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

Premise Bryophytes 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, which have highlighted exten...

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Published in:	American journal of botany Vol. 110; no. 11; pp. e16249 - n/a
Main Authors:	Bechteler, Julia, Peñaloza‐Bojacá, Gabriel, Bell, David, Gordon Burleigh, J., McDaniel, Stuart F., Christine Davis, E., Sessa, Emily B., Bippus, Alexander, Christine Cargill, D., Chantanoarrapint, Sahut, Draper, Isabel, Endara, Lorena, Forrest, Laura L., Garilleti, Ricardo, Graham, Sean W., Huttunen, Sanna, Lazo, Javier Jauregui, Lara, Francisco, Larraín, Juan, Lewis, Lily R., Long, David G., Quandt, Dietmar, Renzaglia, Karen, Schäfer‐Verwimp, Alfons, Lee, Gaik Ee, Sierra, Adriel M., Konrat, Matt, Zartman, Charles E., Pereira, Marta Regina, Goffinet, Bernard, Villarreal A., Juan Carlos
Format:	Journal Article
Language:	English
Published:	United States Botanical Society of America, Inc 01-11-2023
Subjects:	Aquatic plants Bryophyta Bryophyta - genetics Bryophytes Coalescence Cretaceous Cretaceous diversification Diversification Exons Hepatophyta - genetics Homoplasy hornworts Jurassic land plants liverworts Mosses New orders Nodes phylogenetic discordance Phylogenetics Phylogeny Plant biomass Plants - genetics rapid diversification target capture Topology mosses target capture liverworts phylogenetic discordance hornworts rapid diversification Cretaceous diversification land plants
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Summary:	Premise Bryophytes 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, which have highlighted extensive homoplasy in various traits and repeated bursts of diversification. However, the timing of key events in the phylogeny, patterns, and processes of diversification across bryophytes remain unclear. Methods Using the GoFlag probe set, we sequenced 405 exons representing 228 nuclear genes for 531 species from 52 of the 54 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 10 new orders of mosses. Most orders originated in the Jurassic 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 loci across a broad phylogenetic spectrum spanning at least 450 Ma of evolution; 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 this important group of plants.
Bibliography:	Julia Bechteler, Gabriel Peñaloza‐Bojacá, J. Gordon Burleigh, Bernard Goffinet, and Juan Carlos Villarreal A. contributed equally to this article. ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	0002-9122 1537-2197
DOI:	10.1002/ajb2.16249