WickettMirarabNamEtAl2014

Référence

Wickett, N.J., Mirarab, S., Nam, N, Warnow, T., Carpenter, E., Matasci, N., Ayyampalayam, S., Barker, Mi.S., Burleigh, J. G., Gitzendanner, M.A., Ruhfel, B.R., Wafula, E., Der, Joshua P., Graham, S.W., Mathews, S., Melkonian, M., Soltis, D.E., Soltis, P.S., Miles, N.W., Rothfels, C.J., Pokorny, L., Shaw, A. J., DeGironimo, L., Stevenson, D.W., Surek, B., Villarreal, J.C., Roure, B., Philippe, H., dePamphilis, C.W., Chen, T., Deyholos, M.K., Baucom, R.S., Kutchan, T.M., Augustin, M.M., Wang, J., Zhang, Y., Tian, Z., Yan, Z., Wu, X., Sun, X., Wong, G.K.-S., Leebens-Mack, J. (2014) Phylotranscriptomic analysis of the origin and early diversification of land plants. Proceedings of the National Academy of Sciences of the United States of America, 111(45):E4859-E4868.

Résumé

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.

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@ARTICLE { WickettMirarabNamEtAl2014,
    AUTHOR = { Wickett, N.J. and Mirarab, S. and Nam, N and Warnow, T. and Carpenter, E. and Matasci, N. and Ayyampalayam, S. and Barker, Mi.S. and Burleigh, J. G. and Gitzendanner, M.A. and Ruhfel, B.R. and Wafula, E. and Der, Joshua P. and Graham, S.W. and Mathews, S. and Melkonian, M. and Soltis, D.E. and Soltis, P.S. and Miles, N.W. and Rothfels, C.J. and Pokorny, L. and Shaw, A. J. and DeGironimo, L. and Stevenson, D.W. and Surek, B. and Villarreal, J.C. and Roure, B. and Philippe, H. and dePamphilis, C.W. and Chen, T. and Deyholos, M.K. and Baucom, R.S. and Kutchan, T.M. and Augustin, M.M. and Wang, J. and Zhang, Y. and Tian, Z. and Yan, Z. and Wu, X. and Sun, X. and Wong, G.K.-S. and Leebens-Mack, J. },
    TITLE = { Phylotranscriptomic analysis of the origin and early diversification of land plants },
    JOURNAL = { Proceedings of the National Academy of Sciences of the United States of America },
    YEAR = { 2014 },
    VOLUME = { 111 },
    NUMBER = { 45 },
    PAGES = { E4859-E4868 },
    MONTH = { nov },
    ISSN = { 0027-8424 },
    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. },
    DOI = { 10.1073/pnas.1323926111 },
    ORCID-NUMBERS = { Graham, Sean/0000-0001-8209-5231 Wang, Jun/0000-0002-8540-8931 Wong, Gane Ka-Shu/0000-0001-6108-5560 Mathews, Sarah/0000-0002-5518-7541 Wang, Jun/0000-0002-2113-5874 Gitzendanner, Matthew/0000-0002-7078-4336 Mirarab, Siavash/0000-0001-5410-1518 Der, Joshua/0000-0001-9668-2525 Baucom, Regina/0000-0001-7960-498X },
    RESEARCHERID-NUMBERS = { Kutchan, Toni/L-4625-2013 Graham, Sean/L-3944-2014 Wang, Jun/C-8434-2016 Wong, Gane Ka-Shu/G-5784-2013 Soltis, Pamela/L-5184-2015 dePamphilis, Claude/P-6652-2016 Pokorny, Lisa/H-1233-2013 Mathews, Sarah/A-6513-2015 },
    UNIQUE-ID = { ISI:000344526800010 },
}

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