Genetic variation and phenotypic plasticity in a trophically polymorphic population of pumpkinseed sunfish (Lepomis gibbosus)

Summary Adaptive variation can exist at a variety of scales in biological systems, including among species, among local populations of a single species and among individuals within a single population. Trophic or resource polymorphisms in fishes are a good example of the lowest level of this hierarchy. In lakes without bluegill sunfish (Lepomis macrochirus), pumpkinseed sunfish (Lepomis gibbosus) can be trophically polymorphic, including a planktivorous limnetic form found in the pelagic habitat, in addition to the usual benthic form found in the littoral zone. In this paper we examine the degree to which morphological differences between the two forms are caused by genetic differences versus phenotypic plasticity. Adults from pelagic and littoral sites in Paradox Lake, NY, were bred separately and their progeny were raised in cages both in the open water and shallow water habitats of an artificial pond. The experimental design permitted two tests of genetic differences between the breeding stocks (in open and shallow water cages, respectively) and two tests of phenotypic plasticity (in the limnetic and benthic offspring, respectively). Limnetic progeny were more fusiform than benthic progeny raised in the same habitat. In addition, progeny of both stocks displayed limnetic-type characteristics when raised in the open water and benthic-type characteristics in the shallow water. Thus, genetic differences and phenotypic plasticity both contributed to the trophic polymorphism. Phenotypic plasticity and genetic differentiation accounted for 53 and 14%, respectively, of the variation in morphology. This study addresses the nature of subtle phenotypic differences among individuals from a single population that is embedded within a complex community, a condition that is likely to be the norm for most natural populations, as opposed to very large differences that have evolved in relatively few populations that reside in species-poor environments.     

Macrophyte development in unimpacted lowland rivers in Poland

Three ecologically and morphologically distinct forms of Arctic charr (Salvelinus alpinus L.) have been identified in Loch Rannoch, Scotland, whose evolutionary status and origins are incompletely understood. A study was made of restriction fragment length polymorphism (RFLPs) detected variation in the D-loop, ND1 and cytochrome b regions of the mitochondrial genome, encompassing >3500 bp. Eight RFLP haplotypes were identified that clustered into three distinct clans based on restriction differences and into four clans based on sequence differences. Significant differences in RFLP frequencies were found among all morph groups. The pelagic morph was highly divergent from the two benthic forms, with the benthic forms having variants from only one genetic clan while the pelagic was dominated by a single variant from another clan. The relative divergence observed among benthic and pelagic forms is ~10 fold greater when nucleotide divergence among the haplotypes, as well as haplotype frequency differences, is taken into account. Sequence divergence between haplotypes in the two main clans is of a similar order to that between haplotypes in these clans and a charr from North America. In contrast, divergence among the two benthic morphs relates entirely to differences in haplotype frequencies. The study confirms the genetic distinctiveness of the pelagic and benthic forms as well as of the two benthic forms. It strongly supports previous evidence that the genetic divergence between the pelagic and benthic populations is allopatric in origin. Additionally, the results strongly suggest that the two benthic populations have undergone peripatric divergence through the sequential colonisation of the two basins by one lineage, followed by their spatial separation and reproductive isolation.     

The relative importance of plasticity versus genetic differentiation in explaining between population differences; a meta‐analysis

Both plasticity and genetic differentiation can contribute to phenotypic differences between populations. Using data on non‐fitness traits from reciprocal transplant studies, we show that approximately 60% of traits exhibit co‐gradient variation whereby genetic differences and plasticity‐induced differences between populations are the same sign. In these cases, plasticity is about twice as important as genetic differentiation in explaining phenotypic divergence. In contrast to fitness traits, the amount of genotype by environment interaction is small. Of the 40% of traits that exhibit counter‐gradient variation the majority seem to be hyperplastic whereby non‐native individuals express phenotypes that exceed those of native individuals. In about 20% of cases plasticity causes non‐native phenotypes to diverge from the native phenotype to a greater extent than if plasticity was absent, consistent with maladaptive plasticity. The degree to which genetic differentiation versus plasticity can explain phenotypic divergence varies a lot between species, but our proxies for motility and migration explain little of this variation.     

