Introduction:

Parallel evolution is an evolutionary process and outcome by which similar phenotypes arise and establish in multiple independent populations in separate environments (Bolnick et al., 2018; Elmer & Meyer, 2011; Schluter, 1996). These replicate evolutionary outcomes suggest that similar environments impose similar selective pressures on organismal phenotypes, with only a small number of phenotypic solutions favoured in that context. While the existence of parallel phenotypes is well established in natural populations (Oke et al., 2017; Siwertsson et al., 2013), the extent to which those are associated with similarly shared genomic underpinnings is rarely examined (Magalhaes et al., 2021; McGirr & Martin, 2018; Ravinet et al., 2016). Indeed, the appearance of the same phenotypes through parallel evolution processes does not mean that the same genomic processes underpin those similar evolutionary outcomes across replicates (Conte et al., 2012; Elmer & Meyer, 2011). Similar phenotypic outcomes could result from alternative genetic pathways. This might arise because of differing demographic histories (Elmer et al., 2014), variable genetic backgrounds (Arendt & Reznick, 2008; Kowalko et al., 2013) or the involvement of alternative splicing, differential gene expression or post-translational modifications resulting in phenotypic parallelism (Filteau et al., 2013; Jacobs & Elmer, 2021; McGirr & Martin, 2018).
One classic example of parallel evolution is the replicated divergence across northern freshwater lakes of distinct trophic specialists, also known as ecomorphs or ecotypes. These occur abundantly in salmonid fishes in recently glaciated lakes, such as lake whitefish (Coregonus clupeaformis) (Landry et al., 2007), lake trout or lake charr (Salvelinus namaycush) (Baillie et al., 2016), and Arctic charr (Salvelinus alpinus) (Doenz et al., 2019; Jensen et al., 2017). In Arctic charr, ecomorphs associated with divergence along the depth axis and ecological niche, typically forming pelagic and benthic foraging specialists (Elmer, 2016; Klemetsen, 2010). Two key traits involved in this divergence are head shape and body shape, both having functional significance; head shape being important for foraging and prey specialisation and body shape important for swimming behaviour and niche use (Adams & Huntingford, 2002; Skoglund et al., 2015). Additionally, ecomorphs often differ in other complex traits such as body size, colouration and spawning time (Garduño-Paz et al., 2012; Jonsson & Jonsson, 2001).