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, ?? , ??–??.     

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.     

Alternative migration and host parasitism strategies and their long-term stability in river lampreys from the River Endrick, Scotland

The stability of a discrete body size dimorphism of sexually mature river lamprey Lampetra fluviatilis from the River Endrick, Scotland, was examined over a 21 year period. Stable isotope analysis was used to test the hypothesis that the two size forms comprise individuals with differing migration and parasitic foraging strategies. Maturing river lamprey and the brook lamprey Lampetra planeri were trapped over 3 months each year in the periods 1983–1984 and 2004–2005. Brook lamprey catches and catches of both species combined showed no significant trend in catch rate with time. The catch rate of small body size river lamprey declined between 1983–1984 and 2004–2005 (although the difference did not reach statistical significance; P = 0·055). In contrast, there was a significant increase in the catch rate of the large body size river lamprey and as a consequence, a significant change in the relative proportion of each of the two river lamprey morphs over the study period. Analysis of the stable isotopes of C and N in muscle tissue showed that brook lamprey tissue derived its carbon from a freshwater source and had a δ¹³C more consistent with that of the River Endrick than with Loch Lomond. δ¹⁵N values for this species showed it to be feeding at the base of the food chain, consistent with filter feeding as an ammocoete. The large body size and the small body size river lamprey adults differed substantially in their δ¹³C values, with the small body size δ¹³C signature indicative of a freshwater carbon source and the large body size morph of a marine source. The small body size morph had a δ¹³C signature that was consistent with that of Loch Lomond powan Coregonus lavaretus suggesting that they share a common carbon source. The large body size morph was clearly feeding at a higher trophic level than the small body size morph. A single small body size river lamprey individual with typical morphology for that group, however, had C and N signatures that clustered with those of the large body size morphs. This individual had either migrated to sea to forage, as is typical for the species, or had been feeding on an anadromous fish with a strong marine C signature in fresh water. It is concluded that the body size dimorphism is indicative of a differential migration and foraging strategy in the parasitic phase of the life cycle of river lamprey at this site.     

Effects of population,family, and diet on craniofacial morphology of Icelandic Arctic charr (Salvelinus alpinus)

We evaluated hypotheses of intralacustrine diversification and plastic responses to two diet environments in Icelandic Arctic charr (Salvelinus alpinus). Full‐sib families of progeny of wild polymorphic charr from two lakes where morphs vary in their degree of phenotypic and ecological divergence were split, with half of the offspring reared on a benthic and half on a limnetic type of diet to estimate family norms of reaction. We focused on variation in craniofacial traits because they are probably functionally related to diet and complement a previous study of body shape in these charr. A hierarchical analysis of phenotypic variation between lakes, pairs of morphs within each lake, and two families within each morph found that phenotypic variation partitioned between families relative to morphs was reduced in the more ecologically diversified population, which is consistent with adaptive diversification. The effect size of plastic responses between lake populations was similar, suggesting little difference in the degree of canalization in contrast to a previous analysis of body form plasticity. Thus, the role that plastic morphological responses play in the adaptive diversification of morphs and different lake populations of Arctic charr may depend on the trait. © 2013 The Linnean Society of London     

Variation in scale shape among alternative sympatric phenotypes of Arctic charr Salvelinus alpinus from two lakes in Scotland

Landmark‐based geometric morphometric analysis was used to detect differences in scale shape between ecologically distinct phenotypes of Arctic charr Salvelinus alpinus coexisting in the same lake. Relative warp analysis and standard multivariate analyses of the partial warps, obtained after a Procrustes superimposition, showed that scale landmarks were efficient in discriminating among two closely related alternative phenotypes within each of the two lakes. In Loch Tay, S. alpinus exhibited a bimodal body size‐frequency distribution among sexually mature fish, whereas in Loch Awe, S. alpinus are unimodal in body size but segregated into two distinct spawning phenotypes. In both lakes, alternative phenotypes showed significant differences in foraging ecology, habitat use and life history. It is probable that differences in scale shape reflect differences in ecology of these forms.     

