RAD_LDna_sample_Rcode

Compressed file with all necessary files (data, custom functions and R-code) to reproduce figures 3,4 and 5 in the original paper

Stickleback_r2

Pairwise r-squared values between all SNPs from file: "Stickleback_SNPs_filtered

Stickleback_SNPs_filtered

Filtered Stickleback SNP dat

R script and code for cluster-based association and QTL mapping

R script and code for cluster-based association and QTL mappin

RAD_baimaii_BLAT

BLAT results against the A. dirus draft genom (https://olive.broadinstitute.org/genomes/anop_diru_wrair2.1). Contains results from both RAD landscape genomics loci and the linkage map. Loci denoted with a "u" means the loci are unique to the linkage map

RAD_baimaii_RAW_alleles

This file contains RAW data from the software STACKS containing the RAD genotypes. The file "RAD_baimaii_RAW_numbers" contains the corresponding stack depths for each allele and these provided the raw data for quality filtering of the RAD sequence data set as described in the original paper. See also STACKs documentation for more details

RAD_baimaii_filtered_SNPs

This file contains all bi-allelic SNPs with a minimum allele frequency>0.1 from the RAD sequence data set: RAD_baimaii_filtered_fullsequence.tsv. The first part of the locus name give the RAD locus and the second part (after ".") gives the position of the SNP (starting from 1) along the 96 bp sequence. 3828 loci and 184 individuals

RAD_baimaii_RAW_numbers

This file contains RAW data from the software STACKS containing stack depths for the RAD genotypes for Anopheles baimaii. The file "RAD_baimaii_RAW_alleles" contains the corresponding alleles. These two files provided the raw data for quality filtering of the RAD sequence data set as described in the original paper. See also STACKs documentation for more details

RAD_baimaii_filtered_fullsequence

Same information as file "RAD_baimaii_filtered.tsv" except contains the full sequence (96 bps including restriction site overhang)

RAD_baimaii_filtered

Contains the filtered Anopheles baimaii RAD sequence data set. (184 individuals and 3008 RAD loci). The rad sequence here contains only sites that were polymorphic in the RAW data (e.g. file "RAD_baimaii_RAW_alleles.tsv"). Monomorphic loci have alleles called "consensus"