Paul J. Kores

A phylogenetic analysis of the Orchidaceae: evidence from rbcL nucleotide sequences

Cladistic parsimony analyses of rbcL nucleotide sequence data from 171 taxa representing nearly all tribes and subtribes of Orchidaceae are presented here. These analyses divide the family into five primary monophyletic clades: apostasioid, cypripedioid, vanilloid, orchidoid, and epidendroid orchids, arranged in that order. These clades, with the exception of the vanilloids, essentially correspond to currently recognized subfamilies. A distinct subfamily, based upon tribe Vanilleae, is supported for Vanilla and its allies. The general tree topology is, for the most part, congruent with previously published hypotheses of intrafamilial relationships; however, there is no evidence supporting the previously recognized subfamilies Spiranthoideae, Neottioideae, or Vandoideae. Subfamily Spiranthoideae is embedded within a single clade containing members of Orchidoideae and sister to tribe Diurideae. Genera representing tribe Tropideae are placed within the epidendroid clade. Most traditional subtribal units are supported within each clade, but few tribes, as currently circumscribed, are monophyletic. Although powerful in assessing monophyly of clades within the family, in this case rbcL fails to provide strong support for the interrelationships of the subfamilies (i.e., along the spine of the tree). The cladograms presented here should serve as a standard to which future morphological and molecular studies can be compared.

Molecular phylogenetics of Diseae (Orchidaceae): a contribution from nuclear ribosomal ITS sequences

We present here the first molecular phylogeny of tribe Diseae (Orchidoideae: Orchidaceae). Nuclear ribosomal ITS1, 5.8S rDNA, and ITS2 sequences were compared for 30 Diseae, 20 Orchideae, and four Cranichideae and Diurideae outgroups. ITS - rDNA sequences exhibited a transition:transversion ratio of 1.3 and extensive ITS length polymorphism. Phylogenetic analyses using maximum parsimony identified seven major core orchidoid groups. The branching order of the five Diseae and two Orchideae clades was weakly supported but indicated paraphyly of Diseae, with Disperis sister to the rest, followed by successive divergence of Brownleea, Disinae, Coryciinae sensu stricto (s.s.), Satyriinae, and terminated by Orchidinae plus Habenariinae. Within the monophyletic Disinae, Herschelia and Monadenia were nested within a paraphyletic Disa and clustered with D. sect. Micranthae. Within monophyletic Satyriinae, Satyridium rostratum plus Satyrium bicallosum was sister to the rest of Satyrium, and then Satyrium nepalense plus S. odorum was distinct from a cluster of six species. Coryciinae are paraphyletic because Disperis is sister to all other core orchidoids. Coryciinae s.s. are sister to Satyriinae plus Orchideae, with Pterygodium nested within Corycium. Maximum likelihood analysis supported possible affinities among Disinae, Brownleeinae, and Coryciinae but did not support monophyly of Diseae or an affinity between Disinae and Satyriinae. Morphological characters are fully congruent with the well-supported groups identified in the ITS phylogeny.

AN EXPANDED PLASTID DNA PHYLOGENY OF ORCHIDACEAE AND ANALYSIS OF JACKKNIFE BRANCH SUPPORT STRATEGY

An expanded plastid DNA phylogeny for Orchidaceae was generated from sequences of rbcL and matK for representatives of all five subfamilies. The data were analyzed using equally weighted parsimony, and branch support was assessed with jackknifing. The analysis supports recognition of five subfamilies with the following relationships: (Apostasioideae (Vanilloideae (Cypripedioideae (Orchidoideae (Epidendroideae))))). Support for many tribal-level groups within Epidendroideae is evident, but relationships among these groups remain uncertain, probably due to a rapid radiation in the subfamily that resulted in short branches along the spine of the tree. A series of experiments examined jackknife parameters and strategies to determine a reasonable balance between computational effort and results. We found that support values plateau rapidly with increased search effort. Tree bisection-reconnection swapping in a single search replicate per jackknife replicate and saving only two trees resulted in values that were close to those obtained in the most extensive searches. Although this approach uses considerably more computational effort than less extensive (or no) swapping, the results were also distinctly better. The effect of saving a maximal number of trees in each jackknife replicate can also be pronounced and is important for representing support accurately.

Phylogenetics of Arethuseae (Orchidaceae) Based on Plastid matK and rbcL Sequences

Abstract Circumscriptions of Arethuseae have varied since the tribe was first described by John Lindley in 1840, containing over ninety genera among the different authors. The latest system of Arethuseae defined by Dressler, including around thirty genera, is the most commonly accepted today. The goals of this study are to assess whether Arethuseae sensu Dressler and component subtribes are monophyletic and evaluate the position(s) of Arethuseae within Orchidaceae. Sequences of two plastid genes, matK and rbcL, have been obtained for 24 representative genera of Arethuseae in Dresslers latest two taxonomic systems for the tribe, plus 46 other genera throughout Orchidaceae. Both separate and combined analyses of the matK and rbcL data indicate that the tribe may not be monophyletic, which is also true for most subtribes within Arethuseae. Furthermore, matK data suggest that this gene may be non-functional within Orchidaceae. Communicating Editor: Kathleen A. Kron

Phylogenetic relationships within Korthalsella (Viscaceae) based on nuclear ITS and plastid trnL-F sequence data

The nuclear encoded internal transcribed spacer (ITS) region and the plastid encoded trnL-F region were sequenced for 25 populations of Korthalsella, a genus of reduced, monoecious, Old World misletoes. The molecular study confirms the hypothesis that branch shape and cladotaxy (the arrangement of branches with respect to their parent axis) are unreliable indicators of relationship in the genus and demonstrates that many of the taxa previously recognized are not monophyletic. Both gene regions identify three major subgroups within the genus and find lower level relationships within these subgroups highly correlated with geographic distance. An analysis based upon 18S and rbcL sequences identifiesGinalloa as the sister group to Korthalsella, which together with the branching order within the genus, indicates that Korthalsella originated in Papuasia and aids in elucidating evolution of the peculiar inflorescence structure. There are problems associated with species delimitation when evolutionary units are more restricted than morphological lineages, and justification is offered for recognizing only morphologically diagnosable monophyletic lineages as species. Varying substitution rates and differing modes of inheritance in ITS and trnL-F result in complementary utility of the two regions for elucidating infrageneric relationships in Korthalsella.

Inexpensive digital data acquisition for morphometric study

Three programs for digital (i.e. not requiring RGB video input) image analysis on IBM-PC compatible computers, and one on Macintosh computers, are discussed with regard to their use in morphometric applications. Measurement-TV provides a least-cost solution for IBM compatibles, though with reduced capabilities compared to other programs. The Image family of public domain programs provide excellent capabilities on high-end Macintoshes.