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

 

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Title Geneland coordinates
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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
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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
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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
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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
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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 Individual sample names have been replaced by x and y coordinates in meters.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
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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
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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
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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
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Description MtDNA alignment in phylip format for PartitionFinder analysis.
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Title PartitionFinder infile
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Description Input file for PartitionFinder analysis.
Download partition_finder.cfg (545bytes)
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Title Infile for SGoF+ analysis
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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
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Description This is the complete data file.
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Title All SDM points
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Description This file contains latitude and longitude coordinates for the 91 unique localities used to construct species distribution models.
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Title subset point localities
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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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When using this data, please cite the original publication:

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. http://dx.doi.org/10.1111/mec.12196

Additionally, please cite the Dryad data package:

Devitt TJ, Cameron Devitt SE, Hollingsworth BD, McGuire JA, Moritz C (2013) Data from: Montane refugia predict population genetic structure in the Large-blotched Ensatina salamander. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.k9g50
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