000000000010000000000000000000000000000000000000000000000000000000000000101????????? Limodorum_abortivum ?????????????????????????00000010001??????????????????????????0?000000000001?0?10000000000 Listera_smallii 000000000000000010000000000000000000000000000000000000000000000000000000000000100000000000 Listera_cordata 000000000000000010000001000000000000000000000000000000000000000000000000000000100000000100 Neottia_nidus_avis 00000000000000001000000000000000000000000000000000000001000000000000000000000010000000000? Corymborkis_vert_ER66 000000000000000011000000000000000000000001000000000000000000000000000000000000?10000000000 Tropidia_effusa 000000000000000010000000000000000000000000000000000000000000000000000000000000100000000000 Tropidia_sp 000000000000000010000000000000000000000000000000000100000000000000000000000000100000000000 Epilyna_jimenzeii ?????????????????????????????????????????????????????????????????????????????????????????? Epilyna_hirtzii 000000000000000000000000000000000000000000000000000000000000000000000100000000100000000000 Sertifera_columbiana_ER38 10000000000101?0100110001001???00000000000000000000000000000000000000000000000100000000000 Sertifera_sp 10000000000101?0100110001001???00000000000000000000000000000000000000000000000100000000000 Elleanthus_lancifolius_ER36 ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_sp 000000000000000010000000000000000000000000000000000000000000000000000000000000100000000000

356 Sobralia_crocea_w533 000000000000000010000000000000000000000000000000000000000000000000000000000000100000000000 Sobralia_mucronata_w535 000000000000000010000000000000000000000000000000000000000000000000000000000000100000000000 Diceratostele_gabonensis_ER44 0000000000000000100000000000?1?00000110010000000000000100000000000000100000010100000010000 Epipogium_aphyllum 000000000000000010000000000000000000000000?1??1?00??00001100??1?00??????????????0??0000000 Gastrodia_procera_ER64 000000000000000010000000000000010000000100000000001?1?100?10000100000100000000000010000?10 Xerorchis_amazonica_0799 00000000001?00001?100000000000001000011000000000000000000000000?10???????????????????????? Nervilia_plicata 0000000000000000100000000000000000000000000000000000000000000000000000?1????????0000000000 Nervilia_shirensis 000000000000000??????????????????????????????????????????????????????????????????????????? Triphora_amazonica_ERP ????????????????????????????????????????????????????????????????00???????????????????????? Triphora_trianthophora 00100000000000001000000100000000000000000000000000000000000000000010??00?0?00010010?1????0 Triphora_gentianoides_ER01 00000001000000101000000000101000?100100000000000000000000000000000?1????????????00010?0?00 Monophyllorchis_maculta 000000000000000010000000000000000000000000000000000000000000000000000000000000100000000001 Psilochilus_macrophyllus_ER02 0000000000000001?000000000000000000000000000000000000000000000000000000000000010000000000? Psilochilus_LJ6914 0000000000010011?100001000000000000000000000000000000000000000000000000000000010000000000? Didymoplexis_pallens 0000?10??000000010000000000000001000000000000000000000000000?10?00000000001010?10000000000 Calypso_bulbosa 000000000000000010000000000000000000000000000000000000000000000000000000000000100000000000 Chysis_bractescens 000000000000000010000000000000000000000000000000000000000000000000000000000000100000000000 Isochilus_amparoana 000000000000000010000000000000000000000000000000000000000000000000000000000000100000000000 C_trifida ?????????????????????????????????????????????????????????????????????????????????????????? Oreorchis_patens ??????????????????????????????????????????????????????????????????????????????????????????

Continued

Table A.4 Continued

Codonorchis_lessonii 000000000000010000000000000000000000000000000000000000000001???00???0?00000000000000100100 Corycium_sp 000000000000010000000000000000000000000000000000000000000000000000000000000000000000000100 Goodyera_sp 000000000000010000000000000000000000000000000000000000000000000000000100000000000000000100 Brownleea_coerulea 000000000000010000000000000000000000000000000000000000000000000000000000000000000000000100 Palmorchis_trilobulata 00000?100??0??0001?10000??10000000000000000000000000000000000000000000000?1??0000000000100 Palmorchis_sp 000000000000010000000000000000000000000000000000000000000000000000000000000000000000000100 Cephalanthera_damasonium 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000100 Cephalanthera_aus 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000100 Aphyllorchis_montana 000000000100010000000000000000000100000000000010000000000000000000000000000000100000000100 Epipactis_sp 00??00000000010000000000?10000000000000000000000000000000000????1???0??0??0000000000000100 Limodorum_abortivum 00000??10??0??0000000000000000001000000000000000000001000000000000000000000000000000000100 Listera_smallii 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000100 Listera_cordata 000?1??00??0??00011000010000000000000000001?00?10?0000000000000000010?00000000?1??00000100 Neottia_nidus_avis ?1??0?0000001000000000000000000000000000?1?????????00?000000???10???0??0?00000000000000100 Corymborkis_vert_ER66 000100000100010000000000000000000000010000000000000000000000000000000000000000000100000100 Tropidia_effusa 000000000100010000000000000000000000000000000000000000000000000000000000000000000000000100 Tropidia_sp 000000000100010000000000000000000000000000000000000001000000000000000100000000000000000000 Epilyna_jimenzeii ?????????????????????????????????????????????????????????????????????????????????????????? Epilyna_hirtzii 000000000100010000000000???100000000000000000000000000000000000000000000000000000000000100 357 Sertifera_columbiana_ER38 000000000100010000000000???100000000000000000000000000000000000000000000000000000000000100 Sertifera_sp 000000000100010000000000???100000000000000000000000000000000000000000000000000000000000100 Elleanthus_lancifolius_ER36 ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_sp 000000000100010000000000???100000000000000000000000000000000000000000000000000000000000100 Sobralia_crocea_w533 000000000100010000000000???100000000000000000000000000000000000000000000000000000000000100 Sobralia_mucronata_w535 000000000100010000000000???100000000000000000000000000000000000000000000000000000000000100 Diceratostele_gabonensis_ER44 000001000100010000?1000010000000010001000000000000000?100000000000000100100010000000000?10 Epipogium_aphyllum 0001000001000??10?????0??????0000000001?????????????0??0?000000000000010?00000000000000100 Gastrodia_procera_ER64 000001000?10??0001?10000??100000000000000000000000000000?100?00001??0?00100000000000000100 Xerorchis_amazonica_0799 ????0?000?0001000000000000001001????0?0??00010?000000??1??00??0000010?00000100000000000100 Nervilia_plicata 00000???1??0????0?????0??????00000000000100000000?100?000000100000000000100000001000000??1 Nervilia_shirensis ?????????????????????????????????????????????????????????????????????????????????????????? Triphora_amazonica_ERP 00??000001000???1????????????????????????????????????????????????????????????????????????? Triphora_trianthophora 000000000100010000????1???????00?0??1?0??0???0??0?0000000000?10000010?00100000000000100100 Triphora_gentianoides_ER01 0001000001000100000000000000010001?10?0000000000010000000000?100000?1????????????????????? Monophyllorchis_maculta 00??00000100010000000000000000000000000000000000000000000000??1000?00100000000000000000100 Psilochilus_macrophyllus_ER02 10??0?000100010000000000000000000000000000010000000000000000000000000000100000000000000100 Psilochilus_LJ6914 10??0?000100010000000000000000000000000000010000000000000000000000000000100000000000000100 Didymoplexis_pallens 000000000100010000?100000000000000000000000000??1??00?0000000000000000000000?1?????0000100 Calypso_bulbosa 000000000100010000000000000000000000000000000000000000000000000000000000000000000000000100 Chysis_bractescens 000000000100000000000000000000000000000000000000000000000000000000000000000000000000000100

Continued

Table A.4 Continued

Isochilus_amparoana 000000000100010000000000000000000000000000000000000000000000000000000000000000000000000100 C_trifida ?????????????????????????????????????????????????????????????????????????????????????????? Oreorchis_patens ??????????????????????????????????????????????????????????????????????????????????????????

Codonorchis_lessonii 1?000100000000000000000000000000000000000000000000000000?1?0?00?00000000000000000000000000 Corycium_sp 1?000100000000000000000000000000000000000000000000000000?1?0?00?00000000000000000000001?00 Goodyera_sp 0??1??000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Brownleea_coerulea 1?0001000?100???000000000001000000000000100010??00???00??0?0?00000000000000000000000000100 Palmorchis_trilobulata 000000?1?000000000000100000?1000000000?0000000000?00000000000000000000000001000000000?0000 Palmorchis_sp 000000?1?000000000000000000000000000000000000000000000000000000000000000000000000000000000 Cephalanthera_damasonium 00000000000000000000000000000000000000000000000000000000000000000?1??000??0000000000000000 Cephalanthera_aus 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Aphyllorchis_montana 01000010000000000000000000000100000?1?00??000000000000000000100000000000001?????0000000000 Epipactis_sp 000000?1?000000000000000000000000000000000000000000000000000000000000000000000000000000000 Limodorum_abortivum 00001?0010000010000000001000000000000000000000000000000010?000000000?100??0?0000?1?000???? Listera_smallii 000000?1?000000000000000000000000000000000000000000000000000000000000000000000000000000000 Listera_cordata 000000?1?0000000000000010000000000010?00?00000000000100??0?0001??????000??0?00000000000?1? 358 Neottia_nidus_avis 0000000000000000000000000000000000000000000000000000000000000000010010000000000000?100???? Corymborkis_vert_ER66 000000000000000000000000000000000000000000000000000000000010000000000000000001??0000000000 Tropidia_effusa 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Tropidia_sp 0000001000000000010000000000000000000000000000000000000000100000000000000000001?0000001?00 Epilyna_jimenzeii ??????????????????????????????????????0??????????0???????????????????????????????????0???? Epilyna_hirtzii 000000000100000000000000000000000000000000000000000000000000000000000000100000000000000000 Sertifera_columbiana_ER38 0000000000000000000000000000000000000?1??????????0???????????????????????????????????0???? Sertifera_sp 000000000000000000000000000000000000000000?1?????0???????????0????????00????????0000?1???? Elleanthus_lancifolius_ER36 ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_sp 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Sobralia_crocea_w533 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Sobralia_mucronata_w535 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Diceratostele_gabonensis_ER44 0??1??00010000000?100?0000000?1?00000100000000000000??1??????0???????000??0?00000000000000 Epipogium_aphyllum 000000000???1????????????????????0????0??????????0??????????????????????????????????00???? Gastrodia_procera_ER64 0?1000000??10???????0?000000000000000000000000?100???00??0?000000000??10?????????0?000??00 Xerorchis_amazonica_0799 000000000000010000000001000000000000000000000000000000000000000000010000010000000000000000 Nervilia_plicata 0000000000000000010000001000000000100000?1000010000100000010000100000000000100010000000000 Nervilia_shirensis ?????????????????????????????????????????????????????????????????????????????????????????? Triphora_amazonica_ERP ??????????????????????????????????????0??????????0???????????????????????????????????0???? Triphora_trianthophora 000000000000000000000100?1???00100000001???0?0??00????0??????00??????000??000001001000??00 Triphora_gentianoides_ER01 ???????????00???0000000000000000000000000000000000010001?0?0000?1?0??000?00001??0000000000 Monophyllorchis_maculta 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Psilochilus_macrophyllus_ER02 0000000000000000000000000000000000000000000000000000000000000000000000000000000010?000??00

Continued

Table A.4 Continued

Psilochilus_LJ6914 0000000000000000000000001000000000000000000000000000000000000000000000000000000010?000??00 Didymoplexis_pallens 0??1??0000000100000000000000000000000000000000000000?10????0?00?0000???1?????????0?000??0? Calypso_bulbosa 000000000000001000000000000000000000000000000000000000000000000000000000000000000000000000 Chysis_bractescens 000000?1?00000100000000000000000000000?0000000000?00000000000000000000000000000000000?0000 Isochilus_amparoana 000000000000001000000000000000000000000000000000000000000000000000000000000000000000000000 C_trifida ?????????????????????????????????????????????????????????????????????????????????????????? Oreorchis_patens ??????????????????????????????????????????????????????????????????????????????????????????

Codonorchis_lessonii 00010?00000??1?0?0?0000000000000000000000000000000000000000000000000?100000000000000000000 Corycium_sp 00010?00000??1?0?0?0000000001000000?1?????0?0?1?????0?00?00?0?001?????000000001??????????? Goodyera_sp 00010?00000??1?0?0?0000000000000000000000000000000000000000000010000?100000000000000000000 Brownleea_coerulea 00010?00000??1?0?0?0000000000000000000000000000000000000000000000000?100000000000000000000 Palmorchis_trilobulata 0?1000000001000000000000000?0?0000000000000000?00000?0???????????????????????????????????? Palmorchis_sp 000000000001000000000000000000000000000000000000000000000000000000000000000000000000000000 Cephalanthera_damasonium 000000000001000000000000000000000000000000000000000000000000000000000000000000000000000000 Cephalanthera_aus 000000000001000000000000000000000000000000000000000000000000000000000000000000000000000000

359 Aphyllorchis_montana 01000000000?1000100100010?0000000000000000000000000000000000000000000000000000000000000000 Epipactis_sp 000000000001000000000000000000000000000000000000000000000000000000000000000000000000000000 Limodorum_abortivum 0???0?0?000000100000000001000000010?00?0010100000000000000000000000100000000000??10?0001?? Listera_smallii 00000000000100000000000000000?000000000000000000000000000000000000000000000000000000000000 Listera_cordata 0??00001001??0?001??0000000010000?1?0?????0000001000000010000000001010000101000???0?00000? Neottia_nidus_avis ????0????0???0?0001???1?0?00?1???????????????????????????????????????????????????????????? Corymborkis_vert_ER66 01000000000100000000000000000000000000001000000000000000?10?0???00000000000000000000000000 Tropidia_effusa 00000000000100000000000000000000010?00?000000000000000000000000000000000000000000000000000 Tropidia_sp 00000000000100000000000000000000000000000000000000100?10??0?0???00000000000000000000000000 Epilyna_jimenzeii ???????????????????????????0?0????????????????????????????????????????????????0??????????? Epilyna_hirtzii 010001000001000000100000000000000000000010000000010000000000010000100000000000000000000000 Sertifera_columbiana_ER38 ???????????????????????????0?0????????????????????????????????????????????????0??????????? Sertifera_sp ???????????????????????????0?0????????????????????????????????????????????????0??????????? Elleanthus_lancifolius_ER36 ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_sp 000000000001000000000000000000000000000000000000000000000000000000000000000000000000000000 Sobralia_crocea_w533 000000000001000000000000000000000000000000000000000000000000000000000000000000000000000000 Sobralia_mucronata_w535 000000000001000000000000000000000000000000000000000000000000000000000000000000000000000000 Diceratostele_gabonensis_ER44 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Epipogium_aphyllum ????0??????????0?0?0000?1??0?0????????????0??00000100001????????????????????000??????????? Gastrodia_procera_ER64 0000000001?????0?0?000000000000000000000000000000000000000010?000000???10???000???0?000000 Xerorchis_amazonica_0799 00000?1?00010000000??100000000?100000000001??00000000100001?0???00?0000000000001000100000? Nervilia_plicata 01000001000100000010000000000000000100?1?00?100000???????????????????????????????????????? Nervilia_shirensis ?????????????????????????????????????????????????????????????????????????????????????????? Triphora_amazonica_ERP ???????????????????????????0?0????????????????0????10000000?1???????????????000???????????

Continued

Table A.4 Continued

Triphora_trianthophora 0000000000010000000000000010?0000000000000000000010000000000001001??00000000000000000?10?? Triphora_gentianoides_ER01 0100000000010001?0?00000000000000000000000000000000000000000000000000000000000000000000000 Monophyllorchis_maculta 000000000001000000000000000000000000000000000000000000000000000000000000000000000000000000 Psilochilus_macrophyllus_ER02 0000000000010000000?100000000010000001????0000000000000000000000000000000000000000001?00?0 Psilochilus_LJ6914 0000000000010000000?100000000010000001????0000000000000000000000000000000000000000001?00?0 Didymoplexis_pallens 0000000?10???0?000000000000000??1?????????0??0000000000000000000000000001???000???0????0?? Calypso_bulbosa 000000000001000000000000000000000000000000000000000000000000000000000000000000000000000000 Chysis_bractescens 000000000001000000000000000?0?000000000000000000000000000000000000000000000000?00000000000 Isochilus_amparoana 000000000001000000000000000000000000000000000000000000000000000000000000000000000000000000 C_trifida ?????????????????????????????????????????????????????????????????????????????????????????? Oreorchis_patens ??????????????????????????????????????????????????????????????????????????????????????????

Codonorchis_lessonii 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Corycium_sp ????????????0??????????????????????????????????????????????????????????????????0?????0???? Goodyera_sp 000000000000000000000000100?00000000000000000000000000000000000000000000000000000000000000 Brownleea_coerulea 000000000000000000000000000000000000000000010000000000000000000000000000000000000000000000

360 Palmorchis_trilobulata ?????????????????????????????????????????????????????????????????????????????????????????? Palmorchis_sp 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Cephalanthera_damasonium 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000100 Cephalanthera_aus 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Aphyllorchis_montana 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Epipactis_sp 000000000000000000000000000000000000?10?00001000000000000000000000000000000000000000000000 Limodorum_abortivum ????0??????00??0000?00000?1????????1??????????????????????????????0????????????0?????0???? Listera_smallii 000000000000?000000000000000000000000000000000000000000000000000000000000000000?00000?0000 Listera_cordata ?????????????????????????????????????????????????????????????????????????????????????????? Neottia_nidus_avis ????????????0??????????????????????????????????????????????????????????????????0?????0???? Corymborkis_vert_ER66 0000000000000000?1?????????????????0??????????????????????????????0????????????0?????0???0 Tropidia_effusa 0000000000000000?1?????????????????0??????????????????????????????0????????????0?????0???0 Tropidia_sp 0000000000000000?1?????????????????0??????????????????????????????0????????????0?????0???0 Epilyna_jimenzeii ????0???????0?????????????????????????????????????????????????????0????????????0?????0???? Epilyna_hirtzii 001000000000000000000000000000000000000000000000000010000000000001000000000000000000000000 Sertifera_columbiana_ER38 ????0???????0?????????????????????????????????????????????????????0????????????0?????0???? Sertifera_sp ????0???????0?????????????????????????????????????????????????????0????????????0?????0???? Elleanthus_lancifolius_ER36 ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_sp 0000000000000000000000000000000000000000000000000000?1000000000000000000000000000000000000 Sobralia_crocea_w533 0000000000000000000000000000000000000000000000000000?1000000000000000000000000000000000000 Sobralia_mucronata_w535 0000000000000000000000000000000000000000000000000000?1000000000000000000000000000000000000 Diceratostele_gabonensis_ER44 00000000000000000000000000000000000000000000?10?000000000000000000000000000000000000000000 Epipogium_aphyllum ????0??????00???000???????????????0010010?1?00010?10????1?????????0????????????0?????0??00 Gastrodia_procera_ER64 00????????????????????????????????????????????????????????????????????????????????????????

Continued

Table A.4 Continued

Xerorchis_amazonica_0799 ?1?000010100010000000000010???00?010001?0?00??1?0000???10???0?10001????????????0?????0???? Nervilia_plicata ?????????????????????????????????????????????????????????????????????????????????????????? Nervilia_shirensis ?????????????????????????????????????????????????????????????????????????????????????????? Triphora_amazonica_ERP ????0??????00??0000?????00000110?00000000000??1?00010000000100001?0000000000?100?01?000000 Triphora_trianthophora ?0000?1??0000000000000000000000000000000000000001???000000101001??00010?00?1?0000000000000 Triphora_gentianoides_ER01 0000000000000010000000?1000000000000000000000000000000000000110000010001000010000000000000 Monophyllorchis_maculta 00000000000000000000000000000000000000000000000000000000000000000000000?100000000000000000 Psilochilus_macrophyllus_ER02 0000010?00100000000000000000000000000000000000000000?100000000000000010?001000000000000000 Psilochilus_LJ6914 0000010?00100000000100000000000010000000000000000000??100000000000000?1?001000000001000000 Didymoplexis_pallens ???00?0?00000001000???????0???00?1000000000000000000?100000000000000000000000000000?100100 Calypso_bulbosa 00000000000000000000000000000000000000000000?10?000000000000000000000000000000000000000000 Chysis_bractescens 0000?0000000?0000000000000000000000?00000000?10?000000000000100000?010000000000?00000?0000 Isochilus_amparoana 00000000000000000000000000000000000000000000?10?010000000100000000000000000000000000000000 C_trifida ?????????????????????????????????????????????????????????????????????????????????????????? Oreorchis_patens ??????????????????????????????????????????????????????????????????????????????????????????

361 Codonorchis_lessonii 0000000000000000000000000000000000000000000000000000000000000000000000000000000001?0????00 Corycium_sp ???????????????????????????????????????????????????????????????????????????????????0?????? Goodyera_sp 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Brownleea_coerulea 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Palmorchis_trilobulata ????00000000000000000000000000000100000000001000100000000100000000000000000000000000000000 Palmorchis_sp 000000000000000010000000000000000000000000000000000000010000000000000000000010000000000000 Cephalanthera_damasonium 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Cephalanthera_aus 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Aphyllorchis_montana 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Epipactis_sp 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Limodorum_abortivum ??0?000?10000000001001001000001000000?1?????????????????????????0??0????00000000000000???1 Listera_smallii 01010000000000000000000000000000000000000000000000000000000000000000000000000000000?000000 Listera_cordata ?????????????????????????????????????????????????????????????????????????????????????????? Neottia_nidus_avis ?????????????????????????????????????????????????????????????????????????????????????????? Corymborkis_vert_ER66 ?00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Tropidia_effusa ?00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Tropidia_sp ?00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Epilyna_jimenzeii ??0?000000100101???000000?1010000100100000001001000?1000101010010000100010000101001011?100 Epilyna_hirtzii 0000000000000000?1?00000000000000000000000000000000000000000000000000000000000000000000000 Sertifera_columbiana_ER38 ?????0???0??????????????000000000000000000000000000000000000000000000000000000000000000000 Sertifera_sp ?????0???0????????????????0000000000000000000000000000000000000000000000000000000000000000 Elleanthus_lancifolius_ER36 ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_sp 0000000000000000?1?00000000000000000000000000000000000000000000000000000000000000000000000 Sobralia_crocea_w533 0000000000000000?1?00000000000000000000000000000000000000000000000????????????????????????

Continued

Table A.4 Continued

Sobralia_mucronata_w535 0000000000000000?1?00000000000000000000000000000000000000000000000???????????????????????? Diceratostele_gabonensis_ER44 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Epipogium_aphyllum 001??00??0??0?001000100011000001???0??0?00010?1???????????????0000?1?????0?00?1?0001?????? Gastrodia_procera_ER64 ?????????????????????????????????????????????????????????????????????????????????????????? Xerorchis_amazonica_0799 ?????0???0????????????????????????????0???0?0000001???????01000?1??????????????????0?????0 Nervilia_plicata ?????????????????????????????????????????????????????????????????????????????????????????? Nervilia_shirensis ?????????????????????????????????????????????????????????????????????????????????????????? Triphora_amazonica_ERP 1101000?1001001???????1?000000000000000000000000100100000000000000000100000000000000000000 Triphora_trianthophora 01010001000?1?00?000000000000000000000000000000000000000000000000000000000010000000000??10 Triphora_gentianoides_ER01 01010001000?1?00?000000000000000000000000000000000000000000000000000000000100000000000??10 Monophyllorchis_maculta 00000000000000000000000000000000000000000000000000000010000001000100001?001000000000000000 Psilochilus_macrophyllus_ER02 0000000000000000000000000000000000000000010?0000000000000000000000000000000000000000000000 Psilochilus_LJ6914 0001000000000100100100010?100000010000001?0?0000000000000000000000000001000100000010001000 Didymoplexis_pallens 00000000000000000000000000000000101000000?1??000?10001????0000000000000001?????????0?????0 Calypso_bulbosa 000100000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Chysis_bractescens 00?000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Isochilus_amparoana 0000000001?????????????????????????????????????????????????????????????????????????0??????

362 C_trifida ?????????????????????????????????????????????????????????????????????????????????????????? Oreorchis_patens ??????????????????????????????????????????????????????????????????????????????????????????

Codonorchis_lessonii ??001???00000000000010000000000000000000000100?000000000000000000000000000???1??00??0?0000 Corycium_sp ??????????????????0??0?000000000000000001???00?000000000000000000000000001?0000100??0?0000 Goodyera_sp ?1001???000000000000100001?????0?00000001???00?00000000000000000000001000010000100??0?0000 Brownleea_coerulea 00000000000000000000100000000000000000001???00?000000000000000000000000001?0000100??0?0000 Palmorchis_trilobulata 0000000000000000000010000000000000000000000100?0000000000000000000000000000000000000000000 Palmorchis_sp 0000000000001000000010000000000000000000001?00?0000000000000100000000000000000000000000000 Cephalanthera_damasonium 0000000000000000000000000000000000000000000100?0000000000000000000000000000000000000000000 Cephalanthera_aus 0000000000000000000000000000000000000000000100?0000000000000000000000000000000000000000000 Aphyllorchis_montana 0000000000000000000000000000000000000000000100?0000000000000000000000000000000000000000000 Epipactis_sp ?1000??100000000000110000000000000000000000100?0000000000000000000000000000000000000000000 Limodorum_abortivum ???0????0000010010001001000010000001??????????????00001????000100010???0?0??10?000??1?000? Listera_smallii 0000000000000000000000000?0000????????00000100?0000000000000000000000000000000000000000000 Listera_cordata ?????????????????????????????????????????????????????????????????????????????????????????? Neottia_nidus_avis ???????????????????????????????0?????????????????????????????????????????????????0???????? Corymborkis_vert_ER66 0000000000000000000010000000000000000000000100?0000000000000000000000000000000000000000000 Tropidia_effusa 0000000000000000000010000000000000000000000100?0000000000000000000000000000000000000000000 Tropidia_sp 0000000000000000000010000000000000000000000100?0000000000000000000000000000000000000000000 Epilyna_jimenzeii ?0000?1000000001?10??010101??00010101000001?00?001010?01010100010000100011?000000000000000 Epilyna_hirtzii 0000000000000000000010000000000000000000000100?0000000000000000000000000000000000000000000 Sertifera_columbiana_ER38 0000000000000000000010000000000000000000010100?0100000000000000000000000000000000010000000

Continued

Table A.4 Continued

Sertifera_sp 0000000000000000000010000000000000000000010100?0100000000000000000000000000000000010000000 Elleanthus_lancifolius_ER36 ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_sp 0000000000000000000010000000000000000000000100?0000000000000000000000000000000000000000000 Sobralia_crocea_w533 ?????????????????????????????????????????????????????????????????????????????????????????? Sobralia_mucronata_w535 ?????????????????????????????????????????????????????????????????????????????????????????? Diceratostele_gabonensis_ER44 0000000000000000000010000000000000000000000100?0000000000000000000000000000000000000000000 Epipogium_aphyllum ???????????????????????????????0?????????????????????????????????????????????????0???????? Gastrodia_procera_ER64 ?????????????????????????????????????????????????????????????????????????????????????????? Xerorchis_amazonica_0799 ???00??00001?????000?1???000?10000000100000100?0000000000010?1??0000101010?100???1???????? Nervilia_plicata ?????????????????????????????????????????????????????????????????????????????????????????? Nervilia_shirensis ?????????????????????????????????????????????????????????????????????????????????????????? Triphora_amazonica_ERP 1000010001000000100010000000000000000010?????0???0000000000000000000100000000000000000000? Triphora_trianthophora ??0000000100001??00010000000000000000010?????0???00000000000000??100??0000000000000000000? Triphora_gentianoides_ER01 ??00000001000000000010000000??10?0000000000?10???00000000000000?1000??0000000000000000000? Monophyllorchis_maculta 0000000000000000000010000000000000000010?????0???00000001??0000000000000000000100000000000 Psilochilus_macrophyllus_ER02 0000000000000000000010000000000000000010?????0???00001000000000000000000001000000000000000 Psilochilus_LJ6914 0000000000000000000010000001000000000000000??1????0?1?000000000000000000001000000000000000

363 Didymoplexis_pallens ??00000000000000000010000000000000000000000100?0000000000000000000000000000000000000000000 Calypso_bulbosa 0000000000000000000010000000000000000000000000?1000000000000000000000000000000000000000000 Chysis_bractescens 000000000000000000001000000000000000000000000000000000000000000000000000000000000000000000 Isochilus_amparoana ???0????0000000000001000000000000000000000000000000000000000000000000000000000000000000000 C_trifida ?????????????????????????????????????????????????????????????????????????????????????????? Oreorchis_patens ??????????????????????????????????????????????????????????????????????????????????????????

Codonorchis_lessonii 000100001000100000000000000100000000000000000000000000000000000000000000000000000000000000 Corycium_sp 00000000000000000000000100010000000000000000000000000100?000?00000000000000000000000010?00 Goodyera_sp 00000000000000000000000000010000?????10??????????????0000000???1??????0?00?0??000000000000 Brownleea_coerulea 000000000000100000000000000100000000000000000000000000000000000000000000000000000000000000 Palmorchis_trilobulata 000000000000000000000000000000000000000000000000000000000000?1000?000000000000000000000000 Palmorchis_sp 000000000000000000000001000000000000000000000000000000000000?1000?000000000000000000000000 Cephalanthera_damasonium 000000000000000000000000000000000000000000010000000000000000?1000?000000000000000000000000 Cephalanthera_aus 000000000000000000000000100000000000000000010000000000000000?1000?000000000000000000000000 Aphyllorchis_montana 00000000000000000000000000000000?100000?00010000000000000000?1000?000000000000000000000000 Epipactis_sp 00000000000000000??1?0???????0000000000000000000000000000000?1000?000000000000000000000000 Limodorum_abortivum 0?0??10????00001??0000?000000010000000010?1????????000000000000000000000000000000000000000 Listera_smallii 000000000000000000000000000000000000000000010000000000000010??00????0000000000000000000000 Listera_cordata ?????????????????????????????????????????????????????????????????????????????????????????? Neottia_nidus_avis ???????????????????????????????????????????????????????????0??00????00000000000101?0000000 Corymborkis_vert_ER66 000000000000000000000000000001?0????000?000?000100100000000000000000000?1?????????????0??? Tropidia_effusa 0000000000000000000000000000000000000000000??10?000000000000?1000?000000000000000000000000

Continued

Table A.4 Continued

Tropidia_sp 0000000000000000000000000000000000000000000??10?00000000000010000000000100?0??000000010?00 Epilyna_jimenzeii 010100001000001011000001000000000000000000000000010000000000000000000000000000000000000000 Epilyna_hirtzii 000100000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Sertifera_columbiana_ER38 000100000001?????????????????00000000000010??000000000000000000000000?1?00?0????0000000110 Sertifera_sp 000100000001?????????????????00000000000010??000000000000000000000000?1?00?0????0000000110 Elleanthus_lancifolius_ER36 ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_sp 000?100???00000000000000000000000000000000000000000000000000000000000000000000000000000000 Sobralia_crocea_w533 ?????????????????????????????????????????????????????????????????????????????????????????? Sobralia_mucronata_w535 ?????????????????????????????????????????????????????????????????????????????????????????? Diceratostele_gabonensis_ER44 00000000000000000000000000000000000000000000000?1?0000000000100000000000000000000000000000 Epipogium_aphyllum ?????00???0001?000000000000000000000001???????????????????00??00??0000000000100000000?1??? Gastrodia_procera_ER64 ?????????????????????????????????????????????????????????????????????????????????????????? Xerorchis_amazonica_0799 ?????????????????????????????????????????????????????????????????????????????????????????? Nervilia_plicata ?????????????????????????????????????????????????????????????????????????????????????????? Nervilia_shirensis ?????????????????????????????????????????????????????????????????????????????????????????? Triphora_amazonica_ERP 1??00000000000000000000000000000????100???0???????000000000010000000000001??????????0?0?00 Triphora_trianthophora 1??000000?100000000010???????0?1?????00???0???????000?10??00?0000000000000000?1?00??1?0??0

364 Triphora_gentianoides_ER01 1??00000010000000000?1???????0?1?????00???0???????000?10??00?0000000000000?1???????0000000 Monophyllorchis_maculta 00000000000000000000000000000000???1000?000?000000000100?000?00000000000000000000000000000 Psilochilus_macrophyllus_ER02 00100001000000000000000000000000????100???0???????000??1??00??000?00010000?0?0000000010?00 Psilochilus_LJ6914 00100001000000000000000000000000????100???0???????000??1??00??000?00010000?0?0000000010?00 Didymoplexis_pallens 000???1????0?000000000100?1??0000000000?1?0???????00100000?1????????????00?0????0010000000 Calypso_bulbosa 00000000000000000000000000000000000000000000000000000100?000?00000000000000000000000000000 Chysis_bractescens 00000000000000000000000000000000000000000000000000000100?000?00000000000000000000000000000 Isochilus_amparoana 00000000000000000000000000000000000000000000000000000100?000?00000000000000000000000000000 C_trifida ?????????????????????????????????????????????????????????????????????????????????????????? Oreorchis_patens ??????????????????????????????????????????????????????????????????????????????????????????

