Comprehensive phylogenomic time tree of bryophytes reveals deep relationships and uncovers gene incongruences in the last 500 million years of diversification

However, the timing of key events in the phylogeny, and the degree to which the observed homoplasy represents error or biological processes, remain poorly resolved.

Methods

Using the GoFlag probe set, we sampled 405 exons representing 228 nuclear genes for 531 species from 51 of the 53 orders of bryophytes. We inferred the species phylogeny from gene tree analyses using concatenated and coalescence approaches, assessed gene conflict, and estimated the timing of divergences based on 29 fossil calibrations. Results The phylogeny resolves many relationships across the bryophytes, enabling us to resurrect five liverwort orders and recognize three more, and propose ten new orders of mosses.

Most orders originated in the Jurassic or earlier and diversified in the Cretaceous or later. The phylogenomic data also highlight topological conflict in parts of the tree, suggesting complex processes of diversification that cannot be adequately captured in a single gene tree topology. Conclusions We sampled hundreds of homologous loci across a broad phylogenetic spectrum spanning at least 450 Ma of evolution, and these data resolved many of the critical nodes of the diversification of bryophytes.

The data also highlight the need to explore the mechanisms underlying the phylogenetic ambiguity at specific nodes. The phylogenomic data provide an expandable framework toward reconstructing a comprehensive phylogeny of bryophytes and for investigating the transformations of traits in this important group of plants.