Inter- and intra-morph patterns in helminth communities of sympatric whitefish morphs

Infection patterns of trophically transmitted helminth parasites were compared with feeding ecology in two sympatric whitefish Coregonus lavaretus morphs from two lake systems in northern Norway. In both lakes, the pelagic morph was an obligate zooplanktivore, while the benthic morph utilized both the benthivore and zooplanktivore trophic niches. The differences in niche utilization between the two morphs were associated with differences in trophic morphology (gill raker numbers), suggesting that they were genetically dissimilar and reproductively isolated. The benthic morph had the highest number of helminth species, probably because they exhibited a broader niche width compared to the pelagic morph. In both lakes, the species composition and intensities of helminths reflected the trophic diversification of the whitefish ecotypes with respect to different habitat choice (benthic v . pelagic) and dietary specialization (benthivore v . zooplanktivore feeding strategies within the benthic whitefish morph). Zooplanktivorous fish from both morphs acquired parasites mainly from pelagic copepods and in almost equal quantities. The benthivore feeders within the benthic morph had the highest proportion of parasites with transmission stages from benthic organisms. Host feeding behaviour seemed to be a major determinant of the helminth community structure, and helminths appeared to be useful indicators of long-term trophic specialization of whitefish ecotypes.     

Ecological speciation in postglacial European whitefish: rapid adaptive radiations into the littoral,pelagic, and profundal lake habitats

Understanding how a monophyletic lineage of a species diverges into several adaptive forms has received increased attention in recent years, but the underlying mechanisms in this process are still under debate. Postglacial fishes are excellent model organisms for exploring this process, especially the initial stages of ecological speciation, as postglacial lakes represent replicated discrete environments with variation in available niches. Here, we combine data of niche utilization, trophic morphology, and 17 microsatellite loci to investigate the diversification process of three sympatric European whitefish morphs from three northern Fennoscandian lakes. The morphological divergence in the gill raker number among the whitefish morphs was related to the utilization of different trophic niches and was associated with reproductive isolation within and across lakes. The intralacustrine comparison of whitefish morphs showed that these systems represent two levels of adaptive divergence: (1) a consistent littoral–pelagic resource axis; and (2) a more variable littoral–profundal resource axis. The results also indicate that the profundal whitefish morph has diverged repeatedly from the ancestral littoral whitefish morph in sympatry in two different watercourses. In contrast, all the analyses performed revealed clustering of the pelagic whitefish morphs across lakes suggesting parallel postglacial immigration with the littoral whitefish morph into each lake. Finally, the analyses strongly suggested that the trophic adaptive trait, number of gill rakers, was under diversifying selection in the different whitefish morphs. Together, the results support a complex evolutionary scenario where ecological speciation acts, but where both allopatric (colonization history) and sympatric (within watercourse divergence) processes are involved.     

Patterns of morphological changes and hybridization between sympatric whitefish morphs (Coregonus spp.) in a Swiss lake: a role for eutrophication?

Whitefish, genus Coregonus, show exceptional levels of phenotypic diversity with sympatric morphs occurring in numerous postglacial lakes in the northern hemisphere. Here, we studied the effects of human‐induced eutrophication on sympatric whitefish morphs in the Swiss lake, Lake Thun. In particular, we addressed the questions whether eutrophication (i) induced hybridization between two ecologically divergent summer‐spawning morphs through a loss of environmental heterogeneity, and (ii) induced rapid adaptive morphological changes through changes in the food web structure. Genetic analysis based on 11 microsatellite loci of 282 spawners revealed that the pelagic and the benthic morph represent highly distinct gene pools occurring at different relative proportions on all seven known spawning sites. Gill raker counts, a highly heritable trait, showed nearly discrete distributions for the two morphs. Multilocus genotypes characteristic of the pelagic morph had more gill rakers than genotypes characteristic of benthic morph. Using Bayesian methods, we found indications of recent but limited introgressive hybridization. Comparisons with historical gill raker data yielded median evolutionary rates of 0.24 haldanes and median selection intensities of 0.27 for this trait in both morphs for 1948–2004 suggesting rapid evolution through directional selection at this trait. However, phenotypic plasticity as an alternative explanation for this phenotypic change cannot be discarded. We hypothesize that both the temporal shifts in mean gill raker counts and the recent hybridization reflect responses to changes in the trophic state of the lake induced by pollution in the 1960s, which created novel selection pressures with respect to feeding niches and spawning site preferences.     

