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

Premise Bryophytes, land plants defined by a free-living gametophyte and
an unbranched sporophyte, form a major component of terrestrial plant
biomass, structuring ecological communities in all biomes. Our
understanding of the evolutionary history of hornworts, liverworts and
mosses has been significantly reshaped by inferences from molecular data,
highlighting extensive homoplasy in various traits and repeated bursts 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.