On the performance of tests for the detection of signatures of selection : a case study with the Spanish autochthonous beef cattle populations

Autores
González Rodríguez, Aldemar; Munilla Leguizamón, Sebastián; Mouresan, Elena Flavia; Cañas Alvarez, Jhon J.; Díaz, Clara; Piedrafita, Jesús; Altarriba, Juan; Baro, Jesús A.; Molina, Antonio; Varona, Luis
Año de publicación
2016
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Fil: González Rodríguez, Aldemar. Universidad de Zaragoza. Departamento de Anatomía, Embriología y Genética. Saragossa, España.
Fil: Munilla Leguizamón, Sebastián. Universidad de Zaragoza. Departamento de Anatomía, Embriología y Genética. Saragossa, España.
Fil: Munilla Leguizamón, Sebastián. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal. Buenos Aires, Argentina.
Fil: Mouresan, Elena Flavia. Universidad de Zaragoza. Departamento de Anatomía, Embriología y Genética. Saragossa, España.
Fil: Altarriba, Juan. Universidad de Zaragoza. Departamento de Anatomía, Embriología y Genética. Saragossa, España.
Fil: Varona, Luis. Universidad de Zaragoza. Departamento de Anatomía, Embriología y Genética. Saragossa, España.
Background: Procedures for the detection of signatures of selection can be classified according to the source of information they use to reject the null hypothesis of absence of selection. Three main groups of tests can be identified that are based on: (1) the analysis of the site frequency spectrum, (2) the study of the extension of the linkage disequilibrium across the length of the haplotypes that surround the polymorphism, and (3) the differentiation among populations. The aim of this study was to compare the performance of a subset of these procedures by using a dataset on seven Spanish autochthonous beef cattle populations. Results: Analysis of the correlations between the logarithms of the statistics that were obtained by 11 tests for detecting signatures of selection at each single nucleotide polymorphism confirmed that they can be clustered into the three main groups mentioned above. A factor analysis summarized the results of the 11 tests into three canonical axes that were each associated with one of the three groups. Moreover, the signatures of selection identified with the first and second groups of tests were shared across populations, whereas those with the third group were more breed-specific. Nevertheless, an enrichment analysis identified the metabolic pathways that were associated with each group; they coincided with canonical axes and were related to immune response, muscle development, protein biosynthesis, skin and pigmentation, glucose metabolism, fat metabolism, embryogenesis and morphology, heart and uterine metabolism, regulation of the hypothalamic-pituitary-thyroid axis, hormonal, cellular cycle, cell signaling and extracellular receptors. Conclusions: We show that the results of the procedures used to identify signals of selection differed substantially between the three groups of tests. However, they can be classified using a factor analysis. Moreover, each canonical factor that coincided with a group of tests identified different signals of selection, which could be attributed to processes of selection that occurred at different evolutionary times. Nevertheless, the metabolic pathways that were associated with each group of tests were similar, which suggests that the selection events that occurred during the evolutionary history of the populations probably affected the same group of traits.
Fuente
Genetics selection evolution
Vol.48
1-12
http://www.biomedcentral.com/
Materia
SELECTION
BEEF CATTLE
Nivel de accesibilidad
acceso abierto
Condiciones de uso
acceso abierto
Repositorio
FAUBA Digital (UBA-FAUBA)
Institución
Universidad de Buenos Aires. Facultad de Agronomía
OAI Identificador
snrd:2016gonzalezrodriguez

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oai_identifier_str snrd:2016gonzalezrodriguez
network_acronym_str FAUBA
repository_id_str 2729
network_name_str FAUBA Digital (UBA-FAUBA)
spelling On the performance of tests for the detection of signatures of selection : a case study with the Spanish autochthonous beef cattle populationsGonzález Rodríguez, AldemarMunilla Leguizamón, SebastiánMouresan, Elena FlaviaCañas Alvarez, Jhon J.Díaz, ClaraPiedrafita, JesúsAltarriba, JuanBaro, Jesús A.Molina, AntonioVarona, LuisSELECTIONBEEF CATTLEFil: González Rodríguez, Aldemar. Universidad de Zaragoza. Departamento de Anatomía, Embriología y Genética. Saragossa, España.Fil: Munilla Leguizamón, Sebastián. Universidad de Zaragoza. Departamento de Anatomía, Embriología y Genética. Saragossa, España.Fil: Munilla Leguizamón, Sebastián. