DOI: 10.5061/dryad.k9g50
title: Data from: Montane refugia predict population genetic structure in the Large-blotched Ensatina salamander

description: Understanding the biotic consequences of Pleistocene range shifts and
 fragmentation remains a fundamental goal in historical biogeography and
 evolutionary biology. Here, we combine species distribution models (SDM)
 from the present and two late Quaternary time periods with multilocus
 genetic data (mitochondrial DNA and microsatellites) to evaluate the
 effect of climate-induced habitat shifts on population genetic structure
 in the Large-blotched Ensatina (Ensatina eschscholtzii klauberi), a
 plethodontid salamander endemic to middle and high-elevation conifer
 forest in the Transverse and Peninsular Ranges of southern California and
 northern Baja California. A composite SDM representing the range through
 time predicts two disjunct refugia, one in southern California
 encompassing the core of the species range and the other in the Sierra San
 Pedro Mártir of northern Baja California at the southern limit of the
 species range. Based on our spatial model, we would expect a pattern of
 high connectivity among populations within the northern refugium and,
 conversely, a pattern of isolation due to long-term persistence of the
 Sierra San Pedro Mártir population. Our genetic results are consistent
 with these predictions based on the hypothetical refugia in that (i)
 historical measures of population connectivity among stable areas are
 correlated with gene flow estimates; and (ii) there is strong geographical
 structure between separate refugia. These results provide evidence for the
 role of recent climatic change in shaping patterns of population
 persistence and connectivity within the Transverse and Peninsular Ranges,
 an evolutionary hotspot.
description: Geneland
 coordinatesThis is the spatial
 coordinate file (in UTM format) for Geneland analyses. There is one line
 per individual and two columns representing the x-axis and y-axis
 coordinate. Original latitude/longitude coordinates were collected in the
 field using a hand-held GPS (WGS84 datum) and subsequently converted to
 UTM format in ArcView.Geneland
 genotypesThis is the
 microsatellite genotypes file for Geneland analyses. There is one line per
 individual with 20 columns (diploid, codominant data). Missing data are
 represented by 000.Geneland individual
 labelsThis is the file of
 individual labels for Geneland analyses in the same order as the genotypes
 and coordinates files.Structure
 infileThis is the input file
 for Structure analyses. The second column contains sample group
 information used as a prior. Missing data are represented by
 -9.structure.txtGenepop infileThis is the input file for Genepop v4 analyses. Individual sample names have been replaced by x and y coordinates in meters. Microsatellite and mitochondrial data are included. Missing data are represented by 000.Genepop.txtMrBayesDir infileNexus file for modified version of MrBayes 3.1.2 with Dirichlet priors on branch lengths. Partitioning scheme and substitution models determined using PartitionFinder.mbdir.nexIBDWS infile for IBD regressionMatrixes of geographic distance (in meters; above diagonal) and genetic distance (below diagonal) for Isolation by Distance Web Service analysis. Genetic distances calculated as Fst/(1-Fst) in Genepop v4.2.IBDWS euclidean.txtIBDWS infile for IBR regressionMatrixes of resistance distance (above diagonal) and genetic distance (below diagonal) for Isolation by Distance Web Service analysis. Genetic distances calculated as Fst/(1-Fst) in Genepop v4.2.IBDWS resistance.txtAlignment phylip formatMtDNA alignment in phylip format for PartitionFinder analysis.klauberi.phyPartitionFinder infileInput file for PartitionFinder analysis.partition_finder.cfgInfile for SGoF+ analysisInput file for sequential goodness-of-fit test to correct for multiple comparisons implemented in SGoF+. The file consists of an integer indicating the total number of tests (102) and after it two columns with pairs of identifiers and p-values.PvalSGoF.datFull data fileThis is the complete data file.data full.txtAll SDM pointsThis file contains latitude and longitude coordinates for the 91 unique localities used to construct species distribution models.all point localities.csvsubset point localitiesThis file contains latitude and longitude coordinates for the 23 localities representing a subset of the total data used to construct species distribution models. California records were filtered to one locality record per 10 km2 grid cell, resulting in a total of N=23 records. We performed this analysis to investigate whether the greater number of records in California unduly influenced the model.