Kocyan, A; Vogel, E F; Conti, E; Gravendell, B (2008). Molecular phylogeny of Aerides (Orchidaceae) based on one nuclear and two plastid markers: a step in understanding the evolution of the Aeridinae. Molecular Phylogenetics and Evolution, 48(2):422-443. Postprint available at: http://www.zora.uzh.ch University of Zurich Posted at the Zurich Open Repository and Archive, University of Zurich. Zurich Open Repository and Archive http://www.zora.uzh.ch Originally published at: Molecular Phylogenetics and Evolution 2008, 48(2):422-443. Winterthurerstr. 190 CH-8057 Zurich http://www.zora.uzh.ch Year: 2008 Molecular phylogeny of Aerides (Orchidaceae) based on one nuclear and two plastid markers: a step in understanding the evolution of the Aeridinae Kocyan, A; Vogel, E F; Conti, E; Gravendell, B Kocyan, A; Vogel, E F; Conti, E; Gravendell, B (2008). Molecular phylogeny of Aerides (Orchidaceae) based on one nuclear and two plastid markers: a step in understanding the evolution of the Aeridinae. Molecular Phylogenetics and Evolution, 48(2):422-443. Postprint available at: http://www.zora.uzh.ch Posted at the Zurich Open Repository and Archive, University of Zurich. http://www.zora.uzh.ch Originally published at: Molecular Phylogenetics and Evolution 2008, 48(2):422-443. Molecular phylogeny of Aerides (Orchidaceae) based on one nuclear and two plastid markers: a step in understanding the evolution of the Aeridinae Abstract Phylogenetic relationships of the orchid genus Aerides (Epidendroideae, Vandeae, Aeridinae) from Southeast Asia were inferred from DNA sequences of one nuclear (nrITS) and two plastid (matK, trnL-trnL-F) regions of 48 taxa (21 Aerides, 25 other Aeridinae, 2 outgroup). Analyses of the combined datasets with parsimony, maximum likelihood and Bayesian methods revealed that Aerides is monophyletic and consists of three well-supported subclades which are only partly in accordance with previous sectional delimitations based on floral characters. The two different flower types in Aerides (hidden versus open spur entrance) seem to have evolved at least twice in geographically distinct areas. The phylogeny presented here is yet another example in Orchidaceae where floral morphology cannot be relied on to reconstruct phylogenetic history but rather is the result of pollinator-driven selection. The Aerides subclades are characterized by three different length classes of the mutation-rich P8 region in the trnL intron. To our knowledge, this is the first time that the P8 region was studied in orchids. The matK gene has been assumed to be a pseudogene in orchids due to occasional occurrence of frameshift indels, low transition/transversion (ts:tv) ratios and low substitution rates at the 3rd codon position. However, matK does not appear to be a pseudogene in Aerides and a comparison with data from other angiosperms suggests that ts:tv ratios and low substitution rates have been overestimated as arguments for a pseudogene status of matK in orchids. Accepted Manuscript Molecular phylogeny of Aerides (Orchidaceae) based on one nuclear and two plastid markers: a step forward in understanding the evolution of the Aeridinae Alexander Kocyan, Ed F. de Vogel, Elena Conti, Barbara Gravendeel PII: S1055-7903(08)00059-6 DOI: 10.1016/j.ympev.2008.02.017 Reference: YMPEV 2790 To appear in: Molecular Phylogenetics and Evolution Received Date: 5 July 2007 Revised Date: 19 January 2008 Accepted Date: 2 February 2008 Please cite this article as: Kocyan, A., de Vogel, E.F., Conti, E., Gravendeel, B., Molecular phylogeny of Aerides (Orchidaceae) based on one nuclear and two plastid markers: a step forward in understanding the evolution of the Aeridinae, Molecular Phylogenetics and Evolution (2008), doi: 10.1016/j.ympev.2008.02.017 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. ACCEPTED MANUSCRIPT 1 Running head: Phylogeny of Aerides (Orchidaceae) 2 3 Molecular phylogeny of Aerides (Orchidaceae) based on one 4 nuclear and two plastid markers: a step forward in understanding 5 the evolution of the Aeridinae 6 7 Alexander Kocyan a,b,*, Ed F. de Vogel a, Elena Conti b, Barbara 8 Gravendeel a 9 10 a Nationaal Herbarium Nederland, Universiteit Leiden Branch, P.O. Box 9514, 2300 RA 11 Leiden, The Netherlands 12 b Institute of Systematic Botany, University of Zurich, Zollikerstrasse 107, CH-8008 Zurich, 13 Switzerland 14 * Corresponding author. [email protected]; present address: Institute of 15 Systematic Botany, Ludwig Maximilian University, Menzinger Strasse 67, D-80638 Munich, 16 Germany; Tel.: 0049 89 17861 228, Fax: 0049 