DOI: 10.5061/dryad.gm1td
title: Data from: How sea-level change mediates genetic divergence in coastal species across regions with varying tectonic and sediment processes

description: 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.
description: Genbank-mtDNA-accessionsAccession IDs for all DNA sequences uploaded to Genbank for this projectallelic-richness-test-steep-broadData used for linear mixed model to test whether populations on broad coasts have higher allelic richness than narrow coasts (they do).Mol_Ecol_Allelic_Richness_Broad-steep-resultsResults in HTML format from linear mixed model run in JMP showing that allelic richness is higher on broad coasts than narrow coasts.Mol_Ecol_Allelic_Richness_Broad-steep.htmlRefugia-geospatial-size-dataThis is all the attribute data used for discriminant function analyses and generalized linear models to determine: 1) the predictors of present-day species distributions; 2) whether lowstand size attributes were similar to present-day size attributes; 3) relative size of habitats on steep versus broad coasts.Geospatial-size-data.xlsxSample sitesGoogle Earth file of sampling localitiesMolEcolsites.kmzMicrosat data: Fundulus parvipinnisFull microsatellite dataset in STRUCTURE format for F. parvipinnisFMAdata3Oct2012bCONVERT.strMicrosat data: Gillichthys mirabilisFull microsatellite dataset in STRUCTURE format for G. mirabilisGmi_fulldata_7May2015_orderfixed.strMicrosat data: Quietula y-caudaFull microsatellite dataset in STRUCTURE format for Quietula y-caudaQMA_fulldata_7May2015_orderfixed.strABC input file: FpaInput file for DIYABC2 for F. parvipinnisFMA_test_PACIFIC.mssABC input file: Gmi, PacificDIYABC input file for G. mirabilis Pacific populationsGMA_MolEcol_DIYABC_pac_Scen1.mssABC input file: Gmi, GulfDIYABC input file for G. mirabilis Gulf samplesGMA_MolEcol_DIYABC_Gulf.mssABC input file: Qyc, PacificDIYABC input file for Q. y-cauda Pacific samplesQMA_PAC_7May2015_orderfixed_forDIYABC.mssABC input file: Qyc, GulfDIYABC input file for Q. y-cauda Gulf samplesQMA_GULF_DIYABC_test_Refugia_missingQMA9,28.mss