Genetic and morphological variation between two forms of lacustrine brook charr

Genetic data suggest that the littoral and pelagic forms of brook charr Salvelinus fontinalis in Lake Bondi are two populations with partial reproductive isolation and non-random mating. Genetic differentiation between the two groups was supported by differences in allele frequencies and by deviation from Hardy-Weinberg equilibrium when the two groups were pooled; no such deviation was observed when fish were divided into littoral and pelagic groups. In contrast to Lake Bondi, no clear evidence of genetic differentiation was observed in Lake Ledoux. Discriminant function analyses of morphological characters support the existence of littoral and pelagic groups in Bondi and Ledoux Lakes. In Lake Bondi, the two groups differed significantly in two shape variables (pelagic fish had shorter dorsal fins, and longer body length posterior to the dorsal fin than littoral ones) whereas in Lake Ledoux, the groups differed in four shape variables (pelagic fish had shorter pectoral fins, shorter dorsal fins, and a shorter and higher caudal peduncle than littoral ones). Discriminant analyses of these characters were effective in reclassifying fish into their appropriate groups in both populations, with an efficiency of 78% for juveniles in Lake Bondi and 69% for adults in Lake Ledoux. Differences in morphology between the two forms are consistent with adaptations required to forage in each zone, i.e. benthic form in the littoral zone and planktivorous form in the pelagic zone.     

Extensive genetic differentiation between recently evolved sympatric Arctic charr morphs

The availability of diverse ecological niches can promote adaptation of trophic specializations and related traits, as has been repeatedly observed in evolutionary radiations of freshwater fish. The role of genetics, environment, and history in ecologically driven divergence and adaptation, can be studied on adaptive radiations or populations showing ecological polymorphism. Salmonids, especially the Salvelinus genus, are renowned for both phenotypic diversity and polymorphism. Arctic charr (Salvelinus alpinus) invaded Icelandic streams during the glacial retreat (about 10,000 years ago) and exhibits many instances of sympatric polymorphism. Particularly, well studied are the four morphs in Lake Þingvallavatn in Iceland. The small benthic (SB), large benthic (LB), planktivorous (PL), and piscivorous (PI) charr differ in many regards, including size, form, and life history traits. To investigate relatedness and genomic differentiation between morphs, we identified variable sites from RNA‐sequencing data from three of those morphs and verified 22 variants in population samples. The data reveal genetic differences between the morphs, with the two benthic morphs being more similar and the PL‐charr more genetically different. The markers with high differentiation map to all linkage groups, suggesting ancient and pervasive genetic separation of these three morphs. Furthermore, GO analyses suggest differences in collagen metabolism, odontogenesis, and sensory systems between PL‐charr and the benthic morphs. Genotyping in population samples from all four morphs confirms the genetic separation and indicates that the PI‐charr are less genetically distinct than the other three morphs. The genetic separation of the other three morphs indicates certain degree of reproductive isolation. The extent of gene flow between the morphs and the nature of reproductive barriers between them remain to be elucidated.     

Effects of geography and life history traits on genetic differentiation in benthic marine fishes

Dispersal of planktonic larvae can create connections between geographically separated adult populations of benthic marine animals. How geographic context and life history traits affect these connections is largely unresolved. We use data from genetic studies (species level F_ST) of benthic teleost fishes combined with linear models to evaluate the importance of transitions between biogeographic regions, geographic distance, egg type (benthic or pelagic eggs), pelagic larval duration (PLD), and type of genetic marker as factors affecting differentiation within species. We find that transitions between biogeographic regions and egg type are significant and consistent contributors to population genetic structure, whereas PLD does not significantly explain population structure. Total study distance frequently contributes to significant interaction terms, particularly in association with genetic markers, whereby F_ST increases with study distance for studies employing mtDNA sequences, but allozyme and microsatellite studies show no increase in F_ST with study distance. These results highlight the importance of spatial context (biogeography and geographic distance) in affecting genetic differentiation and imply that there are inherent differences in dispersal ability associated with egg type. We also find that the geographic distance over which the maximum pairwise F_ST between populations occurs (relative to total study distance) is highly variable and can be observed at any scale. This result is consistent with stochastic processes inflating genetic differentiation and/or insufficient consideration of geographic and biological factors relevant to connectivity.     

Phenotypic plasticity and genetic isolation-by-distance in the freshwater mussel <Emphasis Type="Italic">Unio pictorum</Emphasis> (Mollusca: Unionoida)

Freshwater mussels (Unionoida) show high intraspecific morphological variability, and some shell morphological traits are believed to be associated with habitat conditions. It is not known whether and which of these ecophenotypic differences reflect underlying genetic differentiation or are the result of phenotypic plasticity. Using 103 amplified fragment length polymorphism (AFLP) markers, we studied population genetics of three paired Unio pictorum populations sampled from two different habitat types (marina and river) along the River Thames. We found genetic differences along the Thames which were consistent with a pattern of isolation by distance and probably reflect limited dispersal via host fish species upon which unionoid larvae are obligate parasites. No consistent genetic differences were found between the two different habitat types suggesting that morphological differences in the degree of shell elongation and the shape of dorso-posterior margin are caused by phenotypic plasticity. Our study provides the first good evidence for phenotypic plasticity of shell shape in a European unionoid and illustrates the need to include genetic data in order properly to interpret geographic patterns of morphological variation.     

