Dual ancestry and adaptation in the reconstructed genome of the dire wolf (Aenocyon dirus)
The dire wolf (Aenocyon dirus) is an extinct canid predator that inhabited much of continental North America during the Pleistocene, but whose evolutionary history remains poorly resolved. Dire wolves were phenotypically similar to living wolves and jackals, which previous genomic analysis attributed to potential post-divergence admixture with a basal wolf-like lineage. To test this hypothesis, we assembled paleogenomes data from two of the best preserved dire wolf fossils: an individual from Sheriden Pit, Ohio, that dates to around 11,500 years ago and an individual from a 72,000-year-old site near Gigantobison Bay, Idaho. We used an iterative mapping approach to generate 3.4x and 12.8x coverage dire wolf paleogenomes. We used these data to estimate consensus species trees for an alignment of 11 canid species. Our results reveal that the dire wolf had a hybrid ancestry, with around one third of of its ancestry derived from a basal Canini lineage that pre-dates Cerdocyonina (~4-5 Mya) and the remaining ancestry derived from a basal wolf-like lineage that emerged after the appearance of African wild dogs some 4.8 million years ago. We identified 32 genes exhibiting episodic positive selection at dire wolf specific residues aligning to functional protein domains, including skeletal, muscular, circulatory, and sensory adaptations relevant to successfully hunting Pleistocene megafauna. Our results underscore the power of paleogenomes to resolve longstanding taxonomic questions and highlight another instance in evolutionary history in which related lineages hybridize following divergence.