Parasite burdens differ between sympatric three-spined stickleback species

The ecological theory of adaptive radiation states that differences in ecological circumstances among local populations are the cause of divergence that leads to speciation. The role of parasites in contributing to divergence has seldom been considered, despite their ubiquity and known selective effects. The potential for parasites to contribute to divergence between closely related taxa was examined by quantifying the variation in parasite burdens between sympatric three-spined stickleback species ( Gasterosteus aculeatus complex) in two lakes in coastal British Columbia, Canada. In doing so the relative importance of geographical differences between lakes and trophic or microhabitat differences between species within lakes were evaluated. The entire metazoan parasite burdens of a total of 255 limnetic and benthic sticklebacks in Paxton and Priest lakes were assayed over five time points between spring and autumn. Despite their sympatric distributions, there were large differences in parasite burdens between benthic and limnetic sticklebacks within lakes and these were consistent across both lakes. In particular, limnetics suffered greater burdens of the parasites Schistocephalus solidus and Diplostomum scudderi and benthics had much higher burdens of parasitic glochidia (mollusc larvae). Parasite burdens also differed quantitatively between lakes, but in general such differences were less pronounced than those between the stickleback species. The documented differences in parasite burdens between stickleback species have potential to contribute to divergent selection on life history, immunological and secondary sexual characters that could contribute to reproductive isolation between the species.     

Adaptive plasticity and genetic divergence in feeding efficiency during parallel adaptive radiation of whitefish (Coregonus spp.)

Parallel phenotypic divergence in replicated adaptive radiations could either result from parallel genetic divergence in response to similar divergent selection regimes or from equivalent phenotypically plastic response to the repeated occurrence of contrasting environments. In post‐glacial fish, replicated divergence in phenotypes along the benthic‐limnetic habitat axis is commonly observed. Here, we use two benthic‐limnetic species pairs of whitefish from two Swiss lakes, raised in a common garden design, with reciprocal food treatments in one species pair, to experimentally measure whether feeding efficiency on benthic prey has a genetic basis or whether it underlies phenotypic plasticity (or both). To do so, we offered experimental fish mosquito larvae, partially burried in sand, and measured multiple feeding efficiency variables. Our results reveal both, genetic divergence as well as phenotypically plastic divergence in feeding efficiency, with the phenotypically benthic species raised on benthic food being the most efficient forager on benthic prey. This indicates that both, divergent natural selection on genetically heritable traits and adaptive phenotypic plasticity, are likely important mechanisms driving phenotypic divergence in adaptive radiation.     

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.     

Phenotypic Plasticity and the Ecotypic Differentiation of Aggressive Behavior in Threespine Stickleback

The threespine stickleback fish, Gasterosteus aculeatus, has undergone a remarkable postglacial adaptive radiation in which an ancient oceanic ancestor has given rise to uncountable freshwater populations. The radiation is characterized by repeated, independent evolution of similar derived phenotypes under similar environmental conditions. A common pattern of divergence is caused by differences in habitat that favor morphological and behavioral features that enhance efficiency of feeding on plankton (limnetic ecotypes) vs. those that enhance efficiency of feeding on benthic invertebrates (benthic ecotypes). These two ecotypes exhibit consistently different patterns of courtship and of foraging and cannibalistic behavior (divergent behavioral syndromes). Here, we demonstrate that there also exist differences in aggression toward conspecifics that are likely to be characteristic of the ecotypes. We report differences in patterns of aggression toward rivals between the ecotypes and offer evidence of differences in the patterns of phenotypic plasticity (norms of reaction) for these traits across population types, and of differences in the incorporation of aggressive elements of behavior in courtship. These data support an earlier suggestion that differences in aggressive tendencies could have facilitated assortative mating between the four benthic–limnetic species pairs found in British Columbia lakes, and they demonstrate the need to evaluate divergent behavioral phenotypes in this radiation as phenotypic norms of reaction rather than as fixed traits.     

