Ancient DNA from Palaeoloxodon naumanni in Japan reveals early evolution of Eurasian Palaeoloxodon

Palaeoloxodon, the extinct genus of straight-tusked elephants, originated in Africa and dispersed across Eurasia. We analyzed ancient mitochondrial DNA of Palaeoloxodon naumanni, a species of the Japanese archipelago that went extinct during the late Late Pleistocene. The data indicate that P. naumanni forms a monophyletic group nested within the Eurasian-wide WE clade (defined by the Weimar-Ehringsdorf specimen and also represented in China) and represents an early-diverging lineage, with a split estimated at ∼1.05 Ma. Combined with fossil cranial morphology, the results support an early eastward spread of the plesiomorphic "Stuttgart morph" into East Asia, followed by continental predominance of the derived "namadicus morph", while P. naumanni persisted as a relict in the Japanese archipelago under island isolation. These results enhance our understanding of the evolutionary trajectory of Palaeoloxodon and underscore the importance of ancient mitochondrial DNA analysis in shedding light on Pleistocene extinctions, with particular emphasis on the Japanese archipelago.