Phylogenomic reappraisal of the Neotropical catfish family Loricariidae (Teleostei: Siluriformes) using ultraconserved elements
Autor(a) principal: | |
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Data de Publicação: | 2019 |
Outros Autores: | , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1016/j.ympev.2019.02.017 http://hdl.handle.net/11449/190212 |
Resumo: | Neotropical freshwaters host more than 6000 fish species, of which 983 are suckermouth armored catfishes of the family Loricariidae – the most-diverse catfish family and fifth most species-rich vertebrate family on Earth. Given their diversity and ubiquitous distribution across many habitat types, loricariids are an excellent system in which to investigate factors that create and maintain Neotropical fish diversity, yet robust phylogenies needed to support such ecological and evolutionary studies are lacking. We sought to buttress the systematic understanding of loricariid catfishes by generating a genome-scale data set (1041 loci, 328,330 bp) for 140 species spanning 75 genera and five of six previously proposed subfamilies. Both maximum likelihood and Bayesian analyses strongly supported the monophyly of Loricariidae. Our results also reinforced the established backbone of loricariid interrelationships: Delturinae as sister to all other analyzed loricariids, with subfamily Rhinelepinae diverging next, followed by Loricariinae sister to Hypostominae + Hypoptopomatinae. Previous DNA-based relationships within Hypostominae and Loricariinae were strongly supported. However, we evaluated for the first time DNA-based relationships among many Hypoptopomatinae genera and found significant differences with this subfamily's current genus-level classification, prompting several taxonomic changes. Finally, we placed our topological results within a fossil-calibrated temporal context indicating that early Loricariidae diversification occurred across the Cretaceous-Paleogene boundary ∼65 million years ago (Ma). Our study lays a strong foundation for future research to focus on relationships among species and the macroevolutionary processes affecting loricariid diversification rates and patterns. |
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Phylogenomic reappraisal of the Neotropical catfish family Loricariidae (Teleostei: Siluriformes) using ultraconserved elementsBiodiversityCascudosNeotropicsPhylogenomicsSouth AmericaTimetreeNeotropical freshwaters host more than 6000 fish species, of which 983 are suckermouth armored catfishes of the family Loricariidae – the most-diverse catfish family and fifth most species-rich vertebrate family on Earth. Given their diversity and ubiquitous distribution across many habitat types, loricariids are an excellent system in which to investigate factors that create and maintain Neotropical fish diversity, yet robust phylogenies needed to support such ecological and evolutionary studies are lacking. We sought to buttress the systematic understanding of loricariid catfishes by generating a genome-scale data set (1041 loci, 328,330 bp) for 140 species spanning 75 genera and five of six previously proposed subfamilies. Both maximum likelihood and Bayesian analyses strongly supported the monophyly of Loricariidae. Our results also reinforced the established backbone of loricariid interrelationships: Delturinae as sister to all other analyzed loricariids, with subfamily Rhinelepinae diverging next, followed by Loricariinae sister to Hypostominae + Hypoptopomatinae. Previous DNA-based relationships within Hypostominae and Loricariinae were strongly supported. However, we evaluated for the first time DNA-based relationships among many Hypoptopomatinae genera and found significant differences with this subfamily's current genus-level classification, prompting several taxonomic changes. Finally, we placed our topological results within a fossil-calibrated temporal context indicating that early Loricariidae diversification occurred across the Cretaceous-Paleogene boundary ∼65 million years ago (Ma). Our study lays a strong foundation for future research to focus on relationships among species and the macroevolutionary processes affecting loricariid diversification rates and patterns.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Departamento de Morfologia Instituto de Biociências Universidade Estadual Paulista (UNESP)Departamento de Zoologia Instituto de Biociências Universidade Estadual Paulista (UNESP)Department of Ichthyology Academy of Natural Sciences of Drexel UniversityDepartment of Biology University of Toronto ScarboroughDepartment of Herpetology and Ichthyology Museum of Natural HistoryDepartment of Vertebrate Zoology National Museum of Natural History Smithsonian InstitutionDepartment of Biology University of Louisiana at LafayetteDepartment of Ecology and Evolutionary Biology University of CaliforniaDepartamento de Morfologia Instituto de Biociências Universidade Estadual Paulista (UNESP)Departamento de Zoologia Instituto de Biociências Universidade Estadual Paulista (UNESP)Universidade Estadual Paulista (Unesp)Academy of Natural Sciences of Drexel UniversityUniversity of Toronto ScarboroughMuseum of Natural HistorySmithsonian InstitutionUniversity of Louisiana at LafayetteUniversity of CaliforniaRoxo, Fábio F. [UNESP]Ochoa, Luz E. [UNESP]Sabaj, Mark H.Lujan, Nathan K.Covain, RaphaëlSilva, Gabriel S.C. [UNESP]Melo, Bruno F. [UNESP]Albert, James S.Chang, JonathanForesti, Fausto [UNESP]Alfaro, Michael E.Oliveira, Claudio [UNESP]2019-10-06T17:05:53Z2019-10-06T17:05:53Z2019-06-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article148-165http://dx.doi.org/10.1016/j.ympev.2019.02.017Molecular Phylogenetics and Evolution, v. 135, p. 148-165.1095-95131055-7903http://hdl.handle.net/11449/19021210.1016/j.ympev.2019.02.0172-s2.0-85063227382Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengMolecular Phylogenetics and Evolutioninfo:eu-repo/semantics/openAccess2021-10-22T21:09:56Zoai:repositorio.unesp.br:11449/190212Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T20:15:44.218833Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Phylogenomic reappraisal of the Neotropical catfish family Loricariidae (Teleostei: Siluriformes) using ultraconserved elements |