Resource polymorphism in a Patagonian fish Percichthys trucha (Percichthyidae): phenotypic evidence for interlake pattern variation

Within-species differentiation in phenotypic characters related to resource use (resource polymorphism) is frequently thought to result from divergent natural selection in a heterogeneous environment with 'open niches'. In this study we found consistent resource-based polymorphism within three different populations of Percichthys trucha , a lake-dwelling fish native to the southern Andes. In each of three lakes we found two morphotypes that could be clearly distinguished by differences in gill raker length. However, the magnitude of the polymorphism, and the suite of phenotypic characteristics associated with the polymorphism, differed between lakes. Patterns of divergence were more similar between the two northern lakes which ultimately drain into a common river, than between these two lakes and a more southern, unconnected lake. The southern population, which had the largest divergence in gill raker length (32% vs. 16% and 19%), also showed substantial differences in diet. Evidence from the southern population suggests that polymorphism in P. trucha is present early during ontogeny. We conclude that while there are some strong parallels among lakes in the development of a trophic polymorphism, differences in environmental ­conditions and/or colonization history have led to substantial differences in the evolutionary history, resulting in ­different ecological roles of common morphotypes within different lakes.  © 2003 The Linnean Society of London . Biological Journal of the Linnean Society , 2003, 78 , 497–515.     

Discrete foraging niches promote ecological, phenotypic, and genetic divergence in sympatric whitefish (Coregonus lavaretus)

Natural populations often vary in their degree of ecological, morphological and genetic divergence. This variation can be arranged along an ecological speciation continuum of increasingly discrete variation, with high inter-individual variation at one end and well defined species in the other. In postglacial fishes, evolutionary divergence has commonly resulted in the co-occurrence of a pelagic and a benthic specialist. We studied three replicate lakes supporting sympatric pelagic and benthic European whitefish (Coregonus lavaretus (L.)) morphs in search for early signs of possible further divergence into more specialized niches. Using stomach content data (recent diet) and stable isotope analyses (time-integrated measure of trophic niche use), we observed a split in the trophic niche within the benthic whitefish morph, with individuals specializing on either littoral or profundal resources. This divergence in resource use was accompanied by small but significant differences in an adaptive morphological trait (gill raker number) and significant genetic differences between fish exploiting littoral and profundal habitats and foraging resources. The same pattern of parallel divergence was found in all three lakes, suggesting similar natural selection pressures driving and/or maintaining the divergence. The two levels of divergence (a clear and robust benthic – pelagic and a more subtle littoral – profundal divergence) observed in this study apparently represent different stages in the process of ecological speciation.     

Genetic differentiation in gill raker number and length in sympatric anadromous and nonanadromous morphs of sockeye salmon, Oncorhynchus nerka

The genetic and environmental basis for polymorphism in gill raker number and length in sympatric anadromous and nonanadromous morphs of sockeye salmon, Oncorhynchus nerka, was investigated. Analysis of 30 full sib families involving pure types and reciprocal hybrids revealed that the variation was partitioned significantly among families within cross types and among cross types in both traits. As in the wild, kokanee displayed more gill rakers than sockeye; reciprocal hybrids displayed intermediate counts. Gill raker length also varied markedly among cross types, with pure sockeye displaying 19% longer gill rakers than comparable sized kokanee. This difference was in the opposite direction predicted, given the common positive association between gill raker number and length in sympatric morphs of the same species in fishes. Gill raker number and length were generally not correlated within cross types, suggesting independent divergence of the traits. The results are discussed in relation to genetic and trophic divergence of the morphs and to factors selecting for differentiation in the two gill raker traits.     

Parallel evolution of ecomorphological traits in the European whitefish Coregonus lavaretus (L.) species complex during postglacial times

The extensive phenotypic polymorphism in the European whitefish has triggered evolutionary research in order to disentangle mechanisms underlying diversification. To illuminate the ecological distinctiveness in polymorphic whitefish, and evaluate taxonomic designations, we studied nine Norwegian lakes in three watercourses, which each harboured pairs of divergent whitefish morphs. We compared the morphology and life history of these morphs, documented the extent of genetic differentiation between them, and contrasted the niche use of sympatric morphs along both the habitat and resource axes. In all cases, sympatric morphs differed in the number of gill rakers, a highly heritable trait related to trophic utilization. Individual growth rate, age and size at maturity, diet and habitat use also differed between morphs within lakes, but were remarkably similar across lakes within the same morph. Microsatellite analyses confirmed for all but one pair that sympatric morphs were significantly genetically different, and that similar morphs from different lakes likely have a polyphyletic origin. These results are most compatible with the process of parallel evolution through recurrent postglacial divergence into pelagic and benthic niches in each of these lakes. We propose that sparsely and densely rakered whitefish sympatric pairs may be a likely case of ecological speciation, mediated in oligotrophic lakes with few trophic competitors.     

