Quantitative genetic inheritance of morphological divergence in a lake-stream stickleback ecotype pair: implications for reproductive isolation

Directional epistasis is common in morphological divergence

Epistasis is often portrayed as unimportant in evolution. While random patterns of epistasis may have limited effects on the response to selection, systematic directional epistasis can have substantial effects on evolutionary dynamics. Directional epistasis occurs when allele substitutions that change a trait also modify the effects of allele substitution at other loci in a systematic direction. In this case, trait evolution may induce correlated changes in allelic effects and additive genetic variance (evolvability) that modify further evolution. Although theory thus suggests a potentially important role for directional epistasis in evolution, we still lack empirical evidence about its prevalence and magnitude. Using a new framework to estimate systematic patterns of epistasis from line-crosses experiments, we quantify its effects on 197 size-related traits from diverging natural populations in 24 animal and 17 plant species. We show that directional epistasis is common and tends to become stronger with increasing morphological divergence. In animals, most traits displayed negative directionality toward larger size, suggesting that epistatic constraints reducing evolvability toward larger size. Dominance was also common but did not systematically alter the effects of epistasis.

Repeated genetic divergence plays a minor role in repeated phenotypic divergence of lake-stream stickleback

Recent studies have shown that the repeated evolution of similar phenotypes in response to similar ecological conditions (here "parallel evolution") often occurs through mutations in the same genes. However, many previous studies have focused on known candidate genes in a limited number of systems. Thus, the question of how often parallel phenotypic evolution is due to parallel genetic changes remains open. Here, we used quantitative trait locus (QTL) mapping in F2 intercrosses between lake and stream threespine stickleback (Gasterosteus aculeatus) from four independent watersheds on Vancouver Island, Canada to determine whether the same QTL underlie divergence in the same phenotypes across, between, and within watersheds. We find few parallel QTL, even in independent crosses from the same watershed or for phenotypes that have diverged in parallel. These findings suggest that different mutations can lead to similar phenotypes. The low genetic repeatability observed in these lake-stream systems contrasts with the higher genetic repeatability observed in other stickleback systems. We speculate that differences in evolutionary history, gene flow, and/or the strength and direction of selection might explain these differences in genetic parallelism and emphasize that more work is needed to move beyond documenting genetic parallelism to identifying the underlying causes.

Does genetic differentiation underlie behavioral divergence in response to migration barriers in sticklebacks? A common garden experiment

Abstract

Water management measures in the 1970s in the Netherlands have produced a large number of “resident” populations of three-spined sticklebacks that are no longer able to migrate to the sea. This may be viewed as a replicated field experiment, allowing us to study how the resident populations are coping with human-induced barriers to migration. We have previously shown that residents are smaller, bolder, more exploratory, more active, and more aggressive and exhibited lower shoaling and lower migratory tendencies compared to their ancestral “migrant” counterparts. However, it is not clear if these differences in wild-caught residents and migrants reflect genetic differentiation, rather than different developmental conditions. To investigate this, we raised offspring of four crosses (migrant ♂ × migrant ♀, resident ♂ × resident ♀, migrant ♂ × resident ♀, resident ♂ × migrant ♀) under similar controlled conditions and tested for differences in morphology and behavior as adults. We found that lab-raised resident sticklebacks exhibited lower shoaling and migratory tendencies as compared to lab-raised migrants, retaining the differences in their wild-caught parents. This indicates genetic differentiation of these traits. For all other traits, the lab-raised sticklebacks of the various crosses did not differ significantly, suggesting that the earlier-found contrast between wild-caught fish reflects differences in their environment. Our study shows that barriers to migration can lead to rapid differentiation in behavioral tendencies over contemporary timescales (~ 50 generations) and that part of these differences reflects genetic differentiation.

Significance statement

Many organisms face changes to their habitats due to human activities. Much research is therefore dedicated to the question whether and how organisms are able to adapt to novel conditions. We address this question in three-spined sticklebacks, where water management measures cut off some populations, prohibiting their seasonal migration to the North Sea. In a previous study, we showed that wild-caught “resident” fish exhibited markedly different behavior than migrants. To disentangle whether these differences reflect genetic differentiation or differences in the conditions under which the wild-caught fish grew up, we conducted crosses, raising the F1 offspring under identical conditions. As their wild-caught parents, the F1 of resident × resident crosses exhibited lower migratory and shoaling tendencies than the F1 of migrant × migrant crosses, while the F1 of hybrid crosses were intermediate. This suggests that ~ 50 years of isolation are sufficient to induce behaviorally relevant genetic differentiation.

