title: The deepest divergences in land plants inferred from phylogenomic evidence.
abstract: Phylogenetic relationships among the four major lineages of land plants (liverworts, mosses, hornworts, and vascular plants) remain vigorously contested; their resolution is essential to our understanding of the origin and early evolution of land plants. We analyzed three different complementary data sets: a multigene supermatrix, a genomic structural character matrix, and a chloroplast genome sequence matrix, using maximum likelihood, maximum parsimony, and compatibility methods. Analyses of all three data sets strongly supported liverworts as the sister to all other land plants, and analyses of the multigene and chloroplast genome matrices provided moderate to strong support for hornworts as the sister to vascular plants. These results highlight the important roles of liverworts and hornworts in two major events of plant evolution: the water-to-land transition and the change from a haploid gametophyte generation-dominant life cycle in bryophytes to a diploid sporophyte generation-dominant life cycle in vascular plants. This study also demonstrates the importance of using a multifaceted approach to resolve difficult nodes in the tree of life. In particular, it is shown here that densely sampled taxon trees built with multiple genes provide an indispensable test of taxon-sparse trees inferred from genome sequences.
authors.affiliation: Department of Ecology and Evolutionary Biology, University Herbarium, University of Michigan, Ann Arbor, MI 48109-1048, USA. ylqiu@umich.edu
authors.forename: Yin-Long
authors.initials: YL
authors.lastname: Qiu
authors.forename: Libo
authors.initials: L
authors.lastname: Li
authors.forename: Bin
authors.initials: B
authors.lastname: Wang
authors.forename: Zhiduan
authors.initials: Z
authors.lastname: Chen
authors.forename: Volker
authors.initials: V
authors.lastname: Knoop
authors.forename: Milena
authors.initials: M
authors.lastname: Groth-Malonek
authors.forename: Olena
authors.initials: O
authors.lastname: Dombrovska
authors.forename: Jungho
authors.initials: J
authors.lastname: Lee
authors.forename: Livija
authors.initials: L
authors.lastname: Kent
authors.forename: Joshua
authors.initials: J
authors.lastname: Rest
authors.forename: George F
authors.initials: GF
authors.lastname: Estabrook
authors.forename: Tory A
authors.initials: TA
authors.lastname: Hendry
authors.forename: David W
authors.initials: DW
authors.lastname: Taylor
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Testa
authors.forename: Mathew
authors.initials: M
authors.lastname: Ambros
authors.forename: Barbara
authors.initials: B
authors.lastname: Crandall-Stotler
authors.forename: R Joel
authors.initials: RJ
authors.lastname: Duff
authors.forename: Michael
authors.initials: M
authors.lastname: Stech
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Frey
authors.forename: Dietmar
authors.initials: D
authors.lastname: Quandt
authors.forename: Charles C
authors.initials: CC
authors.lastname: Davis
mesh_terms: D018745:Genome, Plant; D016013:Likelihood Functions; D008969:Molecular Sequence Data; D005810:Multigene Family; D010802:Phylogeny; D010944:Plants / Q000145:classification / Q000235:genetics