Phylogeny and divergence times of suckers (Cypriniformes: Catostomidae) inferred from Bayesian total-evidence analyses of molecules, morphology, and fossils
Autor(a) principal: | |
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Data de Publicação: | 2018 |
Outros Autores: | , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.7717/peerj.5168 http://hdl.handle.net/11449/164378 |
Resumo: | Catostomidae (suckers) is a diverse (76 species) and broadly distributed family of Holarctic freshwater fishes with a rich fossil record and a considerable number (similar to 35%) of threatened and imperiled species. We integrate DNA sequences (three mitochondrial genes, three nuclear genes), morphological data, and fossil information to infer sucker phylogenetic relationships and divergence times using Bayesian total-evidence methods, and then test hypotheses about the temporal diversification of the group. Our analyses resolved many nodes within subfamilies and clarified Catostominae relationships to be of the form ((Thoburniini, Moxostomatini), (Erimyzonini, Catostomini)). Patterns of subfamily relationships were incongruent, but mainly supported two placements of the Myxocyprininae; distinguishing these using Bayes factors lent strongest support to a model with Myxocyprininae sister to all remaining sucker lineages. We improved our Bayesian total-evidence dating analysis by excluding problematic characters, using a clock-partitioning scheme identified by Bayesian model selection, and employing a fossilized birth-death tree prior accommodating morphological data and fossils. The resulting chronogram showed that suckers evolved since the Late Cretaceous-Eocene, and that the Catostomini and Moxostomatini clades have accumulated species diversity since the early to mid-Miocene. These results agree with the fossil record and confirm previous hypotheses about dates for the origins of Catostomide and catostomine diversification, but reject previous molecular hypotheses about the timing of divergence of ictiobines, and between Asian-North American lineages. Overall, our findings from a synthesis of multiple data types enhance understanding of the phylogenetic relationships, taxonomic classification, and temporal diversification of suckers, while also highlighting practical methods for improving Bayesian divergence dating models by coupling phylogenetic informativeness profiling with relaxed-clock partitioning. |
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Phylogeny and divergence times of suckers (Cypriniformes: Catostomidae) inferred from Bayesian total-evidence analyses of molecules, morphology, and fossilsMolecular phylogeneticsCatostomidaeFossilized birth-death processDivergence time estimationRelaxed molecular clockPhylogenetic informativeness profilesCatostomidae (suckers) is a diverse (76 species) and broadly distributed family of Holarctic freshwater fishes with a rich fossil record and a considerable number (similar to 35%) of threatened and imperiled species. We integrate DNA sequences (three mitochondrial genes, three nuclear genes), morphological data, and fossil information to infer sucker phylogenetic relationships and divergence times using Bayesian total-evidence methods, and then test hypotheses about the temporal diversification of the group. Our analyses resolved many nodes within subfamilies and clarified Catostominae relationships to be of the form ((Thoburniini, Moxostomatini), (Erimyzonini, Catostomini)). Patterns of subfamily relationships were incongruent, but mainly supported two placements of the Myxocyprininae; distinguishing these using Bayes factors lent strongest support to a model with Myxocyprininae sister to all remaining sucker lineages. We improved our Bayesian total-evidence dating analysis by excluding problematic characters, using a clock-partitioning scheme identified by Bayesian model selection, and employing a fossilized birth-death tree prior accommodating morphological data and fossils. The resulting chronogram showed that suckers evolved since the Late Cretaceous-Eocene, and that the Catostomini and Moxostomatini clades have accumulated species diversity since the early to mid-Miocene. These results agree with the fossil record and confirm previous hypotheses about dates for the origins of Catostomide and catostomine diversification, but reject previous molecular hypotheses about the timing of divergence of ictiobines, and between Asian-North American lineages. Overall, our findings from a synthesis of multiple data types enhance understanding of the phylogenetic relationships, taxonomic classification, and temporal diversification of suckers, while also highlighting practical methods for improving Bayesian divergence dating models by coupling phylogenetic informativeness profiling with relaxed-clock partitioning.U.S. National Science Foundation (NSF)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Virginia Commonwealth Univ, Dept Biol, Richmond, VA 23284 USAUniv Brasilia, Dept Zool, Brasilia, DF, BrazilUniv Estadual Paulista, Dept Zool & Bot, IBiLCE, Sao Jose Do Rio Preto, SP, BrazilSt Louis Univ, Dept Biol, St Louis, MO 63103 USAUniv Alabama, Dept Biol Sci, Tuscaloosa, AL USAUniv Estadual Paulista, Dept Zool & Bot, IBiLCE, Sao Jose Do Rio Preto, SP, BrazilU.S. National Science Foundation (NSF): EF-0431326U.S. National Science Foundation (NSF): EF-0431263CNPq: 314724/2014-1Peerj IncVirginia Commonwealth UnivUniversidade de Brasília (UnB)Universidade Estadual Paulista (Unesp)St Louis UnivUniv AlabamaBagley, Justin C. [UNESP]Mayden, Richard L.Harris, Philip M.2018-11-26T17:54:18Z2018-11-26T17:54:18Z2018-07-04info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article35application/pdfhttp://dx.doi.org/10.7717/peerj.5168Peerj. London: Peerj Inc, v. 6, 35 p., 2018.2167-8359http://hdl.handle.net/11449/16437810.7717/peerj.5168WOS:000437258800012WOS000437258800012.pdfWeb of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengPeerj1,087info:eu-repo/semantics/openAccess2024-01-04T06:29:20Zoai:repositorio.unesp.br:11449/164378Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T22:08:31.432040Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Phylogeny and divergence times of suckers (Cypriniformes: Catostomidae) inferred from Bayesian total-evidence analyses of molecules, morphology, and fossils |
