Paleogenomes reveal the evolutionary relationship between modern and cave lions
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Stanton, D.W.G., Bergström, A., Heintzman, P.D., van der Valk, T., Carmagnini, A., Ersmark, E., Pawar, H., Sandoval-Velasco, M., Androsov, S., Fedorov, S., Kuhlwilm, M., Nagel, D., Plotnikov, V., Protopopov, A., Shapiro, B., Barnett, R., Sinding, M.-H.S., Marques-Bonet, T., Yamaguchi, N., Gilbert, M.T.P., Götherström, A., Skoglund, P., Frantz, L., Dalén, L., 2026. Paleogenomes reveal the evolutionary relationship between modern and cave lions. Cell 189, 4425-4436.e4411.
Highlights
• Cave and modern lions were distinct evolutionary lineages with independent histories
• Cave lions possessed many unique functional mutations across the genome
• Gene flow occurred between modern and cave lions during the Late Pleistocene
• Cave lions were highly connected across their distribution
Summary
The Eurasian cave lion was abundant across the Northern Hemisphere before the Late Pleistocene megafaunal extinctions. However, the extent of the distinction between cave and modern lions and their adaptive differences have remained unclear. Using 12 cave lion genomes spanning more than 100,000 years, we show that modern and cave lions were distinct evolutionary lineages with separate demographic histories and unique non-synonymous variants. We also identify evidence of ancient gene flow between them, with the best modern lion proxy for this ancestry being an extinct Southwest Asian population. This admixture correlates with global ice extent, with 3.2%–4.4% modern lion ancestry detected in a ∼20,000-year-old cave lion from Central East Asia. These findings provide insight into the evolutionary history of the cave lion, once one of the Northern Hemisphere’s most ecologically impactful megafaunal species