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Molecular Phylogeny of the Portulacaceous Cohort Wendy Linn Applequist Iowa State University

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Molecular Phylogeny of the Portulacaceous Cohort Wendy Linn Applequist Iowa State University Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 1999 Molecular phylogeny of the portulacaceous cohort Wendy Linn Applequist Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Botany Commons, and the Genetics Commons Recommended Citation Applequist, Wendy Linn, "Molecular phylogeny of the portulacaceous cohort " (1999). Retrospective Theses and Dissertations. 12438. https://lib.dr.iastate.edu/rtd/12438 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Retrospective Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. INFORMATION TO USERS This manuscript has been reproduced from the microfilm master. UMI films the text directly from the original or copy submitted. Thus, some thesis and dissertation copies are in typewriter face, while others may be from any type of computer printer. The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleedthrough, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send UMI a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, charts) are reproduced by sectioning the original, beginning at tine upper left-hand comer and continuing from left to right in equal sections with small overlaps. Photographs included in the original manuscript have been reproduced xerographically in this copy. Higher quality 6" x 9" black and white photographic prints are available for any photographs or illustrations appearing in this copy for an additional charge. Contact UMI directiy to order. Bell & Howell Information and Leaming 300 North Zeeb Road, Ann Arbor, Ml 48106-1346 USA UIVQ 800-521-0600 Molecular phylogeny of the portulacaceous cohort by Wendy Linn Appiequist A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Botany (Systematics and Evolution) Major Professor: Robert S. Wallace Iowa State University Ames, Iowa 1999 Copyright © Wendy Lirm Appiequist, 1999. All rights reserved. UMI Number 9950074 UMI ® UMI Microform9950074 Copyright 2000 by Bell & Howell Information and Learning Company. All rights reserved. This microform edition is protected against unauthorized copying under Title 17, United States Code. Bell & Howell infonnation and Learning Company 300 North Zeeb Road P.O. Box 1346 Ann Arbor, Ml 48106-1346 ii Graduate College Iowa State University This is to certify that the Doctoral dissertation of Wendy Linn Applequist has met the dissertation requirements of Iowa State University Signature was redacted for privacy. Signature was redacted for privacy. For the Major Program Signature was redacted for privacy. For the Graduate College iii TABLE OF CONTENTS GENERAL INTRODUCTION 1 Taxonomic Problems in the Portulacaceous Cohort 1 Dissertation Organization 2 Literature Cited 4 HISTORY OF TAXONOMIC CLASSIFICATION DM THE PORTULACACEOUS COHORT 6 Monophyly of the Order Caryophyllales 6 Phylogenetic Affinities of the Basellaceae Moquin-Tandon 8 Phylogenetic Affinities of the Cactaceae A. L. de Jussieu 9 Phylogenetic Affinities of the Didiereaceae Drake del Castillo 10 Phylogenetic Affinities of the Portulacaceae A. L. de Jussieu 11 Molecular Support for the Portulacaceous Cohort 12 Infrafamilial Classification of the Portulacaceae 13 Literature Cited 19 PHYLOGENY OF THE PORTULACACEOUS COHORT BASED ON NDHF SEQUENCE DATA 25 Abstract 25 Introduction 25 Materials and Methods 28 Results 31 Discussion 33 Acknowledgements 40 Literature Cited 41 PHYLOGENY OF THE MADAGASCAN ENDEMIC FAMILY DIDIEREACEAE 54 Abstract 54 Introduction 54 Material and Methods 56 Results 58 Discussion 60 Acknowledgements 64 References 64 MOLECULAR PHYLOGENY AND NOMENCLATURE IN TYGSEANACAMPSEROTEAE {PORTUIACACEAE) 74 Abstract 74 Introduction 74 Materials and Methods 76 Results 78 Discussion 79 Acknowledgements 82 Literature Cited 83 iv GENERAL CONCLUSIONS 91 General Conclusions and Recommendations for Future Research 91 Literature Cited 94 ACKNOWLEDGMENTS 96 1 GENERAL INTRODUCTION Taxonomic Problems in the Portulacaceous Cohort The portulacaceous cohort or alliance generally refers to the four families Basellaceae, Cactaceae, Didiereaceae, and Portulacaceae. These families belong to the order Caryophyllales, which is strongly supported as monophyletic due to the presence of many unique synapomorphies (Cronquist 1981). Succulence and a variety of adaptations to xerophytism are found in several families of the