Adaptation in Sitka Spruce
Studies such as GWAS are ideally suited to conifers due to the characteristics of their genome which is marked by a slow rate of evolution and low diversity despite the large range of ecological niches the populations occupy (Farjon, 2010). The low rates of LD and the large range of physical distance slow the rate of evolution and lead to clines of locally adapted genotypes. This, however, is ideal for GEA and GWAS studies, as high LD is problematic for the discovery of loci via GWAS, due to the linkage of adaptive loci causing false discovery (Christoforou et al., 2012). High LD does however necessitate very high marker density. However linkage of adaptive loci can lead to evolution by adaption through divergence, so harsh LD filtering is also not recommended. Here we have discovered 694 loci that have positive effects on the growth of spruce. We have discovered a split between the northern and southern populations shows loci involved with increases in height in the southern population. This is similar to what has been presented previously (Mimura & Aitken, 2010), with reductions in growth rate in northern populations and slowing of bud set and burst. The allelic distribution pattern suggests local adaptation in the northern and southern populations. The distribution of these adaptive loci suggests these alleles occurred in the farthest extent north and are naturally selected until it meets the southern range in central British Columbia. In the southern range, natural selection favours loci with positive correlations toward height. This highlights a range ideal for breeding programs that focus on height.
Previous studies in conifers have shown subtle shifts in MAF responsible for adaptation (De La Torre et al., 2019). Here we see adaptive loci with very high MAF compared to overall MAF. This indicates recent local adaption due to the non-conserved alleles (Günther & Coop, 2013). This would agree with what is seen previously with post glaciation spread of Sitka spruce creating the need for local adaptation (Byrne et al., 2022; Gapare et al., 2005). Here we found shifts in MAF associated with some climactic adaptive alleles. Traits identified as associated with southern conditions (Fig.6) had subtle to moderate increases in MAF in southern ranges indicating recent adaption. The same is seen in northern ranges where traits associated with cold and snowfall saw subtle increases in MAF. This subtle to moderate change in MAF is characteristic of adaptations in conifers, as shown in Picea glauca and Pinus taeda (De La Torre et al., 2019; Hornoy et al., 2015). This indicates local adaption across a cline.