Codonorchis_lessonii 00000000000000000000000000000000010?000000??10?????000?10???0?00000000?100??????0000000000 Corycium_sp 00000000000000000000000000000000010?000000??10?????000?10???0?0000000000000000000000000000 Goodyera_sp 00000000000000000000000000000000010?000000??10?????000000000000000000000000000000000000000 Brownleea_coerulea 00000000000000000000000000000000010?000000??10?????00000000000000000000010??????0000000000 Palmorchis_trilobulata 00000000000000000000?1?0?0000000010?000000000000000000000000000000000000000000000000000000 Palmorchis_sp 00000000000000000000000000000000010?000000000000000000000000000000000000000000000000000000 Cephalanthera_damasonium 00000000000000000000000000000000010?000000000000000000000000000000000000000000000000000000 Cephalanthera_aus 00000000000000000000000000000000010?000000000000000000000000000000000000000000000000000000 Aphyllorchis_montana 00000000000000000000000000000000010?000000000000000000000000000000000000000000000000000000 Epipactis_sp 00000000000000000000000000000000010?000000???1??????????????0?0000000000000000000000000000 Limodorum_abortivum 00000000010000000000000000000000010?000000000000000000000000000000000000000000000100000000

Continued

Table A.4 Continued

Listera_smallii 00000000000000000000000000000000010?000000000000000000000000000000000000000000000000000000 Listera_cordata ?????????????????????????????????????????????????????????????????????????????????????????? Neottia_nidus_avis 00000000000000000000000000000000010?000000000000000000000000000000000000000000000000000000 Corymborkis_vert_ER66 0????0??00000000000000000000000?1???000000000000000000000000000000000000000000000000000000 Tropidia_effusa 00000000000000000000000000000000010?000000000000000000000000000000000000000000000000100000 Tropidia_sp 00?100?000000000000000000000000?1???000000000000000000000000000000000000000000000000000000 Epilyna_jimenzeii 00000010100001000000000000100000010?010000000000000000000000000000000000000000000000000000 Epilyna_hirtzii 00000000000000000000000000000000010?000000000000000000000000000000000000000000000000000101 Sertifera_columbiana_ER38 00100001000100000001000000001000010?001?0000000001?000000100000000010000000??????????????? Sertifera_sp 00100001000100000001000000001000010?001?0000000001?0000001000000000100000001?????????????? Elleanthus_lancifolius_ER36 ?????????????????????????????????????????????????????????????????????????????????????????? Elleanthus_sp 00000000000000000000000000000000010?000000000000000000000000000000000000000000000000000000 Sobralia_crocea_w533 ?????????????????????????????????????????????????????????????????????????????????????????? Sobralia_mucronata_w535 ?????????????????????????????????????????????????????????????????????????????????????????? Diceratostele_gabonensis_ER44 00000000000000000000000000000000010?000000000000000000000000000000000000000000010001?00100 Epipogium_aphyllum ???????????????????????????001????????0000?100?0?0?0000000000000000001???0??????0000100000 Gastrodia_procera_ER64 ??????????????????????????????????????????????????????????????????????????????????????????

365 Xerorchis_amazonica_0799 ????????????????????????????????????????????????????????????0?00010?10?000001?1?0000000000 Nervilia_plicata ?????????????????????????????????????????????????????????????????????????????????????????? Nervilia_shirensis ?????????????????????????????????????????????????????????????????????????????????????????? Triphora_amazonica_ERP 0000000010000?100010000010000000010?0000001000000000?1000?1?0?0000000000000000001000000000 Triphora_trianthophora 01?000?0000000001000000000000000010?000000000010?0?00000000?1????????0?0000??000101??00000 Triphora_gentianoides_ER01 01?000?0000000000010000000000000010?0001000000?1???00000010001000000000000000000101??00000 Monophyllorchis_maculta 00000000000000000000000000000000010?00000000000000000000000001001?010000000000000000000000 Psilochilus_macrophyllus_ER02 00000000100000000000100010000000010?000000000000000000000000010001000000000001001000010011 Psilochilus_LJ6914 00000000000000000000000000000000010?000000100000000000000000000000000000000000001000000100 Didymoplexis_pallens 1???????0000000000000010?10000010?1?0100100000001011????????0?000000000000000?1?0000000000 Calypso_bulbosa 000000000000000000000000000000000000000000000000000000000000000000000000000000000000001000 Chysis_bractescens 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 Isochilus_amparoana 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 C_trifida ?????????????????????????????????????????????????????????????????????????????????????????? Oreorchis_patens ??????????????????????????????????????????????????????????????????????????????????????????

Codonorchis_lessonii 00000000000000000000000000000000100000000000000 Corycium_sp 00000000000000000000000000000000000000000000000 Goodyera_sp 00000000000000000000000000000000100000000000000 Brownleea_coerulea 00000000000000000000000000000000100000000000000 Palmorchis_trilobulata 00000000000000000000000???????????????????????? Palmorchis_sp 00000000???????????????????????????????????????

Continued

Table A.4 Continued

Cephalanthera_damasonium 00000000000000000000000000000000000000000000000 Cephalanthera_aus 00000000000000000000000000000000000000000000000 Aphyllorchis_montana 00000000000000000000000000000000010000000000000 Epipactis_sp 00000000000000000000000000000000000000000000000 Limodorum_abortivum 00010000000001000100000001??1?0100?1?0000100000 Listera_smallii 00000000000000000000000000000000000000000000000 Listera_cordata ??????????????????????????????????????????????? Neottia_nidus_avis 00000000000000000000000000000000000000000000000 Corymborkis_vert_ER66 0000000000010?0000000000000000000000000000000?? Tropidia_effusa 00000000000000000000000000000000000000000000000 Tropidia_sp 00000000000000000000000000000000000000000000000 Epilyna_jimenzeii 00000000001000000001000000000000000000000101000 Epilyna_hirtzii 000011101000000000011000001000000010000?1???000 Sertifera_columbiana_ER38 ??????????????????????????????????????????????? Sertifera_sp ??????????????????????????????????????????????? Elleanthus_lancifolius_ER36 ??????????????????????????????????????????????? Elleanthus_sp 00000000000000000000000000000000000000000000000

366 Sobralia_crocea_w533 ??????????????????????????????????????????????? Sobralia_mucronata_w535 ??????????????????????????????????????????????? Diceratostele_gabonensis_ER44 10100001010000000011010000000000000000100000010 Epipogium_aphyllum 00000000000000000000000000000000000000000000000 Gastrodia_procera_ER64 ??????????????????????????????????????????????? Xerorchis_amazonica_0799 00000000000000000000000000000000000000000000000 Nervilia_plicata ??????????????????????????????????????????????? Nervilia_shirensis ??????????????????????????????????????????????? Triphora_amazonica_ERP 0000000000001?001001001110??011?01001000001?1?? Triphora_trianthophora 00000000000000000000000000000001000000000000000 Triphora_gentianoides_ER01 00000000000000000000000000000000000000000000000 Monophyllorchis_maculta 00000000000000000000000000000000000000000000000 Psilochilus_macrophyllus_ER02 0000000000000001000100010000??????????????????? Psilochilus_LJ6914 ?1000000000000100000000000010001000000010000011 Didymoplexis_pallens 00000000000000000000000000000000000000000000000 Calypso_bulbosa 00000000000000000000000000000000000000000000000 Chysis_bractescens 00000000000000000000000000000000000000000000000 Isochilus_amparoana 00000000000000000000000000000000000000000000000 C_trifida ??????????????????????????????????????????????? Oreorchis_patens ???????????????????????????????????????????????

APPENDIX B

NUCLEAR, CHLOROPLAST, MITOCHONDRIAL DNA SEQUENCES AND GAP

MATRICES INCLUDING 30 MORPHOLOGICAL CHARACTER USED IN

CHAPTER 3: A PHYLOGENETIC HYPOTHESIS OF THE BASAL

EPIDENDROIDEAE FROM MORPHOLOGY AND MOLECULAR DATA: A TOTAL

EVIDENCE APPROACH.

367

DIMENSIONS NTAX=34 NCHAR=4858; (281 w/ ITS characters already excluded) FORMAT DATATYPE=DNA MISSING=? GAP=- ;

Codonorchis TCGAGACCCGGA-GAGACCG--AGCGATCCTG-GAACCCATGA-TTAA--AATTGGCCGC----GGCG-CGCCGC----- Goodyera ------A------Palmorchis -C-AAACC---ATGAGATGGG-AGCGATTTTGCGAACTCGTGAACGAA-GTGATGGCAGTTGCTATCA-CGAAACAA--C Cephalanthera TCGAGACCAAAA-GAGATGGG-AG--ATTCAGAGAACTCATGAACTAA-GCGGTGACAGTCACTGTCA-CGAAACAA--A Aphyllorchis ???????????????????????????????????????????????????????????????????????????????? Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis TCGAGACCAAAA-GAAATGGGGAG--ATTTAGAGAACTCATGAACCAA-GTGGTGGCAGTCAATGCCA-CAAAACAT--A Limodorum TCGAGACCAAAA-GAGATGGGGAG--ATCTAGAGAACTCACGAACCAA-GTGGTGGCAGTAACTGTCA-TGAAACAA--A Listera TCGAGACCAAAA--AGATTGAGAG--ATTTAGAGAACTCATGAACCAA-GTGGTGGCAGACATTGTCA-CGGAACAA--T Neottia TCGAGACCAAAA-TTGATTGAGAG--ATTCAGATAACTCATGAACCAA-GTGGTGACAGTCACTGTCA-CACAATAA--A Corymborkis ------GTGGCAG---TTGCTATCA-CGGAGCAA--C Tropidia TCGAG-CCGGAA-GATATTT--AGCGATTCGGAGAACTCGTGAAATAA-GTGGCAGCA-TTGCTATCA-CGGAGCAA--C Epilyna TCGAGACCCAGA-AAGA-GG------CAA-A-TCGCTG-CGGCGGAGCAG--C Sertifera TCGAGACCGAAA-AAGA-GGG-AGTGATTTAGAGAACTCGT-AAAGAAAGTGACAACAGTTGCTG-CAGCAGTGCAG--A Elleanthus TCGAAGC-GAA--AAGC-CGG-A-CGATCTAT-GAACTCGT-AAAGAAAGCGG------G------AG--C Sobralia TCGAGACCGAAA-GAGA-GGG-AGTGATTCAGCGAACCCGTAAAAGAA-GCGGTAACAGTTGCTG-CGGCGGAGCAG--G Diceratostele ------GG------CGT----GA---CGG---CAGTCGCCGTCA-CGGCACAT--C Didymoplexis TC-A-A-CGA-A--A-ATG-G-ATCGAGCCACCAAACCCGYGAAACA-G-CGGC--CA-CCGC-G--ACCG---CATTCT

368 Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium ------GACCCCATAAAA-AAC---TGG-CAGTTGCTG-CC-T--AGCAA--C Xerorchis ------AT------CA-----GC--CA-T------CG-AA--TT-- Nervilia ------GAAA-GAGA-CGG-AGCGACTAGGAGAACGCGTGA--TG--GCCGTGGCAGTTGCTGTCA-CG-AA-ACTAC Triphora TC-AGATCG--AT----TGTG-AATGATTTAGAGAMCACGTCAAGTTCC-TG------TTGCC-TCCGT-AATC----- Monophyllorchis TCGAGATC----T-----G-G-TTTGATTGTGCAAATTTGTGAAATAAG-TGGGT--A-TT------GG-TCCA--C Psilochilus ???????????????????????????????????????????????????????????????????????????????? Wullschlaegelia TCGAGACCGAAA-G-GAT-G------ATTCATTGAACTCGTGGGAATAAGCGGCGGCAATCGCTGTC-ATGGA-CAA--T Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso TCGAGACCGAAGTTA--TG-G-AGTGATTCAGCGAACTCGTGAAATT--GCGATTGCAAT-GATGTT-GTGA-TTAG--C Chysis TCGAGACCCAAATTA--TCG--AGCGATTCGGAGAACCCGTGAA-TGA-GCGGCGGCAGT-GCCGTC-GCGAAATTG--C Gastrodia_sesamoides_534 ???????????????????????????????????????????????????????????????????????????????? gastrodia_sp_reunion_ER214 ???????????????????????????????????????????????????????????????????????????????? gastrodia_confusa_0801 ???????????????????????????????????????????????????????????????????????????????? gastrodia_zyl_16313 ????????????????????????????????????????????????????????????????????????????????

Continued

Table B.1. Primitive Epidendroideae combined Total Evidence analysis. 30 Morphological characters, ITS, trnL-F, trnL-F gaps, nad1b-c, nad1b-c gaps.

Table B.1 Continued

Codonorchis -GTCC-A-GCTTCTG--TCCTGCCTCC---TGA-CGGA---GGATG-GAAAA-ATC--AAA-CCAGCATAGCC-CGCGCC Goodyera ------Palmorchis CGTCC-A-GTCTTTG--CCCCGCCTCC---AGGGTGAA---GGCTGGATGAG-A-CCCGAG-CAGGCACAGCTTCGTGCC Cephalanthera CATTC-A-GTCT-CG--CACGATCTCC---ACGGCGAA---GGCTGGATGAA-A-CCCGAG-CTAGCGCATTTTCGCGCC Aphyllorchis ???????????????????????????????????????????????????????????????????????????????? Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis CGTCC-A-ACCTTTG--CTTCAACTCC---GCGGTAAA---GGTTGGATGAATAACCCAAG-CTAGCGCATTATCGCGCC Limodorum CATCC-A-AC-ATCG--CCTCTTCTCC---GCGGTGAA---GGTTGGATGA-TAACCCGAA-CCAGCGCAATTTCGCGCC Listera CATAC-A-AC-TTAT--C-TTGTCTCC---AAGGTAAA---GGTTGGATGAA-AACTCGAG-CTAGCGCATTTTCGCGCC Neottia CATAC-A-GCCT-AG--CCTTGTATCC---ATGGTGAA---GGTTGTATGAA-AACCCGAG-CTAGCGCAATTTCGCGCC Corymborkis CAACCCA-GTCGTTG--CCTCATCTCCCC-ACGATGAAA--GGTCGGATGAA-AACTCGAG-CCGGCGCAGTTCCGCGCC Tropidia CATCCCA-GTCGTTG--CCTCATCTCCC--ACGATGAA---GTTCGGATGAA-A-CTCGAG-CCGGCGCAGTTCCGCGCC Epilyna CATCCCA-ACCATTG--TTGCGTCTCCCCCGCGATGAAAAAGGTTGGATAAA-AACTCAAAATCGGCGCAGTCTCGCGCC Sertifera CATCCCA-ATTGTTG--CC--A-C------ACGATGACGAAGGTTGGATGAA-AACTCAAAATCGGCGCAGTCTCGCGCC Elleanthus CATCCCA-ACTGTTG--CCGCATCTCCCCCGCGGTGCAGAAGGTTGGATGAA-AACTCAAAACCGGCGCAGTCTCGCGCC Sobralia CATCCCA-ATTGTTG--CCACATGTCC---ACGATAAAGAAGGTTGGATGAA-AACTCAAA-CCGGCGCAGCTTCGCGCC Diceratostele CGTCCCCGAC-GT-G--TCCCCCCATC---ACGGGGGAGG-GGCCGGATGAA-A-CTCGAG-CCGGCGCAGATCTGCGCC Didymoplexis GCTCC---ATC-TCGCCTCCCCAGTGGCGCGCGGTGCC---GGCCGGATGAA---TTTGAAAGGGGCG--GA-CTGGGCC 369 Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium CTTCCT--TCTGTTG----AC--CTCC---ACGACGCG---GGTCGG-TGAA-A-CCCGAG-CCGGCGCAGCTTCGCGCC Xerorchis CGTC---GCCCGT-G--TCACCAC------ACGATGGG---GGATGGATGAT-A-CTCAAG-CCGGCGCAATCCCGCGCC Nervilia CG-CCC-GATCGTCGCCGTGGTGCGTC---ACGGAGGA---GGTAGGATGAA-AACTCGAT-CCGGCGCAGCTACGCGCC Triphora --TCC--GAT-GCTG----AAC--ACC-----G-TGAAG--TGCCGGATGA----TACTAA-TTGGCGCAGCGCCGCGTC Monophyllorchis C-TC------TCAACACACC-CAACGATGAA---TGT-GG--GAA-AATCCTAAATGAGCGCAAGTAAGCGCC Psilochilus ???????????????????????????????????????????????????????????????????????????????? Wullschlaegelia AAGCCC--ATC------CATCTCCTCGACG-TC-----GGGTCGACGAA-A-CACGAA-CTGACACAGGTTTGCGTC Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso CGTCCCA-ATTGTTT--CCCCACGTT----GCGATGAA---GGATGGATTAA-AACTCAAA-CCGGCGCAGTTACGCGCC Chysis CGTCCCAGC-CG-GG--CCTCGTC-A----ACGAGGAA---GGACGGATGAA-A-CTCAAA-CCGGCGCAGCTACGCGCC Gastrodia_sesamoides_534 ???????????????????????????????????????????????????????????????????????????????? gastrodia_sp_reunion_ER214 ???????????????????????????????????????????????????????????????????????????????? gastrodia_confusa_0801 ???????????????????????????????????????????????????????????????????????????????? gastrodia_zyl_16313 ????????????????????????????????????????????????????????????????????????????????

Continued

Table B.1 Continued

Codonorchis AAGCGAGA-TGTACAGA-TGTGATCGGCG--TGGCGTATCCTCGGACGTCGGG---GAT--CGC------TTATA--GA Goodyera ------AAG------T---TT----AGCGGAATG------TTGTA---T Palmorchis AAGGCAAA-TGCGCAAA-CAGGAGCCCTT--GCGGGTGCAGTAGCACGGAGCG--CTATT-CGC------TTATA---C Cephalanthera AAGGCAA--TGTGCAAAACACGAGCCCCA--ACAGGTTTGGTGGCATTGA------TTATA---T Aphyllorchis ???????????????????????????????????????????????????????????????????????????????? Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis AAGGGAA--TGTGCAAAACACGAGCCACA--TAAAGTTTGGTGGCATGTA------TA------TTATA---T Limodorum AAGGGAA--TGTGCAAAACACGAGCCCCA--GCAGGTCTGGTGGCATGGA------TTATA---T Listera AAGGTAA--TGTGCAAAATATGAGCCCCA--GCAAGTCTGGTGGCATGGA------TTATA---T Neottia AAGGTAA--TGTGCAAAACATGATTCCCA--GCATGTCTGGTGGCATGGA------TTATA---T Corymborkis AAGG-AAA-TGTGCAAA--ATGAGCCCCGCAGCGGGCTTAGTAGCGTGGAGTG--CTGTTT-GCACGCCATTT--AACAC Tropidia AAGTGAA--TGTGCAAA--ATGAGCCCTACACCGGGTTTAGTAGCGTGGGGTG--CTGT--CGCACACCACTT--AACAC Epilyna AAGGGAAAGTTTGCAAA-CATAAGCCCTACTGCGGGCTTAGCGGTGTGGAGTG--TT-----GC-CACCATTTATAACAT Sertifera AAGGGAAAATTTGCAAA-CGTAAGCCCTGTTGCGGGTTTAGCGGCGTGGAGTG--TTGTTACGCACACCATTTAAAATAT Elleanthus AAGGGAAA-TTTGCAAA-CATAAGCCCTGCAGCGGGCTTAGCGGTGTGGAGTG--CTGTTACGCATACCATC-ATAACAT Sobralia AAGGGAAAATATGCAAA-CGTAAGCCCTGCTGTGGGTTTAGTGGTGCGGAGTG--TTGCTACGC--ACCATTTATAATAT Diceratostele AAGGGAA--TATGCAAA-CG--AGCCCCGCAGCGGGCTTAGCGGCGTGGAGCG--CCGTC-CGCACAC---TT--AACAC Didymoplexis AAGGGAA----CGCGA--TG-GA-CCC-G---TGGAA--CAAGGGCCGGA-CG--CCGTT-C--TCA-CATTT---ACAC Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium AAGG-AA--TTTGC----C---AGCCC-GCAGCGGGCCA--CG---AGGAGTG--CTATT-CGC------CTA-AACAT 370 Xerorchis AAGTGAA--TTTGCAA--T-T-AGCCCCA-AGCGGGTTTAGTGGAATGGG-CG--CCG---CGC--ACCATTT--GACAC Nervilia AAGGGGAA-TATAAGAA-CG--AGCCC---GGCGGGCTG--CGCCGAGCAGCCC---GCT-CGT----C-TTT--GACAC Triphora AAGTCAATCTA-G-AAA--TCTTCTCC-A--GCAAATTTATTGGATTGAAGCG--CACTC-C-C------TC--AACAC Monophyllorchis AAGTGAACAGACG-AAA-----AG-CC-A--GCAA-TGTGGCGATGTGAA-T---CACTT-CTTA---CATTG-T-ACAT Psilochilus ???????????????????????????????????????????????????????????????????????????????? Wullschlaegelia AAGGTAA--TATGCAGCCCACGATCCC-A--GC------TG-A-----C-GTT-CGC--ACCGTTT--AAAAT Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso AAGGGAA--TACG-AAAGCACGAGCCT--CATTGGGTTTAGTGTTGTGGAGTG--C-ATT--GCACACCATTT--GACAT Chysis AAGGGAA--TACG-AAAACACGAGCCC--TATCGGGTTTAGTGGCGTGGAGTG--C-GTC--GCACACCACTC--GACAC Gastrodia_sesamoides_534 ???????????????????????????????????????????????????????????????????????????????? gastrodia_sp_reunion_ER214 ???????????????????????????????????????????????????????????????????????????????? gastrodia_confusa_0801 ???????????????????????????????????????????????????????????????????????????????? gastrodia_zyl_16313 ????????????????????????????????????????????????????????????????????????????????

Codonorchis GATTCTCGGTAATGGATATCTTGGTTCTCGCATCGATGAAGAGCACAGTGAAATGCGATACGTGGTGCGAATTGCAGAAT Goodyera GACTCTCGGCAATGGATATCTTGGCTCTTGCATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGTGAATTGCAGAAT Palmorchis GACTCTCGGCAACGGATATCTTGGCTCTCGCATCGATGAAGAGCGCAGCGAAATGCGATACGTAGTGCGAATTGCAGAAT Cephalanthera GACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAAT Aphyllorchis ???????????????????????????????????????????????????????????????????????????????? Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis GACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAAT Limodorum GACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAAT

Listera GACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAAT Neottia GACTCTCGACAACGGATATCTCGGCTCTCGCATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAAT Corymborkis GACTCTCGGCAATGGATATCTCGGCTCTCGCATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAAT Tropidia GACTCTCGGCAATGGATATCTCGGCTCTCGCATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGTGAATTGCAGAAT Epilyna GACTCTCGGCAATGGATATCTCGGCTCTCGCATCGATGAAGAGCGCAGCGAAATGCGATACATGGTGCGAATTGCAGAAT Sertifera GACTCTCGGCAATGGATATCTCGGCTCTCGCATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAAT Elleanthus GACTCTCGGCAATGGATATCTCGGCTCTCGCATCGATGAAGAGCGCAGCGAAATGCGATACATGGTGCGAATTGCAGAAT Sobralia GACTCTCGGCAATGGATATCTCGGCTCTCGCATCGATGAAGAGCGCAGCGAAATGCGATACATGGTGCGAATTGCAGAAT Diceratostele GACTCTCGGCAATGGATATCTCGGCTCTCGCATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAAT Didymoplexis GACTCTTGGCAATGGATATCTCGGTTCTCGCATCGATGAAGATCATAGTGAAATGAAATACGTGGTGTAAATTGCAGAAT Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium GACTCTCGGCAATGGATATCTCGGCTCCCGCATCGATGAAGAACGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAAT Xerorchis GACTCTCGGCAATGGATATCTCGGCTCTCGCATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGTGAATTGCAGAAT Nervilia GACTCTCGGCAATGGATATCTCGGCTCTCGCATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAAT Triphora GACTCTCGGCAATGGATATCTCGGCTCTCGCAACGATGAAGAGCGCAGCAAAATGCGACACATGGTGCGAATTGCAGAAT Monophyllorchis GACCCTCGGCAATGGATATCTCAACTCTTGCTTCGATGAAGGACGCAGCAAAATGCGAGATTTGATGCGAATTGCAGAAT Psilochilus ???????????????????????????????????????????????????????????????????????????????? Wullschlaegelia GACTCTCAGCAATGGATATCTCGGCTCTCGCATCGATGAAGAGCACAACGAAATATGATACGTGGTGTGAATTACAGAAT Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso GACTCTCGGCAATGGATATCTCGGCTCTCGCATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAAT Chysis GACTCTCGGCAATGGATATCTCGGCTCTCGCATCGATGAAGAGCGCAGCGAAATGCGATACGTGGTGCGAATTGCAGAAT

371 Gastrodia_sesamoides_534 ???????????????????????????????????????????????????????????????????????????????? gastrodia_sp_reunion_ER214 ???????????????????????????????????????????????????????????????????????????????? gastrodia_confusa_0801 ???????????????????????????????????????????????????????????????????????????????? gastrodia_zyl_16313 ????????????????????????????????????????????????????????????????????????????????

Codonorchis CCCTTGAACCATCAAATTTTTGAACGCAAGTTGCGTCGGAGGCCTGCTGACCGAGGGCACGTCCGCCTGGGCGTCTAGCA Goodyera CCCGTGAACCATCGAGTTTTTGAACGCAAGTTGCGCCTGAGGCCAATTGGCTAAGGGCACGTCCGCCTGGGCGTCAAGCA Palmorchis CCCGTGAACCATCGAGTATTTGAACGCAAGTTGCGCCCGAGGCCAGCCGGCCGAGGGCACGTCTGCTTGGGCGTGAAGCA Cephalanthera CCCGTGAACCATCAAGTCTTTGAACGCAAGTTGCGCCCGAGGCCAATCGGCTAAGGGCACGTCCGCCTGGGCGTCAAGCG Aphyllorchis ???????????????????????????????????????????????????????????????????????????????? Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis CCCGTGAACCATCAAGTCTTTGAACGCAAGTTGCGCCCGAGGCCAATCGGCTAAGGGCACGTCTGCCTGGGCGTCAAGCG Limodorum CCCGTGAACCATCAAGTCTTTGAACGCAAGTTGCGCCCGAGGCCAATCGGCCAAGGGCACGTCTGCCTGGGCGTCAAGCG Listera CCCGTGAACCATCAAGTCTTTGAACGCAAGTTGCGCCCGAGGCCAATCGGCCAAGGGCACGTCTGCCTGGGCGTCAAGCG Neottia CCCGTGAACCATCAAGTCTTTGAACGCAAGTTGCGCCCGAGGCCAATCGGCCAAGGGCACGTCTGCCTGGGCGTCAAGCG Corymborkis CCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAGGCCAACCGGCCAAGGGCAAGTCTGCCTGGGCGTCAAGCG Tropidia CCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAGGCCAACCGGCCAAGGGCACGTCTGCCTGGGCGTCAAGCG

Continued

Table B.1 Continued

Epilyna CCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAGGTCAATCGACCGAGGGCACGTCTGCCTGGGCGTCAAGCA Sertifera CCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAGGCCAATCGACCGAGGGCACGTCTGCCTGGGCGTCAAGCA Elleanthus CCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAGGCCAATCGACCGAGGGCACGTCCGCCTGGGCGTCAAGCA Sobralia CCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAGGCCAATCGGCCAAGGGCACGTCTGCCTGGGCGTCAAGCA Diceratostele CCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCTGAGGCCAACCGGCCAAGGGCACGTCCGCCTGGGCGTCAAGCG Didymoplexis CCTGCGAACCATCTAGTCTATGAATGCAAGTTGCGCCTGAGGCTAATCGGCTGAGGGCACGCCCGCCTGG------CA Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium CCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCAAGGCCCTTAGGCCAAGGGCACGCCTGCCTGGGCGTCATGCA Xerorchis CCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAGGCCAACCGGCCAAGG-CACGTCCGCCTGGGAGTCGAGCA Nervilia CCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAGGCCCACCGGCCGAGGGCACGCCCGCCTGGGCGTCAAGCA Triphora CCCGCGAACCATCGAGTACTTGAACGCAAGTTGCGCCCAAGGCCAACATGCCGAGGGCACGTCCGCCTGGGGGTCCAGCA Monophyllorchis CCCGTGAATCATCAAAAATTTGAACGCAAGTTGCGCTCGAGGCCATTAGGCCAAGGGCACGCCTGCTTGGGAGACATGCT Psilochilus ???????????????????????????????????????????????????????????????????????????????? Wullschlaegelia CCCACGAACCATCGAGTCTTTGAACGCAAGTTGCTCCCGAAGCCAACCGGCCTAGGGCACATCCACCTGGGCGTTAGGCA Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso CCCGCGAACCATCGAGTTTTTGAACGCAAGTTGCGCCCGAGGCCTGTCGGCCAAGGGCACGTCTGCCTGGGCGTCATGCG Chysis CCCGCGAACCATCGAGAATTTGAACGCAAGTTGCGCCCGAGGCCAGCCGGCCAAGGGCACGTCCGCCTGGGCGTCAAGCG Gastrodia_sesamoides_534 ???????????????????????????????????????????????????????????????????????????????? 372 gastrodia_sp_reunion_ER214 ???????????????????????????????????????????????????????????????????????????????? gastrodia_confusa_0801 ???????????????????????????????????????????????????????????????????????????????? gastrodia_zyl_16313 ????????????????????????????????????????????????????????????????????????????????

Codonorchis CCGCCTCGCTCCGT--C-GG--CACGA-GCCTC-GA-TA-GATGCGTTGGT------GG-CCC---AT------Goodyera TTACGTCGCTTCAA-TC-GT--CACCAAGCC---AA-TA---TTGTTGCGGGCC---GG--TTTGAAT------GC Palmorchis TTGCATCGCTCCGAGCCAGCGCCATCC-CCT---AATTTGGGTGCGTTGCTGC--A-AG-CTC-GGAT------GT Cephalanthera TTGCATCGCTTCGTGCCGCCACCACAC-ACC---AAT--GTGCGTGGTCGTGC--G-GG-CTC-GAAT------GC Aphyllorchis ???????????????????????????????????????????????????????????????????????????????? Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis TTGCGTCACTTCGTACCATCACCACAC-ACT---AAT--GGGTGTGTTGCTGT--A-GG-CTC-GAAT------GT Limodorum TTGCGTCGCTTCGTGCCATCACCACCC-TCC----ATT-CGGTGTGTTGGTGC--A-GG-CTC-GAAT------GT Listera TTGCGTCGCTTCGTGCCATCACCACCC-ACC---GAT--AGGTGTGTTAGTGC--A-TG-CTC-GAAT------GT Neottia TTGCGTCACTTCGTGTCATCACCACCC-ACC----ATT-GGGTGTGTTGGTGC--A-TG-CTC-GAAT------GT Corymborkis CTGCGTCGCTCCGTGCCAACGTCATCCCACC---GAT--GGGTGGGTGGG-GC-GA-GG-CGC-GGAC------GT Tropidia CTGCGTCGCTCCGTGCCAACGCCATCCCGCC---AA---GGGTGTGTGGG-GC-CAAGG-CTC-GGAT------GT Epilyna TCACATCGCTCCATGCCGACGCCATCCCACC---GA---GGGTGTGTCGG-G-G-AAGG-CCT-GGAT------GT Sertifera TTGCATCGCTCCATGCAGGCACCAACCCACC---TA---GGGTGAGCAGGTGYG---GG-CAT-GGAT------GT Elleanthus CCGCATCGCTCCATGCCGACGCCATCCCGCC---GA---GGGTGTGTTGG--CGCAAGG-CCT-GGAT------GT

Continued

Table B.1 Continued

Sobralia TTGCATCGCTCCATGCCAACACTATCCCACC---AA---GGGTGTGTTAGTGCACA-GG-CTT-GGAT------GT Diceratostele CCGCATCGCTCCGTGCCAGCGCCATCCC-CG---GG---GGGWGTGCCGGCGCA---GG-CAC-GGAT------GT Didymoplexis TTGCGTCR-TCCGCGTCGG-GCCA------GC-TTCCTG-----GG-G-C-AAAT------GC Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium TTACGTCG-TCC-T---A-CCCTATCC------TGTGA-GG---A-A-CT-CTT-GGAT------GC Xerorchis TTGCGTCGCTCCGTGCAGACACCGTCCCAC----TGA--GG-TGTGCGGGTGCG---GG-CTC-GGAT------GC Nervilia TCACGTCA-TCCTCGCCAAGACCATCCCG------T-GG---AC------GGATGGGCGGGGACGT Triphora CCA--TCCATCCGCCGCAGCCT---CCCACG---GATA----TGTGGGGAGAAAG--AT-CGC-GGAT------GA Monophyllorchis TTGCTTTG-TCCGAACC-TCAC------TT----TGT------CCT-GGAC------GT Psilochilus ???????????????????????????????????????????????????????????????????????????????? Wullschlaegelia TTTTGTAGCTTCATGCTGACACTCGTGTGGC------G-GAGAG-CGGACAAA--GG-CAC-GGAC------GT Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso TTGCATCG-TCCGTGCCAACACCATCACACC---TAT--GAGTGT-TTGGGGAA---GG-CTC-GGAT------GT Chysis TTGCGTCG-TCCGTGCCAACTCCATCCCATC---GAT--GGGTGTGTCGGTCGA---GG-CTC-GGAC------GT Gastrodia_sesamoides_534 ???????????????????????????????????????????????????????????????????????????????? gastrodia_sp_reunion_ER214 ???????????????????????????????????????????????????????????????????????????????? gastrodia_confusa_0801 ???????????????????????????????????????????????????????????????????????????????? gastrodia_zyl_16313 ???????????????????????????????????????????????????????????????????????????????? 373

Codonorchis ------CGCGT-GTGCT-A--GC-----GCAGTGGGCTGAAGAGCGGCTGCCCTCCT------GGCCCTG----ACG Goodyera GGAGAGTGGCCCTTCGCGCA-ATTGT-----GCGACGGGTTGAAGAACAGTTTGCTTCC------GGCAATG----TTT Palmorchis GCAGAGTGGCTCGTCGTGCTTATTGGT----ACGGCGGGTTGAAGAGCGGGTTGTCGTCTT--CG-GGCCATGCTGGACA Cephalanthera GAAGAGTGGTCCGCCGTGCTCATCGGT----GCGGCGGATTGAAGAGCGGGTTGTCGTCTC--AT-GGCCACGATCGAC- Aphyllorchis ???????????????????????????????????????????????????????????????????????????????? Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis GAAGAGTGGTTCGCCGTGCCCATTGGT----GCGACGGACTGAAGAGCGGGTTGTTGTCTC--AT-GGCCACGATTGACA Limodorum GAAGAGTGGTTCGCCGTGCTAATTGGT----GCGACGGACTGAAGAGTGGGTTGTTGTCTC--AT-GGCCACGATCGAC- Listera GAAGAGTGGTTCGCCGTGCCC-TTGGT----GCGGCGGATTGAAGAGCGGGT-GTTGTCTC--CT-GGCCACGATAGAC- Neottia GGAGAGTGGTTCTCCGTGTCC-TTGAT----GCGGCGGACTGAAGAACGGGTTGTTGTCTC--CT-GGCCACGATAGAC- Corymborkis GAAGAGTGGCTCGCCGTACCAATTGGTGC--ACGGCGGGCTGAAGAGTGGGTTATCGTCTC--ATTGGCCACTATCGATA Tropidia GCAGAGTGGCTCGCCGTGCCGTTTGGTGC--GCGGCGGGCTGAAGAGCGGGTTACCGTCTC--ATTGGCCACGATCGATA Epilyna GCAGAGTGGCCCGTCGTTCTCATCGGTGC-TGCGGCGGGCTAAAGAGCGGGCTTTT-TCTT--ATCAGCCACACTTGACG Sertifera GTAGAGTGGCTCGTCGTTCTCATTGGTGCGTGCGGCGGGCTAAAGAGCGGGCTTTCGTCTC--ATTAGCCACATCTGACG Elleanthus GCAGATTGGCCCGCCGTTCTCATCGGTGCGTGCGGCGGGCTAAAGAGCGGGCTTTCGTCTC--ATCGGCCACACTTGACG Sobralia GTAGAGTGGCTCGTCGTTCTCATTGGTGCG-GCGGCGGGCTGAAGAGTGAGTTTTCGTCTT--ATTAGCCATGTTTGACG Diceratostele GCAGAGTGGCCCGCCGTGCCCGTCGGC----GCGGCGGGCTGAAGAGCGGGTTATATTCTT--ATTGGCCACGATCG-CA Didymoplexis GCATGATGAGCCGCTGTTCCAAAGGGC------GGTAGTTCGAAGGGTGCGACGGCGCCTC--GTCGACCGCGGTCG-C-

Continued

Table B.1 Continued

Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium GGAAATTGGCCCTTCGTGCTC--CGGC----ATGGCGGGTTGAAGAGTGGGTTTTC----TGCTGT-G--AC----G-TT Xerorchis GTAGAGTGACTCGCCGTGCCCATCCGC----ACGACGGTC-GAAGATTGGGTTGGCATGGT--GTGGACCATGATA-AC- Nervilia GCAGAGTGGCCCGCCGTGC-CGTCGGT----GCGGCGGGCTGAAGAGCGGGCGATCGTCTTGCTGTGGCCACGAACA-TG Triphora CTTGATTGGCTCGCCGTGGTGTGTTAT----GCGGCGGGCTGAAGATCATTTTCTGGTTTC--ATCTGTCATGAT-GA-T Monophyllorchis GGACATTGACTCGTCGTCCCCATCTA-----GCGGCGGGTTGAAGGTCAATTTTTTGTCTT--CCTGCCCCCAATCGA-G Psilochilus ???????????????????????????????????????????????????????????????????????????????? Wullschlaegelia GTAGCGTGGCCCACTGCGTCCGACAAT----CTAGCGGGTTGAAGAGTAGGCACTGCACTTCTATCGACCATGAGCGAC- Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso GCATATTGGCTCATCGTGCCCATTGGC----GCGGCGGGTTGAAGAGTGGGTTATCGCCTC--ACTGGCCACGAACAAC- Chysis GCAGAGTGGCTCGTCGTGCCCGTCGGT----GCGGCGGGCTGAAGAGGGGGTCGTCGTCTC--ATCGGCCACGAACAAC- Gastrodia_sesamoides_534 ???????????????????????????????????????????????????????????????????????????????? gastrodia_sp_reunion_ER214 ???????????????????????????????????????????????????????????????????????????????? gastrodia_confusa_0801 ???????????????????????????????????????????????????????????????????????????????? gastrodia_zyl_16313 ????????????????????????????????????????????????????????????????????????????????

