Multilocus species trees and species delimitation in a temporal context: application to the water shrews of the genus Neomys

[Background] Multilocus data are becoming increasingly important in determining the phylogeny of closely related species and delimiting species. In species complexes where unequivocal fossil calibrations are not available, rigorous dating of the coalescence-based species trees requires accurate muta...

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Detalles Bibliográficos
Autores: Igea, Javier, Aymerich, Pere, Bannikova, Anna A., Gosálbez, Joaquim, Castresana, José
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2015
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/125554
Acceso en línea:http://hdl.handle.net/10261/125554
Access Level:acceso abierto
Palabra clave:Gene flow
Introns
Mutation rates
Relaxed clock
Speciation
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spelling Multilocus species trees and species delimitation in a temporal context: application to the water shrews of the genus NeomysIgea, JavierAymerich, PereBannikova, Anna A.Gosálbez, JoaquimCastresana, JoséGene flowIntronsMutation ratesRelaxed clockSpeciation[Background] Multilocus data are becoming increasingly important in determining the phylogeny of closely related species and delimiting species. In species complexes where unequivocal fossil calibrations are not available, rigorous dating of the coalescence-based species trees requires accurate mutation rates of the loci under study but, generally, these rates are unknown. Here, we obtained lineage-specific mutation rates of these loci from a higher-level phylogeny with a reliable fossil record and investigated how different choices of mutation rates and species tree models affected the split time estimates. We implemented this strategy with a genus of water shrews, Neomys, whose taxonomy has been contentious over the last century.[Results] We sequenced 13 introns and cytochrome b from specimens of the three species currently recognized in this genus including two subspecies of N. anomalus that were originally described as species. A Bayesian multilocus species delimitation method and estimation of gene flow supported that these subspecies are distinct evolutionary lineages that should be treated as distinct species: N. anomalus (sensu stricto), limited to part of the Iberian Peninsula, and N. milleri, with a larger Eurasian range. We then estimated mutation rates from a Bayesian relaxed clock analysis of the mammalian orthologues with several fossil calibrations. Next, using the estimated Neomys-specific rates for each locus in an isolation-with-migration model, the split time for these sister taxa was dated at 0.40 Myr ago (with a 95 % confidence interval of 0.26 – 0.86 Myr), likely coinciding with one of the major glaciations of the Middle Pleistocene. We also showed that the extrapolation of non-specific rates or the use of simpler models would lead to very different split time estimates.[Conclusions] We showed that the estimation of rigorous lineage-specific mutation rates for each locus allows the inference of robust split times in a species tree framework. These times, in turn, afford a better understanding of the timeframe required to achieve isolation and, eventually, speciation in sister lineages. The application of species delimitation methods and an accurate dating strategy to the genus Neomys helped to clarify its controversial taxonomy.This work was financially supported by research project CGL2011-22640/BOS of the “Plan Nacional I + D + I del Ministerio de Ciencia e Innovación” (Spain) to J.C. with contribution of project 014/2008 of the “Convocatoria de ayudas a proyectos de investigación en la Red de Parques Nacionales” (Spain) to J.G. The research of A.A.B. was supported by the Russian Foundation for Basic Research, project 14-04-00034. We acknowledge support of the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI).Peer reviewedBioMed CentralMinisterio de Ciencia e Innovación (España)Russian Foundation for Basic ResearchCSIC - Unidad de Recursos de Información Científica para la Investigación (URICI)Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2015201520152015info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/125554reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Ingléshttp://dx.doi.org/10.1186/s12862-015-0485-zSíinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/1255542026-05-22T06:33:51Z
dc.title.none.fl_str_mv Multilocus species trees and species delimitation in a temporal context: application to the water shrews of the genus Neomys
title Multilocus species trees and species delimitation in a temporal context: application to the water shrews of the genus Neomys
spellingShingle Multilocus species trees and species delimitation in a temporal context: application to the water shrews of the genus Neomys
Igea, Javier
Gene flow
Introns
Mutation rates
Relaxed clock
Speciation
title_short Multilocus species trees and species delimitation in a temporal context: application to the water shrews of the genus Neomys
title_full Multilocus species trees and species delimitation in a temporal context: application to the water shrews of the genus Neomys
title_fullStr Multilocus species trees and species delimitation in a temporal context: application to the water shrews of the genus Neomys
title_full_unstemmed Multilocus species trees and species delimitation in a temporal context: application to the water shrews of the genus Neomys
title_sort Multilocus species trees and species delimitation in a temporal context: application to the water shrews of the genus Neomys
dc.creator.none.fl_str_mv Igea, Javier
Aymerich, Pere
Bannikova, Anna A.
Gosálbez, Joaquim
Castresana, José
author Igea, Javier
author_facet Igea, Javier
Aymerich, Pere
Bannikova, Anna A.
Gosálbez, Joaquim
Castresana, José
author_role author
author2 Aymerich, Pere
Bannikova, Anna A.
Gosálbez, Joaquim
Castresana, José
author2_role author
author
author
author
dc.contributor.none.fl_str_mv Ministerio de Ciencia e Innovación (España)
Russian Foundation for Basic Research
CSIC - Unidad de Recursos de Información Científica para la Investigación (URICI)
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Gene flow
Introns
Mutation rates
Relaxed clock
Speciation
topic Gene flow
Introns
Mutation rates
Relaxed clock
Speciation
description [Background] Multilocus data are becoming increasingly important in determining the phylogeny of closely related species and delimiting species. In species complexes where unequivocal fossil calibrations are not available, rigorous dating of the coalescence-based species trees requires accurate mutation rates of the loci under study but, generally, these rates are unknown. Here, we obtained lineage-specific mutation rates of these loci from a higher-level phylogeny with a reliable fossil record and investigated how different choices of mutation rates and species tree models affected the split time estimates. We implemented this strategy with a genus of water shrews, Neomys, whose taxonomy has been contentious over the last century.
publishDate 2015
dc.date.none.fl_str_mv 2015
2015
2015
2015
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/125554
url http://hdl.handle.net/10261/125554
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv http://dx.doi.org/10.1186/s12862-015-0485-z
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,81155

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