The potential of genome-wide RAD sequences for resolving rapid radiations: a case study in Cactaceae
Autor(a) principal: | |
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Data de Publicação: | 2020 |
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.2020.106896 http://hdl.handle.net/11449/202010 |
Resumo: | The reconstruction of relationships within recently radiated groups is challenging even when massive amounts of sequencing data are available. The use of restriction site-associated DNA sequencing (RAD-Seq) to this end is promising. Here, we assessed the performance of RAD-Seq to infer the species-level phylogeny of the rapidly radiating genus Cereus (Cactaceae). To examine how the amount of genomic data affects resolution in this group, we used datasets and implemented different analyses. We sampled 52 individuals of Cereus, representing 18 of the 25 species currently recognized, plus members of the closely allied genera Cipocereus and Praecereus, and other 11 Cactaceae genera as outgroups. Three scenarios of permissiveness to missing data were carried out in iPyRAD, assembling datasets with 30% (333 loci), 45% (1440 loci), and 70% (6141 loci) of missing data. For each dataset, Maximum Likelihood (ML) trees were generated using two supermatrices, i.e., only SNPs and SNPs plus invariant sites. Accuracy and resolution were improved when the dataset with the highest number of loci was used (6141 loci), despite the high percentage of missing data included (70%). Coalescent trees estimated using SVDQuartets and ASTRAL are similar to those obtained by the ML reconstructions. Overall, we reconstruct a well-supported phylogeny of Cereus, which is resolved as monophyletic and composed of four main clades with high support in their internal relationships. Our findings also provide insights into the impact of missing data for phylogeny reconstruction using RAD loci. |
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The potential of genome-wide RAD sequences for resolving rapid radiations: a case study in CactaceaeCereusddRAD-SeqMissing dataPhylogenomicsRadiationThe reconstruction of relationships within recently radiated groups is challenging even when massive amounts of sequencing data are available. The use of restriction site-associated DNA sequencing (RAD-Seq) to this end is promising. Here, we assessed the performance of RAD-Seq to infer the species-level phylogeny of the rapidly radiating genus Cereus (Cactaceae). To examine how the amount of genomic data affects resolution in this group, we used datasets and implemented different analyses. We sampled 52 individuals of Cereus, representing 18 of the 25 species currently recognized, plus members of the closely allied genera Cipocereus and Praecereus, and other 11 Cactaceae genera as outgroups. Three scenarios of permissiveness to missing data were carried out in iPyRAD, assembling datasets with 30% (333 loci), 45% (1440 loci), and 70% (6141 loci) of missing data. For each dataset, Maximum Likelihood (ML) trees were generated using two supermatrices, i.e., only SNPs and SNPs plus invariant sites. Accuracy and resolution were improved when the dataset with the highest number of loci was used (6141 loci), despite the high percentage of missing data included (70%). Coalescent trees estimated using SVDQuartets and ASTRAL are similar to those obtained by the ML reconstructions. Overall, we reconstruct a well-supported phylogeny of Cereus, which is resolved as monophyletic and composed of four main clades with high support in their internal relationships. Our findings also provide insights into the impact of missing data for phylogeny reconstruction using RAD loci.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Departamento de Biologia Centro de Ciências Humanas e Biológicas Universidade Federal de São Carlos (UFSCar)Programa de pós-graduação em Biologia Comparada Faculdade de Filosofia Ciências e Letras de Ribeirão Preto Universidade de São Paulo (USP)Departamento de Genética e Biologia Evolutiva Universidade de São Paulo (USP)Department of Ecology Evolution and Environmental Biology Columbia UniversityInstituto de Biotecnologia (IBTEC) e Instituto de Biociências de Botucatu (IBB) Universidade Estadual Paulista (UNESP)Singapore Botanic Gardens (National Parks Board), 1 Cluny RoadInstituto Tecnológico Vale / Museu Paraense Emilio Goeldi Coord. BotânicaInstituto de Biotecnologia (IBTEC) e Instituto de Biociências de Botucatu (IBB) Universidade Estadual Paulista (UNESP)FAPESP: 2014/25227-0FAPESP: 2018/03428-5Universidade Federal de São Carlos (UFSCar)Universidade de São Paulo (USP)Columbia UniversityUniversidade Estadual Paulista (Unesp)Singapore Botanic Gardens (National Parks Board)Coord. BotânicaBombonato, Juliana Rodriguesdo Amaral, Danilo TrabucoSilva, Gislaine Angélica RodriguesKhan, GulzarMoraes, Evandro M.da Silva Andrade, Sónia CristinaEaton, Deren A.R.Alonso, Diego Peres [UNESP]Ribolla, Paulo Eduardo Martins [UNESP]Taylor, NigelZappi, DanielaFranco, Fernando Faria2020-12-12T02:47:34Z2020-12-12T02:47:34Z2020-10-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1016/j.ympev.2020.106896Molecular Phylogenetics and Evolution, v. 151.1095-95131055-7903http://hdl.handle.net/11449/20201010.1016/j.ympev.2020.1068962-s2.0-85089358974Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengMolecular Phylogenetics and Evolutioninfo:eu-repo/semantics/openAccess2021-10-23T04:24:24Zoai:repositorio.unesp.br:11449/202010Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T23:57:49.091935Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
