Fig. 1

A Maximum likelihood tree estimated using the GTR + G model by Iqtree based on 94,142 single nucleotide polymorphisms detected in GRAS-Di analysis. Mid-point rooting was used to construct the phylogeny. The numerals above the branches are bootstrap values estimated by ultrafast bootstrap approximation (10,000 replications). These values are only shown for the clades of each island in the Seto Inland Sea and close relationships between these islands A–F. Full information regarding the terminal samples and bootstrap values is shown in Additional File 4. B Sampling localities of the examined individuals and genetic relationships (red enclosures) demarcated on the basis of the phylogenetic tree A. The inset in the lower right corner shows a wider map of western Japan with longitude and latitude information. Letters (A–F and each locality code) are consistent with the letters in A. The gray lines in the Seto Inland Sea are ancient rivers that are currently submerged, according to estimations by QGIS. The gray lines in Honshu and Shikoku are extant rivers. C Comparisons between PC1 and PC2 obtained by a principal component analysis with the program PLINK1.9. Letters (A–E and each locality code in the legend) are consistent with the letters in A and B. D The same as for C except for removal of individuals A–E. Letter F and locality code in the legend are consistent with those in A, B, and C