374 Codonorchis ACTGG??????????????????????????????????????????????????????TGGAAACCTGCTAAGTGGTAA Goodyera GAGGGGTGGATGTA?????????????????????????????????????????????TGG-AACCTGCTAAGTGGTAA Palmorchis AAGGGGTGGATGGAAGCCGTAAGCATG-C------TGTCTCATGCTGGCCAGATGAAATGGAAACCTGCTAAGTGGTAA Cephalanthera AAGGGGTGGACGGAAGCCACGAGCACGGCCAAACAGTGTCTCACGCTGGCCTGAGGAC-TGGAAACCTGCTAAGTGGTAA Aphyllorchis ???????????????????????????????????????????????????????????????????????????????? Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis AA-GGGTGGACGAAAGCCACGAGCACGACCAAACATTGTCTAATTCTGGCCTGAGGAA-TGGAA--CTGCTAAGTGGTA- Limodorum AAGGGGTGGACGTATGCCACGAGCACGGCCAAACAATGTCCCATGGTGGCCTGAGGAA------Listera AAGGGGTGGACGGAAGCCACGAGCACGGCCAAACAGTGTCTCATGCTGGTATGAGGAA-TGGAAACCTGCTAAGTGGTAA Neottia AAGGGGTGGACGGATGCCACGAGCACGGCCAAACAGTGTCTCATGTTGGCCTGAGGAA-????????????????????? Corymborkis AAGGGGTGGATAAAAGCTGTGAGGAAGGCTTA-CGCTGTCTCATGCTGGCCTGA-GAAA------Tropidia AAGGGGTGGATAAAAGCTGTGAGCGAGGCTTA-CGTTGTCTCATGCTGGCCTGA-GAAGTGGAAACCTGCTAAGTGGTAA Epilyna A-TGGGTGGATAAAAGCTGTGAGCATGACCTG-TGTCGCCTCGTGTTGGCCGGAGGAAA-GGAAANNNGNTGAGNNNNNN Sertifera A-TGGGTGGATAAAAGCTATGAGCATGACCTA-CGTCGCCTCATGTTGGCTGGATGAAATGGAAACCTGCTCAGTGGTAA Elleanthus A-TGGGTGGAGAAAAGCTATGAGCACGACCTA-TGTCGCCTCGTGCTGGCCGGAGGAAA-GGAAANNNGNTGAGNNNNNN Sobralia A-TGGGTGGAAAAAAGCTATGAGCATGACCTA-CGTCGCCTCATGTTGGCTTGAGGAAATGGAA-CCTGCTAAGTGGTAA Diceratostele A-GGGGTGGATA-AAGCCGCGGGCGCG---T--CGTTCGC--AT---GCCCCGAGGGAA????????????????????? Didymoplexis A-CARGTGGGTTGT-GCCGACTGCAT---CAG-TGCTGACTCGTC--GGC-TGAGGCAG????????????????????? Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium A-TAGG-GGATTGGAGC-AT-AGCTTG------C-TTGGCCC-----GCCC-GCCGAA-????????????????????? Xerorchis A-GGGGTGGATGAAATC--TGATCATGTCC-GAC-TC---TTAAA----CG---GG-A-TGGAAACCTGCTAAGTGGTAA Continued

Table B.1 Continued

Nervilia A-GGGGTGGATAGAAGCTATGGGCACGG--TGACGTGGCATCG------???????????TGAGTGCTAA Triphora A-AGAGTGGATGA--GCA-----CACGTCCTGA-TTTG--TCCTGCTGAC---AAG-T-TGGAA-CCTGGTAAGTGGTAA Monophyllorchis G-TGGGTGGATGGGCGCTTT--GCATGCCCTA-CAT-G-CTCATGATG-C-TGAAGAT-TGGAAACCTGCTAAGTGGTAA Psilochilus ???????????????????????????????????????????????????????????TGGAA-CCTT-TTAGTGATAA Wullschlaegelia G--TTGTGG-TAAACGCCATGAGCTCGGCCT--GGTCGT-GCATGCTGGCC------????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso G-AGCGTGGATGAAAGCTGTGAGCAAGGCTTA-TGTTGTCTCGTTTTGGCTTGA-GAAATGGAAACCTGCTAAGTGGTAA Chysis A-AGGGTGGATGAGAGCTGTGAGCAAGGCCTA-CGTTGTCTCGTGCCGGCCTGA-GAAATGGAAACCTGCTAAGTGGTAA Gastrodia_sesamoides_534 ???????????????????????????????????????????????????????????????????????????????? gastrodia_sp_reunion_ER214 ???????????????????????????????????????????????????????????????????????????????? gastrodia_confusa_0801 ???????????????????????????????????????????????????????????????????????????????? gastrodia_zyl_16313 ????????????????????????????????????????????????????????????????????????????????

Codonorchis CTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTTTTTT------Goodyera CTTCCAAATTCAGAGAA-CCCTGGAACTAAAAATGGGCATCCCTGAGCCAAATYTTTTTTTTGAGAAAAAAAA--CAAAA 375 Palmorchis CTTCCAAATTCAGAGAAACCCTGGAACTAATAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAAAAGTAA-GGAAAA Cephalanthera CTTCCAAATTCAGAGAA-CCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAAAAAAAAAATGGAAAA Aphyllorchis ??????????????????????????????????????????????????????????????????????????GGTGAA Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis CTTCCAAATTCAGAGAAACC-TGG-ACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAAAAAAAATGGAAAA Limodorum ------AGTGGAAAA Listera CTTTCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTTTTTTGAGAAAAAAA-TGGAAAA Neottia ????????????????????????????????????????????????CAAATCTTTTTT--AA------TGTAAAA Corymborkis ------ATCCTGAGCCAAATCTTTGTTTTGAGAGAAAAAATGGACAA Tropidia CTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCCTTTTTTTG????????????????? Epilyna CTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAGAAAAAAGGGCAAA Sertifera CTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAGAAAAAATGGAAAA Elleanthus CTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAGAAAAAATGGAAAA Sobralia CTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAGAAAAAATGGAAAA Diceratostele ???????????????????????????????????????????????????????????????????????????????? Didymoplexis ???????????????????????????????????????????????????????????????????????????????? Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium ???????????????????????????????????????????????????????????????????????????????? Xerorchis CTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCCTTATTTTGAGA-TAA-GA-GGAAAA Nervilia CTTCCAAATTCAGAGAAACCCTGGAACTAAGAATGGGCAATCCTGAGCCAAATCCTTGTTTTGAGAGAAAAAATGG---- Triphora CTTCCAAATTCAGAGANTTCATGGAACTAATAATGGGCAATCCTGAGCCAAATCCTTTTT-A-AGAAAGA---TGGAAAA Monophyllorchis CTTCCAAATTCAGAGAAACCCTGGAACTAAGAAAGGGCAATCCTGAGCCAAATCTTTTTT-A-AGAAAAA---TGGAAAA

Continued

Table B.1 Continued

Psilochilus CTTCCAAATTCAGAGAAATCCTGGAACTAAGAATGGGCAATCCTGAGCCAAATCTTTTTTTT-AGAAAAAA---GGAAAA Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso CTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCAAATCTTTGTTTTGAGAGAAAAAATGGAAAA Chysis CTTCCAAATTCAGAGAAACCCTGGAACTAAAAATGGGCAATCCTGAGCCGAATCTTTGTTTTGAGAGAAAAAATGGAAAA Gastrodia_sesamoides_534 ???????????????????????????????????????????????????????????????????????????????? gastrodia_sp_reunion_ER214 ???????????????????????????????????????????????????????????????????????????????? gastrodia_confusa_0801 ???????????????????????????????????????????????????????????????????????????????? gastrodia_zyl_16313 ????????????????????????????????????????????????????????????????????????????????

Codonorchis TTAGAA--AAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAAAGAATGAAA-TTTACTACGTTAGATTAGTAGC Goodyera TGAGAATAAAAAGAGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTTACTACGTTAGATTAGTAGT Palmorchis TGAGAATAAAAAGGGATAGGTGCAGACACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAGC Cephalanthera TTAGAATAAAAAGGGATAGGTGCAAAAACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTA--A-- Aphyllorchis TGAGAATAAAA-GGGATAGGTGCAGAGACTCAATGGAAGCTTTTCTAACANATGAAA-TTGACTACGTTACGTTAGTAGC 376 Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis TGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAGC Limodorum TGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACAAATGAAA-TTGACTACGTTACGTTAGTAGC Listera TGAGAATAAAA-GGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGT------Neottia TGATAATAAAAAGGGATAGGTGCAGAGACCCAATGGAAGCTATTCTAACAAATAAAAATTAAATTGACTACGTTAGTAGA Corymborkis TGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAGC Tropidia ???????????????????????????????????????????????????????????????????????????????? Epilyna TGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAGC Sertifera TGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAGC Elleanthus TGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAGC Sobralia TGAGAAGAAAAAGGGATAGGTGCAGAGACTCAATGGAAGTTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAGC Diceratostele ???????????????????????????????????????????????????????????????????????????????? Didymoplexis ???????????????????????????????????????????????????????????????????????????????? Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium ???????????????????????????????????????????????????????????????????????????????? Xerorchis TGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTTACTACGTTACATTAGGAGT Nervilia ------ATAGGTGCAGAGACTCAATGGAAGATGTTCTAACGAATGAAA-TTGATTACGTGACGTTAGTAGC Triphora TGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTA--A-A Monophyllorchis ---GAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTGCGCTACGTTAGTAGA Psilochilus TGAGAATAAAAAGGGATAGGGGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTATGTTACGTTAGTAGC Wullschlaegelia ????????????????????????????????????????????????????????????????????????????????

Continued

Table B.1 Continued

Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso TGAGAATAAAAAAGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACAAATGAAA-TTGACTACGTTACGTTAGTAGC Chysis TGAGAATAAAAAGGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATGAAA-TTGACTACGTTACGTTAGTAGC Gastrodia_sesamoides_534 ???????????????????????????????????????????????????????????????????????????????? gastrodia_sp_reunion_ER214 ???????????????????????????????????????????????????????????????????????????????? gastrodia_confusa_0801 ???????????????????????????????????????????????????????????????????????????????? gastrodia_zyl_16313 ????????????????????????????????????????????????????????????????????????????????

Codonorchis TAAAATCCTTCTATCAAAA------GAAATGACAGAAAGGATAACCTTATATATTTAATACGTACGTATACATACTT Goodyera TAAAATACTTCTATCAAGATAAAAGATTGAAATGACAGAAAGGATGACCTTATGTACCTAATAAATATGTATACATACTT Palmorchis TAAAATCCGTCTATC------GAAATGACAGAAAGGATAACCTTATATACCTAATACGTACGTATACATACTG Cephalanthera ------GGATAACCTTATATACCTAATACGTACGTATACATACTG Aphyllorchis TAAGATCCTTCTATC------GAAATGACAGAAAGGATAACCTTCTATACCTAATACGTACGTATACATACTG Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis TAAAATCCTTC------CAGAAAGGATAACCTTATATACCTAATACATACGTATACATACTG 377 Limodorum TAAAATCCCCCCATC------AAGATGACAGAACGGATAACCTTATATACCTAATACGTACGTATACATACTG Listera ------ATACATACTG Neottia TAAAATCCTTCTATC------AAAAT------GG---ACCCCAGATAACTAATGAGTAC--ATACATACTG Corymborkis TAAAAT-CTTCTATC------GAAATGACAGAGAGG------TTATATACCTAATACGTACGTATACATACTG Tropidia ???????????????????????????????????????????????????????????????????????????????? Epilyna TAAGATTCTTCTATC------GAAATGACAGAAAGGATAACCTTATATACCTAATACGTACGTATACATACTG Sertifera TAAGATCCTTCTATC------GAAATGACAGAAAGGATAACCTTATATACCTAAGACGTACGTATACATACTG Elleanthus TAAAATTCTTCTATC------GAAATGACAGAAAGGATAACCTTATATACCTAATACGTACGTATACATACTG Sobralia TAAAATTCTTCTATC------GAAATGACAGAAAGGATAACCTTATATACCTAATACGTACGTATACATACTG Diceratostele ???????????????????????????????????????????????????????????????????????????????? Didymoplexis ???????????????????????????????????????????????????????????????????????????????? Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium ???????????????????????????????????????????????????????????????????????????????? Xerorchis TAAAATCCTTCTATT------GAAATGAAAGAAAGGATAACCTTATATACCTAATACGTACGTATACATACTG Nervilia TAAAATATTTCTATC------GAAATGACAGAAAGGATAACCTTATATACCTAATACGTACGTATACATACTG Triphora TGA--TT-TTCT--C------TAAATGACATAA-GGATTACCTTATGTACCTAATACATACAT-TATACATTT Monophyllorchis TAAAATCATT-TATC------TAAATGACATACA------AATACGTACGTATACATACTT Psilochilus TAAAAT-TT-CTAAC------TAAATGACATATAGG------TA-TAAGTACATATACATACTG Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ????????????????????????????????????????????????????????????????????????????????

Continued

Table B.1 Continued

Calypso TAAAATCCTTCTAAC------GAAATGACAGAAAGGATAACCTTATATACCTAATACATACGTATACATACTG Chysis TAAAATCCTTCTATC------GAAATGACAGAAAGGATAACCTTATATACCTAATACGTACGTATACATACTG Gastrodia_sesamoides_534 ???????????????????????????????????????????????????????????????????????????????? gastrodia_sp_reunion_ER214 ???????????????????????????????????????????????????????????????????????????????? gastrodia_confusa_0801 ???????????????????????????????????????????????????????????????????????????????? gastrodia_zyl_16313 ????????????????????????????????????????????????????????????????????????????????

Codonorchis GCATAGCAAACGATTAATCACAT------TCTTATATACA------GA------Goodyera ACATAGCAAGCGATTAATCACAT------TCTTATAAA------CTATGAAAAGTT------A Palmorchis ACATAGCAAACGATTAA-----TCCCAA-----ATAGAGATCAAAAAATCTATGAAAGATT-AAGAATTATTGTGAATCA Cephalanthera ACATAGCAAACGATTAATCACAACCCAAATCTTATAGAGATCAAAAAATCTATGAAAAATTGAAGAATTATTGTGAATCA Aphyllorchis ACATAGCAAACGATTAATCACAACCCGAATCTTATAGAGATCAAAGAATCTATGAAAATTTGAAGAATTATTGTGAATCA Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis ACATAGCAAACGATTAATCACAACCCGAACCTTATAGAGATCAAAAAATCTATCAAAAATTGAAGAATTATTGTGAATCA Limodorum ACATAGCAAACGATTAATCACAACCCGAATCTTATAGAGATCAAAAA-TATAGGAAAAATTGAAGAATTATTGTGAATCA Listera ATATAGCAAACGATTAATCACAACCCAAATCTTATAGAGATCAAAAAATCTATGAAAAATTGAAGAATTATTTTGAATAA Neottia ATATATAAAATTATTAATCACAACCCAAATCTTATATATATCAAAAAATATATGAA-CATTTAAGAATTATTG-G----- 378 Corymborkis ACATAGCAAACGATTAATCACAATCCGAAT------Tropidia ???????????????????????????????????????????????????????????????????????????????? Epilyna ACATAGCAAACGATTAATCACAACCCGAATCTTATAGAGATCAAGAAATATATGAAAAATTGAAGAGTTATTGTCAATCA Sertifera ACATAGCAAACGATTAATCACAACCCGAATCTTATAGAGATCAAAAA-TATATGAAAAATTGAAGAGTTATTGTCAATCA Elleanthus ACATAGCAAACGATTAATCACAACCCGAATCTTATAGAGATCAAAAAATATATGAAAAATTGAAGAGTTATTGTCAATCA Sobralia ACATAGCAAACGATTAATCACAACCCGAATCTTATAGAGATCAAAAAATCTATGAAAAATTGAAGAGTTATTGTCAATCA Diceratostele ???????????????????????????????????????????????????????????????????????????????? Didymoplexis ???????????????????????????????????????????????????????????????????????????????? Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium ???????????????????????????????????????????????????????????????????????????????? Xerorchis ACATAGCAAACGATTAATCAAAACCCAA------Nervilia ACATAGCAAACGATTAATCACAACCCGAATCTTATAGAGATCAAAAAATATATGAAAAATCGAAG--TT------Triphora ACATAG------TAA--ACAATTCGAATCTTATAGAGATCAAAAAATCTATGGAGATTTGAAGAGTTATTGTGTTGTA Monophyllorchis ACATAGCAAACAATTCATCACAATTCAAATCTTATAGAGATCAAAAAATATATGAAAAATGGAAGAGTTCTTGTTTTGTA Psilochilus ACATATCAAACAATTAATCACAATTTGAATCTTATAGAGATCGAAAAATCTATGAAAAAATGAAGAGTTATTGTGTTGTA Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso ACATAGCAAACGATTAATCACAACCCAAATTTTATAGGGATCAAAAAATATATGAAAAATTGAAGAGTTATTGTGAATCA Chysis ACATAGCAAACGATTAATCACAACCCAAATCTTATAGAGATAAAAAAATATATGAAAAATTGAAGAGTTATTGTGAATCA Gastrodia_sesamoides_534 ????????????????????????????????????????????????????????????????????????????????

Continued

Table B.1 Continued

gastrodia_sp_reunion_ER214 ???????????????????????????????????????????????????????????????????????????????? gastrodia_confusa_0801 ???????????????????????????????????????????????????????????????????????????????? gastrodia_zyl_16313 ????????????????????????????????????????????????????????????????????????????????

Codonorchis ------TTGAAGTTGAAAAAAGAATCGAATTTGAA------TATTCAGT-GATCGAATGATTCATTCCAGAGTTTGA Goodyera ATTATAATTGAAGTTGAAAAAAGAATCGAATTCAAA------TATTCAGT-GATCAAATGAGTCATTCCAGAGTTTGA Palmorchis ATTCCAATTGAAGT-GAAAAAAGAATCGAATTCAAA------TATTCAGT-GATCAAAAGATTCATTCCAGAGTTGGA Cephalanthera ATTCCAATTGAAGTTGAAAAAAGAATCGAATTCGAA------TATTCAGT-GATCAAATGATTCATTCCAGAGTTTGA Aphyllorchis ATTCCAATTGAA------Auxopus ???????????????????????????????????????????????????????????????????????????????A Epipactis ATTCCAATTGAAGTTGAAAAAAGAATCGAATTCAAA------TATTCAGT-GATCAAATGATTCATTCCAGAGTTTGA Limodorum ATTCCAAT--A------GAA------Listera ATTCCAATTGAAGTTGAAAAAAGAATCGAATTTGAA------TATTCAGT-GATCAAATGATTCATTCCAGAGTTTGA Neottia ------GGATAAATTTTGAA------TAATCAGT-GATAAAATGATTCATT-GAGAGTTTGA Corymborkis ------Tropidia ???????????????????????????????????????????????????????????????????????????????? 379 Epilyna ATTCCGATTGAAGG-GAAAAAAGAATCGAATTCGAA------TATTCAGG-GATCAAATGATTCATTCCAGAGTTTGA Sertifera ATTCCAATTGAAGTT-AAAAA-GAATCGAATTTTAA------TATT-AGT-GATCAAATGATTCCTTCCAGAGTTTGA Elleanthus ATTCCAATTGAAGTT-AAAAAAGAATCGAATTCGAA------TATTCAGT-GATCAAACGATTCATTCCAGAGTTTGA Sobralia ATTCCAATTGAAGTTCAAAAA-GAATCGAATTCGAA------TATTCAGT-GATCAAATGATTCATT----AGTTTGA Diceratostele ???????????????????????????????????????????????????????????????????????????????A Didymoplexis ???????????????????????????????????????????????????????????????????????????????? Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium ???????????????????????????????????????????????????????????????????????????????? Xerorchis ------Nervilia ------GAAAAAAGA------TTCGAA------TATTCAGT-GATAAAATGATTCATTCCAGAGTT-GA Triphora AATCCA-TTGAAGTTGAAAAAGGAATCAAATTCGAATTTTCAGTTATTCAGT-AATCAAATGATTCATTCCAGAGTTTGA Monophyllorchis AATCCA-TTGAAGTTGAAAAAAGAATAGAATTCGAAT-----GTT---CAGT-AATCAAATGATTCATTCCAGAGTTTGA Psilochilus AATCCA-TTGAAGTTCAAA---GAAAAGAAT-CGA-T---CAGTTATTCAGT-AATCAAATGATTCATTCCAGAGTTTGA Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso ATTCCAATTGAAGTTGAAAAAAGAATCGAATTCAAA------TATTCAGT-GATCAAATGATTCATTCCAGAGTTTGA Chysis ATTCCAATTGAAGTTGAAAAAAGAATCGAATTCGAA------TATTCAGT-GATCAAATGATTCA------TTTGA Gastrodia_sesamoides_534 ???????????????????????????????????????????????????????????????????????????????? gastrodia_sp_reunion_ER214 ???????????????????????????????????????????????????????????????????????????????? gastrodia_confusa_0801 ???????????????????????????????????????????????????????????????????????????????? gastrodia_zyl_16313 ???????????????????????????????????????????????????????????????????????????????? Continued

Table B.1 Continued

Codonorchis TAAATCTTTTAAAGATTAATCGGACGAGAATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTA Goodyera TAGATTTTTTGAAGATAAATCGGACGAGAATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTA Palmorchis TAGATCTTTTGAAGATTAATCGGACGAGAATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTA Cephalanthera TAGATCTTTTGAAGATTAATCGGACGAGAATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTA Aphyllorchis ------GAAGATTAATCGGACGAGAATAAAGAGAGAGTCCCGTTTTACATGTCAATACCGACAACAATGAAATTTA Auxopus TAGATCTTTTGAAGATTAATCGGACGAGAATAAAGAGAGAGTCC--TTTTACATGTNNATACCGNCAACAATGAAATTTN Epipactis TAGATCTTTTGAAGATTAATTGGACGAGAATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGATATTTA Limodorum ------GAAGATTAATCGGACGAGAATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTA Listera TAGATCTTTTGAAGATTAATCGGACAAGAATAAAGAGAGAGTCCCGTTTAACATGTCAATACCGACAACAATGAAATTTA Neottia TAGATCTTTTGGAGATTAATTGGACGAGAATAAAGATAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTA Corymborkis ------Tropidia ???????????????????????????????????????????????????????????????????????????????? Epilyna TAGATCTTTTGAAGRTTAATCGGACGRGAA-AAAGGGAGGGGCCCCTTTTACATGGCCAT-CCGACAACCATGGAATTTT Sertifera TAGATYTTTTGAAGATTAATCGGGCGAGAATAAAGAGAGAGTCCCCTTTTTCATKTCAATWCCGGCAACAATGAAATTTT Elleanthus TAGATCTTTTGAAGATTA-TCGGACGAGAATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAAGGAAATTTA Sobralia TAGATCTTTTGAAGATTAATCGGACGAGAATAAAGAGAGAGTCCCCTTTTACATGTCAAAACCGACAACAATGAAATTTA Diceratostele TAGATCTTTTGAAGATTAATCGGACGAGAATAAAGAGAGAGTCC--TTTTACATGTNNATACCGNCAACAATGAAATTTN Didymoplexis ???????????????????????????????????????????????????????????????????????????????? Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium ???????????????????????????????????????????????????????????????????????????????? 380 Xerorchis ----TCTT------ATT---CGGACGAGAATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTA Nervilia TAGATCTTTTGAAGATTAATCGGACGAGAATAAAGAGAGAGTCCCTTTTTACATGTCAATACCGACAACAATGAAATTTA Triphora AAGATCTTTTGAAGATTAATCATACGAGAATAAAGAGAGAGTCCCTTTTTACATGTCAATACCGACAACAATGAAATTTA Monophyllorchis TAGATCTTTTAAAGATTAATCGAACGAGAATAAAGAGAGAGTCCCTTTT-ACATGTCAATACCGACAAAAATGAAATTTA Psilochilus TAGATCTTTTGAAGATTAATCGGACGAGAATAAAGAGAGAGTCCCTTTTTACATGTCAATACCGACAACAATGAAATTTC Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso TAGATCTTTTGAAGATTAATTGGACGAGAATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTA Chysis TAGATCTTTTGAAGATTAATCGGACGAGAATAAAGAGAGAGTCCCATTTTACATGTCAATACCGACAACAATGAAATTTA Gastrodia_sesamoides_534 ???????????????????????????????????????????????????????????????????????????????? gastrodia_sp_reunion_ER214 ???????????????????????????????????????????????????????????????????????????????? gastrodia_confusa_0801 ???????????????????????????????????????????????????????????????????????????????? gastrodia_zyl_16313 ????????????????????????????????????????????????????????????????????????????????

Codonorchis TAGTAAGAGGAAAATCCGTCGAATTG-AAAATCGTGAGGGTTCAAGTCCCTCTATCCCCAA--AAAAGCCCATTTT---- Goodyera GAGTAAGAGGAAAATCCGTCGAATTG-AAAATCGTGAGGGTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCATTTT---- Palmorchis TAGTAAGAGGAAAATCCGTCGAATTTTAAAATCGTGAGGGTTCAAGTCCTTCTATCCCCAAGAAAAAGCCCATTTT---- Cephalanthera TAGTAAGAGGAAAATCCGTCGAATT-GAAAATCGTGAGGGTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCATTTT----

Continued

Table B.1 Continued

Aphyllorchis TAGTAAGAGGAAAATCCGTCGAATTTGAAAATCGTGAGGGTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCATTTT---- Auxopus TAGTAAGAGGAAAATCCGTCGAATTTTCAAATCGTGAGGGTTCAAGTCCCTCTATCCCCAAGAAGAAGCCCTTCTTCTTT Epipactis TAGTAAGAG---AATC-GTCGA-TT-GAAAATCGTGAGGGTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCATTT----- Limodorum TAGTAAGAGGAAAATCCGTCGAATTT-AAAATCGTGAGGGTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCATTTT---- Listera TAGTAAGAGGAAAATCCGTCGAATTTGAAAATCGTGAGGGTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCATTTA---- Neottia TAGTAATAGGAAAATCCGTCGAATTTGAAAATCGTGAGGGTTCAAGTCCCTCTATCCCCAATAAAAAGCCCATTTT---- Corymborkis ------Tropidia ?????????????????????????????????????GGGTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCATTTT---- Epilyna TAGGAAG-GGAAAATCCGTCGAATTTTAAAATCGGGGGGGTTCAAGGCCCCCCTTCCCCCAGAAAAACCCCATTTT---- Sertifera TAGTAAGAGGAAA-TCCGTTGAATTTTAAAATTGGGGGGGTTCAAGTCCCTTTTTCCCCAAGAAAAAACCCCTTTT---- Elleanthus TGGTAAGAGGAAAATCCGTCGAATTTTAAAATCGTGAGGGTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCATTTT---- Sobralia TAGTAAGAGGAAAATCCGTCGAATTTGAAAATCGTGAGGGTTCAAGTCCCTCTATCCCCCAGAAAAAGCCCCTTTT---- Diceratostele TAGTAAGAGGAAAATCCGTCGAATTTTCAAATCGTGAGGGTTCAAGTCCCTCTATCCCCAAGAAGAAGCCCTTCTTCTTT Didymoplexis ???????????????????????????????????????????????????????????????????????????????? Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium ???????????????????????????????????????????????????????????????????????????????? Xerorchis TAGTAAGAGGAAAATCCGTCGAATTTTAAA-TCGTGAGGGTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCATTTT---- Nervilia TAGTAAGAGGAAAATCCGTCGAATTTTCAAATCGTGAGGGTTCAAGTCCCTCTATCCCCAAGAAGAAGCCCTTCTTCTTT Triphora TAGTAAGAGGAAAATCCGTCGAATTTTAAAATCGTGAGGGTTCAAGTCCCTCTATCCCCAAGAAAA-GCCCATTTT---- 381 Monophyllorchis TAGTAAGAGGAAAATCCGTCGAATTTCAAAATCGTGAGGGTTCAAGTCC-TCTATCCCCAATAAAAAGCCCATTTT---- Psilochilus TAGTAAAAGGAAAATCCGTCGAATTTTAAAATCGTGAGGGTTCAAGTCCCTCTATCCCCAAGAAAGAGCCCTTTTT---- Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso --GTAT------Chysis TAGTAAGAGGAAAATCCGTCGAATTTTAA--TCGTGAGGGTTCAAGTCCCTCTATCCCCAATAAAAAGCCCATTTT---- Gastrodia_sesamoides_534 ???????????????????????????????????????????????????????????????????????????????? gastrodia_sp_reunion_ER214 ???????????????????????????????????????????????????????????????????????????????? gastrodia_confusa_0801 ???????????????????????????????????????????????????????????????????????????????? gastrodia_zyl_16313 ????????????????????????????????????????????????????????????????????????????????

Codonorchis -ACTTCC------TCATCCTATTTGTT--CAT---CAGTTGTTAAGTTCAAACAAAATTCAATATCTTT Goodyera -AATTCCCCACTCTTTTTTTACTCTCATTCTCTTTTTTTT-AT---CAGTTGTTCAGTTCAAACAAAATTAAATATCTTT Palmorchis -ACTTCCTCACTCTTTATTTATCCTCATCCTATTTTTTTTCAT---CAGTGGTTCAGTTCAAACAAAATTCAATATCTTT Cephalanthera -ACTTCCTCACTCTTTATTTATCCTCATCCTCTTTTT---CAT---CAGAGGTTCAGTTCAAACAAAATTAAATATCTTT Aphyllorchis -ACTTCCTCACTCTTTATTTATCCTCATCCTTTTTTT---CAT---CAGTGGTTTAGTTCAAACAAAATTCAATATCTTT Auxopus TACTTTNTCTCTCTTTATTTATCCTCATCATAT--CTTTTCAT---TAGTGGATCAGTTCAAA------

Continued

Epipactis -ACTTCCTCACTCTTTATTTATCCTCATCCTCTTTTTTTTAAT---CAGTGGTTCAGTTCAAACAAAATTCAATATCTTT Limodorum -ACTTCCTC------CAAAATTCAATATTTTT Listera -ACTTCCTCACTCTTTATTTATCCTCATCCTCTTTTTTTTCAT---CAGTGGTTCAGTTCAAACAAAATTCAAT------Neottia -ACTTCCTC------A--TA------CTTT-TTTTCAT---CTGTGGTTCAGTTCAACCAAAATT-AAG-T---- Corymborkis ------Tropidia -ACTTCCTCGCTCTTTATTTATCCTCATCTTCTTTCTTTTCAT---CAGTGGCTCAGTTCAAACAAAATTCAATATCTTT Epilyna -CCT-CCCCGCCCTTTGTT-ATCCCCHACCCATTTCCTTTCATTTTCA-TAA-TAAGTTCAAAAAAGATTCAATATCTTT Sertifera -AWTTCCCCGCTCTTTATTTATCCTCATCCTCTTTTTTTTCATTTTCA-TAA-TCAGTTCAAACAAAATTCAATATATTT Elleanthus -ACTTCCTCGCTCTTTATTTATCCTCATCCTATTTCTTTTCATTTTCA-TAA-TAAGTTCAAACAAAATTCAATATCTTT Sobralia -ACTTCCCCGCTCTTTATTTATCCTCATCCTCTTTCTTTTCATTTTCA-TAA-TCAGTTCAAACAAAATTCAATATATTT Diceratostele TACTTTNTCTCTCTTTATTTATCCTCATCATAT--CTTTTCAT---TAGTGGATCAGTTCAAA------Didymoplexis ???????????????????????????????????????????????????????????????????????????????? Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium ???????????????????????????????????????????????????????????????????????????????? Xerorchis -AATTCCTCGTTCTTTATTTATCCTCATCCTTTTTTTTTTCAT---CAGTGGCTCAGTTCAAACAAAATTTAATATCCTT Nervilia TACTTTCTCTCTCTTTAATTATCCTCATCATAT--CTTTTCAT---TAGTGGATCAGTTCAAACAAA------Triphora -ACTTCCTTG------TCCAATATCTTT Monophyllorchis -ACTTCCTCGCTCTTTATTTATCCTCATCCTCTTTC----CAT---CAGTGACTCGATTCAAACAAAATCCAATATTTTT Psilochilus -ACTTCTTAAATCTTTTTTTATCCTCATCCTCTTTCTTTT------CAGTGGCTCGGTTCAAA-AAAATCCAATATCTTT Wullschlaegelia ????????????????????????????????????????????????????????????????????????????????