Clinal genomic analysis reveals strong reproductive isolation across a steep habitat transition in stickleback fish

How ecological divergence causes strong reproductive isolation between populations in close geographic contact remains poorly understood at the genomic level. We here study this question in a stickleback fish population pair adapted to contiguous, ecologically different lake and stream habitats. Clinal whole-genome sequence data reveal numerous genome regions (nearly) fixed for alternative alleles over a distance of just a few hundred meters. This strong polygenic adaptive divergence must constitute a genome-wide barrier to gene flow because a steep cline in allele frequencies is observed across the entire genome, and because the cline center closely matches the habitat transition. Simulations confirm that such strong divergence can be maintained by polygenic selection despite high dispersal and small per-locus selection coefficients. Finally, comparing samples from near the habitat transition before and after an unusual ecological perturbation demonstrates the fragility of the balance between gene flow and selection. Overall, our study highlights the efficacy of divergent selection in maintaining reproductive isolation without physical isolation, and the analytical power of studying speciation at a fine eco-geographic and genomic scale.

How ecological divergence causes reproductive isolation between populations in close contact remains poorly understood at the genomic level. This study presents a clinal investigation based on whole-genome sequencing to characterize reproductive isolation between threespine stickleback adapted to contiguous but ecologically different lake and stream habitats.

An assessment of terminology for intraspecific diversity in fishes, with a focus on "ecotypes" and "life histories"

Understanding and preserving intraspecific diversity (ISD) is important for species conservation. However, ISD units do not have taxonomic standards and are not universally recognized. The terminology used to describe ISD is varied and often used ambiguously. We compared definitions of terms used to describe ISD with use in recent studies of three fish taxa: sticklebacks (Gasterosteidae), Pacific salmon and trout (Oncorhynchus spp., "PST"), and lampreys (Petromyzontiformes). Life history describes the phenotypic responses of organisms to environments and includes biological parameters that affect population growth or decline. Life-history pathway(s) are the result of different organismal routes of development that can result in different life histories. These terms can be used to describe recognizable life-history traits. Life history is generally used in organismal- and ecology-based journals. The terms paired species/species pairs have been used to describe two different phenotypes, whereas in some species and situations a continuum of phenotypes may be expressed. Our review revealed overlapping definitions for race and subspecies, and subspecies and ecotypes. Ecotypes are genotypic adaptations to particular environments, and this term is often used in genetic- and evolution-based journals. "Satellite species" is used for situations in which a parasitic lamprey yields two or more derived, nonparasitic lamprey species. Designatable Units, Evolutionary Significant Units (ESUs), and Distinct Population Segments (DPS) are used by some governments to classify ISD of vertebrate species within distinct and evolutionary significant criteria. In situations where the genetic or life-history components of ISD are not well understood, a conservative approach would be to call them phenotypes.

Repeatability of Adaptive Radiation Depends on Spatial Scale: Regional Versus Global Replicates of Stickleback in Lake Versus Stream Habitats

The repeatability of adaptive radiation is expected to be scale-dependent, with determinism decreasing as greater spatial separation among "replicates" leads to their increased genetic and ecological independence. Threespine stickleback (Gasterosteus aculeatus) provide an opportunity to test whether this expectation holds for the early stages of adaptive radiation-their diversification in freshwater ecosystems has been replicated many times. To better understand the repeatability of that adaptive radiation, we examined the influence of geographic scale on levels of parallel evolution by quantifying phenotypic and genetic divergence between lake and stream stickleback pairs sampled at regional (Vancouver Island) and global (North America and Europe) scales. We measured phenotypes known to show lake-stream divergence and used reduced representation genome-wide sequencing to estimate genetic divergence. We assessed the scale dependence of parallel evolution by comparing effect sizes from multivariate models and also the direction and magnitude of lake-stream divergence vectors. At the phenotypic level, parallelism was greater at the regional than the global scale. At the genetic level, putative selected loci showed greater lake-stream parallelism at the regional than the global scale. Generally, the level of parallel evolution was low at both scales, except for some key univariate traits. Divergence vectors were often orthogonal, highlighting possible ecological and genetic constraints on parallel evolution at both scales. Overall, our results confirm that the repeatability of adaptive radiation decreases at increasing spatial scales. We suggest that greater environmental heterogeneity at larger scales imposes different selection regimes, thus generating lower repeatability of adaptive radiation at larger spatial scales.