Frequency dependent natural selection during character displacement in sticklebacks

Abstract We know little about how natural selection on a species is altered when a closely related species consuming similar resources appears in its environment. In a pond experiment with threespine sticklebacks I tested the prediction that divergent natural selection between competitors is frequency-dependent, changing with the distribution of phe-notypes in the environment. Differential growth and survival of phenotypes in a target stickleback population were contrasted between two treatments. In one treatment an offshore zooplankton feeder (the limnetic stickleback species) was added to the same pond as the target. In the other treatment I added the benthic stickleback instead, a species adapted to feeding on invertebrates from sediments and inshore vegetation. The target population was ecologically and morphologically intermediate with phenotypic variance artificially inflated by hybridization. Growth rates of phenotypes within the target population differed between treatments as predicted by character displacement. The impact of adding a second species always fell most heavily on those phenotypes in the target population resembling the added species most closely. However, those individuals in the target population that most resembled the added species did not experience reduced survival. Instead, consistent survival differences between populations suggested the presence of an inshore –offshore gradient in mortality risk. These results provide further support for the hypothesis of character displacement in sympatric sticklebacks. They suggest that displacement along the resource gradient also led to divergence in vulnerability to agents of mortality, probably including predation.     

Evolutionary history of an adaptive radiation in species pairs of threespine sticklebacks (Gasterosteus): insights from mitochondrial DNA

Species pairs of threespine stickleback, Gasterosteus aculeatus, co-exist in several lakes in the Strait of Georgia, southwestern British Columbia. One species, ‘benthics’ is robust-bodied and is morphologically and behaviourally specialized for benthivory. The other species, ‘limnetics’ is specialized for planktivory in open-water habitats of the lakes. We examined mitochondrial DNA restriction site variation in benthic and limnetic sticklebacks as well as in solitary freshwater, anadromous (sea-run), and marine populations to test: (i) if benthic and limnetic pairs have evolved only once or multiple times (parallel evolution) and (ii) if the species have evolved sympatrically, or allopatrically from ‘double invasions’ of lakes by ancestral anadromous/marine sticklebacks. Stickleback mtDNA comprised a single clade with a low (mean = 0.40%) degree of sequence divergence among the 77 haplotypes resolved. Most nucleotide diversity (97%) was found within (rather than among) populations of anadromous/marine sticklebacks whereas most diversity (77%) was found among populations in freshwater sticklebacks. Significant differences in haplotype frequencies were found between benthics and limnetics in three of the four species pair lakes examined, but in all cases the pairs within lakes were characterized by unique assemblages of closely related haplotypes. Hierarchical clustering of divergence estimates suggested that comparable species from different lakes have originated independently in all lakes because in no case did comparable species from different lakes cluster together. Divergent species within lakes tended to be more closely related to one another than to species in other lakes and there were two cases were benthics and limnetics within a particular lake were monophyletic. In two of the four two-species lakes, limnetics were less divergent from putative ancestral anadromous/marine stickleback as predicted by the double invasion hypothesis, but in the two other lakes benthics were less divergent. Our data argue strongly that the species pairs have evolved independently in each lake were they now co-exist. Further, in two lakes our data are consistent with the species having evolved by sympatric divergence, but allopatric divergence followed by introgression of mtDNA that has obscured ancestral relationships cannot be discounted completely. Finally, despite remaining uncertainty about the geography of speciation, the species appear to have evolved in the face of gene flow arguing that natural selection acting on trophic ecology has been a major component of ecological speciation in sticklebacks.     

Axial variation in the three-spine stickleback: genetic and environmental factors

Subtle differences in the pattern of arrangement of types of vertebrae and associated median skeletal structures between a benthic and limnetic species pair of threespine stickleback from Paxton Lake, British Columbia, are typical of those found throughout the range of the Gasterosteus aculeatus species complex. We established laboratory colonies from just three individuals of each species, and studied the effect of three generations of inbreeding on axial morphology. There was sufficient divergence in the location of individual elements between families to regenerate close to the entire range of axial diversity seen in threespine sticklebacks worldwide. Analysis of the patterns of variance and covariance between the axial locations of elements provides evidence for the action of both meristic and homeotic processes in the generation of morphological divergence within each species. Hybrid sticklebacks produced by the cross of limnetic and benthic parents tend to have intermediate morphologies, with dominance of either parental type evident for some elements. Effects of temperature and salinity were found to be small in direct comparison with between-family effects, and varied according to genetic background. These results demonstrate that considerable genetic variation for axial morphology is maintained in natural populations of threespine stickleback, and that differences between populations may be brought about rapidly by changes in frequency of alleles that have coordinated effects along the body axis.     