title |
Phylogenomic reappraisal of the Neotropical catfish family Loricariidae (Teleostei: Siluriformes) using ultraconserved elements |
spellingShingle |
Phylogenomic reappraisal of the Neotropical catfish family Loricariidae (Teleostei: Siluriformes) using ultraconserved elements Roxo, Fábio F. [UNESP] Biodiversity Cascudos Neotropics Phylogenomics South America Timetree |
title_short |
Phylogenomic reappraisal of the Neotropical catfish family Loricariidae (Teleostei: Siluriformes) using ultraconserved elements |
title_full |
Phylogenomic reappraisal of the Neotropical catfish family Loricariidae (Teleostei: Siluriformes) using ultraconserved elements |
title_fullStr |
Phylogenomic reappraisal of the Neotropical catfish family Loricariidae (Teleostei: Siluriformes) using ultraconserved elements |
title_full_unstemmed |
Phylogenomic reappraisal of the Neotropical catfish family Loricariidae (Teleostei: Siluriformes) using ultraconserved elements |
title_sort |
Phylogenomic reappraisal of the Neotropical catfish family Loricariidae (Teleostei: Siluriformes) using ultraconserved elements |
author |
Roxo, Fábio F. [UNESP] |
author_facet |
Roxo, Fábio F. [UNESP] Ochoa, Luz E. [UNESP] Sabaj, Mark H. Lujan, Nathan K. Covain, Raphaël Silva, Gabriel S.C. [UNESP] Melo, Bruno F. [UNESP] Albert, James S. Chang, Jonathan Foresti, Fausto [UNESP] Alfaro, Michael E. Oliveira, Claudio [UNESP] |
author_role |
author |
author2 |
Ochoa, Luz E. [UNESP] Sabaj, Mark H. Lujan, Nathan K. Covain, Raphaël Silva, Gabriel S.C. [UNESP] Melo, Bruno F. [UNESP] Albert, James S. Chang, Jonathan Foresti, Fausto [UNESP] Alfaro, Michael E. Oliveira, Claudio [UNESP] |
author2_role |
author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) Academy of Natural Sciences of Drexel University University of Toronto Scarborough Museum of Natural History Smithsonian Institution University of Louisiana at Lafayette University of California |
dc.contributor.author.fl_str_mv |
Roxo, Fábio F. [UNESP] Ochoa, Luz E. [UNESP] Sabaj, Mark H. Lujan, Nathan K. Covain, Raphaël Silva, Gabriel S.C. [UNESP] Melo, Bruno F. [UNESP] Albert, James S. Chang, Jonathan Foresti, Fausto [UNESP] Alfaro, Michael E. Oliveira, Claudio [UNESP] |
dc.subject.por.fl_str_mv |
Biodiversity Cascudos Neotropics Phylogenomics South America Timetree |
topic |
Biodiversity Cascudos Neotropics Phylogenomics South America Timetree |
description |
Neotropical freshwaters host more than 6000 fish species, of which 983 are suckermouth armored catfishes of the family Loricariidae – the most-diverse catfish family and fifth most species-rich vertebrate family on Earth. Given their diversity and ubiquitous distribution across many habitat types, loricariids are an excellent system in which to investigate factors that create and maintain Neotropical fish diversity, yet robust phylogenies needed to support such ecological and evolutionary studies are lacking. We sought to buttress the systematic understanding of loricariid catfishes by generating a genome-scale data set (1041 loci, 328,330 bp) for 140 species spanning 75 genera and five of six previously proposed subfamilies. Both maximum likelihood and Bayesian analyses strongly supported the monophyly of Loricariidae. Our results also reinforced the established backbone of loricariid interrelationships: Delturinae as sister to all other analyzed loricariids, with subfamily Rhinelepinae diverging next, followed by Loricariinae sister to Hypostominae + Hypoptopomatinae. Previous DNA-based relationships within Hypostominae and Loricariinae were strongly supported. However, we evaluated for the first time DNA-based relationships among many Hypoptopomatinae genera and found significant differences with this subfamily's current genus-level classification, prompting several taxonomic changes. Finally, we placed our topological results within a fossil-calibrated temporal context indicating that early Loricariidae diversification occurred across the Cretaceous-Paleogene boundary ∼65 million years ago (Ma). Our study lays a strong foundation for future research to focus on relationships among species and the macroevolutionary processes affecting loricariid diversification rates and patterns. |
publishDate |
2019 |
dc.date.none.fl_str_mv |
2019-10-06T17:05:53Z 2019-10-06T17:05:53Z 2019-06-01 |
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/10.1016/j.ympev.2019.02.017 Molecular Phylogenetics and Evolution, v. 135, p. 148-165. 1095-9513 1055-7903 http://hdl.handle.net/11449/190212 10.1016/j.ympev.2019.02.017 2-s2.0-85063227382 |
url |
http://dx.doi.org/10.1016/j.ympev.2019.02.017 http://hdl.handle.net/11449/190212 |
identifier_str_mv |
Molecular Phylogenetics and Evolution, v. 135, p. 148-165. 1095-9513 1055-7903 10.1016/j.ympev.2019.02.017 2-s2.0-85063227382 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Molecular Phylogenetics and Evolution |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
148-165 |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1808129180746907648 |