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

Abstract

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.

Phylogenetic relationships within Orchidaceae based on a low-copy nuclear coding gene, Xdh: Congruence with organellar and nuclear ribosomal DNA results

“…Other molecular studies have produced results more similar to ours. Cameron (2006) found Earina to be sister (but with less than 50% bootstrp support) to Calypsoeae using combined atpB and rbcL plastid data, but his study did not include other Agrostophyllinae. Our result is clearly in contradiction to that of Van den Berg et al (2005), who used the same DNA samples.…”

Understanding angiosperm diversification using small and large phylogenetic trees

“…For example, while many analyses place Amborella as sister to the rest of angiosperms, there is also the possibility that Amborella and Nymphaeales go together ( Leebens-Mack et al, 2005 ;Soltis et al, 2007 ). We also examined alternative relationships among the major clades within the Mesangiospermae (i.e., the placement of Chloranthaceae; Jansen et al, 2007 ), among the early-branching lineages within Monocotyledonae (i.e., the placement of Acorales; Davis et al, 2004 ;Chase et al, 2006 ), within Orchidaceae (i.e., the arrangement of Vanilloideae and Cyprepedioideae; Cameron, 2006 ;Ramirez et al, 2007 ), and within Asteraceae (i.e., the arrangement of Stiffi oideae, Mutisioideae, and Wunderlichioideae; Funk, 2002 , 2008 ;Funk et al, 2005 ).…”

“…For relationships within monocots, we relied on Chase et al (2006) , and for eudicots, we used Worberg et al (2007) . For Orchidaceae, we relied on Cameron (2006) , and we used the Grass Phylogeny Working Group (2001) tree for Poaceae. Finally, we referred to the trees of Wojciechowski et al (2004) and Bruneau et al (2008) for relationships within Fababceae and to the study of Panero and Funk (2008) for backbone relationships within Asteraceae.…”

Conserved differential expression of paralogous DEFICIENS‐ and GLOBOSA‐like MADS‐box genes in the flowers of Orchidaceae: refining the ‘orchid code’

“…Therefore, we investigated the wider applicability of the 'orchid code' by measuring and comparing the expression of the unique GLO-like gene and the four DEF-like genes in the outer tepals, inner lateral tepals, labellum, gynostemium and ovary of Vanilla planifolia and Phragmipedium longifolium, as well as in wild-type and peloric flowers of the horticultural variety Phalaenopsis hybrid 'Athens'. Vanilla planifolia and Phragmipedium longifolium represent the Vanilloideae and Cypripedioideae, two groups of orchids with an intermediate phylogenetic position between the diverse Orchidoideae and Epidendroideae and the basalmost Apostasioideae (Figure 1c; Cameron, 2006). Unfortunately, we were not able to include species from the Apostasioideae in our analyses because they are not available in cultivation beyond their range in Southern Asia.…”