Submerged corridors of ancient gene flow in an insular caecilian amphibian

Many island archipelagos sit on shallow continental shelves. During the Pleistocene, these islands were often connected as global sea levels dropped following glaciation. Given a continental shelf only 30–60 m below sea level, the terrestrial biota of the Seychelles archipelago likely dispersed amongst now isolated islands during the Pleistocene. _Hypogeophis rostratus_ is a caecilian amphibian found on ten islands in the Seychelles. Despite the seemingly limited dispersal abilities of a terrestrial, salt-intolerant, and primarily fossorial amphibian, this broad geographical distribution suggests historic dispersal across now submerged continental shelf corridors. Here, we tested for the genetic signature of these historic corridors despite thousands of generations spent isolated on different islands. Using fine-scale genomic data (ddRADseq) we found that genomic clusters often did not correspond to islands in the archipelago. Additionally, isolation-by-distance patterns were more consistent with gene flow across a continuous landscape than isolated island populations. Using effective migration surfaces and ancestral range expansion prediction we found support for contemporary populations originating near the large southern island of Mahé and dispersing to northern islands via the isolated Frégate island, with additional historic migration across the flat expanse of the Seychelles bank. Collectively, our results suggest that biogeographic patterns can retain signals from Pleistocene ‘palaeo-islands’, and that present-day islands can be thought of as hosting bottlenecks or transient refugia rather than discrete genetic units. Thus, the signatures of gene flow associated with palaeo-islands may be stronger than the isolating effects of contemporary islands in terrestrial species distributed on continental shelf islands.