382 Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso ------Chysis -ACTTCCTCGCTCTTTATTTATCCTCATCCTCTTTCTTTTCAT---CAGTGGCTCAGTTTCAACAAAATGAAATATCTTT Gastrodia_sesamoides_534 ???????????????????????????????????????????????????????????????????????????????? gastrodia_sp_reunion_ER214 ???????????????????????????????????????????????????????????????????????????????? gastrodia_confusa_0801 ???????????????????????????????????????????????????????????????????????????????? gastrodia_zyl_16313 ????????????????????????????????????????????????????????????????????????????????

Codonorchis CTCATTTCATTCACTCTGTACTTTCACAAGTGGATCCGAATAGAAATTATCGTATCTTC-TTCCAATTTAATCCAATTTC Goodyera CTAATTTCATTCACTCTGTTCTTTCACAAATGGATACGAATAGAAATTCTCGTATCTT-ATTCCAATT-A---CAATTTC Palmorchis CTCATTTCATTCACTCTGTTCTTTCACAAATGGATCCGAATAGAAATCCTCGTATCTTC-TTCTAATC-----CAATTTC Cephalanthera CTCATTTCATTCACTCTGTTCTTTCACAAATGGATCCAAATAGAAATCCTCGTATCTTC-TTCCAATC-----AAATTTC Aphyllorchis CTCATTTCATTCACTCTGTTCTTTCACAACTGGATCCAAATATAAATCCTCGTATCTTC-TTCCAATC-----CAATTTC Auxopus ------CAATT-----CNATTTC Epipactis CTCATTTCATTCACTCTGTTCTTTTGCAACTGGATCCAAATAGAAATCCTCGTATCTTC-TTCCAATC------Limodorum CTCATTTCATTCACTCTGTTCTTTCACAACTGGATCCAAATGGAAATCCTCATATCTTC-TTCCAATC-----CAATTTC Listera TTCATTTCATTCACTCTGTTCTTTCACAACTGGATCCAAATAGAAATCCTCGTATCTTC-TTCCAATC-----CAATTTC

Continued

Table B.1 Continued

Neottia TTCATTTCATTTACTCAGTTCTTTAATAACTAGATCCAAATATAAATCCTCATACATCC-TTTCAATA-----CAATTTA Corymborkis ------Tropidia CTCATTTCATTCACTCTGTTCTTTCACAAATGGATC------TCCTCGTATCTTC-TTCCAATC-----CAATTTC Epilyna CTCATTTCATTCACTCTGTTCTTTCACAAATGGATCCGRATAGAAATCCTCGTATCTTA-TTCCAATC-----CMATTCC Sertifera CTCATTTCATTCACTCTTTTCTTTCACAAATGGATCCGAATAGAAATCCTCGTATCTTC-TTCCAATC-----CAATTTC Elleanthus CTCATTTCATTCAGTGTGTTCTTTCACAAATGAATCCGAATAGAAATCCTCGTATCTTC-TTCCAATC-----CAATTTC Sobralia CTCATTTCATTCACTCTGTTCTTTCACAAATGGATCCGAATAGAAATCCTCGTATCTTC-TTCCAATC-----CAATTTC Diceratostele ------CAATT-----CNATTTC Didymoplexis ???????????????????????????????????????????????????????????????????????????????? Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium ???????????????????????????????????????????????????????????????????????????????? Xerorchis CTCATTTCATTCACTCTGTTCTTTCACAAATGGATCCGAATAAAAATCCTCGTAT------ATA-----GAATTTC Nervilia ------TC-----CAATTTC Triphora CTTATTTCATTCACTCTGTTCTTTAACAAAAGGATTCGAATATAAATCCTCACATCTTC-TTCCAATC-----CAATTTC Monophyllorchis CTCATTTCTTTCCCTCTTTTCTTTAACAAAAGGATCCGAATAGAAATCCTCATATCTTC-TTCCAATC-----CAATTTC Psilochilus CTCATTTCATTAACTCTGTTCTTTAACAAAAGGATCCGAATATAAATCCTCATATCTTC-TTCCAATC-----CAATTTC Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso ------383 Chysis CTCATTTCATTCACTCTGTTCTTTCACAAATGGATCCGAATAGAAATCCTCGTATCTTC-TTCCAATC-----CAATCTC Gastrodia_sesamoides_534 ???????????????????????????????????????????????????????????????????????????????? gastrodia_sp_reunion_ER214 ???????????????????????????????????????????????????????????????????????????????? gastrodia_confusa_0801 ???????????????????????????????????????????????????????????????????????????????? gastrodia_zyl_16313 ????????????????????????????????????????????????????????????????????????????????

Codonorchis ATTTG----GTATAGATACGATACCTGCACAAATGAACATATATGTTCAAGGAATCTCCGTTATTTAAT--CATTCACAG Goodyera -TTTGTTTTGTATAGATACGATACCTGCACAAATGAACATATATATTCAAGGAATCTCCCTTATTGAATAACATTCACAG Palmorchis ATTT-----GTATAG-TACGATACCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT--CATTCACAG Cephalanthera ATTT-----GTATAG-TACGATACCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT--CATTCACAG Aphyllorchis ATTT-----ATAGAG-TACGATATCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT--CATTCACAG Auxopus ATTTGTTTTGTATAG-CACAATGCCTGCACAAATGASCATATATGTTGGGGGAATCTCCGTTACTGAAC--CATTCACAG Epipactis --TT-----GTATAG-TACGATACCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT--CATTCACAG Limodorum ATTT-----GTATAG-TACGATACCTGTAC----G------Listera ATTT-----GTATAG-TACGATACCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT--CATTCACAG Neottia ATTT-----CTAT---TTTTTTACCTGTACAAAAGAACATATATGTTCAAGGAATTTCCGTTATTGAAT------Corymborkis ------Tropidia ATTTGTTTTGTATAG-TACGATACCTGTAAAAATGAACATACATGTTCAAGGAATCTCCGTTATTGAAT--CATTCACAG Continued

Table B.1 Continued

Epilyna ATTTGTTTTGTATAG-TACGATACCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT--CATTCACAG Sertifera ATTTGTTTTTTATAG-TACGATACCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT--CATTCACAG Elleanthus ATTTGTTTTGTATAG-TACGATACCTGTACAAATGA------Sobralia ATTTGTTTTGTATAG-TACGATACCTGTACAAATGAACATATATGTTAAAGGAATCTCCGTTATTGAAT--CATTCACAG Diceratostele ATTTGTTTTGTATAG-CACAATGCCTGCACAAATGASCATATATGTTGGGGGAATCTCCGTTACTGAAC--CATTCACAG Didymoplexis ???????????????????????????????????????????????????????????????????????????????? Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium ???????????????????????????????????????????????????????????????????????????????? Xerorchis ATTTGTTTTGTAGAG-TACGATGCCTGTACTAATGAACATATATGTTCAAGGAATCTCCGTTATTGAAT--CATTCGCAG Nervilia ATTTGTTTTGTATAG-CACAATGCCTGCACAAATG------TATGTTCAAGGAATCTCCGTTATTGAAC--CATTCCCAG Triphora CTTTGTT---AATAG-TACAATATCTGTACAAAGGAACATATATGTTAAAGGAATCCGCCTTAT------CA- Monophyllorchis CTCTGTTTTTTCTAG-TACAATATCTGTACAAATGAACATATATGTTCAAGGAATCCGCGTTATTGAAT--CATTCACAG Psilochilus CTTTGTTTTTTATAG-TACGATACCTGTACAAAGGAACATCTATCTTCAAGGAATTCACATTCTTGAAT--CATTCACAT Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso ------Chysis ATTTGTTTTGTATAA-TACGATA--TG------AACATATATGTTCAAGGAATCTCCGTTATGGAAT--CATTCATAG Gastrodia_sesamoides_534 ???????????????????????????????????????????????????????????????????????????????? gastrodia_sp_reunion_ER214 ???????????????????????????????????????????????????????????????????????????????? 384 gastrodia_confusa_0801 ???????????????????????????????????????????????????????????????????????????????? gastrodia_zyl_16313 ????????????????????????????????????????????????????????????????????????????????

Codonorchis TCCATATCATTCTCCTTTCATTT-----ACAAAGAAAAT------GAATATCTAA------Goodyera TTCATATCATTATCTTTACATTT-----ACAAAGAAAGTTTT------Palmorchis TCCATATCATT------TTT-----ACAAAGAAAGTCTTCTTTTTGAAGATTCAAGAAATTCAGGGGCTAGGTCCAA Cephalanthera TCCATATCATT------ATT------ACAAAGAAAGTCTTCTTTTTGAAGACCTAAGAAATTCAGGGGCTAGGTCCAA Aphyllorchis TCCATATCACTATCCTTACACTT-----AC------Auxopus TCCATA-----ATCCTTACATTTCATTTACAAAGAAAGTCTTCTTKTTGAAGNTCTNAGAGAGTCAGGGTCTAGGTACAN Epipactis TCCATAT------CATTA----TACAAAGAAAGTCTTCTTTTTGAAGACCTAAGAAATTCAGGGGCTAGGTCCAA Limodorum ------Listera TCCATATCATTATCCTTACATA------AAAAAAAATCTTCTTTTTGAAGACCTAAGAAATTCGGGGGCTAGGTCCCA Neottia ------CATTT------AAAGTTTTATTTTTGAAGACGTAATAAATTAAGG--CTAGGTCCAA Corymborkis ------Tropidia TCCATATCTTTTTCCTTACATTT-----ACAAAGAAAGTCTTCTTT------Epilyna TCCAT------Sertifera TCCATAT----AT------Elleanthus ------Sobralia TCCATAT----AT------

Continued

Table B.1 Continued Diceratostele TCCATA-----ATCCTTACATTTCATTTACAAAGAAAGTCTTCTTKTTGAAGNTCTNAGAGAGTCAGGGTCTAGGTACAN Didymoplexis ???????????????????????????????????????????????????????????????????????????????? Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium ???????????????????????????????????????????????????????????????????????????????? Xerorchis TCCATATCTCTATCCTTACATTT-----ACAAAGAAAGTCTTC------Nervilia TCCATA-----ATCCTTACATTTCATTTACAAAGAAAGTCTTCTTTTTGAAGATCTAAGAGATTCAGGGTCTAGGTACAA Triphora TCCTTA-----ATCCTTACATTT-----A-AAA---ATACTT------Monophyllorchis TCCTTATCTTTATCCTTACATTT-----A-AAA------TTTT----GAAGATCTAAGAAATTCAGGGGCTAGGTCCAA Psilochilus TCCTTA------TCCTTACATTT-----A-AAAAGAAG------Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso ------Chysis TCCATATCTTTTTCCTTACATTG-----ACAAAGAAAGTCTTCTTTTAGAAGATCTAAGAAATTCAGGGGCTAGGGCCAA Gastrodia_sesamoides_534 ???????????????????????????????????????????????????????????????????????????????? gastrodia_sp_reunion_ER214 ???????????????????????????????????????????????????????????????????????????????? gastrodia_confusa_0801 ???????????????????????????????????????????????????????????????????????????????? gastrodia_zyl_16313 ????????????????????????????????????????????????????????????????????????????????

385 Codonorchis ------TTTAGTTTTTTTCATTGACA------TAGATACAAGTACTCTGCTAGGATAATGCACAGGAA Goodyera ------ATTTTTTAGTTCTTTTCGTTTACA------TAGATACAAGTACTCTGCTAGGATTATGCA-GG-TA Palmorchis TTTGTTAAGACTTTTTT----AGTTCTTTTCATTGACA------TAGATACAAGTCCTCTGCTAGGATGATGCACGAGAA Cephalanthera TTTGTTAAGACTTTTTT----AGTTCTTTTCATTGACA------TAGATACAAGTACTTTGCTAGGATGATGCACGGGAA Aphyllorchis ------Auxopus TTTGTTAAGACTCTCTNGTNTAGCTCTCTTCATTGAGA------AGCTCGAAGTNCTCGGCNAGGATGATGCACGGGAA Epipactis TTTGTTAAGACTTTTTT----AGTTCCTTTCATTGACA------TAGATACAAGTACTTTGCTAGGATGATGCACGGGAA Limodorum ------Listera TTTGTTAATACTTTTTT----AGTTTTTTTCATTGACA------TAGATAAAAGTACTTTGCTAGGATGATGCACGGGAA Neottia TTTGTTAAGACTTTTTT----AGTTCTTTTAATTAAAA------Corymborkis ------Tropidia ------AGTTATTTTCATTGACA------TAGATATAAGTACTCTGCTAGGATGATGCACGGGAA Epilyna ------Sertifera ------AAGTACTCTGCTAGGATGATTCACGGGAA Elleanthus ------Sobralia ------AAGTACTCTGCTAGGATGATTCACGGGAA Diceratostele TTTGTTAAGACTCTCTNGTNTAGCTCTCTTCATTGAGA------AGCTCGAAGTNCTCGGCNAGGATGATGCACGGGAA Didymoplexis ???????????????????????????????????????????????????????????????????????????????? Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium ???????????????????????????????????????????????????????????????????????????????? Xerorchis ------CTTTTT-----AGTTCTTTTCATTGACA------TAGATAGAAGTGCTCTGCTAGGATGATGCAAGGGAA

Continued

Table B.1 Continued

Nervilia TTTGTTAAGACTCTCTTTTTTAGTTCTTTTCATTGAC??????????????AAGTACTCGGCTAGGATGAT------Triphora ------TTTATTTTTTAGTTCTTTTCATTGACATTG-AC-AGATATAAW------GATAGGATCAACTAAGGGAA Monophyllorchis TTWGTTAAGACGTTCTTTTTTAGTTCTTTTCATTGACA------AGATAT--GT------Psilochilus ------ACTTTATTTTTTAGTTCTTTTCATTGACATAGGAC-AGATATAAGTACT-TTATAGGATGATGCAAGGGAA Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso ------Chysis TTTGTTAAGATTTTCTTTTTTAGTTCTTTTCATTGACAT------AGATA-AAGTACTCTGCTAGGATGATGCACGGGAA Gastrodia_sesamoides_534 ???????????????????????????????????????????????????????????????????????????????? gastrodia_sp_reunion_ER214 ???????????????????????????????????????????????????????????????????????????????? gastrodia_confusa_0801 ???????????????????????????????????????????????????????????????????????????????? gastrodia_zyl_16313 ????????????????????????????????????????????????????????????????????????????????

Codonorchis A0000000000000000000000??10???????????0?0001000000000000010000000000000000000010 Goodyera C1000000000010000000000000000000000?10000000000000000000010000000000000000000000 386 Palmorchis A0000000000000000000000000000000000100000000000000000000010000000000000000010??0 Cephalanthera A00000000000100000000000000000000000000000000000000000000101?1????????????0????? Aphyllorchis -????????????????????????????????????0000000100000000000010000000000000000010??0 Auxopus C??????????????????????????????????????????????????????????????????????????????? Epipactis A1000100010001100000000000000000000000000000000000000000010000000000?10???0????0 Limodorum -???????????????0????????00?0??0000000000000000000000000010000000000000000010??0 Listera A0000000000000000000000000000000001000000000100000000000011???????????????0????? Neottia -???????????????000?1?0000001????0?000000000000000000000000000000000000000010??1 Corymborkis -???????????????0000000000000000000000000000000000000000010000010000000000010??0 Tropidia A000000000000000?00000?0???????????????????????????????????????????????????????? Epilyna -0000000000000000000000000000000000000000000000000000000010000000000000000010??0 Sertifera A0000000000000000000000000000000000000000000000000000000010000000000000000010??0 Elleanthus -0000000000000000000000000000000000000000000000000000000010000000000000000010??0 Sobralia A0010000000000000000000000000000000000000000000000000000010000000000000000010??0 Diceratostele C??????????????????????????????????????????????????????????????????????????????? Didymoplexis ???????????????????????????????????????????????????????????????????????????????? Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium ???????????????????????????????????????????????????????????????????????????????? Xerorchis A0000000000000000000000000000110000100000000000000000000010000000000000000010??0 Nervilia -??????00000000000000000000000000000001????????000000000010000000000000000010??0 Triphora C00100000000000000010001000000?1?0?000000000000000000000010110101000000100010??0 Monophyllorchis -00000000000000000010001000000?1?0?000001000000000000000010000000001000000010??0

Continued

Table B.1 Continued

Psilochilus A0010010000000000000000100000000?1??00000000000000000000010000010010000000010??0 Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso -0000000000000000000000000000000000000000000000000000000010000000000000000010??0 Chysis A0000000000000000000000000000000000000000000000000000000010000000000000000010??0 Gastrodia_sesamoides_534 ???????????????????????????????????????????????????????????????????????????????? gastrodia_sp_reunion_ER214 ???????????????????????????????????????????????????????????????????????????????? gastrodia_confusa_0801 ???????????????????????????????????????????????????????????????????????????????? gastrodia_zyl_16313 ????????????????????????????????????????????????????????????????????????????????

Codonorchis 000000000000000000000000000000000100000000001?1???????0??0?00??00000000000000000 Goodyera 00000000000000000000000000000000010000000001??00000??100?0?00?000000000000000000 Palmorchis 00000000000000000000000000000?100000010?0000000000010000000000000010000000000000 Cephalanthera 0?000000000000000000000000000000000000000000000000000000000000000000000000000000 Aphyllorchis 000000000000000000000000000000000000000000000000000000000000000001?????????????? Auxopus ???????????????????????????????????????????????????????????????????????????????? 387 Epipactis 00000000000000000000000000000000000000000000000000000000000000000000000000000000 Limodorum 000000000000000000000000000000000000000000000100000000000000000110?????0???1???? Listera ?????????????????0?0000000000000000000000000000000000000000000000000000000000000 Neottia 0?00100000000000001000000000000000000000000000001000000000101????0?????000000000 Corymborkis 0000?1000000000000000000000000000000000????????????????????????????????????????? Tropidia ???????????????????????????????????????????????????????????????????????????????? Epilyna 00000000000000000000000000000000000000000000000000000000000000000010000000000000 Sertifera 00000000000000000000000000000000000000000000010000000000000000000001001000000000 Elleanthus 00000000000000000000000000000000000000000000000000000000000000000001000000000000 Sobralia 00000000000000000000000000000000000000000000000000000000000000000000001000000000 Diceratostele ???????????????????????????????????????????????????????????????????????????????? Didymoplexis ???????????????????????????????????????????????????????????????????????????????? Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium ???????????????????????????????????????????????????????????????????????????????? Xerorchis 0000000000000000000000000000000000000?1??????????????????????????0?????????0???? Nervilia 0000000000000000000000000000000000000000000000000000000011?00???00?00001??00?000 Triphora 010000000000000000001000001?0100000000000000000000000000000000100000000000000000 Monophyllorchis 001????????000000000000000000000000000000000000000000000000000100000000000000000 Psilochilus 0000???10??0100000000000000000000000000000000000000000000000001000001??000000100 Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Continued

Table B.1 Continued

Calypso 00000000000000000000000000000000000000000000000000000000000000000000000000000000 Chysis 00000000000000000000000000000000000000000000000000000000000000000000000000000000 Gastrodia_sesamoides_534 ???????????????????????????????????????????????????????????????????????????????? gastrodia_sp_reunion_ER214 ???????????????????????????????????????????????????????????????????????????????? gastrodia_confusa_0801 ???????????????????????????????????????????????????????????????????????????????? gastrodia_zyl_16313 ????????????????????????????????????????????????????????????????????????????????

Codonorchis 01??0010000000000000000000000010000010001000?1?00???00000001?0000100000000000000 Goodyera 01??0010000000000000000000000010000000001000000000000000000001000100000000000000 Palmorchis 01??0010000000000000000000000000000000001000000000000000000000000100000000000000 Cephalanthera 01??0010000000000000000000000100000000001000000000000000001??0000100000000000000 Aphyllorchis ????????????0?000000000000000000000000001000000000000000001??0000100000000000000 Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis 01??001000000000000000000101110000000010?000000000000000000000000100000000000000 Limodorum ????????????0?00000000000000001000000000100000?10?????????????????????0000000000 Listera 01??00100000000000000000000000000000000010000000000000000000000001000000000000?1 388 Neottia 01??001001000000000000000000000000000000100000100?101?00100000000100000000010010 Corymborkis ???????????????????????????????????????????????????????????????????????????????? Tropidia ??????????????????????????????????0000001000000000000000000000000100000000000000 Epilyna 01??0010000000001000100010000000000000001010000000010000000000000011000000000000 Sertifera 01??0110000000000000000000100000000000001000000000000000000000000011000000000000 Elleanthus 01??0010000000010000000000000000000000001000000000000000000000000011000000000000 Sobralia 01??00100?1000000000000000000000000000001000000000000000000000000011000000000000 Diceratostele ????????????0000010000000000000000000000000000000000001?00000000010000?1??0????? Didymoplexis ???????????????????????????????????????????????????????????????????????????????? Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium ???????????????????????????????????????????????????????????????????????????????? Xerorchis ????????????1?1?0000000000000000100000001000000000000000000000000100000000000000 Nervilia 01??001000010000000000000000000000000000000000000000001?00000000010000000?1????? Triphora 0000001000000000000000000000000000000100100000001??????????????????????0?0000000 Monophyllorchis 00?1101000000000001000000000000000100000100000000000000001???0000100000000000000 Psilochilus 1010001000000000000000000000000000000000100000000000000000000?10??00001000000000 Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso 01??00100000000000000001???????????????????????????????????????????????????????? Chysis 01??00101??000000000000000000001?00000001000000000000000000000000100000000000000

Continued

Table B.1 Continued

Gastrodia_sesamoides_534 ???????????????????????????????????????????????????????????????????????????????? gastrodia_sp_reunion_ER214 ???????????????????????????????????????????????????????????????????????????????? gastrodia_confusa_0801 ???????????????????????????????????????????????????????????????????????????????? gastrodia_zyl_16313 ????????????????????????????????????????????????????????????????????????????????

Codonorchis 000000000000000001000000000010000000000000000010000000000000000?10000000100000?0 Goodyera 000000000000000010010000110000000000000000000000000000000000000?100000000?1????0 Palmorchis 0000000000000000010?1000?001?000000010000000001000000000??10000?1000000000000000 Cephalanthera 0000000000000000010?1000?001?000000010000000001000000000?100010??000000000000000 Aphyllorchis 0000000000000000010?1000?001?0000000100000000010000000000000000?100????????????? Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis 0000000000000000010????1??01?0000000100000000010000000?1?00000010000000000000000 Limodorum 0000000000000000010?1000?001?000000010001??????????????????????????????????????? Listera ?000000000000000010?1000?001?00000001000000000100000000000000?1??0?0000000000000 Neottia 1000000000000000010?1000?001?00001?0?000000000?1?????????000000??1?0000000000000 Corymborkis ???????????????????????????????????????????????????????????????????????????????? 389 Tropidia 000000000?10?000010?1000?00000000000100000000010000000000000000?1000000000000001 Epilyna 0000000000000000010?1000?00000000000100000000010000????????????????????????????? Sertifera 0000000000000000010?1000?0000000000010000000001000000010000?1??????????????????? Elleanthus 0000000000000000010?1000?00000000000100000?????????????????????????????????????? Sobralia 0000000000000000010?1000?0000000000010000000001000000010000?1??????????????????? Diceratostele ???????????0?0?0??0?1000?00000000000100000000010000100?0000000000000000000000000 Didymoplexis ???????????????????????????????????????????????????????????????????????????????? Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium ???????????????????????????????????????????????????????????????????????????????? Xerorchis 0000000000000001??0?1000?00000000000100000000010000000000000000?10000000000?10?0 Nervilia ???????????0?0????0?1000?00000000000100001000010000100?00000?0000000000000000000 Triphora 0000000000000000010?1000?000001000001000000010?0?01100?00000000?101100?0010??0?0 Monophyllorchis 0000000000000000010?1000?00000000000100000000010000000000000000?101?10?000000010 Psilochilus 0000000000000000010?1000?00000000000100000000010000?10?0?000000?10100001?00?00?0 Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso ???????????????????????????????????????????????????????????????????????????????? Chysis 0000000000000000010?1000?000000000001011?0000010000000000000000?1000000000000000 Gastrodia_sesamoides_534 ???????????????????????????????????????????????????????????????????????????????? gastrodia_sp_reunion_ER214 ???????????????????????????????????????????????????????????????????????????????? gastrodia_confusa_0801 ???????????????????????????????????????????????????????????????????????????????? gastrodia_zyl_16313 ????????????????????????????????????????????????????????????????????????????????

Continued

Table B.1 Continued

Codonorchis 1????00001000?00000000000GCGAAGGCA-TCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGG Goodyera 0????00001000?00000000011GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGG Palmorchis 0000001??1000?00000000000-CGAAGGCAATCTCTCGGATGTTCCCCTAACCCACCCCGGGAACGGACCGTATGG Cephalanthera 0000001??1000?00000000000GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGVANGG Aphyllorchis ?????????????????????????------Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis 0000001??1000?00000000000GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGG Limodorum ?????????????????????????CCGAAGGGAATCGGGCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGG Listera 0000001??1000?00000000000GCGAAGGCAATCGCTCGGMTGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGG Neottia 0010001??????????????????GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGG Corymborkis ?????????????????????????------TCCCCTAACCCTACCCGGGAACGGACCGGAGGG Tropidia ?????????1000?00000000000G-GAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGG Epilyna ?????????????????????????------Sertifera ????????????????000000000TCGAAGGCA-TCGC--GGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGG Elleanthus ???????????????????????????????????????????????????????????????????????????????? Sobralia ????????????????000000000------Diceratostele 000000000?10???0000000000GCTTAGGCGATCACGCTTATGTTCCCCTACCCCTTCCC-TTAAC---CCTTTAGT Didymoplexis ?????????????????????????GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCC------GGAGGG 390 Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium ?????????????????????????GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGG Xerorchis 0????1???1000?00000000000GAGAA------GCTCATATGTTCCCCTGACCCAACCCGGGAAGGGACCGGAGGG Nervilia 000000000???????0000000??TC-AAGGCA-TCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGG Triphora 0????0000000011000?1??000GCGAAGGCA-----TCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGG Monophyllorchis 000000000?10???01000?????GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGG Psilochilus 0??0?00000000010000010000GCGAAGGCA-TCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGG Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso ?????????????????????????GSGAAGGCAATCGCTCGGATGTTCCMCTAACCCAACCCGGGAACGGACCGGAGGG Chysis 0000000000001??1000000000GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGG Gastrodia_sesamoides_534 ?????????????????????????GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCCGGTTA----CCGGAGGG gastrodia_sp_reunion_ER214 ?????????????????????????------CGGATGTTCCCCTAACCCAACCCGGGAACGGACCGGAGGG gastrodia_confusa_0801 ?????????????????????????GCGAAGG------TCGGATGTTCCCCTAACCCAACCCGGT--C---CCGGAGGG gastrodia_zyl_16313 ?????????????????????????GCGAAGGCAATCGCTCGGATGTTCCCCTAACCCAACCC------GGAGGG

Continued

Table B.1 Continued

Codonorchis AACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTT------GGGCGGGCAG Goodyera AACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTT------SGGCGGGCAG Palmorchis AACCGCATCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGATTTTTGGGGGGCGAGCTTTGGGCGGGCAG Cephalanthera AACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTTGGGGGNSSAGCTTTGGGCGGGCAG Aphyllorchis --CCG-AGCG-GAGGA-TGTCCGCGTCTCGTCGCAGGGCGC-TGCGTTTGAGTTTTGGGGGGCGA-CTTTGGGCGGGCAG Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis AACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTTGGG----GAGCTTTGGGCGGGCAG Limodorum AACCGCAGCATGAGGAATGGCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTTGGGGGGCGAGCTTTGGGCGGGCAG Listera AACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTTGGGGGGCGAGCTTTGGGC----AG Neottia AACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTTGGGGTCTGA-CTTA--GCG----- Corymborkis AACCGCAGCTTGAGGAATGTCCGCGTCTCGGCGAAGGGCGCTTGCGTTTGAGTTTTGGGTGGTGAGCTTTGGGCGGGCAG Tropidia AACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTTGGGGGGCGAGCTTTGGGCGGGCAG Epilyna ------Sertifera AACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTATGGGGGGCGAGCTTTGGG----CAG Elleanthus ???????????????????????????????????????????????????????????????????????????????? Sobralia ------Diceratostele ACCCTTATCTTGTGGTATGACCACGTCTGCTCTCACAGAACTTA--ATCGAGCTCTGGGGGGCGAGCTTTGGGCGGGCAG Didymoplexis AACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTTGGGGGGCGAGCTTTGGGCGGGCAG Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? 391 Epipogium AACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTTTGGGGGCGAGCTTTGGGCGGGCAG Xerorchis AACCTCAGCATGGGGGATGTCCGCGTCTCGTCTCTCGGCTCAT---TTT--GT--TGGGGGGC-AGCTTTGGG------Nervilia AACCGCATCCTGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTTGGGGGGCGAGCTTTGGGCGGGCAG Triphora AACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCA----CGTTTGAG----GG--GGCGAGCTTTGGGCGGGCAG Monophyllorchis AACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCG???????TTTGGGGGGCGAGCTTTGGGCGGGCAG Psilochilus AACCGCAGCATGAGGAAT-TCCGCGTCTCGTCGCAAGGCGCTTGCG------GG-GGGCGAGCTTTGGGCGGGC-- Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso AACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTNNGNGGG-GAGCTTTGGGCGGGCAG Chysis AACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTTGGGGGGCGAGCTTTGGGCGGGCAG Gastrodia_sesamoides_534 AACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTRCGTTTGAGTTBSGGGGGGCGAGCTTTGGGCGGGCAG gastrodia_sp_reunion_ER214 AACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTTGGGGGGCGAGCTTTGGG------gastrodia_confusa_0801 GACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGG---TTA--TTTGAGTTTTGGGGGGCGAGCTTTGGGCGGGCAG gastrodia_zyl_16313 AACCGCAGCATGAGGAATGTCCGCGTCTCGTCGCAAGGCGCTTGCGTTTGAGTTTTGGGGGGCGAGCTTTGGGCGGGCAG

Continued

Table B.1 Continued

Codonorchis TGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTCAATGAGATAA Goodyera TGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTTACTTCAATGAGAGAA Palmorchis TGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAAGTGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAA Cephalanthera TGCAGTCCGGGGCGGGG--CACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAA Aphyllorchis TGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAA Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis TGCAGTCCGGGGCGGGG--CACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGG-GACTTCAATGAGAGAA Limodorum TGCAGTCCGGGGCGGGG--CACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTC-ATGA-A-AA Listera TGCAGTCCGGGGCGGGG--CACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTAAATTAGAGAA Neottia ------GGGGCGGGG--CACAAGGGTCA-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTGAAATTAGAGAA Corymborkis TGCAATCC-GGGC------CCCAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAA Tropidia TGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAA Epilyna ------Sertifera TGCAGTCCGGGG------CAAAAGG-TCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTCAATGAGATAA Elleanthus ???????????????????????????????????????????????????????????????????????????????? Sobralia ------Diceratostele TGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAA Didymoplexis TGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGGTGCGAATAACCC------AATGAGAGAA Didymoplexiella ????????????????????????????????????????????????????????????????????????????????