order, including these four. In Cronquist's view, the Portulacaceae and Basellaceae were sister lineages, while the Cactaceae and Didiereaceae were more closely related to the Aizoaceae. The cohort was first recognized by Thome (1976), and its monophyly is supported by both morphological data (Hershkovitz 1993) and rbcL sequence analysis (Rettig et al. 1992). Relationships among the four constiment families are complicated by evidence (Hershkovitz and Zimmer 1997) that the Cactaceae, Basellaceae, and Didiereaceae may all have arisen from within a paraphyletic Portulacaceae. The Portulacaceae comprise about 500 species in over 20 genera. Many of these are highly modified succulents subjected to various selective pressures that may have complicated traditional infrafamilial classifications based on morphology. Pax and Hoffman's (1934) treatment of the family in Die natiirlichen Pflanzenfamilien recognized two subfamilies; however, later researchers have unanimously rejected this taxonomy. Recent attempts at classification have divided the family into as many as eight tribes (Nyananyo 1990), with tribes consisting of only one or a few genera. Nevertheless, these 2 classifications (see also McNeill 1974; Carolin 1987, 1993) propose directly conflicting relationships among major genera. As morphological smdies have failed to provide satisfactory understanding of evolutionary pattem within the cohort, the use of molecular methods is desirable. Hershkovitz and Zinmier (1997) performed a phylogenetic analysis of ITS sequences, which indicated that the Portulacaceae were paraphyletic. The intent of the present research was to use chloroplast DNA sequences to explore this finding fiarther, as weU as to achieve better resolution of the major lineages within the Portulacaceae. Sequences of the chloroplast gene ndhF were used to produce a phylogeny of the entire cohort. This gene evolves somewhat faster than rbcL, providing considerable resolution at the familial level, but is not variable enough to resolve closely related subclades in these plants. More rapidly evolving, noncoding regions of chloroplast DNA were therefore employed to study evolutionary pattem within two clearly monophyletic lineages, the Didiereaceae and Tribe Anacampseroteae. Dissertation Organization The first chapter of this dissertation, entitled "History of taxonomic classification in the portulacaceous cohort," summarizes the progress of understanding of the relationships among the four families of the cohort, from initial placement within different orders to the recognition of close kinship. Additionally, the literature pertaining to classification solely within the Portulacaceae is reviewed; major competing classifications are summarized, and their shared features and inconsistencies are addressed. Areas of the family that have presented particular taxonomic challenges are noted, as well as certain potentially paraphyletic or polyphyletic generic concepts. 3 The second chapter, entitled "Phylogeny of the portuJacaceous cohort based on ndhF sequence data," is a manuscript prepared for submission to Systematic Botany. Technical information is presented regarding the use of ndhF, including Caryophyllales-specific primer sequences and suitable protocols. The results of phylogenetic analyses of sequences from almost forty portulacaceous taxa are presented. The Portulacaceae sensu lato were divided into two main lineages, one of which included the Cactaceae, Portulaca, Talinella, the Anacampseroteae, and most of Talinum, and the other of which included the Basellaceae, Didiereaceae, Portulacarieae, Calyptrotheca, the Western North American genera of Portulacaceae, and all of the taxa formerly considered as Calandrinia sensu lato. Evidence is presented that the generic circumscriptions of Talinum and Cistantke remain overly broad. The congruence of these results with competing previous classifications is briefly discussed, as are the possible implications for future classification of the cohort. The third chapter, entitled "Phylogeny of the Madagascan endemic family Didiereaceae," is a manuscript that has been submitted to Plant Systematics and Evolution. The Didiereaceae are a family of eleven species with a unique vegetative morphology and a very limited range. This paper, which uses sequences of three non-coding cpDNA regions, presents the first evidence that the sister group of the family is the East African genus Calyptrotheca, a result that is strongly supported. Very little cpDNA variation
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