Prehistoric genomes reveal the genetic foundation and cost of horse domestication

Schubert, Michael et al.
The domestication of the horse ∼5.5 kya and the emergence of mounted riding, chariotry, and cavalry dramatically transformed human civilization. However, the genetics underlying horse domestication are difficult to reconstruct, given the near extinction of wild horses. We therefore sequenced two ancient horse genomes from Taymyr, Russia (at 7.4- and 24.3-fold coverage), both predating the earliest archeological evidence of domestication. We compared these genomes with genomes of domesticated horses and the wild Przewalski's horse and found genetic structure within Eurasia in the Late Pleistocene, with the ancient population contributing significantly to the genetic variation of domesticated breeds. We furthermore identified a conservative set of 125 potential domestication targets using four complementary scans for genes that have undergone positive selection. One group of genes is involved in muscular and limb development, articular junctions, and the cardiac system, and may represent physiological adaptations to human utilization. A second group consists of genes with cognitive functions, including social behavior, learning capabilities, fear response, and agreeableness, which may have been key for taming horses. We also found that domestication is associated with inbreeding and an excess of deleterious mutations. This genetic load is in line with the "cost of domestication" hypothesis also reported for rice, tomatoes, and dogs, and it is generally attributed to the relaxation of purifying selection resulting from the strong demographic bottlenecks accompanying domestication. Our work demonstrates the power of ancient genomes to reconstruct the complex genetic changes that transformed wild animals into their domesticated forms, and the population context in which this process took place. © 2014, National Academy of Sciences. All rights reserved.
This work was supported by the Danish Council for Independent Research, Natural Sciences (FNU); the Danish National Research Foundation (DNFR94); a Marie-Curie Career Integration Grant (FP7 CIG-293845); and the International Research Group Program (IRG14-08), Deanship of Scientific Research (King Saud University, Saudi Arabia). H.J. was supported by a Marie-Curie Initial Training Network Grant (EUROTAST; FP7 ITN-290344); A.G. and L. Ermini were supported by Marie-Curie Intra-European Fellowships (FP7 IEF-299176 and FP7 IEF-302617); M.S. was supported by a Lundbeck Foundation Grant (R52-A5062); I.D., A.F., and L. Excoffier were supported by a Swiss National Science Foundation Grant (31003A-143393); M.H. was supported by a European Research Council (ERC) Consolidator Grant (310763); T.M.-B. was supported by an ERC Starting Grant (260372) and by a Ministerio de Ciencia e Innovación (MICINN) Grant (BFU2011-28549); B.S. was supported by the Packard Foundation; and D.C. was supported by start-up funds to B.S. from the University of California, Santa Cruz.