Application of Targeted Y‐Chromosomal Capture Enrichment to Increase the Resolution of Native American Haplogroup Q

Autores
Köksal, Zehra; Børsting, Claus; Bailliet, Graciela; Burgos, Germán; Carvalho, Elizeu; Casas Vargas, Andrea; Castillo, Adriana; Brito Gomes, Marilia; Martínez, Beatriz; Ossa, Humberto; Parolin, María Laura; Quiroz, Alfredo; Toscanini, Ulises; Usaquén, William; Velázquez, Irina Florencia; Vullo, Carlos; Gusmão, Leonor; Pereira, Vania
Año de publicación
2024
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Y-chromosomal haplogroups and the Y-SNPs defining them are relevant for the exploration of male lineages, inference of paternal ancestry, and reconstruction of migration pathways, to name a few. Currently, over 300,000 Y-SNPs have been reported, defining 20 main haplogroups. However, ascertainment bias in the investigations has led to some haplogroups being overlooked, which hinders a representative depiction of certain populations and their migration events. For migration pattern analyses of the first settlers of the Americas, the Native American main founding lineage Q-M3 needs to be further investigated to allow clear genetic differentiation of individuals of different ethnogeographic origins. To increase the resolution within this haplogroup, a total of 7.45 Mb of the Y chromosome of 59 admixed South Americans of haplogroup Q was targeted for sequencing using hybridization capture enrichment. Data were combined with 218 publicly available sequences of Central and South Americans of haplogroup Q. After rigorous data processing, variants not meeting the quality criteria were excluded and 4128 reliable Y- SNPs were reported. A total of 2224 Y-SNPs had previously unknown positions in the phylogenetic tree, and 1291 of these arenovel. The phylogenetic relationships between the Y-SNPs were established using the software SNPtotree in order to report a redesigned phylogenetic tree containing 300 branches, defined by 3400 Y-SNPs. The new tree introduces 117 previously undescribed branches and is the most comprehensive phylogenetic tree of the Native American haplogroup Q lineages to date. The 214 sequences were assigned to 135 different low- to high-resolution branches, while in the previous phylogenetic tree, only 195 sequences could be sorted into 14 low-resolution branches with the same quality criteria. The improved genetic differentiation of subhaplogroup Q-M3 has a great potential to resolve migration patterns of Native Americans.
Fil: Köksal, Zehra. Universidad de Copenhagen; Dinamarca
Fil: Børsting, Claus. Universidad de Copenhagen; Dinamarca
Fil: Bailliet, Graciela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto Multidisciplinario de Biología Celular. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Instituto Multidisciplinario de Biología Celular. Universidad Nacional de La Plata. Instituto Multidisciplinario de Biología Celular; Argentina. Ministerio de Ciencia. Tecnología e Innovación Productiva. Agencia Nacional de Promoción Científica y Tecnológica; Argentina
Fil: Burgos, Germán. Universidad de Las Américas; Ecuador
Fil: Carvalho, Elizeu. Universidade Federal do Rio de Janeiro; Brasil
Fil: Casas Vargas, Andrea. Universidad Nacional de Colombia; Colombia
Fil: Castillo, Adriana. Universidad Industrial Santander; Colombia
Fil: Brito Gomes, Marilia. Universidade Federal do Rio de Janeiro; Brasil
Fil: Martínez, Beatriz. Universidad de Cartagena; Colombia
Fil: Ossa, Humberto. Pontificia Universidad Javeriana; Colombia. Instituto de Previsión Social; Paraguay
Fil: Parolin, María Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Diversidad y Evolución Austral; Argentina
Fil: Quiroz, Alfredo. Instituto de Previsión Social; Paraguay
Fil: Toscanini, Ulises. Fundación Favaloro; Argentina
Fil: Usaquén, William. Universidad Nacional de Colombia; Colombia
Fil: Velázquez, Irina Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Diversidad y Evolución Austral; Argentina
Fil: Vullo, Carlos. Equipo Argentino de Antropología Forense; Argentina
Fil: Gusmão, Leonor. Universidade Federal do Rio de Janeiro; Brasil
Fil: Pereira, Vania. Universidad de Copenhagen; Dinamarca
Materia
Y-SNPS
NATIVA AMERICAN
Q BRANCHES
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:11336/265443
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/265443