Two morphotypes of lacustrine threespine stickleback,Gasterosteus aculeatus, in Benka Lake, Alaska

Synopsis Within freshwater fishes, a common pattern of diversification of body form and trophic structure has recently been recognized. Two different suites of co-occurring characters appear to allow fish to efficiently forage on either benthic invertebrates or plankton. For threespine stickleback,Gasterosteus aculeatus, these suites of characters have been labeled benthic and limnetic. The forms differ in several morpholoical traits, with the limnetic having a more fusiform shape, larger eyes, longer and more numerous gill rakers, and a smaller more tubular mouth. Benthic and limnetic threespine stickleback are usually found in allopatry or parapatry, and less frequently in sympatry. Within the range of the threespine stickleback, which comprises perhaps tens of thousands of lacustrine populations, the sympatric occurrence of the benthic and limnetic forms has only been established for six lakes within a small region of the Strait of Georgia, British Columbia. We present the first evidence for the presence of sympatric morphotypes of threespine stickleback outside of British Columbia. We examine the nature and extent of this diversification, and present possible explanations for the sympatric occurrence of these morphotypes. We also explore possible reasons for the small number of documented sympatric benthic and limnetic forms of threespine stickleback despite the existence of thousands of apparently suitable lakes.     

Niche specialization influences adaptive phenotypic plasticity in the threespine stickleback

Phenotypic plasticity may be favored in generalist populations if it increases niche width, even in temporally constant environments. Phenotypic plasticity can increase the frequency of extreme phenotypes in a population and thus allow it to make use of a wide resource spectrum. Here we test the prediction that generalist populations should be more plastic than specialists. In a common-garden experiment, we show that solitary, generalist populations of threespine sticklebacks inhabiting small coastal lakes of British Columbia have a higher degree of morphological plasticity than the more specialized sympatric limnetic and benthic species. The ancestral marine stickleback showed low levels of plasticity similar to those of sympatric sticklebacks, implying that the greater plasticity of the generalist population has evolved recently. Measurements of wild populations show that those with mean trait values intermediate between the benthic and limnetic values indeed have higher morphological variation. Our data indicate that plasticity can evolve rapidly after colonization of a new environment in response to changing niche use.     

Resource diversity promotes among‐individual diet variation,but not genomic diversity,in lake stickleback

Many generalist species consist of specialised individuals that use different resources. This within‐population niche variation can stabilise population and community dynamics. Consequently, ecologists wish to identify environmental settings that promote such variation. Theory predicts that environments with greater resource diversity favour ecological diversity among consumers (via disruptive selection or plasticity). Alternatively, niche variation might be a side‐effect of neutral genomic diversity in larger populations. We tested these alternatives in a metapopulation of threespine stickleback. Stickleback consume benthic and limnetic invertebrates, focusing on the former in small lakes, the latter in large lakes. Intermediate‐sized lakes support generalist stickleback populations using an even mixture of the two prey types, and exhibit greater among‐individual variation in diet and morphology. In contrast, genomic diversity increases with lake size. Thus, phenotypic diversity and neutral genetic polymorphism are decoupled: trophic diversity being greatest in intermediate‐sized lakes with high resource diversity, whereas neutral genetic diversity is greatest in the largest lakes.     

A test of hybrid growth disadvantage in wild, free-ranging species pairs of threespine stickleback (Gasterosteus aculeatus) and its implications for ecological speciation

Ecological speciation is the evolution of reproductive isolation as a direct or indirect consequence of divergent natural selection. Reduced performance of hybrids in nature is thought to be an important process by which natural selection can favor the evolution of assortative mating and drive speciation. Benthic and limnetic sympatric species of threespine stickleback (Gasterosteus aculeatus) are adapted to alternative trophic niches (bottom browsing vs. open water planktivory, respectively) and reduced feeding performance of hybrids is thought to have contributed to the evolution of reproductive isolation. We tested this “hybrid‐disadvantage hypothesis” by inferring growth rates from otoliths sampled from wild, free‐ranging benthic, limnetic, and hybrid sticklebacks in two lakes. There were significant differences in growth rate between lakes, life‐history stages, and among years (maximum P = 0.02), as well as interactions between most factors, but not between hybrid and parental species sticklebacks in most comparisons. Our results provide little evidence of a growth disadvantage in hybrid sticklebacks when free‐ranging in nature. Although trophic ecology per se may contribute less to ecological speciation than envisioned, it may act in concert with other aspects of stickleback biology, such as interactions with parasites, predators, competitors, and/or sexual selection, to present strong multifarious selection against hybrids.     

