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dc.contributor.author Devitt, Thomas J.
dc.contributor.author Cameron Devitt, Susan E.
dc.contributor.author Hollingsworth, Bradford D.
dc.contributor.author McGuire, Jimmy A.
dc.contributor.author Moritz, Craig
dc.coverage.spatial California
dc.coverage.spatial United States of America
dc.coverage.spatial Baja California
dc.coverage.spatial Mexico
dc.coverage.temporal Pleistocene
dc.coverage.temporal Holocene
dc.coverage.temporal Quaternary
dc.date.accessioned 2012-12-06T20:00:08Z
dc.date.available 2012-12-06T20:00:08Z
dc.date.issued 2013-02-04
dc.identifier doi:10.5061/dryad.k9g50
dc.identifier.citation Devitt TJ, Cameron Devitt SE, Hollingsworth BD, McGuire JA, Moritz C (2013) Montane refugia predict population genetic structure in the Large-blotched Ensatina salamander. Molecular Ecology 22(6): 1650–1665.
dc.identifier.uri http://hdl.handle.net/10255/dryad.44586
dc.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.
dc.relation.haspart doi:10.5061/dryad.k9g50/1
dc.relation.haspart doi:10.5061/dryad.k9g50/2
dc.relation.haspart doi:10.5061/dryad.k9g50/3
dc.relation.haspart doi:10.5061/dryad.k9g50/4
dc.relation.haspart doi:10.5061/dryad.k9g50/5
dc.relation.haspart doi:10.5061/dryad.k9g50/6
dc.relation.haspart doi:10.5061/dryad.k9g50/7
dc.relation.haspart doi:10.5061/dryad.k9g50/8
dc.relation.haspart doi:10.5061/dryad.k9g50/9
dc.relation.haspart doi:10.5061/dryad.k9g50/10
dc.relation.haspart doi:10.5061/dryad.k9g50/11
dc.relation.haspart doi:10.5061/dryad.k9g50/12
dc.relation.haspart doi:10.5061/dryad.k9g50/13
dc.relation.haspart doi:10.5061/dryad.k9g50/14
dc.relation.isreferencedby doi:10.1111/mec.12196
dc.relation.isreferencedby PMID:23379992
dc.subject Amphibians
dc.subject Climate Change
dc.subject Phylogeography
dc.subject Landscape Genetics
dc.subject Conservation Genetics
dc.subject Niche Modelling
dc.title Data from: Montane refugia predict population genetic structure in the Large-blotched Ensatina salamander
dc.type Article *
dwc.ScientificName Ensatina eschscholtzii klauberi
dwc.ScientificName Ensatina klauberi
dc.contributor.correspondingAuthor Devitt, Thomas J.
prism.publicationName Molecular Ecology

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To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data.

Title Geneland coordinates
Downloaded 33 times
Description This 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.
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Title Geneland genotypes
Downloaded 38 times
Description This 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.
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Title Geneland individual labels
Downloaded 14 times
Description This is the file of individual labels for Geneland analyses in the same order as the genotypes and coordinates files.
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Title Structure infile
Downloaded 18 times
Description 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.
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Title Genepop infile
Downloaded 15 times
Description This 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.
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Title MrBayesDir infile
Downloaded 5 times
Description Nexus file for modified version of MrBayes 3.1.2 with Dirichlet priors on branch lengths. Partitioning scheme and substitution models determined using PartitionFinder.
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Title IBDWS infile for IBD regression
Downloaded 5 times
Description Matrixes 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.
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Title IBDWS infile for IBR regression
Downloaded 4 times
Description 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.
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Title Alignment phylip format
Downloaded 5 times
Description MtDNA alignment in phylip format for PartitionFinder analysis.
Download klauberi.phy (57.96Kb)  View File Details
Title PartitionFinder infile
Downloaded 6 times
Description Input file for PartitionFinder analysis.
Download partition_finder.cfg (545bytes)  View File Details
Title Infile for SGoF+ analysis
Downloaded 4 times
Description 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.
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Title Full data file
Downloaded 12 times
Description This is the complete data file.
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Title All SDM points
Downloaded 7 times
Description This file contains latitude and longitude coordinates for the 91 unique localities used to construct species distribution models.
Download all point localities.csv (2.184Kb)  View File Details
Title subset point localities
Downloaded 5 times
Description This 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.
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