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Application of Targeted Y‐Chromosomal Capture Enrichment to Increase the Resolution of Native American Haplogroup QKöksal, ZehraBørsting, ClausBailliet, GracielaBurgos, GermánCarvalho, ElizeuCasas Vargas, AndreaCastillo, AdrianaBrito Gomes, MariliaMartínez, BeatrizOssa, HumbertoParolin, María LauraQuiroz, AlfredoToscanini, UlisesUsaquén, WilliamVelázquez, Irina FlorenciaVullo, CarlosGusmão, LeonorPereira, VaniaY-SNPSNATIVA AMERICANQ BRANCHEShttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Y-chromosomal haplogroups and the Y-SNPs defining them are relevant for the exploration of male lineages, inference of paternal ancestry, and reconstruction of migration pathways, to name a few. Currently, over 300,000 Y-SNPs have been reported, defining 20 main haplogroups. However, ascertainment bias in the investigations has led to some haplogroups being overlooked, which hinders a representative depiction of certain populations and their migration events. For migration pattern analyses of the first settlers of the Americas, the Native American main founding lineage Q-M3 needs to be further investigated to allow clear genetic differentiation of individuals of different ethnogeographic origins. To increase the resolution within this haplogroup, a total of 7.45 Mb of the Y chromosome of 59 admixed South Americans of haplogroup Q was targeted for sequencing using hybridization capture enrichment. Data were combined with 218 publicly available sequences of Central and South Americans of haplogroup Q. After rigorous data processing, variants not meeting the quality criteria were excluded and 4128 reliable Y- SNPs were reported. A total of 2224 Y-SNPs had previously unknown positions in the phylogenetic tree, and 1291 of these arenovel. The phylogenetic relationships between the Y-SNPs were established using the software SNPtotree in order to report a redesigned phylogenetic tree containing 300 branches, defined by 3400 Y-SNPs. The new tree introduces 117 previously undescribed branches and is the most comprehensive phylogenetic tree of the Native American haplogroup Q lineages to date. The 214 sequences were assigned to 135 different low- to high-resolution branches, while in the previous phylogenetic tree, only 195 sequences could be sorted into 14 low-resolution branches with the same quality criteria. The improved genetic differentiation of subhaplogroup Q-M3 has a great potential to resolve migration patterns of Native Americans.Fil: Köksal, Zehra. Universidad de Copenhagen; DinamarcaFil: Børsting, Claus. Universidad de Copenhagen; DinamarcaFil: Bailliet, Graciela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto Multidisciplinario de Biología Celular. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Instituto Multidisciplinario de Biología Celular. Universidad Nacional de La Plata. Instituto Multidisciplinario de Biología Celular; Argentina. Ministerio de Ciencia. Tecnología e Innovación Productiva. Agencia Nacional de Promoción Científica y Tecnológica; ArgentinaFil: Burgos, Germán. Universidad de Las Américas; EcuadorFil: Carvalho, Elizeu. Universidade Federal do Rio de Janeiro; BrasilFil: Casas Vargas, Andrea. Universidad Nacional de Colombia; ColombiaFil: Castillo, Adriana. Universidad Industrial Santander; ColombiaFil: Brito Gomes, Marilia. Universidade Federal do Rio de Janeiro; BrasilFil: Martínez, Beatriz. Universidad de Cartagena; ColombiaFil: Ossa, Humberto. Pontificia Universidad Javeriana; Colombia. Instituto de Previsión Social; ParaguayFil: Parolin, María Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Diversidad y Evolución Austral; ArgentinaFil: Quiroz, Alfredo. Instituto de Previsión Social; ParaguayFil: Toscanini, Ulises. Fundación Favaloro; ArgentinaFil: Usaquén, William. Universidad Nacional de Colombia; ColombiaFil: Velázquez, Irina Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Diversidad y Evolución Austral; ArgentinaFil: Vullo, Carlos. Equipo Argentino de Antropología Forense; ArgentinaFil: Gusmão, Leonor. Universidade Federal do Rio de Janeiro; BrasilFil: Pereira, Vania. Universidad de Copenhagen; DinamarcaWiley-liss, div John Wiley & Sons Inc.2024-07info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/265443Köksal, Zehra; Børsting, Claus; Bailliet, Graciela; Burgos, Germán; Carvalho, Elizeu; et al.; Application of Targeted Y‐Chromosomal Capture Enrichment to Increase the Resolution of Native American Haplogroup Q; Wiley-liss, div John Wiley & Sons Inc.; Human Mutation; 2024; 1; 7-2024; 1-101059-7794CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/10.1155/2024/3046495info:eu-repo/semantics/altIdentifier/doi/10.1155/2024/3046495info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-15T14:48:10Zoai:ri.conicet.gov.ar:11336/265443instacron: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:34982025-10-15 14:48:10.515CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Application of Targeted Y‐Chromosomal Capture Enrichment to Increase the Resolution of Native American Haplogroup Q