Molecular genetic examination of the polymorphic Arctic charr Salvelinus alpinus of Thingvallavatn, Iceland

Thingvallavatn, Iceland contains two sympatric morphotypes (benthic and limnetic) of Arctic charr Salvelinus alpinus. Each morphotype is composed of two morphs and these differ markedly in ecology, behaviour and life history. We used molecular genetic approaches to test whether (i) genetic heterogeneity exists among morphs and (ii) if morphs arose in allopatry and came into secondary contact or arose sympatrically within the lake through genetic segregation and/or phenotypic plasticity. Direct sequencing of 275 bp of the mitochondrial DNA (mtDNA) control region, mtDNA restriction fragment length polymorphisms and single locus minisatellite analyses detected insufficient variation to test our hypotheses. Analysis of multilocus minisatellite band sharing detected no significant differences between morphs within the same morphotype. However, significant differences among morphs belonging to different morphotypes suggest some genetic heterogeneity in Thingvallavatn charr. Limnetic charr from Thingvallavatn were more similar to sympatric benthic charr than to allopatric limnetics from two other Icelandic lakes. This suggests that the Thingvallavatn morphs arose sympatrically within the lake rather than in allopatry followed by secondary contact.     

Individual variations in habitat use and morphology in brook charr

The specific objectives of this study were to determine if there is individual specialization in habitat use by lacustrine brook charr Salvelinus fontinalis and if so, if specialization is related to fish morphology. Localizations of 28 brook charr equipped with thermosensitive radiotransmitters were recorded during three summers (1991, 1992, and 1993) in two lakes of the Mastigouche Reserve (Québec, Canada). Fifty per cent of the fish were found mainly in the benthic zone (hereafter benthic individuals), 18% in the pelagic zone (pelagic individuals), and 32% travelled regularly between the two zones (generalist individuals). The observed interindividual differences in habitat preference were related to differences in body morphology and coloration: (i) the pectoral fins of benthic and generalist individuals were significantly longer than those of pelagic ones; and (ii) the coloration of the lower flank of benthic and generalist individuals was silver-grey while that of pelagic individuals was red. The results of this study suggest that brook charr inhabiting oligotrophic lakes of the Canadian Shield exhibit trophic polymorphisms, where some individuals are specialists better adapted to feeding in the littoral zone whereas others are specialists better adapted to feeding in the pelagic zone. The potential for reproductive isolation between the two morphs is discussed.     

Lifestyle and Ice: The Relationship between Ecological Specialization and Response to Pleistocene Climate Change

Major climatic changes in the Pleistocene had significant effects on marine organisms and the environments in which they lived. The presence of divergent patterns of demographic history even among phylogenetically closely-related species sharing climatic changes raises questions as to the respective influence of species-specific traits on population structure. In this work we tested whether the lifestyle of Antarctic notothenioid benthic and pelagic fish species from the Southern Ocean influenced the concerted population response to Pleistocene climatic fluctuations. This was done by a comparative analysis of sequence variation at the cyt b and S7 loci in nine newly sequenced and four re-analysed species. We found that all species underwent more or less intensive changes in population size but we also found consistent differences between demographic histories of pelagic and benthic species. Contemporary pelagic populations are significantly more genetically diverse and bear traces of older demographic expansions than less diverse benthic species that show evidence of more recent population expansions. Our findings suggest that the lifestyles of different species have strong influences on their responses to the same environmental events. Our data, in conjunction with previous studies showing a constant diversification tempo of these species during the Pleistocene, support the hypothesis that Pleistocene glaciations had a smaller effect on pelagic species than on benthic species whose survival may have relied upon ephemeral refugia in shallow shelf waters. These findings suggest that the interaction between lifestyle and environmental changes should be considered in genetic analyses.     

