Prehistoric genomes reveal the genetic foundation and cost of horse domestication

The domestication of the horse provided, for the first time, a means of rapid transportation on land and consequently had a tremendous impact on the politico-economical trajectory of our societies, revolutionizing communication and the circulation of ideas, languages and religions. Horse chariotry and cavalry also changed warfare and equestrian technologies greatly stimulated agricultural productivity. However, the 5,500 year long history of their domestication, which redirected the natural evolution of wild horses into the hundreds of modern breeds living today, is difficult to reconstruct from archeozoological data and modern genetics. Yet, with archeogenetics, one can access the genetic information from past individuals and thereby directly access past population histories. We therefore reconstructed high-quality genomes from two ancient wild horses dating to the Late Pleistocene period, which predates the onset of horse domestication by thousands of years. Their direct comparison to the genomes of living horses, including a diversity of domesticated breeds and the wild Przewalski’s horse, allowed us to reconstruct the population context in which domestication took place. We found that horse domestication was associated with inbreeding and an excess of deleterious mutations, in line with the ‘cost of domestication’ hypothesis also reported for rice, tomatoes and dogs, and generally attributed to the relaxation of purifying selection resulting from demographic bottlenecks accompanying domestication. Additionally, we identified a conservative set of 125 potential domestication targets using four complementary scans for genes that have undergone positive selection, revealing the genetic basis for the behavioral, physiological, and other biological changes that accompanied horse domestication