Whole-genome sequences of extinct and living lions revealed their population history, with special emphasis on characterising the evolutionary relationships between cave and modern lions. We also assessed the genetic heterozygosity in different present-day lion populations.. The evolutionary history of extinct and living lions

Lions are one of the world’s most iconic megafauna, yet little is known about their temporal and spatial demographic history and population differentiation. We analysed a genomic dataset of 20 specimens: two ca. 30,000-year-old cave lions (Panthera leo spelaea), 12 historic lions (Panthera leo leo/Panthera leo melanochaita) that lived between the 15th and 20th centuries outside the current geographic distribution of lions, and 6 present-day lions from Africa and India. We found that cave and modern lions shared an ancestor ca. 500,000 years ago and that the two lineages likely did not hybridise following their divergence. Within modern lions, we found two main lineages that diverged ca. 70,000 years ago, with clear evidence of subsequent gene flow. Our data also reveal a nearly complete absence of genetic diversity within Indian lions, probably due to well-documented extremely low effective population sizes in the recent past. Our results contribute towards the understanding of the evolutionary history of lions and complement conservation efforts to protect the diversity of this vulnerable species.