Low but significant genetic differentiation underlies biologically meaningful phenotypic divergence in a large Atlantic salmon population

Despite decades of research assessing the genetic structure of natural populations, the biological meaning of low yet significant genetic divergence often remains unclear due to a lack of associated phenotypic and ecological information. At the same time, structured populations with low genetic divergence and overlapping boundaries can potentially provide excellent models to study adaptation and reproductive isolation in cases where high‐resolution genetic markers and relevant phenotypic and life history information are available. Here, we combined single nucleotide polymorphism (SNP)‐based population inference with extensive phenotypic and life history data to identify potential biological mechanisms driving fine‐scale subpopulation differentiation in Atlantic salmon (Salmo salar) from the Teno River, a major salmon river in Europe. Two sympatrically occurring subpopulations had low but significant genetic differentiation (F_ST = 0.018) and displayed marked differences in the distribution of life history strategies, including variation in juvenile growth rate, age at maturity and size within age classes. Large, late‐maturing individuals were virtually absent from one of the two subpopulations, and there were significant differences in juvenile growth rates and size at age after oceanic migration between individuals in the respective subpopulations. Our findings suggest that different evolutionary processes affect each subpopulation and that hybridization and subsequent selection may maintain low genetic differentiation without hindering adaptive divergence.     

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.     

Phenotypic plasticity allows the Mediterranean parsley frog Pelodytes punctatus to exploit two temporal niches under continuous gene flow

Environmental changes, such as climate change, lead to the opening of new niches. In such situations, species that adapt to new niches can survive and/or expand their ranges. However, gene flow can hamper genetic adaptation to new environments. Alternatively, recent models have highlighted the importance of phenotypic plasticity in tracking environmental change. Here, we investigate whether phenotypic plasticity or genetic evolution (or both) allows an amphibian species to exploit two divergent climatic niches. In the Mediterranean region, the parsley frog Pelodytes punctatus breeds both in spring, as do most other species, and in autumn, a temporal niche not exploited by most other species, but which may become increasingly important with global warming. Conditions of development are dramatically different between the two seasons and deeply impact tadpole life-history traits. To determine whether these temporal niches are exploited by two genetically differentiated subpopulations, or whether the bimodal phenology arises in a panmictic population displaying plastic life-history traits, we use two complementary approaches. We measure both molecular genetic differentiation and quantitative-trait differentiation between spring and autumn cohorts, using microsatellites and common garden experiments, respectively. Seasonal cohorts were not genetically differentiated and differences in tadpole life history between cohorts were not maintained in laboratory conditions. We conclude that phenotypic plasticity, rather than genetic adaptation, allows Parsley frog to exploit two contrasting temporal niches.     

Plastic responses to parents and predators lead to divergent shoaling behaviour in sticklebacks

Population divergence in antipredator defence and behaviour occurs rapidly and repeatedly. Genetic differences, phenotypic plasticity or parental effects may all contribute to divergence, but the relative importance of each of these mechanisms remains unknown. We exposed juveniles to parents and predators to measure how induced changes contribute to shoaling behaviour differences between two threespine stickleback species (benthics and limnetics: Gasterosteus spp). We found that limnetics increased shoaling in response to predator attacks, whereas benthics did not alter their behaviour. Care by limnetic fathers led to increased shoaling in both limnetic and benthic offspring. Shoaling helps limnetics avoid trout and avian predation; our results suggest that this adaptive behaviour is the result of a combination of paternal effects, predator-induced plasticity and genetic differences between species. These results suggest that plasticity substantially contributes to the rapid divergence in shoaling behaviour across the post-Pleistocene radiation of sticklebacks.     

No effect of elevation and fragmentation on genetic diversity and structure in Polylepis australis trees from central Argentina

Phenological differences in flowering arising along elevational gradients may be caused by either local adaptation or phenotypic plasticity. Local adaptation can lead to reproductive isolation of populations at different elevational zones and thus produce elevational genetic structuring, while phenotypic plasticity does not produce elevational genetic structuring. In this study, we examined the effects of elevation and fragmentation on genetic diversity and structure of Polylepis australis populations, where individuals exhibit phenological differences in flowering along an elevational gradient. We assessed the polymorphism of amplified fragment length polymorphism markers in adults and saplings from one conserved and one fragmented forest covering elevations from 1600 to 2600 m asl. Over 98% of variation was found within populations, and we found very low and similar genetic differentiation along elevational gradients for adults and saplings in both continuous and fragmented forests. In addition, there was no significant relationship between genetic diversity and elevation. Results indicated that phenological differences along elevational gradients are more likely caused by phenotypic plasticity than local adaptation, and fragmentation does not appear to have affected genetic diversity and differentiation in the studied populations. Results therefore imply that if necessary, seeds for reforestation purposes may be collected from different elevations to the seeding or planting sites.     

