Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data

Autores
Hughes, Lily C.; Ortí, Guillermo; Huang, Yu; Sun, Ying; Baldwin, Carole C.; Thompson, Andrew W.; Arcila, Dahiana; Betancur, Ricardo; Li, Chenhong; Becker, Leandro Anibal; Bellora, Nicolás; Zhao, Xiaomeng; Li, Xiaofeng; Wang, Min; Fang, Chao; Xie, Bing; Zhoui, Zhuocheng; Huang, Hai; Chen, Songlin; Venkatesh, Byrappa; Shi, Qiong
Año de publicación
2018
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
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.
Fil: Hughes, Lily C.. National Museum of Natural History; Estados Unidos. The George Washington University; Estados Unidos
Fil: Ortí, Guillermo. National Museum of Natural History; Estados Unidos. The George Washington University; Estados Unidos
Fil: Huang, Yu. Beijing Genomics Institute; China. Chinese Academy of Sciences; República de China
Fil: Sun, Ying. China National Genebank; China. Beijing Genomics Institute; China
Fil: Baldwin, Carole C.. National Museum of Natural History; Estados Unidos
Fil: Thompson, Andrew W.. National Museum of Natural History; Estados Unidos. The George Washington University; Estados Unidos
Fil: Arcila, Dahiana. National Museum of Natural History; Estados Unidos. The George Washington University; Estados Unidos
Fil: Betancur, Ricardo. National Museum of Natural History; Estados Unidos. Universidad de Puerto Rico, Recinto de Rio Piedras; Puerto Rico
Fil: Li, Chenhong. Shanghai Ocean University; China
Fil: Becker, Leandro Anibal. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales. Universidad Nacional del Comahue. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales.; Argentina. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche; Argentina
Fil: Bellora, Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales. Universidad Nacional del Comahue. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales.; Argentina. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche; Argentina
Fil: Zhao, Xiaomeng. Chinese Academy of Sciences; República de China. Beijing Genomics Institute; China
Fil: Li, Xiaofeng. Chinese Academy of Sciences; República de China. Beijing Genomics Institute; China
Fil: Wang, Min. Beijing Genomics Institute; China
Fil: Fang, Chao. Chinese Academy of Sciences; República de China
Fil: Xie, Bing. Bgi-shenzhen; China
Fil: Zhoui, Zhuocheng. China Fisheries Association; China
Fil: Huang, Hai. Hainan Tropical Ocean University; China
Fil: Chen, Songlin. Yellow Sea Fisheries Research Institute Chinese Academy Of Fishery Science; China
Fil: Venkatesh, Byrappa. A-star, Institute Of Molecular And Cell Biology;
Fil: Shi, Qiong. Chinese Academy of Sciences; República de China
Materia
BONY FISH
DIVERGENCE TIMES
PARALOGY
PHYLOGENOMICS
TREE OF LIFE
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/89324
Acceder
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network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic dataHughes, Lily C.Ortí, GuillermoHuang, YuSun, YingBaldwin, Carole C.Thompson, Andrew W.Arcila, DahianaBetancur, RicardoLi, ChenhongBecker, Leandro AnibalBellora, NicolásZhao, XiaomengLi, XiaofengWang, MinFang, ChaoXie, BingZhoui, ZhuochengHuang, HaiChen, SonglinVenkatesh, ByrappaShi, QiongBONY FISHDIVERGENCE TIMESPARALOGYPHYLOGENOMICSTREE OF LIFEhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1https://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Our 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.Fil: Hughes, Lily C.. National Museum of Natural History; Estados Unidos. The George Washington University; Estados UnidosFil: Ortí, Guillermo. National Museum of Natural History; Estados Unidos. The George Washington University; Estados UnidosFil: Huang, Yu. Beijing Genomics Institute; China. Chinese Academy of Sciences; República de ChinaFil: Sun, Ying. China National Genebank; China. Beijing Genomics Institute; ChinaFil: Baldwin, Carole C.. National Museum of Natural History; Estados UnidosFil: Thompson, Andrew W.. National Museum of Natural History; Estados Unidos. The George Washington University; Estados UnidosFil: Arcila, Dahiana. National Museum of Natural History; Estados Unidos. The George Washington University; Estados UnidosFil: Betancur, Ricardo. National Museum of Natural History; Estados Unidos. Universidad de Puerto Rico, Recinto de Rio Piedras; Puerto RicoFil: Li, Chenhong. Shanghai Ocean University; ChinaFil: Becker, Leandro Anibal. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales. Universidad Nacional del Comahue. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales.; Argentina. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche; ArgentinaFil: Bellora, Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales. Universidad Nacional del Comahue. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales.; Argentina. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche; ArgentinaFil: Zhao, Xiaomeng. Chinese Academy of Sciences; República de China. Beijing Genomics Institute; ChinaFil: Li, Xiaofeng. Chinese Academy of Sciences; República de China. Beijing Genomics Institute; ChinaFil: Wang, Min. Beijing Genomics Institute; ChinaFil: Fang, Chao. Chinese Academy of Sciences; República de ChinaFil: Xie, Bing. Bgi-shenzhen; ChinaFil: Zhoui, Zhuocheng. China Fisheries Association; ChinaFil: Huang, Hai. Hainan Tropical Ocean University; ChinaFil: Chen, Songlin. Yellow Sea Fisheries Research Institute Chinese Academy Of Fishery Science; ChinaFil: Venkatesh, Byrappa. A-star, Institute Of Molecular And Cell Biology;Fil: Shi, Qiong. Chinese Academy of Sciences; República de ChinaNational Academy of Sciences2018-06info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/89324Hughes, Lily C.; Ortí, Guillermo; Huang, Yu; Sun, Ying; Baldwin, Carole C.; et al.; Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data; National Academy of Sciences; Proceedings of the National Academy of Sciences of The United States of America; 115; 24; 6-2018; 6249-62540027-8424CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/http://www.pnas.org/lookup/doi/10.1073/pnas.1719358115info:eu-repo/semantics/altIdentifier/doi/10.1073/pnas.1719358115info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:47:34Zoai:ri.conicet.gov.ar:11336/89324instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 10:47:34.296CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data
title Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data
spellingShingle Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data
Hughes, Lily C.
BONY FISH
DIVERGENCE TIMES
PARALOGY
PHYLOGENOMICS
TREE OF LIFE
title_short Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data
title_full Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data
title_fullStr Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data
title_full_unstemmed Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data
title_sort Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data
dc.creator.none.fl_str_mv Hughes, Lily C.
Ortí, Guillermo
Huang, Yu
Sun, Ying
Baldwin, Carole C.
Thompson, Andrew W.
Arcila, Dahiana
Betancur, Ricardo
Li, Chenhong
Becker, Leandro Anibal
Bellora, Nicolás
Zhao, Xiaomeng
Li, Xiaofeng
Wang, Min
Fang, Chao
Xie, Bing
Zhoui, Zhuocheng
Huang, Hai
Chen, Songlin
Venkatesh, Byrappa
Shi, Qiong
author Hughes, Lily C.
author_facet Hughes, Lily C.
Ortí, Guillermo
Huang, Yu
Sun, Ying
Baldwin, Carole C.
Thompson, Andrew W.
Arcila, Dahiana
Betancur, Ricardo
Li, Chenhong
Becker, Leandro Anibal
Bellora, Nicolás
Zhao, Xiaomeng
Li, Xiaofeng
Wang, Min
Fang, Chao
Xie, Bing
Zhoui, Zhuocheng
Huang, Hai
Chen, Songlin
Venkatesh, Byrappa
Shi, Qiong
author_role author
author2 Ortí, Guillermo
Huang, Yu
Sun, Ying
Baldwin, Carole C.
