Phylogeography of terrestrial mammals on islands is complicated because of the geological changes in the island configuration or their past population dynamics on the nearby landmass. To understand the function of Shodoshima Island in the Seto Inland Sea in preserving lineages of Japanese macaques (Macaca fuscata) and sika deer (Cervus nippon), we investigated the molecular phylogeny of these species on the island. We analyzed a partial sequence of the mitochondrial DNA (mtDNA) control region of the two species. We identified four mtDNA haplotypes in macaques, including western and eastern Japan lineages. Two mtDNA haplotypes for deer were discovered, which were categorized into only the northern Japan lineage. Their nucleotide sequences were identical except for a tandem repeat. These results suggest that the phylogeographic trend was remarkably different between the two species, which may be due to the migration of multiple lineages of macaques to the island when it was connected to Honshu Island, and a bottleneck effect on the deer population caused by overhunting. Some haplotypes were probably unique to the Shodoshima population of both species. The presence of region-specific haplotypes suggests the importance of Shodoshima Island to maintain genetic diversity of the species.

Published online 30 January, 2024; Print publication 30 April, 2024