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

We develop an in-solution target-enrichment approach, based on a reasonable number of 80-mer RNA species probes, to characterize in single experiments the mitochondrial genetic variation from eight domesticated animal species of major economic interest, including cattle, chickens, dogs, donkeys, goats, horses, pigs and sheep. We illustrate how our design can be adapted to enrich DNA library content and map the Y-chromosomal diversity within Equus caballus. 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 characterize mitogenomes to an average depth-of-coverage between 19.43 to 2003.7 -folds. 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 bisons and cave hyenas. Our methodology will prove especially useful to minimize costs related to the genetic analysis of maternal and paternal lineages of a range of domesticated and wild animal species, and for mapping their diversity change over space and time, including from environmental samples.