Loch Dughaill and in particular Loch Tay often showed notable high genomic divergence between ecomorphs for many of the associated SNPs for each trait. Additionally, the associated SNPs for both traits showed high DXY values compared to the background subsets at both of these lakes. While increased levels of DXY or FST compared to genomic background can be indicative of positive selection , they might also be expected for loci resisting introgression following secondary contact , as is likely the case in Loch Tay and Loch Dughaill . The associated SNPs we found are widespread across the genome (Figure 2) indicating these are not single linked regions of divergence as found in studies on Atlantic cod and rainbow trout but instead are diffused and highly polygenic, similar to patterns for body shape in lake whitefish .

Functional genomic regions for head and body shape:

Roughly half of the associated SNPs identified for each of head and body shape were found within or proximal to an annotated gene in the charr genome. A number of the GO terms that appeared as significantly overrepresented or enriched in our study have been identified in other studies investigating adaptive divergences or parallel evolution in various fish species. Odontogenesis (GO:0042476), sensory perception of sound (GO:0007605), blood vessel remodelling (GO:0001974), response to muscle activity (GO:0014850), ventricular trabecula myocardium morphogenesis (GO:0003222), common-partner SMAD protein phosphorylation (GO:0007182), cellular response to ethanol (GO:0071361), and neuromuscular synaptic transmission (GO:0007274) have shown significance in other Arctic charr studies investigating ecomorph divergence . The GO terms for associative learning (GO:0008306), regulation of cell shape (GO:0008360), and UDP-glucuronate biosynthetic process (GO:0006065) also appear in overrepresented groups in a study on the divergence of a sympatric lake whitefish species pair (Corgeonus clupeaformis ) in the USA . Finally, in pupfishes (Cyprinodon. sp. ), the divergent expression of a number of genes involved in cranial skeletal system development was seen between different trophic specialists with the GO term for this process (GO:1904888) significant in our study . Differences in ossification rate have been related to adaptive morphological differentiation in other freshwater fish and the over enrichment or overexpression of genes related to formation of various bones in our study indicates a similarly important role in adaptive divergences between ecomorphs of Arctic charr . Indeed, previous work has noted the importance of differences in bone structure and sizes between different ecomorphs of Arctic charr .
The QTL database that we have developed allows us to explore whether rapid replicated diversification of ecomorphs in different salmonid species is underlined by the use of the same functional regions as has been previously suggested for salinity tolerance . Our results suggest that this is true to some extent with QTLs related to body shape in lake trout and whitefish found in proximity to SNPs that we identified as being associated with phenotypic differences in Arctic charr ecomorphs. Whilst we only identified a small number of QTLs located near the associated SNPs, this is line with other work which suggests that shared basis for ecomorph divergence across species may be limited . This QTL marker database will be a valuable resource for future salmonid research.