Divergence in social foraging among morphs of the three‐spined stickleback,Gasterosteus aculeatus

Foraging in social groups has a number of benefits but can also increase the risk of exploitation. High tendency to shoal may be correlated with groups foraging, although facultatively social fish adjust both shoaling decisions and food resource defence based on intrinsic and extrinsic factors. The main aim of this study was to examine the relationships between shoaling, solitary foraging and aggression, forager tolerance of conspecifics joining at a discovered food patch and forager exploitation of resources discovered by others. We used two intra‐lacustrine three‐spined stickleback morph pairs, lava and mud, and monomorphic morphs from each of lava and mud habitats. The lava morph formed less cohesive shoals, was bolder during solitary foraging, approached and entered an occupied food patch less frequently than the mud morph, suggesting a link between shoaling and the propensity for social foraging. However, shoaling tendency and joiner tolerance were not correlated at a population level. Intralacustrine lava and mud morphs differed more markedly in joiner tolerance than morphs from single habitat lakes, whereas the opposite was true for shoaling tendency. We conclude that, in addition to differentiation in shoaling tendency, the lava and mud morphs differ in social foraging and these variations may act to promote population divergence. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 194–203.     

Inter and intra‐population phenotypic and genotypic structuring in the European whitefish Coregonus lavaretus,a rare freshwater fish in Scotland

This study revealed between‐lake genetic structuring between Coregonus lavaretus collected from the only two native populations of this species in Scotland, U.K. (Lochs Eck and Lomond) evidenced by the existence of private alleles (12 in Lomond and four in Eck) and significant genetic differentiation (F_ST = 0·056) across 10 microsatellite markers. Juvenile C. lavaretus originating from eggs collected from the two lakes and reared in a common‐garden experiment showed clear phenotypic differences in trophic morphology (i.e. head and body shape) between these populations indicating that these characteristics were, at least partly, inherited. Microsatellite analysis of adults collected from different geographic regions within Loch Lomond revealed detectable and statistically significant but relatively weak genetic structuring (F_ST = 0·001–0·024) and evidence of private alleles related to the basin structure of the lake. Within‐lake genetic divergence patterns suggest three possibilities for this observed pattern: (1) differential selection pressures causing divergence into separate gene pools, (2) a collapse of two formerly divergent gene pools and (3) a stable state maintained by balancing selection forces resulting from spatial variation in selection and lake heterogeneity. Small estimates of effective population sizes for the populations in both lakes suggest that the capacity of both populations to adapt to future environmental change may be limited.     

Calanoid copepods from South Georgia,with special reference to size dimorphism within the genus Pseudoboeckella

Summary Three species of calanoid copepods, Boeckella michaelseni, Parabroteas sarsii and Pseudoboeckella poppei were recorded from 6 freshwater localities in the Husvik area, South Georgia. Of the latter species two distinct size morphs occurred, with no overlap in size even in closely situated populations. The large morph was recorded in lakes, the small was found in ponds. The small morph did not coexist with the large predatory P. sarsii, and we suggest predation pressure from this species as the major cause for the observed distribution of these morphs. The pronounced size segregation as well as small morphological dissimilarities suggest that these morphs are reproductively isolated. While the large morphotype corresponds to that of P. poppei, the taxonomic affinities of the small morph are uncertain.     

Differentiation of deep-water lake charr <Emphasis Type="Italic">Salvelinus namaycush</Emphasis> in North American lakes

Deep-water morphs of lake charr, Salvelinus namaycush, are found, with one exception, in four of the largest lakes in the world: lakes Superior and Mistassini (QC) and Great Bear and Slave lakes. This paper advances a hypothesis for resource polymorphisms involving two types of deep-water morph, one of which is characteristic of the humper and the other of the siscowet charrs of Lake Superior. My hypothesis states that, first, the humper, or a humper-like morph, diverged postglacially in sympatry from the ancestral common (shallow-water) lake charr and became a feeding specialist on Mysis relicta. Second, in at least two of the four lakes the siscowet, or a siscowet-like charr, diverged as a feeding specialist on postglacially derived forms of deep-water ciscoes. In Lake Superior a successional process may have resulted in dominance of the siscowet at the expense of the humper charr. I concur with a previous inference that the one occurrence of a deep-water charr in a small lake (the above exception) represents emigration from Lake Superior. I further infer that this event involved an early humper charr, which implies that this morphotype had differentiated in Lake Superior in less than 1,900 year. I suggest that innate differences in plasticity, breeding behavior and assortive mating, and philopatry account for why Arctic charr isolate readily in small lakes whereas lake charr do not. My hypothesis assumes divergence of deep-water morphs occurred postglacially, an idea consistent with genetic and biogeographical evidence.     

