Validating a Target-Enrichment Design for Capturing Uniparental Haplotypes in Ancient Domesticated Animals
More K.D. Lebrasseur O. Garrido J.L. Seguin-Orlando A. Discamps E. Estrada O. Tonasso-Calvière L. Chauvey L. Tressières G. Schiavinato S. Gibert M. Padula H. Chiavazza H. Fernández P.M. Guardia N.M. Borges C. Bertani S. Contreras-Mancilla J. Allccarima-Crisóstomo D. Fhon M. Barrey E. Charliquart L. Robbe E. de Noblet T. Zhumatayev R. Shakenov S. Vila E. Berthon R. Mashkour M. Khazaeli R. Nikgoftar A. Vahdati A.A. Kosintsev P. Houle J.-L. Bayarsaikhan J. Wilczynski J. Moskal-del Hoyo M. Nowak M. Taylor W. Bălășescu A. Dobrescu R. Benecke N. Arbuckle B. Steadman S. McMahon G. Šikanjić P.R. Buric M. Vukičević T.T. Alvarez N. Castel J.-C. Boudadi-Maligne M. Star B. Post-Melbye J.R. Rødsrud C.L. Stanton D.W.G. Charlton S. Mullin V.E. Daly K.G. Burgos N.S. Pablos A. Dalen L. Bradley D.G. Frantz L. Larson G. Orlando L.
October 2025John Wiley and Sons Inc
Molecular Ecology Resources
2025#25Issue 7
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.
ancient DNA , domestication , environmental DNA , palaeogenomics , target enrichment
Text of the article Перейти на текст статьи
Centre for Anthropobiology and Genomics of Toulouse (CNRS UMR5288/Université de Toulouse), Toulouse, France
TRACES UMR 5608, CNRS-Université de Toulouse-Jean Jaurès, Toulouse, France
Centro de Interpretaciòn de Arqueologìa y Paleontologìa ‘Mario Silveira’, Dirección General de Patrimonio, Museos y Casco Històrico, Buenos Aires, Argentina
Instituto de Arqueología y Etnología, Facultad de Filosofía y Letras, Universidad Nacional de Cuyo, Mendoza, Argentina
National Institute of Anthropology and Latin American Thought (INAPL), Buenos Aires, Argentina
National Scientific and Technical Research Council (CONICET), Buenos Aires, Argentina
Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Arqueología y Etnología, Facultad de Filosofía y Letras, Universidad Nacional de Cuyo, Mendoza, Argentina
Universidade Federal Rural de Pernambuco Recife, PE, Recife, Brazil
UMR 152 PHARMADEV, IRD, UPS, Université de Toulouse, Toulouse Cedex 9, France
International Joint Laboratory of Molecular Anthropological Oncology (LOAM), National Cancer Institute (INEN), Lima, Peru
Museo de Sitio Bodega y Quadra, Lima, Peru
Université Paris-Saclay, INRAE, AgroParisTech, Paris, France
Musée de lArmée, Hôtel Des Invalides, Paris, France
Department of Archaeology, Ethnology and Museology, Al Farabi Kazakh National University, Almaty, Kazakhstan
UMR 5133-Archéorient, CNRS-Université Lyon 2, France
Centre National de Recherche Scientifique, Muséum National dHistoire Naturelle, Archéozoologie, Archéobotanique (AASPE), CP, Paris, France
Central Laboratory, Bioarchaeology Laboratory, Archaeozoology Section, University of Tehran, Tehran, Iran
Ministry of Cultural Heritage, Tourism and Handicrafts, Shahr-e Belqays National Research Base, Esfarayen, Iran
Ministry of Cultural Heritage, Tourism and Handicrafts, North Khorasan Office, Bojnord, Iran
Paleoecology Laboratory, Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russian Federation
Department of History of the Institute of Humanities, Ural Federal University, Ekaterinburg, Russian Federation
Department of Folk Studies and Anthropology, Western Kentucky University, Bowling Green, KY, United States
Max Planck Institute of Geoanthropology, Jena, Germany
Institute of Archaeology, Mongolian Academy of Science, Ulaanbaatar, Mongolia
Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland
Institute of Archeology, Jagiellonian University, Kraków, Poland
Museum of Natural History, University of Colorado-Boulder, Boulder, CO, United States
Vasile Pârvan Institute of Archeology, Bucarest, Romania
Eurasia Department of the German Archaeological Institute, Berlin, Germany
Department of Anthropology, Alumni Building, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
