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

<i>Palaeoloxodon</i>, the extinct genus of straight-tusked elephants, originated in Africa and dispersed across Eurasia. We analyzed ancient mitochondrial DNA of <i>Palaeoloxodon naumanni</i>, a species of the Japanese archipelago that went extinct during the late Late Pleistocene. The data indicate that <i>P. naumanni</i> 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 "<i>namadicus</i> morph", while <i>P. naumanni</i> persisted as a relict in the Japanese archipelago under island isolation. These results enhance our understanding of the evolutionary trajectory of <i>Palaeoloxodon</i> and underscore the importance of ancient mitochondrial DNA analysis in shedding light on Pleistocene extinctions, with particular emphasis on the Japanese archipelago.