Colour-associated foraging success and population genetic structure in a sit-and-wait predator Nephila maculata (Araneae: Tetragnathidae)

Giant wood spiders, Nephila maculata (Fabricius 1793), typically have a greenish cephalothorax and a dark abdomen decorated with striking yellow bands and spots. However, in Taiwan and neighbouring coastal islands we also found some morphologically indistinguishable individuals that were totally dark. As insects are attracted to ultraviolet (UV) light, we compared the UV reflectance property and insect-catching ability of the two morphs to see whether variation in colour affected foraging success. We also examined the population genetic structure to estimate indirectly the level of gene flow between these two colour morphs. Body surface UV reflection rate was measured from six areas of the spider with a spectrometer. To compare the insect-catching ability of different morphs, we recorded the spiders' body colour, orb size and insect-interception rates. The typical morph of N. maculata reflected significantly more UV in four of the six areas examined and caught significantly more insects than the melanic morph. We estimated population genetic structure by allozyme electrophoresis, using 20 loci from 17 enzymes. The population differentiation index (F_ST) derived from all eight polymorphic loci was 0.023, indicating a minimum level of genetic differentiation. These results indicate that the two morphs ofN. maculata may be members of an interbreeding population, and melanics have lower foraging success because of a lower body surface reflectance.     

Immune function, parasitization and extended phenotypes in colour polymorphic pygmy grasshoppers

Ecological and evolutionary consequences of host–parasite interactions have attracted considerable attention from evolutionary biologists. Previous studies have suggested that immune responsiveness may be genetically or developmentally linked with colour pattern, such that the evolution of animal colour patterns may be influenced by correlated responses to selection for parasite resistance. We studied interactions between the endoparasitic fly Leiophora innoxia (Meigen) (Diptera: Tachinidae) and its colour polymorphic pygmy grasshopper host Tetrix undulata (Sow.) (Orthoptera: Tetrigidae) to test for morph‐specific differences in parasitization and immune defence, and host‐induced variation in parasite phenotypes. Our results revealed that c. 2 and 30% of adult grasshoppers collected from the same natural population in two subsequent years, respectively were parasitized. Parasite prevalence was independent of host sex and colour morph. Pupae were larger if the parasite had developed in a female than in a male host, possibly reflecting host resource value or a physical constraint on larval growth imposed by host body size. Pupal size was also associated with host colour morph, with individuals that had developed in dark morphs being smaller at pupation compared to those that developed in paler morphs. However, immune defence, measured as the encapsulation response to a novel antigen, did not differ among individuals belonging to alternative colour morphs or sexes. Darker morphs warm up more quickly and prefer higher body temperatures than paler ones. Encapsulation was not influenced by maintenance temperature (15 vs. 30 °C), however, suggesting that indirect effects of coloration on parasite resistance mediated via differential body temperature are unlikely. The dependence of parasite body size on host colour morph may thus reflect plasticity of growth and development of the larvae in response to differential host body temperature, rather than variable host immune defence. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 85 , 373–383.     

Empirical evaluation of phenotype–environment correlation and trait utility with allopatric and sympatric whitefish, Coregonus lavaretus (L.), populations in subarctic lakes

Adaptive phenotypic divergence of sympatric morphs in a single species may have significant evolutionary consequences. In the present study, phenotypic impacts of predator on zooplankton prey populations were compared in two northern Finnish lakes; one with an allopatric whitefish, Coregonus lavaretus (L.), population and the other with three sympatric whitefish populations. First, we examined whether there were phenotypic associations with specific niches in allopatric and sympatric whitefish. Second, trait utility (i.e. number of gillrakers) of allopatric and sympatric whitefish in utilizing a pelagic resource was explored by comparing predator avoidance of prey, prey size in environment, and prey size in predator diet. The allopatric living large sparsely rakered (LSR) whitefish morph, was a generalist using both pelagic and benthic niches. In contrast, sympatric living whitefish morphs were specialized: LSR whitefish was a littoral benthivore, small sparsely rakered whitefish was a profundal benthivore and densely rakered (DR) whitefish was a pelagic planktivore. In the lake with allopatric whitefish, zooplankton prey did not migrate vertically to avoid predation whereas, in the lake with sympatric whitefish, all important prey taxa migrated significantly. Trait utility was observed as significantly smaller size of prey in environment and predator diet in the lake with DR whitefish than in the lake with only LSR whitefish.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 561–572.     

