Phylogenomic species delimitation in microendemic frogs of the Brazilian Atlantic Forest
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.2019.106627 http://hdl.handle.net/11449/194929 |
Resumo: | The advent of next-generation sequencing allows researchers to use large-scale datasets for species delimitation analyses, yet one can envision an inflection point where the added accuracy of including more loci does not offset the increased computational burden. One alternative to including all loci could be to prioritize the analysis of loci for which there is an expectation of high informativeness. Here, we explore the issue of species delimitation and locus selection with montane species from two anuran genera that have been isolated in sky islands across the southern Brazilian Atlantic Forest: Melanophryniscus (Bufonidae) and Brachycephalus (Brachycephalidae). To delimit species, we obtained genetic data using target enrichment of ultraconserved elements from 32 populations (13 for Melanophryniscus and 19 for Brachycephalus), and we were able to create datasets that included over 800 loci with no missing data. We ranked loci according to their number of parsimony-informative sites, and we performed species delimitation analyses using BPP with the most informative 10, 20, 40, 80, 160, 320, and 640 loci. We identified three types of phylogenetic node: nodes with either consistently high or low support regardless of the number of loci or their informativeness and nodes that were initially poorly supported where support became stronger as we included more data. When viewed across all sensitivity analyses, our results suggest that the current species richness in both genera is likely underestimated. In addition, our results show the effects of different sampling strategies on species delimitation using phylogenomic datasets. |
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Phylogenomic species delimitation in microendemic frogs of the Brazilian Atlantic ForestAnuraTerraranaeBrachycephalusMelanophryniscusUltraconserved elementsUCEsThe advent of next-generation sequencing allows researchers to use large-scale datasets for species delimitation analyses, yet one can envision an inflection point where the added accuracy of including more loci does not offset the increased computational burden. One alternative to including all loci could be to prioritize the analysis of loci for which there is an expectation of high informativeness. Here, we explore the issue of species delimitation and locus selection with montane species from two anuran genera that have been isolated in sky islands across the southern Brazilian Atlantic Forest: Melanophryniscus (Bufonidae) and Brachycephalus (Brachycephalidae). To delimit species, we obtained genetic data using target enrichment of ultraconserved elements from 32 populations (13 for Melanophryniscus and 19 for Brachycephalus), and we were able to create datasets that included over 800 loci with no missing data. We ranked loci according to their number of parsimony-informative sites, and we performed species delimitation analyses using BPP with the most informative 10, 20, 40, 80, 160, 320, and 640 loci. We identified three types of phylogenetic node: nodes with either consistently high or low support regardless of the number of loci or their informativeness and nodes that were initially poorly supported where support became stronger as we included more data. When viewed across all sensitivity analyses, our results suggest that the current species richness in both genera is likely underestimated. In addition, our results show the effects of different sampling strategies on species delimitation using phylogenomic datasets.Fundacao Grupo Boticario de Protecao a NaturezaConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Univ Fed Parana, Dept Zool, BR-81531980 Curitiba, Parana, BrazilMater Nat Inst Estudos Ambientais, BR-80250020 Curitiba, Parana, BrazilUniv Estadual Paulista, Inst Biociencias, Praca Infante Dom Henrique S-No,Parque Bitaru, BR-11330900 Sao Paulo, BrazilPontificia Univ Catolica Parana, Escola Ciencias Vida, BR-80215901 Curitiba, Parana, BrazilLouisiana State Univ, Dept Biol Sci, Baton Rouge, LA 70803 USALouisiana State Univ, Museum Nat Sci, Baton Rouge, LA 70803 USAOccidental Coll, Moore Lab Zool, 1600 Campus Rd, Los Angeles, CA 90041 USAUniv Estadual Paulista, Inst Biociencias, Praca Infante Dom Henrique S-No,Parque Bitaru, BR-11330900 Sao Paulo, BrazilFundacao Grupo Boticario de Protecao a Natureza: 0895_20111Fundacao Grupo Boticario de Protecao a Natureza: A0010_2014CNPq: 301636/2016-8Elsevier B.V.Univ Fed ParanaMater Nat Inst Estudos AmbientaisUniversidade Estadual Paulista (Unesp)Pontificia Univ Catolica ParanaLouisiana State UnivOccidental CollPie, Marcio R.Bornschein, Marcos R. [UNESP]Ribeiro, Luiz F.Faircloth, Brant C.McCormack, John E.2020-12-10T16:58:59Z2020-12-10T16:58:59Z2019-12-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article8http://dx.doi.org/10.1016/j.ympev.2019.106627Molecular Phylogenetics And Evolution. San Diego: Academic Press Inc Elsevier Science, v. 141, 8 p., 2019.1055-7903http://hdl.handle.net/11449/19492910.1016/j.ympev.2019.106627WOS:000492748200015Web of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengMolecular Phylogenetics And Evolutioninfo:eu-repo/semantics/openAccess2021-10-23T02:05:38Zoai:repositorio.unesp.br:11449/194929Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T16:24:02.554600Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Phylogenomic species delimitation in microendemic frogs of the Brazilian Atlantic Forest |
