Phylotranscriptomic analysis of the origin and early diversification of land plants
Norman J. Wickett,Siavash Mirarab,Nam Nguyen,Tandy Warnow,Eric J. Carpenter,Naim Matasci,Saravanaraj Ayyampalayam,Michael S. Barker,J. Gordon Burleigh,Matthew A. Gitzendanner,Brad R. Ruhfel,Brad R. Ruhfel,Eric K. Wafula,Joshua P. Der,Sean W. Graham,Sarah Mathews,Michael Melkonian,Douglas E. Soltis,Douglas E. Soltis,Pamela S. Soltis,Pamela S. Soltis,Nicholas W. Miles,Carl J. Rothfels,Carl J. Rothfels,Lisa Pokorny,Lisa Pokorny,A. Jonathan Shaw,Lisa DeGironimo,Dennis W. Stevenson,Barbara Surek,Juan Carlos Villarreal,Béatrice Roure,Hervé Philippe,Hervé Philippe,Claude W. dePamphilis,Tao Chen,Michael K. Deyholos,Regina S. Baucom,Toni M. Kutchan,Megan M. Augustin,Jun Wang,Yong Zhang,Zhijian Tian,Zhixiang Yan,Xiaolei Wu,Xiao Sun,Gane Ka-Shu Wong,Jim Leebens-Mack +47 more
TLDR
Strong and robust support is found for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.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.read more
Citations
More filters
Journal ArticleDOI
An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II
TL;DR: A revised and updated classification for the families of the flowering plants is provided in this paper, which includes Austrobaileyales, Canellales, Gunnerales, Crossosomatales and Celastrales.
Journal ArticleDOI
RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference.
Alexey M. Kozlov,Diego Darriba,Tomas Flouri,Benoit Morel,Alexandros Stamatakis,Alexandros Stamatakis +5 more
TL;DR: RAxML-NG is presented, a from-scratch re-implementation of the established greedy tree search algorithm of RAxML/ExaML, which offers improved accuracy, flexibility, speed, scalability, and usability compared with RAx ML/ exaML.
Journal ArticleDOI
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees.
TL;DR: ASTRAL-III is a faster version of the ASTRAL method for phylogenetic reconstruction and can scale up to 10,000 species and removes low support branches from gene trees, resulting in improved accuracy.
Journal ArticleDOI
A community-derived classification for extant lycophytes and ferns
Eric Schuettpelz,Harald Schneider,Alan R. Smith,Peter Hovenkamp,Jefferson Prado,Germinal Rouhan,Alexandre Salino,Michael A. Sundue,Thaís Elias Almeida,Barbara S. Parris,Emily B. Sessa,Ashley R. Field,André Luís de Gasper,Carl J. Rothfels,Michael D. Windham,Marcus Lehnert,Benjamin Dauphin,Atsushi Ebihara,Samuli Lehtonen,Pedro Bond Schwartsburd,Jordan S. Metzgar,Li-Bing Zhang,Li-Yaung Kuo,Patrick J. Brownsey,Masahiro Kato,Marcelo D. Arana,Francine Costa Assis,Michael S. Barker,David S. Barrington,Ho-Ming Chang,Yi-Han Chang,Yi-Shan Chao,Cheng-Wei Chen,De-Kui Chen,Wen-Liang Chiou,Vinícius Antonio de Oliveira Dittrich,Yi-Fan Duan,Jean-Yves Dubuisson,Donald R. Farrar,Susan Fawcett,Jose María Gabriel y Galán,Luiz Armando de Araújo Góes-Neto,Jason R. Grant,Amanda L. Grusz,Christopher H. Haufler,Warren D. Hauk,Hai He,Sabine Hennequin,Regina Y. Hirai,Layne Huiet,Michael Kessler,Petra Korall,Paulo H. Labiak,Anders Larsson,Blanca León,Chun-Xiang Li,Fay-Wei Li,Melanie A. Link-Pérez,Hong-Mei Liu,Ngan Thi Lu,Esteban I. Meza-Torres,Xin-Yuan Miao,Robbin C. Moran,Claudine M. Mynssen,Nathalie S. Nagalingum,Benjamin Øllgaard,Alison M. Paul,Jovani B. S. Pereira,Leon R. Perrie,M. Mónica Ponce,Tom A. Ranker,Christian Schulz,Wataru Shinohara,Alexander Shmakov,Erin M. Sigel,Filipe Soares de Souza,Lana da Silva Sylvestre,Weston Testo,Luz Amparo Triana-Moreno,Chie Tsutsumi,Hanna Tuomisto,Ivan A. Valdespino,Alejandra Vasco,Raquel Stauffer Viveros,Alan S. Weakley,Ran Wei,Stina Weststrand,Paul G. Wolf,George Yatskievych,Xiao-Gang Xu,Yue-Hong Yan,Liang Zhang,Xian-Chun Zhang,Xin-Mao Zhou +93 more
TL;DR: A modern, comprehensive classification for lycophytes and ferns, down to the genus level, utilizing a community‐based approach, that uses monophyly as the primary criterion for the recognition of taxa, but also aims to preserve existing taxa and circumscriptions that are both widely accepted and consistent with the understanding of pteridophyte phylogeny.
