title: Phylogenetic relationships in Epidendroideae (Orchidaceae), one of the great flowering plant radiations: progressive specialization and diversification.
abstract: OBJECTIVE
  The largest subfamily of orchids, Epidendroideae, represents one of the most significant diversifications among flowering plants in terms of pollination strategy, vegetative adaptation and number of species. Although many groups in the subfamily have been resolved, significant relationships in the tree remain unclear, limiting conclusions about diversification and creating uncertainty in the classification. This study brings together DNA sequences from nuclear, plastid and mitochrondrial genomes in order to clarify relationships, to test associations of key characters with diversification and to improve the classification.
  
  
  METHODS
  Sequences from seven loci were concatenated in a supermatrix analysis for 312 genera representing most of epidendroid diversity. Maximum-likelihood and parsimony analyses were performed on this matrix and on subsets of the data to generate trees and to investigate the effect of missing values. Statistical character-associated diversification analyses were performed.
  
  
  RESULTS
  Likelihood and parsimony analyses yielded highly resolved trees that are in strong agreement and show significant support for many key clades. Many previously proposed relationships among tribes and subtribes are supported, and some new relationships are revealed. Analyses of subsets of the data suggest that the relatively high number of missing data for the full analysis is not problematic. Diversification analyses show that epiphytism is most strongly associated with diversification among epidendroids, followed by expansion into the New World and anther characters that are involved with pollinator specificity, namely early anther inflexion, cellular pollinium stalks and the superposed pollinium arrangement.
  
  
  CONCLUSIONS
  All tested characters show significant association with speciation in Epidendroideae, suggesting that no single character accounts for the success of this group. Rather, it appears that a succession of key features appeared that have contributed to diversification, sometimes in parallel.
authors.affiliation: Herbarium, Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43212, USA, Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey TW9 3AE, UK and School of Plant Biology, The University of Western Australia, Crawley, WA 600, Australia freudenstein.1@osu.edu.
authors.forename: John V
authors.initials: JV
authors.lastname: Freudenstein
authors.affiliation: Herbarium, Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43212, USA, Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey TW9 3AE, UK and School of Plant Biology, The University of Western Australia, Crawley, WA 600, Australia Herbarium, Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43212, USA, Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey TW9 3AE, UK and School of Plant Biology, The University of Western Australia, Crawley, WA 600, Australia.
authors.forename: Mark W
authors.initials: MW
authors.lastname: Chase
mesh_terms: D044822:Biodiversity; D005075:Biological Evolution; D002467:Cell Nucleus / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D029595:Orchidaceae / Q000033:anatomy & histology / Q000737:chemistry / Q000145:classification* / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D018087:Plastids / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial; D010940:Plant Proteins
keywords: Epidendroideae; Orchidaceae; diversification; epiphytism; missing data; phylogenetics