Data from: Sea-level driven glacial-age refugia and post-glacial mixing on subtropical coasts, a palaeohabitat and genetic study

Using a novel combination of palaeohabitat modelling and genetic mixture analyses, we identify and assess a sea-level driven recolonisation process following the Last Glacial Maximum (LGM). Our palaeohabitat modelling reveals dramatic changes in estuarine habitat distribution along the coast of California (USA) and Baja California (Mexico). At LGM (~20 kya), when sea level was ~130 m lower, the palaeo-shoreline was too steep for tidal estuarine habitat formation, eliminating this habitat type from regions where it is currently most abundant, and limiting such estuaries to a northern and a southern refugium separated by 1,000 km. We document the recolonisation of estuaries formed during post-LGM sea-level rise through examination of refugium-associated alleles and Approximate Bayesian Computation in three species of estuarine fishes. Results reveal sourcing of modern populations from both refugia, which admix in the newly formed habitat between the refuges. We infer a dramatic peak in habitat distribution and area between 15–10 kya. Overall, this approach revealed a previously undocumented dynamic and integrated relationship between sea-level change, coastal processes, and population genetics. These results extend glacial refugial dynamics to unglaciated subtropical coasts, and have significant implications for biotic response to predicted sea-level rise.