Genome-Scale Phylogenetics: Inferring the Plant Tree of Life from 18,896 Gene Trees

被引:79
作者
Burleigh, J. Gordon [1 ,2 ]
Bansal, Mukul S. [3 ,4 ]
Eulenstein, Oliver [3 ]
Hartmann, Stefanie [5 ,6 ]
Wehe, Andre [3 ]
Vision, Todd J. [2 ,5 ]
机构
[1] Univ Florida, Dept Biol, Gainesville, FL 32609 USA
[2] NESCent, Durham, NC 27705 USA
[3] Iowa State Univ, Dept Comp Sci, Ames, IA 50011 USA
[4] Tel Aviv Univ, Sch Comp Sci, IL-69978 Tel Aviv, Israel
[5] Univ N Carolina, Dept Biol, Chapel Hill, NC 27599 USA
[6] Univ Potsdam, Inst Biochem & Biol, D-14476 Potsdam, Germany
基金
美国国家卫生研究院; 美国国家科学基金会;
关键词
Gene tree-species tree reconciliation; gene tree parsimony; plant phylogeny; phylogenomics; SPECIES TREES; RECONCILED TREES; ANGIOSPERMS; EVOLUTION; RECONSTRUCTION; IMPROVEMENT; LIKELIHOOD; PARSIMONY; RESOLVES; PROGRAM;
D O I
10.1093/sysbio/syq072
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
Phylogenetic analyses using genome-scale data sets must confront incongruence among gene trees, which in plants is exacerbated by frequent gene duplications and losses. Gene tree parsimony (GTP) is a phylogenetic optimization criterion in which a species tree that minimizes the number of gene duplications induced among a set of gene trees is selected. The run time performance of previous implementations has limited its use on large-scale data sets. We used new software that incorporates recent algorithmic advances to examine the performance of GTP on a plant data set consisting of 18,896 gene trees containing 510,922 protein sequences from 136 plant taxa (giving a combined alignment length of >2.9 million characters). The relationships inferred from the GTP analysis were largely consistent with previous large-scale studies of backbone plant phylogeny and resolved some controversial nodes. The placement of taxa that were present in few gene trees generally varied the most among GTP bootstrap replicates. Excluding these taxa either before or after the GTP analysis revealed high levels of phylogenetic support across plants. The analyses supported magnoliids sister to a eudicot + monocot clade and did not support the eurosid I and II clades. This study presents a nuclear genomic perspective on the broad-scale phylogenic relationships among plants, and it demonstrates that nuclear genes with a history of duplication and loss can be phylogenetically informative for resolving the plant tree of life.
引用
收藏
页码:117 / 125
页数:9
相关论文
共 62 条
[1]   Polyploidy and genome evolution in plants [J].
Adams, KL ;
Wendel, JF .
CURRENT OPINION IN PLANT BIOLOGY, 2005, 8 (02) :135-141
[2]   Simultaneous Bayesian gene tree reconstruction and reconciliation analysis [J].
Akerborg, Oerjan ;
Sennblad, Bengt ;
Arvestad, Lars ;
Lagergren, Jens .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2009, 106 (14) :5714-5719
[3]  
ARVESTAD L, 2004, GENE TREE RECONSTRUC, P326
[4]  
Bansal MS, 2007, LECT NOTES COMPUT SC, V4453, P238
[5]   Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models [J].
Bansal, Mukul S. ;
Burleigh, J. Gordon ;
Eulenstein, Oliver .
BMC BIOINFORMATICS, 2010, 11
[6]   The evolution of supertrees [J].
Bininda-Emonds, ORP .
TRENDS IN ECOLOGY & EVOLUTION, 2004, 19 (06) :315-322
[7]   NOTUNG: A program for dating gene duplications and optimizing gene family trees [J].
Chen, K ;
Durand, D ;
Farach-Colton, M .
JOURNAL OF COMPUTATIONAL BIOLOGY, 2000, 7 (3-4) :429-447
[8]  
Cotton J.A., 2004, PHYLOGENETIC SUPERTR, P107
[9]   Going nuclear: gene family evolution and vertebrate phylogeny reconciled [J].
Cotton, JA ;
Page, RDM .
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 2002, 269 (1500) :1555-1561
[10]   Supertrees join the mainstream of phylogenetics [J].
Cotton, James A. ;
Wilkinson, Mark .
TRENDS IN ECOLOGY & EVOLUTION, 2009, 24 (01) :1-3