Data from: Sun skink landscape genomics: assessing how microevolutionary processes shape genetic and phenotypic diversity across a heterogeneous and fragmented landscape

Barley AJ, Monnahan PJ, Thomson RC, Grismer LL, Brown RM

Date Published: March 12, 2015

DOI: http://dx.doi.org/10.5061/dryad.v6726

 

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Title Allele Frequency Data
Downloaded 26 times
Description This file contains allele frequency data for each of the 14 populations used in the fst-pst analyses. The format of the file format for each population is as follows, for each line: locus number, the total number of genes in the population for the locus, the number of alleles for the locus, the number of copies of each allele in the population.
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Title Barcodes
Downloaded 6 times
Description This file contains information on the barcode sequence assigned to each individual in our study.
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Title Structure
Downloaded 8 times
Description This is a structure formatted file containing genotypic data for each individual used in the study.
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Title BEDASSLE
Downloaded 29 times
Description This is an R object file that was used to run the BEDASSLE analyses.
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Title Bootstrap
Downloaded 12 times
Description This R script contains the code for the bootstrapping procedure for obtaining confidence intervals for the global pst data as described in the manuscript.
Download Bootstrap_Phenos.R (1.24 Kb)
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Title Calculate_Fsts
Downloaded 14 times
Description This python script contains the code for calculating global Fst's for each locus as described in the manuscript.
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Title FastSimCoal
Downloaded 20 times
Description This archive contains the files used to run fastsimcoal2 to obtain the isolation-migration parameter estimates as in the manuscript.
Download FastSimCoal.tar.gz (8.117 Kb)
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Title Fst_Bootstrap
Downloaded 7 times
Description This R script contains the code for calculating bootstrapped confidence intervals for global Fst as described in the manuscript.
Download Fst_boot.R (187 bytes)
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Title IBDWS
Downloaded 7 times
Description This text file contains the distance matrix information used for testing for isolation by distance using the Isolation by distance web server.
Download IBDWS_input.txt (5.943 Kb)
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Title Maxent ASCII
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Description This is the habitat suitability output file from Maxent.
Download multifasciata.asc (193.2 Mb)
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Title Morphological Data
Downloaded 10 times
Description This file contains the morphological data used for calculating Psts.
Download MorphData.csv (15.35 Kb)
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Title Population Coordinates
Downloaded 5 times
Description This file contains the geographic coordinates (WGS84) for each population used in the landscape genetic analyses.
Download PopulationCoordinates.csv (625 bytes)
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When using this data, please cite the original publication:

Barley AJ, Monnahan PJ, Thomson RC, Grismer LL, Brown RM (2015) Sun skink landscape genomics: assessing how microevolutionary processes shape genetic and phenotypic diversity across a heterogeneous and fragmented landscape. Molecular Ecology 24(8): 1696-1712. http://dx.doi.org/10.1111/mec.13151

Additionally, please cite the Dryad data package:

Barley AJ, Monnahan PJ, Thomson RC, Grismer LL, Brown RM (2015) Data from: Sun skink landscape genomics: assessing how microevolutionary processes shape genetic and phenotypic diversity across a heterogeneous and fragmented landscape. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.v6726
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