A new study on multiple genomes from the extinct cave lion has discovered that it represented a highly distinct evolutionary lineage, which separated from modern lions more than a million years ago. The results also show that the cave lion had a history of interbreeding with modern lions that was tightly linked to past climatic changes. These findings are published in the journal Cell in a study led by Swedish and British scientists.

The research was done at the Centre for Palaeogenetics (CPG), which is a joint initiative by Stockholm University and the Swedish Museum of Natural History. The researchers analyzed 12 genomes from cave lions sampled across Eurasia and northernmost North America, spanning a period of over 100,000 years, and compared these with 20 genomes from modern lions in Africa and southern Asia. The cave lion DNA was extracted from teeth and bones, but also some soft-tissue specimens, including two exceptionally well-preserved cave lion cubs from Northern Siberia.

“Cave lions have often been portrayed as just a larger, more rugged version of modern lions,” says lead author David Stanton, a former postdoc in Stockholm and now a Lecturer at Cardiff University in the UK. “But what we see in their genomes is something much more remarkable – a lineage that has been evolving independently for over a million years, accumulating its own unique biological features.”

A comparison of the genomes show that cave lions and modern lions formed clearly distinct groups, indicating long term evolutionary separation. While earlier estimates have suggested a relatively recent divergence, the new analyses support a much deeper split that may extend back well over 1.5 million years.

The researchers also identified genetic differences that likely contributed to the distinctive biology of cave lions. The researchers found mutations unique to cave lions that are predicted to affect protein function, along with an excess of genetic changes in genes linked to brain function, vision, growth, and circulatory development. These findings are consistent with evidence from fossils and cave art suggesting that cave lions differed from modern lions in size, behaviour, and ecological adaptation.

Despite this long period of separation, cave lions and modern lions did not evolve in complete isolation. The team identified multiple episodes of interbreeding between the two lineages across tens of thousands of years. Although the genetic contribution from modern lions was relatively small, these events were widespread and occurred at different points in time.

Strikingly, the timing of this gene flow appears to be closely linked to past changes in global climate. The researchers found that the level of modern lion ancestry in cave lion genomes increased during periods when ice sheets were most extensive. During these colder phases, cave lion populations likely expanded southward, bringing them into contact with modern lions in regions such as Central and Southwest Asia.

“Our results suggest that past climate change did more than reshape habitats. It actively brought species together, creating brief opportunities for interbreeding that would not have existed otherwise”, says senior author Love Dalén, a Professor and research group leader at the Centre for Palaeogenetics in Stockholm.

Genetic evidence points to a recently extinct population of modern lions in Southwest Asia as the most likely source of this gene flow. These lions appear to have served as a contact zone between the two lineages during colder periods.

At the same time, cave lion populations themselves were highly dynamic. The data reveal extensive genetic connectivity between cave lion populations across Eurasia, with ancestry spreading rapidly over large distances, within relatively short time spans.