Nuclear genes, matK and the phylogeny of the Poales

Phylogenetic relationships within the monocot order Poales have been well studied, but several unrelated questions remain. These include the relationships among the basal families in the order, family delimitations within the restiid clade, and the search for nuclear single-copy gene loci to test the relationships based on chloroplast loci. To this end two nuclear loci (PhyB, Topo6) were explored both at the ordinal level, and within the Bromeliaceae and the restiid clade. First, a plastid reference tree was inferred based on matK, using 140 taxa covering all APG IV families of Poales, and analyzed using parsimony, maximum likelihood and Bayesian methods. The trees inferred from matK closely approach the published phylogeny based on whole-plastome sequencing. Of the two nuclear loci, Topo6 supported a congruent, but much less resolved phylogeny. By contrast, PhyB indicated different phylogenetic relationships, with, inter alia, Mayacaceae and Typhaceae sister to Poaceae, and Flagellariaceae in a basally branching position within the Poales. Within the restiid clade the differences between the three markers appear less serious. The Anarthria clade is first diverging in all analyses, followed by Restionoideae, Sporadanthoideae, Centrolepidoideae and Leptocarpoideae in the matK and Topo6 data, but in the PhyB data Centrolepidoideae diverges next, followed by a paraphyletic Restionoideae with a clade consisting of the monophyletic Sporadanthoideae and Leptocarpoideae nested within them. The Bromeliaceae phylogeny obtained from Topo6 is insufficiently sampled to make reliable statements, but indicates a good starting point for further investigations. We find that matK is remarkably good at retrieving the chloroplast phylogeny, that Topo6, despite low resolution, is suitable to test the generality of the plastid phylogeny as a taxic phylogeny, that PhyB might be too complex to be really useful at the level of families within an order, that the inclusion of the centrolepids in Restionaceae might be valid, but that there is no phylogenetic support for or against including the Anarthria clade in Restionaceae. The basal arrangement of families in the Poales (Bromeliaceae, Typhaceae, Rapateaceae) remains unresolved.