Because of their vital role in foraging and swimming, the genetics of head and body morphology has been explored as QTL studies in many fish species, including salmonids (Boulding et al., 2008; Küttner et al., 2014; Laporte et al., 2015; Smith et al., 2020). For example, in lake whitefish, as many as 138 different quantitative trait loci (QTLs) related to body shape have been identified, implying that the trait is highly polygenic in this species (Laporte et al., 2015). In other species, body shape has been found to be less polygenic, with a small number of QTLs identified related to benthic-limnetic differences between ecomorphs of lake trout (Smith et al., 2020) and a single region that differentiates ecomorphs in Atlantic cod (Gadus morhua) (Hemmer-Hansen et al., 2013). However, the extent to which parallel phenotypes have the same genomic underpinnings across replicates seems to vary greatly between species and locality. Studies in three-spine stickleback (Gasterosteus aculeatus), rainbow trout (Oncorhynchus mykiss), and sockeye salmon (Oncorhynchus nerka) all suggest that while some genetic variation that underlies morphological variation can be shared across replicates, this is rarely the case across the species’ entire range and the degree of genetic parallelism that is shared is often low (Fang et al., 2020; Larson et al., 2019; Weinstein et al., 2019). Often only a few key genes or loci are shared across replicates, and in some cases, they underlie morph differentiation in multiple species (Jacobs et al., 2017; Salisbury & Ruzzante, 2021).