Data from: How sea-level change mediates genetic divergence in coastal species across regions with varying tectonic and sediment processes

Plate tectonics and sediment processes control regional continental shelf topography. We examine the genetic consequences of how glacial-associated sea-level change interacted with variable near-shore topography since the last glaciation. We reconstructed the size and distribution of areas suitable for tidal estuary formation from the Last Glacial Maximum, ~20 thousand years ago, to present from San Francisco, California, USA (~38 °N) to Reforma, Sinaloa, Mexico (~25 °N). We assessed range-wide genetic structure and diversity of three co-distributed tidal estuarine fishes (California Killifish, Shadow Goby, Longjaw Mudsucker) along ~4,600 km using mitochondrial control region and cytB sequence, and 16–20 microsatellite loci from a total of 524 individuals. Results show that glacial-associated sea-level change limited estuarine habitat to few, widely separated refugia at glacial lowstand, and present-day genetic clades were sourced from specific refugia. Habitat increased during postglacial sea-level rise and refugial populations admixed in newly formed habitats. Continental shelves with active tectonics and/or low sediment supply were steep and hosted fewer, smaller refugia with more genetically differentiated populations than on broader shelves. Approximate Bayesian computation favored the refuge-recolonization scenarios from habitat models over isolation by distance and seaway alternatives, indicating isolation at lowstand is a major diversification mechanism among estuarine (and perhaps other) coastal species. Because sea-level change is a global phenomenon, we suggest this top-down physical control of extirpation-isolation-recolonization may be an important driver of genetic diversification in coastal taxa inhabiting other topographically complex coasts globally during the Mid- to Late Pleistocene and deeper timescales

ABC input file: Qyc, Gulf

DIYABC input file for Q. y-cauda Gulf sample

allelic-richness-test-steep-broad

Data used for linear mixed model to test whether populations on broad coasts have higher allelic richness than narrow coasts (they do)

PRSB_qyc_forDIYABC_3pops

input data file for DIYABC v. 2 for Quietula y-caud

Microsatellite allele copy number data

allele copy number data for all 3 species used for the genetic Discriminant Function Analysis ('genetic DFA). Microsatellite fragment lengths are alleles, and individuals can have 0 copies of an allele, 1 copy of an allele (heterozygous) or 2 copies of an allele (homozygous)

ABC input file: Fpa

Input file for DIYABC2 for F. parvipinni

ABC input file: Gmi, Gulf

DIYABC input file for G. mirabilis Gulf sample

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 recolonization 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 the LGM (approx. 20 kya), when sea level was approximately 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 1000 km. We assess the recolonization 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 area between 15 and 10 kya with subsequent decline. 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