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal. Buenos Aires, Argentina.Fil: Mouresan, Elena Flavia. Universidad de Zaragoza. Departamento de Anatomía, Embriología y Genética. Saragossa, España.Fil: Altarriba, Juan. Universidad de Zaragoza. Departamento de Anatomía, Embriología y Genética. Saragossa, España.Fil: Varona, Luis. Universidad de Zaragoza. Departamento de Anatomía, Embriología y Genética. Saragossa, España.Background: Procedures for the detection of signatures of selection can be classified according to the source of information they use to reject the null hypothesis of absence of selection. Three main groups of tests can be identified that are based on: (1) the analysis of the site frequency spectrum, (2) the study of the extension of the linkage disequilibrium across the length of the haplotypes that surround the polymorphism, and (3) the differentiation among populations. The aim of this study was to compare the performance of a subset of these procedures by using a dataset on seven Spanish autochthonous beef cattle populations. Results: Analysis of the correlations between the logarithms of the statistics that were obtained by 11 tests for detecting signatures of selection at each single nucleotide polymorphism confirmed that they can be clustered into the three main groups mentioned above. A factor analysis summarized the results of the 11 tests into three canonical axes that were each associated with one of the three groups. Moreover, the signatures of selection identified with the first and second groups of tests were shared across populations, whereas those with the third group were more breed-specific. Nevertheless, an enrichment analysis identified the metabolic pathways that were associated with each group; they coincided with canonical axes and were related to immune response, muscle development, protein biosynthesis, skin and pigmentation, glucose metabolism, fat metabolism, embryogenesis and morphology, heart and uterine metabolism, regulation of the hypothalamic-pituitary-thyroid axis, hormonal, cellular cycle, cell signaling and extracellular receptors. Conclusions: We show that the results of the procedures used to identify signals of selection differed substantially between the three groups of tests. However, they can be classified using a factor analysis. Moreover, each canonical factor that coincided with a group of tests identified different signals of selection, which could be attributed to processes of selection that occurred at different evolutionary times. Nevertheless, the metabolic pathways that were associated with each group of tests were similar, which suggests that the selection events that occurred during the evolutionary history of the populations probably affected the same group of traits.2016info:eu-repo/semantics/articlepublishedVersioninfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfdoi:10.1186/s12711-016-0258-1issn:0999-193Xhttp://ri.agro.uba.ar/greenstone3/library/collection/arti/document/2016gonzalezrodriguezGenetics selection evolutionVol.481-12http://www.biomedcentral.com/reponame:FAUBA Digital (UBA-FAUBA)instname:Universidad de Buenos Aires. Facultad de Agronomíaenginfo:eu-repo/semantics/openAccessopenAccesshttp://ri.agro.uba.ar/greenstone3/library/page/biblioteca#section42025-09-29T13:41:34Zsnrd:2016gonzalezrodriguezinstacron:UBA-FAUBAInstitucionalhttp://ri.agro.uba.ar/Universidad públicaNo correspondehttp://ri.agro.uba.ar/greenstone3/oaiserver?verb=ListSetsmartino@agro.uba.ar;berasa@agro.uba.ar ArgentinaNo correspondeNo correspondeNo correspondeopendoar:27292025-09-29 13:41:35.306FAUBA Digital (UBA-FAUBA) - Universidad de Buenos Aires. Facultad de Agronomíafalse
dc.title.none.fl_str_mv On the performance of tests for the detection of signatures of selection : a case study with the Spanish autochthonous beef cattle populations
title On the performance of tests for the detection of signatures of selection : a case study with the Spanish autochthonous beef cattle populations
spellingShingle On the performance of tests for the detection of signatures of selection : a case study with the Spanish autochthonous beef cattle populations
González Rodríguez, Aldemar
SELECTION
BEEF CATTLE
title_short On the performance of tests for the detection of signatures of selection : a case study with the Spanish autochthonous beef cattle populations
title_full On the performance of tests for the detection of signatures of selection : a case study with the Spanish autochthonous beef cattle populations
title_fullStr On the performance of tests for the detection of signatures of selection : a case study with the Spanish autochthonous beef cattle populations
title_full_unstemmed On the performance of tests for the detection of signatures of selection : a case study with the Spanish autochthonous beef cattle populations
title_sort On the performance of tests for the detection of signatures of selection : a case study with the Spanish autochthonous beef cattle populations
dc.creator.none.fl_str_mv González Rodríguez, Aldemar
Munilla Leguizamón, Sebastián
Mouresan, Elena Flavia
Cañas Alvarez, Jhon J.
Díaz, Clara
Piedrafita, Jesús
Altarriba, Juan
Baro, Jesús A.
Molina, Antonio
Varona, Luis
author González Rodríguez, Aldemar
author_facet González Rodríguez, Aldemar
Munilla Leguizamón, Sebastián
Mouresan, Elena Flavia
Cañas Alvarez, Jhon J.
Díaz, Clara
Piedrafita, Jesús
Altarriba, Juan
Baro, Jesús A.
