Montane refugia predict population genetic structure in the Large-blotched Ensatina salamander

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

PartitionFinder infile

Input file for PartitionFinder analysis

Data from: Montane refugia predict population genetic structure in the Large-blotched Ensatina salamander

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

All SDM points

This file contains latitude and longitude coordinates for the 91 unique localities used to construct species distribution models

Infile for SGoF+ analysis

Input 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

Alignment phylip format

MtDNA alignment in phylip format for PartitionFinder analysis

Structure infile

This is the input file for Structure analyses. The second column contains sample group information used as a prior. Missing data are represented by -9

Geneland individual labels

This is the file of individual labels for Geneland analyses in the same order as the genotypes and coordinates files

MrBayesDir infile

Nexus file for modified version of MrBayes 3.1.2 with Dirichlet priors on branch lengths. Partitioning scheme and substitution models determined using PartitionFinder

IBDWS infile for IBR regression

Matrixes 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