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 relationship..., , , =====================Files correspond to
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Comprehensive phylogenomic time tree of bryophytes reveals deep relationships and uncovers gene incongruences in the last 500 million years of diversification

Julia Bechteler\*, Gabriel Peñaloza-Bojacá\*, David Bell, Gordon Burleigh\*, Stuart McDaniel, Christine Davis, Emily Sessa, Alexander Bippus, D.Christine Cargill, Sahut Chantanoarrapint, Isabel Draper, Lorena Endara, Laura L. Forrest, Ricardo Garilleti,Sean W. Graham, Sanna Huttunen, Javier Jauregui Lazo, Francisco Lara, Juan Larraín, Lily Lewis, David Long, Dietmar Quandt, Karen Renzaglia, Alfons Schäfer-Verwimp, Adriel Sierra Pinilla, Matt von Konrat, Charles Zartman, Marta Regina Pereira, Bernard Goffinet *& Juan Carlos Villarreal A.*

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1\. Scripts used in this study are listed in 1\_Scripts\_GoFlag\_BryophytePhylogenomics\.txt

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2\. Nucleotide \(NT\) dataset and corresponding analyses
2-1) Nucleotide-Alignments are stored in t...