Body size influences differently the detectabilities of colour morphs of cryptic prey

Body size and coloration may contribute to variation in performance and fitness among individuals; for example, by influencing vulnerability to predators. Yet, the combined effect of size and colour pattern on susceptibility to visual predators has received little attention, particularly in camouflaged prey. In the colour polymorphic pygmy grasshopper Tetrix subulata (Linnaeus, 1758), females are larger than males, although there is a size overlap between sexes. In the present study, we investigated how body size and colour morph influenced detection of these grasshoppers, and whether differences in protective value among morphs change with size. We conducted a computer‐based experiment and compared how human ‘predators’ detected images of large, intermediate or small grasshoppers belonging to black, grey or striped colour morphs when embedded in photographs of natural grasshopper habitats. We found that time to detection increased with decreasing size, that differences in time to detection of the black, grey and striped morphs depended differently on body size, and that no single morph provided superior or inferior protection in all three size classes. By comparing morph frequencies in samples of male and female grasshoppers from natural populations, we also examined whether the joint effects of size and colour morph on detection could explain evolutionary dynamics in the wild. Morph frequency differences between sexes were largely in accordance with expectations from the results of the detection experiment. The results of the present study demonstrate that body size and colour morph can interactively influence detection of camouflaged prey. This may contribute to the morph frequency differences between male and female pygmy grasshoppers in the wild. Such interactive effects may also influence the dynamics of colour polymorphisms, and contribute to the evolution of ontogenetic colour change and sexual dichromatism. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 112–122.     

Morphological variation in Bosmina longirostris (O.F. Müller, 1785) (Crustacea: Cladocera): consequence of cyclomorphosis or indication of cryptic species?

Samples of the polymorphic cladoceran Bosmina longirostris were collected in several lakes and ponds in Western Germany between 1993 and 1999. The shape of the first antennule was used as a qualitative criterion to classify 1241 individuals to three morphs (`longirostris', `cornuta', `pellucida') according to Lieder (Crustacea: Cladocera: Bosminidae. Stuttgart, Germany: Gustav. Fischer Verlag, 1996). Eight morphometric variables were subsequently measured in each individual to quantify size‐ and shape‐related features. Principal component and discriminant analyses were used to describe the morphological variation within and among the three morphs. Seasonal environmental changes modified several traits and thus, cyclomorphosis accounted for a high proportion of within‐morph variation. However, there was no gradual change from one morph to another. As well among‐morph variation was considerably greater than within‐morph variation. Consequently, the disagreement between the qualitative pre‐classification and the assignment basing on morphometric discriminant functions was low (4.6–12.0%). Considering that each morph is morphologically well‐defined, and that the different morphs coexisted over several generations in the same lake we conclude that they represent different species rather than variants of one polymorphic species. Therefore, we recognize beside the nominal taxon Bosmina longirostris ( 26 ) two more species: Bosmina cornuta ( 10 ) and Bosmina pellucida 30 .     

Polychromatism of the scale-eaterPerissodus microlepis (Cichlidae,Teleostei) in relation to foraging behavior

Variation in foraging behavior in a population of the scale-eaterPerissodus microlepis was studied on the northwest coast of Lake Tanganyika. Differences in body coloration were found among adult and subadult individuals, which were classified into 4 color morphs designated as Beige, Dark, Grey and Stripe. These color morphs were not strictly related to either sex or size. Each morph spent much time in specific microhabitats and had a major hunting technique that differed from other morphs. Beige morph. which predominated in number, ambushed prey at open surfaces of the substrate, whereas Dark morph used the shade of rock as an ambush site. Grey morph mixed in schools of fisheds hovering in midwater to attack school members, and Stripe morph cruised in the water column and stooped mainly at bottom-fishes. Prey preference differed among the morphs corresponding to their hunting techniques but successful attack rates were similar among them. Observations of marked individuals demonstrated adherence to particular hunting techniques and, in some cases, to particular hunting sites. Intraspecific foraging specialization is discussed in relation to the function of body color and diversity of life styles of prey fishes.     

The functional significance of inherited differences in feeding morphology in a sympatric polymorphic population of Arctic charr

Artificially fertilised eggs from wild-caught Arctic charr parents of two sympatric morphs (benthivorous and planktivorous) from Loch Rannoch, Scotland were reared in the laboratory under identical conditions. During the subsequent 2 years, aspects of their trophic anatomy and feeding behaviour were compared. As previously described for wild-caught fish, charr derived from the benthivorous morph had an increasingly wider mouth gape for a given body length than those derived from the planktivorous morph. The functional significance of these differences in gape was tested by comparing the maximum size of prey that could be handled by each of the two morphs. In both forms, a larger gape enabled larger food particles to be eaten, but the elevation of the regression of maximum prey size on gape was higher in the benthivorous form, indicating the existence of additional morphological and/or behavioural differences influencing the size of prey consumed. When offered a choice between a typical benthic prey item and a typical pelagic food item, charr of benthivorous origin were more likely to feed on the former, whereas those of planktivorous origin were more likely to feed on the latter. Thus inherited differences in gape place constraints on foraging ability and are associated with inherited differences in dietary preference. We conclude that the functional significance of the foraging specialisations indicate a strong selection pressure for the evolution of the divergence and propose that heterochronic growth is the mechanism resulting in the divergence of tropic anatomy.     