392 Epipogium TGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGG------ATTAGAGAA Xerorchis ------CACAAGGGTCC-TGGWACAATCCAGGTGCGAAGAACCCCGGAGGTGACTGCAATGAGAGAA Nervilia TGCA-TCCGGGG------ACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTCAATTAGAGAA Triphora TGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGGTGCGAATAACCCCGGAGGTGACTTCAATGAGAGAA Monophyllorchis TGCAGTCCGGGG------CACAAGGSTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAA Psilochilus TGAACTCCGGGG------CACAAGGG-----GGTACTACCCAGGTGCGAAGAATCCCGGTGGCGACTT------GAGAA Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso TGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAA Chysis TGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGTGACTTCAATGAGAGAA Gastrodia_sesamoides_534 THCAGTCC------GGGTCC-TGGTACTACCCAGGTGCGAATAACCCCGGAGGCG----C--GGAGA--- gastrodia_sp_reunion_ER214 ------CCGGGGCGGGG--CACAAGGGTCC-TGGTACTATCCAGGTGCGAAGAACCCCGGAGGTGACTTCAATTAGAGAA gastrodia_confusa_0801 TGCAGTCC------GGGTCC-TGGTACTACCCAGGTGCGAAGAACCCCGGAGGC------A gastrodia_zyl_16313 TGCAGTCCGGGG------CACAAGGGTCC-TGGTACTACCCAGGTGCGAATAACCC------AATGAGAGAA

Continued

Table B.1 Continued

Codonorchis ATTGAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAA Goodyera ATTGAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAA Palmorchis ATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAA Cephalanthera ATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGCCGAGCTCCAA Aphyllorchis ATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAA Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis ATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGCCGAGCTCCAA Limodorum ATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAAC-AATGGCC-AGCTCCAA Listera ATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAA Neottia ATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGCCGAGCTCCAA Corymborkis ATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAA Tropidia ATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAA Epilyna ------Sertifera ATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAA Elleanthus ???????????????????????????????????????????????????????????????????????????????? Sobralia ------Diceratostele ATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAA Didymoplexis ATGTAACTCACTGGCCTAAACGACGAACAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAA Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium ATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAA 393 Xerorchis ATATAACTCACCGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCCGACAAATGGACCAGTTCT-- Nervilia ATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAA Triphora ATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCCAACGAATGGA--A---CC-- Monophyllorchis ATGTCACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTBAGAGCAAGGGATCACCAAACGAATGGACGAGC----- Psilochilus ATGTCACTCACTGGCCTAAACGACGAGCAAACATTCAAACGTGAGAGCAAGGGATCACCAAACGAATGG-CGAGCTCCAA Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso ATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAA Chysis ATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAA Gastrodia_sesamoides_534 -KGTAACTAACTGGCCTAAACGACGAAAAAACACTCGAACGTTAGACCAAGGGATCACCAAACGAATGGACGAGCTCCAA gastrodia_sp_reunion_ER214 ATGTAACTCACTGGCCTAAACGACGAGCAAACACTCGAACGTGAGAGCAAGGGATCACCCAACGAATGGTCGAGCACCGA gastrodia_confusa_0801 ATGTAACTCACTGGCCTAAACGACGAAAAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATG------CTCCAA gastrodia_zyl_16313 ATGTAACTCACTGGCCTAAACGACGAACAAACACTCGAACGTGAGAGCAAGGGATCACCAAACGAATGGACGAGCTCCAA

Continued

Table B.1 Continued

Codonorchis GGAGGTAGGAGAAAGGGGGGC-AAGAACCATGCTTT----CATAGATGACATATTTTCACTCTGAACTGCGATAATAACT Goodyera GGAGGTAGGAGAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATGACATATTTBCACTCTGAACTGCGAGAAGAACT Palmorchis GGAGGGAGGAGAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATTACATATTTTCACTCTGAACTGCGATAATAACT Cephalanthera GGAGGGAGGAGAAAGGGGGGC-AATAACCATGCTTT----CAGAGATGACATATCT-CACTCTGAAC-----TAATCACT Aphyllorchis GGAGGGAGGAGAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATTACATATTTTCACTCTGAACCGCGAGAATAACT Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis GGAGGGAGGAGAAAGGGGGGC-AATAACCATGCTTT----CAGAGATGACATATTTTCACTCTGAACTGCAAAAATCACT Limodorum GGAGG-AGGA-AAAGGGGGGC-AATAACCCTGCTTT----CAAA--TGAC-----TGAACTCTGAAC------ACT Listera GGAGGGAGGAGAAAGGGGGGC-AATAACCATGCTTT----CAGAGATTACCTATTTTAACTCTGAACTGCAAAAAGAACT Neottia GGAGGGAGGAGAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATGACAGATTTGAACTAGGAA-----A-AAGAACT Corymborkis GGAGGGAGGAGAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATTACATATTTTCACTCTGAACCGCGAGAATAACT Tropidia GGAGGGAGGAGAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATTACATATTTTCACTCTGAACTGCGAGAATAACT Epilyna ------Sertifera GGAGGGAGGAGAAAGGGGGGC-AAGAACCATGCTTG----AAGAGATTACAGATTTGAACTATGAACTGCGAGAAGAACT Elleanthus ???????????????????????????????????????????????????????????????????????????????? Sobralia ------Diceratostele GGAGGGAGGAGAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATGACATATTTTCACTCTGAAC-----GAATAACT Didymoplexis ------GGGGGG------CC-TGCTGTAAT----AGATTACATA-TTGAACTTTGAACTGCGAGAATAACT Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? 394 Epipogium GGAGGGAGGAGAAAGG------CCATGCTTG-ATG------ACATCTTTTCACTCTGAAC-----GAAGAA-- Xerorchis GAA------GA--GTG------AGAATCATGCTTT----CAAAGA---CAT---TTCGGTC-CTA--GCGAAAAAGACT Nervilia GGAGGGAGGAGAAAGGGGGGC-AAGAACCATGCTTT----CAGAGATTACATCTTTTCACTCTGAACTGCGAGAATAACT Triphora -GA---AGG-----GGT---CC--GAA---T-CGT-----C-----TT-CG------TGAAC---GAG------Monophyllorchis GGAGGGAGGAGAAAGG----C-AAGA------TTT----CAGAGATTACATATTTTCAC------GAGAATAACT Psilochilus GGAGGGAGGAGAAAGG----C-AAGAACCATGCTTT----CA-AGATGACGTATATGA--TTGGAAC---GAGAATCACT Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso GGAGGGAGGAGAAAGGGGG-C-AAGAACTATGCTTT----CAGAGATTACATATTTKCACTCTGAACTGCGATAATAACT Chysis GGAGGGAGGAGAAAGGGGG-C-AAGAACCATGCTTT----CAGAGATTACATATTTTCACTCTGAACTGCGAGAATAACT Gastrodia_sesamoides_534 GGA------GG----C------CCGTGC--GAATGCTAAG-GTCCATATTTGAACTCTGAACTGCGAGAATAACT gastrodia_sp_reunion_ER214 GGAGGGAGGAGAAAGGGGGG--AA------TTCCATATTTGAACTCTGAACTGCGAGAATAACT gastrodia_confusa_0801 GGAGGGAGGGGCTCTTGGAG---AGAG--ATG---GAA------TTCCATATTTGAACTCTGAACTGCGAGAATAACT gastrodia_zyl_16313 ------GGGGGG---A---CCCTGCTGTAAT--AGA--TTACATA-TTGAACTTTGAACTGCGAGAATAACT

Continued

Table B.1 Continued

Codonorchis GACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGACAGAT Goodyera GACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGACAGAT Palmorchis GACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGATTGTATGGGTGACAGAT Cephalanthera GACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCAAGAATGTATGGGTGACAGAT Aphyllorchis TACTCAGCCGTGCCTCC-----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGACAGAT Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis GACTCAGCCGTGCCTCCC----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGACAGAT Limodorum GACTCAGCCG-GCCTCCA----GGGGGCATTC???????????????????????????????????????????????? Listera GACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGGCGGGACGGGGCCAAGCC------GGGTGACAGAT Neottia GACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGGTGGGACGGGGCCAAGCC------GGGTGACAGAT Corymborkis TACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGACAGAT Tropidia TACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGACAGAT Epilyna ------Sertifera TACTCAGCCGTGCCTCCA----GG-----TTCTCCACACGGG----ACGGGGCCAAGCCC--AATGTATGGGTGACAGAT Elleanthus ???????????????????????????????????????????????????????????????????????????????? Sobralia ------GTATGGGTGACAGAT Diceratostele TACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCA-AATGTATGGGTGACAGAT Didymoplexis GACTAAGCCGTGCCTCCA---CGGGG-CATTCTCCACACGGG------CC--GCCCAGAATGTATGGGTGACAGAT Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? 395 Epipogium ------CC-GGGCGGGGGCATTCTCCACAC------ACGG------CCAGAATGTATGGGTGACAGAT Xerorchis GACTC-GCCGCTATAACA------C-T-----A-A------ACGGG---AAAC--AGTTTGT-TGGGTGACATAT Nervilia GACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGACAGAT Triphora GACTAAGCC---CC------GGT--CATTCTC-----G------ACGGGGCC------GA-TGT-TGGGTGACAGAT Monophyllorchis KACTCAGACGT---TCC-----GGGG-CATTCTCCACACGGG----ACGGGGGCAAGCCCAGAATGTATCGGTSACAGAT Psilochilus GACTAAGCCGTGCCTCC-----GGGGGCATTCTCCCCACGGG----ACGGGGCCAAGCCC-AAATGTATGGGTGACAGAT Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso GACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGG----ACGGGGCCAAGCCCAGAATGTATGGGTGACAGAT Chysis GACTCAGCCGTGCCTCCA----GGGGGCATTCTCCACACGGG----RCGGGGCCAAGCCCAGANTGTATGGGTGACAGAT Gastrodia_sesamoides_534 GACTAAGCCGTGCCTCCA----GGGGG------ACGGG------AATGTCTGGGTGACAGAT gastrodia_sp_reunion_ER214 GA-TAAGCCGTGCCTCCAGGGCGG------ACGGGG------AATGTATGGGTGACAGAT gastrodia_confusa_0801 GACTAAGCCGTGCCTCCAGGGCGG------ACGGGG------AATGTATGGGTGACAGAT gastrodia_zyl_16313 GACTAAGCCGTGCCTCCA---CGGGG-AATTCTCCACACGGG------CC--GCCCAGAATGTATGGGTGACAGAT

Continued

Table B.1 Continued

Codonorchis CGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGT Goodyera CGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGT Palmorchis CGGCTATACGGGTACTACGGGGTATACACCAGGGCAC-GCA-TGTCGAGCATACGACGATGCCGCCCGTGTTCTTTTCCT Cephalanthera CGGCCATAGGGGTACTCCGGGGTATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGT Aphyllorchis CGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATAC-ACGATCCCGCCCGTTTTCATTTCGT Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis CGGCCATAGGGGTACTCCGGGGTATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGT Limodorum ???????????????????????????????????????????????????????????TGCCGCCCGTTTTCATCTCAC Listera CGGCCATAGGGGTACTCCGGGGTATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGT Neottia CAGCCATAGGGGTACTCCGGGGTATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGT Corymborkis CGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAA-TGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGT Tropidia CGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGT Epilyna ------Sertifera CGGCCATAGGG-TACTCCGGGATATAC-CCAG--CAA-CAAATGTC-AGC-TACGA---TGCCGCCCGTTTTCATTT--- Elleanthus ???????????????????????????????????????????????????????????????????????????????? Sobralia CGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGT Diceratostele CGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTC-- Didymoplexis CGGCCATAGGGGTACTCCGGG------ACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGT Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium CGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGT 396 Xerorchis CGGCCATATGATTACTCCGGGATATA-----GGGCAA-CCA--GTTGAGCATACGACAATGCCCCCCGTTTTCATTTCAT Nervilia CGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGT Triphora CGGCCATACCAG-ACTCCGGGATAGACACCAGGGCAA-CAAATGTCGAGCATAC-ACGATGCCGCCCGTTTTCATTTCGT Monophyllorchis CGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGT Psilochilus CGGCCATAAGGGTACTCCGGGATATACACCAGGGCA--CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGT Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso CGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGT Chysis CGGCCATAGGGGTMCTCCGGGWTATHCACCAGGGCAV-CAAATGTCGAGCATACGACGATGCCGBCCGTTTTCATTTCGT Gastrodia_sesamoides_534 CGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-AAAAGGTCGAGCATATGACGATGCCGCCCGTTTTCCTTTCGT gastrodia_sp_reunion_ER214 CGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-AAAATGTCGAGCATATGACGATGCCGCCCGTTTTCCTTTCGT gastrodia_confusa_0801 CGGCCATAGGGGTACTCCGGGATATACACCAGGGCAA-AAAATGTCGAGCATATGACGATGCCGCCCGTTTTCCTTTCGT gastrodia_zyl_16313 CGGCCATAGGGGTACTCCGGGA------CCAGGGCAA-CAAATGTCGAGCATACGACGATGCCGCCCGTTTTCATTTCGT

Codonorchis GGAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGA----GCGTTCTGCTTCTTAGGGCGCA-AA--ATCGTGACTCTGGGG Goodyera GGAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGA----GCCTTCTGCTTATTAGGGCGCATAA--ATCGTGACTCTGGGG Palmorchis GGAAGTCCCCGGGGGAGGAATGGGCTGTATGTGA-GGTGCGTTCTGCTTCTTAGG-CGCAGA----TTGTTCCTAT---- Cephalanthera GGAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCT-GGGGCGCAGAA--ATCGTTCCTATGGGT Aphyllorchis G-AAGTCCCCGGCCGAG-AAAGAGATGTAGGTGATGGATCGTTCTGCTTCTTACGGAGGAAAA---TCGTTCCTTTCG-G

Continued

Table B.1 Continued

Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis GGAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCTTAGGGCGCAGAA--A------GGGG Limodorum G-AAGTCCCCG------GGGCGG--AA---TCGGCTGTAT---- Listera GGAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCTTAGGGCGCAGAA--ATCGTACCTCTGGGT Neottia GGAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTT-TGCTTCTTAGGGCGCATAA--ATCGTTCC-----G- Corymborkis GGAAGTCCCCGGCAGAGGAAAGGGCTGTAG-TGATGGCGCGTTCTGCTTCTTAGGGAGCAAAA---TCRTTCCTT-GG-G Tropidia GGAAGTACCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCTTAGGGCGCATAA--ATCGTTCCTATGG-G Epilyna ------Sertifera -GAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCGCAGGGCGCATAA--ATCGTTCCTATGG-G Elleanthus ???????????????????????????????????????????????????????????????????????????????? Sobralia GGAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCTTAGGGCGCATAA--ATCGTTCCTATGG-G Diceratostele GGAATTCCCCGGCA-AG-AAAGGGCTG-AGGGGATGGCCCGT-CTGCTTCTTAGG-CGCA-AA--ATCGT-CCTAT-G-G Didymoplexis GGAA-TCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGTGTTCTACTTCT--GATTG-A-AA---TCGTTCCTATGG-G Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium GGAAGTCCCCGGCAGAGGAAAGGGCTGTAGG--A-----CGTTC-GG-TCT------TTCCTA-GG-G Xerorchis GGAA-TCCCAGGCAGAG-A--GGGCTGTAGATGATGGCGCGTTCATCTTCTT------G Nervilia GGAAGTCCCCGGCAGAGGAAAGGGCTGTATGTGATGGCGCGTTCTGCTTCTTAGGG------TCGTTCCTAT---- Triphora GGAAGTCCCCGGCGGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTATAA------AAAA--AT-G----TATGG-G Monophyllorchis GGAAGTTCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCTTAGGGCGCATAA--ATCGTTCC---GG-G 397 Psilochilus GGAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCTTAGGGCGCAGAA--ATTGTTCC----G-G Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso GGAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCTGAGGGCGCATAA--ATCGTTCCTATGG-G Chysis GGAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGCGTTCTGCTTCTTAGGGCGCAGAA--ATCGTACCTCTGG-A Gastrodia_sesamoides_534 GGAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTGAT----CGTTCTGC---TTAGGGCGCATAAGCATAAT-CCTATGG-G gastrodia_sp_reunion_ER214 GGAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTTTT-----GTTCTTCTTCTTATA-T---TAAGCTTA-T---TAAGG-G gastrodia_confusa_0801 GGAAGTCCCCGGCAGAGGAAAGGGCTGTAGGTTTT------TTCTTT--CT-ATA-TAGA-AA---TCGTTCCTATGG-G gastrodia_zyl_16313 GGAA-TCCCCGGCAGAGGAAAGGGCTGTAGGTGATGGCGTGTTCTACTTCTGAT--T-GA-AA---TCGTTCCTATGG-G

Codonorchis ----TCGTGCGTGGCACTGGTATAGATGATGAAAGGCGG------CCGGGACCTC-T-C--T-TGAAGAGGCGGCAAGC Goodyera ----TCGTGCGTGGCACTGGTATAGATGATGAAAGGCGGGCTTGA-CCGGGACCTCTT-CT---TGAATAGGCGGCAAGC Palmorchis ----TC-T--G---CACTGGTATAGATGATGAAAGGCGGGCTTGAACC---ACCTATT-CTCTT--AATAG-CCACA--C Cephalanthera GGGGTCGTGCGTGGCACTGGTATAGATGATGAAAGGCGGGCTTGAACCGGGACCTATT-CTCTTATAATAGGCGGCAAGC Aphyllorchis ----TCGTGCGTGGGACTGGT-GAGATGATGAA-GGGGGGCTTGAACAGGC-CCCCTT-TT-TT-TAATAGGCAGCAAA- Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis ----TCGTGCG--GCACTGGTATAGATGATGAAAGGCGGG------GGACCTATT-CTCTT--AATAGGCGGCAAGC

Continued

Table B.1 Continued

Limodorum ------GTGCGTGGGGCTGG-ATAGATGATGAAAGG-GGGCTTGAACCGGGACCTATT-CTC--A-AA-AGGCGG-AAGC Listera GGGGTCGTGCGTGGCACTGGTATAGATGATGAAAGGCGGGCTTGAACCGGGACCTATT-CTCTT--AATAGGCGGCAAGC Neottia GGGGTCGTGCGTGGCACTGGTATAGAT------GGG------GGGACCTATT-CTATTATAATAGGCGGCAAGC Corymborkis ----TCGTGCGTGGCACTGGTATA-ATGATGAATGGCGGGCTTGAACCGGGACT-ATT-CTCTTATAAAAGGCGGCAAGC Tropidia ----TCGTGCGTAGCACTGGTATAGATGATGAAAGGCGGGTTTGAACCGGGACCTATT-CTCTTATAAGAGGCGGCAAGC Epilyna ------Sertifera ----TCGTGCG----ACTGGTATAGATGATGAAAGGCGGGCTTGAACCGGGACCTATT-CTCTTATAAAAAGCGGCAAGC Elleanthus ???????????????????????????????????????????????????????????????????????????????? Sobralia ----TCGTGCG----ACTGGTATAGATGATGAAAGGCGGGCTTGAACCGGGACCTATT-CTCTTATAATAGGCGGCAAGC Diceratostele ----TCGG--G-GGCACTGGT-TA-ATGATGAAAGG--GGCTTGA-C-GG-ACTTATT--T---AT-ATA--AGGAAAG- Didymoplexis ----TCGT--GTGGCACTGGTATAGATGATGAA----GGGAATGTACCGG------TT-CT---ACA-TAGGCGGCAAGC Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium ------TTGGTCTAG------CTTGAA--GGGGCCTATT-CTCTGAT------Xerorchis ----TCGTGAGGA---A------T----AT------G--CCG-TATCTAAT-CTTTTATA-AAGGG--CAAGC Nervilia ------CTGGTATAAAT-ATGAAA---GGG-TTGAAC-GGGAC-TATT---TTTATAATA-GCGG-AAGC Triphora ----TCCT------AT------TGGG--TG--C-GGGACCTA-T-CTATTATAATAG-CGT----C Monophyllorchis ----TCGTGCGTGGCACTGGTATAGATGATGAAAGACAGG----A-CCGGGACCTATT-CTCTTATAATAGGCGGCAAGC Psilochilus ----TCGTGCGTGGCACTGGTATAGATGA-GAAAGGCAGGCTTGAAC-GGGACCTATT-CTCTTATAATAGGCGGCAAGC

398 Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso ----TCGTGCGTGGCACTGGTATAGATGATGAGAGGCGGGCTTGAACCGGGACCTATT-CTGTTATAA-AGGCGGCAAGC Chysis GGGGTCGTGCGTGGCACTGGTATAGATGATGAAAGGCGGGCTTGAACCGGGACCTATT-CTCTT--AA-AGGCGGCAAGC Gastrodia_sesamoides_534 ----TCGTGCGTGGCACTGGTATAGATGATGAAAGGCG---T----C-GGGACCTATT-CT--GAT------GGCAAGC gastrodia_sp_reunion_ER214 ------GCACTGGT-T-GA--ATGA-----G--CTT-AA--CTCACCT----CT--TC-AAAA-----CCTAC gastrodia_confusa_0801 ----TCGTGCGTGGCACTGGTATAGATGATGAAA------TT-AA-----TTCTAT--CT-TTCTAAATGGAGGCAAGC gastrodia_zyl_16313 ----TCGT--GTGGCACTGGTATAGATGATGAA-GG-T------AAAGGGCTTCTA---CTCTTCT-ATTGGCGGCAAGC

Codonorchis AAGAAGAGGAAAGGG------TTATGAGTGCCTTTTTAG--AAAAA------GGGTGGAATGTGGAGCTAACCTGGC Goodyera AAGAATAGGAAAGGGGGCGGCTGATGAGTGCCTTTTTAG--AAAAA------GGGTTGAATGTCGAGCTAACCTGGC Palmorchis AAGAATAGGAAAGGGGGCGGCTGATGA-TGCCTTTTTA--CATAAA-TAGAAAAAGGGTTGAATGTGGAGCTAACCTGGC Cephalanthera AATAATAGGAAAGGGGGCGGG-----AGTGCCTTTTTAGTCATAAA-TAGAAAAAGGGTGGAATGTGGAGCTAACCTGGC Aphyllorchis AA-----GGAAAGGGGG-GGGTGATG------TTTTTA-TCAGAAA--A-AAAAAGG-T--AATGTGGAGCTAACCTGGC Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis AATAATAGGAAAGGGGGCGGCTGATGAGTGCCTTTTTAGTCAGAAA-TAGAAAAAGGGTGGAATGTGGAGCTAACCTGGC Limodorum AATAATAGGAAAGGG--CGGGCG------CC------GAAAA--GGCTATGGGTG-AATGT----C-AA-ATCAC

Continued

Table B.1 Continued

Listera AATAATAGGAAAGGGGGCGGCTGATGAGTGCCTTTTTAGTCCTAAA-TAGAAAAAGGGTGGAATGTGGAGCTAACCTGGC Neottia AAGAATAGGAAAGGTTACGAA-G-TGAGTGCCC------GAAAA-GG----A------Corymborkis AAGAATAGGAAAGGGG-CGGYTGATGRA----TTTTTA-TCAAAAA-TAAAAAAAGGGTTGAATGKGGAG-TAACCTGGC Tropidia AAGAATAGGAAAGGGGGCGGCTGATGAGTGCCTTTTTAGTCAGAAA-GAGAAAAAGGGTTGAATGT----CTAACCTGGC Epilyna ------Sertifera AAG------Elleanthus ???????????????????????????????????????????????????????????????????????????????? Sobralia AAGAATAGGAAAGGGGGCGGCTGATGAGTGCCTTTTTAGTAAGAAA-GAGAAAAAGGGTTGAATGTGGAGCTAACCTGGC Diceratostele --G-CTAAGAAA------GCCTTTTTAGTCATAAAATAGAAAAAGGGTTGAATGTGGAGCTAACCTGGC Didymoplexis AAGAATAGGAAA------TG------GTC------GAAAAAGGGTGGAA------TGGC Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium ------GGT------TGGC Xerorchis ATGAGTGGGAAAACGCATTTCT-CC-AATGCGTTAGCAGT---AAA-TCGAACTCGG---GAA--TGGAGTT-----GGC Nervilia A--AA--G-AA-GGGG-TGG-TGATGA-TGC-TTTTTA-TA-TAAA-TAAAAAA-GGGTTGAATGTG-A--TAA--TGGT Triphora -AGA------GTGC-T----AGTCATAAA-GAGAAAAAGGGTGG--TGTGGAGCTCACCTGG- Monophyllorchis AAGAATAGGAAAGGGGGCGACTGATGAGTGCCTTTTTAGTCAGAAA-GAGAAAAAGGGTTGAATGTGGAGCTCACCTGGC Psilochilus AAGAATAGGAAAGGGGGCGACTGATGAGTGCG-----AGTCAGAAA-GAGAAAAAGG--CGAA-GTGG-----ACCTGGC Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? 399 Calypso AAGAGTAGGAAAGGGGGCGGCTGATGAGTGCCTTTKTAGTCATAAA-TAGAAAAAGGGTTGAATGTGGAGCTAACCTGGC Chysis AATAATAGGAAAGGGGGCGGCTGATGAGTGCCTTTTTAGTCCTAAA-TAGRAAAAGGGTGGAATGTGGAGCTAACCTGGC Gastrodia_sesamoides_534 AAGAATA------GC-TTCTGAGTCA------TGGTTGAATGTGGAGCTAACCTGGC gastrodia_sp_reunion_ER214 ------GGTGGAT-TAACCTGGA gastrodia_confusa_0801 AAGAATAG------C-TTCT-AGTCA------TGGTTGAATGTGGAGCTAACCTGGA gastrodia_zyl_16313 AAGAATAGGAAATGGAA------TCAAAAA------GGGTGGAA------TGGC

Codonorchis TACAAGTATAGCCAAAGAAAGA----CGGGACGGACTGTAAGAGGCCGCAGCGGGACGACCAGAGGAAAGCCCGCCCCCG Goodyera TACAAGTCTAGC-AAAGAAAGA----CGGGACGGACTGTAAGACGCCGCAGCGGGACGACCAGAGGAAA----GCCCCCG Palmorchis TACAA??????????????????????????????????????????????????????????????????????????? Cephalanthera TACAAGTATAGCCAAAGAAAGAGAGACGGGACGGACTTTCAGAGGCCGCAGCGGGACGACCAGAGGAAAGCCCGCCCCCG Aphyllorchis TACAAGTATAGCCAAAGAAAGAGAGACGGGACGGACTTTCAGAGGCCGCAGCGGGACGACCAGAGGAAAGCCCGCCCCCG Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis TACAAGTATAGCCAAAGAAAGAGAGACGGGACGGACTTTCAGAGGCCGCAGCGGGACGACCAGAGGAAAGCCCGCCCCCG Limodorum TTGGTCTCGACTGAAAG-----GAGAGGTGA-----T------GAAAG------Listera TACAAGTATAGCCAAAGAAAGAGAGACGGGACGGACTTTCAGAGGCCGCAGCGGGACGACCAGAGGAAAGCCCGCCCCCG Neottia ------Corymborkis TMCAA------AAAGAAAGAGAGATGGGACGGACTGTCAGAGGCCGCAGCGGGACGACCA------

Continued

Table B.1 Continued

Tropidia TACAAGTATAGCCAAAGAAAGAGAGACGGGACGGACTGTCAGAGGCCGCAGCGAGACGACCA------Epilyna ------Sertifera ------Elleanthus ???????????????????????????????????????????????????????????????????????????????? Sobralia TACAAGTATAGCCAAAGAAAGAGAGACGGGACGGACTGTCAGAGGCCGCAGCGGGACGACCAGAGGAAAGCCCGCCCCCG Diceratostele TACAAGTATAGCCAAAGAAAGAGAGACGGGACGGACTGTCAGAGGCCGCAGCGGGACGACCAGAGGAAAGCCCGCCCCCG Didymoplexis TACAAGTATAGCCAAAGAAAGAGA------CGGGACGACC------Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium -ACA------Xerorchis TTC--GT------GAAAAACACAA-GG--TTT------CCG-AGC---A-GACCACAGCGAGA------Nervilia ------Triphora TACAAGTATA-CCA------GAGACGGGACGGAC-----GAGGCC-----GGGACGACCAGAGGAAAGCCCGCCCCCG Monophyllorchis TACAAGTATAGCAAAAGAAAGAGAGACGGGACGGACTGTCAGAGGCCGCAGCGGGACGACCAGAGGAAAGCCCGCCCCCG Psilochilus TACAAGTATAGCCAAAGAAAGAGAGACGGGACGGA----AAGAGGCT--AGTGGC-CGACCATAGGAAAGCCCGCCCCCG Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso TACAAGTATAGCCAAAGAAAGAGAGACGGGACGGACTGTGAGAGGCCGCAGCGGGACGACCAGAGGAAAGCCCGCCCCCG Chysis TACAAGTATAGCCAAAGAAAGAGAGACGGGACGGACTTTCAGAGGCCGCAGCGGGACGACCAGAGGRAAGCCCGCCMCCG Gastrodia_sesamoides_534 TACTTGTA--GCCAAAGAAAGG------TGTTATAGGCCGCAGCGGCACGACCAGAGGA--GCCCGCTC--- 400 gastrodia_sp_reunion_ER214 -GCCA-TCTAGCCAAAGAAAGAGAGACGG------gastrodia_confusa_0801 -GCCA-TCTAGCCAAAGAAAGAGAGACGG------gastrodia_zyl_16313 TACAAGTATAGCCAA-GAAAGA-AGACGGGAC------GACCA------

Codonorchis CTAGCTAACATAGTATTCTCGGTGCGCATATTCTAGATTGAGAATAGATTACCGACCAGGCCAGGCCGAATCGGGCCACC Goodyera CTAGCTAACATAGTATTCTCGGTGCGCATATTCTCTCTGTAGAATCTATTCCCGACCAGGCCAGGCCGAATCGGGCCACC Palmorchis ???????????????????????????????????????????????????????????????????????????????? Cephalanthera CTAGCTAACATATTATTCTCGGTGCGCATATTCTCTCTTTAGAATCTATTCCCGACCAGACCAGGCCGAATCGG-CCACC Aphyllorchis CTAGCTAACATATTATTCTCGGTGCGCATATTCTCTCTTTAGAATCTATTCCCGACCAGACCAGGCCGAATCGGGCCACC Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis CTAGC------AG-ATTCTCGGTGCGCATATTCTCTCTTTAGAATCTATTCCCGACCAGACCAGGCCGAATCGGGCCACC Limodorum --A------Listera CTAGCTCACATATTATTCTCGGTGCGCATATTCTCTCTTTAGAATCTATTCCCGACCAGACCAGGCCGAATCGGGCCAC- Neottia ------Corymborkis ------Tropidia ------Epilyna ------Sertifera ------Elleanthus ????????????????????????????????????????????????????????????????????????????????

Continued

Table B.1 Continued

Sobralia CTAGCTAACATAGGATTCTCGG----CATATTCTCTCTTTAGAATCTATTCCCGACCAGGCCAGGCCGAATCGGGCCACC Diceratostele CTAGCTAACATAG--TTCTCGGTGCGCATATTCTCTCTTAAGAATAGATTCCCGACCAGGCCAGGCCGAATCGGGCCACC Didymoplexis C-AGCTCACATAGGATTCTCGG----CATATTCTCTATTTCGAATAGATTCCCGACCAGGCCAGGC------GG-CCGCC Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium ---GC-A-CAT--G-TT--CGG------ACC Xerorchis CTA-CT------G----CTCCG------CT--CTTT------Nervilia ------Triphora CTATCTAACATAGGA------GTGCGC---TT-TCT-----GAA--GA------CAGGCCGAATCGGGTCAC- Monophyllorchis YTAGCTAACATAGGATTCTCGGTGCGCATATTCTCTATTTAGAAT------CAGGCCAGGCCGAATCGGGCCACC Psilochilus CTAGCTAACATATGATTCTCGG----CAGATTCTCTATTCAGAA--GA------GGCCAGGCCGAATCGGGCCACC Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso CTAGCTAACATAG--TTCTCGGTGCGCATATTCTCTCTTTAGAATCTATTCCCGACCAGGCCAGGCCGAATCGGGCCACC Chysis ATAGCTYACATAT--TTCTCGGTGCGCATWTT-TCTCTTTAGA-TCTATTCCCGACCAGGCCAGGCCGAATCGGGCCACC Gastrodia_sesamoides_534 --A-CTCACATAGGATTCTCGG----CATATTCTCTCTTTAGAATAGATTACCGACCAGGCCAGGCCGAATC-----ACC gastrodia_sp_reunion_ER214 ------CCGAC------gastrodia_confusa_0801 ----CTAAC------GAACC------GG--A---CGA------gastrodia_zyl_16313 ----CTCACAT-GGATTCTCGG----CATATTCTCTATTT------401

Codonorchis ACTTGGGATGGGAATGGCTCAGCCCACATGCATCATTTGATGAAAGCATTCCAGTCGCCTCCGATCAGTGGCTTGTCAAC Goodyera ACTTGGGATGGGAATGGCTCAGCCCACATGCATCATTTGATGRAAGCATTCCAGTCGCCTCCGATCAGTGGCTTGTCAAC Palmorchis ???????ATGGGAAGGGTCCAGCCCCCCTGCCTCATTTGCGGAAA-CTTTCCAGT-GC-TTCGATCAGT-GCTTGTCAAA Cephalanthera ACTTGGGATGGGAATGGCTCAGCCCACATGCATCATTTGAGGAAAGCATTCCAGTCGCCTCCGATCAGTGGCTTGTCAAC Aphyllorchis ACTTGGGATGGGAATGGCTCAGCCCACATGCATCATTTGAGGAAAGCATTCCAGTCGCCTCCGATCAGTGGCTTGTCAAC Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis ACTTGGGATGGGAATGGCTCAGCCCACATGCATCATTTGAGGAAAGCATTCCAGTCGCCTCCGATCAGTGGCTTGTCAAC Limodorum ------TGCT--CACTATAGA-GAGATG-ATC-TTTCTT-AAAGGA------Listera ----GG-ATGGGAATGGCTCAGCCCACATGCATCATTTGAGGAAAGCATTCCAGTCGCCTCCGATCAGTGTCTTGTCAAC Neottia ------Corymborkis -CTTGGGATGGGGATGGCTCAGCTCACATGCATCATTTGATGAAAGCATTCCAGTCGCCTCCGATCAGTGGCTTGTCAAC Tropidia -CTTGGGATGGGGATGGCTCAGCCCACATGCATCATTTGATGAAAGCATTCCAGTCGCCTCCGATCAGTGGCTTGTCAAC Epilyna ------GA-GG-TC------CATGCATCATT--A-GAAA-C-TTTCAGT-G-CT--GATCAG-GG-TT-TC-AC Sertifera ------AATTTGATGAAAGCATTCCAGTCGCCTCCGATCAGTGGCTTGTAAAC Elleanthus ???????????????????????????????????????????????????????????????????????????????? Sobralia ACTTGGGATGGGGATGGCTCA-----CATGCATCATTTGATGAAAGCATTCCAGTCCCCTCCGATCAGTGGCTTGTCAAC Diceratostele ACTTGGGATGGGGATGGCTCAGCCCACATGCATCATTTGATGAAAGCATTCCAGTCGCCTCCGATCAGTGGCTTGTCAAC

Continued

Table B.1 Continued

Didymoplexis ACTTGGGATGGGGATGGCTCAGCCCACATGCATCATTTGATGAT-G-AATCCA---GC--CC------GCTTGTCAAC Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium A------CA-CCCACA-GGATC-GA-GATGG------AG-C------AAC Xerorchis ------CGCG------C--GTC--- Nervilia ------Triphora ----AG-ATCGG-ATT------CCCACATGCATCATTTGATGAAAGCATTCCAGTCGCCTCTGATCAGTGGCTTGTCAAC Monophyllorchis ACTTGGGATGGGGATGGCTCAGCCCACATGCATCATTTGATTCAAGCATTCCAGTCGCCTCCGG--AGTGGTTTA-CAAA Psilochilus GCTTGGGATGGGGATGGCTCAGCCCACATGCATCATTTGATGAAATCATTCCA--CGTCTCCGATCAGTGGCTTGTCAAC Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso ACTTGG-ATGGGGATGGCTCAGCCCACATGCATCATTTGATGAAAGCATTCCAGTCGCCTCCGATCAGTGGCTTGTCAAC Chysis ACCT?GGATGGGGATGGCTCAGCCCACATGCATCATTTGATGAAAGCATTCCAGTCGCCTCCGATCAGTGGCTTGTCAAC Gastrodia_sesamoides_534 ACTTGGG------GCTCAGCCCACATGCATCATTT------T-CC-AGTC------GATCAGTGGCTTGTAAAC gastrodia_sp_reunion_ER214 ------gastrodia_confusa_0801 ------gastrodia_zyl_16313 ------