The potential of genome-wide RAD sequences for resolving rapid radiations: a case study in Cactaceae |
title |
The potential of genome-wide RAD sequences for resolving rapid radiations: a case study in Cactaceae |
spellingShingle |
The potential of genome-wide RAD sequences for resolving rapid radiations: a case study in Cactaceae Bombonato, Juliana Rodrigues Cereus ddRAD-Seq Missing data Phylogenomics Radiation |
title_short |
The potential of genome-wide RAD sequences for resolving rapid radiations: a case study in Cactaceae |
title_full |
The potential of genome-wide RAD sequences for resolving rapid radiations: a case study in Cactaceae |
title_fullStr |
The potential of genome-wide RAD sequences for resolving rapid radiations: a case study in Cactaceae |
title_full_unstemmed |
The potential of genome-wide RAD sequences for resolving rapid radiations: a case study in Cactaceae |
title_sort |
The potential of genome-wide RAD sequences for resolving rapid radiations: a case study in Cactaceae |
author |
Bombonato, Juliana Rodrigues |
author_facet |
Bombonato, Juliana Rodrigues do Amaral, Danilo Trabuco Silva, Gislaine Angélica Rodrigues Khan, Gulzar Moraes, Evandro M. da Silva Andrade, Sónia Cristina Eaton, Deren A.R. Alonso, Diego Peres [UNESP] Ribolla, Paulo Eduardo Martins [UNESP] Taylor, Nigel Zappi, Daniela Franco, Fernando Faria |
author_role |
author |
author2 |
do Amaral, Danilo Trabuco Silva, Gislaine Angélica Rodrigues Khan, Gulzar Moraes, Evandro M. da Silva Andrade, Sónia Cristina Eaton, Deren A.R. Alonso, Diego Peres [UNESP] Ribolla, Paulo Eduardo Martins [UNESP] Taylor, Nigel Zappi, Daniela Franco, Fernando Faria |
author2_role |
author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Federal de São Carlos (UFSCar) Universidade de São Paulo (USP) Columbia University Universidade Estadual Paulista (Unesp) Singapore Botanic Gardens (National Parks Board) Coord. Botânica |
dc.contributor.author.fl_str_mv |
Bombonato, Juliana Rodrigues do Amaral, Danilo Trabuco Silva, Gislaine Angélica Rodrigues Khan, Gulzar Moraes, Evandro M. da Silva Andrade, Sónia Cristina Eaton, Deren A.R. Alonso, Diego Peres [UNESP] Ribolla, Paulo Eduardo Martins [UNESP] Taylor, Nigel Zappi, Daniela Franco, Fernando Faria |
dc.subject.por.fl_str_mv |
Cereus ddRAD-Seq Missing data Phylogenomics Radiation |
topic |
Cereus ddRAD-Seq Missing data Phylogenomics Radiation |
description |
The reconstruction of relationships within recently radiated groups is challenging even when massive amounts of sequencing data are available. The use of restriction site-associated DNA sequencing (RAD-Seq) to this end is promising. Here, we assessed the performance of RAD-Seq to infer the species-level phylogeny of the rapidly radiating genus Cereus (Cactaceae). To examine how the amount of genomic data affects resolution in this group, we used datasets and implemented different analyses. We sampled 52 individuals of Cereus, representing 18 of the 25 species currently recognized, plus members of the closely allied genera Cipocereus and Praecereus, and other 11 Cactaceae genera as outgroups. Three scenarios of permissiveness to missing data were carried out in iPyRAD, assembling datasets with 30% (333 loci), 45% (1440 loci), and 70% (6141 loci) of missing data. For each dataset, Maximum Likelihood (ML) trees were generated using two supermatrices, i.e., only SNPs and SNPs plus invariant sites. Accuracy and resolution were improved when the dataset with the highest number of loci was used (6141 loci), despite the high percentage of missing data included (70%). Coalescent trees estimated using SVDQuartets and ASTRAL are similar to those obtained by the ML reconstructions. Overall, we reconstruct a well-supported phylogeny of Cereus, which is resolved as monophyletic and composed of four main clades with high support in their internal relationships. Our findings also provide insights into the impact of missing data for phylogeny reconstruction using RAD loci. |
publishDate |
2020 |
dc.date.none.fl_str_mv |
2020-12-12T02:47:34Z 2020-12-12T02:47:34Z 2020-10-01 |
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.2020.106896 Molecular Phylogenetics and Evolution, v. 151. 1095-9513 1055-7903 http://hdl.handle.net/11449/202010 10.1016/j.ympev.2020.106896 2-s2.0-85089358974 |
url |
http://dx.doi.org/10.1016/j.ympev.2020.106896 http://hdl.handle.net/11449/202010 |
identifier_str_mv |
Molecular Phylogenetics and Evolution, v. 151. 1095-9513 1055-7903 10.1016/j.ympev.2020.106896 2-s2.0-85089358974 |
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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1808129566791696384 |