Phylogenomic analysis of the Neotropical fish subfamily Characinae using ultraconserved elements (Teleostei: Characidae)
Autor(a) principal: | |
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Data de Publicação: | 2022 |
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.2022.107462 http://hdl.handle.net/11449/223740 |
Resumo: | Characinae is one of the most species-rich subfamilies of Characidae and holds special taxonomic importance because it includes Charax, type-genus of Characidae and Characiformes. Currently, the monophyly and the hypotheses of intergeneric and interspecific relationships of Characinae are based on a few morphological and molecular studies but all with low species coverage. Given their diversity, taxonomic importance, and the lack of a taxon-dense phylogeny, we sought to buttress the systematic understanding of Characinae collecting DNA sequence data from ultraconserved elements (UCEs) of the genome from 98 specimens covering 57 species (61%) plus 17 characiforms as outgroups. We used maximum likelihood, Bayesian inference, and coalescent-based species tree approaches and the resulting phylogeny with 1,300 UCE loci (586,785 characters) reinforced the monophyly of the subfamily as well as of six genera: Acestrocephalus, Charax, Cynopotamus, Galeocharax, Phenacogaster, and Roeboides. The phylogeny provides a hypothesis of intergeneric and interspecific relationships for the subfamily with Phenacogaster sister to all genera, and Acanthocharax sister to Cynopotamini (Cynopotamus (Acestrocephalus Galeocharax)) and Characini (Charax Roeboides). We propose a new tribe Acanthocharacini to allocate Acanthocharax, two subclades for Phenacogaster, two for Cynopotamus, three for Charax, and reinforced the four subclades for Roeboides previously identified by morphological studies. Additionally, we generated a time-calibrated phylogeny for Characinae that suggested an initial diversification during the Miocene at around 19 million years ago and discussed historical biogeographic events for major subclades. The results obtained here will contribute to the development of further research on the evolutionary processes modulating species diversification in Characinae. |
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Phylogenomic analysis of the Neotropical fish subfamily Characinae using ultraconserved elements (Teleostei: Characidae)BiodiversityCharaciformesFreshwater fishNeotropicsOstariophysiSystematicsCharacinae is one of the most species-rich subfamilies of Characidae and holds special taxonomic importance because it includes Charax, type-genus of Characidae and Characiformes. Currently, the monophyly and the hypotheses of intergeneric and interspecific relationships of Characinae are based on a few morphological and molecular studies but all with low species coverage. Given their diversity, taxonomic importance, and the lack of a taxon-dense phylogeny, we sought to buttress the systematic understanding of Characinae collecting DNA sequence data from ultraconserved elements (UCEs) of the genome from 98 specimens covering 57 species (61%) plus 17 characiforms as outgroups. We used maximum likelihood, Bayesian inference, and coalescent-based species tree approaches and the resulting phylogeny with 1,300 UCE loci (586,785 characters) reinforced the monophyly of the subfamily as well as of six genera: Acestrocephalus, Charax, Cynopotamus, Galeocharax, Phenacogaster, and Roeboides. The phylogeny provides a hypothesis of intergeneric and interspecific relationships for the subfamily with Phenacogaster sister to all genera, and Acanthocharax sister to Cynopotamini (Cynopotamus (Acestrocephalus Galeocharax)) and Characini (Charax Roeboides). We propose a new tribe Acanthocharacini to allocate Acanthocharax, two subclades for Phenacogaster, two for Cynopotamus, three for Charax, and reinforced the four subclades for Roeboides previously identified by morphological studies. Additionally, we generated a time-calibrated phylogeny for Characinae that suggested an initial diversification during the Miocene at around 19 million years ago and discussed historical biogeographic events for major subclades. The results obtained here will contribute to the development of further research on the evolutionary processes modulating species diversification in Characinae.Departamento de Biologia Estrutural e Funcional Instituto de Biociências Universidade Estadual Paulista, R. Prof. Dr. Antônio C. W. Zanin 250, SPDepartment of Ichthyology Division of Vertebrate Zoology American Museum of Natural History, Central Park West at 79th StreetLaboratório de Ictiologia de Sorocaba Departamento de Biologia Universidade Federal de São Carlos, Rod. João Leme dos Santos km 110, SPDepartamento de Biologia Estrutural e Funcional Instituto de Biociências Universidade Estadual Paulista, R. Prof. Dr. Antônio C. W. Zanin 250, SPUniversidade Estadual Paulista (UNESP)American Museum of Natural HistoryUniversidade Federal de São Carlos (UFSCar)Souza, Camila S. [UNESP]Melo, Bruno F.Mattox, George M.T.Oliveira, Claudio [UNESP]2022-04-28T19:52:49Z2022-04-28T19:52:49Z2022-06-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1016/j.ympev.2022.107462Molecular Phylogenetics and Evolution, v. 171.1095-95131055-7903http://hdl.handle.net/11449/22374010.1016/j.ympev.2022.1074622-s2.0-85127348247Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengMolecular Phylogenetics and Evolutioninfo:eu-repo/semantics/openAccess2022-04-28T19:52:49Zoai:repositorio.unesp.br:11449/223740Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T19:12:51.132497Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Phylogenomic analysis of the Neotropical fish subfamily Characinae using ultraconserved elements (Teleostei: Characidae) |
