From the Cover: PNAS Plus: Prehistoric genomes reveal the genetic foundation and cost of horse domestication

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.The domestication of the horse had a far-reaching impact on the sociopolitical and economic trajectories of human societies (1). It not only provided meat and milk (2) but also enabled the development of continent-sized nomadic empires, by transforming warfare and allowing for the rapid spread of goods and information over long distances. However, despite the characterization of the genome of modern horses (3), an understanding of the genetic processes underlying horse domestication is still lacking. In other organisms, such an understanding is usually achieved by comparing the genomes of domesticated species and their wild relatives (4–6), but this approach is not directly applicable to horses. Recent genome-wide analyses have shown that Przewalski’s horse, the last truly wild horse population remaining today, is not the direct ancestor of domesticated horses (7, 8). Instead, it likely represents a sister population that separated from the ancestral population of domesticated horses some 38–72 kya (9). This date significantly predates not only the widely accepted date for the beginning of horse domestication, ca. 5.5 kya (2), but also the earliest potential evidence for horse domestication, ca. 7.5 kya (10). In addition, the current Przewalski’s horse population descends from a captive stock consisting of only 13 founder individuals (7). This severe demographic bottleneck, together with inbreeding resulting from unequal contributions from different captive lineages, likely caused a substantial loss of the diversity once present in Przewalski’s horses. As a result, no modern horse population can fully represent the genetic diversity ancestral to the modern, domesticated gene pool (11–13).Ancient DNA allows tracking of past population histories through time, accessing the gene pools of wild animals predating domestication and exploring genetic variation that has been lost in extant populations. Recovery of ancient DNA, coupled with low-throughput gene candidate analyses, has previously been used to investigate changes in the genetic diversity of horses over time. This approach revealed coat color variation as one early result of domestication, by showing that the selection of multiple alleles driving diverse coloration patterns was already ongoing in the Early Bronze Age (14). It has also revealed a loss of Y-chromosomal haplotypes on both the Przewalski’s and domestic horse lineages (12).Using next-generation sequencing, the complete genome sequence of ancient individuals can now be deciphered (15), with qualities rivaling the qualities of modern genomes (16–18). We characterized complete genome sequences of two ancient horse specimens predating the earliest evidence of horse domestication to reveal the population context in which horse domestication took place. We compared the genomic information of these specimens with genomic information of six domestic horses, representing five breeds, and one Przewalski’s horse (9), ranging from a 7.4- to 32.7-fold average depth of coverage. We also included the domestic donkey as an outgroup, which represents a sister lineage of modern horses and shares a most common recent ancestor with horses 4.0–4.5 Mya ago (9). This comparison enabled us to reconstruct the relationships between wild and domesticated horses, and to explore the genetic mechanisms underlying the behavioral, physiological, and other biological changes that accompanied horse domestication.