Validating a target-enrichment design for capturing uniparental haplotypes in ancient domesticated animals

In the last three decades, DNA sequencing of ancient animal osteological assemblages has become an important tool complementing standard archaeozoological approaches to reconstruct the history of animal domestication. However, osteological assemblages of key archaeological contexts are not always av...

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Detalhes bibliográficos
Autores: More, Kuldeep D., Lebrasseur, Ophélie, Lira Garrido, Jaime, Seguin-Orlando, Andaine, Discamps, Emmanuel, Estrada, Oscar, Tonasso-Calvière, Laure, Sala Burgos, Nohemi, Pablos Fernández, Adrián
Formato: artículo
Fecha de publicación:2025
País:España
Recursos:Universidad Complutense de Madrid (UCM)
Repositorio:Docta Complutense
Idioma:inglés
OAI Identifier:oai:docta.ucm.es:20.500.14352/131225
Acesso em linha:https://hdl.handle.net/20.500.14352/131225
Access Level:acceso abierto
Palavra-chave:575
Ancient DNA
Domestication
Environmental DNA
palaeogenomics
Target enrichment
Genética
2409 Genética
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oai_identifier_str oai:docta.ucm.es:20.500.14352/131225
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spelling Validating a target-enrichment design for capturing uniparental haplotypes in ancient domesticated animalsMore, Kuldeep D.Lebrasseur, OphélieLira Garrido, JaimeSeguin-Orlando, AndaineDiscamps, EmmanuelEstrada, OscarTonasso-Calvière, LaureSala Burgos, NohemiPablos Fernández, Adrián575Ancient DNADomesticationEnvironmental DNApalaeogenomicsTarget enrichmentGenética2409 GenéticaIn the last three decades, DNA sequencing of ancient animal osteological assemblages has become an important tool complementing standard archaeozoological approaches to reconstruct the history of animal domestication. However, osteological assemblages of key archaeological contexts are not always available or do not necessarily preserve enough ancient DNA for a cost-effective genetic analysis. Here, we develop an in-solution target-enrichment approach, based on 80-mer species-specific RNA probes (ranging from 306 to 1686 per species) to characterise (in single experiments) the mitochondrial genetic variation from eight domesticated animal species of major economic interest: cattle, chickens, dogs, donkeys, goats, horses, pigs and sheep. We also illustrate how our design can be adapted to enrich DNA library content and map the Y-chromosomal diversity within Equus caballus. By applying our target-enrichment assay to an extensive panel of ancient osteological remains, farm soil, and cave sediments spanning the last 43 kyrs, we demonstrate that minimal sequencing efforts are necessary to exhaust the DNA library complexity and to characterise mitogenomes to an average depth-of-coverage of 19.4 to 2003.7-fold. Our assay further retrieved horse mitogenome and Y-chromosome data from Late Pleistocene coprolites, as well as bona fide mitochondrial sequences from species that were not part of the probe design, such as bison and cave hyena. Our methodology will prove especially useful to minimise costs related to the genetic analyses of maternal and paternal lineages of a wide range of domesticated and wild animal species, and for mapping their diversity changes over space and time, including from environmental samples.WileyUniversidad Complutense de Madrid20252025-04-0920252025-04-09journal articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/20.500.14352/131225reponame:Docta Complutenseinstname:Universidad Complutense de Madrid (UCM)Inglésengopen accesshttp://purl.org/coar/access_right/c_abf2Attribution-NonCommercial-NoDerivatives 4.0 Internationalhttp://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/openAccessoai:docta.ucm.es:20.500.14352/1312252026-06-02T12:44:21Z
dc.title.none.fl_str_mv Validating a target-enrichment design for capturing uniparental haplotypes in ancient domesticated animals
title Validating a target-enrichment design for capturing uniparental haplotypes in ancient domesticated animals
spellingShingle Validating a target-enrichment design for capturing uniparental haplotypes in ancient domesticated animals
More, Kuldeep D.
575
Ancient DNA
Domestication
Environmental DNA
palaeogenomics
Target enrichment
Genética
2409 Genética
