A Comparison and Combination of Plastid atpB and rbcL Gene Sequences for Inferring Phylogenetic Relationships within Orchidaceae

Parsimony analyses of DNA sequences from the plastid genes atpB and rbcL were completed for 173 species of Orchidaceae (representing 150 different genera) and nine genera from outgroup families in Asparagales. The atpB tree topology is similar to the rbcL tree, although the atpB data contain less homoplasy and provide greater jackknife support than rbcL alone. In combination, the two-gene tree recovers five monophyletic clades corresponding to subfamilies within Orchidaceae, and fully resolves them with moderate to high jackknife support as follows: Epidendroideae are sister to Orchidoideae, followed by Cypripedioideae, then Vanilloideae, and with Apostasioideae sister to the entire family. Although this two-gene hypothesis of orchid phylogeny is an improvement over all single-gene studies published to date, there is still no consensus as to how all the tribes of Epidendroideae are related to one another. Nevertheless, these new topologies help to clarify some of the anomalous results recovered when rbcL was previously analyzed alone, and demonstrate the value of continued plastid gene sequencing within Orchidaceae.