Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data
文献类型： 外文期刊
作者： Hughes, Lily C. 1 ; Orti, Guillermo 1 ; Huang, Yu 3 ; Sun, Ying 3 ; Baldwin, Carole C. 2 ; Thompson, Andrew W. 1 ; Arc 1 ;
作者机构： 1.George Washington Univ, Dept Biol Sci, Washington, DC 20052 USA
2.Smithsonian Inst, Natl Museum Nat Hist, Washington, DC 20560 USA
3.Beijing Genom Inst, Beijing Genom Inst Marine, Guangdong Prov Key Lab Mol Breeding Marine Econ A, Shenzhen Key Lab Marine Genom,Acad Marine Sci, Shenzhen 518083, Peoples R China
4.Univ Chinese Acad Sci, Beijing Genom Inst, Educ Ctr, Shenzhen 518083, Peoples R China
5.China Natl GeneBank, Beijing Genom Inst Shenzhen, Shenzhen 518120, Peoples R China
6.Univ Puerto Rico Rio Piedras, Dept Biol, San Juan, PR 00931 USA
7.Shanghai Ocean Univ, Minist Educ, Key Lab Explorat & Utilizat Aquat Genet Resources, Shanghai 201306, Peoples R China
8.Univ Nacl Comahue, CONICET, Lab Ictiol & Acuicultura Expt, RA-8400 San Carlos De Bariloche, Rio Negro, Argentina
9.China Fisheries Assoc, Profess Comm Native Aquat Organisms & Water Ecosy, Beijing 100125, Peoples R China
10.Hainan Trop Ocean Univ, Coll Life Sci & Ecol, Sanya 572022, Peoples R China
11.Chinese Acad Fishery Sci, Yellow Sea Fisheries Res Inst, Qingdao 266071, Peoples R China
12.ASTAR, Biopolis, Inst Mol & Cell Biol, Comparat Genom Lab, Singapore 138673, Singapore
关键词： phylogenomics; divergence times; bony fish; paralogy; tree of life
期刊名称：PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA （ 影响因子：11.205； 五年影响因子：12.291 ）
ISSN： 0027-8424
年卷期： 2018 年 115 卷 24 期
页码：
收录情况： SCI
摘要： Our understanding of phylogenetic relationships among bony fishes has been transformed by analysis of a small number of genes, but uncertainty remains around critical nodes. Genomescale inferences so far have sampled a limited number of taxa and genes. Here we leveraged 144 genomes and 159 transcriptomes to investigate fish evolution with an unparalleled scale of data: >0.5 Mb from 1,105 orthologous exon sequences from 303 species, representing 66 out of 72 ray-finned fish orders. We apply phylogenetic tests designed to trace the effect of whole-genome duplication events on gene trees and find paralogy-free loci using a bioinformatics approach. Genome-wide data support the structure of the fish phylogeny, and hypothesis-testing procedures appropriate for phylogenomic datasets using explicit gene genealogy interrogation settle some long-standing uncertainties, such as the branching order at the base of the teleosts and among early euteleosts, and the sister lineage to the acanthomorph and percomorph radiations. Comprehensive fossil calibrations date the origin of all major fish lineages before the end of the Cretaceous.
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