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.