Post-bottleneck increase in mitochondrial DNA diversity in Yaku sika deer (Cervus nippon yakushimae) on Yakushima Island, Japan

We investigated the genetic diversity and divergence of sika deer (Cervus nippon) descended from survivors of a catastrophic pyroclastic flow event approximately 7,300 years ago by analyzing the 894 base pairs mitochondrial DNA control region extracted from fecal samples. We focused on Yaku sika deer (C. n. yakushimae) across the remote islands Yakushima and Kuchinoerabujima in southern Japan. On Yakushima, 18 haplotypes were detected, with significant regional variation. Two subpopulation structures on Yakushima aligned with the distribution of pyroclastic flow deposits. Two haplotypes were found on Kuchinoerabujima, one shared with Yakushima. Reconstructed haplotype networks with sika deer from various regions of the Japanese Archipelago suggested that a historical simultaneous dispersal event occurred in the Yakushima population. The Yakushima and Tanegashima populations (C. n. mageshimae) formed their own clusters and were clearly separated from other southwestern Japanese populations. The lack of common haplotypes between these populations suggests that the Yakushima population experienced sufficient generational changes for genetic drift to fix region-specific mutations after geographical isolation approximately 37,500 years ago. The high genetic diversity of the current Yakushima population may have been acquired through simultaneous dispersal approximately 4,900-6,500 years ago after the pyroclastic flow-induced population bottleneck approximately 7,300 years ago.