Present-day domestic horses are immensely diverse in their maternally inherited mitochondrial DNA, yet theyshow very little variation on their paternally inherited Y chromosome. Although it has recently been shown thatY chromosomal diversity in domestic horses was higher at least until the Iron Age, when and why this diversitydisappeared remain controversial questions. We genotyped 16 recently discovered Y chromosomal single-nucleotidepolymorphisms in 96 ancient Eurasian stallions spanning the early domestication stages (Copper and BronzeAge) to the Middle Ages. Using this Y chromosomal time series, which covers nearly the entire history of horsedomestication, we reveal how Y chromosomal diversity changed over time. Our results also show that the lack ofmultiple stallion lineages in the extant domestic population is caused by neither a founder effect nor randomdemographic effects but instead is the result of artificial selection—initially during the Iron Age by nomadic peoplefrom the Eurasian steppes and later during the Roman period. Moreover, the modern domestic haplotype probablyderived from another, already advantageous, haplotype, most likely after the beginning of the domestication.In line with recent findings indicating that the Przewalski and domestic horse lineages remained connectedby gene flow after they diverged about 45,000 years ago, we present evidence for Y chromosomal introgressionof Przewalski horses into the gene pool of European domestic horses at least until medieval times.
This is very interesting, as it clearly suggests that horses were domesticated by various cultures of the Neolithic. The earliest domestic horses came from northern Anatolia (2700-2200 B.C.E.), followed by Portuguese Zambujal culture whose population seems to have domesticated horses who carried Przewalski Y-DNA haplotypes. There are several Y-DNA turnovers before the emergence of modern domesticates. The Y-DNA haplotypes of modern domesticates first appears in the Hatvan culture of Slovakia in the Bronze Age.

The supplement includes 3 Y-DNA haplogroups from Andronovo horses. These are associated with Anatolia (n=2) and Slovakia (n=1)

Link: http://advances.sciencemag.org/content/4/4/eaap9691