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 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.

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Publication Details

Journal
Molecular Ecology Resources
Published
2025-04-09
DOI
https://doi.org/10.1111/1755-0998.14112
Citations
2
Primary Topic
Identification and Quantification in Food
Type
article
Field-Weighted Citation Impact
1.61

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article

Validating a Target‐Enrichment Design for Capturing Uniparental Haplotypes in Ancient Domesticated Animals

Sharon R. Steadman, Nadir Álvarez, Rinat Zhumatayev, Andaine Seguin‐Orlando et al.
2 citations
Molecular Ecology Resources
Identification and Quantification in Food
1.61
article

Validating a Target‐Enrichment Design for Capturing Uniparental Haplotypes in Ancient Domesticated Animals

Sharon R. Steadman, Nadir Álvarez, Rinat Zhumatayev, Andaine Seguin‐Orlando, Petra Rajić Šikanjić, Ali A. Vahdati, Magdalena Moskal‐del Hoyo, Julian Post-Melbye, Éric Barrey, Myriam Boudadi‐Maligne, Jean‐Luc Houle, Greger Larson, Juan Contreras‐Mancilla, Gregory McMahon, Rémi Berthon, Horacio Chiavazza, Emmanuel Discamps, Sophy Charlton, Laurent Frantz, Oscar Estrada, Ludovic Orlando, Jamsranjav Bayarsaikhan, Stéphane Bertani, Love Dalén, Loreleï Chauvey, Léa Charliquart, Émilie Robbe, Stéphanie Schiavinato, Jean‐Christophe Castel, Bastiaan Star, Norbert Benecke, Roxana Dobrescu, П. А. Косинцев, Marjan Mashkour, Emmanuelle Vila, Victoria E. Mullin, Laure Tonasso‐Calvière, Roya Khazaeli, Gaétan Tressières, Nicolás Guardia, Tajana Trbojević Vukičević, Jaime Lira Garrido, Benjamin S. Arbuckle, William Taylor, Samat Shakenov, Kevin G. Daly, Ophélie Lebrasseur, A. Nikgoftar, Kuldeep Dilip More, Caroline Borges, Christian Løchsen Rødsrud, Adrián Pablos, David W. G. Stanton, Daniel G. Bradley, Adrian Bălăşescu, Marcel Burić, Jarosław Wilczyński, Marek Nowak, Pablo Marcelo Fernández, Morgane Gibert, Horacio Padula, Diana Allccarima‐Crisóstomo, Miguel Fhon, Thibault de Noblet, Nohemi Sala Burgos
article en
2 citations

Abstract

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.

Molecular Ecology ResourcesVol. 25(7)
Université Claude Bernard Lyon 1 (FR), University College Dublin (IE), University of North Carolina at Chapel Hill (US), University of Geneva (CH), Universidad Complutense de Madrid (ES), Jagiellonian University (PL), Centre National de la Recherche Scientifique (FR), Ural Federal University (RU), Université Toulouse III - Paul Sabatier (FR), Mongolian Academy of Sciences (MN), Université de Bordeaux (FR), Consejo Nacional de Investigaciones Científicas y Técnicas (AR), Universidad Nacional de Cuyo (AR), University of New Hampshire (US), Stockholm University (SE), Queen Mary University of London (GB), Université Fédérale de Toulouse Midi-Pyrénées (FR), University of Zagreb (HR), University of Oslo (NO), Al-Farabi Kazakh National University (KZ), University of Colorado Boulder (US), Trinity College Dublin (IE), AgroParisTech (FR), University of Tehran (IR), Université Paris-Saclay (FR), Deutsches Archäologisches Institut, Zentrale (DE), Swedish Museum of Natural History (SE), Natural History Museum of Geneva (CH), University of Oxford (GB), Institute for Anthropological Research (HR), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR), Museum of Boulder (US), Centro Científico Tecnológico - San Juan (AR), Centro Nacional de Investigación sobre la Evolución Humana (ES), De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (FR), Archéozoologie et Archéobotanique (FR), Institute of Plant and Animal Ecology (RU), Pharmacochimie et Biologie pour le Développement (FR), Oxford Archaeology (GB), Instituto de Histología y Embriología de Mendoza (AR), Travaux et Recherches Archéologiques sur les Cultures, les Espaces et les Sociétés (FR), Université Toulouse - Jean Jaurès (FR), Centre for Palaeogenetics (SE), Archéorient (FR), Max Planck Institute for the Science of Human History (DE), Musée de l'Homme (FR), Władysław Szafer Institute of Botany (PL), Institut de Recherche pour le Développement (FR), Institute of Systematics and Evolution of Animals (PL), Max Planck Institute of Geoanthropology, University of York (GB), Universidade Federal Rural de Pernambuco (BR), Universidad de Sevilla (ES), Cardiff University (GB), Ludwig-Maximilians-Universität München (DE), SUNY Cortland (US), Western Kentucky University (US), Polish Academy of Sciences (PL)
European Commission, Agence Nationale de la Recherche, Knut och Alice Wallenbergs Stiftelse, Vetenskapsrådet, Université de Toulouse, Centre National de la Recherche Scientifique, Science for Life Laboratory, Junta de Andalucía, Junta de Comunidades de Castilla-La Mancha, Horizon 2020 Framework Programme, Agencia Estatal de Investigación, Uppsala Multidisciplinary Center for Advanced Computational Science, European Social Fund, H2020 Marie Skłodowska-Curie Actions
Life in Land
Openalex Percentile: Top 18%
Identification and Quantification in Food
1.61
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