Patterns, Predictors, and Consequences of Dominance in Hybrids

AbstractCompared to those of their parents, are the traits of first-generation (F₁) hybrids typically intermediate, biased toward one parent, or mismatched for alternative parental phenotypes? To address this empirical gap, we compiled data from 233 crosses in which traits were measured in a common environment for two parent taxa and their F₁ hybrids. We find that individual traits in F₁s are halfway between the parental midpoint and one parental value. Considering pairs of traits together, a hybrid's bivariate phenotype tends to resemble one parent (parent bias) about 50% more than the other, while also exhibiting a similar magnitude of mismatch due to different traits having dominance in conflicting directions. Using data from an experimental field planting of recombinant hybrid sunflowers, we illustrate that parent bias improves fitness, whereas mismatch reduces fitness. Our study has three major conclusions. First, hybrids are not phenotypically intermediate but rather exhibit substantial mismatch. Second, dominance is likely determined by the idiosyncratic evolutionary trajectories of individual traits and populations. Finally, selection against hybrids likely results from selection against both intermediate and mismatched phenotypes.

Ecological factors and morphological traits are associated with repeated genomic differentiation between lake and stream stickleback

The repeated evolution of similar phenotypes in independent populations (i.e. parallel or convergent evolution) provides an opportunity to identify genetic and ecological factors that influence the process of adaptation. Threespine stickleback fish ( Gasterosteus aculeatus) are an excellent model for such studies, as they have repeatedly adapted to divergent habitats across the Northern hemisphere. Here, we use genomic, ecological and morphological data from 16 independent pairs of stickleback populations adapted to divergent lake and stream habitats. We combine a population genomic approach to identify regions of the genome that are likely under selection in these divergent habitats with an association mapping approach to identify regions of the genome that underlie variation in ecological factors and morphological traits. Over 37% of genomic windows are repeatedly differentiated across lake-stream pairs. Similarly, many genomic windows are associated with variation in abiotic factors, diet items and morphological phenotypes. Both the highly differentiated windows and candidate trait windows are non-randomly distributed across the genome and show some overlap. However, the overlap is not significant on a genome-wide scale. Together, our data suggest that adaptation to divergent food resources and predation regimes are drivers of differentiation in lake-stream stickleback, but that additional ecological factors are also important. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.

Rapid Divergence of Predator Functional Traits Affects Prey Composition in Aquatic Communities

Identifying traits that underlie variation in individual performance of consumers (i.e., trait utility) can help reveal the ecological causes of population divergence and the subsequent consequences for species interactions and community structure. Here, we document a case of rapid divergence (over the past 100 generations, or ∼150 years) in foraging traits and feeding efficiency between a lake and stream population pair of threespine stickleback. Building on predictions from functional trait models of fish feeding, we analyzed foraging experiments with a Bayesian path analysis and elucidated the traits explaining variation in foraging performance and the species composition of ingested prey. Despite extensive previous research on the divergence of foraging traits among populations and ecotypes of stickleback, our results provide novel experimental evidence of trait utility for jaw protrusion, gill raker length, and gill raker spacing when foraging on a natural zooplankton assemblage. Furthermore, we discuss how these traits might contribute to the differential effects of lake and stream stickleback on their prey communities, observed in both laboratory and mesocosm conditions. More generally, our results illustrate how the rapid divergence of functional foraging traits of consumers can impact the biomass, species composition, and trophic structure of prey communities.

Heterochronic development of lateral plates in the three-spined stickleback induced by thyroid hormone level alterations

The three-spined stickleback Gasterosteus aculeatus is an important model for studying microevolution and parallel adaptation to freshwater environments. Marine and freshwater forms differ markedly in their phenotype, especially in the number of lateral plates, which are serially repeated elements of the exoskeleton. In fishes, thyroid hormones are involved in adaptation to salinity, as well as the developmental regulation of serially repeated elements. To study how thyroid hormones influence lateral plate development, we manipulated levels of triiodothyronine and thiourea during early ontogeny in a marine and freshwater population with complete and low plate phenotypes, respectively. The development of lateral plates along the body and keel was heterochronic among experimental groups. Fish with a low dosage of exogenous triiodothyronine and those treated with thiourea exhibited retarded development of bony plates compared to both control fish and those treated with higher a triiodothyronine dosage. Several triiodothyronine-treated individuals of the marine form expressed the partial lateral plate phenotype. Some individuals with delayed development of lateral plates manifested 1–2 extra bony plates located above the main row of lateral plates.