title_short Validating a target-enrichment design for capturing uniparental haplotypes in ancient domesticated animals
title_full Validating a target-enrichment design for capturing uniparental haplotypes in ancient domesticated animals
title_fullStr Validating a target-enrichment design for capturing uniparental haplotypes in ancient domesticated animals
title_full_unstemmed Validating a target-enrichment design for capturing uniparental haplotypes in ancient domesticated animals
title_sort Validating a target-enrichment design for capturing uniparental haplotypes in ancient domesticated animals
dc.creator.none.fl_str_mv More, Kuldeep D.
Lebrasseur, Ophélie
Lira Garrido, Jaime
Seguin-Orlando, Andaine
Discamps, Emmanuel
Estrada, Oscar
Tonasso-Calvière, Laure
Sala Burgos, Nohemi
Pablos Fernández, Adrián
author More, Kuldeep D.
author_facet More, Kuldeep D.
Lebrasseur, Ophélie
Lira Garrido, Jaime
Seguin-Orlando, Andaine
Discamps, Emmanuel
Estrada, Oscar
Tonasso-Calvière, Laure
Sala Burgos, Nohemi
Pablos Fernández, Adrián
author_role author
author2 Lebrasseur, Ophélie
Lira Garrido, Jaime
Seguin-Orlando, Andaine
Discamps, Emmanuel
Estrada, Oscar
Tonasso-Calvière, Laure
Sala Burgos, Nohemi
Pablos Fernández, Adrián
author2_role author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Universidad Complutense de Madrid
dc.subject.none.fl_str_mv 575
Ancient DNA
Domestication
Environmental DNA
palaeogenomics
Target enrichment
Genética
2409 Genética
topic 575
Ancient DNA
Domestication
Environmental DNA
palaeogenomics
Target enrichment
Genética
2409 Genética
description In the last three decades, DNA sequencing of ancient animal osteological assemblages has become an important tool complementing standard archaeozoological approaches to reconstruct the history of animal domestication. However, osteological assemblages of key archaeological contexts are not always available or do not necessarily preserve enough ancient DNA for a cost-effective genetic analysis. Here, we develop an in-solution target-enrichment approach, based on 80-mer species-specific RNA probes (ranging from 306 to 1686 per species) to characterise (in single experiments) the mitochondrial genetic variation from eight domesticated animal species of major economic interest: cattle, chickens, dogs, donkeys, goats, horses, pigs and sheep. We also illustrate how our design can be adapted to enrich DNA library content and map the Y-chromosomal diversity within Equus caballus. By applying our target-enrichment assay to an extensive panel of ancient osteological remains, farm soil, and cave sediments spanning the last 43 kyrs, we demonstrate that minimal sequencing efforts are necessary to exhaust the DNA library complexity and to characterise mitogenomes to an average depth-of-coverage of 19.4 to 2003.7-fold. Our assay further retrieved horse mitogenome and Y-chromosome data from Late Pleistocene coprolites, as well as bona fide mitochondrial sequences from species that were not part of the probe design, such as bison and cave hyena. Our methodology will prove especially useful to minimise costs related to the genetic analyses of maternal and paternal lineages of a wide range of domesticated and wild animal species, and for mapping their diversity changes over space and time, including from environmental samples.
publishDate 2025
dc.date.none.fl_str_mv 2025
2025-04-09
2025
2025-04-09
dc.type.none.fl_str_mv journal article
http://purl.org/coar/resource_type/c_6501
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://hdl.handle.net/20.500.14352/131225
url https://hdl.handle.net/20.500.14352/131225
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution-NonCommercial-NoDerivatives 4.0 International
http://creativecommons.org/licenses/by-nc-nd/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution-NonCommercial-NoDerivatives 4.0 International
http://creativecommons.org/licenses/by-nc-nd/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Wiley
publisher.none.fl_str_mv Wiley
dc.source.none.fl_str_mv reponame:Docta Complutense
instname:Universidad Complutense de Madrid (UCM)
instname_str Universidad Complutense de Madrid (UCM)
reponame_str Docta Complutense
collection Docta Complutense
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,812429

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