Long term diet differences between morphs in trophically polymorphic Perdchthys trucha (Pisces: Percichthyidae) populations from the southern Andes

Divergent natural selection is often believed to be the driving force behind phenotypic differentiation in characters related to resource acquisition, leading to trophic polymorphism in fishes. Here we use variation in the fatty acid composition of adipose and muscle tissues to look at differences in resource use by two recently described sympatric morphs of Percichthys trucha , a common freshwater fish of the Andean and Patagonian regions of South America. Because dietary fatty acids are often stored in carnivorous animals with litde modification after consumption, they can be used to infer information about dietary habits of individuals. We found that the two morphs differed in the overall composition of fatty acids in both adipose and muscle tissue, but that there were some differences in how die morphs differed in lakes from the northern vs southern part of the range. Furthermore, we found that certain fatty acids were correlated with diet as determined by gut content analysis. Consumption of anisopteran larvae was highly correlated widi 14:0 in adipose and muscle tissue; and higher levels of longer chain unsaturated fatty acids (i.e. 20 and 22 carbons) were correlated with die presence offish and also amphipods in die diets. Taken togetiier, die results suggest that diere are marked differences in die foraging ecology of die two morphs of P. trucha inhabiting southern Andean lakes.     

Incipient speciation through niche expansion: an example from the Arctic charr in a subarctic lake

Two reproductive isolated morphs of Arctic charr (Salvelinus alpinus), termed profundal and littoral charr according to their different spawning habitats, co-occur in the postglacial lake Fjellfr?svatn in North Norway. All profundal charr live in deep water their entire life and have a maximum size of 14cm, while the littoral charr grow to 40cm. Some small and young littoral charr move to the profundal zone in an ontogenetic habitat shift in the ice-free season and the rest of the population remains in epilimnic waters. The two morphs had different diet niches in the profundal zone: the profundal charr ate typical soft-bottom prey (chironomid larvae, pea mussels and benthic copepods), while the young littoral charr mainly consumed crustacean zooplankton. In four other lakes without a profundal morph (i.e. monomorphic populations), young charr also performed ontogenetic habitat shifts to the profundal zone and fed on zooplankton. The profundal morph of Fjellfr?svatn therefore utilize a food resource niche that neither the littoral morph nor comparable monomorphic populations exploit. This suggests that intraspecific resource competition has driven incipient ecological speciation of the profundal charr of Fjellfr?svatn. The exploitation of the soft-bottom resources by the profundal charr supports earlier experimental findings that the profundal morph is genetically different in trophic behaviour and morphology. The sympatric ecological divergence within the profundal habitat is possible because unexploited food resources (soft-bottom profundal prey) are available. Apparently, this represents a case of incipient segregation by expansion to new resource types (niche invasion), and not by subdivision of one broad ancestral niche.     

Experimental evidence for trait utility of gill raker number in adaptive radiation of a north temperate fish

North temperate fish in post‐glacial lakes are textbook examples for rapid parallel adaptive radiation into multiple trophic specialists within individual lakes. Speciation repeatedly proceeded along the benthic–limnetic habitat axis, and benthic–limnetic sister species diverge in the number of gill rakers. Yet, the utility of different numbers of gill rakers for consuming benthic vs. limnetic food has only very rarely been experimentally demonstrated. We bred and raised families of a benthic–limnetic species pair of whitefish under common garden conditions to test whether these species (i) show heritable differentiation in feeding efficiency on zooplankton, and (ii) whether variation in feeding efficiency is predicted by variation in gill raker numbers. We used zooplankton of three different size classes to investigate prey size dependency of divergence in feeding efficiency and to investigate the effect strength of variation in the number of gill rakers. Our results show strong interspecific differences in feeding efficiency. These differences are largest when fish were tested with the smallest zooplankton. Importantly, feeding efficiency is significantly positively correlated with the number of gill rakers when using small zooplankton, also when species identity is statistically controlled for. Our results support the hypothesis that a larger number of gill rakers are of adaptive significance for feeding on zooplankton and provide one of the first experimental demonstrations of trait utility of gill raker number when fish feed on zooplankton. These results are consistent with the suggested importance of divergent selection driven feeding adaptation during adaptive radiation of fish in post‐glacial lakes.     

