Genotype Data
We had previously generated GBS data to assess genetic diversity and structure of a diverse population of Picea sitchensis (Byrne et al., 2022) so were able to utilize that dataset for this study. GBS data from 1177 genotypes of the IUFRO population, representing 80 sampling points, were therefore obtained from NCBI BioProject PRJNA852515 (Byrne et al., 2022). This data was generated with 150bp paired-end GBS using Pst1-Apek1 following (Elshire et al., 2011). Sequences were aligned to the Q903-v1-1000 plus Sitka spruce genome (GCA_010110895.2) (Gagalova et al., 2022) using BWA-mem with default parameters (Li & Durbin, 2009). Variant calling was completed using SAMtools v1.9 mpileup (Li et al., 2009). VCFtools was used for filtering (Danecek et al., 2021). Indels were removed, multi-allelic SNPs were removed, minimum genotype quality was filtered to 20, read depth was filtered to 5, max missing data was filtered to 0.7 and MAF was set to 0.05. This resulted in 66974 loci which were transformed into an allelic matrix for further study.