Paleogenomes reveal the evolutionary relationship between modern and cave lions

Stanton, David W. G., Bergström, Anders ORCID: https://orcid.org/0000-0002-4096-9268, Heintzman, Peter D., van der Valk, Tom, Carmagnini, Alberto, Ersmark, Erik, Pawar, Harvinder, Sandoval-Velasco, Marcela, Androsov, Semyon, Fedorov, Sergey, Kuhlwilm, Martin, Nagel, Doris, Plotnikov, Valeri, Protopopov, Albert, Shapiro, Beth, Barnett, Ross, Sinding, Mikkel-Holger S., Marques-Bonet, Tomas, Yamaguchi, Nobuyuki, Gilbert, M. Thomas P., Götherström, Anders, Skoglund, Pontus, Frantz, Laurent and Dalén, Love (2026) Paleogenomes reveal the evolutionary relationship between modern and cave lions. Cell. ISSN 0092-8674

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Abstract

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.

Item Type:	Article
Additional Information:	Data and code availability: All short-read sequencing data generated in this study have been deposited in the European Nucleotide Archive (ENA) under project accession PRJEB83684. Individual experiment accessions are available under ERX13487333–ERX13500950 and are listed in Table S2. All original code used to perform forward simulations has been deposited at Zenodo (DOI: https://doi.org/10.5281/zenodo.19890537) and is publicly available as of the date of publication. Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.
Uncontrolled Keywords:	ancient dna,demography,evolution,genomics,hybridization,paleogenomics,panthera spelaea,speciation,general biochemistry,genetics and molecular biology ,/dk/atira/pure/subjectarea/asjc/1300/1300
Related URLs:	https://www.scopus.com/pages/publication...
Depositing User:	LivePure Connector
Date Deposited:	17 Jun 2026 14:14
Last Modified:	18 Jun 2026 21:01
URI:	https://ueaeprints.uea.ac.uk/id/eprint/103422
DOI:	10.1016/j.cell.2026.05.007

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