Phylogenetic relationships among the mosses based on heterogeneous Bayesian analysis of multiple genes from multiple genomic compartments

Nucleotide sequences fromeight nuclear, chloroplast, andmitochondrial genes were obtained from30mosses (plus four outgroup liverworts) in order to resolve phylogenetic relationships among the major clades of division Bryophyta. Phylogenetic analyses were conducted using maximum parsimony, maximum likelihood (ML), and Bayesian inference. Inferences were compared from Bayesian analyses using homogeneous and several heterogeneous models. Estimates of clade con dence were based on bootstrap analyses, posterior probabilities (in Bayesian analyses) and novel combined approaches. Most ingroup relationships were congruent among analyses, but support for individual clades depended on the analytical approach. Increasingly parameterized models of nucleotide substitution in the likelihood analyses provided signi cantly higher goodness-of- t to the data. The results suggest that 1) the Bryophyta, including Sphagnum and Takakia, are monophyletic, 2) Andreaea and Andreaeobryum form a monophyletic group, 3) Oedipodium grif thianum is sister to all other operculate taxa, 4) mosses with nematodontous peristomes are paraphyletic and basal to arthrodontous mosses, 5) Diphyscium is sister to all other arthrodontous mosses, 6) Encalypta is sister to the Funariaceae, and 6) mosses with diplolepideousalternate peristomes form a monophyletic group. Implications of the phylogenetic hypothesis formorphological evolution in mosses include 1) a pseudopodium has arisen independently in Sphagnum and Andreaea, 2) the mucilage hairs of Andreaeobryum and Takakia are non-homologous, 3) the stomata found in Sphagnum are not homologous to those of other mosses, and 4) that stomata were absent in the ancestor of all mosses