BioProject

The members of the Equidae family, including horses, asses and zebras, can develop first-generation (F1-) hybrids, despite their striking karyotypic and phenotypic differences. More...

The members of the Equidae family, including horses, asses and zebras, can develop first-generation (F1-) hybrids, despite their striking karyotypic and phenotypic differences. Such F1 hybrids are mostly infertile, but often present characters of considerable interests for breeders. They were, thus, extremely valued in antiquity, especially for trade, transport and the military applications, and relatively commonly represented in art and on coinage. Surprisingly, hybrids show a relatively limited appearance in archaeological faunal assemblages. This is mostly because taxonomic identification using only morphological traits and/or morphometrical data is extremely difficult. In this study, we developed a methodological framework that exploits high-throughput sequencing data retrieved from archaeological material to identify F1-equine hybrids. Our computational methodology is distributed in the open-source Zonkey pipeline, as part of the PALEOMIX package (https://github.com/MikkelSchubert/paleomix), together with full documentation and examples. Using a combination of approaches, including synthetic sequence datasets, and real sequence datasets retrieved from living and ancient F1-hybrids, we find that Zonkey shows high sensitivity and specificity, even following limited sequencing efforts. Zonkey is thus well suited to the identification of equine hybrids in the archeological record, even in cases where DNA preservation is limited. In addition to the detection of F1-hybrids and the gender of ancient animals, Zonkey allows taxonomic identification at the species level, which advantageously complements morphological data in cases fragmentary material and/or multiple candidate equine species coexisted in sympatry. Less...