Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences

Autores
Colonna, Vicenza; Ayub, Qasim; Chen, Yua; Pagani, Luca; Luisi, Pierre; Pybus, Marc; Garrison, Erik; Xue, Yali; Tyler Smith, Chris; Genomes Project Consortium
Año de publicación
2016
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Population differentiation has proved to be effective for identifying loci under geographically localized positive selection, and has the potential to identify loci subject to balancing selection. We have previously investigated the pattern of genetic differentiation among human populations at 36.8 million genomic variants to identify sites in the genome showing high frequency differences. Here, we extend this dataset to include additional variants, survey sites with low levels of differentiation, and evaluate the extent to which highly differentiated sites are likely to result from selective or other processes. We demonstrate that while sites with low differentiation represent sampling effects rather than balancing selection, sites showing extremely high population differentiation are enriched for positive selection events and that one half may be the result of classic selective sweeps. Among these, we rediscover known examples, where we actually identify the established functional SNP, and discover novel examples including the genes ABCA12, CALD1 and ZNF804, which we speculate may be linked to adaptations in skin, calcium metabolism and defense, respectively. We identify known and many novel candidate regions for geographically restricted positive selection, and suggest several directions for further research.
Fil: Colonna, Vicenza. National Research Council; Italia. The Wellcome Trust Sanger Institute; Reino Unido
Fil: Ayub, Qasim. The Wellcome Trust Sanger Institute; Reino Unido
Fil: Chen, Yua. The Wellcome Trust Sanger Institute; Reino Unido
Fil: Pagani, Luca. The Wellcome Trust Sanger Institute; Reino Unido
Fil: Luisi, Pierre. Universitat Pompeu Fabra; España. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; Argentina
Fil: Pybus, Marc. Universitat Pompeu Fabra; España
Fil: Garrison, Erik. Boston College; Estados Unidos
Fil: Xue, Yali. The Wellcome Trust Sanger Institute; Reino Unido
Fil: Tyler Smith, Chris. The Wellcome Trust Sanger Institute; Reino Unido
Fil: Genomes Project Consortium. 1000 Genomes Proyect Consortium; Estados Unidos
Materia
POSITIVE SELECTION
BALANCING SELECTION
SELECTIVE SWEEP
SOFT SWEEP
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/102804
Acceder
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network_acronym_str CONICETDig
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network_name_str CONICET Digital (CONICET)
spelling Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequencesColonna, VicenzaAyub, QasimChen, YuaPagani, LucaLuisi, PierrePybus, MarcGarrison, ErikXue, YaliTyler Smith, ChrisGenomes Project ConsortiumPOSITIVE SELECTIONBALANCING SELECTIONSELECTIVE SWEEPSOFT SWEEPhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1https://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1https://purl.org/becyt/ford/6.1https://purl.org/becyt/ford/6Population differentiation has proved to be effective for identifying loci under geographically localized positive selection, and has the potential to identify loci subject to balancing selection. We have previously investigated the pattern of genetic differentiation among human populations at 36.8 million genomic variants to identify sites in the genome showing high frequency differences. Here, we extend this dataset to include additional variants, survey sites with low levels of differentiation, and evaluate the extent to which highly differentiated sites are likely to result from selective or other processes. We demonstrate that while sites with low differentiation represent sampling effects rather than balancing selection, sites showing extremely high population differentiation are enriched for positive selection events and that one half may be the result of classic selective sweeps. Among these, we rediscover known examples, where we actually identify the established functional SNP, and discover novel examples including the genes ABCA12, CALD1 and ZNF804, which we speculate may be linked to adaptations in skin, calcium metabolism and defense, respectively. We identify known and many novel candidate regions for geographically restricted positive selection, and suggest several directions for further research.Fil: Colonna, Vicenza. National Research Council; Italia. The Wellcome Trust Sanger Institute; Reino UnidoFil: Ayub, Qasim. The Wellcome Trust Sanger Institute; Reino UnidoFil: Chen, Yua. The Wellcome Trust Sanger Institute; Reino UnidoFil: Pagani, Luca. The Wellcome Trust Sanger Institute; Reino UnidoFil: Luisi, Pierre. Universitat Pompeu Fabra; España. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; ArgentinaFil: Pybus, Marc. Universitat Pompeu Fabra; EspañaFil: Garrison, Erik. Boston College; Estados UnidosFil: Xue, Yali. The Wellcome Trust Sanger Institute; Reino UnidoFil: Tyler Smith, Chris. The Wellcome Trust Sanger Institute; Reino UnidoFil: Genomes Project Consortium. 1000 Genomes Proyect Consortium; Estados UnidosBioMed Central2016-06-30info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/102804Colonna, Vicenza; Ayub, Qasim; Chen, Yua; Pagani, Luca; Luisi, Pierre; et al.; Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences; BioMed Central; Genome Biology; 15; 30-6-2016; 1-141474-760X1474-7596CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-6-r88info:eu-repo/semantics/altIdentifier/doi/10.1186/gb-2014-15-6-r88info:eu-repo/semantics/altIdentifier/url/https://www.ncbi.nlm.nih.gov/pubmed/24980144info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2026-04-15T10:44:29Zoai:ri.conicet.gov.ar:11336/102804instacron: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:34982026-04-15 10:44:30.367CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences
title Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences
spellingShingle Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences
Colonna, Vicenza
POSITIVE SELECTION
BALANCING SELECTION
SELECTIVE SWEEP
SOFT SWEEP
title_short Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences
title_full Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences
title_fullStr Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences
title_full_unstemmed Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences
title_sort Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences
dc.creator.none.fl_str_mv Colonna, Vicenza
Ayub, Qasim
Chen, Yua
Pagani, Luca
Luisi, Pierre
Pybus, Marc
Garrison, Erik
Xue, Yali
Tyler Smith, Chris
Genomes Project Consortium
author Colonna, Vicenza
author_facet Colonna, Vicenza
Ayub, Qasim
Chen, Yua
Pagani, Luca
Luisi, Pierre
Pybus, Marc
Garrison, Erik
Xue, Yali
Tyler Smith, Chris
Genomes Project Consortium
author_role author
author2 Ayub, Qasim
Chen, Yua
Pagani, Luca
Luisi, Pierre
Pybus, Marc
Garrison, Erik
Xue, Yali
Tyler Smith, Chris
Genomes Project Consortium
author2_role author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv POSITIVE SELECTION
BALANCING SELECTION
SELECTIVE SWEEP
SOFT SWEEP
topic POSITIVE SELECTION
BALANCING SELECTION
SELECTIVE SWEEP
SOFT SWEEP
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
https://purl.org/becyt/ford/6.1
https://purl.org/becyt/ford/6
dc.description.none.fl_txt_mv Population differentiation has proved to be effective for identifying loci under geographically localized positive selection, and has the potential to identify loci subject to balancing selection. We have previously investigated the pattern of genetic differentiation among human populations at 36.8 million genomic variants to identify sites in the genome showing high frequency differences. Here, we extend this dataset to include additional variants, survey sites with low levels of differentiation, and evaluate the extent to which highly differentiated sites are likely to result from selective or other processes. We demonstrate that while sites with low differentiation represent sampling effects rather than balancing selection, sites showing extremely high population differentiation are enriched for positive selection events and that one half may be the result of classic selective sweeps. Among these, we rediscover known examples, where we actually identify the established functional SNP, and discover novel examples including the genes ABCA12, CALD1 and ZNF804, which we speculate may be linked to adaptations in skin, calcium metabolism and defense, respectively. We identify known and many novel candidate regions for geographically restricted positive selection, and suggest several directions for further research.
Fil: Colonna, Vicenza. National Research Council; Italia. The Wellcome Trust Sanger Institute; Reino Unido
Fil: Ayub, Qasim. The Wellcome Trust Sanger Institute; Reino Unido
Fil: Chen, Yua. The Wellcome Trust Sanger Institute; Reino Unido
Fil: Pagani, Luca. The Wellcome Trust Sanger Institute; Reino Unido
Fil: Luisi, Pierre. Universitat Pompeu Fabra; España. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; Argentina
Fil: Pybus, Marc. Universitat Pompeu Fabra; España
Fil: Garrison, Erik. Boston College; Estados Unidos
Fil: Xue, Yali. The Wellcome Trust Sanger Institute; Reino Unido
Fil: Tyler Smith, Chris. The Wellcome Trust Sanger Institute; Reino Unido
Fil: Genomes Project Consortium. 1000 Genomes Proyect Consortium; Estados Unidos
description Population differentiation has proved to be effective for identifying loci under geographically localized positive selection, and has the potential to identify loci subject to balancing selection. We have previously investigated the pattern of genetic differentiation among human populations at 36.8 million genomic variants to identify sites in the genome showing high frequency differences. Here, we extend this dataset to include additional variants, survey sites with low levels of differentiation, and evaluate the extent to which highly differentiated sites are likely to result from selective or other processes. We demonstrate that while sites with low differentiation represent sampling effects rather than balancing selection, sites showing extremely high population differentiation are enriched for positive selection events and that one half may be the result of classic selective sweeps. Among these, we rediscover known examples, where we actually identify the established functional SNP, and discover novel examples including the genes ABCA12, CALD1 and ZNF804, which we speculate may be linked to adaptations in skin, calcium metabolism and defense, respectively. We identify known and many novel candidate regions for geographically restricted positive selection, and suggest several directions for further research.
publishDate 2016
dc.date.none.fl_str_mv 2016-06-30
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/11336/102804
Colonna, Vicenza; Ayub, Qasim; Chen, Yua; Pagani, Luca; Luisi, Pierre; et al.; Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences; BioMed Central; Genome Biology; 15; 30-6-2016; 1-14
1474-760X
1474-7596
CONICET Digital
CONICET
url http://hdl.handle.net/11336/102804
identifier_str_mv Colonna, Vicenza; Ayub, Qasim; Chen, Yua; Pagani, Luca; Luisi, Pierre; et al.; Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences; BioMed Central; Genome Biology; 15; 30-6-2016; 1-14
1474-760X
1474-7596
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://genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-6-r88
info:eu-repo/semantics/altIdentifier/doi/10.1186/gb-2014-15-6-r88
info:eu-repo/semantics/altIdentifier/url/https://www.ncbi.nlm.nih.gov/pubmed/24980144
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
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 13.203462

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