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
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/68380
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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 Técnicas2025-09-29T09:51:59Zoai: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:34982025-09-29 09:51:59.997CONICET 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 |
_version_ |
1844613596614492160 |
score |
13.070432 |