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.