- Tytuł:
- Validating a target‐enrichment design for capturing uniparental haplotypes in ancient domesticated animals
- Autorzy:
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Larson, Greger
Rødsrud, Christian Løchsen
Bayarsaikhan, Jamsranjav
Charliquart, Léa
Vila, Emmanuelle
Orlando, Ludovic
Bălășescu, Adrian
Dobrescu, Roxana
Zhumatayev, Rinat
Chauvey, Loreleï
Discamps, Emmanuel
Vahdati, Ali A.
More, Kuldeep D.
Fernández, Pablo M.
Buric, Marcel
Daly, Kevin G.
Benecke, Norbert
Taylor, William
Garrido, Jaime Lira
Nikgoftar, Ahmad
Burgos, Nohemi Sala
de Noblet, Thibault
Chiavazza, Horacio
Moskal‐del Hoyo, Magdalena
Bradley, Daniel G.
Steadman, Sharon
Robbe, Emilie
Frantz, Laurent
Guardia, Nicolás M.
Nowak, Marek
Berthon, Rémi
Star, Bastiaan
Padula, Horacio
Allccarima‐Crisóstomo, Diana
Kosintsev, Pavel
Borges, Caroline
Contreras‐Mancilla, Juan
Vukičević, Tajana Trbojević
Post‐Melbye, Julian Robert
Mullin, Victoria E.
Dalen, Love
Wilczynski, Jaroslaw
Lebrasseur, Ophélie
Schiavinato, Stéphanie
Tressières, Gaëtan
Stanton, David W. G.
Boudadi‐Maligne, Myriam
Arbuckle, Benjamin
Shakenov, Samat
Castel, Jean‐Christophe
Houle, Jean‐Luc
Charlton, Sophy
Seguin‐Orlando, Andaine
Šikanjić, Petra Rajić
Mashkour, Marjan
McMahon, Gregory
Bertani, Stéphane
Barrey, Eric
Gibert, Morgane
Estrada, Oscar
Pablos, Adrian
Alvarez, Nadir
Fhon, Miguel
Tonasso‐Calvière, Laure
Khazaeli, Roya - Opis:
- 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.
- Dostawca treści:
- Repozytorium Uniwersytetu Jagiellońskiego
Artykuł