Morphological divergence between three Arctic charr morphs – the significance of the deep‐water environment

Morphological divergence was evident among three sympatric morphs of Arctic charr (Salvelinus alpinus (L.)) that are ecologically diverged along the shallow‐, deep‐water resource axis in a subarctic postglacial lake (Norway). The two deep‐water (profundal) spawning morphs, a benthivore (PB‐morph) and a piscivore (PP‐morph), have evolved under identical abiotic conditions with constant low light and temperature levels in their deep‐water habitat, and were morphologically most similar. However, they differed in important head traits (e.g., eye and mouth size) related to their different diet specializations. The small‐sized PB‐morph had a paedomorphic appearance with a blunt head shape, large eyes, and a deep body shape adapted to their profundal lifestyle feeding on submerged benthos from soft, deep‐water sediments. The PP‐morph had a robust head, large mouth with numerous teeth, and an elongated body shape strongly related to their piscivorous behavior. The littoral spawning omnivore morph (LO‐morph) predominantly utilizes the shallow benthic–pelagic habitat and food resources. Compared to the deep‐water morphs, the LO‐morph had smaller head relative to body size. The LO‐morph exhibited traits typical for both shallow‐water benthic feeding (e.g., large body depths and small eyes) and planktivorous feeding in the pelagic habitat (e.g., streamlined body shape and small mouth). The development of morphological differences within the same deep‐water habitat for the PB‐ and PP‐morphs highlights the potential of biotic factors and ecological interactions to promote further divergence in the evolution of polymorphism in a tentative incipient speciation process. The diversity of deep‐water charr in this study represents a novelty in the Arctic charr polymorphism as a truly deep‐water piscivore morph has to our knowledge not been described elsewhere.     

Resource polymorphism and diversity of Arctic charr Salvelinus alpinus in a series of isolated lakes

Morphological, dietary and life‐history variation in Arctic charr Salvelinus alpinus were characterized from three geographically proximate, but isolated lakes and one large lake into which they drain in south‐western Alaska. Polymorphism was predicted to occur in the first three lakes because S. alpinus tend to become polymorphic in deep, isolated lakes with few co‐occurring species. Only one morph was evident in the large lake and two of the three isolated lakes. In the third isolated lake, Lower Tazimina Lake, small and large morphs were found, the latter including two forms differing in growth rate. The small morph additionally differed from the two large forms by having more gill rakers and a deeper body than same‐sized individuals of the large morph, consuming more limnetic and fewer benthic resources, having a greater gonado‐somatic index and maturing at a smaller size. The two large forms consumed only slightly different foods (more terrestrial insects were consumed by the medium‐growth form; more snails by the high‐growth form). Trends in consumption of resources with body shape also differed between lakes. Variability in life history of S. alpinus in these Alaskan lakes was as broad as that found elsewhere. This variability is important for understanding lake ecosystems of remote regions where this species is commonly dominant.     

Convergent evolutionary processes driven by foraging opportunity in two sympatric morph pairs of Arctic charr with contrasting post‐glacial origins

The expression of two or more discrete phenotypes amongst individuals within a species (morphs) provides multiple modes upon which selection can act semi‐independently, and thus may be an important stage in speciation. In the present study, we compared two sympatric morph systems aiming to address hypotheses related to their evolutionary origin. Arctic charr in sympatry in Loch Tay, Scotland, exhibit one of two discrete, alternative body size phenotypes at maturity (large or small body size). Arctic charr in Loch Awe segregate into two temporally segregated spawning groups (breeding in either spring or autumn). Mitochondrial DNA restriction fragment length polymorphism analysis showed that the morph pairs in both lakes comprise separate gene pools, although segregation of the Loch Awe morphs is more subtle than that of Loch Tay. We conclude that the Loch Awe morphs diverged in situ (within the lake), whereas Loch Tay morphs most likely arose through multiple invasions by different ancestral groups that segregated before post‐glacial invasion (i.e. in allopatry). Both morph pairs showed clear trophic segregation between planktonic and benthic resources (measured by stable isotope analysis) but this was significantly less distinct in Loch Tay than in Loch Awe. By contrast, both inter‐morph morphological and life‐history differences were more subtle in Loch Awe than in Loch Tay. The strong ecological but relatively weak morphological and life‐history divergence of the in situ derived morphs compared to morphs with allopatric origins indicates a strong link between early ecological and subsequent genetic divergence of sympatric origin emerging species pairs. The emergence of parallel specialisms despite distinct genetic origins of these morph pairs suggests that the effect of available foraging opportunities may be at least as important as genetic origin in structuring sympatric divergence in post‐glacial fishes with high levels of phenotypic plasticity. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Habitat use of arctic charrSalvelinus alpinus in Thingvallavatn,Iceland

