Molecular phylogeography of the riffle beetle Urumaelmis uenoi (Coleoptera: Elmidae) in the Ryukyu Islands, Japan

Islands are regarded as "nature's laboratories" and are important model systems for examining biological phenomena. In phylogeographic studies of continental islands, estimating divergence periods has often been used to examine the relationship between island formation history and species evolution. However, when only post-island-formation events are used for calibration, earlier geological processes may be overlooked, potentially introducing bias into divergence period estimates and their interpretation. In this study, we investigated the relationship between evolutionary history and the formation history of the Ryukyu Islands using the riffle beetle Urumaelmis uenoi (Elmidae), which inhabits river systems in the Ryukyu Islands. Divergence period estimation was conducted using multiple DNA markers and analytical approaches. Three major geographically distinct lineages (Northern Ryukyu, Amami Iss. and Okinawa Iss.) were identified within U. uenoi, one of which was separated by the Tokara Gap between the Palearctic and Oriental regions. Mito-nuclear discordance was detected in the phylogenetic relationships of U. uenoi and its related species, and mitochondrial DNA did not support species-level monophyly of U. uenoi. In contrast, nuclear DNA supported species-level monophyly and suggested that divergence among intraspecific lineages predates the formation of the Ryukyu Islands. These results indicate that geological history prior to island formation, as well as post-formation inter-island dispersal, played important roles in shaping genetic structure. Our findings highlight the importance of integrating multiple DNA markers, including related species, as well as carefully selecting calibration points, in phylogeographic studies of continental islands. In addition, this study is the first to apply genome-wide SNPs to the Elmidae.