Ancient Horse Genomes In the Next-Next Generation Sequencing Era

Horses have played a critical role in human societies and the rich fossil record of the horse family is one of the most widely known examples of macroevolutionary change. Hence, horses offer a unique paradigm to understand the processes of domestication and speciation. However, horses have become mostly extinct in the wild precluding direct comparison of domestic and wild horse genomes. In this project, we aim at using state-of-the-art ancient DNA methods in combination with 2nd and 3rd generation sequencing technologies to characterize the complete genomes of two Pleistocene horses conserved in permafrost soils together with the 6 complete genomes of modern equids. We have explored the potential of third-generation sequencing, performing ‘true single molecule sequencing’ of ancient DNA on the Helicos HeliScope. Our results indicate that the molecular biology tools used to generate ancient DNA sequencing libraries introduce biases, that reduce the efficiency of the sequencing process and limit our ability to fully explore the molecular complexity of ancient DNA extracts. Our results suggest that paleogenomes could be sequenced in an unprecedented manner by combining current second- and third- generation sequencing approaches. Using this strategy, we have characterized the genomes of horses before the domestication started. Comparative genomics with modern domestic breeds reveals the loci that have been positively selected by humans early in the process of horse domestication.