Input files for various analyses for population N1 of Timema cristinae -------------------------------------------------------------- PCA input file: N1_ordered_s099.maf0.01.unlinked_geno.csv (99% of individuals covered; filtered for MAF and linked SNPs) this file contains joint posterior probabilities for genotypes and allele frequencies collapsed into a single value per individual and locus (i.e., posterior mean of alternative allele dosage, ranging from zero to two) N1_EMallelefreqsPCAclusters.csv (allele frequency estimates for each PCA cluster obtained from genotype likelihoods using an iterative soft expectation-maximization algorithm) N1_ordered_s090.lowcovClustmm.txt (snps that were not covered/had low coverage in melanistic cluster and were excluded from some analyses are tagged with 1 in second column) fastPHASE input files: N1_All.maf0.01.lg8.inp or N1_PCA_nonOutl.maf0.01.lg8.inp (all individuals or without PCA outliers; for SNPs on LG8 filtered for MAF and low coverge in melanistic cluster, 90% of individuals covered) fastPHASE ran with the following flags: -KL10 -KU20 -Ki2 -em4 -Pp -q0.9 STRUCTURE input files: N1_All.ord626364.maf0.01.lg8.str (all individuals and SNPs on scaffolds 931, 318, and 1440; generated from fastPHASE output) N1_PCA_nonOutl.maf0.01.lg8.str (without PCA outliers and SNPs on LG8; generated from fastPHASE output) running STRUCTURE with local copy of software with bug for site-by-site output fixed: In structure.c, InitializeR, comment /* sumR[ind] = 0.0 */ and /* varR[ind] = 0.0 */, run make to compile --------------------------------------------------------------