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.     

Mixed support for an alignment between phenotypic plasticity and genetic differentiation in damselfly wing shape

The relationship between genetic differentiation and phenotypic plasticity can provide information on whether plasticity generally facilitates or hinders adaptation to environmental change. Here, we studied wing shape variation in a damselfly (Lestes sponsa) across a latitudinal gradient in Europe that differed in time constraints mediated by photoperiod and temperature. We reared damselflies from northern and southern populations in the laboratory using a reciprocal transplant experiment that simulated time-constrained (i.e. northern) and unconstrained (southern) photoperiods and temperatures. After emergence, adult wing shape was analysed using geometric morphometrics. Wings from individuals in the northern and southern populations differed significantly in shape when animals were reared in their respective native environment. Comparing wing shape across environments, we found evidence for phenotypic plasticity in wing shape, and this response differed across populations (i.e. G × E interactions). This interaction was driven by a stronger plastic response by individuals from the northern population and differences in the direction of plastic wing shape changes among populations. The alignment between genetic and plastic responses depended on the specific combination of population and rearing environment. For example, there was an alignment between plasticity and genetic differentiation under time-constrained, but not under non-time-constrained conditions for forewings. We thus find mixed support for the hypothesis that environmental plasticity and genetic population differentiation are aligned. Furthermore, although our laboratory treatments mimicked the natural climatic conditions at northern and southern latitudes, the effects of population differences on wing shape were two to four times stronger than plastic effects. We discuss our results in terms of time constraints and the possibility that natural and sexual selection is acting differently on fore- and hindwings.     

Does plasticity enhance or dampen phenotypic parallelism? A test with three lake–stream stickleback pairs

Parallel (and convergent) phenotypic variation is most often studied in the wild, where it is difficult to disentangle genetic vs. environmentally induced effects. As a result, the potential contributions of phenotypic plasticity to parallelism (and nonparallelism) are rarely evaluated in a formal sense. Phenotypic parallelism could be enhanced by plasticity that causes stronger parallelism across populations in the wild than would be expected from genetic differences alone. Phenotypic parallelism could be dampened if site‐specific plasticity induced differences between otherwise genetically parallel populations. We used a common‐garden study of three independent lake–stream stickleback population pairs to evaluate the extent to which adaptive divergence has a genetic or plastic basis, and to investigate the enhancing vs. dampening effects of plasticity on phenotypic parallelism. We found that lake–stream differences in most traits had a genetic basis, but that several traits also showed contributions from plasticity. Moreover, plasticity was much more prevalent in one watershed than in the other two. In most cases, plasticity enhanced phenotypic parallelism, whereas in a few cases, plasticity had a dampening effect. Genetic and plastic contributions to divergence seem to play a complimentary, likely adaptive, role in phenotypic parallelism of lake–stream stickleback. These findings highlight the value of formally comparing wild‐caught and laboratory‐reared individuals in the study of phenotypic parallelism.     

The role of phenotypic plasticity in driving genetic evolution

Models of population divergence and speciation are often based on the assumption that differences between populations are due to genetic factors, and that phenotypic change is due to natural selection. It is equally plausible that some of the differences among populations are due to phenotypic plasticity. We use the metaphor of the adaptive landscape to review the role of phenotypic plasticity in driving genetic evolution. Moderate levels of phenotypic plasticity are optimal in permitting population survival in a new environment and in bringing populations into the realm of attraction of an adaptive peak. High levels of plasticity may increase the probability of population persistence but reduce the likelihood of genetic change, because the plastic response itself places the population close to a peak. Moderate levels of plasticity arise whenever multiple traits, some of which are plastic and others not, form a composite trait involved in the adaptive response. For example, altered behaviours may drive selection on morphology and physiology. Because there is likely to be a considerable element of chance in which behaviours become established, behavioural change followed by morphological and physiological evolution may be a potent force in driving evolution in novel directions. We assess the role of phenotypic plasticity in stimulating evolution by considering two examples from birds: (i) the evolution of red and yellow plumage coloration due to carotenoid consumption; and (ii) the evolution of foraging behaviours on islands. Phenotypic plasticity is widespread in nature and may speed up, slow down, or have little effect on evolutionary change. Moderate levels of plasticity may often facilitate genetic evolution but careful analyses of individual cases are needed to ascertain whether plasticity has been essential or merely incidental to population differentiation.