Cave lion (Panthera spelaea) genomes from a 150 KYA time series to investigate ecology and evolution of an extinct apex predator

The Eurasian cave lion (Panthera spelaea) was abundant in the Northern Hemisphere prior to the megafaunal extinctions at the end of the Late Pleistocene. However, the extent to which cave lions were distinct from modern lions (Panthera leo) has been debated, and little is known about the adaptive differences that distinguished these two lion lineages or the population dynamics of cave lions leading up to their disappearance. Using 12 cave lion genomes spanning more than 100,000 years, we demonstrate that modern and cave lions were distinct evolutionary lineages with separate demographic histories and differentiated non-synonymous genetic variation in protein-coding genes. Cave lions and modern lions have been hypothesised to have had several contact zones. We identified the first evidence of ancient gene flow between these two lion lineages, with the best modern lion proxy being an extinct population from Southwest Asia. This admixture appears to be associated with global ice extent, with up to 5% modern lion ancestry in a cave lion from Central East Asia dated to the Last Glacial Maximum. These results provide valuable insight into the evolutionary history of the cave lion, historically one of the Northern Hemisphere's most ecologically impactful megafaunal species.