Wickett, Norman J., Mirarab, Siavash ORCID: 0000-0001-5410-1518, Warnow, Tandy, Carpenter, Eric, Matasci, Naim ORCID: 0000-0003-4416-048X, Ayyampalayam, Saravanaraj, Barker, Michael S., Burleigh, J. Gordon, Gitzendanner, Matthew A., Ruhfel, Brad R., Wafula, Eric, Der, Joshua P., Graham, Sean W., Mathews, Sarah ORCID: 0000-0002-5518-7541, Melkonian, Michael, Soltis, Douglas E., Soltis, Pamela S., Miles, Nicholas W., Rothfels, Carl J., Pokorny, Lisa ORCID: 0000-0002-2478-8555, Shaw, A. Jonathan, DeGironimo, Lisa, Stevenson, Dennis W., Surek, Barbara, Villarreal, Juan Carlos, Roure, Beatrice, Philippe, Herve, dePamphilis, Claude W., Chen, Tao, Deyholos, Michael K., Baucom, Regina S., Kutchan, Toni M., Augustin, Megan M., Wang, Jun ORCID: 0000-0002-8540-8931, Zhang, Yong, Tian, Zhijian, Yan, Zhixiang, Wu, Xiaolei, Sun, Xiao, Wong, Gane Ka-Shu and Leebens-Mack, James ORCID: 0000-0003-4811-2231 (2014). Phylotranscriptomic analysis of the origin and early diversification of land plants. Proc. Natl. Acad. Sci. U. S. A., 111 (45). S. E4859 - 10. WASHINGTON: NATL ACAD SCIENCES. ISSN 0027-8424

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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 inmolecular 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 datamatrix or to phylogeneticmethod, 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.

Item Type: Journal Article
Creators:
CreatorsEmailORCIDORCID Put Code
Wickett, Norman J.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Mirarab, SiavashUNSPECIFIEDorcid.org/0000-0001-5410-1518UNSPECIFIED
Warnow, TandyUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Carpenter, EricUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Matasci, NaimUNSPECIFIEDorcid.org/0000-0003-4416-048XUNSPECIFIED
Ayyampalayam, SaravanarajUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Barker, Michael S.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Burleigh, J. GordonUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Gitzendanner, Matthew A.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Ruhfel, Brad R.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wafula, EricUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Der, Joshua P.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Graham, Sean W.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Mathews, SarahUNSPECIFIEDorcid.org/0000-0002-5518-7541UNSPECIFIED
Melkonian, MichaelUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Soltis, Douglas E.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Soltis, Pamela S.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Miles, Nicholas W.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Rothfels, Carl J.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Pokorny, LisaUNSPECIFIEDorcid.org/0000-0002-2478-8555UNSPECIFIED
Shaw, A. JonathanUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
DeGironimo, LisaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Stevenson, Dennis W.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Surek, BarbaraUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Villarreal, Juan CarlosUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Roure, BeatriceUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Philippe, HerveUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
dePamphilis, Claude W.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Chen, TaoUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Deyholos, Michael K.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Baucom, Regina S.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Kutchan, Toni M.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Augustin, Megan M.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wang, JunUNSPECIFIEDorcid.org/0000-0002-8540-8931UNSPECIFIED
Zhang, YongUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Tian, ZhijianUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Yan, ZhixiangUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wu, XiaoleiUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Sun, XiaoUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wong, Gane Ka-ShuUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Leebens-Mack, JamesUNSPECIFIEDorcid.org/0000-0003-4811-2231UNSPECIFIED
URN: urn:nbn:de:hbz:38-423454
DOI: 10.1073/pnas.1323926111
Journal or Publication Title: Proc. Natl. Acad. Sci. U. S. A.
Volume: 111
Number: 45
Page Range: S. E4859 - 10
Date: 2014
Publisher: NATL ACAD SCIENCES
Place of Publication: WASHINGTON
ISSN: 0027-8424
Language: English
Faculty: Unspecified
Divisions: Unspecified
Subjects: no entry
Uncontrolled Keywords:
KeywordsLanguage
CHLOROPLAST GENOME SEQUENCE; CLOSEST LIVING RELATIVES; GREEN-ALGA MOUGEOTIA; SEED PLANTS; PHYLOGENETIC RECONSTRUCTION; EARLIEST ANGIOSPERMS; MULTIGENE PHYLOGENY; EXTANT GYMNOSPERMS; PLASTID GENOMES; EARLY EVOLUTIONMultiple languages
Multidisciplinary SciencesMultiple languages
URI: http://kups.ub.uni-koeln.de/id/eprint/42345

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