title |
Phylogeny and divergence times of suckers (Cypriniformes: Catostomidae) inferred from Bayesian total-evidence analyses of molecules, morphology, and fossils |
spellingShingle |
Phylogeny and divergence times of suckers (Cypriniformes: Catostomidae) inferred from Bayesian total-evidence analyses of molecules, morphology, and fossils Bagley, Justin C. [UNESP] Molecular phylogenetics Catostomidae Fossilized birth-death process Divergence time estimation Relaxed molecular clock Phylogenetic informativeness profiles |
title_short |
Phylogeny and divergence times of suckers (Cypriniformes: Catostomidae) inferred from Bayesian total-evidence analyses of molecules, morphology, and fossils |
title_full |
Phylogeny and divergence times of suckers (Cypriniformes: Catostomidae) inferred from Bayesian total-evidence analyses of molecules, morphology, and fossils |
title_fullStr |
Phylogeny and divergence times of suckers (Cypriniformes: Catostomidae) inferred from Bayesian total-evidence analyses of molecules, morphology, and fossils |
title_full_unstemmed |
Phylogeny and divergence times of suckers (Cypriniformes: Catostomidae) inferred from Bayesian total-evidence analyses of molecules, morphology, and fossils |
title_sort |
Phylogeny and divergence times of suckers (Cypriniformes: Catostomidae) inferred from Bayesian total-evidence analyses of molecules, morphology, and fossils |
author |
Bagley, Justin C. [UNESP] |
author_facet |
Bagley, Justin C. [UNESP] Mayden, Richard L. Harris, Philip M. |
author_role |
author |
author2 |
Mayden, Richard L. Harris, Philip M. |
author2_role |
author author |
dc.contributor.none.fl_str_mv |
Virginia Commonwealth Univ Universidade de Brasília (UnB) Universidade Estadual Paulista (Unesp) St Louis Univ Univ Alabama |
dc.contributor.author.fl_str_mv |
Bagley, Justin C. [UNESP] Mayden, Richard L. Harris, Philip M. |
dc.subject.por.fl_str_mv |
Molecular phylogenetics Catostomidae Fossilized birth-death process Divergence time estimation Relaxed molecular clock Phylogenetic informativeness profiles |
topic |
Molecular phylogenetics Catostomidae Fossilized birth-death process Divergence time estimation Relaxed molecular clock Phylogenetic informativeness profiles |
description |
Catostomidae (suckers) is a diverse (76 species) and broadly distributed family of Holarctic freshwater fishes with a rich fossil record and a considerable number (similar to 35%) of threatened and imperiled species. We integrate DNA sequences (three mitochondrial genes, three nuclear genes), morphological data, and fossil information to infer sucker phylogenetic relationships and divergence times using Bayesian total-evidence methods, and then test hypotheses about the temporal diversification of the group. Our analyses resolved many nodes within subfamilies and clarified Catostominae relationships to be of the form ((Thoburniini, Moxostomatini), (Erimyzonini, Catostomini)). Patterns of subfamily relationships were incongruent, but mainly supported two placements of the Myxocyprininae; distinguishing these using Bayes factors lent strongest support to a model with Myxocyprininae sister to all remaining sucker lineages. We improved our Bayesian total-evidence dating analysis by excluding problematic characters, using a clock-partitioning scheme identified by Bayesian model selection, and employing a fossilized birth-death tree prior accommodating morphological data and fossils. The resulting chronogram showed that suckers evolved since the Late Cretaceous-Eocene, and that the Catostomini and Moxostomatini clades have accumulated species diversity since the early to mid-Miocene. These results agree with the fossil record and confirm previous hypotheses about dates for the origins of Catostomide and catostomine diversification, but reject previous molecular hypotheses about the timing of divergence of ictiobines, and between Asian-North American lineages. Overall, our findings from a synthesis of multiple data types enhance understanding of the phylogenetic relationships, taxonomic classification, and temporal diversification of suckers, while also highlighting practical methods for improving Bayesian divergence dating models by coupling phylogenetic informativeness profiling with relaxed-clock partitioning. |
publishDate |
2018 |
dc.date.none.fl_str_mv |
2018-11-26T17:54:18Z 2018-11-26T17:54:18Z 2018-07-04 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.7717/peerj.5168 Peerj. London: Peerj Inc, v. 6, 35 p., 2018. 2167-8359 http://hdl.handle.net/11449/164378 10.7717/peerj.5168 WOS:000437258800012 WOS000437258800012.pdf |
url |
http://dx.doi.org/10.7717/peerj.5168 http://hdl.handle.net/11449/164378 |
identifier_str_mv |
Peerj. London: Peerj Inc, v. 6, 35 p., 2018. 2167-8359 10.7717/peerj.5168 WOS:000437258800012 WOS000437258800012.pdf |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
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Peerj 1,087 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
35 application/pdf |
dc.publisher.none.fl_str_mv |
Peerj Inc |
publisher.none.fl_str_mv |
Peerj Inc |
dc.source.none.fl_str_mv |
Web of Science reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
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UNESP |
reponame_str |
Repositório Institucional da UNESP |
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Repositório Institucional da UNESP |
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Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
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1808129396651851776 |