The First Complete Genome of Extinct Equus hydruntinus

Equus hydruntinus, commonly known as European wild ass, once roamed in a range from Western Europe to east of Zagros Mountains in Iran, globally went extinct in the Holocene. Mixed morphological characteristics obstructed proper taxonomic placement of this species on Equid family tree in the past, but ancient DNA studies based on mitochondrial DNA showed close relationship with Equus hemionus, Asian wild ass. However, tracking only maternal genetic lineage would veil more complex interspecies interactions and result in poor understanding in population history. Here, we present the first whole genome of this extinct species from Central Anatolia, dating back to the Iron Age and two other lesser quality genomes. Our taxonomic analysis places ancient Anatolian wild asses in a cluster with previously published European wild asses. Demographical analyses implied European wild ass as a distinct clade and indicated a complex population history involving African and Asian subgenera with hints of sex-dependent gene flow. Extinction mechanisms of this species were also put in a genomic point-of-view with decrease of genetic variation and inbreeding. Our findings suggest a deeper relationship network between non-caballine equids, more than previously thought.