title |
Phylogenomic analysis of the Neotropical fish subfamily Characinae using ultraconserved elements (Teleostei: Characidae) |
spellingShingle |
Phylogenomic analysis of the Neotropical fish subfamily Characinae using ultraconserved elements (Teleostei: Characidae) Souza, Camila S. [UNESP] Biodiversity Characiformes Freshwater fish Neotropics Ostariophysi Systematics |
title_short |
Phylogenomic analysis of the Neotropical fish subfamily Characinae using ultraconserved elements (Teleostei: Characidae) |
title_full |
Phylogenomic analysis of the Neotropical fish subfamily Characinae using ultraconserved elements (Teleostei: Characidae) |
title_fullStr |
Phylogenomic analysis of the Neotropical fish subfamily Characinae using ultraconserved elements (Teleostei: Characidae) |
title_full_unstemmed |
Phylogenomic analysis of the Neotropical fish subfamily Characinae using ultraconserved elements (Teleostei: Characidae) |
title_sort |
Phylogenomic analysis of the Neotropical fish subfamily Characinae using ultraconserved elements (Teleostei: Characidae) |
author |
Souza, Camila S. [UNESP] |
author_facet |
Souza, Camila S. [UNESP] Melo, Bruno F. Mattox, George M.T. Oliveira, Claudio [UNESP] |
author_role |
author |
author2 |
Melo, Bruno F. Mattox, George M.T. Oliveira, Claudio [UNESP] |
author2_role |
author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (UNESP) American Museum of Natural History Universidade Federal de São Carlos (UFSCar) |
dc.contributor.author.fl_str_mv |
Souza, Camila S. [UNESP] Melo, Bruno F. Mattox, George M.T. Oliveira, Claudio [UNESP] |
dc.subject.por.fl_str_mv |
Biodiversity Characiformes Freshwater fish Neotropics Ostariophysi Systematics |
topic |
Biodiversity Characiformes Freshwater fish Neotropics Ostariophysi Systematics |
description |
Characinae is one of the most species-rich subfamilies of Characidae and holds special taxonomic importance because it includes Charax, type-genus of Characidae and Characiformes. Currently, the monophyly and the hypotheses of intergeneric and interspecific relationships of Characinae are based on a few morphological and molecular studies but all with low species coverage. Given their diversity, taxonomic importance, and the lack of a taxon-dense phylogeny, we sought to buttress the systematic understanding of Characinae collecting DNA sequence data from ultraconserved elements (UCEs) of the genome from 98 specimens covering 57 species (61%) plus 17 characiforms as outgroups. We used maximum likelihood, Bayesian inference, and coalescent-based species tree approaches and the resulting phylogeny with 1,300 UCE loci (586,785 characters) reinforced the monophyly of the subfamily as well as of six genera: Acestrocephalus, Charax, Cynopotamus, Galeocharax, Phenacogaster, and Roeboides. The phylogeny provides a hypothesis of intergeneric and interspecific relationships for the subfamily with Phenacogaster sister to all genera, and Acanthocharax sister to Cynopotamini (Cynopotamus (Acestrocephalus Galeocharax)) and Characini (Charax Roeboides). We propose a new tribe Acanthocharacini to allocate Acanthocharax, two subclades for Phenacogaster, two for Cynopotamus, three for Charax, and reinforced the four subclades for Roeboides previously identified by morphological studies. Additionally, we generated a time-calibrated phylogeny for Characinae that suggested an initial diversification during the Miocene at around 19 million years ago and discussed historical biogeographic events for major subclades. The results obtained here will contribute to the development of further research on the evolutionary processes modulating species diversification in Characinae. |
publishDate |
2022 |
dc.date.none.fl_str_mv |
2022-04-28T19:52:49Z 2022-04-28T19:52:49Z 2022-06-01 |
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.2022.107462 Molecular Phylogenetics and Evolution, v. 171. 1095-9513 1055-7903 http://hdl.handle.net/11449/223740 10.1016/j.ympev.2022.107462 2-s2.0-85127348247 |
url |
http://dx.doi.org/10.1016/j.ympev.2022.107462 http://hdl.handle.net/11449/223740 |
identifier_str_mv |
Molecular Phylogenetics and Evolution, v. 171. 1095-9513 1055-7903 10.1016/j.ympev.2022.107462 2-s2.0-85127348247 |
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.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 |
|
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1808129033893838848 |