title Application of Targeted Y‐Chromosomal Capture Enrichment to Increase the Resolution of Native American Haplogroup Q
spellingShingle Application of Targeted Y‐Chromosomal Capture Enrichment to Increase the Resolution of Native American Haplogroup Q
Köksal, Zehra
Y-SNPS
NATIVA AMERICAN
Q BRANCHES
title_short Application of Targeted Y‐Chromosomal Capture Enrichment to Increase the Resolution of Native American Haplogroup Q
title_full Application of Targeted Y‐Chromosomal Capture Enrichment to Increase the Resolution of Native American Haplogroup Q
title_fullStr Application of Targeted Y‐Chromosomal Capture Enrichment to Increase the Resolution of Native American Haplogroup Q
title_full_unstemmed Application of Targeted Y‐Chromosomal Capture Enrichment to Increase the Resolution of Native American Haplogroup Q
title_sort Application of Targeted Y‐Chromosomal Capture Enrichment to Increase the Resolution of Native American Haplogroup Q
dc.creator.none.fl_str_mv Köksal, Zehra
Børsting, Claus
Bailliet, Graciela
Burgos, Germán
Carvalho, Elizeu
Casas Vargas, Andrea
Castillo, Adriana
Brito Gomes, Marilia
Martínez, Beatriz
Ossa, Humberto
Parolin, María Laura
Quiroz, Alfredo
Toscanini, Ulises
Usaquén, William
Velázquez, Irina Florencia
Vullo, Carlos
Gusmão, Leonor
Pereira, Vania
author Köksal, Zehra
author_facet Köksal, Zehra
Børsting, Claus
Bailliet, Graciela
Burgos, Germán
Carvalho, Elizeu
Casas Vargas, Andrea
Castillo, Adriana
Brito Gomes, Marilia
Martínez, Beatriz
Ossa, Humberto
Parolin, María Laura
Quiroz, Alfredo
Toscanini, Ulises
Usaquén, William
Velázquez, Irina Florencia
Vullo, Carlos
Gusmão, Leonor
Pereira, Vania
author_role author
author2 Børsting, Claus
Bailliet, Graciela
Burgos, Germán
Carvalho, Elizeu
Casas Vargas, Andrea
Castillo, Adriana
Brito Gomes, Marilia
Martínez, Beatriz
Ossa, Humberto
Parolin, María Laura
Quiroz, Alfredo
Toscanini, Ulises
Usaquén, William
Velázquez, Irina Florencia
Vullo, Carlos
Gusmão, Leonor
Pereira, Vania
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Y-SNPS
NATIVA AMERICAN
Q BRANCHES
topic Y-SNPS
NATIVA AMERICAN
Q BRANCHES
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Y-chromosomal haplogroups and the Y-SNPs defining them are relevant for the exploration of male lineages, inference of paternal ancestry, and reconstruction of migration pathways, to name a few. Currently, over 300,000 Y-SNPs have been reported, defining 20 main haplogroups. However, ascertainment bias in the investigations has led to some haplogroups being overlooked, which hinders a representative depiction of certain populations and their migration events. For migration pattern analyses of the first settlers of the Americas, the Native American main founding lineage Q-M3 needs to be further investigated to allow clear genetic differentiation of individuals of different ethnogeographic origins. To increase the resolution within this haplogroup, a total of 7.45 Mb of the Y chromosome of 59 admixed South Americans of haplogroup Q was targeted for sequencing using hybridization capture enrichment. Data were combined with 218 publicly available sequences of Central and South Americans of haplogroup Q. After rigorous data processing, variants not meeting the quality criteria were excluded and 4128 reliable Y- SNPs were reported. A total of 2224 Y-SNPs had previously unknown positions in the phylogenetic tree, and 1291 of these arenovel. The phylogenetic relationships between the Y-SNPs were established using the software SNPtotree in order to report a redesigned phylogenetic tree containing 300 branches, defined by 3400 Y-SNPs. The new tree introduces 117 previously undescribed branches and is the most comprehensive phylogenetic tree of the Native American haplogroup Q lineages to date. The 214 sequences were assigned to 135 different low- to high-resolution branches, while in the previous phylogenetic tree, only 195 sequences could be sorted into 14 low-resolution branches with the same quality criteria. The improved genetic differentiation of subhaplogroup Q-M3 has a great potential to resolve migration patterns of Native Americans.