402 Codonorchis CACCGGACCGTAGCTC------GG------AAACACAGCGCAT-----GAGTAGTTCGTTCAAGGACCA Goodyera CACCGGACCGTAGCTCCTCACAAAATGCCC--GG------AAACACAGCGCAT-----GAGTAG------GACCA Palmorchis CACCGGATGGTAGCTCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACAT-----GAGTAGTTCGTTCAAGGACCA Cephalanthera CACCGGACCGTAGCTCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACATCACATGAATAGTTCGTTCAAGGACCA Aphyllorchis CACCGGACCGTAGCTCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACATCACATGAATAGTTCGTTCAAGGACCA Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis CACCGGACCGTAGCTCCTCACCAAATGCCC--GGG------AAACACAGCAC-T-----GAATAGTTCGTTCAAGGACCA Limodorum ------AGCGTGAAGCACTTGATATCATA------TATCA-AGG-CGT-----GA-TTCTTC-TTAAAGGA--- Listera CACCGGACCGTAGCTCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACATCACATGRATAGTTCGTTCA??????? Neottia ------Corymborkis CACCGGACGGTAGCTCCTCACCAAATGCGCTTGGGTTGGGGAAACACACCACAT-----GAGTAGTTCGTTCAAGGACCA Tropidia CACCGGACCGTAGCTCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACAT-----GAGTAGTTCGTTCAAGGACCA Epilyna CA-CGG---GTAG-T-CTC-CCAA-T-CC--TGGG---GGGAACCACA-C------G-GT-GT---TTCA-GG-CC- Sertifera CACCGGACCGTAGCTACTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACAT-----GAGTAGTTCGTTCAAGGACCA Elleanthus ???????????????????????????????????????????????????????????????????????????????? Sobralia C------Diceratostele CACCGGACCGTAGCTCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACAT-----GAGTAGTTCGTTCAAGGACCA Didymoplexis CACCGGAC------GGTTGGGGAAACACAGCGCAT-----GAGTAGTTCGTGAAAGGACCA Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium C------TAG------ACC------Xerorchis ------GGG------CAT------C--TCCACGTGAA Nervilia ------Continued

Table B.1 Continued

Triphora CACCGGACGG-ACCGCCTCACCAAATGCC----GGTTGG------AC----CAT-----GAGTAGTTCGTTCAAGGACCA Monophyllorchis --CC--ACG-CCGCTCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCGCAT-----GAGTAGTTCGTTCAAGGACCA Psilochilus CACCGGACCGTAGCTCCTCACCAAATGCGCTTGGGTTGGGGAAAGACAGCACAT-----GAGTAGTTCGTTCAAGGACCA Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso CACCGGACCGTAGCTCCTCACAAAATGCCCTTGGGTTGGGGAAACACAGCACAT-----GAGTAGTTCGTTCAAGGACCA Chysis CACSGGACCGTAGCCCCTCACCAAATGCCCTTGGGTTGGGGAAACACAGCACAT-----GAGTAGTYCGTTCAAGGACCA Gastrodia_sesamoides_534 C-----ACCGTAGCTCCTCACCAAAAGCCC----G-TAGG------CAGCACAT-----GAGTAGTTCGTGAAAG----- gastrodia_sp_reunion_ER214 ------gastrodia_confusa_0801 ------gastrodia_zyl_16313 ------

Codonorchis CACCCTTTC---GAGAGCAGGATGCTGGCCGAGATGGAGCTGGGATAAAA------CGCGCCTT-GG-TT-----GCCCC Goodyera CAACC------AGAGCAGGATGCTGGCCGAGATGGAGC-GGGATAAAA-CG---CGCGCCTTGCGCTTGCCTTGCCCC Palmorchis CACCCTCTC---GAGAGCAGGATGCTGGCCGAGATGGAGCTGGGAGTCAACCTATACTTTCCTTGGGCTTGCCTTGCCCC 403 Cephalanthera CACCCTCTC---GAGAGCAGGATGCTGGCCGAGATGGAGCTGGGAGCCAACCTAGACTTTCCTTGGGCTTGCCTTGCCCC Aphyllorchis CACCCTCTC---GAGAGCAGGATGCTGGCCGAGATGGAGCTGGGAGCCAACCTATACTTTCCTTGGGCTTGCCTTGCCCC Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis CACCCTCCC---GAGAGCAGGATGCTGGCCGAGATGGAGCTGGGAGCCAACCTAGACTTTCCTTGGGCTTGCCTTGCCCC Limodorum ------AGG------CG---TG------AA---A------CTT------CTG---- Listera ???CCYCYC---GAGAGCAGGATGCTGGCCGAGATGGAGCTGGGAGCCAACCTAGACTTTCCTTGGGCTTGCCTTGCCCC Neottia ------Corymborkis CACCCTCTC---GAGAGCAGGATGCTGGCCGAGATGGAGCTGGAAGCCAACCTAGACTTTCCTTGGGCTTGCCTTGCCCC Tropidia CACCCTCTC---GAGAGCAGGATGCTGGCCGAGATGGAGCTGGGAGCCAACCTAGACTTTCCTTGGGCTTGCCTTGCCCC Epilyna ---CCTTT----GAGA-C--GAT--T-GC-GAGA--GAG-TGGGA-CCA--CTAGACTTT-CTT-CG-TCGCCT--CCCC Sertifera CACCCA--C---GA-AGCAGGATGCTGGCCGAGATGGAGCTGGGAGCCAACCTA-ACTTTCCTT-CGCT------Elleanthus ???????????????????????????????????????????????????????????????????????????????? Sobralia ------Diceratostele CACCCTCTC---GAGAGCAGGATGCTGGCCGAGATGGAGCTGGGAGCCAACCTAGACTTTCCTTGGGCTTGCCTTGCCCC Didymoplexis CACCCTCTC---GAGAGCAGGATGCTGGCCGAGATGGAGCTGGGAGCCAACCTATACTTTCCTT------GCCCC Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium ------CC---CCAC Xerorchis TA---TTTG---TGGCACCGCATCATA-CC------AG-T--GA-CAAA--T------Nervilia ------Triphora CACC------GCAGGATGCTGGCCGAGA------TGAGCCAACCTAGAATT-----GGGC-----TTGCCCC Monophyllorchis CACC------GCAGGATG----CCGAGATGGAGCTGGGAGCCCAC-TAGACTTTCCTTGGGCTTGCCTTGCCCC Psilochilus CACC------GCA-GATGCTGGCCGAGATGGAGCTGGGAGCCCA-CTAGACTTTC---GG-CTTGCCTTGCCCC Wullschlaegelia ????????????????????????????????????????????????????????????????????????????????

Continued

Table B.1 Continued

Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso CACCCTCTCGA---GAGCAGGATGCTGGCCGAGATGGAGCTGGGAGCCAACCTAGACTTTCCTTGGGCTTGCCTTGCCCC Chysis CACCCTCTCGAGGAGAGCAGGATGCTGGCCGAGATGGAGCTGGGAGCCAACCTATACTTSCCTTGGGCTTGCCTTGCCCC Gastrodia_sesamoides_534 ---CCTCTC---GAAA------TGCTGGCCGAGATGGAGCTGGGAGCCAACCTATACTT-CCTTGGGCTTGCCTTGCCCC gastrodia_sp_reunion_ER214 ------gastrodia_confusa_0801 ------gastrodia_zyl_16313 ------

Codonorchis ACCATCTA-ATCAAGGGCGGGCGCCGAAAAGGAAAGGAACCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGC Goodyera ACCATCAA-ATCAA------GGAA------CCATTTCGACGAAAGCTTAGCTTGGTAGGCGC Palmorchis CCCATCTAAATAAAGGGCGGGTGCCGAAAAGGAA-----CCAGTGACGCCTTTTCAACGAAAGCTTAGCTTGGTAGGCGC Cephalanthera ACCATCTAAATAAAGGGCTTA-GCCGAAAAGGAA-----CCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGC Aphyllorchis ACCATCTAAAGAAA-----GG-GCCGAAAAGGAA-----CCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGC Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis AC------AAAGGGCGGGCGCCGAAAAGGAA-----CCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGC Limodorum -----CTAAGTAA---G-TT------AAGGAAAGGAACCAGTGACGCCTTTTCGACGAAAGCTTAGCTTG-TAGGCGC 404 Listera ACCATCTAAATAAAGGGCTAA-GSCGAAAAGGA------GACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGC Neottia ------GAC---T---CGACGAAAGCTTAGCTTGGTAGGCGC Corymborkis ACCATATAAATA------G-CT--AAAAAAAGGAACCA------CTTGGTAGGCGC Tropidia ACCATCTAAATAAAGGGCGGG---CGAAAAGGAA-----CCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGC Epilyna -C-AT-TAAAGAAAGGGCGGGCGC-GAAAAGGAAAGGAACCAGTGACGCCTTTTCGACGAAAG-TTAGCT-GGTAGGCG- Sertifera ------CCGCGG---CCAAAAAGGAAAGGAACC------TTTTC-AC-AA-GCTTA-CTTGGTAG-CGC Elleanthus ???????????????????????????????????????????????????????????????????????????????? Sobralia ------Diceratostele ACCATCTAAAGAAAGGGCGGGCT--GAAAAGGAA-CGAACCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGC Didymoplexis ACCA-CT---GAAAGGG------CAAA-GGA------TT--CGACG------TTGGTAGGCGC Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium ACCATCTCAAGAAAGG------GTT-CGCCTTTT------Xerorchis ------Nervilia ------Triphora ACC------GAA------GAAAA------AACCATTGA----TT------A----TTAGCTTGGTAGGCGC Monophyllorchis ACCATCTAAAGAAA------GCCGAAAA-----GAAACCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGC Psilochilus ACCATCTCAAGATA------GAAAA------CC-----CGCCTTTT----GAAAGCTTAGCT-GGTAGGCGC Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso ACCATCTAAATAAAGGGCGGGCGCCGAAAA-----GGAACCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGC Chysis ACCATATAAATAAAGGGCGGGCGCCGAAAA-----GGAACCAGTGACGCCTTTTCGACGAAAGCTTAGCTTGGTAGGCGC Gastrodia_sesamoides_534 AC----T-AAGAAAGGGCGGGCTC-AA---GGAA------CCCTTTTCGACTGGGCTTGGTATTGGTAGGCGC Continued

Table B.1 Continued

gastrodia_sp_reunion_ER214 ------TGG----CGC gastrodia_confusa_0801 ------TGG----CGC gastrodia_zyl_16313 ------

Codonorchis TGCTTACTCACCCTATTCCCTCATACAATGCCCTGAA--CACTCAA------TT-----CCATTTTCCCAT------Goodyera TGCTTACTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAA------TGAATCCCCCTTTTCCCATGCGGAGT Palmorchis TGCTTACTCACC------TCAGACAATGCCCTGAA--CACGAAAGTTTGCAGTTCAGCCCCCTTTTCCCATGCGGAGT Cephalanthera TGCTTACTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAAGTTTGCAGTTCAGCCCCCTTTTCCCATGCGGAGT Aphyllorchis TGCTTACTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAAGTTTGCAGTTCAGCCCCCTTTTCCCATGCGGAGT Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis TGCTTACTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAA------TTTCCCCATGCGGAGT Limodorum TGCTTACTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAAGTTTGCAGTTAAGCCCCCTTTTCCCATGCGGAGT Listera TGCTTACTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAAGTTTGCAGTTCAGCCCCCTTTTCCCATGCGGAGT Neottia TGCTTACTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAAGTTTGCAGTTCAGCCCGCTTTTCCCATGCGGAGT Corymborkis TGCTTACTCACCCTATTCCTTCAGACAATGCCCT------CGAAAGTTTGCTGTTCCGCCCCCTTTTCCCATGCGGAGT Tropidia TGCTTACTGACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAAGTTTGCAGTTCCGCCCCCTTTTCCCATGCGGAGT Epilyna -GCTTACTCACCCTATTCCCT--GACAATGCCCTGAA--CA-GAAAGTTTGCAGTTCTGCCCCCTTTTCCCATGCGGAGT 405 Sertifera TGCTTACTC-CCCTATTCCCTCA-ACAATGCCCTGAA--CAC--AAGTGT----TTCC-CCCCCTTTTCC-ATGCAGAG- Elleanthus ???????????????????????????????????????????????????????????????????????????????? Sobralia ------Diceratostele TGCTTACTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAAGTTTGCAGTTCCGCCCCCTTTTCCCATGCGGAGT Didymoplexis TGCTTTGTCACCCC-GGCC---ATACAATGCCCC-AA---A-GAA-GTT-G-A------CCTTTTCCCATGCGGAGT Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium ------GAC------GAAA------GTTCACTCACCTATTCCA------Xerorchis ------TTT-CC------TTG Nervilia ------Triphora T-----CTCACCCTATTCCCTCAGAGAATGCCCTGAA--CACGAGACT----AGTTTCG------Monophyllorchis TGCTTACTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAAGTTTGCAGTTCCGC-CCCT---CC-ATGCGGAGT Psilochilus TGCTGACTCACC-TATTCC-TCAGACAATGCCCTGAA--CACGAAAGTTTGCAGTTCCGC-CCCTTT-CCCATGCGGAGT Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso TGCTTACTCACCCTATTCCCTCAGACAATGCCCTGAACTCACGAAAGTTTGCAGTTCCGCCCCCTTTTCCCATGCGGAGT Chysis TGCTTACTCACCCTATTCCCTCAGACAATGCCCTGAACTCACGAAAGTTTGCAGTTCCGCCCCCTTTTCCCATGCGGAGT Gastrodia_sesamoides_534 TGCTTACTCACCCTATTCCCTCAGACAATGCCCTGAA--CACGAAAGTGTGAAG-TCTCTC------gastrodia_sp_reunion_ER214 T------GGC-----GAAAA-----AGAA--CAAGAG------TT-CGC-CCC------G--- gastrodia_confusa_0801 ------GGCC-TC--AAAA-----AGAA--CAAGAG------TT-CGC-CCCCCCT------CGGA-- gastrodia_zyl_16313 ------Continued

Table B.1 Continued

Codonorchis ------GCCTCGGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCG Goodyera CACAGGCAGCGCCTCGGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCG Palmorchis CACAGGCAGCGCCTCGGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCATGGGTGGTTCTGGCCGGGGACCCCG Cephalanthera CACAGGNAGCGCCTCGGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCG Aphyllorchis CACAGGCAGCGCCTCGGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCG Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis CACAGGCAGCGCCTCGGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCSGGGCACCCSG Limodorum CACATGCAGCGCCTCGG-AAAAAGCACGGACGAGCCACATGCAGG-TGTGGAGCCTGTGTGTTTCTGGCCGGGGAC-CCG Listera CACAGGCAGCGCCTCGGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCG Neottia CACAGGCAGCGCCTCGGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCG Corymborkis CCCAGGCAGCGCCTCGGAAAAAAGCACGGACGACCCACATGCAGGGAAACTTGCACGGGTGGTTCTGGCCGG-----CCG Tropidia SACAGGCAGCGCCTCGGAAAAA-GCAYGGACGAGCGACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCG Epilyna CACAGGCAGCGCCTCGGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCGGGGGTGGTT-TGGCCGGGGACCCCG Sertifera ------Elleanthus ???????????????????????????????????????????????????????????????????????????????? Sobralia ------Diceratostele CACAGG----GCCTCGGAAAG--GCA-TTACGATC-ACA-GCAGGGAATGATTT-CTTATAG-TAACAATCAGTACCCCG Didymoplexis GACAG-----GCCTCGTAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCG Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? 406 Epipogium ------CCTCAGAAAAT-GCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCG Xerorchis T--CA-----GCCAKGCTGTAAAGCACGGACGAGCCACATGCAGGGAAACTCGCACGTGTGGTTCTGGCTGGGGACCCCG Nervilia ------Triphora ----GGCAGCGC----GAA----GCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCG Monophyllorchis CACAGGCAGCGCCTCGGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCG Psilochilus CACAG-CAGCGC----GAAAGAA-CACGG-CGA-CCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCG Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso CAAAGGCAGCGCCTCGGAAANNNN-ACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACSCCG Chysis CACAGGCAGCGCCTCGGAAAAAAGCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCG Gastrodia_sesamoides_534 ----GCKTTCGCCTCGTCAAAAAB-ACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCG gastrodia_sp_reunion_ER214 ------AAAAAAGCACGGACGAGCCACATGCGGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCG gastrodia_confusa_0801 ------GCCTCGGAAAAA-GCACGGACGAGCCACATGCGGGGAAACTTGCACGTGTGGTTCTGGCCGGGGACCCCG gastrodia_zyl_16313 ------

Codonorchis GTATACTGTACTAATATGTGTAGGTCCCTGTAATTCGAG-GAGATTGTCATGGCGCAAAAGCAGA000000100000000 Goodyera GTATACTGTACTAATATGTGTAGGTCCCTGTAATTCGAG-GAGATTGTCATGGCGCAAAAGCAGA000000000000000 Palmorchis GTATACTGTACTAATAT------000000000000000 Continued

Cephalanthera GTATACTGTACTAATATGTGTAGGTCCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAAGCAGA000000000000000 Aphyllorchis GTATACTGTACTAATATGTGTAGGTCCCAGTAATTCGAGC-AGATTGTCATGGCGCAAAAGCAGA??????????????? Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis GTATACTGTACTAATATGTGTAGGTCCCTGTAATTCGAGTGAGATTGTCATGGCGCRCAAGCAGA000000000000000 Limodorum GCAGGA--TCCGAATAGGGGTAGG------A---GA-TG---TTG-CATGCCACAAAAGCAGA000000000000000 Listera GTATACTGTACTAATATGTGTAGGTCCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAAGCAGA000000000000000 Neottia GTCTACTGTACTAATATGTGTAGGTCCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAAGCAGA000000000000000 Corymborkis GTATACTGTACTAATATGTGTAGGTCCCTGTAATTCGAGTCTGATTGTCATGGCG------??????????????? Tropidia GTCTACTGTACTAATATGTGTAGGTCCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAAGCAGA100000000000000 Epilyna GTATACTGTA-TAATATGTGTAGGTCCCTGTAATTCGAGCATGATTG-CA-GGCGCAAAAGCAGA??????????????? Sertifera ------000000100010000 Elleanthus ???????????????????????????????????????????????????????????????????????????????? Sobralia ------??????????????? Diceratostele GATTACTG-A-TAA--TTAACAGGAACCTGTAATATGAGTGAGAT-GTCATAGCACAAA-GCACA000000000000000 Didymoplexis GTATACTGTACTAATATGTGTAGGTCCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAAGCAGA000000000000000 Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium GTATACTGTACTAATATGTGTAGGTCCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAAGCAGA000000000000000 Xerorchis GTATACTGTACTAATATGTGTAGGTCCCCGTAATTCGAGTGGGATTGTCATGGCGCAAAAGCAGA00?1?0?00000000 Nervilia ------010000100000000 Triphora GTCTACTGTACTAATATGTGTAGGTCCCTGTAATTCGA-TGAGATTGTCATGGCGCAAAAGCAGA000000?1??00000

407 Monophyllorchis GTATACTGTACTAATATGTGTAGGTCCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAAGCAGA000000000000000 Psilochilus GT-TACTGTA-TAATATG-GTAGGTCCCTGTAA------000000100000000 Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso GTATACTGTACTAATATGTGTAGGTCCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAAGCAGA000000000000000 Chysis GTATACTGTACTAATATGTGTAGGTCCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAAGCAGA000000000000000 Gastrodia_sesamoides_534 GTATACTGTACTAATATGTGTAGGTCCCTGTAATTCGAGTGAGATTGTCATGGCGCAAAAGCAGA000000000000000 gastrodia_sp_reunion_ER214 GTATACTGTACTAATATGTGTAGGTCCCTGTAATTCGAGTGAAA-TGTCATGGCGCAAAAGCAGA??????????00000 gastrodia_confusa_0801 GTATACTGTACTAATATGTGTAGGTCCCTGTAATTCGAGTGAAATTGTCATGGCGCAAAAGCAGA000001????00000 gastrodia_zyl_16313 ------000000000000000

Codonorchis 0000000000000000000000000000000000001???0?????000000000000000000100??00000100000 Goodyera 0000000000000000000000000000000000001???0?????000000000000000000100??00000100000 Palmorchis 0000000000000000000000000000000000000000000000000000000000000000100??00000100000 Cephalanthera 00000000000000000000000000000000000000000000000000000000000000000000100000100000 Aphyllorchis 0???????????0101001000010000000000000000000010000000000000000000100??00000100000 Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis 00000000000000000000000000000000000000010??0000000000000000000000000100000100000 Continued

Table B.1 Continued

Limodorum 00000000000000000000000000000000000000000000000000000000000000000000100000100000 Listera 00000000000000000000000000000000000000000000000000000100000000000000100000100000 Neottia 0000000000000000000000000000000000000000000010100000001?????00000000100000100000 Corymborkis 00000000000000000000000000000000000000000000000000000000000000100001?00000100000 Tropidia 0000000000000000000000000000000000000000000000000000000000000000100??00000100000 Epilyna ???????????????????????????????????????????????????????????????????????????????? Sertifera 0000000000000000000000000000000000000000000000000010000000000000100??00100100000 Elleanthus ???????????????????????????????????????????????????????????????????????????????? Sobralia ???????????????????????????????????????????????????????????????????????????????? Diceratostele 0000010000100000000000000100000000000000000000000000000000000000100??00000100000 Didymoplexis 00000??1???00000000000000000000000000000000000000000000000000000100??0000010000? Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium 0000000000000000000000000000000000000000000000000000000000000000100??00000100000 Xerorchis 0000000000000000000000001?000100010000000001000000??1??????????0?00??00000100000 Nervilia 0000000000000000000000000000000000000000000000000000000000010000?10???0000100000 Triphora 00000000000000000000001?000000010?000?10000000000000000000000000100??00000100000 Monophyllorchis 00000000000000000000000000???????0000000000000000000000000000000100??00000100000 Psilochilus 000000000000000000010000001?????0?0001000000000000000001?0000000100??000?1???000

408 Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso 0000000000000000000000000000000000000000001000000000000000000000100??00000100000 Chysis 0000000000000000000000000000000000000000000000000000000000000000100??00000100000 Gastrodia_sesamoides_534 0000000001?000000000000000000000000000000000000000000000000000?1??????0000100000 gastrodia_sp_reunion_ER214 00000000000000000000000000000000000000000000000000?10?0?????00000000100000100000 gastrodia_confusa_0801 00000000101000000000010001000000000000000000000000000000000000?1??????0000100000 gastrodia_zyl_16313 00000??1???00000000000000000000000000000000000000000000000000000100??0000010000?

Codonorchis 00000000000000000000000000000000000000000000000000000010000000000000000?10000000 Goodyera 00000000000000000000000000000000000000000000000000000010000000000000000?10000000 Palmorchis 00000000000000000000000000000000000000000000000000000010000000000000000?10000000 Cephalanthera 00000000000000000000000000000000000000000000000000000010000000000000000?10000000 Aphyllorchis 00000000000000000000000000000000000000000000000000000010000000000000000?10000000 Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis 00010000000000000000000000000000000000000000000000000010000000000000000?10000000 Limodorum 00?00000100110000000010000100000000000010010000000000010000000000000000?10000001 Listera 00000000000000000000000000000000000000000000000000000010000000000000000?10000000 Continued

Table B.1 Continued

Neottia 00000000000000000000000000000000000000000000000000000010000000000000000?10000000 Corymborkis 00000000000000000000000000000000000000000000000000000010000000000000000?10000000 Tropidia 00000000000000000000000000000000000000000000000000000010000000000000000?10000000 Epilyna ???????????????????????????????????????????????????????????????????????????????? Sertifera 00000000000000000000000000000000000000000000000000000010000000000000000?10000000 Elleanthus ???????????????????????????????????????????????????????????????????????????????? Sobralia ??0????????????????????????????????????????????????????????????????????????????? Diceratostele 00000000000000000000000000000000000000000000000000000010000000000000000?10000000 Didymoplexis 1?0?00?000000000000000000000000000?1????0???0000000??1??????00000100000000?100?0 Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium 000?10?0?00000000000000000000000000000000000?1????0?????????00000000000100001??? Xerorchis 000000000000000000000000000000010?00?10?000100?10?0??0?0000000000000000?10000000 Nervilia 00000000000000000000000000000000000000000000000000000010000000000000000?10000000 Triphora 00000000000000000000000001?1000?1?00100?01??00100?0000001?00000?1?10010??00001?? Monophyllorchis 000000000000000000000000000001??0?000000000010?00?00001000000?1????0000?10000000 Psilochilus 00000001???00000000000001000000000000000000010?00?000010000000000000000?10000010 Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso 00000000000000000000000000000000000000000000000001000010000000000000000?10000000 409 Chysis 00000000000000000000000000000000000000000000000001000010000000000000000?10000000 Gastrodia_sesamoides_534 00000010?100?10000000000000000000000??1?0???10?00?0000?1????00000000100000000000 gastrodia_sp_reunion_ER214 000000000000000000000000000000000000000000000000000100?000??1???????????????0??? gastrodia_confusa_0801 000001???????00000000001???000000000000000000000000?10?0000000010001?00001??0??? gastrodia_zyl_16313 1?0?00?000000000000000000000000000?1????0???0000000?10?000?100000000000000100001

Codonorchis 00000000000000000000000000000000000000?10000000000000000010000000000000000000000 Goodyera 00000000000000000000000000000000000000?10000000000000000010000000000000000000000 Palmorchis 00000000000000000000000000000000000000?10000000000000000010000000000000000000000 Cephalanthera 000000000100000000?10?0000000000000000?10000000000000000010000000000000000000000 Aphyllorchis 000000000000000000000000000000000000?1??0000000000000000010000000000000000000000 Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis 00000000000000000000000000000000000000?10000000000000000010000000000000000000000 Limodorum ?00010???000000000??1??000000010000000?100?000?0???????????????????????????????? Listera 00000000000000000000000000000000000000?1000000000000000000000000000000000??1???? Neottia 0000000000000000?1?00?1000000000000000?1000000000000000000000000000000000??1???? Corymborkis 00000000000000000000000000000000000000?10000000000000000010000000000000000000000 Tropidia 00000000000000000000000000000000000000?10000000000000000010000000000000000000000 Epilyna ???????????????????????????????????????????????????????????????????????????????? Sertifera 00000000000000000000000000000000000000?1010???0?0000000001000000000000000000?10?

Continued

Table B.1 Continued

Elleanthus ???????????????????????????????????????????????????????????????????????????????? Sobralia ???????????????????????????????????????????????????????????????????????????0???? Diceratostele 000000000000000000?10?0000000000000000?10000000000000000010000000000000000000001 Didymoplexis 000000001000000000000000000000000000001000001000000000000??1?0000010?00000000000 Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium ?00000000000000000?10?001????????0001000000000000000010?0?0001?00??0????00000000 Xerorchis 010?00?1?00000101000000000010000000000??100??00110101?0?0?0000100?00000010000000 Nervilia 00000000000000000000000000000000000000?10000000000000000010000000000000000000000 Triphora ?00101???????00000100?01000001?0001?????0001?00001??00010?00000000?1??????00?000 Monophyllorchis 00000000000001???0?00?0000000001?000?1??0000100000000000010000000000000000000000 Psilochilus 0000000000?1?00000100?00000000000000?1??0000000000000000010000000000000000001000 Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso 00000000000000000000000000000000000000?10000000000000000010000000000000000000000 Chysis 00000000000000000000000000000000000000?10000000000000000010000000000000000000000 Gastrodia_sesamoides_534 10000000000000000000000000000000000000?100000?1???????0?0?0000?1??????????00??0? gastrodia_sp_reunion_ER214 ?0000000000000000000000001000000000000000?1???????????0?0?0000001?????????00??0? gastrodia_confusa_0801 ?0000000000000000000000000000000000000000?1???????????0?0?0000001?????????00??0? 410 gastrodia_zyl_16313 ?00000001000000000000000000000000000001000001000000000000??1?0000010?00000000000

Codonorchis 000000000000000000000000001000000000000000000000000000?10000?0000000000000000000 Goodyera 000000000000000000000000001000000000000000000000000000?10000?0000000000000000000 Palmorchis 00000000000000000000000000110000000000000000000000000010000000000000000000000001 Cephalanthera 00000000000000000000000000100000000000000000000000000000000000000000001000000000 Aphyllorchis 00000000000000000000000000100000010000000100000100000000000000000000000000000000 Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis 00000000000000000000000000100000000000000000000000000000000000000000000000000000 Limodorum ???????????????????????????????????00000010001??????????????????????????0?000000 Listera ?????000000000000000000000100000000000000000000000000000000000000000000000000000 Neottia ?????000000000000000000000100000000000000000000000000000000000000100000000000000 Corymborkis 00000000000000000000000000110000000000000000000000010000000000000000000000000000 Tropidia 00000000000000000000000000100000000000000000000000000000000000000000000000000000 Epilyna ???????????????????????????????????????????????????????????????????????????????? Sertifera 000000000010000000000101?0100110001001???000000000000000000000000000000000000000 Elleanthus ???????????????????????????????????????????????????????????????????????????????? Sobralia 0?000000000000000000000000100000000000000000000000000000000000000000000000000000 Diceratostele 00000000000000000000000000100000000000?1?000001100100000000000001000000000000001 Continued

Table B.1 Continued

Didymoplexis 00000000000000?10??000000010000000000000001000000000000000000000000000?10?000000 Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium 0000000000000000000000000010000000000000000000000000?1??1?00??00001100??1?00???? Xerorchis 000100000000000000001?00001?100000000000001000011000000000000000000000000?10???? Nervilia 00000000000000000000000000100000000000000000000000000000000000000000000000000000 Triphora 010100000000100000000000001000000100000000000000000000000000000000000000000010?? Monophyllorchis 00000000000000000000000000100000000000000000000000000000000000000000000000000000 Psilochilus 00000000000000000000000001?00000000000000000000000000000000000000000000000000000 Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso 00000000000000000000000000100000000000000000000000000000000000000000000000000000 Chysis 00000000000000000000000000100000000000000000000000000000000000000000000000000000 Gastrodia_sesamoides_534 000000000000000000000000001000000000000000000000000000000100??00000??10000000000 gastrodia_sp_reunion_ER214 000000000000000000000000001000000000000000000000000000000?10??000000000000000001 gastrodia_confusa_0801 000000000000000000000000001000000000000000000000000000000??1????000?101000000001 gastrodia_zyl_16313 00000000000000001???0?000010000000000000001000000000000000000000000000000000001?

411

Codonorchis 00000010100000000000000000000000010000000000000000000000000000000000000000000001 Goodyera 00000000100000000000000000000000010000000000000000000000000000000000000000000000 Palmorchis 00000001??000000000000000?100??0??0001?10000??1000000000000000000000000000000000 Cephalanthera 00000000100000000000000000000000000000000000000000000000000000000000000000000000 Aphyllorchis 00000000?10000000000000000000100010000000000000000000100000000000010000000000000 Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis 00000000101?????????00??00000000010000000000?10000000000000000000000000000000000 Limodorum 000001?0?1000000000000000??10??0??0000000000000000001000000000000000000001000000 Listera 00000000100000000000000000000000000000000000000000000000000000000000000000000000 Neottia 0000000010000000000??1??0?0000001000000000000000000000000000?1?????????00?000000 Corymborkis 00000000?10000000000000100000100010000000000000000000000010000000000000000000000 Tropidia 00000000100000000000000000000100010000000000000000000000000000000000000000000000 Epilyna ???????????????????????????????????????????????????????????????????????????????? Sertifera 00000000100000000000000000000100010000000000???100000000000000000000000000000000 Elleanthus ???????????????????????????????????????????????????????????????????????????????? Sobralia 00000000100000000000000000000100010000000000???100000000000000000000000000000000 Diceratostele 00000010100000010000000001000100010000?1000010000000010001000000000000000?100000 Didymoplexis 00001010?10000000000000000000100010000?100000000000000000000000000??1??00?000000 Didymoplexiella ????????????????????????????????????????????????????????????????????????????????

Continued

Table B.1 Continued

Epipogium ??????????0??00000000001000001000??10?????0??????0000000001?????????????0??0?000 Xerorchis ????????????????????????0?000?0001000000000000001001????0?0??00010?000000??1??00 Nervilia ?1????????000000000000000???1??0????0?????0??????00000000000100000000?100?000000 Triphora 00?0?00010010?1????0000000000100010000????1???????00?0??1?0??0???0??0?0000000000 Monophyllorchis 0000000010000000000100??00000100010000000000000000000000000000000000000000000000 Psilochilus 0000000010000000000?10??0?000100010000000000000000000000000000010000000000000000 Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso 00000000100000000000000000000100010000000000000000000000000000000000000000000000 Chysis 00000000100000000000000000000100000000000000000000000000000000000000000000000000 Gastrodia_sesamoides_534 0000000000000001000000000000010001000000000000000000000000000000000000000000?100 gastrodia_sp_reunion_ER214 00?1?0000000100?1??00000000001000?100?????0???00000001100001?00001?????00?001000 gastrodia_confusa_0801 00000010?100000000000000000001000100000000000000000000000000000000000???1??0??00 gastrodia_zyl_16313 00100010?10000000000000000000100010000?1000000000000000000000000001000000100??10

Codonorchis ???00???0?000000000000001001001?000100000000000000000000000000000000000000000000 412 Goodyera 0000000001000000000000000001000??1??00000000000000000000000000000000000000000000 Palmorchis 0000000000000?1??0000000000100000000?1?000000000000100000?1000000000?0000000000? Cephalanthera 00000000000000000000000000010000000000000000000000000000000000000000000000000000 Aphyllorchis 00000000000000000010000000010001000010000000000000000000000100000?1?00??00000000 Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis ????1???0??0??0000000000000100000000?1?00000000000000000000000000000000000000000 Limodorum 00000000000000000000000000010000001?00100000100000000010000000000000000000000000 Listera 000000000000000000000000000100000000?1?00000000000000000000000000000000000000000 Neottia ???10???0??0?0000000000000010000000000000000000000000000000000000000000000000000 Corymborkis 00000000000000000000010000010000000000000000000000000000000000000000000000000000 Tropidia 00000000000000000000000000010000000000000000000000000000000000000000000000000000 Epilyna ????????????????????????????????????????????????????????????????????0??????????0 Sertifera 0000000000000000000000000001000000000000000000000000000000000000000?1??????????0 Elleanthus ???????????????????????????????????????????????????????????????????????????????? Sobralia 00000000000000000000000000010000000000000000000000000000000000000000000000000000 Diceratostele 000000000100100010000000000?100??1??00010000000?100?0000000?1?000001000000000000 Didymoplexis 0000000000000000?1?????00001000??1??00000001000000000000000000000000000000000000 Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium 000000000010?00000000000000100000000000???1????????????????????0????0??????????0 Xerorchis ??0000010?0000010000000000010000000000000001000000000100000000000000000000000000 Nervilia 100000000000100000001000000??10000000000000000010000001000000000100000?100001000 Triphora ?10000010?00100000000000100100000000000000000000000100?1???00100000001???0?0??00

Continued

Table B.1 Continued

Monophyllorchis ??1000?0010000000000000000010000000000000000000000000000000000000000000000000000 Psilochilus 00000000000010000000000000010000000000000000000000000000000000000000000000000000 Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso 00000000000000000000000000010000000000000000100000000000000000000000000000000000 Chysis 000000000000000000000000000100000000?1?00000100000000000000000000000?0000000000? Gastrodia_sesamoides_534 ?00001??0?001000000000000001000?1000000??10???????0?0000000000000000000000?1??00 gastrodia_sp_reunion_ER214 000000100010?000000000?1????000?100000100000000???1???0000000??1????0??????????0 gastrodia_confusa_0801 ?000001000?1?????0000000001?000100000000000000000000000000000000000000000000??10 gastrodia_zyl_16313 ???000?00000000000000000?1??0000000000010000000000000000000000000000000000000000

Codonorchis 000000?1?0?00?0000000000000000000000000000010?00000??1?0?0?000000000000000000000 Goodyera 000000000000000000000000000000000000000000010?00000??1?0?0?000000000000000000000 Palmorchis 00000000000000000000000001000000000?00000?1000000001000000000000000?0?0000000000 Cephalanthera 000000000000000?1??000??00000000000000000000000000010000000000000000000000000000 Aphyllorchis 0000000000100000000000001?????000000000001000000000?1000100100010?00000000000000

413 Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis 00000000000000000000000000000000000000000000000000010000000000000000000000000000 Limodorum 00000010?000000000?100??0?0000?1?000????0???0?0?000000100000000001000000010?00?0 Listera 000000000000000000000000000000000000000000000000000100000000000000000?0000000000 Neottia 00000000000000010010000000000000?100????????0????0???0?0001???1?0?00?1?????????? Corymborkis 0000000010000000000000000001??00000000000100000000010000000000000000000000000000 Tropidia 000000000000000000000000000000000000000000000000000100000000000000000000010?00?0 Epilyna ???????????????????????????????????0???????????????????????????????0?0?????????? Sertifera ???????????????????????????????????0???????????????????????????????0?0?????????? Elleanthus ???????????????????????????????????????????????????????????????????????????????? Sobralia 00000000000000000000000000000000000000000000000000010000000000000000000000000000 Diceratostele 00??1??????0???????000??0?000000000000000000000000000000000000000000000000000000 Didymoplexis 00?10????0?00?0000???1?????????0?000??0?0000000?10???0?000000000000000??1??????? Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium ??????????????????????????????????00????????0??????????0?0?0000?1??0?0?????????? Xerorchis 000000000000000001000001000000000000000000000?1?00010000000??100000000?100000000 Nervilia 010000001000010000000000010001000000000001000001000100000010000000000000000100?1 Triphora ????0??????00??????000??000001001000??000000000000010000000000000010?00000000000 Monophyllorchis 00000000000000000000000000000000000000000000000000010000000000000000000000000000 Psilochilus 00000000000000000000000000000010?000??000000000000010000000?100000000010000001?? Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Continued

Table B.1 Continued

Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso 00000000000000000000000000000000000000000000000000010000000000000000000000000000 Chysis 00000000000000000000000000000000000?0000000000000001000000000000000?0?0000000000 Gastrodia_sesamoides_534 ???????????0???????000??0?000100000000000000000001?????0?0?000000000000000000000 gastrodia_sp_reunion_ER214 ??????????????????????????????????00????????????????????????????0??0?00000000000 gastrodia_confusa_0801 ???????????0????????00??0?000100000001000000000001?????0?0?000000000000000000000 gastrodia_zyl_16313 0000000000?1???????????????????0?000??0?0?000000000??1?0?0?00000000000??1???????