EXPERIMENTAL CONFIRMATION THAT BODY SIZE DETERMINES MATE PREFERENCE VIA PHENOTYPE MATCHING IN A STICKLEBACK SPECIES PAIR

Mate choice by phenotype matching, whereby individuals prefer a mate whose phenotype is similar to their own, should facilitate speciation with gene flow. This is because the genes that control mate signal (the phenotype being matched) also determine the preferred mate signal (“mate preference”). Speciation is made even easier if phenotype matching is based on a trait under divergent natural selection. In this case, assortative mating should readily evolve as a byproduct of divergent selection on the trait. Previous observational studies of assortative mating between sympatric, hybridizing threespine stickleback species (Gasterosteus aculeatus complex) suggested that phenotype matching might occur by body size, a trait under divergent natural selection. To test this, we used experimental manipulation of body size to rule out the effects of confounding variables. We found that size‐manipulated benthic and limnetic stickleback females prefer mates whose body size more closely matches their own. It is thus likely that assortative mating by phenotype matching has facilitated the origin and persistence of benthic and limnetic threespine sticklebacks in the face of gene flow.     

Lake Malawi cichlid evolution along a benthic/limnetic axis

Divergence along a benthic to limnetic habitat axis is ubiquitous in aquatic systems. However, this type of habitat divergence has largely been examined in low diversity, high latitude lake systems. In this study, we examined the importance of benthic and limnetic divergence within the incredibly species‐rich radiation of Lake Malawi cichlid fishes. Using novel phylogenetic reconstructions, we provided a series of hypotheses regarding the evolutionary relationships among 24 benthic and limnetic species that suggests divergence along this axis has occurred multiple times within Lake Malawi cichlids. Because pectoral fin morphology is often associated with divergence along this habitat axis in other fish groups, we investigated divergence in pectoral fin muscles in these benthic and limnetic cichlid species. We showed that the eight pectoral fin muscles and fin area generally tended to evolve in a tightly correlated manner in the Lake Malawi cichlids. Additionally, we found that larger pectoral fin muscles are strongly associated with the independent evolution of the benthic feeding habit across this group of fish. Evolutionary specialization along a benthic/limnetic axis has occurred multiple times within this tropical lake radiation and has produced repeated convergent matching between exploitation of water column habitats and locomotory morphology.     

Evolutionary interplay between ecology,morphology and reproductive behavior in threespine stickleback,Gasterosteus aculeatus

Synopsis Throughout its range, freshwater populations in the Gasterosteus aculeatus species complex display remarkable differentiation of morphology and behavior, much of which reflects differences in ecological conditions among habitats. We first describe the ecological conditions that have led to morphological and behavioral divergence in two common lake types in British Columbia, Canada. Deep, oligotrophic lakes have favored the evolution of slender fish well adapted for feeding on plankton (limnetic, sensu McPhail 1984), whereas shallow, more eutrophic lakes with extensive littoral zones favor fish that are deeper-bodied and well adapted for feeding on benthic invertebrates. The latter forage in large groups that attack nests guarded by males and cannibalize the young within. Courtship in these lakes is relatively inconspicuous, a feature that apparently enhances nest survivorship. In limnetic populations, this form of cannibalism is usually absent and courtship is conspicuous. Because benthic populations tend to have larger bodies and hence, larger gapes than do limnetic fish we suggest that cannibalism may be facilitated by large body size or a correlated trait. We test this by comparing the morphology of populations exhibiting both group cannibalism and a second kind of cannibalism in which solitary females court males, gain access to nests as a consequence, and then cannibalize eggs without spawning. Our results suggest that differences in body size cannot explain variation among populations in cannibalistic tendencies but that body size may affect the effectiveness of cannibalism by females within populations.     