Fil: Köksal, Zehra. Universidad de Copenhagen; Dinamarca
Fil: Børsting, Claus. Universidad de Copenhagen; Dinamarca
Fil: Bailliet, Graciela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto Multidisciplinario de Biología Celular. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Instituto Multidisciplinario de Biología Celular. Universidad Nacional de La Plata. Instituto Multidisciplinario de Biología Celular; Argentina. Ministerio de Ciencia. Tecnología e Innovación Productiva. Agencia Nacional de Promoción Científica y Tecnológica; Argentina
Fil: Burgos, Germán. Universidad de Las Américas; Ecuador
Fil: Carvalho, Elizeu. Universidade Federal do Rio de Janeiro; Brasil
Fil: Casas Vargas, Andrea. Universidad Nacional de Colombia; Colombia
Fil: Castillo, Adriana. Universidad Industrial Santander; Colombia
Fil: Brito Gomes, Marilia. Universidade Federal do Rio de Janeiro; Brasil
Fil: Martínez, Beatriz. Universidad de Cartagena; Colombia
Fil: Ossa, Humberto. Pontificia Universidad Javeriana; Colombia. Instituto de Previsión Social; Paraguay
Fil: Parolin, María Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Diversidad y Evolución Austral; Argentina
Fil: Quiroz, Alfredo. Instituto de Previsión Social; Paraguay
Fil: Toscanini, Ulises. Fundación Favaloro; Argentina
Fil: Usaquén, William. Universidad Nacional de Colombia; Colombia
Fil: Velázquez, Irina Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Diversidad y Evolución Austral; Argentina
Fil: Vullo, Carlos. Equipo Argentino de Antropología Forense; Argentina
Fil: Gusmão, Leonor. Universidade Federal do Rio de Janeiro; Brasil
Fil: Pereira, Vania. Universidad de Copenhagen; Dinamarca
description Y-chromosomal haplogroups and the Y-SNPs defining them are relevant for the exploration of male lineages, inference of paternal ancestry, and reconstruction of migration pathways, to name a few. Currently, over 300,000 Y-SNPs have been reported, defining 20 main haplogroups. However, ascertainment bias in the investigations has led to some haplogroups being overlooked, which hinders a representative depiction of certain populations and their migration events. For migration pattern analyses of the first settlers of the Americas, the Native American main founding lineage Q-M3 needs to be further investigated to allow clear genetic differentiation of individuals of different ethnogeographic origins. To increase the resolution within this haplogroup, a total of 7.45 Mb of the Y chromosome of 59 admixed South Americans of haplogroup Q was targeted for sequencing using hybridization capture enrichment. Data were combined with 218 publicly available sequences of Central and South Americans of haplogroup Q. After rigorous data processing, variants not meeting the quality criteria were excluded and 4128 reliable Y- SNPs were reported. A total of 2224 Y-SNPs had previously unknown positions in the phylogenetic tree, and 1291 of these arenovel. The phylogenetic relationships between the Y-SNPs were established using the software SNPtotree in order to report a redesigned phylogenetic tree containing 300 branches, defined by 3400 Y-SNPs. The new tree introduces 117 previously undescribed branches and is the most comprehensive phylogenetic tree of the Native American haplogroup Q lineages to date. The 214 sequences were assigned to 135 different low- to high-resolution branches, while in the previous phylogenetic tree, only 195 sequences could be sorted into 14 low-resolution branches with the same quality criteria. The improved genetic differentiation of subhaplogroup Q-M3 has a great potential to resolve migration patterns of Native Americans.
publishDate 2024
dc.date.none.fl_str_mv 2024-07
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/11336/265443
Köksal, Zehra; Børsting, Claus; Bailliet, Graciela; Burgos, Germán; Carvalho, Elizeu; et al.; Application of Targeted Y‐Chromosomal Capture Enrichment to Increase the Resolution of Native American Haplogroup Q; Wiley-liss, div John Wiley & Sons Inc.; Human Mutation; 2024; 1; 7-2024; 1-10
1059-7794
CONICET Digital
CONICET
url http://hdl.handle.net/11336/265443
identifier_str_mv Köksal, Zehra; Børsting, Claus; Bailliet, Graciela; Burgos, Germán; Carvalho, Elizeu; et al.; Application of Targeted Y‐Chromosomal Capture Enrichment to Increase the Resolution of Native American Haplogroup Q; Wiley-liss, div John Wiley & Sons Inc.; Human Mutation; 2024; 1; 7-2024; 1-10
1059-7794
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/10.1155/2024/3046495
info:eu-repo/semantics/altIdentifier/doi/10.1155/2024/3046495
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
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Wiley-liss, div John Wiley & Sons Inc.
publisher.none.fl_str_mv Wiley-liss, div John Wiley & Sons 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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