Genomic signatures of adaptive divergence among lake trout (Salvelinus namaycush) ecomorphotypes

Adaptive radiations generate biodiversity via ecological specialization, with the emergence of ecotypes representing an intermediate step toward speciation. We investigated the genomic basis of diversification in Lake Superior Lake Trout (Salvelinus namaycush), which exhibit three distinct ecomorphotypes—leans, siscowets, and humpers—each adapted to habitats at different depths. We identified 601 single nucleotide polymorphisms within multiple islands of divergence where allele frequencies were highly differentiated between ecomorphotypes. Some of the strongest signals of adaptive divergence were within, or near, genes in the Wnt signaling pathway (Wnt5a, Frizzled-1-like, Dishevelled 2-like), suggesting this highly conserved pathway associated with early morphological development likely played a key role in the emergence of ecomorphological variation. Additional candidate genes related to lipid metabolism, circadian rhythm, immune function, eye development, and other traits were also identified. Population genetic analyses revealed that the primary axis of genetic differentiation within the Lake Superior metapopulation was between ecomorphotypes, rather than between geographic locations, prior to and during the 1990s. Individual ancestry coefficients suggest that hybridization occurred primarily between leans and humpers or humpers and siscowets, but rarely between leans and siscowets. Historical samples indicate that hybridization rates likely increased between the 1960s and 1990s, providing a mechanism for the previously documented genetic homogenization among ecomorphotypes and highlighting challenges associated with conserving ecotypic diversity.