Morphological variation in pumpkinseed Lepomis gibbosus introduced into Iberian lakes and reservoirs; adaptations to habitat type and diet?

The morphology of pumpkinseed Lepomis gibbosus populations from five Catalonian waterbodies (north-eastern Spain) that vary in hydromorphometry was examined and compared to a native North American reference site that contained two morphological variants of this species. Populations exhibited significant differences in fin location, body depth and caudal peduncle length, which are known to have functional significance in the hydrodynamics of swimming and hence the foraging mode. Differences were also noted in internal morphological traits functionally related to prey selection. Pumpkinseed populations that fed extensively on zooplankton showed narrow gill raker spacing, and mollusc-feeding populations had longer and wider pharyngeal bones. Discriminant function analysis (DFA) provided significant separation of all populations on the basis of both external and internal morphology, with the main axis of separation being geographical rather than environmental. The secondary DFA axis, however, did separate populations that fed primarily on zooplankton from those that were primarily benthic invertebrate feeders. In this regard, a population that occupied an Iberian steep-sided reservoir with an unstable littoral zone showed similar morphological adaptations to the limnetic morphological variant native in North America, supporting previous studies showing that fish morphology is strongly affected by prey type and feeding mode. The results suggest that pumpkinseeds are able to adapt, morphologically, to the types of habitats and prey present in Catalonian waterbodies, and this may partially explain why they are so successful in areas where they have been introduced.     

Ancestral Plasticity and Allometry in Threespine Stickleback Fish Reveal Phenotypes Associated with Derived, Freshwater Ecotypes

For over a century, evolutionary biologists have debated whether and how phenotypic plasticity impacts the processes of adaptation and diversification. The empirical tests required to resolve these issues have proven elusive, mainly because it requires documentation of ancestral reaction norms, a difficult prospect where many ancestors are either extinct or have evolved. The threespine stickleback radiation is not limited in this regard, making it an ideal system in which to address general questions regarding the role of plasticity in adaptive evolution. As retreating ice sheets have exposed new habitats, oceanic stickleback founded innumerable freshwater populations, many of which have evolved parallel adaptations to their new environments. Because the founding oceanic population is extant, we can directly evaluate whether specific patterns of ancestral phenotypic expression in the context of novel environments (plasticity), or over ontogeny, predisposed the repeated evolution of "benthic" and "limnetic" ecotypes in shallow and deep lakes, respectively. Consistent with this hypothesis, we found that oceanic stickleback raised in a complex habitat and fed a macroinvertebrate diet expressed traits resembling derived, benthic fish. Alternatively, when reared in a simple environment on a diet of zooplankton, oceanic stickleback developed phenotypes resembling derived, limnetic fish. As fish in both treatments grew, their body depths increased allometrically, as did the size of their mouths, while their eyes became relatively smaller. Allometric trajectories were subtly but significantly impacted by rearing environment. Thus, both environmental and allometric influences on development, along with their interactive effects, produced variation in phenotypes consistent with derived benthic and limnetic fish, which may have predisposed the repeated genetic accommodation of this specific suite of traits. We also found significant shape differences between marine and anadromous stickleback, which has implications for evaluating the ancestral state of stickleback traits.     

Character shifts in the defensive armor of sympatric sticklebacks

Natural enemies may contribute to the morphological divergence of sympatric species, yet their role has received little attention to date. We tested for character shifts in defensive armor of sympatric threespine sticklebacks (Gasterosteus aculeatus complex) previously shown to exhibit ecological character displacement in traits related to resource use. We scored five defensive armor traits in sympatric benthic and limnetic stickleback species from southwestern British Columbia and compared them with the same traits in nearby allopatric populations in the presence of the same predatory fish (Oncorhynchus sp.). This approach is analogous to tests of ecological character displacement that compare trophic traits of sympatric and allopatric species in the presence of the same community of resource types. Three patterns consistent with character displacement in defensive armor were found. First, limnetics in different lakes had consistently more armor than sympatric benthics. Second, the average amount of armor, averaged over both species, was reduced in sympatry compared to allopatric populations. This reduction was almost entirely the result of shifts by benthic species, whereas armor in limnetics was more similar to that in allopatric populations. Third, differences between sympatric benthics and limnetics in total armor were greater than expected from comparisons with allopatric populations. We interpret these patterns as the result of differences in habitat-specific predation regimes accompanying ecological character displacement and indirect interactions between sympatric stickleback species mediated by their top predators. These results suggest that predation may facilitate, rather than hinder, the process of divergence in sympatry.     

