Validating a target-enrichment design for capturing uniparental haplotypes in ancient domesticated animals

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 sufficient amounts of 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 1,686 per species) to characterize (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..., We screened the literature to collect an extensive representation of full mitogenome sequences from a total of eight species of domesticated animals, namely cattle (Bos taurus), chickens (Gallus gallus), dogs (Canis familiaris), donkeys (Equus asinus), goats (Capra aegagrus hircus), horses (Equus caballus), pigs (Sus scrofa domesticus), and sheep (Ovis aries) (Table S2). We then added the mitochondrial haplotypes from three equid and three canid outgroups (Equus hemionus, N=1; E, africanus somaliensis, N=1, and E. hydruntinus, N=1; Canis latrans, N=5; Canis himalayensis, N=2, and C. lupus signatus, N=2, respectively) to the E. asinus and C. familiaris data sets. We also added to this dataset 476 full mitogenome sequences from hominins, including 433 Homo sapiens sapiens with a worldwide distribution, 34 Homo sapiens neanderthaliensis, seven Homo altaiensis and two Homo heidelbergensis. We also included a total of 409 bear mitochondrial sequences. Independent multiple sequence align..., , # Validating a target-enrichment design for capturing uniparental haplotypes in ancient domesticated animals

[https://doi.org/10.5061/dryad.612jm64cr](https://doi.org/10.5061/dryad.612jm64cr)

## Description of the data and file structure

We screened the literature to collect an extensive representation of full mitogenome sequences from a total of eight species of domesticated animals, namely cattle (*Bos taurus*), chickens (*Gallus gallus*), dogs (*Canis familiaris*), donkeys (*Equus asinus*), goats (*Capra aegagrus hircus*), horses (*Equus caballus*), pigs (*Sus scrofa domesticus*), and sheep (*Ovis aries*) (Table S2). We then added the mitochondrial haplotypes from three equid and three canid outgroups (*Equus hemionus*, N=1; *E, africanus somaliensis*, N=1, and *E. hydruntinus*, N=1; *Canis latrans*, N=5; *Canis himalayensis*, N=2, and *C. lupus signatus*, N=2, respectively) to the *E. asinus* and *C. familiaris *data sets. We also added to this dataset 476 full mitogenome sequenc...,