Signatures of adaptation
These associations, indicating local adaptation, were found despite high
levels of gene flow among populations across the distribution as it is
common in eucalypt species (Supple et al., 2018; Murray et al., 2019;
Ahrens et al., 2019a; Jones et al., 2002). Low differentiation among
populations indicates that application of EAA in jarrah is appropriate
to identify alleles putatively under selection. Overall, the distinct
EAA approaches identified different sets of SNPs as potential candidates
under selection for each climate variable, which is expected given the
different statistical frameworks of the methods (Forester et al., 2018;
Caye et al., 2019). One limitation of EEAs is the identification of SNPs
that are found to be under selection but are in fact not (false
positives). While false positives are an inherent limitation in EAA
studies, it is considered that they are useful in consistently
identifying adaptive SNPs, even if the adaptive coefficient is small
(Ahrens et al., 2021a). We focus our interpretation on SNPs that are
within gene space to lessen the impact of false positives, despite that
candidate SNPs identified outside of gene space could also be true
positives. For instance, SNPs could be in promoter regions, regions that
are known to have high proportion of adaptive variants (Wittkopp &
Kalay, 2012), SNPs could share a large haplotype with genes that are
under selection (Todesco et al., 2020), or SNPs could be in linkage
disequilibrium with adaptive SNPs. Future work should focus on improving
the genomic resources of the species to elucidate these complex issues
that are beyond the scope of this work.