Genomic architecture of ecologically divergent body shape in a pair of sympatric crater lake cichlid fishes

Determining the genetic bases of adaptations and their roles in speciation is a prominent issue in evolutionary biology. Cichlid fish species flocks are a prime example of recent rapid radiations, often associated with adaptive phenotypic divergence from a common ancestor within a short period of time. In several radiations of freshwater fishes, divergence in ecomorphological traits — including body shape, colour, lips and jaws — is thought to underlie their ecological differentiation, specialization and, ultimately, speciation. The Midas cichlid species complex (Amphilophus spp.) of Nicaragua provides one of the few known examples of sympatric speciation where species have rapidly evolved different but parallel morphologies in young crater lakes. This study identified significant QTL for body shape using SNPs generated via ddRAD sequencing and geometric morphometric analyses of a cross between two ecologically and morphologically divergent, sympatric cichlid species endemic to crater Lake Apoyo: an elongated limnetic species (Amphilophus zaliosus) and a high‐bodied benthic species (Amphilophus astorquii). A total of 453 genome‐wide informative SNPs were identified in 240 F₂ hybrids. These markers were used to construct a genetic map in which 25 linkage groups were resolved. Seventy‐two segregating SNPs were linked to 11 QTL. By annotating the two most highly supported QTL‐linked genomic regions, genes that might contribute to divergence in body shape along the benthic–limnetic axis in Midas cichlid sympatric adaptive radiations were identified. These results suggest that few genomic regions of large effect contribute to early stage divergence in Midas cichlids.     

Intraguild predation leads to genetically based character shifts in the threespine stickleback

Intraguild predation is a common ecological interaction that occurs when a species preys upon another species with which it competes. The interaction is potentially a mechanism of divergence between intraguild prey (IG‐prey) populations, but it is unknown if cases of character shifts in IG‐prey are an environmental or evolutionary response. We investigated the genetic basis and inducibility of character shifts in threespine stickleback from lakes with and without prickly sculpin, a benthic intraguild predator (IG‐predator). Wild populations of stickleback sympatric with sculpin repeatedly show greater defensive armor and water column height preference. We laboratory‐raised stickleback from lakes with and without sculpin, as well as marine stickleback, and found that differences between populations in armor, body shape, and behavior persisted in a common garden. Within the common garden, we raised stickleback half‐families from multiple populations in the presence and absence of sculpin. Although the presence of sculpin induced trait changes in the marine stickleback, we did not observe an induced response in the freshwater stickleback. Behavioral and morphological trait differences between freshwater populations thus have a genetic basis and suggest an evolutionary response to intraguild predation.     

Crater lake cichlids individually specialize along the benthic–limnetic axis

A common pattern of adaptive diversification in freshwater fishes is the repeated evolution of elongated open water (limnetic) species and high‐bodied shore (benthic) species from generalist ancestors. Studies on phenotype‐diet correlations have suggested that population‐wide individual specialization occurs at an early evolutionary and ecological stage of divergence and niche partitioning. This variable restricted niche use across individuals can provide the raw material for earliest stages of sympatric divergence. We investigated variation in morphology and diet as well as their correlations along the benthic‐limnetic axis in an extremely young Midas cichlid species, Amphilophus tolteca, endemic to the Nicaraguan crater lake Asososca Managua. We found that A. tolteca varied continuously in ecologically relevant traits such as body shape and lower pharyngeal jaw morphology. The correlation of these phenotypes with niche suggested that individuals are specialized along the benthic‐limnetic axis. No genetic differentiation within the crater lake was detected based on genotypes from 13 microsatellite loci. Overall, we found that individual specialization in this young crater lake species encompasses the limnetic‐ as well as the benthic macro‐habitat. Yet there is no evidence for any diversification within the species, making this a candidate system for studying what might be the early stages preceding sympatric divergence.