Zonkey: A simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages

Abstract

Horses, asses and zebras, can produce first-generation F1-hybrids, despite their striking karyotypic and phenotypic differences. Such F1-hybrids are mostly infertile, but often present characters of considerable interest to breeders. They were extremely valued in antiquity, and commonly represented in art and on coinage. However, hybrids appear relatively rarely in archaeological faunal assemblages, mostly because identification based on morphometric data alone is extremely difficult. Here, 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, now part of PALEOMIX (https://github.com/MikkelSchubert/paleomix), together with full documentation and examples. Using both synthetic and real sequence datasets, from living and ancient F1-hybrids, we find that Zonkey shows high sensitivity and specificity, even with limited sequencing efforts. Zonkey is thus well suited to the identification of equine F1-hybrids in the archaeological record, even in cases where DNA preservation is limited. Zonkey can also help determine the sex of ancient animals, and allows species identification, which advantageously complements morphological data in cases where material is fragmentary and/or multiple candidate equine species coexisted in sympatry.

Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series

“…Following low-depth sequencing, a total of 278 ancient equids reached a nuclear DNA coverage higher than 0.01X and were investigated for sex and species identification using the methodology implemented in Zonkey ( Table S1 ) ( Schubert et al., 2017 ). Additionally, 87 pure horses recovered from museum and/or private collections, palaeontological and archaeological sites spread across Eurasia, showing moderate to high endogenous DNA content 0.06-0.78 were selected for whole-genome sequencing at a depth-of-coverage higher than 1-fold.…”

“…Some of those pits contained several individuals, potentially buried simultaneously. In total, 22 individuals dating back to the C2 nd and C3 rd have been discovered, including Boinville_GVA125_1817, an 8-to-10-year-old male, genetically identified as a donkey ( Schubert et al., 2017 ).…”

“…BCE), and shows an over-representation of domestic animals such as cattle, sheep and goats but also a significant number of wild herbivores, such as hemiones and gazelles ( Sheikhi Seno et al., 2012 ). Individual TepeMehrAli_Trj12x31_CopperAge was genetically identified as a pure hemione specimen ( Schubert et al., 2017 ).…”

“…Preliminary sequence data obtained while screening the DNA libraries, typically considering 1-5 million sequencing reads, were processed with the Zonkey package, as part of PALEOMIX ( https://github.com/MikkelSchubert/paleomix ) ( Schubert et al., 2017 ) in order to identify first-generation equine hybrids and determine the molecular sex of each individual. Among the 278 individuals included in this study, we detected three hemiones, three asses, 27 mules, 245 pure horses.…”

Finding Archaeology in 2017: What Is Archaeology and Why Are We Doing It? Why Should We Be Doing It?

“…Researchers are using DNA techniques on animal remains to reinvigorate studies of traditional interest, such as domestication (MacHugh, Larson, and Orlando ) and species identification (Schubert et al. ), but also to look at other less typical issues, including human migrations (Kemp et al. ) and trade (Star et al.…”