89 172638 CCEPTED MANUSCRIPT A 1 ACCEPTED MANUSCRIPT 17 Abstract 18 Phylogenetic relationships of the orchid genus Aerides (Epidendroideae, Vandeae, 19 Aeridinae) from Southeast Asia were inferred from DNA sequences of one nuclear (nrITS) 20 and two plastid (matK, trnL-trnL-F) regions of 48 taxa (21 Aerides, 25 other Aeridinae, 2 21 outgroup). Analyses of the combined datasets with parsimony, maximum likelihood and 22 Bayesian methods revealed that Aerides is monophyletic and consists of three well-supported 23 subclades which are only partly in accordance with previous sectional delimitations based on 24 floral characters. The two different flower types in Aerides (hidden versus open spur 25 entrance) seem to have evolved at least twice in geographically distinct areas. The phylogeny 26 presented here is yet another example in Orchidaceae where floral morphology can not be 27 relied on to reconstruct phylogenetic history but rather is the result of pollinator driven 28 selection. The Aerides subclades are characterized by three different length classes of the 29 mutation-rich P8 region in the trnL intron. To our knowledge, this is the first time that the P8 30 region was studied in orchids. The matK gene has been assumed to be a pseudogene in 31 orchids due to occasional occurrence of frameshift indels, low transition/transversion (ts:tv) 32 ratios and low substitution rates at the 3rd codon position. However, matK does not appear to 33 be a pseudogene in Aerides and a comparison with data from other angiosperms suggests that 34 ts:tv ratios and low substitution rates have been overestimated as arguments for a pseudogene 35 status of matK in orchids. 36 37 Keywords: Bayesian analysis, biogeography, inversion, maximum likelihood, matK, orchids, 38 pseudogene, pollinatCCEPTEDor-driven selection, parsimony , MANUSCRIPTsecondary folding, sectional 39 reorganisation, trAnL intron 40 41 1. Introduction 2 ACCEPTED MANUSCRIPT 42 43 The orchid genus Aerides Lour. consists of approximately 21 southeast Asian species 44 ranging from India to Papua New Guinea. Aerides has a monopodial growth habit with more 45 or less succulent leaves. Plants are medium to large-sized epi- or lithophytes with mostly 46 pinkish coloured, heavily scented flowers. Their fragrance has made them a valuable source 47 for the production of numerous artificial hybrids and cultivars. Aerides was described by 48 Loureiro in 1790. The scientific name (gr. aer = air, eides = coming from) refers to the 49 epiphytic growth habit, which was extraordinary for scientists in the eighteenth century. 50 After Aerides was first described, many species previously placed in other genera have 51 been moved to it. Conversely, dozens of orchid species once included in Aerides have now 52 been removed from it (Table 1). Additionally, some species were described more than once 53 under different names, reflecting the widespread occurrence of the genus throughout tropical 54 Asia. Over the past two centuries, it gradually became clear that a combination of specialized 55 column, lip, and spur morphology provides useful diagnostic characters for generic 56 circumscription (Christenson, 1986). The flowers of Aerides species have a long column foot, 57 i.e., a ventral extension of the column to which the lateral sepals and the lip are connected 58 (Fig. 1). The lip is mostly three-lobed, bears longitudinal ridges and is attached to the top of 59 the column foot with or without a hinge. The spur is curved forward and the rostellum has a 60 longitudinal incision that divides it in two parts. 61 Lindley (1833) included 26 species in Aerides and was the first who proposed an 62 infrageneric delimitation advocating five sections (Cuculla, Tubera, Fornicaria, Pilearia, 63 Ornithochilus). OnlyCCEPTED three of the species included byMANUSCRIPT Lindley were considered to be 64 congeneric with Aerides by later authors. Bentham (1883) recognized 16 species, of which six 65 remained in Aerides in two sections (Planifoliae, Teretifoliae). Pfitzer (1889) also proposed a 66 subgeneric classification of Aerides. In his treatment, five sections (Euaerides, Fieldingia, 3 ACCEPTED MANUSCRIPT 67 Teretifolia, Ornithochilus, Phalaenidium) were described comprising 15 species, of which 68 only three (A. odorata, A. quinquevulnera, A. rosea [= A. fieldingii]) are still placed in 69 Aerides. Later, Hooker (1894) proposed three sections containing a total of 15 species. Only 70 two of these sections include species still recognised as belonging to Aerides. Subsequent 71 authors, e. g. Garay