Ancient Genomic Changes Associated with Domestication of the Horse

The genomic changes underlying both early and late stages of horse domestication remain largely unknown. We examined the genome sequences of fourteen early domestic horses from the Bronze and Iron Ages, dating to between ~4 and 2.3 thousand years before present (kyr BP). We find selection patterns during early domestication stages supporting the neural crest hypothesis, which provides a unified developmental origin for most common domestic traits. Horses lost genetic diversity and archaic ancestry from a now-extinct lineage. However we observe deleterious mutations arising later than expected under the cost-of-domestication hypothesis, probably following the recent selection of a limited number of reproductive stallions. We also reveal breeding strategies implemented by the Iron Age Scythian steppe nomads, involving selection for robust forelimbs, coat-color variation and no detectable inbreeding.