New insights from whole‑genome sequencing into the genetic structure and the evolutionary history of the Asiatic lion (Panthera leo persica)

The Asiatic lion (Panthera leo persica), once distributed from Southern Europe to Southeast Asia, is now restricted to a single population in Indian Gir Forest. In order to investigate its population structure and evolutionary history, we generated a comparative whole-genome dataset of 37 lions, comprising 16 newly sequenced captive Asiatic individuals, 3 wild ones, and modern and ancient African lions from the literature. Heterozygosity, runs of homozygosity, and identity by descent fragments reveal extreme inbreeding and prolonged bottlenecks in Asiatic lions, contrasting with higher diversity in African populations. Principal Component Analysis (PCA) separates African from Asiatic individuals while highlighting proximity to the extinct North African Barbary population. We then assembled a mitochondrial dataset comprising 51 samples, including two Roman era lions recovered during an archaeological excavation of the Colosseum’s southern sewer conduit. Mitochondrial phylogeny places the Roman specimens within the North African lineage and confirms a genetic link between Barbary and Asiatic lions. Our results provide a historical framework for conservation: targeted relocations or assisted gene flow from genetically compatible lineages may help restore diversity while respecting the Asiatic lion’s unique heritage.