Codonorchis 0000000000000000000000000000?100000000000000000000000000000000000000000000000000 Goodyera 0000000000000000000000010000?100000000000000000000000000000000000000000000100?00 Palmorchis 000000?00000?0?????????????????????????????????????????????????????????????????? Cephalanthera 00000000000000000000000000000000000000000000000000000000000000000000000000000000 Aphyllorchis 00000000000000000000000000000000000000000000000000000000000000000000000000000000 Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis 00000000000000000000000000000000000000000000000000000000000000000000000000000000 Limodorum 010100000000000000000000000100000000000??10?0001??????0??????00??0000?00000?1??? 414 Listera 00000000000000000000000000000000000000000000000000000000000000?00000000000000000 Neottia ??????????????????????????????????????????????????????????????0????????????????? Corymborkis 1000000000000000?10?0???000000000000000000000000000000000000000000?1???????????? Tropidia 000000000000000000000000000000000000000000000000000000000000000000?1???????????? Epilyna ??????????????????????????????????????0???????????????0???????0????????????????? Sertifera ??????????????????????????????????????0???????????????0???????0????????????????? Elleanthus ???????????????????????????????????????????????????????????????????????????????? Sobralia 00000000000000000000000000000000000000000000000000000000000000000000000000000000 Diceratostele 00000000000000000000000000000000000000000000000000000000000000000000000000000000 Didymoplexis ??0??0000000000000000000000000001???000???0????0?????00?0?00000001000???????0??? Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium ??0??00000100001????????????????????000???????????????0??????00???000??????????? Xerorchis 001??00000000100001?0???00?0000000000001000100000??1?000010100010000000000010??? Nervilia ?00?100000?????????????????????????????????????????????????????????????????????? Triphora 00000000010000000000001001??00000000000000000?10???0000?1??000000000000000000000 Monophyllorchis 00000000000000000000000000000000000000000000000000000000000000000000000000000000 Psilochilus ??0000000000000000000000000000000000000000001?00?00000010?0010000000000000000000 Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso 00000000000000000000000000000000000000000000000000000000000000000000000000000000 Chysis 00000000000000000000000000000000000000?000000000000000?0000000?00000000000000000 Continued

Table B.1 Continued

Gastrodia_sesamoides_534 000000000000000000010?000000???10???000???0?000000000000000000000000000100000000 gastrodia_sp_reunion_ER214 100000000010000010000000000000000000?10???????????????0??????00????00??????????? gastrodia_confusa_0801 000000000010000010000000000000000000100???????????????0??????00????00??????????? gastrodia_zyl_16313 ??0??00000000000000000000010100000000000001????0?????00??????00?00100???????????

Codonorchis 00000000000000000000000000000000000000000000000000000000000000000000000000000000 Goodyera 00000000000000000000000000000000000000000000000000000000000000000000000000000000 Palmorchis ????????????????????????????????????????????????????????????????0000000000000000 Cephalanthera 00000000000000000000000000000000000000000000000000000000010000000000000000000000 Aphyllorchis 00000000000000000000000000000000000000000000000000000000000000000000000000000000 Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis 000000?10?0000100000000000000000000000000000000000000000000000000000000000000000 Limodorum ?????1??????????????????????????????0????????????0?????0??????0?000?100000000010 Listera 0000000000000000000000000000000000000000000000000?00000?000001010000000000000000 Neottia ?????????????????????????????????????????????????0?????0???????????????????????? 415 Corymborkis ?????0??????????????????????????????0????????????0?????0???0?0000000000000000000 Tropidia ?????0??????????????????????????????0????????????0?????0???0?0000000000000000000 Epilyna ????????????????????????????????????0????????????0?????0??????0?000000100101???0 Sertifera ????????????????????????????????????0????????????0?????0?????????0???0?????????? Elleanthus ???????????????????????????????????????????????????????????????????????????????? Sobralia 0000000000000000000000?10000000000000000000000000000000000000000000000000000?1?0 Diceratostele 00000000000000?10?00000000000000000000000000000000000000000000000000000000000000 Didymoplexis 00?1000000000000000000?100000000000000000000000000000?10010000000000000000000000 Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium ????0010010?1?00010?10????1?????????0????????????0?????0??00001??00??0??0?001000 Xerorchis 00?010001?0?00??1?0000???10???0?10001????????????0?????0?????????0???0?????????? Nervilia ???????????????????????????????????????????????????????????????????????????????? Triphora 0000000000000000001???000000101001??00010?00?1?000000000000001010001000?1?00?000 Monophyllorchis 00000000000000000000000000000000000000000?10000000000000000000000000000000000000 Psilochilus 0000000000000000000000?100000000000000010?00100000000000000000000000000000000000 Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso 00000000000000?10?00000000000000000000000000000000000000000000010000000000000000 Chysis 00000?00000000?10?000000000000100000?010000000000?00000?000000?00000000000000000 Continued

Table B.1 Continued

Gastrodia_sesamoides_534 ?1??100000000000000000?1000000000000000000000000000000001?000000100??0?000000000 gastrodia_sp_reunion_ER214 ?????0????????????????????0?????????0?????000000?1?????????????????????????????? gastrodia_confusa_0801 ?????000001???????????????0?????????00000001?00000110001???????????????????????? gastrodia_zyl_16313 ?????00000010000000000?1000000000000????????????????????????????????????????????

Codonorchis 00000000000000000000000000000000000000000000000000000000000001?0????00??001???00 Goodyera 0000000000000000000000000000000000000000000000000000000000000000000000?1001???00 Palmorchis 00000000000001000000000010001000000001000000000000000000000000000000000000000000 Cephalanthera 00000000000000000000000000000000000000000000000000000000000000000000000000000000 Aphyllorchis 00000000000000000000000000000000000000000000000000000000000000000000000000000000 Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis 0000000000000000000000000000000000000000000000000000000000000000000000?1000??100 Limodorum 01001000001000000?1?????????????????????????0??0????00000000000000???1???0????00 Listera 000000000000000000000000000000000000000000000000000000000000000?0000000000000000 Neottia ???????????????????????????????????????????????????????????????????????????????? Corymborkis 00000000000000000000000000000000000000000000000000000000000000000000000000000000 416 Tropidia 00000000000000000000000000000000000000000000000000000000000000000000000000000000 Epilyna 00000?1010000100100000001001000?1000101010010000100010000101001011?100?0000?1000 Sertifera ????0000000000000000000000000000000000000000000000000000000000000000000000000000 Elleanthus ???????????????????????????????????????????????????????????????????????????????? Sobralia 0000000000000000000000000000000000000000000000?????????????????????????????????? Diceratostele 00000000000000000000000000000000000000000000000000000000000000000000000000000000 Didymoplexis 000000000000101000000?1??000?10001????0000000000000001?????????0?????0??00000000 Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium 100011000001???0??0?00010?1???????????????0000?1?????0?00?1?0001???????????????? Xerorchis ??????????????????0???0?0000001???????01000?1??????????????????0?????0???00??000 Nervilia ???????????????????????????????????????????????????????????????????????????????? Triphora 000000000000000000000000000000000000000000000000000000010000000000??10??00000001 Monophyllorchis 000000000000000000000000000000000010000001000100001?0010000000000000000000000000 Psilochilus 00000000000000000000010?00000000000000000000000000000000000000000000000000000000 Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso 00000000000000000000000000000000000000000000000000000000000000000000000000000000 Chysis 00000000000000000000000000000000000000000000000000000000000000000000000000000000

Continued

Table B.1 Continued

Gastrodia_sesamoides_534 00000001???0???001010000010???0??000000000000010????000000000000000000??10010000 gastrodia_sp_reunion_ER214 ???????????????????????????????????????????????????????????????????????????????? gastrodia_confusa_0801 ???????????????????????????????????????????????????????????????????????????????? gastrodia_zyl_16313 ????????????????????????????????????????????????????????????????????????????????

Codonorchis 000000000010000000000000000000000100?000000000000000000000000000???1??00??0?0000 Goodyera 0000000000100001?????0?00000001???00?00000000000000000000001000010000100??0?0000 Palmorchis 000000000010000000000000000000000100?0000000000000000000000000000000000000000000 Cephalanthera 000000000000000000000000000000000100?0000000000000000000000000000000000000000000 Aphyllorchis 000000000000000000000000000000000100?0000000000000000000000000000000000000000000 Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis 000000000110000000000000000000000100?0000000000000000000000000000000000000000000 Limodorum 00010010001001000010000001??????????????00001????000100010???0?0??10?000??1?000? Listera 000000000000000?0000????????00000100?0000000000000000000000000000000000000000000 Neottia ?????????????????????0?????????????????????????????????????????????????0???????? Corymborkis 000000000010000000000000000000000100?0000000000000000000000000000000000000000000 Tropidia 000000000010000000000000000000000100?0000000000000000000000000000000000000000000 417 Epilyna 000001?10??010101??00010101000001?00?001010?01010100010000100011?000000000000000 Sertifera 000000000010000000000000000000010100?0100000000000000000000000000000000010000000 Elleanthus ???????????????????????????????????????????????????????????????????????????????? Sobralia ???????????????????????????????????????????????????????????????????????????????? Diceratostele 000000000010000000000000000000000100?0000000000000000000000000000000000000000000 Didymoplexis 000000000010000000000000000000000100?0000000000000000000000000000000000000000000 Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium ?????????????????????0?????????????????????????????????????????????????0???????? Xerorchis 01?????000?1???000?10000000100000100?0000000000010?1??0000101010?100???1???????? Nervilia ???????????????????????????????????????????????????????????????????????????????? Triphora 00001??00010000000000000000010?????0???00000000000000??100??0000000000000000000? Monophyllorchis 000000000010000000000000000010?????0???00000001??0000000000000000000100000000000 Psilochilus 000000000010000000000000000010?????0???00001000000000000000000001000000000000000 Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso 000000000010000000000000000000000000?1000000000000000000000000000000000000000000 Chysis 00000000001000000000000000000000000000000000000000000000000000000000000000000000 Gastrodia_sesamoides_534 10?000000010000000000001?0?000000100?00?1???000000000000000000000000000000000001 gastrodia_sp_reunion_ER214 ?????????????????????0?????????????????????????????????????????????????0???????? gastrodia_confusa_0801 ?????????????????????0?????????????????????????????????????????????????0???????? gastrodia_zyl_16313 ???????????????????????????????????????????????????????????????????????????????? Continued

Table B.1 Continued

Codonorchis 00010000100010000000000000010000000000000000000000000000000000000000000000000000 Goodyera 00000000000000000000000000010000?????10??????????????0000000???1??????0?00?0??00 Palmorchis 000000000000000000000000000000000000000000000000000000000000?1000?00000000000000 Cephalanthera 000000000000000000000000000000000000000000010000000000000000?1000?00000000000000 Aphyllorchis 00000000000000000000000000000000?100000?00010000000000000000?1000?00000000000000 Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis 00000000000000000??1?0???????0000000000000000000000000000000?1000?00000000000000 Limodorum 0?0??10????00001??0000?000000010000000010?1????????00000000000000000000000000000 Listera 000000000000000000000000000000000000000000010000000000000010??00????000000000000 Neottia ???????????????????????????????????????????????????????????0??00????000000000001 Corymborkis 000000000000000000000000000001?0????000?000?000100100000000000000000000?1??????? Tropidia 0000000000000000000000000000000000000000000??10?000000000000?1000?00000000000000 Epilyna 01010000100000101100000100000000000000000000000001000000000000000000000000000000 Sertifera 000100000001?????????????????00000000000010??000000000000000000000000?1?00?0???? Elleanthus ???????????????????????????????????????????????????????????????????????????????? Sobralia ???????????????????????????????????????????????????????????????????????????????? Diceratostele 00000000000000000000000000000000000000000000000?1?000000000010000000000000000000 Didymoplexis 000???1????0?000000000100?1??0000000000?1?0???????00100000?1????????????00?0???? Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? 418 Epipogium ?????00???0001?000000000000000000000001???????????????????00??00??00000000001000 Xerorchis ???????????????????????????????????????????????????????????????????????????????? Nervilia ???????????????????????????????????????????????????????????????????????????????? Triphora 1??000000?100000000010???????0?1?????00???0???????000?10??00?0000000000000000?1? Monophyllorchis 00000000000000000000000000000000???1000?000?000000000100?000?0000000000000000000 Psilochilus 00100001000000000000000000000000????100???0???????000??1??00??000?00010000?0?000 Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso 00000000000000000000000000000000000000000000000000000100?000?0000000000000000000 Chysis 00000000000000000000000000000000000000000000000000000100?000?0000000000000000000 Gastrodia_sesamoides_534 00000000000000000?1000??0100000000000000000000000101?0000000??10????0?0000?0??00 gastrodia_sp_reunion_ER214 ???????????????????????????????????????????????????????????????????????????????? gastrodia_confusa_0801 ???????????????????????????????????????????????????????????????????????????????? gastrodia_zyl_16313 ????????????????????????????????????????????????????????????????????????????????

Codonorchis 000000000000000000000000000000000000000000010?000000??10?????000?10???0?00000000 Goodyera 000000000000000000000000000000000000000000010?000000??10?????0000000000000000000 Palmorchis 000000000000000000000000000000?1?0?0000000010?0000000000000000000000000000000000 Cephalanthera 000000000000000000000000000000000000000000010?0000000000000000000000000000000000 Continued

Table B.1 Continued

Aphyllorchis 000000000000000000000000000000000000000000010?0000000000000000000000000000000000 Auxopus ???????????????????????????????????????????????????????????????????????????????? Epipactis 000000000000000000000000000000000000000000010?000000???1??????????????0?00000000 Limodorum 000000000000000000010000000000000000000000010?0000000000000000000000000000000000 Listera 000000000000000000000000000000000000000000010?0000000000000000000000000000000000 Neottia 01?000000000000000000000000000000000000000010?0000000000000000000000000000000000 Corymborkis ??????0???0????0??00000000000000000000000?1???0000000000000000000000000000000000 Tropidia 000000000000000000000000000000000000000000010?0000000000000000000000000000000000 Epilyna 000000000000000010100001000000000000100000010?0100000000000000000000000000000000 Sertifera 000000011000100001000100000001000000001000010?001?0000000001?0000001000000000100 Elleanthus ???????????????????????????????????????????????????????????????????????????????? Sobralia ???????????????????????????????????????????????????????????????????????????????? Diceratostele 000000000000000000000000000000000000000000010?0000000000000000000000000000000000 Didymoplexis 00100000001???????0000000000000010?10000010?1?0100100000001011????????0?00000000 Didymoplexiella ???????????????????????????????????????????????????????????????????????????????? Epipogium 00000?1??????????????????????????????001????????0000?100?0?0?0000000000000000001 Xerorchis ??????????????????????????????????????????????????????????????????????0?00010?10 Nervilia ???????????????????????????????????????????????????????????????????????????????? Triphora 00??1?0??001?000?0000000001000000000000000010?000000000010?0?00000000?1????????0 Monophyllorchis 000000000000000000000000000000000000000000010?00000000000000000000000001001?0100 419 Psilochilus 0000010?0000000000100000000000100010000000010?0000000000000000000000000100010000 Wullschlaegelia ???????????????????????????????????????????????????????????????????????????????? Stereosandra ???????????????????????????????????????????????????????????????????????????????? Uleiorchis ???????????????????????????????????????????????????????????????????????????????? Calypso 00000000000000000000000000000000000000000000000000000000000000000000000000000000 Chysis 00000000000000000000000000000000000000000000000000000000000000000000000000000000 Gastrodia_sesamoides_534 000000000000000000000000000000000000000000010?000000000000000010000000001??????0 gastrodia_sp_reunion_ER214 ??????0???????????001?0000?1???0?1???00010010?0000?1???0?????0001000000101????00 gastrodia_confusa_0801 ??????0???????????001?0001?????0?01001?010010?0000?1???0?????0001000000100001?00 gastrodia_zyl_16313 ????????????????????????????????????????????????????????????????????????????????

Codonorchis ?100??????00000000000000000000000000000000000000000010000000000000011?00???0?110 Goodyera 000000000000000000000000000000000000000000000000000010000000000000010100?0000010 Palmorchis 0000000000000000000000000000000000000000000????????????????????????0001001001110 Cephalanthera 00000000000000000000000000000000000000000000000000000000000000000000001001100110 Aphyllorchis 000000000000000000000000000000000000000000000000000001000000000000000-3???100110 Auxopus ???????????????????????????????????????????????????????????????????0?-3????011?0 Epipactis 00000000000000000000000000000000000000000000000000000000000000000000001021100110 Continued

Table B.1 Continued

Limodorum 0000000000010000000000010000000001000100000001??1?0100?1?000010000000-3????00110 Listera 00000000000000000000000000000000000000000000000000000000000000000000000021100110 Neottia 000000000000000000000000000000000000000000000000000000000000000000000-3?21-01110 Corymborkis 000000000000000000000000000000010?0000000000000000000000000000000??0001001010000 Tropidia 00000000000000100000000000000000000000000000000000000000000000000000101001000000 Epilyna 00000000000000000000000000000010000000010000000000000000000001010000--202-100010 Sertifera 00000??????????????????????????????????????????????????????????????01-11---1---0 Elleanthus ???????????????????????????????????????????????????????????????????01-112-100110 Sobralia ???????????????????????????????????????????????????????????????????0101120000100 Diceratostele 00000000010001?00100101000010100000000110100000000000000001000000100101001010000 Didymoplexis 0000000?1?00000000000000000000000000000000000000000000000000000000002-3????01110 Didymoplexiella ???????????????????????????????????????????????????????????????????02-3?2??00110 Epipogium ???0??????0000100000000000000000000000000000000000000000000000000000203?20?01110 Xerorchis ?000001?1?00000000000000000000000000000000000000000000000000000000000-10---00000 Nervilia ???????????????????????????????????????????????????????????????????0001020000110 Triphora ?0000??000101??000000000000000000000000000000000000100000000000000000000?000?011 Monophyllorchis 00000000000000000000000000000000000000000000000000000000000000000000--10--00?101 Psilochilus 000000010010000100110000000000000001000100010000???????????????????0--10--00?111

420 Wullschlaegelia ???????????????????????????????????????????????????????????????????0013?2??0?110 Stereosandra ???????????????????????????????????????????????????????????????????02?3?---00010 Uleiorchis ???????????????????????????????????????????????????????????????????0013????0???0 Calypso 000000000000000010000000000000000000000000000000000000000000000000001010?0011110 Chysis 00000000000000000000000000000000000000000000000000000000000000000000???????????0 Gastrodia_sesamoides_534 ?0000??0000000001000000000000000000000000000000000000000000000000000203?2??01110 gastrodia_sp_reunion_ER214 0001???????000000000000000000000000000000000000000000000010000000000303?2??01110 gastrodia_confusa_0801 00001?????0000100000000000000000000000000000000000000000000000000000303?2??01110 gastrodia_zyl_16313 ???????????????????????????????????????????????????????????????????0303?2??01110

Codonorchis ??000201010?01110 Goodyera 01110201010022010 Palmorchis 00001?000001?0001 Cephalanthera 00000100000111001 Aphyllorchis ??000100010112000 Auxopus ??111-00000-2---- Epipactis 00100100000012000 Limodorum 00000100000-?0000 Continued

Table B.1 Continued

Listera 00100100000010000 Neottia 00100100000-10000 Corymborkis 0011--10110-22010 Tropidia 00110?10110122011 Epilyna ?-10--0000212---- Sertifera ---0--00002-2---- Elleanthus 0110--0000212---- Sobralia 01101210002112001 Diceratostele ??-0--00000-02000 Didymoplexis ?-103200000122200 Didymoplexiella ?-10--00000-2---- Epipogium 01120201000120000 Xerorchis ------00001-22000 Nervilia 01120200010112011 Triphora 10124200000012101 Monophyllorchis --12020000011---- Psilochilus 0012020000001---- Wullschlaegelia 01110?00010-22000 Stereosandra --114110010102001 Uleiorchis ---1-?00010-12200 421 Calypso 01101210100122101 Chysis 01?????0????????? Gastrodia_sesamoides_534 ??12020000001???? gastrodia_sp_reunion_ER214 0112?200OO00????? gastrodia_confusa_0801 0112?200OO00????? gastrodia_zyl_16313 0112?200OO00?????

APPENDIX C

DNA ALIGNMENTS FOR THE CHLOROPLAST TRNLF INTERGENIC SPACER

REGION AND GAP MATRICES USED IN CHAPTER 5: A PHYLOGENY OF

PSILOCHILUS (TRIPHOREAE) USING THE PLASTID

TRNL-F INTERGENIC SPACER.

422 Monophyllorchis_sp GGAAACTAAGAAAGGGCAATCCTGAGCCAAATCTTTTTT-ATAGAAAAATGGAAAAGATAA----GAATAAAAAGGGATAGGTGCAGAGA Monophyllorchis_micorstyloides ????????????????????????????????????????????????????????GATAATTGAGAATAAAAACGGATAGGTGCAGAGA Triphora_amazonica_Emerson_A06 GGAA-CTAATAATGGGCAATCCTGAGCCAAATCTTTTTTTATAGAAAAATG-AAAAGATGATTGAGAATAAAAAGGGATAGGTGCAGAGA Triphora_trianthophora_ER19A GGAA-CTAATAATGGGCAATCCTGAGCCAAATCCTTTTT-ATAGAAAGATGGAAAAGATAATTGAGAATAAAAAGGGATAGGTGCAGAGA Triphora_gentianoides_ER01 GGAA-CTAATAAAGGGCAATCCTGAGCCAAATCTTTTT--ATAGAAAAATGGAAGAGATAATTGAGAATAAAAAGGGATAGGTGCAGAGA Psilochilus_carinatus_er113_tr ?????????????????????????????????????????????????????????????????????????????????????????? Psilochilus_modestus_ER65 GGAA-CTAAGAATGGGCAATCCTGAGCCAAATCTTTTTTTTTAGAAAAA-GGGAAAGATAATTGAGAATAAAAAGGGATAGGTGCAGAGA Psilochilus_macrophyllus_ER02 GGAA-CTAAGAATGGGCAATCCTGAGCCAAATCTTTTTTTTTAGAAAAAAGGAAAAGATAATTGAGAATAAAAAGGGATAGGGGCAGAGA Psilochilus_indet_015111 ??????????????????ATCCAGAGCCAAATCTTTTTTTTTGGAAAAAAGGGAAAGATACCTGGGAATAAAAGGGGTTGGGGGCRAGGN ER207 GGAA-CTAAGAATGGGCAATCCTGAGCCAAATCTTTTTTTTTAAAAAAGGGGAAAAGATATTTGGAAAAAAAAGGGGGTGGGGGCAAAAC LJ8264 GGAA-CTAAGAATGGGCAATCCTGAGCCAAATCTTTTTTTTTARAAAAATGGAAAAGATAATTGAGATAAAA-AGGGATAGGKGCAGAGA ER92 ???????????????????????????????????????????????????????????AAGTGGGACTAAAAAGGGATAGGTGCAGAGA Psilochilus_sp.LJ5413_trnlF GGAA-CTAAGANAGGGCAATCCTGAGCCAAATCTTTTTTTTTAGAAAAAGGGAWANNNTATTTGGGATAACACCGGGATAGGGGCARAGA Psilochilus_ER208_1Mera GGAA-CTAAGAATGGGCAATCCTGAGCCAAATCTTTTTTTTTAGAAAAATGGAAAAGATAATTGA-AATAAAAAGGGATAGGGGCAGAGA LJ7955 ?????????????GGGCAATCCTGAGCCAAATCTTTTTTTTTAAAAAAAGGGAAAAGATAATTGA-AAAAAAAGGGGNTGGGGGCRAAGC LJ5381_trnlf__part ?????????????????????????????????????????????????????????????????????????????????????????? LJ6914_loja_outx GGAA-CTAAGAATGGGCAATCCTGAGCCAAATCTTTTTTTTTAGAAAAATGGAAAAGATAATTGAGATAAAA-GGGGATAGGGGCARAGA LJ6860 GGAA-CTAAGAATGGGCAATCCTGAGCCAAATCTTTTTTTTTARAAAAAAGGAAAAGATAATTGAGAWAAAAAAGGGATAGGKGCAGAGA

Monophyllorchis_sp CTCAATGG-AAGCTGTTCTAACGAATGAAATTGACTGCGCTACGTTAGTAGATAAAAT------CATTTTATCTAAATGACATACAAA Monophyllorchis_micorstyloides CTCAAAGG-AAGCTGTTCTAACGAATGAAATTGACTGCGCTACGTTAGTAGATAAAAT------CTCTTTATCTAAATGACATACAAA Triphora_amazonica_Emerson_A06 CTCAATGG-AAGCTGTTCTAACGAATGAAATTGACTACGTTGCGTTA------AAT------GATTTTCTCTAAATGACATAC--- Triphora_trianthophora_ER19A CTCAATGG-AAGCTGTTCTAACGAATGAAATTGACTACGTTACGTTA------AAT------GATTTTCTCTAAATGACATAA--- Triphora_gentianoides_ER01 CTCAATGG-AAGCTGTTCTAACGAATGAAATTGATTACGTTACGTTA------AAT------GATTTTCTATAAATGACATAAA-- 423 Psilochilus_carinatus_er113_tr ?????????????????????????????????????????????????????????????????????????????????????????? Psilochilus_modestus_ER65 CTCAATGG-AAGCTGTTCTAACGAATGAAATTGACTATGTTACGTTAGTAGCTAAAATATCTAAACGATTTTAGATAAATGACATTTA-- Psilochilus_macrophyllus_ER02 CTCAATGG-AAGCTGTTCTAACGAATGAAATTGACTATGTTACGTTAGTAGCTAAAATTTCTAAACGATTTTAGATAAATGACATATAA- Psilochilus_indet_015111 CNCA-TGGGAGGCTGTTCTAAGGAAGGAAATAGACTTTTTTCGGTTGGTNGCAAAAATTTGSCCCCTATTTTAGATAAATGACATTTAA- ER207 CCCC-TGGGAAGCKGTTYTAACGAAGGAAATTGACTTTTTTCCGTTAGAACCAAAAA-ATTTAAACGATTTTAAA-AAAGGGGATTTAA- LJ8264 CTCAATGG-AAGCTGTTCTAACGAATGAAATTGACTATTTTACGTTAGTAGCTAAAATATCTAAACGATTTTAGATAAATGACATATAA- ER92 CTCAATGG-AAGCTGTTCTAACGAATGAAATTGACTACGTTACGTTAGTAGCTAAAAT-TCAT--CTAT----G--AAATGACAGA-AA- Psilochilus_sp.LJ5413_trnlF CTCAAKGG-AAGCTGTTCTAACGAATGAAATTGACTATTTTACGTTAGTAGCTAAAATATTTAAACGATTTTAGATAAATGACATATAA- Psilochilus_ER208_1Mera CTCAATGG-AAGCTGTTCTAACGAATGAAATTGACTATTTTACGTTAGTAGCTAAAATAT-AAAACGATTTTAGATAAATGACATATAA- LJ7955 CCCA-TGGGAAGCTGTTCTACCGAAKGAAATTGACTTTGTTACGTTGGGGGTTAAAAAAGTTA--C--TTTT-G-----TGGC-TAAAA- LJ5381_trnlf__part ?????????????????????????????????????????????????????????????????????????????????????????? LJ6914_loja_outx CTCAATGG-AAGCTGTTCTAACGAATGAAATTGACTATTTTACGTTAGTAGCTAAAATATCTAAACGATTTTAGATAAATGACATATAA- LJ6860 CTCAAKGG-AAGCTGTTCTAACGAATGAAATTGACTATTTTACGTTAGTAGTTAAAATATCTAAACGATTTTARATAAATGACATATAA-

Continued

Table C.1: Alignment of the trnL-F sequcnes data including gap characters coded using simple gaps methods.

