Horses have played a critical role in human societies, warfare and for facilitating the exploration of novel territories. In addition, the rich fossil record of the horse family over the past 55 million years has made it an icon for the patterns and processes of macroevolution. However, most horses have become extinct in the wild precluding direct comparison of domestic and wild horse genomes to understand the processes of domestication and speciation. Here, I propose to use state-of-the-art ancient DNA methods in combination with 2nd and 3rd generation sequencing technologies to characterize the complete genomes of the modern donkey, the Przewalski's horse and of two Pleistocene horses, dating back to more than 12,000 years ago. Through comparative genomics, these genomes will deliver the sequence of all horse genes before humans started breed selection and will identify the genetic changes that occurred in the course of the domestication process. In addition, direct comparison between the genomes of the Przewalski's horse and those of pre-domestic Pleistocene horses will clarify the conservation status of this highly endangered horse. While promising to supersede 2nd generation approaches, no 3rd generation sequencing technology has been so far used in ancient DNA context. This project is the first exploring the potential of 3rd generation approaches for ancient DNA, which could open access to a whole range of fossils previously considered as devoid of any trace of DNA. At the genetic level, the domestication process has never previously been studied through the merger of ancient and modern genome-wide data. Therefore, this project represents an unprecedented attempt to understand the dynamics of genomic changes over time in relation with animal domestication.
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