Journal ArticleDOI
One thousand plant transcriptomes and the phylogenomics of green plants.
TL;DR: It is found that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns.
References
More filters
Journal ArticleDOI
Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Journal ArticleDOI
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
TL;DR: UNLABELLED RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML) that has been used to compute ML trees on two of the largest alignments to date.
Journal ArticleDOI
An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II
TL;DR: A revised and updated classification for the families of the flowering plants is provided in this paper, which includes Austrobaileyales, Canellales, Gunnerales, Crossosomatales and Celastrales.
Journal ArticleDOI
The rapid generation of mutation data matrices from protein sequences
TL;DR: An efficient means for generating mutation data matrices from large numbers of protein sequences is presented, by means of an approximate peptide-based sequence comparison algorithm, which is fast enough to process the entire SWISS-PROT databank in 20 h on a Sun SPARCstation 1, and is fastenough to generate a matrix from a specific family or class of proteins in minutes.
Related Papers (5)
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Kazutaka Katoh,Daron M. Standley +1 more
Whole-genome analyses resolve early branches in the tree of life of modern birds
Erich D. Jarvis,Siavash Mirarab,Andre J. Aberer,Bo Li,Bo Li,Bo Li,Peter Houde,Cai Li,Cai Li,Simon Y. W. Ho,Brant C. Faircloth,Benoit Nabholz,Jason T. Howard,Alexander Suh,Claudia C. Weber,Rute R. da Fonseca,Jianwen Li,Fang Zhang Zhang,Hui Li,Long Zhou,Nitish Narula,Nitish Narula,Liang Liu,Ganesh Ganapathy,Bastien Boussau,Shamsuzzoha Bayzid,Volodymyr Zavidovych,Sankar Subramanian,Toni Gabaldón,Salvador Capella-Gutierrez,Jaime Huerta-Cepas,Bhanu Rekepalli,Bhanu Rekepalli,Kasper Munch,Mikkel H. Schierup,Bent E. K. Lindow,Wesley C. Warren,David A. Ray,Richard E. Green,Michael William Bruford,Xiangjiang Zhan,Xiangjiang Zhan,Andrew Dixon,Shengbin Li,Ning Li,Yinhua Huang,Elizabeth P. Derryberry,Elizabeth P. Derryberry,Mads F. Bertelsen,Frederick H. Sheldon,Robb T. Brumfield,Claudio V. Mello,Claudio V. Mello,Peter V. Lovell,Morgan Wirthlin,Maria Paula Cruz Schneider,Francisco Prosdocimi,José Alfredo Samaniego,Amhed Missael Vargas Velazquez,Alonzo Alfaro-Núñez,Paula F. Campos,Bent O. Petersen,Thomas Sicheritz-Pontén,An Pas,Thomas L. Bailey,R. Paul Scofield,Michael Bunce,David M. Lambert,Qi Zhou,Polina L. Perelman,Amy C. Driskell,Beth Shapiro,Zijun Xiong,Yongli Zeng,Shiping Liu,Zhenyu Li,Binghang Liu,Kui Wu,Jin Xiao,Xiong Yinqi,Quiemei Zheng,Yong Zhang,Huanming Yang,Jian Wang,Linnéa Smeds,Frank E. Rheindt,Michael J. Braun,Jon Fjeldså,Ludovic Orlando,F. Keith Barker,Knud A. Jønsson,Warren E. Johnson,Klaus-Peter Koepfli,Stephen J. O'Brien,David Haussler,Oliver A. Ryder,Carsten Rahbek,Eske Willerslev,Gary R. Graves,Gary R. Graves,Travis C. Glenn,John E. McCormack,Dave Burt,Hans Ellegren,Per Alström,Scott V. Edwards,Alexandros Stamatakis,David P. Mindell,Joel Cracraft,Edward L. Braun,Tandy Warnow,Tandy Warnow,Wang Jun,M. Thomas P. Gilbert,M. Thomas P. Gilbert,Guojie Zhang,Guojie Zhang +116 more