Department of Sociology/Anthropology, College at Cortland, State University of New York, New York, NY, United States
Classics, Humanities and Italian Studies Department, University of new Hampshire, Durham, NH, United States
Institute for Anthropological Research, Zagreb, Croatia
Department of Archaeology, Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia
Department of Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
Geneva Natural History Museum, Geneva, Switzerland
Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
Muséum dhistoire Naturelle, Secteur Des Vertébrés, Geneva, Switzerland
UMR 5199 De la Préhistoire à lActuel: Culture, Environnement et Anthropologie (PACEA), CNRS, Université de Bordeaux, Pessac Cedex, France
Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
Museum of Cultural History, Department of Archaeology, University of Oslo, Oslo, Norway
Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany
Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom
BioArCh, Department of Archaeology, University of York, York, United Kingdom
Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland
Centro Nacional de Investigación Sobre Evolución Humana (CENIEH), Burgos, Spain
Centro Mixto UCM-ISCIII de Investigaciòn Sobre Evoluciòn y Comportamiento Humanos, Madrid, Spain
Departamento de Geodinamica, Estratigrafía y Paleontología, Universidad Complutense de Madrid, Madrid, Spain
Departamento de Prehistoria y Arqueología, Universidad de Sevilla, Sevilla, Spain
Centre for Palaeogenetics, Stockholm, Sweden
Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
Department of Zoology, Stockholm University, Stockholm, Sweden
School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford, United Kingdom
Centre for Anthropobiology and Genomics of Toulouse (CNRS UMR5288/Université de Toulouse)
TRACES UMR 5608
Centro de Interpretaciòn de Arqueologìa y Paleontologìa ‘Mario Silveira’
Instituto de Arqueología y Etnología
National Institute of Anthropology and Latin American Thought (INAPL)
National Scientific and Technical Research Council (CONICET)
Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
Universidade Federal Rural de Pernambuco Recife
UMR 152 PHARMADEV
International Joint Laboratory of Molecular Anthropological Oncology (LOAM)
Museo de Sitio Bodega y Quadra
Université Paris-Saclay
Musée de lArmée
Department of Archaeology
UMR 5133-Archéorient
Centre National de Recherche Scientifique
Central Laboratory
Ministry of Cultural Heritage
Ministry of Cultural Heritage
Paleoecology Laboratory
Department of History of the Institute of Humanities
Department of Folk Studies and Anthropology
Max Planck Institute of Geoanthropology
Institute of Archaeology
Institute of Systematics and Evolution of Animals
W. Szafer Institute of Botany
Institute of Archeology
Museum of Natural History
Vasile Pârvan Institute of Archeology
Eurasia Department of the German Archaeological Institute
Department of Anthropology
Department of Sociology/Anthropology
Classics
Institute for Anthropological Research
Department of Archaeology
Department of Anatomy
Geneva Natural History Museum
Department of Genetics and Evolution
Muséum dhistoire Naturelle
UMR 5199 De la Préhistoire à lActuel: Culture
Centre for Ecological and Evolutionary Synthesis (CEES)
Museum of Cultural History
Palaeogenomics Group
Cardiff School of Biosciences
BioArCh
Smurfit Institute of Genetics
School of Agriculture and Food Science
Centro Nacional de Investigación Sobre Evolución Humana (CENIEH)
Centro Mixto UCM-ISCIII de Investigaciòn Sobre Evoluciòn y Comportamiento Humanos
Departamento de Geodinamica
Departamento de Prehistoria y Arqueología
Centre for Palaeogenetics
Department of Bioinformatics and Genetics
Department of Zoology
School of Biological and Behavioural Sciences
Palaeogenomics and Bio-Archaeology Research Network
10 лет помогаем публиковать статьи Международный издатель
Книга Публикация научной статьи Волощук 2026 Book Publication of a scientific article 2026