Adaptive and non-adaptive divergence in a common landscape

Species in a common landscape often face similar selective environments. The capacity of organisms to adapt to these environments may be largely species specific. Quantifying shared and unique adaptive responses across species within landscapes may thus improve our understanding of landscape-moderated biodiversity patterns. Here we test to what extent populations of two coexisting and phylogenetically related fishes—three-spined and nine-spined stickleback—differ in the strength and nature of neutral and adaptive divergence along a salinity gradient. Phenotypic differentiation, neutral genetic differentiation and genomic signatures of adaptation are stronger in the three-spined stickleback. Yet, both species show substantial phenotypic parallelism. In contrast, genomic signatures of adaptation involve different genomic regions, and are thus non-parallel. The relative contribution of spatial and environmental drivers of population divergence in each species reflects different strategies for persistence in the same landscape. These results provide insight in the mechanisms underlying variation in evolutionary versatility and ecological success among species within landscapes.

The three-spined stickleback is a model species for the study of adaptive divergence. Here, Raeymaekers et al. compare how the three-spined stickleback and its relative the nine-spined stickleback vary at the phenotypic and genomic levels in response to the same spatial and environmental drivers.

Clines Arc through Multivariate Morphospace

Evolutionary biologists typically represent clines as spatial gradients in a univariate character (or a principal-component axis) whose mean changes as a function of location along a transect spanning an environmental gradient or ecotone. This univariate approach may obscure the multivariate nature of phenotypic evolution across a landscape. Clines might instead be plotted as a series of vectors in multidimensional morphospace, connecting sequential geographic sites. We present a model showing that clines may trace nonlinear paths that arc through morphospace rather than elongating along a single major trajectory. Arcing clines arise because different characters diverge at different rates or locations along a geographic transect. We empirically confirm that some clines arc through morphospace, using morphological data from threespine stickleback sampled along eight independent transects from lakes down their respective outlet streams. In all eight clines, successive vectors of lake-stream divergence fluctuate in direction and magnitude in trait space, rather than pointing along a single phenotypic axis. Most clines exhibit surprisingly irregular directions of divergence as one moves downstream, although a few clines exhibit more directional arcs through morphospace. Our results highlight the multivariate complexity of clines that cannot be captured with the traditional graphical framework. We discuss hypotheses regarding the causes, and implications, of such arcing multivariate clines.

The other 96%: Can neglected sources of fitness variation offer new insights into adaptation to global change?

Mounting research considers whether populations may adapt to global change based on additive genetic variance in fitness. Yet selection acts on phenotypes, not additive genetic variance alone, meaning that persistence and evolutionary potential in the near term, at least, may be influenced by other sources of fitness variation, including nonadditive genetic and maternal environmental effects. The fitness consequences of these effects, and their environmental sensitivity, are largely unknown. Here, applying a quantitative genetic breeding design to an ecologically important marine tubeworm, we examined nonadditive genetic and maternal environmental effects on fitness (larval survival) across three thermal environments. We found that these effects are nontrivial and environment dependent, explaining at least 44% of all parentally derived effects on survival at any temperature and 96% of parental effects at the most stressful temperature. Unlike maternal environmental effects, which manifested at the latter temperature only, nonadditive genetic effects were consistently significant and covaried positively across temperatures (i.e., parental combinations that enhanced survival at one temperature also enhanced survival at elevated temperatures). Thus, while nonadditive genetic and maternal environmental effects have long been neglected because their evolutionary consequences are complex, unpredictable, or seen as transient, we argue that they warrant further attention in a rapidly warming world.