title |
Phylogenomic species delimitation in microendemic frogs of the Brazilian Atlantic Forest |
spellingShingle |
Phylogenomic species delimitation in microendemic frogs of the Brazilian Atlantic Forest Pie, Marcio R. Anura Terraranae Brachycephalus Melanophryniscus Ultraconserved elements UCEs |
title_short |
Phylogenomic species delimitation in microendemic frogs of the Brazilian Atlantic Forest |
title_full |
Phylogenomic species delimitation in microendemic frogs of the Brazilian Atlantic Forest |
title_fullStr |
Phylogenomic species delimitation in microendemic frogs of the Brazilian Atlantic Forest |
title_full_unstemmed |
Phylogenomic species delimitation in microendemic frogs of the Brazilian Atlantic Forest |
title_sort |
Phylogenomic species delimitation in microendemic frogs of the Brazilian Atlantic Forest |
author |
Pie, Marcio R. |
author_facet |
Pie, Marcio R. Bornschein, Marcos R. [UNESP] Ribeiro, Luiz F. Faircloth, Brant C. McCormack, John E. |
author_role |
author |
author2 |
Bornschein, Marcos R. [UNESP] Ribeiro, Luiz F. Faircloth, Brant C. McCormack, John E. |
author2_role |
author author author author |
dc.contributor.none.fl_str_mv |
Univ Fed Parana Mater Nat Inst Estudos Ambientais Universidade Estadual Paulista (Unesp) Pontificia Univ Catolica Parana Louisiana State Univ Occidental Coll |
dc.contributor.author.fl_str_mv |
Pie, Marcio R. Bornschein, Marcos R. [UNESP] Ribeiro, Luiz F. Faircloth, Brant C. McCormack, John E. |
dc.subject.por.fl_str_mv |
Anura Terraranae Brachycephalus Melanophryniscus Ultraconserved elements UCEs |
topic |
Anura Terraranae Brachycephalus Melanophryniscus Ultraconserved elements UCEs |
description |
The advent of next-generation sequencing allows researchers to use large-scale datasets for species delimitation analyses, yet one can envision an inflection point where the added accuracy of including more loci does not offset the increased computational burden. One alternative to including all loci could be to prioritize the analysis of loci for which there is an expectation of high informativeness. Here, we explore the issue of species delimitation and locus selection with montane species from two anuran genera that have been isolated in sky islands across the southern Brazilian Atlantic Forest: Melanophryniscus (Bufonidae) and Brachycephalus (Brachycephalidae). To delimit species, we obtained genetic data using target enrichment of ultraconserved elements from 32 populations (13 for Melanophryniscus and 19 for Brachycephalus), and we were able to create datasets that included over 800 loci with no missing data. We ranked loci according to their number of parsimony-informative sites, and we performed species delimitation analyses using BPP with the most informative 10, 20, 40, 80, 160, 320, and 640 loci. We identified three types of phylogenetic node: nodes with either consistently high or low support regardless of the number of loci or their informativeness and nodes that were initially poorly supported where support became stronger as we included more data. When viewed across all sensitivity analyses, our results suggest that the current species richness in both genera is likely underestimated. In addition, our results show the effects of different sampling strategies on species delimitation using phylogenomic datasets. |
publishDate |
2019 |
dc.date.none.fl_str_mv |
2019-12-01 2020-12-10T16:58:59Z 2020-12-10T16:58:59Z |
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.2019.106627 Molecular Phylogenetics And Evolution. San Diego: Academic Press Inc Elsevier Science, v. 141, 8 p., 2019. 1055-7903 http://hdl.handle.net/11449/194929 10.1016/j.ympev.2019.106627 WOS:000492748200015 |
url |
http://dx.doi.org/10.1016/j.ympev.2019.106627 http://hdl.handle.net/11449/194929 |
identifier_str_mv |
Molecular Phylogenetics And Evolution. San Diego: Academic Press Inc Elsevier Science, v. 141, 8 p., 2019. 1055-7903 10.1016/j.ympev.2019.106627 WOS:000492748200015 |
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 |
8 |
dc.publisher.none.fl_str_mv |
Elsevier B.V. |
publisher.none.fl_str_mv |
Elsevier B.V. |
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 |
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_ |
1808128644039573504 |