Congruence and consensus in the cotton tribe (Malvaceae)

We explored the evolutionary history of the Gossypieae and Gossypium using phylogenetic analysis of biparentally and maternally inherited characters. Separate and combined data sets were analyzed and incongruence between data sets was quantified and statistically evaluated. At the tribal level, phylogenetic analyses of nuclear ribosomal ITS sequences yielded trees that are highly congruent with those derived from the plastid gene ndhF, except for species that have a reticulate evolutionary history or for clades supported by few characters. Problematic taxa were then pruned from the data sets and the phylogeny was inferred from the combined data. Results indicate that 1) the Gossypieae is monophyletic, with one branch from the first split being represented by modem Cienfuegosia; 2) Thespesia is not monophyletic, and 3) Gossypium is monophyletic and sister to an unexpected clade consisting of the Hawaiian genus Kokia and the east African/Madagascan genus Gossypioides. Based on the magnitude of ndhF sequence divergence, we suggest that Kokia and Gossypioides diverged from each other in the Pliocene, subsequent to their apparent loss of a pair of chromosomes via chromosome fusion. Phylogenetic relationships among species and ''genome groups'' in Gossypium were assessed using cpDNA restriction site variation and ITS sequence data. Both data sets support the monophyly of each genome group, once taxa known or suspected to have reticulate histories are pruned from the trees. There was little congruence between these two data sets, however, with respect to relationships among genome groups. Statistical tests indicate that most incongruence is not significant and that it probably reflects insufficient information rather than a biological process that has differentially affected the data sets. We propose thai the differing cpDNA- and ITS-based resolutions of genome groups in Gossypium reflect temporally closely spaced divergence events early in the diversification of the genus. This ''short internode'' phenomenon is suggested to be a common cause of phylogenetic incongruence.