Sexual isolation promotes divergence between parapatric lake and stream stickleback

Speciation can be initiated by adaptive divergence between populations in ecologically different habitats, but how sexually based reproductive barriers contribute to this process is less well understood. We here test for sexual isolation between ecotypes of threespine stickleback fish residing in adjacent lake and stream habitats in the Lake Constance basin, Central Europe. Mating trials exposing females to pairings of territorial lake and stream males in outdoor mesocosms allowing for natural reproductive behaviour reveal that mating occurs preferentially between partners of the same ecotype. Compared to random mating, this sexual barrier reduces gene flow between the ecotypes by some 36%. This relatively modest strength of sexual isolation is surprising because comparing the males between the two ecotypes shows striking differentiation in traits generally considered relevant to reproductive behaviour (body size, breeding coloration, nest size). Analysing size differences among the individuals in the mating trials further indicates that assortative mating is not related to ecotype differences in body size. Overall, we demonstrate that sexually based reproductive isolation promotes divergence in lake-stream stickleback along with other known reproductive barriers, but we also caution against inferring strong sexual isolation from the observation of strong population divergence in sexually relevant traits.

Genetic and phenotypic variation along an ecological gradient in lake trout Salvelinus namaycush

Background

Adaptive radiation involving a colonizing phenotype that rapidly evolves into at least one other ecological variant, or ecotype, has been observed in a variety of freshwater fishes in post-glacial environments. However, few studies consider how phenotypic traits vary with regard to neutral genetic partitioning along ecological gradients. Here, we present the first detailed investigation of lake trout Salvelinus namaycush that considers variation as a cline rather than discriminatory among ecotypes. Genetic and phenotypic traits organized along common ecological gradients of water depth and geographic distance provide important insights into diversification processes in a lake with high levels of human disturbance from over-fishing.

Results

Four putative lake trout ecotypes could not be distinguished using population genetic methods, despite morphological differences. Neutral genetic partitioning in lake trout was stronger along a gradient of water depth, than by locality or ecotype. Contemporary genetic migration patterns were consistent with isolation-by-depth. Historical gene flow patterns indicated colonization from shallow to deep water. Comparison of phenotypic (Pst) and neutral genetic variation (Fst) revealed that morphological traits related to swimming performance (e.g., buoyancy, pelvic fin length) departed more strongly from neutral expectations along a depth gradient than craniofacial feeding traits. Elevated phenotypic variance with increasing water depth in pelvic fin length indicated possible ongoing character release and diversification. Finally, differences in early growth rate and asymptotic fish length across depth strata may be associated with limiting factors attributable to cold deep-water environments.

Conclusion

We provide evidence of reductions in gene flow and divergent natural selection associated with water depth in Lake Superior. Such information is relevant for documenting intraspecific biodiversity in the largest freshwater lake in the world for a species that recently lost considerable genetic diversity and is now in recovery. Unknown is whether observed patterns are a result of an early stage of incipient speciation, gene flow-selection equilibrium, or reverse speciation causing formerly divergent ecotypes to collapse into a single gene pool.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0788-8) contains supplementary material, which is available to authorized users.

Assessing reproductive isolation using a contact zone between parapatric lake-stream stickleback ecotypes

Ecological speciation occurs when populations evolve reproductive isolation as a result of divergent natural selection. This isolation can be influenced by many potential reproductive barriers, including selection against hybrids, selection against migrants and assortative mating. How and when these barriers act and interact in nature is understood for relatively few empirical systems. We used a mark-recapture experiment in a contact zone between lake and stream three-spined sticklebacks (Gasterosteus aculeatus, Linnaeus) to evaluate the occurrence of hybrids (allowing inferences about mating isolation), the interannual survival of hybrids (allowing inferences about selection against hybrids) and the shift in lake-like vs. stream-like characteristics (allowing inferences about selection against migrants). Genetic and morphological data suggest the occurrence of hybrids and no selection against hybrids in general, a result contradictory to a number of other studies of sticklebacks. However, we did find selection against more lake-like individuals, suggesting a barrier to gene flow from the lake into the stream. Combined with previous work on this system, our results suggest that multiple (most weakly and often asymmetric) barriers must be combining to yield substantial restrictions on gene flow. This work provides evidence of a reproductive barrier in lake-stream sticklebacks and highlights the value of assessing multiple reproductive barriers in natural contexts.

