Parallel evolution is an evolutionary process and outcome by which
similar phenotypes arise and establish in multiple independent
populations in separate environments . 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 , the
extent to which those are associated with similarly shared genomic
underpinnings is rarely examined . 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 . Similar phenotypic outcomes could result from
alternative genetic pathways. This might arise because of differing
demographic histories , variable genetic backgrounds or the involvement
of alternative splicing, differential gene expression or
post-translational modifications resulting in phenotypic parallelism .
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).