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.