Modularity: genes, development and evolution

Modularity has emerged as a central concept for evolutionary biology, providing the field with a theory of organismal structure and variation. This theory has reframed long standing questions and serves as a unified conceptual framework for genetics, developmental biology and multivariate evolution. Research programs in systems biology and quantitative genetics are bridging the gap between these fields. While this synthesis is ongoing, some major themes have emerged and empirical evidence for modularity has become abundant. In this review, we look at modularity from an historical perspective, highlighting its meaning at different levels of biological organization and the different methods that can be used to detect it. We then explore the relationship between quantitative genetic approaches to modularity and developmental genetic studies. We conclude by investigating the dynamic relationship between modularity and the adaptive landscape and how this potentially shapes evolution and can help bridge the gap between micro- and macroevolution.

Ecosystem size matters: the dimensionality of intralacustrine diversification in Icelandic stickleback is predicted by lake size

Cases of evolutionary diversification can be characterized along a continuum from weak to strong genetic and phenotypic differentiation. Several factors may facilitate or constrain the differentiation process. Comparative analyses of replicates of the same taxon at different stages of differentiation can be useful to identify these factors. We estimated the number of distinct phenotypic groups in three‐spine stickleback populations from nine lakes in Iceland and in one marine population. Using the inferred number of phenotypic groups in each lake, genetic divergence from the marine population, and physical lake and landscape variables, we tested whether ecosystem size, approximated by lake size and depth, or isolation from the ancestral marine gene pool predicts the occurrence and the extent of phenotypic and genetic diversification within lakes. We find intralacustrine phenotypic diversification to be the rule rather than the exception, occurring in all but the youngest lake population and being manifest in ecologically important phenotypic traits. Neutral genetic data further indicate nonrandom mating in four of nine studied lakes, and restricted gene flow between sympatric phenotypic groups in two. Although neither the phenotypic variation nor the number of intralacustrine phenotypic groups was associated with any of our environmental variables, the number of phenotypic traits that were differentiated was significantly positively related to lake size, and evidence for restricted gene flow between sympatric phenotypic groups was only found in the largest lakes where trait specific phenotypic differentiation was highest.

Fitness differences between parapatric lake and stream stickleback revealed by a field transplant

Molecular comparisons of populations diverging into ecologically different environments often reveal strong differentiation in localized genomic regions, with the remainder of the genome being weakly differentiated. This pattern of heterogeneous genomic divergence, however, is rarely connected to direct measurements of fitness differences among populations. We here do so by performing a field enclosure experiment in threespine stickleback fish residing in a lake and in three replicate adjoining streams, and displaying weak yet heterogeneous genomic divergence between these habitats. Tracking survival over 29 weeks, we consistently find that lake genotypes transplanted into the streams suffer greatly reduced viability relative to local stream genotypes and that the performance of F1 hybrid genotypes is intermediate. This observed selection against migrants and hybrids combines to a total reduction in gene flow from the lake into streams of around 80%. Overall, our study identifies a strong reproductive barrier between parapatric stickleback populations, and cautions against inferring weak fitness differences between populations exhibiting weak overall genomic differentiation.

Strong extrinsic reproductive isolation between parapatric populations of an Australian groundsel

Speciation with gene flow, or the evolution of reproductive isolation between interbreeding populations, remains a controversial problem in evolution. This is because gene flow erodes the adaptive differences that selection creates between populations. Here, we use a combination of common garden experiments in the field and in the glasshouse to investigate what ecological and genetic mechanisms prevent gene flow and maintain morphological and genetic differentiation between coastal parapatric populations of the Australian groundsel Senecio lautus. We discovered that in each habitat extrinsic reproductive barriers prevented gene flow, whereas intrinsic barriers in F1 hybrids were weak. In the field, herbivores played a major role in preventing gene flow, but glasshouse experiments demonstrated that soil type also created variable selective pressures both locally and on a greater geographic scale. Our experimental results demonstrate that interfertile plant populations adapting to contrasting environments may diverge as a consequence of concurrent natural selection acting against migrants and hybrids through multiple mechanisms. These results provide novel insights into the consequences of local adaptation in the origin of strong barriers to gene flow in plants, and suggest that herbivory may play an important role in the early stages of plant speciation.

