Unravelling the genomic basis of sympatric lake trout (Salvelinus namaycush) morphs in Great Bear Lake, Canada

Background/Question/Methods

Studying intraspecific variation at the phenotypic and genomic level has become increasingly important not only for eco-evolutionary processes but for predicting the short- and long-term responses of species to novel and changing environments. Sympatric morphs, such as those often observed in salmonid fishes, represent a valuable component of biodiversity and offer a great opportunity to uncover the mechanisms that give rise to such variation and their stage along the speciation continuum. Lake trout (Salvelinus namaycush) is a large, slow growing and long-lived, mainly lacustrine species important for commercial, recreational, and Indigenous subsistence fisheries in North America. Although morph diversification has been strongly associated with depth partitioning, lake trout in Great Bear Lake represents a remarkable example of intraspecific diversification in shallow water (< 30m) with at least four ecotypes varying in morphology, life history, ecology, and habitat use. Does this variation extend to deep-water and what is the genomic basis of diversification? To address these questions, we collected 400 lake trout samples covering all five arms (spatial axis) and various depth zones (vertical axis; 0-150m). Phenotypic variation was assessed with geometric-morphometric analysis of photographs. For genomic diversity and structure we prepared individual DNA libraries for low-coverage Whole Genome Sequencing (lcWGS).

Results/Conclusions

Preliminary results, from analyzing over 18 million polymorphic sites (SNPs), supported the occurrence of three genomic clusters. Interestingly, the majority of sampled individuals showed evidence of extensive admixture with the overall genomic structure being weakly associated with either spatial and vertical axes. At the phenotypic level, the geometric-morphometric analyses identified four ecotypes which were also weakly associated with a depth gradient. We found some evidence for genomic distinctiveness of larger lake trout ( >900mm) despite little overall genomic differentiation among the main sympatric morphs. Overall, these results suggest ongoing gene flow with rather weak divergent selection depending on environmental contexts. Nevertheless, the genomic resolution offered by lcWGS and adopted in this study allows for genome-wide association analyses to further test whether plasticity and/or a few key genes of large effect drive morph diversification. With overharvesting being a major thread, genomic tools can add valuable information on delineating population structure and their relative contribution to mixed-stock harvests. A change is gonna come for the management and conservation of Great Bear Lake’s exceptional intraspecific diversity of lake trout, important for recreational and Indigenous subsistence fisheries.