PCA infile and scripts

This compressed directory contains the phenotype infile (resid-sizeANDcoord-6vi17-subgroups-NoNA.csv) used for the PCA, as well as the PCA script PCA_sizeANDposition-final.R and an additional script defining the Bayesian model that was used for the 95% PC mean ellipses (fitEllipse.R)

Variant calling script

Shell script used for variant calling with samtools and bcftools

Gemma BSLMM infiles

This compressed directory contains the infiles for the genomic prediction/genome wide association mapping analysis. These are in BIMBAM format and include mean genotype (*geno*) and phenotype (*pheno*) files. We include files for size and position (*coord*) traits. Files are included for all biological levels we considered and for all groups: AN = L. anna, GNP = L-ID-GNP, ID = L. idas, JA = Jackson hole, ME = L. melissa east, MW = L. melissa west, RI = L. anna ricei, SIN = L-ME-SIN, SN = Sierra Nevada, WA - Warner Mt., and YBG = L-AN-YBG. Files without prefixes are for the species-comples level analysis. We have also included a perl wrapper script used to fit the BSLMM in gemma = forkRunGemmaPop.pl

Genetic data (filtered vcf file)

This text file contains the filtered genetic data (SNP set) in variant call format (vcf). This included genetic data for 78,567 SNPs

G- and P-matrix infiles and analyses

This compressed directory includes the genome estimated breeding values from genomic prediction (catbv*csv) for each groups, phenotypic data for P-matrixes (resid*) and a R script that runs analyses on these files, matcomp.R (which has annotations throughout). The R script runs the comparisons of P and G-matrixes and the evolvability/constraint analyses, as well as making related plots

Genomic prediction script

Perl wrapper script (forks to run multiple jobs) to run the genomic prediction option in gemma. This is sued after the standard BSLMM has been fit

Lycaeides melissa linkage map

Text file describing the L. melissa linkage map. There are three columns giving the linkage group (lg), scaffold number (scaf, these match the reference genome scaffold names), and position (pos) in centi Morgans along the relevant linkage group

QLT summaries and scripts

This compressed directory contains three files. sortedCombinedPips.txt contains the SNP posterior inclusions probabilities for all traits and biological levels, averaged across MCMC chains. This is the needed input for the other two files/scripts. pipColocal.R quanties correlations in PIPs across traits, and plotPipLgs.R runs the QTL number/density analyses per LG, along with making some plots

Scripts for processing BSLMM output

This compressed directory contains a series of perl scripts used to summarize the output from gemma's BSLMM. The calpost* scripts summarize the hyperparameter estimates (e.g., pve, pge, etc.), get Bvs* extract breeding values from the standard BSLMM (based only on the polygenic term), getPrdtBvs* extract breeding values from genomic prediction that include SNPs with measurable effects, and grabCalsEffects* extract and summarize the SNP effect estimates. All summaries are across MCMC chains

Variant filtering scripts

This compressed directory contains three perl scrips used for filtering and processing the genetic data (i.e., the vcf file). morefilter_filtered2x-70_varsLycGwa.vcf was generated by running the two filter scripts. Most filters described in the paper are impelemented in the main script, vcfFilter.pl, which was run first. The second script, filterSomeMore.pl applies maximum coverage filters and a filter to drop variants that are near each other (within 3 bp in this case). The final scrips, vcf2gl.pl, extracts the genotype likelihoods from the vcf file