Zooplankton in Loch Lomond: perspectives,predation and powan

Published and unpublished accounts of the zooplankton community of Loch Lomond are reviewed. Loch Lomond's zooplankton community is unique amongst those of Scotland's other large lochs. Holopedium gibberum appeared in Loch Lomond in the years between the studies of Slack & Hamilton in the 1950s and zooplankton surveys in the late 1970s.The annual cycles of Eudiaptomus gracilis, Cyclops strenuus abyssorum and Mesocyclops leuckarti are described for the mid basin of Loch Lomond. E. gracilis overwinter mainly as adult with variable egg production during their lifespan of 5–8 months. The cyclopoid copepods have variable life history characteristics. C. str. abyssorum produce a single generation per year, overwinter by means of resting eggs and a small population of planktonic adults, while M. leuckarti is present in the plankton throughout the year, but in low numbers during winter.Zooplankton populations in Loch Lomond are predated by the diverse fish community which includes a facultative planktivore in the powan, Coregonus lavaretus. Powan feed heavily on zooplankton from late spring until late autumn. Powan display selectivity in the prey species taken, in the size distribution and morph types taken within prey species. Zooplankton species, morphs and forms in Loch Lomond tend to reflect this predation.Zoology Department, University of St. AndrewsZoology Department, University of St. Andrews     

Genetic differentiation of Arctic charr <Emphasis Type="Italic">Salvelinus alpinus</Emphasis> complex from Transbaikalia revealed by microsatellite markers

Variation at eight microsatellite loci was studied in Arctic charr Salvelinus alpinus complex from five Transbaikalian mountain lakes. Samples from three lakes included two sympatric charr forms (dwarf and small) differing in trophic specialization, morphology and life cycle parameters. Sympatric forms were genetically closer to each other than to charr from other lakes which evidences their independent origin in each of these lakes as the result of sympatric speciation. In each lake, gene pools of sympatric forms were segregated to a different degree (estimates of F _ST varying from 0.030–0.184 and those of ρ _ST varying from 0.119–0.359). Hierarchical analysis of allelic frequencies variance (AMOVA) in Arctic charr from Lake Baikal, the Vitim, and the Olekma basins showed that variation among and within these basins accounted for 19.5% of the interpopulational variance each. In the AMOVA design, investigating differences among sympatric forms in three lakes these differences accounted for 7.1% of the total variance.     

Characterizing neutral and adaptive genomic differentiation in a changing climate: The most northerly freshwater fish as a model

Arctic freshwater ecosystems have been profoundly affected by climate change. Given that the Arctic charr (Salvelinus alpinus) is often the only fish species inhabiting these ecosystems, it represents a valuable model for studying the impacts of climate change on species life‐history diversity and adaptability. Using a genotyping‐by‐sequencing approach, we identified 5,976 neutral single nucleotide polymorphisms and found evidence for reduced gene flow between allopatric morphs from two high Arctic lakes, Linne'vatn (Anadromous, Normal, and Dwarf) and Ellasjøen (Littoral and Pelagic). Within each lake, the degree of genetic differentiation ranged from low (Pelagic vs. Littoral) to moderate (Anadromous and Normal vs. Dwarf). We identified 17 highly diagnostic, putatively adaptive SNPs that differentiated the allopatric morphs. Although we found no evidence for adaptive differences between morphs within Ellasjøen, we found evidence for moderate (Anadromous vs. Normal) to high genetic differentiation (Anadromous and Normal vs. Dwarf) among morphs within Linne'vatn based on two adaptive loci. As these freshwater ecosystems become more productive, the frequency of sympatric morphs in Ellasjøen will likely shift based on foraging opportunities, whereas the propensity to migrate may decrease in Linne'vatn, increasing the frequency of the Normal morph. The Dwarf charr was the most genetically distinct group. Identifying the biological basis for small body size should elucidate the potential for increased growth and subsequent interbreeding with sympatric morphs. Overall, neutral and adaptive genomic differentiation between allopatric and some sympatric morphs suggests that the response of Arctic charr to climate change will be variable across freshwater ecosystems.