Genetic isolation of an amphidromous goby species, Luciogobius ryukyuensis, highlights limited gene flow in small island populations.

Amphidromous fish could be transported to other habitats during the marine pelagic larval phase by ocean currents, but extent and mechanism of the larval dispersal is poorly known. Since island stream habitats are generally small and fragile, it is very important to understand the connectivity between streams and between islands from the perspective of biodiversity conservation. In the present study, we investigated the genetic connectivity among populations of an amphidromous goby species, Luciogobius ryukyuensis, on four islands (Okinawa, Kume, Ishigaki, and Iriomote) of the Ryukyu Archipelago, Japan. The genome-wide SNPs analyses revealed that the populations of L. ryukyuensis from the four islands are genetically distinguishable. This suggested that larval transport of this species between these four islands is very limited. On the other hand, the mitochondrial genome analysis clearly divided the species into only two populations (Okinawa + Kume and Ishigaki + Iriomote). This may indicate that there was more recent genetic exchange between the two neighboring islands than between more distant islands. The populations on Kume, Ishigaki, and Iriomote islands are particularly small, with only two or three very small habitats on each island. Maintaining all existing habitats will be critical for conservation of the present diversity of the species.