Species delimitation with abc and other coalescent-based methods: A test of accuracy with simulations and an empirical example with lizards of the liolaemus darwinii complex (Squam...

Autores
Camargo Bentaberry, Arley; Morando, Mariana; Avila, Luciano Javier; Sites Jr., Jack W.
Año de publicación
2012
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Species delimitation is a major research focus in evolutionary biology because accurate species boundaries are a prerequisite for the study of speciation. New species delimitation methods (SDMs) can accommodate nonmonophyletic species and gene tree discordance as a result of incomplete lineage sorting via the coalescent model, but do not explicitly accommodate gene flow after divergence. Approximate Bayesian computation (ABC) can incorporate gene flow and estimate other relevant parameters of the speciation process while testing alternative species delimitation hypotheses. We evaluated the accuracy of BPP, SpeDeSTEM, and ABC for delimiting species using simulated data and applied these methods to empirical data from lizards of the Liolaemus darwinii complex. Overall, BPP was the most accurate, ABC showed an intermediate accuracy, and SpeDeSTEM was the least accurate under most simulated conditions. All three SDMs showed lower accuracy when speciation occurred despite gene flow, as found in previous studies, but ABC was the method with the smallest decrease in accuracy. All three SDMs consistently supported the distinctness of southern and northern lineages within L. darwinii. These SDMs based on genetic data should be complemented with novel SDMs based on morphological and ecological data to achieve truly integrative and statistically robust approaches to species discovery.
Fil: Camargo Bentaberry, Arley. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico; Argentina. University Brigham Young; Estados Unidos
Fil: Morando, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentina
Fil: Avila, Luciano Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentina. Brigham Young University; Estados Unidos
Fil: Sites Jr., Jack W.. University Brigham Young; Estados Unidos
Materia
Divergence
Gene Flow
Gene Trees
Simulation
Speciation
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/68380
Acceder
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network_name_str CONICET Digital (CONICET)
spelling Species delimitation with abc and other coalescent-based methods: A test of accuracy with simulations and an empirical example with lizards of the liolaemus darwinii complex (Squamata: Liolaemidae)Camargo Bentaberry, ArleyMorando, MarianaAvila, Luciano JavierSites Jr., Jack W.DivergenceGene FlowGene TreesSimulationSpeciationhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Species delimitation is a major research focus in evolutionary biology because accurate species boundaries are a prerequisite for the study of speciation. New species delimitation methods (SDMs) can accommodate nonmonophyletic species and gene tree discordance as a result of incomplete lineage sorting via the coalescent model, but do not explicitly accommodate gene flow after divergence. Approximate Bayesian computation (ABC) can incorporate gene flow and estimate other relevant parameters of the speciation process while testing alternative species delimitation hypotheses. We evaluated the accuracy of BPP, SpeDeSTEM, and ABC for delimiting species using simulated data and applied these methods to empirical data from lizards of the Liolaemus darwinii complex. Overall, BPP was the most accurate, ABC showed an intermediate accuracy, and SpeDeSTEM was the least accurate under most simulated conditions. All three SDMs showed lower accuracy when speciation occurred despite gene flow, as found in previous studies, but ABC was the method with the smallest decrease in accuracy. All three SDMs consistently supported the distinctness of southern and northern lineages within L. darwinii. These SDMs based on genetic data should be complemented with novel SDMs based on morphological and ecological data to achieve truly integrative and statistically robust approaches to species discovery.Fil: Camargo Bentaberry, Arley. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico; Argentina. University Brigham Young; Estados UnidosFil: Morando, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; ArgentinaFil: Avila, Luciano Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentina. Brigham Young University; Estados UnidosFil: Sites Jr., Jack W.. University Brigham Young; Estados UnidosWiley Blackwell Publishing, Inc2012-09info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/68380Camargo Bentaberry, Arley; Morando, Mariana; Avila, Luciano Javier; Sites Jr., Jack W.; Species delimitation with abc and other coalescent-based methods: A test of accuracy with simulations and an empirical example with lizards of the liolaemus darwinii complex (Squamata: Liolaemidae); Wiley Blackwell Publishing, Inc; Evolution; 66; 9; 9-2012; 2834-28490014-38201558-5646CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/epdf/10.1111/j.1558-5646.2012.01640.xinfo:eu-repo/semantics/altIdentifier/doi/10.1111/j.1558-5646.2012.01640.xinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-22T11:21:25Zoai:ri.conicet.gov.ar:11336/68380instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-10-22 11:21:25.571CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Species delimitation with abc and other coalescent-based methods: A test of accuracy with simulations and an empirical example with lizards of the liolaemus darwinii complex (Squamata: Liolaemidae)
title Species delimitation with abc and other coalescent-based methods: A test of accuracy with simulations and an empirical example with lizards of the liolaemus darwinii complex (Squamata: Liolaemidae)
spellingShingle Species delimitation with abc and other coalescent-based methods: A test of accuracy with simulations and an empirical example with lizards of the liolaemus darwinii complex (Squamata: Liolaemidae)
Camargo Bentaberry, Arley
Divergence
Gene Flow
Gene Trees
Simulation
Speciation
title_short Species delimitation with abc and other coalescent-based methods: A test of accuracy with simulations and an empirical example with lizards of the liolaemus darwinii complex (Squamata: Liolaemidae)
title_full Species delimitation with abc and other coalescent-based methods: A test of accuracy with simulations and an empirical example with lizards of the liolaemus darwinii complex (Squamata: Liolaemidae)
title_fullStr Species delimitation with abc and other coalescent-based methods: A test of accuracy with simulations and an empirical example with lizards of the liolaemus darwinii complex (Squamata: Liolaemidae)
title_full_unstemmed Species delimitation with abc and other coalescent-based methods: A test of accuracy with simulations and an empirical example with lizards of the liolaemus darwinii complex (Squamata: Liolaemidae)
title_sort Species delimitation with abc and other coalescent-based methods: A test of accuracy with simulations and an empirical example with lizards of the liolaemus darwinii complex (Squamata: Liolaemidae)
dc.creator.none.fl_str_mv Camargo Bentaberry, Arley
Morando, Mariana
Avila, Luciano Javier
Sites Jr., Jack W.