Table C. 1 Continued

Monophyllorchis_sp A------GTACGTATACATACTTACATAGCAAACAATTCATCACAATT-CAATCTT--ATT---CTT--ATATTGAATCCTATTCTT Monophyllorchis_micorstyloides G------TAGTACGTATACATACTTACATAGCAAACAATTCATCACAATT-CAATCTT--ATT---CTT--ATATTGAATCCTTTTCTT Triphora_amazonica_Emerson_A06 G-----GGTAGTA------AACAATTC------GAATCTTCTATTGATATTGAATATTGAATC------Triphora_trianthophora_ER19A G-----GGTAGTACCTATACATAC------Triphora_gentianoides_ER01 G-----GGTAGTACCTATACGTAC------G------Psilochilus_carinatus_er113_tr ?????????????????????????????????????????????????????????????????????????????????????????? Psilochilus_modestus_ER65 GTATAAGGGAGTCCATATTCATTCTGACATATCAAACAATTAATCCCAATTTGAATCTTCTATTGA------ATCC------Psilochilus_macrophyllus_ER02 -TATAAGGTAGTACATATACATACTGACATATCAAACAATTAATCACAATTTGAATCTTCTATTGA------ATCC------Psilochilus_indet_015111 GT-TAA----GTACTTATTCCTACTGGCATTTCAAACAATTAATCCCAATTTGAATCTTCTATGGA------ATCC------ER207 -T-TAA---A--AATAATTCC---GGGAATTTCAAAAAATTAACCCCAATTTGAATCTTCTATGGA------ACCC------LJ8264 GTATAA----GTACATATACATACTGACATATCAAACAATTAATCACAATTTGAATCTTCTATTGA------ATCC------ER92 G-ATAA----GTACGTATACATACTGACATAGCAAACGATTAATCACAACCCGAATCT------Psilochilus_sp.LJ5413_trnlF ATATAA----GTACATATACATACTGGCATATCAAACAATTAATCCCAATTTGAATCTTCTATGGA------ATCC------Psilochilus_ER208_1Mera RTATAA----GTACATATACATACTGACATATCAAACAATTAATCACAATTTGAATCTTCTATTGA------ATCC------LJ7955 -TTT------GTCCAT-TTCCTCCGGCCTTTTCAAA-AATTAACCCCCTTTTGAACCTCCTTTTGA------ACCC------LJ5381_trnlf__part ?????????????????????????????????????????????????????????????????????????????????????????? LJ6914_loja_outx GTATAA----GTACATATACATACTGACATATCAAACAATTAATCACAATTTGAATCTTCTATTGA------ATCC------LJ6860 GTATAA----GTACATATACATACTGACATATCAAACAATTAATCACAATTTGAATCTTCTATTGA------ATCC------

Monophyllorchis_sp ATTCTATATCTCTCTCTATGAAAATAGGA-TCTTCTA---TTCTAATTT--ATT---AGA--AT-GATTATAATGATAGAGATC-AAAAA 424 Monophyllorchis_micorstyloides ATTCTATATCTCTCTCTATTTTCATAGGA-TCTTCTA---TTCTAATTC--ATT---AGAATACCGATTCTAATGATAGAGATC-AAAAA Triphora_amazonica_Emerson_A06 ATTCTATATCT---TCTAT----ATA----TC-TCTA-TC-TCTA------GAATTTAGAATAGAATGAGAGAGATC-AAAAA Triphora_trianthophora_ER19A ATTATACATTT--ACATACTGACATAGAAA--TTCGAATCTTCTA------GGAATAT--ATATAAATGATAGAGATC-AAAAA Triphora_gentianoides_ER01 ------TTT--ACATACTGACATAGAAA--TTCGAATCTTCTA-TT---ATTAT-TGAATAT-----AGAATGATAGAGATC-AAAAA Psilochilus_carinatus_er113_tr ???????????????????------GAATGATAGAGATCGAAAAA Psilochilus_modestus_ER65 ----TATATCTCTCTCTATGAAAATAGAAATCTTCTAATCTTCC-CTTTCTATTCTA----TATAGATTAGAATGATAGAGATCGAAAAA Psilochilus_macrophyllus_ER02 ----TATATCTCTCTCTATGAAAATAGAAATC------TTCT-CTTTCTATTCTA----TATAGATTAGAATGATAGAGATCGAAAAA Psilochilus_indet_015111 ----TATATCNCTCTSTAGGAAAATAGAAATCTTCTAATCTTCT-CTTTCTATTCTA----TATAGATTAGAATGATAGAGATCGAAAAA ER207 ----TATATCCCTCCCTTTGAAAAAAAAAATCTTCWAACCTTCC-CTTTCTATTCTA----TAAAGATTAAAGGG-GAAAGAACCAAAAA LJ8264 ----TATATCTCTCTCTATGAAAATAGAAATCTTCTAATCTTCT-CTTTCTATTCTA----TATAGATTAGAATGATAGAGATCGAAAAA ER92 ------TAT--ATT-GAA------Psilochilus_sp.LJ5413_trnlF ----TATATCTCCCTCTATGAAAATAGAAATCTTCTAATCTTCC-CTTTCTATTCCA----TATAGATTAGAATGATAGAGATCGAAAAA Psilochilus_ER208_1Mera ----TATATCTCTCTCTATGAAAATAGAAATCTTCTAATCTTCT-CTTTCTATTCTA----TATAGATTARAATGATAGAGATCGAAAAA LJ7955 ----TATTTCTCCCCCTATAAAAAAAAAAATCTTCAAATCTTCC-CTTTTTTTTCTA----TATAAATTAAAAGGAAAGAAATCGAAAAA LJ5381_trnlf__part ???????????????????AAAAATAGAAATCTTCTA-TCTTCT-CTTTCTATTCTA----TATAGATTAGAATGATAGAGATCGAAAAA LJ6914_loja_outx ----TATATCTCTCTCTATGAAAATAGAAATCTTCTAATCTTCT-CTTTCTATTCTA----TATAGATTAGAATGATAGAGATCGAAAAA LJ6860 ----TATATCTCTCTCTATGAAAATAGAAATCTTCTAATCTTCY-CTTTCTATTCTA----TATAGATTARAAKGATAGAGATCGAAAAA

Continued

Table C. 1 Continued

Monophyllorchis_sp ATATATGAAAAATGGAAGAGTTCTTGTTTTGTAAATCCATTGAAGTTGAAAAAAGAA---GAAT------TCGAATGTTCAGT Monophyllorchis_micorstyloides ATCTATGAAAAATGGAAGAGTTATTGTTTTGTAAATCCATTGAAGTTGAAAAA-GAA---GAAT------TCGAATGTTCAGT Triphora_amazonica_Emerson_A06 ATCTATGAGAATTTGAAGAGTTATTGTGTTGTAAATCCATTGAAGTTGAAAA--GA----GAATCAAATTCGAATAGTCAGTTATTCAGT Triphora_trianthophora_ER19A ATCTATGGAGATTTGAAGAGTTATTGTGTTGTAAATCCATTGAAGTTGAAAAA-G-----GAATCAAATTCGAATTTTCAGTTATTCAGT Triphora_gentianoides_ER01 -TATATGAAAAATTGAAGAGTTATTGTGTTGTAAATCCCTTGAAGTTGAAAAA-GAAAA-GAATCAAATTCGAATATTCAGTTATTCAGT Psilochilus_carinatus_er113_tr ATCTATGAAAAATTGAAGAGTTATTGGGT-GTAAATCCATTGAAGTTCAAA---GAAAAAGAATCAA------TCAGTTATTCAGT Psilochilus_modestus_ER65 -TCTATGAAAAAATGAAGAGTTATTGTGTTGTAAATCCATTGAAGTTCAAA---GAAAAAGAATCGA------TCAGTTATTCAGT Psilochilus_macrophyllus_ER02 -TCTATGAAAAAATGAAGAGTTATTGTGTTGTAAATCCATTGAAGTTCAAA---GAAAAAGAATCGA------TCAGTTATTCAGT Psilochilus_indet_015111 -TCTATGAAAAATTGAAGAGTTATTGGGTGGTAAATCCATTGAAGTTCAAA---GAAAAAGAATCAA------TCAGTTATTCAGT ER207 -TCTATGAAAAATTGAAGAGTTATTGTGTTGTAAATCCATTGAAGTTCAAA---GAAAAAGAATCAA------TCAGTTATTCAGT LJ8264 -TCTATGAAAAATTGAAGAGTTATTGTGTTGTAAATCCATTGAAGTTCAAA---GAAAAAGAATCAA------TCAGTTATTCAGT ER92 ------CC----NTTCAGN Psilochilus_sp.LJ5413_trnlF -TCTATGAAAAATTGAAGAGTTATTGTGTTGTAAATCCATTGAAGT-CAAA---GAAAGAGAATCAA------TCAGTTATTCAGT Psilochilus_ER208_1Mera -TCTATGAAAAATTGAAGAGTTATTGKGTTGTAAATCCATTGAAGTTCAAA---GAAAAAGAATCAA------TCAGTTATTCAGT LJ7955 -TTTTTGAAAAATTGAA-AGTTTTTGGGTTGTAAATCCTTTGAAGTTCAAA---AAAAAAAAATCGA------CCAGTTTTTC--- LJ5381_trnlf__part -TCTATGAAAAATTGAAGGGTTATTGTGTTGTAAATCCATTGAAGTTCAAA---GAAAAAGAATCA------TCAGTTATTCAGT LJ6914_loja_outx -TCTATGAAAAATTGAAGAGTTATTGTGTTGTAAATCCATTGAAGTTCAAA---GAAAAAGAATCAA------TCAGTTATTCAGT LJ6860 -TCTATGAAAAATTGAAGAGTTATTGKGTTGTAAATCCATTGAAGTTCAAA---GAAAAAGAATCGA------TCAGTTATTCAGT

425 Monophyllorchis_sp AATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTAAAGATTAATCGAACGAGAATAAAGAGAGAGTCCCTTTT-ACATGTCAATACC Monophyllorchis_micorstyloides AATCAAATGATTCATTCCAGAGTTTGATAGATCTTT-AAAGATGAATCGGACGAGAATAAAGAGAGAGTCCCTTTTTACATGTCAATACC Triphora_amazonica_Emerson_A06 AATCAAATGATTCATTCCAGAGTTTGAAAGATCTTTTGAAGATTAATCAGACGAGAATAAAGAGAGAGTCCCTTTTTACATGTCAATACC

Triphora_trianthophora_ER19A AATCAAATGATTCATTCCAGAGTTTGAAAGATCTTTTGAAGATTAATCATACGAGAATAAAGAGAGAGTCCCTTTTTACATGTCAATACC Triphora_gentianoides_ER01 AATCAAATGATTCATTCCAAAGTTTGAAAGATCTTTTGAAGATTAATCGGACGAGAATAAAGAGAGAGTCCCTTTTTACATGTCAATACC Psilochilus_carinatus_er113_tr AATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTCATCGGACGAGAATAAAGAGAGAGTCCCTTTTTCCATGTCAATACC Psilochilus_modestus_ER65 AATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTAATCGGACGAGAATAAAGAGAGAGTCCCTTTTTACATGTCAATACC Psilochilus_macrophyllus_ER02 AATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTAATCGGACGAGAATAAAGAGAGAGTCCCTTTTTACATGTCAATACC Psilochilus_indet_015111 AATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTCATCGGACGAGAATAAAGAGAGAGTCCCTTTTTCCATGTCAATCCC ER207 AATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTCATCGGACGAGAATAAAGAGAGAGTCCCTTTTTCCATGTCAATACC LJ8264 AATCAAAGGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTCATCGGACGAGAATAAAGAGAGAGTCCCTTTTTCCATGTCAATACC ER92 NNTCAAANG-TTCATTCCANGGTTGGAAANATTTNTTGAAGATT-ATCGGACGGGAATAAAGAGAGAGTCCCN-TTTACA-GGCAANNCC Psilochilus_sp.LJ5413_trnlF AATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTCATCGGACGAGAATAAAGAGAGAGTCCCTTTTTCCATGTCAATACC Psilochilus_ER208_1Mera AATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTCATCGGACGAGAATAAAGAGAGAGTCCCTTTTTCCATGTCAATACC LJ7955 ------LJ5381_trnlf__part AATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTCATCGGACGRGAATAAAGAGAGAGTCCCTTTTTCCATGTCAATACC LJ6914_loja_outx AATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTCATCGGACGAGAATAAAGAGAGAGTCCCTTTTTCCATGTCAATACC LJ6860 AATCAAATGATTCATTCCAGAGTTTGATAGATCTTTTGAAGATTAATCGGACGAGAATAAAGAGAGAGTCCCTTTTTCCATGTCAATACC

Continued

Table C. 1 Continued

Monophyllorchis_sp GACAAAAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTCAAAATCGTGAGGGTTCAAGTCC-TCTATCCCCAATAAAAAGCCCAT Monophyllorchis_micorstyloides GACAAAAATGAAATTTATAGTTAGAGGAAAATCCGTCGAATTTCAAAATCGTGAGGGTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCAT Triphora_amazonica_Emerson_A06 GACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTTAAGATCGTGAGGGTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCAT Triphora_trianthophora_ER19A GACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTTAAAATCGTGAGGGTTCAAGTCCCTCTATCCCCAAGAAAA-GCCCAT Triphora_gentianoides_ER01 GACAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGAATTTTAAAATCGTGAGGGTTCAAGTCCCTCTATCCCCAAGAAAAAGCCCAT Psilochilus_carinatus_er113_tr GACAACAATGAAATTTCTAGTAAAAGGAAAATCCGTCGAATTTTAAAATCGTGAGGGTTCAAGTCCCTCTATCCCCAAGAAAGAGCCCCT Psilochilus_modestus_ER65 GACAACAATGAAATTTCTAGTAAAAGGAAAATCCGTCGAATTTTAAAATCGTGAGGGTTCAAGTCCCTCTATCCCCAAGAAAGAGCCCCT Psilochilus_macrophyllus_ER02 GACAACAATGAAATTTCTAGTAAAAGGAAAATCCGTCGAATTTTAAAATCGTGAGGGTTCAAGTCCCTCTATCCCCAAGAAAGAGCCCCT Psilochilus_indet_015111 GACAACAATGAAATTTCTAGTAAAAGGAAAATCCGTCGAATTTTAAAATCGTGAGGGGTCAAGTCCC-CTATCCCCAAAAAAGAGCCCCT ER207 GACAACAATGAAATTTCTAGTAAAAGGAAAATCCGTCGAATTTTAAAATCGTGAGGGTTCAAGTCCCTCTATCCCCAAGAAAGAGCCCCT LJ8264 GACAACAATGAAATTTCTAGTAAAAGGAAAATCCGTCGAATT--AAAATCG-GATGT????????????????????????????????? ER92 GGCNACAATGAANTTT-TNGTAAGGGGAAAATCCGTCGAATTTTAAAATCGGGAGGGTTCAAGTCCCTCTATCCCCAAGAAAA-GCCCAA Psilochilus_sp.LJ5413_trnlF GACAACAATGAAATTTCTAGTAAAAGGAAAATCCGTCGAATTTTAAAATCGTGAGGGTTCAAGTCCCTCTATCCCCAAGAAAGAGCCCCT Psilochilus_ER208_1Mera GACAACAATGAAATTTCTAGTAAAAGGAAAATCCGTCGAATTTTAAAATCGTGAGGGTTCAAGTCCCTCTATCCCCAAGAAAGAGCCCCT LJ7955 ------TTTTAAA-TCGTGAGGGTTCAAGTCCCTCTATCCCCAAGAAAGAGCCCCT LJ5381_trnlf__part GACAACAATGAAATTTCTAGTAAAAGGAAAATCCGTCGAATTTTAAAATCGTGAGGGTTCAAGTCCCTCTATCCCCAAGAAAGAGCCCCT LJ6914_loja_outx GACAACAATGAAATTTTTAGTAAAAGGAAAATCCGTCGAATTTTAAAATCGTGAGGGTTCAAGTCCCTCTATCCCCAAGAAAGAGCCCCT LJ6860 GACAACAATGAAATTTCTAGTAAAAGGAAAATCCGTCGAATTTTAAAATCGKGAKGGTTCAAGTCCCTCTATCCCCAAGAAAGAGCCCCT

Monophyllorchis_sp TTT-ACTTCCTCGCTCTTTATTTATCCTCATCCTCTTTTTTTCCATCAGTGACT-CGATTCAAAATTAAACAAAATCCAATATTTTTCTC

426 Monophyllorchis_micorstyloides TTT-ACTTCCTCGCTCTTTATTTATCCTCATCCTCTTTTTTTTTTCCAGTGA------CAAAACCAAACAAAATCCAATAATTTTCTC Triphora_amazonica_Emerson_A06 TTT-ACTTCCTCG------TCCAATATCTTTCTC Triphora_trianthophora_ER19A TTT-ACTTCCTTG------TCCAATATCTTTCTT

Triphora_gentianoides_ER01 TTT-ACTTCCTCG------TCCAATATCTTTCTC Psilochilus_carinatus_er113_tr TTTTACTTCTTCAATCTTTTTTTATCCTCATCCTCTTTTTCTTTTTCAGTGGCTTCGGTTCAAAAAAAAA-----TCCAATATCTTTCTC Psilochilus_modestus_ER65 TTTTACTTCTTCAATCTTTTTTTATCCTCATCCTCTTTTTCTTTTTCAGTGGCT-CGGTTCAAAAAAA------TCCAATATCTTTCTC Psilochilus_macrophyllus_ER02 TTTTACTTCTTAAATCTTTTTTTATCCTCATCCTCTTTTTCTTTTTCAGTGGCT-CGGTTCAAAAAAA------TCCAATATCTTTCTC Psilochilus_indet_015111 TTTTACTTCT-CAATCTTTTTTTATCCTCATCCTCTTTTTCTTTTTCAGTGGCTTCGGTTCAAAAAAAAA-----TCCAATATCTTTCTC ER207 TTTTACTTCTTCAATCTTTTTTTATCCTCATCCTCTTTTTCTTTTTCAGTGGCTTCGGTTCAAAAAAAA------TCCAATATCTTTCTC LJ8264 ?????????????????????????????????????????????????????????????????????????????????????????? ER92 AAAAA-----TC-CCCNCTTATTATCCNCATCCTCTTTTTCATTTTCA-TAA-TAA-GTTCAAACAAAA------TTCAATATCTTTCTC Psilochilus_sp.LJ5413_trnlF TTTTACTTCTTCAATCTTTTTTTATCCTCATCCTCTTTTTCTTTTTCAGTGGCTTCGGTTCAAAAAAAA------TCCAATATCTTTCTC Psilochilus_ER208_1Mera TTTTACTTCTTCAATCTTTTTTTATCCTCATCCTCTTTTTCTTTTTCAGTGGCTTCGGTTCAAAAAAAA------TCCAATATCTTTCTC LJ7955 TTTTACTTCTTCAATCTTTTTTTATCCTCATCCTCTTTTTCTTTTTCAGTGGCTTCGGTTCAAAAAAAA------TCCAATATCTTTCTC LJ5381_trnlf__part TTTTACTTCTTCAATCTTTTTTTATCCTCATCCTCTTTTTCTTTTTCAGTGGCTTAGGTTCAAAAAAAA------TCCAATATCTTTCTC LJ6914_loja_outx TTTTACTTCTTCAATCTTTTTTTATCCTCATCCTCTTTTTCTTTTTCAGTGGCTTCGGTTCAAAAAAAAA-----TCCAATATCTTTCTC LJ6860 TTTTACTTCTTCAATCTTTTTTTATCCTCATCCTCTTTTTCTTTTTCAGTGGCTTCGGTTCAAAAAAAAA-----TCCAATATCTTTCTC

Continued

Table C. 1 Continued

Monophyllorchis_sp ATTTCTTTCCCTCTTTTCTTTAACAAAA------GGATCCGAATAGAAATCCTCATATCTTCTTCCAATCCAATTT-CCTCTGTTTTTT Monophyllorchis_micorstyloides ATTTCTTTCCCTCTTTTCTTTAACAAAA------GGATCCGAATATAAATCCTCATATCTTCTTCCAATCCAATTT-CCT--GGGGGTT Triphora_amazonica_Emerson_A06 ATTTCATTCACTCTGTTCTTTAACAGAA------GGATTCGAATATAAATACTCATATCTTCTTCCAATCCAATTT-CCTTTGTTTTTA Triphora_trianthophora_ER19A ATTTCATTCACTCTGTTCTTTAACAAAA------GGATTCGAATATAAATCCTCACATCTTCTTCCAATCCAATTT-CCTTTGTT---A Triphora_gentianoides_ER01 ATTTCATTCAATCTGTTCTTTAACAAAG------GGATTCGAATATAAATCCTCATATCTTCTTCCAATCCAATTT-CCTTTGTTTTTA Psilochilus_carinatus_er113_tr ATTTCATTAACTCTGTTCTTTAACAAAA------GGATCCGAATAGAAATCCTCATATCTTCTCCCAATCCAATTTTCCTTTGTTTTTT Psilochilus_modestus_ER65 ATTTCATTAACTCTGTTCTTTAACAAAAAACAAAAGGATCCG-ATATAAATCCTCATATCTTCTTCCAATCCAATTTTCCTTTGTTTTTT Psilochilus_macrophyllus_ER02 ATTTCATTAACTCTGTTCTTTAACAAAAAACAAAAGGATCCGAATATAAATCCTCATATCTTCTTCCAATCCAATTTTCCTTTGTTTTTT Psilochilus_indet_015111 ATTTCATTAACTCTGTTCTTTAACAAAA------GGATCCGAATAGAAATCCTCATATCTTCTCCCAATCCAATATTC??????????? ER207 ATTTCATTAACTCTGTTCTTTAACAAAA------GGATCCGAATAGAAATCCTCATATCTTCTCCCAATCCAATTTTCCTTTGTTGGTT LJ8264 ?????????????????????????????????????????????????????????????????????????????????????????? ER92 ATTTCATTCACTCTGTTNTTTCACAAAT------GGATCCGAATAGAAATCCTCGTATCTTCTTCCAATCCAATTT-CATTTGTTTTGT Psilochilus_sp.LJ5413_trnlF ATTTCATTAACTCTGTTCTTTAACAAAA------GGATCCGAATAGAAATCCTCATATCTTCTCCCAATCCAATTTTCCTTTGTTTTTT Psilochilus_ER208_1Mera ATTTCATTAACTCTGTTCTTTAACAAAA------GGATCCGAATAGAAATCCTCATATCTTCTCCCAATCCAATTTTCCTTTGTTTTTT LJ7955 ATTTCATTAACTCTGTTTTTTAACAAAA------GGATCCGAATAGAAATCCTCATATCTTCTCCCAATCCAATTTTCCTTTGTGTTTT LJ5381_trnlf__part ATTTCATTAACTCTGTTCTTTAACAAAA------GGATCCGAATAGAAATCCTCATATCTTCTCCCAATCCAATTTTCCTTTGTTTTTT LJ6914_loja_outx ATTTCATTAACTCTGTTCTTTAACAAAA------GGATCCGAATAGAAATCCTCATATCTTCTCCCAATCCAATTTTCCTTTGGTTTTT LJ6860 ATTTCATTAACTCTGTTCTTTAACAAAA------GGATCCGAATAGAAATCCTCATATCTTCTCCCAATCCAATTTTCCTTTGTTTTTT

427 Monophyllorchis_sp CTAGTACAATATCTGTACAAATGAACATATATGTTCAAGGAATCCGCGTTATTGAATCATTCACAGTCCTTATCTTTATCCTTACATTTC Monophyllorchis_micorstyloides CTAGTACAATATCTGTACAAA????????????????????????????????????????????????????????????????????? Triphora_amazonica_Emerson_A06 ATAGTACAATACCTGTACAAAGGAACATATATGTTCAAGGAATCCGC------CCTTAT------CCTTACATTTA

Triphora_trianthophora_ER19A ATAGTACAATATCTGTACAAAGGAACATATATGTTAAAGGAATCCGC------CCTTATCATCATCCTTACATTTT Triphora_gentianoides_ER01 ATAGTACAATACCTGTACAAAGGAACATATATGTTCAAGGAATCCGCATTATTGAATCATTCACAGTCCTTATCTTTATCCTTACATTTT Psilochilus_carinatus_er113_tr ATAGTACGATACCTGTACAAAGGAACATCTATCTTCAAGGAATTCAAATTCTTGAATCATTCACATTCCTTATGGGGATCCTTACATTTA Psilochilus_modestus_ER65 ATAG------AATTCACATTCTTGAATCATTCACATTCCTTAT------CCTTACATTTA Psilochilus_macrophyllus_ER02 ATAGTACGATACCTGTACAAAGGAACATCTATCTTCAAGGAATTCACATTCTTGAATCATTCACATTCCTTAT------CCTTACATTTA Psilochilus_indet_015111 ?????????????????????????????????????????????????????????????????????????????????????????? ER207 ATAGTACGATACCTGTACAAAGGAACATCTATCTTCAAGGAATTCAAATTCTTGAATCATTCACATTCCTTATCTTTATCCTTACATTTA LJ8264 ?????????????????????????????????????????????????????????????????????????????????????????? ER92 ATAGTACGATACCTGTACAAATGAACATATATGTTCAAGGAATCTCCGTTATTGAATCATTCACAGTCCATAT----TTCCNTACAT??? Psilochilus_sp.LJ5413_trnlF ATAGTACGATACCTGTACAAAGGAACATCTATCTTCAAGGAATTCAAATTCTTGAATCATTCACATTCCTTATCTTTATCCTTACATTTA Psilochilus_ER208_1Mera ATAGTACGATACCTGTACAAAGGAACATCTATCTTCAAGGAATTCAAATTCTTGAATCATTCACATTCCTTATCTTTATCCTTACATTTA LJ7955 ATAGTACGATACCTGTACAAAGGAACATCTATCTTCAAGGAATTCACATTCTTGAATCATTCACATTCCTTATCTTTATCCTTACATTTA LJ5381_trnlf__part -TA-TACGATACCTGTACAAANGAACATCTATCTTCAAGGAATTCAAATTCTTGAATCATTCACATTCCTTATCTTTATCCTTACATTTA LJ6914_loja_outx ATAGTACGATACCTGTACAAAGGAACATCTATCTTCAAGGAATTCAAATTCTTGAATCATTCACATTCCTTATCTTTATCCTTACATTTA LJ6860 ATAGTACGATACCTGTACAAAGGAACATCTATCTTCAAGGAATTCACATTCTTGAATCATTCACATTCCTTATCTTTATCCTTACATTTA

Continued

Table C. 1 Continued

Monophyllorchis_sp AAAATTTTGAAGATCTAAGAAATTCAGGGGCTAGGTCCAATTWGTTAAGACGTTCTTTTTTAGTTCTTTTCATTGACAT------AGAT Monophyllorchis_micorstyloides ?????????????????????????????????????????????????????????????????????????????????????????? Triphora_amazonica_Emerson_A06 AAAGG------AAGACCTTCCTTCTTAGTTCTTTTCATTGACATTG-ACAGAGAT Triphora_trianthophora_ER19A TAAA------AATACTTTATTTTTTAGTTCTTTTCATTGACATTG-ACAAAGAT Triphora_gentianoides_ER01 AAAAG------AAGACTTTCTTTTTTAGTTCTTTTCGTTGACATAG-ATATAAAT Psilochilus_carinatus_er113_tr AAAGG------AAGACTTTCTTTTTTAGTTCTTTTCATTGACATAGGACA????? Psilochilus_modestus_ER65 AAAAG------AAGACTTTATTTTTTAGTTCTTTTCATTGACATAGGACATAGAT Psilochilus_macrophyllus_ER02 AAAAG------AAGACTTTATTTTTTAGTTCTTTTCATTGACATAGGACATAGAT Psilochilus_indet_015111 ?????????????????????????????????????????????????????????????????????????????????????????? ER207 AAAGG------AAGACTTTCTTTTTTAGTTCTTTTCATTGACATAGGACATAGAT LJ8264 ?????????????????????????????????????????????????????????????????????????????????????????? ER92 ?????????????????????????????????????????????????????????????????????????????????????????? Psilochilus_sp.LJ5413_trnlF AAAGG------AAGACTTTCTTTTTTAGTTCTTTTCATTGACATAGGACATAGAT Psilochilus_ER208_1Mera AAAGG------AAGACTTTCTTTTTTAGTTCTTTTCATTGACATAGGACATAGAT LJ7955 AAAGG------AAGACTTTCTTTTTTAGTTCTTTTCATTGACATAG-ACATCTTG LJ5381_trnlf__part AAAGG------AAGACTTTCTTTTTTAGTTCTTTTCATTGACATAGGAC?????? LJ6914_loja_outx AAAGG------AAGACTTTCTTTTTTAGTTCTTTTCATTGACATAGGACATAGAT LJ6860 AAAGG------AAGACTTTCTTTTTTAGTTCTTTTCATTGACATAGGACATAGAT

428 Monophyllorchis_sp AT?????001001000100?1??000000000000???1????0000000010011010000001000?100000011?01100000100 Monophyllorchis_micorstyloides ????????????0000100?1??000000000000??10?0000000000010011010000001000?100000011?00000000100 Triphora_amazonica_Emerson_A06 AT-AAA-100010000110?1??000000001??0?100?00001??0001?00000010?111?0101010??1????00000000100

Triphora_trianthophora_ER19A AAGATAT101000000110?1??000000001??0?100?0000000?1???00?????0100001000000?10????00?10000100 Triphora_gentianoides_ER01 AGGAAAG11?000000110?1??0000000001?0?100?000000010???10??????1000010000001001?0100??1000110 Psilochilus_carinatus_er113_tr ?????????????????????????????????????????????????????0???????????????????????????????00000 Psilochilus_modestus_ER65 ATGTAAG10010000010000000000000001?00000000000000000000001?01000000000001000000010000000010 Psilochilus_macrophyllus_ER02 ATGTAAG10000000010000000000000000?10000000000000000000001?01000000?1??01000000010000000010 Psilochilus_indet_015111 ????????000000010000000000000000010000010?100000000000001?01000000000001000000010000000010 ER207 ATGTAAG10000000100100000000010000?10000101010010000000001?01000000000001000000010000001010 LJ8264 ???????1000000101000000000000000010000000?100000000000001?01000000000001000000010000000010 ER92 ????????????0000100100101?10?010010100000?100000000001??????????????????????????0?1011???? Psilochilus_sp.LJ5413_trnlF ATGTAAG1000000001000000000000000010000000?100000000000001?01000000000001000000010000000010 Psilochilus_ER208_1Mera ATGTAAG1000001001000010000000000010000000?100000000000001?01000000000001000000010000000010 LJ7955 ATGTAAG?000001010000001101?1?1000?1000001??00100010000001?01000000000001000000010000000011 LJ5381_trnlf__part ?????????????????????????????????????????????????????0????????0000001001000000010000000010 LJ6914_loja_outx ATGTAAG1000000101000000000000000010000000?100000000000001?01000000000001000000010000000010 LJ6860 ATGTAAG1000000001000000000000000010000000?100000000000001?01000000000001000000010000000010

Continued

Monophyllorchis_sp 00000001?1??000000100000100100000001000010100000000001?? Monophyllorchis_micorstyloides 00001001?1??000100000000000100000?1??00010110000???????? Triphora_amazonica_Emerson_A06 0001?01??00000000000000000010001????????101000001?101011 Triphora_trianthophora_ER19A 000011???00000000000000000110001????????101010001001?010 Triphora_gentianoides_ER01 00001000100000000000000000010001????????1010000000001010 Psilochilus_carinatus_er113_tr 101??00000010000000000000000000000000001100000000000100? Psilochilus_modestus_ER65 001??000000100000000000000000000000101??010000010?101000 Psilochilus_macrophyllus_ER02 001??000000100000000000000000000000101??000000000?101000 Psilochilus_indet_015111 001??00000010000000000000100010000000001100????????????? ER207 001??0000001000000000000000000000000001?1000000000001000 LJ8264 001??0000001000000000101???????????????????????????????? ER92 ????????????101011011000001010101100101?10100000010????? Psilochilus_sp.LJ5413_trnlF 011??0000001000000000000000000000000001?1000000000001000 Psilochilus_ER208_1Mera 001??0000001000000000000000000000000001?1000000000001000 LJ7955 001??000000101???????010000000000000001?1000000000001010 LJ5381_trnlf__part 001??000001?000000000000000000000000001?100001100000100? LJ6914_loja_outx 001??000000100000000000000000000000000011000000000001000 LJ6860 001??000000100000000000000000000000000011000000000001000 429

APPENDIX D

TABLE OF ACCESSIONS USED IN THE MOLECULAR ANALYSES OF

CHAPTERS 2, 3, AND 5.

430

Genus species ITS trnL-F nad1B-C Altensteinia palacea O-535 Aphyllorchis montana MWC21777 MWC21777 Aphyllorchis pallida O-797 Aplectrum hyemale O-104 AF519959 JVF104 Bletia purpurea O-581 C342/AY008451 Bletilla striata 556 556 Brownleea caerulea AJ000138 AF360512, AF360455 21870 Calypso bulbosa O-490 AF519960 JVF Cephalanthera austiniae DAT115 DAT115

431 Cephalanthera damasonium AY146446 AJ409381 575

Cephalanthera longifolia AY369083 Chysis bractescens O-436 AF266971 436 Codonorchis lessonii AF348005 AJ409387 O-1398 Coelia triptera MWC324 AF266972 324 Corallorhiza trifida JVF 2080 JVF2080 Corycium carnosum AJ409391 O-692 Corycium nigrescens AJ000126 O-695 Corymborkis sp. O-542 O-542 Corymborkis verticillata ER66 ER66 ER66 Diceratostele gabonensis ER44 ER44

Continued Table D.1. List of accessions used in the molecular analyses. AJ, AY, or AF= Genbank accessions; DAT= S. Datwyler; ER= E. Rothacker; JVF= J. Freudenstein; MWC=M. Chase; O = Kew DNA bank accessions; N and G = M. Whitten et al., V= Vargas

Table D.1 Continued

Genus species ITS trnL-F nad1B-C Didymoplexis pallens ER132 ER132 Disperis lindleyana O-696 Elleanthus cynarocephalus G14 Elleanthus lancifolius ER36 ER36 Elleanthus oliganthus ER37 Elleanthus sp. O-374 O-374 AF314871 Elleanthus tricallosus N565 Ephippianthus schmidtii Inoue, sin. JVF

432 Epilyna hirtzii N526 N526

Epilyna jimenzeii ER67 ER67 W2997 Epipactis fageticola AY351382 Epipactis helleborine AF521059 AJ409408 199 Epipactis lusitanica AY351381 Epipactis sp. O-199 Epipogium aphyllum O-19248 O-19248 Epipogium roseum EPR Eulophia nuda O-292 O-292 O-292 Gastrodia confusia O-8091 Gastrodia procera ER64 ER64 Gastrodia sesamoides O-534 Gastrodia sp. Reunion Island ER214

Continued

Table D.1 Continued

Genus species ITS trnL-F nad1B-C Gastrodia zeylanica O16313 Goodyera macranatha AF366894 Goodyera pubescens O-212 ? O-212 Govenia liliacea AF519916 Govenia sp. O-146 AF314879 Habinaria repens O-381 Isochilus amparoanus MWC204 AF266962 204 Leptotes bicolor 1195 AF267014 1195

433 Limodorum abortivum O-924 O-924 O-924

Limodorum sp. JVF Listera convoluta 2707 Listera cordata JVF2580 JVF2850 Listera smallii AF521058 AJ409422 486 Monadenia bracteata AJ000117 AJ409387 Monophyllorchis maculata ER40 O-435 O-435 Monophyllorchis microstyloides ER108 Monophyllorchis sp. cf maculata MWC435 MWC435 Neottia nidus-avis AY351383 JVF JVF Neottia sp. O-573 Nervilia aragoana AJ409431 Nervilia holochila AF324178

Continued

Table D.1 Continued

Genus species ITS trnL-F nad1B-C Nervilia plicata AF324179 ER48 ER48 Nervilia shirensis C280 AF519945 C280 Orchis quadripunctata O-545 Oreorchis patens Inoue, sin. Inoue, sin. Pachyplectron arifolium O-529 Palmorchis powellii V2115 V2115/ER215 Palmorchis silvicola ER72 Palmorchis sp. ER112

434 Palmorchis sp. ER129

Palmorchis sp. cf trilobulata ER211 ER211 Palmorchis sp. cf. trilobulata O-462 AJ409435 Palmorchis sp.1 ER110 Palmorchis sp.2 ER110 Palmorchis trilobulata ER68 Platylepis polyadenia AJ539520 AJ544501 Ponera striata MWC197 AF266965 Psilochilus ecuadoriensis LJ7955 Psilochilus macrophyllus ER02 ER02 Psilochilus modestus ER65 Psilochilus mollis ER207 Psilochilus mollis ER208-1

Continued

Table D.1 Continued

Genus species ITS trnL-F nad1B-C Psilochilus mollis LJ5381 Psilochilus mollis LJ5413 Psilochilus mollis LJ5414 Psilochilus mollis O15111 Psilochilus mollis LJ8264 Psilochilus mollis LJ6914 LJ6914 Psilochilus mollis LJ6860 Psilochilus physurifolius ER101

435 Psilochilus sp. ER113

Pterygodium catholicum AJ00012 AJ40944 Sertifera columbiana ER38 ER38 ER38 Sertifera sp. N565 N565 Sobralia amabilis G18 Sobralia crocea W533 W533 W533 Sobralia fimbriata ER39 Sobralia mucronata W353 W353 W353 Spiranthes cernua O-402 Stenoglottis longifolia O-1136 Triphora amazonica ER73 ER73 ER73 Triphora gentianoides ER01 ER01 ER01 Triphora trianthophora ER19 ER19 ER19

Continued

Table D.1 Continued

Genus species ITS trnL-F nad1B-C Tropidia bambusifolia O-17721 Tropidia curculigoides O-5560 Tropidia effusa MWC 211 MWC 211/AJ409456 MWC 211 Tropidia graminae O-21775 O-21775 O-21775 Tropidia polystaychya W2830

436 Wullschlaegelia aphylla ER128

Xerorchis amazonica O-799 O-799 O-799 Xerorchis sp. MWC12601

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