Thompson, Andrew W.
Arcila, Dahiana
Betancur, Ricardo
Li, Chenhong
Becker, Leandro Anibal
Bellora, Nicolás
Zhao, Xiaomeng
Li, Xiaofeng
Wang, Min
Fang, Chao
Xie, Bing
Zhoui, Zhuocheng
Huang, Hai
Chen, Songlin
Venkatesh, Byrappa
Shi, Qiong
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv BONY FISH
DIVERGENCE TIMES
PARALOGY
PHYLOGENOMICS
TREE OF LIFE
topic BONY FISH
DIVERGENCE TIMES
PARALOGY
PHYLOGENOMICS
TREE OF LIFE
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv 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.
Fil: Hughes, Lily C.. National Museum of Natural History; Estados Unidos. The George Washington University; Estados Unidos
Fil: Ortí, Guillermo. National Museum of Natural History; Estados Unidos. The George Washington University; Estados Unidos
Fil: Huang, Yu. Beijing Genomics Institute; China. Chinese Academy of Sciences; República de China
Fil: Sun, Ying. China National Genebank; China. Beijing Genomics Institute; China
Fil: Baldwin, Carole C.. National Museum of Natural History; Estados Unidos
Fil: Thompson, Andrew W.. National Museum of Natural History; Estados Unidos. The George Washington University; Estados Unidos
Fil: Arcila, Dahiana. National Museum of Natural History; Estados Unidos. The George Washington University; Estados Unidos
Fil: Betancur, Ricardo. National Museum of Natural History; Estados Unidos. Universidad de Puerto Rico, Recinto de Rio Piedras; Puerto Rico
Fil: Li, Chenhong. Shanghai Ocean University; China
Fil: Becker, Leandro Anibal. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales. Universidad Nacional del Comahue. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales.; Argentina. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche; Argentina
Fil: Bellora, Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales. Universidad Nacional del Comahue. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales.; Argentina. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche; Argentina
Fil: Zhao, Xiaomeng. Chinese Academy of Sciences; República de China. Beijing Genomics Institute; China
Fil: Li, Xiaofeng. Chinese Academy of Sciences; República de China. Beijing Genomics Institute; China
Fil: Wang, Min. Beijing Genomics Institute; China
Fil: Fang, Chao. Chinese Academy of Sciences; República de China
Fil: Xie, Bing. Bgi-shenzhen; China
Fil: Zhoui, Zhuocheng. China Fisheries Association; China
Fil: Huang, Hai. Hainan Tropical Ocean University; China
Fil: Chen, Songlin. Yellow Sea Fisheries Research Institute Chinese Academy Of Fishery Science; China
Fil: Venkatesh, Byrappa. A-star, Institute Of Molecular And Cell Biology;
Fil: Shi, Qiong. Chinese Academy of Sciences; República de China
description 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.
publishDate 2018
dc.date.none.fl_str_mv 2018-06
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/89324
Hughes, Lily C.; Ortí, Guillermo; Huang, Yu; Sun, Ying; Baldwin, Carole C.; et al.; Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data; National Academy of Sciences; Proceedings of the National Academy of Sciences of The United States of America; 115; 24; 6-2018; 6249-6254
0027-8424
CONICET Digital
CONICET
url http://hdl.handle.net/11336/89324
identifier_str_mv Hughes, Lily C.; Ortí, Guillermo; Huang, Yu; Sun, Ying; Baldwin, Carole C.; et al.; Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data; National Academy of Sciences; Proceedings of the National Academy of Sciences of The United States of America; 115; 24; 6-2018; 6249-6254
0027-8424
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/http://www.pnas.org/lookup/doi/10.1073/pnas.1719358115
info:eu-repo/semantics/altIdentifier/doi/10.1073/pnas.1719358115
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv National Academy of Sciences
publisher.none.fl_str_mv National Academy of Sciences
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.070432

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