Sea-level fluctuations during Pleistocene glacial cycles repeatedly connected and isolated islands in the Ryukyu Archipelago, but the extent to which these events promoted gene flow remains unclear for many terrestrial taxa. The tree frog Kurixalus eiffingeri occurs on Ishigaki and Iriomote Islands in the Yaeyama group and in Taiwan, and previous mitochondrial DNA analyses revealed deep divergence among populations despite their geographic proximity. To test whether nuclear genomic data supports this pattern, we analysed genome-wide SNPs generated by MIG-seq. Phylogenetic reconstruction, STRUCTURE analysis, and principal component analysis consistently identified four major genetic clusters corresponding to Ishigaki, Iriomote, northern Taiwan, and central Taiwan, with the Ishigaki and Iriomote clusters forming the Ryukyu clade. Despite the clear genetic distinctiveness between the Ishigaki and Iriomote clusters, model-based demographic inference using dadi identified the secondary contact model as the best-fitting scenario, suggesting a history of long-term genetic divergence followed by secondary contact during Pleistocene land bridge formation. This pattern may reflect either limited suitable habitat on the Pleistocene land bridge, which restricted gene flow, or partial reproductive isolation between the two clusters, with limited gene flow across a hybrid zone on the land bridge.
Continental islands, Genome-wide SNPs; Kurixalus, Rhacophoridae, Ryukyu Archipelago, Secondary contact
