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Understanding horse speciation and domestication through comparative palaeogenomics

Final Report Summary - HORSEDOMESTICATION (Understanding horse speciation and domestication through comparative palaeogenomics)

The second period of the HORSEDOMESTICATION project has built from the methods developed during the first period to address four major themes in equine evolution. First, we have sequenced the complete genomes of each living member of the horse family, including 3 species of zebras, the domestic donkey and the Somali wild ass, as well as the Asiatic wild ass and the Tibetan kiang. Additionally, we have sequenced the genome of the now extinct quagga genome, using ancient DNA preserved in museum specimen. With this extensive genome dataset, we could reveal the 4 million years-long evolutionary history of the horse family, by timing speciation events and deciphering the genetic basis underlying the adaptations of species to their environments. Second, we sequenced the complete genomes of two ancient horse specimens from the Upper Paleolithic, a period when horses were not already domesticated. Their comparison with the genomes from a range of domestic horse breeds helped better understand the genetic foundation of horse domestication, revealing that a substantial fraction of the genome of domesticates originate from a hitherto unknown group of wild horses. This work also identified 125 genes that represented early selection targets during the domestication process, with functions related to locomotion, physiology, development, behavior and cognition. Third, we generated the most extensive genome dataset of Przewalski’s horses, which represent the last truly wild horse population in the planet. The information collected helped refine their evolutionary relationships with domesticated horses and provided guidelines to improve the success of current conservation programs aiming at a long-term survival of this endangered group of horses. Finally, using complete genome sequencing of modern and ancient horses, we uncovered the evolutionary origin of Yakutian horses, living in Far Easter Siberia. Our work revealed the genetic basis of their striking adaptation to the Arctic, enabling them to survive to winter temperature below -70C. Overall, our work has illuminated the evolutionary history of horses in terms of their emergence as a species but also in terms of their further differentiation as populations and breeds. It also provided an extensive genome resource within this family, which stimulated a growing number of collaborations with expert scientists in conservation, veterinary, archeological and genomic research.