Synopsis Habitat use by four morphs of arctic charr,Salvelinus alpinus, was investigated in Thingvallavatn, Iceland, by sampling with pelagic and benthic gill nets. Sampling was done in May/June and August/September. Greatest abundance of fish was recorded in the littoral and epipelagic zone in early autumn. Catches were low in early summer. The four morphs are partly segregated in habitat. Small (SB-) and large benthivorous (LB-) charr have a more restricted spatial distribution than piscivorous (PI-), and especially planktivorous (PL-) charr. Both benthivorous morphs are mainly found in the littoral zone, and occur in largest numbers in stony shallows at depths between 0 and 10 m. PL-charr usually dominates in numbers in all habitats. PI-charr is most abundant in epibenthic habitats, although numbers are always low. All morphs are caught in higher numbers at night than during the day, but the diurnal activity difference is highest among SB-charr. The habitat use by different morphs is as may be expected from their morphology and diets. Within the population of PL-charr, young and small fish are more abundant on the bottom than in the pelagic zone, and there is a surplus of females in the pelagic zone. Along the benthic profile, young, small and immature PL-charr are more abundant in deep than in shallow waters. The results are discussed in relation to food supply, competition and predation. Possible reasons for the occurrence of four arctic charr morphs are also discussed.Contribution from the Thingvallavatn project.     

Extreme polymorphism in a Y-linked sexually selected trait

Males of the livebearing fish, Poecilia parae, exhibit one of the most complex polymorphisms known to occur within populations, whereas females are monomorphic. We describe five distinct male colour morphs and an associated size dimorphism, and demonstrate through pedigree analysis that the locus or loci controlling the male colour polymorphism is linked to the Y-chromosome. Field surveys from 1999 to 2002 of nine populations in Guyana and Suriname, South America, indicate that some morphs are consistently abundant and others are rare, implying that the colour polymorphism has important fitness consequences. By rearing offspring of field-inseminated females, we showed that the common morph is also the most successful morph in terms of reproduction. However, dichotomous choice tests show that two rare morphs are preferred by females over the common morph. These results suggest that alternative male mating strategies, sperm competition, overt male-male competition, or other processes are overriding female preferences in these populations. Furthermore, Y-linkage of the colour polymorphism in P. parae supports the hypothesis that heterogametic sex chromosomes harbour sexually antagonistic traits beneficial to the heterogametic sex.     

Parallel phenotypic evolution of skull-bone structures and head measurements of Arctic charr morphs in two subarctic lakes

Interspecific morph variations in trophic morphology related to skull-bones and head traits is associated to ecological segregation of Arctic charr morphs (genus Salvelinus) in two sub-arctic lakes (Fjellfrøsvatn and Skogsfjordvatn, Norway). The replicated morph pair, the profundal spawning benthivorous PB-morph and the littoral spawning omnivorous LO-morph of Arctic charr, diverge along the shallow-deep-water resource axis. In Skogsfjordvatn there is also a profundal spawning piscivorous PP-morph. The PB-morphs from both lakes have similar skull-bone traits and head morphology such as elongated jaw-bones, small opercular bones and relatively longer heads. The PP-morph also has an elongated head, relatively small opercular bones as well as larger jaw-bones. In contrast, the LO-morphs in both lakes have shorter jaw-bones, larger opercular bones in addition to relatively small heads. However, some small non-parallel differences exist among the morphs from the two lakes. Overall, all profundal morphs (PB and PP) have relatively similar skull-bone structures, suggesting adaptations to the deep-water environment but also to their separated dietary niches. There is strong evidence for parallel evolution with some local adaptations in skull-bones and head morphology of the PB-morph and the LO-morph from separate lakes.     

