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

• DOI: 10.1111/1755-0998.14112
• Publication Date: 2025-04-09T15:08:21Z
• Authors: Kuldeep D. More; Ophélie Lebrasseur; Jaime Lira Garrido; Andaine Seguin‐Or...; Emmanuel Discamps; Oscar Estrada; Laure Tonasso‐Cal...; Loreleï Chauvey; Gaëtan Tressières; Stéphanie Schiavi...; Morgane Gibert; Horacio Padula; Horacio Chiavazza; Pablo M. Fernández; Nicolás M. Guardia; Caroline Borges; Stéphane Bertani; Juan Contreras‐Ma...; Diana Allccarima‐...; Miguel Fhon; Eric Barrey; Léa Charliquart; Emilie Robbe; Thibault de Noblet; Rinat Zhumatayev; Samat Shakenov; Emmanuelle Vila; Rémi Berthon; Marjan Mashkour; Roya Khazaeli; Ahmad Nikgoftar; Ali A. Vahdati; Pavel Kosintsev; Jean‐Luc Houle; Jamsranjav Bayars...; Jaroslaw Wilczynski; Magdalena Moskal‐...; Marek Nowak; William Taylor; Adrian Bălășescu; Roxana Dobrescu; Norbert Benecke; Benjamin Arbuckle; Sharon Steadman; Gregory McMahon; Petra Rajić Šikanjić; Marcel Buric; Tajana Trbojević ...; Nadir Alvarez; Jean‐Christophe C...; Myriam Boudadi‐Ma...; Bastiaan Star; Julian Robert Pos...; Christian Løchsen...; David W. G. Stanton; Sophy Charlton; Victoria E. Mullin; Kevin G. Daly; Nohemi Sala Burgos; Adrian Pablos; Love Dalen; Daniel G. Bradley; Laurent Frantz; Greger Larson; Ludovic Orlando
• Keywords: Ancient DNA; Osteology; Equus; Equidae; mtDNA control region

ABSTRACT In the last three decades, DNA sequencing of ancient animal osteological assemblages has become an important tool complementing standard archaeozoological approaches to reconstruct history domestication. However, key archaeological contexts are not always available or do necessarily preserve enough for a cost‐effective genetic analysis. Here, we develop in‐solution target‐enrichment approach, based on 80‐mer species‐specific RNA probes (ranging from 306 1686 per species) characterise (in single experiments) mitochondrial variation eight domesticated species major economic interest: cattle, chickens, dogs, donkeys, goats, horses, pigs and sheep. We also illustrate how our design can be adapted enrich library content map Y‐chromosomal diversity within Equus caballus . By applying assay extensive panel remains, farm soil, cave sediments spanning 43 kyrs, demonstrate that minimal efforts necessary exhaust complexity mitogenomes average depth‐of‐coverage 19.4 2003.7‐fold. Our further retrieved horse mitogenome Y‐chromosome data Late Pleistocene coprolites, as well bona fide sequences were part probe design, such bison hyena. methodology will prove especially useful minimise costs related analyses maternal paternal lineages wide range wild species, mapping their changes over space time, including environmental samples.