title: Phylotranscriptomic analysis of the origin and early diversification of land plants.
abstract: Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximum-likelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.
authors.affiliation: Chicago Botanic Garden, Glencoe, IL 60022; Program in Biological Sciences, Northwestern University, Evanston, IL 60208; nwickett@chicagobotanic.org gane@ualberta.ca jleebensmack@plantbio.uga.edu.
authors.forename: Norman J
authors.initials: NJ
authors.lastname: Wickett
authors.affiliation: Department of Computer Science, University of Texas, Austin, TX 78712;
authors.forename: Siavash
authors.initials: S
authors.lastname: Mirarab
authors.affiliation: Department of Computer Science, University of Texas, Austin, TX 78712;
authors.forename: Nam
authors.initials: N
authors.lastname: Nguyen
authors.affiliation: Department of Computer Science, University of Texas, Austin, TX 78712;
authors.forename: Tandy
authors.initials: T
authors.lastname: Warnow
authors.affiliation: Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9;
authors.forename: Eric
authors.initials: E
authors.lastname: Carpenter
authors.affiliation: iPlant Collaborative, Tucson, AZ 85721; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721;
authors.forename: Naim
authors.initials: N
authors.lastname: Matasci
authors.affiliation: Department of Plant Biology, University of Georgia, Athens, GA 30602;
authors.forename: Saravanaraj
authors.initials: S
authors.lastname: Ayyampalayam
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721;
authors.forename: Michael S
authors.initials: MS
authors.lastname: Barker
authors.affiliation: Department of Biology and.
authors.forename: J Gordon
authors.initials: JG
authors.lastname: Burleigh
authors.affiliation: Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611;
authors.forename: Matthew A
authors.initials: MA
authors.lastname: Gitzendanner
authors.affiliation: Department of Biology and Department of Biological Sciences, Eastern Kentucky University, Richmond, KY 40475; Florida Museum of Natural History, Gainesville, FL 32611;
authors.forename: Brad R
authors.initials: BR
authors.lastname: Ruhfel
authors.affiliation: Department of Biology, Pennsylvania State University, University Park, PA 16803;
authors.forename: Eric
authors.initials: E
authors.lastname: Wafula
authors.affiliation: Department of Biology, Pennsylvania State University, University Park, PA 16803;
authors.forename: Joshua P
authors.identifier: http://orcid.org/0000-0001-9668-2525
authors.initials: JP
authors.lastname: Der
authors.affiliation: Department of Botany and.
authors.forename: Sean W
authors.initials: SW
authors.lastname: Graham
authors.affiliation: Arnold Arboretum of Harvard University, Cambridge, MA 02138;
authors.forename: Sarah
authors.initials: S
authors.lastname: Mathews
authors.affiliation: Botanical Institute, Universität zu Köln, Cologne D-50674, Germany;
authors.forename: Michael
authors.initials: M
authors.lastname: Melkonian
authors.affiliation: Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611; Florida Museum of Natural History, Gainesville, FL 32611;
authors.forename: Douglas E
authors.initials: DE
authors.lastname: Soltis
authors.affiliation: Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611; Florida Museum of Natural History, Gainesville, FL 32611;
authors.forename: Pamela S
authors.initials: PS
authors.lastname: Soltis
authors.affiliation: Florida Museum of Natural History, Gainesville, FL 32611;
authors.forename: Nicholas W
authors.initials: NW
authors.lastname: Miles
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708; Department of Zoology, University of British Columbia, Vancouver, BC, Canada V6T 1Z4;
authors.forename: Carl J
authors.initials: CJ
authors.lastname: Rothfels
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708; Department of Biodiversity and Conservation, Real Jardín Botánico-Consejo Superior de Investigaciones Cientificas, 28014 Madrid, Spain;
authors.forename: Lisa
authors.initials: L
authors.lastname: Pokorny
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708;
authors.forename: A Jonathan
authors.initials: AJ
authors.lastname: Shaw
authors.affiliation: New York Botanical Garden, Bronx, NY 10458;
authors.forename: Lisa
authors.initials: L
authors.lastname: DeGironimo
authors.affiliation: New York Botanical Garden, Bronx, NY 10458;
authors.forename: Dennis W
authors.initials: DW
authors.lastname: Stevenson
authors.affiliation: Botanical Institute, Universität zu Köln, Cologne D-50674, Germany;
authors.forename: Barbara
authors.initials: B
authors.lastname: Surek
authors.affiliation: Department fur Biologie, Systematische Botanik und Mykologie, Ludwig-Maximilians-Universitat, 80638 Munich, Germany;
authors.forename: Juan Carlos
authors.initials: JC
authors.lastname: Villarreal
authors.affiliation: Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Succursale Centre-Ville, Montreal, QC, Canada H3C 3J7;
authors.forename: Béatrice
authors.initials: B
authors.lastname: Roure
authors.affiliation: Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Succursale Centre-Ville, Montreal, QC, Canada H3C 3J7; CNRS, Station d' Ecologie Expérimentale du CNRS, Moulis, 09200, France;
authors.forename: Hervé
authors.initials: H
authors.lastname: Philippe
authors.affiliation: Department of Biology, Pennsylvania State University, University Park, PA 16803;
authors.forename: Claude W
authors.initials: CW
authors.lastname: dePamphilis
authors.affiliation: Shenzhen Fairy Lake Botanical Garden, The Chinese Academy of Sciences, Shenzhen, Guangdong 518004, China;
authors.forename: Tao
authors.initials: T
authors.lastname: Chen
authors.affiliation: Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9;
authors.forename: Michael K
authors.initials: MK
authors.lastname: Deyholos
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109;
authors.forename: Regina S
authors.initials: RS
authors.lastname: Baucom
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, MO 63132;
authors.forename: Toni M
authors.initials: TM
authors.lastname: Kutchan
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, MO 63132;
authors.forename: Megan M
authors.initials: MM
authors.lastname: Augustin
authors.affiliation: BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: CNRS, Station d' Ecologie Expérimentale du CNRS, Moulis, 09200, France;
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and.
authors.forename: Zhijian
authors.initials: Z
authors.lastname: Tian
authors.affiliation: BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and.
authors.forename: Zhixiang
authors.initials: Z
authors.lastname: Yan
authors.affiliation: BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and.
authors.forename: Xiaolei
authors.initials: X
authors.lastname: Wu
authors.affiliation: BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and.
authors.forename: Xiao
authors.initials: X
authors.lastname: Sun
authors.affiliation: Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9; BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and Department of Medicine, University of Alberta, Edmonton, AB, Canada T6G 2E1 nwickett@chicagobotanic.org gane@ualberta.ca jleebensmack@plantbio.uga.edu.
authors.forename: Gane Ka-Shu
authors.initials: GK
authors.lastname: Wong
authors.affiliation: Department of Plant Biology, University of Georgia, Athens, GA 30602; nwickett@chicagobotanic.org gane@ualberta.ca jleebensmack@plantbio.uga.edu.
authors.forename: James
authors.initials: J
authors.lastname: Leebens-Mack
mesh_terms: D018744:DNA, Plant / Q000235:genetics / Q000378:metabolism; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D018745:Genome, Plant / Q000502:physiology*; D010802:Phylogeny; D019655:Quantitative Trait, Heritable; D016415:Sequence Alignment; D057949:Streptophyta / Q000145:classification / Q000502:physiology*; D059467:Transcriptome / Q000502:physiology*
chemical_list: D018744:DNA, Plant
keywords: Streptophyta; land plants; phylogenomics; phylogeny; transcriptome