TL;DR: Despite substantial variation in the overall rate of molecular evolution among lineages, inferred amounts of change among codon-position data partitions are correlated with each other across the monocot tree, consistent with low incongruence between these partitions.
Abstract: We use multiple photosynthetic, chlororespiratory, and plastid translation apparatus loci and their associated noncoding regions (ca. 16 per taxon, prior to alignment) to make strongly supported inferences of the deep internal branches of monocot phylogeny. Most monocot relationships are robust (an average of ca. 91% bootstrap support per branch examined), including those poorly supported or unresolved in other studies. Our data strongly support a sister-group relationship between Asparagales and the commelinid monocots, the inclusion of the orchids in Asparagales, and the status of Petrosaviaceae as the sister group of all monocots except Acorus and Alismatales. The latter finding supports recognition of the order Petrosaviales. Also strongly supported is a placement of Petermannia disjunct from Colchicaceae (Liliales) and a sister-group relationship between Commelinales and Zingiberales. from highlight the remaining weak areas of monocot phylogeny, including Commelinales and Zingiberales. Liliales, and Pandanales. Despite substantial variation in the overall rate of molecular evolution among lineages, inferred amounts of change among codon-position data partitions are correlated with each other across the monocot tree, consistent with low incongruence between these partitions. Ceratophyllum and Chloranthaceae appear to have a destabilizing effect on the these partitions. Ceratoamong other angiosperms; the issue of monocot placement in broader angiosperm phylogeny remains problematic.
TL;DR: Cumulative analyses of genes ranked by decreasing numbers of informative characters indicated continued fluctuation in support, even as small genes were added to a nearly complete matrix, contrary to the expected pattern of stabilization in support.
TL;DR: The numbers of species in families of the revised Commelinidae are related partly to the extent of adaptive radiation in those families, but seem more strongly related to nonadaptive features promoting speciation, such as restricted seed dispersal, polyploidy, aneuploidsy, and apomixis.
TL;DR: The phylogeny supports the most recent classification of the family with monophyletic tribes Tradescantieae (minus Palisota) and Commelineae, but is highly incongruent with a morphology-based phylogeny.
Abstract: The chloroplast-encoded gene rbcL was sequenced in 30 genera of Commelinaceae to evaluate intergeneric relationships within the family. The Australian Cartonema was consistently placed as sister to the rest of the family. The Commelineae is monophyletic, while the monophyly of Tradescantieae is in question, due to the position of Palisota as sister to all other Tradescantieae plus Commelineae. The phylogeny supports the most recent classification of the family with monophyletic tribes Tradescantieae (minus Palisota) and Commelineae, but is highly incongruent with a morphology-based phylogeny. This incongruence is attributed to convergent evolution of morphological characters associated with pollination strategies, especially those of the androecium and inflorescence. Analysis of the combined data sets produced a phylogeny similar to the rbcL phylogeny. The combined analysis differed from the molecular one, however, in supporting the monophyly of Dichorisandrinae. The family appears to have arisen in the Old World, with one or possibly two movements to the New World in the Tradescantieae, and two (or possibly one) subsequent movements back to the Old World; the latter are required to account for the Old World distribution of Coleotrypinae and Cyanotinae, which are nested within a New World clade.