Validating a Target-Enrichment Design for Capturing Uniparental Haplotypes in Ancient Domesticated Animals
2 UEX - Universidad de Extremadura - University of Extremadura
3 TRACES - Travaux et recherches archéologiques sur les cultures, les espaces et les sociétés
4 PHARMA-DEV - Pharmacochimie et Biologie pour le Développement
5 Universität Bayreuth [Deutschland] = University of Bayreuth [Germany] = Université de Bayreuth [Allemagne]
6 INEN - Instituto Nacional de Enfermedades Neoplasicas [Lima, Pérou]
7 LOAM - Laboratoire Mixte International d'Oncologie Anthropologique Moléculaire = International Joint Laboratory of Molecular Anthropological Oncology
8 PHARMA-DEV - Pharmacochimie et Biologie pour le Développement
9 Musée de l'Armée, Paris
10 KazNU - Al-Farabi Kazakh National University [Almaty]
11 Archéorient - ARCHEORIENT - Environnements et sociétés de l'Orient ancien
12 BioArch - BioArchéologie, Interactions Sociétés Environnements
13 University of Tehran
14 MPI-SHH - Max Planck Institute for the Science of Human History
15 NMM - National Museum of Mongolia
16 PAN - Polska Akademia Nauk = Polish Academy of Sciences = Académie polonaise des sciences
17 UJ - Uniwersytet Jagielloński w Krakowie = Jagiellonian University = Université Jagellon de Cracovie
18 IGDR - Institut de Génétique et Développement de Rennes
19 Romanian Academy
20 DAI - German Archaeological Institute
21 UNC-Chapel Hill - Université de Caroline du Nord à Chapel Hill = University of North Carolina [Chapel Hill]
22 PACEA - De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie
23 CNRS - Centre National de la Recherche Scientifique
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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 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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