Molina, Antonio
Varona, Luis
author_role author
author2 Munilla Leguizamón, Sebastián
Mouresan, Elena Flavia
Cañas Alvarez, Jhon J.
Díaz, Clara
Piedrafita, Jesús
Altarriba, Juan
Baro, Jesús A.
Molina, Antonio
Varona, Luis
author2_role author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv SELECTION
BEEF CATTLE
topic SELECTION
BEEF CATTLE
dc.description.none.fl_txt_mv Fil: González Rodríguez, Aldemar. Universidad de Zaragoza. Departamento de Anatomía, Embriología y Genética. Saragossa, España.
Fil: Munilla Leguizamón, Sebastián. Universidad de Zaragoza. Departamento de Anatomía, Embriología y Genética. Saragossa, España.
Fil: Munilla Leguizamón, Sebastián. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal. Buenos Aires, Argentina.
Fil: Mouresan, Elena Flavia. Universidad de Zaragoza. Departamento de Anatomía, Embriología y Genética. Saragossa, España.
Fil: Altarriba, Juan. Universidad de Zaragoza. Departamento de Anatomía, Embriología y Genética. Saragossa, España.
Fil: Varona, Luis. Universidad de Zaragoza. Departamento de Anatomía, Embriología y Genética. Saragossa, España.
Background: Procedures for the detection of signatures of selection can be classified according to the source of information they use to reject the null hypothesis of absence of selection. Three main groups of tests can be identified that are based on: (1) the analysis of the site frequency spectrum, (2) the study of the extension of the linkage disequilibrium across the length of the haplotypes that surround the polymorphism, and (3) the differentiation among populations. The aim of this study was to compare the performance of a subset of these procedures by using a dataset on seven Spanish autochthonous beef cattle populations. Results: Analysis of the correlations between the logarithms of the statistics that were obtained by 11 tests for detecting signatures of selection at each single nucleotide polymorphism confirmed that they can be clustered into the three main groups mentioned above. A factor analysis summarized the results of the 11 tests into three canonical axes that were each associated with one of the three groups. Moreover, the signatures of selection identified with the first and second groups of tests were shared across populations, whereas those with the third group were more breed-specific. Nevertheless, an enrichment analysis identified the metabolic pathways that were associated with each group; they coincided with canonical axes and were related to immune response, muscle development, protein biosynthesis, skin and pigmentation, glucose metabolism, fat metabolism, embryogenesis and morphology, heart and uterine metabolism, regulation of the hypothalamic-pituitary-thyroid axis, hormonal, cellular cycle, cell signaling and extracellular receptors. Conclusions: We show that the results of the procedures used to identify signals of selection differed substantially between the three groups of tests. However, they can be classified using a factor analysis. Moreover, each canonical factor that coincided with a group of tests identified different signals of selection, which could be attributed to processes of selection that occurred at different evolutionary times. Nevertheless, the metabolic pathways that were associated with each group of tests were similar, which suggests that the selection events that occurred during the evolutionary history of the populations probably affected the same group of traits.
description Fil: González Rodríguez, Aldemar. Universidad de Zaragoza. Departamento de Anatomía, Embriología y Genética. Saragossa, España.
publishDate 2016
dc.date.none.fl_str_mv 2016
dc.type.none.fl_str_mv info:eu-repo/semantics/article
publishedVersion
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 doi:10.1186/s12711-016-0258-1
issn:0999-193X
http://ri.agro.uba.ar/greenstone3/library/collection/arti/document/2016gonzalezrodriguez
identifier_str_mv doi:10.1186/s12711-016-0258-1
issn:0999-193X
url http://ri.agro.uba.ar/greenstone3/library/collection/arti/document/2016gonzalezrodriguez
dc.language.none.fl_str_mv eng
language eng
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
openAccess
http://ri.agro.uba.ar/greenstone3/library/page/biblioteca#section4
eu_rights_str_mv openAccess
rights_invalid_str_mv openAccess
http://ri.agro.uba.ar/greenstone3/library/page/biblioteca#section4
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv Genetics selection evolution
Vol.48
1-12
http://www.biomedcentral.com/
reponame:FAUBA Digital (UBA-FAUBA)
instname:Universidad de Buenos Aires. Facultad de Agronomía
reponame_str FAUBA Digital (UBA-FAUBA)
collection FAUBA Digital (UBA-FAUBA)
instname_str Universidad de Buenos Aires. Facultad de Agronomía
repository.name.fl_str_mv FAUBA Digital (UBA-FAUBA) - Universidad de Buenos Aires. Facultad de Agronomía
repository.mail.fl_str_mv martino@agro.uba.ar;berasa@agro.uba.ar
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score 13.070432