author Camargo Bentaberry, Arley
author_facet Camargo Bentaberry, Arley
Morando, Mariana
Avila, Luciano Javier
Sites Jr., Jack W.
author_role author
author2 Morando, Mariana
Avila, Luciano Javier
Sites Jr., Jack W.
author2_role author
author
author
dc.subject.none.fl_str_mv Divergence
Gene Flow
Gene Trees
Simulation
Speciation
topic Divergence
Gene Flow
Gene Trees
Simulation
Speciation
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Species delimitation is a major research focus in evolutionary biology because accurate species boundaries are a prerequisite for the study of speciation. New species delimitation methods (SDMs) can accommodate nonmonophyletic species and gene tree discordance as a result of incomplete lineage sorting via the coalescent model, but do not explicitly accommodate gene flow after divergence. Approximate Bayesian computation (ABC) can incorporate gene flow and estimate other relevant parameters of the speciation process while testing alternative species delimitation hypotheses. We evaluated the accuracy of BPP, SpeDeSTEM, and ABC for delimiting species using simulated data and applied these methods to empirical data from lizards of the Liolaemus darwinii complex. Overall, BPP was the most accurate, ABC showed an intermediate accuracy, and SpeDeSTEM was the least accurate under most simulated conditions. All three SDMs showed lower accuracy when speciation occurred despite gene flow, as found in previous studies, but ABC was the method with the smallest decrease in accuracy. All three SDMs consistently supported the distinctness of southern and northern lineages within L. darwinii. These SDMs based on genetic data should be complemented with novel SDMs based on morphological and ecological data to achieve truly integrative and statistically robust approaches to species discovery.
Fil: Camargo Bentaberry, Arley. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico; Argentina. University Brigham Young; Estados Unidos
Fil: Morando, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentina
Fil: Avila, Luciano Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentina. Brigham Young University; Estados Unidos
Fil: Sites Jr., Jack W.. University Brigham Young; Estados Unidos
description Species delimitation is a major research focus in evolutionary biology because accurate species boundaries are a prerequisite for the study of speciation. New species delimitation methods (SDMs) can accommodate nonmonophyletic species and gene tree discordance as a result of incomplete lineage sorting via the coalescent model, but do not explicitly accommodate gene flow after divergence. Approximate Bayesian computation (ABC) can incorporate gene flow and estimate other relevant parameters of the speciation process while testing alternative species delimitation hypotheses. We evaluated the accuracy of BPP, SpeDeSTEM, and ABC for delimiting species using simulated data and applied these methods to empirical data from lizards of the Liolaemus darwinii complex. Overall, BPP was the most accurate, ABC showed an intermediate accuracy, and SpeDeSTEM was the least accurate under most simulated conditions. All three SDMs showed lower accuracy when speciation occurred despite gene flow, as found in previous studies, but ABC was the method with the smallest decrease in accuracy. All three SDMs consistently supported the distinctness of southern and northern lineages within L. darwinii. These SDMs based on genetic data should be complemented with novel SDMs based on morphological and ecological data to achieve truly integrative and statistically robust approaches to species discovery.
publishDate 2012
dc.date.none.fl_str_mv 2012-09
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/68380
Camargo Bentaberry, Arley; Morando, Mariana; Avila, Luciano Javier; Sites Jr., Jack W.; Species delimitation with abc and other coalescent-based methods: A test of accuracy with simulations and an empirical example with lizards of the liolaemus darwinii complex (Squamata: Liolaemidae); Wiley Blackwell Publishing, Inc; Evolution; 66; 9; 9-2012; 2834-2849
0014-3820
1558-5646
CONICET Digital
CONICET
url http://hdl.handle.net/11336/68380
identifier_str_mv Camargo Bentaberry, Arley; Morando, Mariana; Avila, Luciano Javier; Sites Jr., Jack W.; Species delimitation with abc and other coalescent-based methods: A test of accuracy with simulations and an empirical example with lizards of the liolaemus darwinii complex (Squamata: Liolaemidae); Wiley Blackwell Publishing, Inc; Evolution; 66; 9; 9-2012; 2834-2849
0014-3820
1558-5646
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/epdf/10.1111/j.1558-5646.2012.01640.x
info:eu-repo/semantics/altIdentifier/doi/10.1111/j.1558-5646.2012.01640.x
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Wiley Blackwell Publishing, Inc
publisher.none.fl_str_mv Wiley Blackwell Publishing, Inc
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 12.982451

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