SsalLocSeln_raw_results.tar

Tar.gz archive containing raw output files from analyses

SsalLocSeln_ggplot.tar

Tar.gz archive containing ggplot2 code and data files for making the figures in the manuscript

SsalLocSeln_genotypes.tar

Tar.gz archive containing genotype data in Plink PED format

SsalLocSeln_results.tar

Tar.gz archive containing final results for all analyses and all SNPs, including package-specific significance tests

Aykanat_et_al_Dryad_files

FILES IN THE BUNDLE: mainparams: parameter file for the structure runs. NOTE that k and n are "number of populations" and "number of replicate", respectively and appropriate number should be used instead of these letters when running the software. teno_MS = The GenABEL format main file. The file includes genotype (n= 2874 SNPs), phenotype as well as location information from 662 individuals, which is sufficient to replicate the main results. Structure raw files.zip = Includes raw results from the structure analysis which is sufficient to replicate all structure related results

PPC_correction.tar.gz

This archive (700MB) contains the following data files for Pritchard et al. (2016), used for calculating and applying the PPC correction: R_code for_PPC_correction.txt: Annotated R code for calculating PPC correction coefficients from data in CALL.txt and INT.txt. CALL.txt: File of genotype calls. INT2.txt: File of A and B allele probe intensities. PPC_correction_coefficients.csv: PPC correction coefficients returned for each SNP. See README file in archive for further information

Genotyping_allelotyping.tar.gz

This archive contains the following data files for Pritchard et al. (2016): B_allele_freq_Naatamo_pools.csv: Uncorrected B allele frequencies for the Naatamo pools. B_allele_freq_New_Teno_pools.csv: Uncorrected B allele frequencies for the New Teno mainstem pools. B_allele_freq_Teno_Finnmark_pools.csv: Uncorrected B allele frequencies for the old Teno and Finnmark pools. B_allele_freqs_all_pops.csv: Corrected B allele frequencies for all populations. Individuals_and_pooling.csv: Details of genotyped individuals. Pritchardetal_genotypes.map; Pritchardetal_genotypes.ped: Individual genotypes in PLINK format. See README file in archive for further information

Hybrid_class_assignment.tar.gz

This archive contains code used for hybrid class assignments, and hybrid class assignment results for Pritchard et al. (2016): Code_for_hybrid_class_assigments.txt: code used to generate NewHybrids and Structure input files and parse results. Folder "Extra_required_files" contains text files required by the above code. Folder "Results" contains hybrid class assignment results. See README file in archive for further information

Bayescan_Fdist2.tar.gz

This archive contains files used by Pritchard et al. (2016) for Fst outlier analyses: Index.txt - index of SNPs. Bayescan*.in - Bayescan input files, SNPs in index order. Fdist*.in -Fdist2 input files, SNPs in index order. datacal.c; fdist2.c; Original_README_fdist2 - Fdist2 source code & information. R_code_for_analysing_Fdist2_output.txt - modified R code from Lotterhos & Whitlock (2014). See README file in archive for further information

Code_and_data_for_figures.tar.gz

This archive contains the ggplot2 code and data files required for making all the figures in Pritchard et al. (2016): Code_for_ggplot.txt contains annotated ggplot code for making figures. See README file in archive for further information