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

Kuldeep More; Ophélie Lebrasseur; Jaime Lira Garrido; Andaine Seguin-Orlando; Emmanuel Discamps; Oscar Estrada; Laure Tonasso-Calvière; Loreleï Chauvey; Gaëtan Tressières; Stéphanie Schiavinato; Morgane Gibert; Horacio Padula; Horacio Chiavazza; Pablo Fernández; Nicolás Guardia; Caroline Borges; Stéphane Bertani; Juan Contreras-Mancilla; Diana Allccarima-Crisóstomo; Miguel Fhon; Léa Charliquart; Emilie Robbe; Thibault de Noblet; Rinat Zhumatayev; Samat Shakenov; Emmanuelle Vila; Rémi Berthon; Marjan Mashkour; Roya Khazaeli; Ahmad Nikgoftar; Ali Vahdati; Pavel Kosintsev; Jean‐luc Houle; Jamsranjav Bayarsaikhan; Jaroslaw Wilczynski; Magdalena Moskal-del Hoyo; Marek Nowak; William Taylor; Adrian Bălășescu; Roxana Dobrescu; Norbert Benecke; Benjamin Arbuckle; Sharon Steadman; Gregory Mcmahon; Petra Rajić Šikanjić; Marcel Buric; Tajana Trbojević Vukičević; Nadir Alvarez; Jean‐christophe Castel; Myriam Boudadi-Maligne; Trbojev Vukičevi; Julian Robert Post-Melbye; Christian Løchsen Rødsrud; David Stanton; Sophy Charlton; Victoria Mullin; Kevin Daly; Nohemi Sala Burgos; Adrian Pablos; Sophy Charl; Victoria Mull; Laurent Frantz; Greger Larson; Ludovic Orlando

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

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2025

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Anglais

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HALSHS : archive ouverte en Sciences de l’Homme et de la Société

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Ce document est lié à :
info:eu-repo/semantics/altIdentifier/doi/10.1111/1755-0998.14112

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Centre pour la communication scientifique directe

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http://creativecommons.org/licenses/by-nd/ , info:eu-repo/semantics/OpenAccess

Mots-clés En Und

ancient DNA domestication environmental DNA palaeogenomics target enrichment

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Deoxyribonucleic acid TNA (Nucleic acid) Desoxyribonucleic acid Thymonucleic acid

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Kuldeep More et al., « Validating a Target-Enrichment Design for Capturing Uniparental Haplotypes in Ancient Domesticated Animals », HALSHS : archive ouverte en Sciences de l’Homme et de la Société, ID : 10.1111/1755-0998.14112

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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 speciesspecific 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 This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

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

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