Middle Pleistocene Cave Bear Genome Calibrates the Evolutionary History of Palaearctic Bears

Palaeogenomes provide the potential to study evolutionary processes in real time⁠, but this potential is limited by our ability to recover genetic data over extended timescales. The Late Pleistocene currently represents the age-limit for temperate-zone palaeogenome retrieval. Consequently, large portions of the evolutionary histories of many organismal clades remain inaccessible for direct genomic investigation. Here, we present the palaeogenome of a 367,000 year old cave bear from Kudaro 1 cave in the Caucasus. Analysis of this genome alongside those of Late Pleistocene representatives almost completely overturns the established view of cave bear evolution based on mitochondrial DNA. The Middle Pleistocene genome further allows us to directly estimate the ursine substitution rate to calibrate our revised nuclear genome phylogeny of Palaearctic bears. This reveals the Middle Pleistocene Transition as a key period in Palaearctic bear evolution, associated with the divergence of the major cave bear lineages, the divergence of brown and polar bears, and the end of gene flow between cave bears and brown bears. With an age encompassing an estimated 23% of the entire evolutionary history of cave bears, the Kudaro 1 genome extends the limit for temperate-zone palaeogenome retrieval well into the Middle Pleistocene.