Polymorphism in northern fishes is common, but the extent to which polymorphism occurs in Lake Trout Salvelinus namaycush, a species generally associated with low intraspecific variation, is not well known. This study examined the polymorphism of Lake Trout inhabiting the shallow‐water zones (≤30 m) of Great Bear Lake, Northwest Territories. We combined an analysis of classical morphometric and traditional linear measures with shape analysis (geometric morphometrics) to quantify morphological differences in body shape, head shape, and fin and body length measurements among 558 adult and 55 juvenile shallow‐water Lake Trout from Great Bear Lake. A UPGMA cluster analysis on adult Lake Trout distinguished three different morphs that coexist in the shallow‐water habitat. The most important differences among adult morphotypes were associated with head and fin measurements, whereas body shape variation was less distinct. A fourth, albeit rarer, morph was supported by a multivariate ANOVA that indicated significant differences in head and fin characteristics among the four groups. The divergent morphologies among the shallow‐water Lake Trout of Great Bear Lake are consistent with traits generally associated with feeding and swimming. In contrast to adult trout, no consistent patterns were found for juveniles, suggesting that phenotypic differences develop at a later stage. This unusual level of endemic diversity in the shallow‐water habitat expands our knowledge of Lake Trout diversity beyond the predominant focus on shallow‐ versus deepwater forms.

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Sympatric diversification in Lake Trout is generally linked to differences in habitat use (especially depth) as a result of foraging on different prey items. However, extensive sympatric divergence has taken place in the shallow waters (≤30 m) of Great Bear Lake, with multiple Lake Trout morphs varying in head and fin characteristics. To investigate diet partitioning as a potential explanatory mechanism for this diversification, we assessed trophic characteristics and relationships among four sympatric shallow‐water morphs of Lake Trout via analyses of fatty acids and stomach contents. Fatty acids and stomach contents both identified Lake Trout, Cisco and Mysis as key prey items in Lake Trout diets. Interestingly, terrestrial invertebrates were also seasonally important among morphs, reflecting temporal variability of available prey in this arctic lake. Some diet partitioning was observed among morphs; Morph 1 was characterised as a generalist, Morph 3 was more benthic‐oriented, and Morphs 2 and 4 were mainly pelagic feeders. Of the latter, Morph 4 was the most specialised, whereas Morph 2 exhibited alternative feeding tactics of benthic cannibalistic and pelagic piscivorous feeding. Our findings demonstrate that complementary dietary methods can elucidate habits of opportunistic feeders, a task that can often be problematic, given their complex and variable diets. Our results add new information and perspectives on the current model of Lake Trout differentiation, demonstrating niche partitioning based on benthic versus pelagic habitat use and generalist versus specialist feeding tactics.

Great Bear Lake is the most northerly lake of its size and provides unique opportunities for intraspecific diversification. Despite increasing attention to intraspecific polymorphism, several knowledge gaps remain (e.g. determining the extent of intraspecific diversification in large relatively pristine lakes and at which spatial scale it can occur). We focused on geographical patterns of morphological differentiation within lake trout (Salvelinus namaycush) to describe two levels of intralake diversification in Great Bear Lake. We used a combination of geometric and traditional linear measurements to quantify differences in body shape, head shape, and fin and body lengths among 910 adult lake trout from the five distinct arms of Great Bear Lake. Although head and fin linear measurements discriminated the three common morphotypes at the whole‐lake level, inter‐arm variation in body shape was observed within each morphotype. A comparison of genetic and morphological distance matrices revealed the lack of an association between the two sets of data, although both comparisons revealed an association in the inter‐arm variation patterns among morphotypes, suggesting a phenotypically plastic response to distinct environments. The whole‐lake and inter‐arm morphological variation observed within lake trout demonstrates the importance of considering scale, especially across large lakes that exhibit marked complexity and a variety of freshwater habitats. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 114, 109–125.

Range expansion in north-temperate fishes subsequent to the retreat of the Wisconsinan glaciers has resulted in the rapid colonization of previously unexploited, heterogeneous habitats and, in many situations, secondary contact among conspecific lineages that were once previously isolated. Such ecological opportunity coupled with reduced competition likely promoted morphological and genetic differentiation within and among post-glacial fish populations. Discrete morphological forms existing in sympatry, for example, have now been described in many species, yet few studies have directly assessed the association between morphological and genetic variation. Morphotypes of Lake Trout, Salvelinus namaycush, are found in several large-lake systems including Great Bear Lake (GBL), Northwest Territories, Canada, where several shallow-water forms are known. Here, we assess microsatellite and mitochondrial DNA variation among four morphotypes of Lake Trout from the five distinct arms of GBL, and also from locations outside of this system to evaluate several hypotheses concerning the evolution of morphological variation in this species. Our data indicate that morphotypes of Lake Trout from GBL are genetically differentiated from one another, yet the morphotypes are still genetically more similar to one another compared with populations from outside of this system. Furthermore, our data suggest that Lake Trout colonized GBL following dispersal from a single glacial refugium (the Mississippian) and support an intra-lake model of divergence. Overall, our study provides insights into the origins of morphological and genetic variation in post-glacial populations of fishes and provides benchmarks important for monitoring Lake Trout biodiversity in a region thought to be disproportionately susceptible to impacts from climate change.