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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.

SUBMITTER: Wickett NJ 

PROVIDER: S-EPMC4234587 | biostudies-literature | 2014 Nov

REPOSITORIES: biostudies-literature

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Phylotranscriptomic analysis of the origin and early diversification of land plants.

Wickett Norman J NJ   Mirarab Siavash S   Nguyen Nam N   Warnow Tandy T   Carpenter Eric E   Matasci Naim N   Ayyampalayam Saravanaraj S   Barker Michael S MS   Burleigh J Gordon JG   Gitzendanner Matthew A MA   Ruhfel Brad R BR   Wafula Eric E   Der Joshua P JP   Graham Sean W SW   Mathews Sarah S   Melkonian Michael M   Soltis Douglas E DE   Soltis Pamela S PS   Miles Nicholas W NW   Rothfels Carl J CJ   Pokorny Lisa L   Shaw A Jonathan AJ   DeGironimo Lisa L   Stevenson Dennis W DW   Surek Barbara B   Villarreal Juan Carlos JC   Roure Béatrice B   Philippe Hervé H   dePamphilis Claude W CW   Chen Tao T   Deyholos Michael K MK   Baucom Regina S RS   Kutchan Toni M TM   Augustin Megan M MM   Wang Jun J   Wang Jun J   Zhang Yong Y   Tian Zhijian Z   Yan Zhixiang Z   Wu Xiaolei X   Sun Xiao X   Wong Gane Ka-Shu GK   Leebens-Mack James J  

Proceedings of the National Academy of Sciences of the United States of America 20141029 45


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  ...[more]

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