Buoyancy studies of three morphs of the Antarctic fish Trematomus newnesi (Nototheniidae) from the South Shetland Islands

Phenotypic plasticity, a widespread phenomenon in boreal freshwater fishes, is less apparent in the marine realm and the organism–environment interactions producing this variation are undetermined. A sample of 40 specimens of Trematomus newnesi, an inshore Antarctic fish from King George/25 de Mayo Island in the South Shetlands, was composed of 52.5% typical morphs, 27.5% large-mouth morphs and 20% intermediate morphs. Measurements of percentage buoyancy on the morphs of this sample were 3.73, 3.84 and 3.83%, respectively with no significant differences among means. Both mean dry skeletal weight as a percentage of body weight and mean oral jaw weight as a percentage of dry skeletal weight were significantly greater in large-mouth morphs compared to typical morphs. Diversification in head and jaw morphology is not accompanied by diversification in ecology as represented by buoyancy and, in spite of external appearances, measurements of buoyancy offer no support for the hypothesis that the large-mouth morph is more benthic than the typical semipelagic morph. Although a trophic basis for this polymorphism is possible, it has not yet been documented. Our discussion centers on the status of key open questions regarding morphism and highlights areas requiring more research.     

Trophic specialization in Arctic charr Salvelinus alpinus (Pisces; Salmonidae): morphological divergence and ontogenetic niche shifts

Lake Thingvallavatn supports four trophic morphs of Arctic charr, Salvelinus alpinus (L.); two of the morphs are benthic (small and large benthivorous charr) one exploits pelagic waters (planktivorous charr) and the fourth is found in both habitats (piscivorous charr). The morphological variation among these morphs was analysed by use of principal component analysis and canonical discriminant analysis. The benihic morphs have a short lower jaw and long pectoral fins. The benthic fish also have fewer gillrakers than the other morphs. Small and large benthivorous charrs attain sexual maturity from 2 and 6 years of age, and at fork lengths from 7 and 22 cm, respectively. Small benthivorous charr retain their juvenile parr marks as adults, have beige ventral colours, and are frequently melanized under the lower jaw. Planktivorous and piscivorous charr attain sexual maturity from 4 and 6 years of age, from fork lengths of 15 and 23 cm, respectively. This phenotypic polymorphism is associated with habitat utilization and diet of the fish, and has probably arisen within the lake system through diversification and niche specialization. The pelagic morphs apparently stem from a single population, and are possibly diversified through conditional niche shifts which affect ontogeny. Juveniles reaching a body length of 23 cm may change from zooplankton to fish feeding. Asymptotic length increases thereby from 20.5 cm in planktivorous charr to 30.2 cm in piscivorous charr. The benthic morphs appear to represent separate populations, although both feed chiefly on the gastropod Lymnaea peregra. Their co-existence seems to be facilitated by size dependent constraints on habitat use. The small morph (asymptotic length 13.3 cm) exploit the interstitial crevices in the lava block substratum, whereas the large morph (asymptotic length 55.4 cm) live epibenthically.     

Niche segregation of coexisting Arctic charr (Salvelinus alpinus) and brown trout (Salmo trutta) constrains food web coupling in subarctic lakes

1. Generalist fish species are recognised as important couplers of benthic and pelagic food‐web compartments in lakes. However, interspecific niche segregation and individual specialisation may limit the potential for generalistic feeding behaviour. 2. We studied summer habitat use, stomach contents and stable isotopic compositions of the generalist feeder Arctic charr coexisting with its common resource competitor brown trout in five subarctic lakes in northern Norway to reveal population‐level and individual‐level niche plasticity. 3. Charr and trout showed partial niche segregation in all five lakes. Charr used all habitat types and a wide variety of invertebrate prey including zooplankton, whereas trout fed mainly on insects in the littoral zone. Hence, charr showed a higher potential to promote habitat and food‐web coupling compared to littoral‐dwelling trout. 4. The level of niche segregation between charr and trout and between pelagic‐caught and littoral‐caught charr depended on the prevailing patterns of interspecific and intraspecific resource competition. The two fish species had partially overlapping trophic niches in one lake where charr numerically dominated the fish community, whereas the most segregated niches occurred in lakes where trout were more abundant. 5. In general, pelagic‐caught charr had substantially narrower dietary and isotopic niches and relied less on littoral carbon sources compared to littoral‐caught conspecifics that included generalist as well as specialised benthivorous and planktivorous individuals. Despite the partially specialised planktivorous niche and thus reduced potential of pelagic‐dwelling charr to promote benthic–pelagic coupling, the isotopic compositions of both charr subpopulations suggested a significant reliance on both littoral and pelagic carbon sources in all five study lakes. 6. Our study demonstrates that both interspecific niche segregation between and individual trophic specialisation within generalist fish species can constrain food‐web coupling and alter energy mobilisation to top consumers in subarctic lakes. Nevertheless, pelagic and littoral habitats and food‐web compartments may still be highly integrated due to the potentially plastic foraging behaviour of top consumers.