Asymmetric reproductive barriers and mosaic reproductive isolation: insights from Misty lake-stream stickleback

Ecological speciation seems to occur readily but is clearly not ubiquitous - and the relative contributions of different reproductive barriers remain unclear in most systems. We here investigate the potential importance of selection against migrants in lake/stream stickleback (Gasterosteus aculeatus) from the Misty Lake system, Canada. This system is of particular interest because one population contrast (Lake vs. Outlet stream) shows very low genetic and morphological divergence, whereas another population contrast (Lake vs. Inlet stream) shows dramatic genetic and morphological divergence apparently without strong and symmetric reproductive barriers. To test whether selection against migrants might solve this "conundrum of missing reproductive isolation", we performed a fully factorial reciprocal transplant experiment using 225 individually marked stickleback collected from the wild. Relative fitness of the different ecotypes (Lake, Inlet, and Outlet) was assessed based on survival and mass change in experimental enclosures. We found that Inlet fish performed poorly in the lake (selection against migrants in that direction), whereas Lake fish outperformed Inlet fish in all environments (no selection against migrants in the opposite direction). As predicted from their phenotypic and genetic similarity, Outlet and Lake fish performed similarly in all environments. These results suggest that selection against migrants is asymmetric and, together with previous work, indicates that multiple reproductive barriers contribute to reproductive isolation. Similar mosaic patterns of reproductive isolation are likely in other natural systems.

Key questions in the genetics and genomics of eco-evolutionary dynamics

Increasing acceptance that evolution can be 'rapid' (or 'contemporary') has generated growing interest in the consequences for ecology. The genetics and genomics of these 'eco-evolutionary dynamics' will be--to a large extent--the genetics and genomics of organismal phenotypes. In the hope of stimulating research in this area, I review empirical data from natural populations and draw the following conclusions. (1) Considerable additive genetic variance is present for most traits in most populations. (2) Trait correlations do not consistently oppose selection. (3) Adaptive differences between populations often involve dominance and epistasis. (4) Most adaptation is the result of genes of small-to-modest effect, although (5) some genes certainly have larger effects than the others. (6) Adaptation by independent lineages to similar environments is mostly driven by different alleles/genes. (7) Adaptation to new environments is mostly driven by standing genetic variation, although new mutations can be important in some instances. (8) Adaptation is driven by both structural and regulatory genetic variation, with recent studies emphasizing the latter. (9) The ecological effects of organisms, considered as extended phenotypes, are often heritable. Overall, the study of eco-evolutionary dynamics will benefit from perspectives and approaches that emphasize standing genetic variation in many genes of small-to-modest effect acting across multiple traits and that analyze overall adaptation or 'fitness'. In addition, increasing attention should be paid to dominance, epistasis and regulatory variation.

Molecular phylogeny and biogeography of percocypris (Cyprinidae, Teleostei)

Fierce predatory freshwater fishes, the species of Percocypris (Cyprinidae, Teleostei) inhabit large rivers or lakes, and have a specific distribution pattern. Only a single species or subspecies occurs in each large-scale drainage basin of the Southeastern Tibetan Plateau. In this study, the molecular phylogenetic relationships for all but one of the described subspecies/species of Percocypris were investigated based on three mitochondrial genes (16S; COI; Cyt b) and one nuclear marker (Rag2). The results of Maximum Likelihood and Bayesian Inference analyses show that Percocypris is a strongly supported monophyletic group and that it is the sister group of Schizothorax. Combined with analyses of morphological characters, our results suggest that Percocypris needs to be reclassified, and we propose that six species be recognized, with corresponding distributions in five main drainages (including one lake). In addition, based on the results of the estimation of divergence times and ancestral drainages, we hypothesize that Percocypris likely originated in the early Miocene from a paleo-connected drainage system containing the contemporary main drainages of the Southeastern Tibetan Plateau. This study suggests that vicariance (due to the uplift of the Tibetan Plateau modifying the large-scale morphologies of drainage basins in the Southeastern Tibetan Plateau) has played an important role in the speciation of the genus. Furthermore, external morphological characters (such as the length of the fins) and an internal trait (the position of pterygiophore) appear to be correlated with different habitats in rivers and the lake.

Repeated lake-stream divergence in stickleback life history within a Central European lake basin

Life history divergence between populations inhabiting ecologically distinct habitats might be a potent source of reproductive isolation, but has received little attention in the context of speciation. We here test for life history divergence between threespine stickleback inhabiting Lake Constance (Central Europe) and multiple tributary streams. Otolith analysis shows that lake fish generally reproduce at two years of age, while their conspecifics in all streams have shifted to a primarily annual life cycle. This divergence is paralleled by a striking and consistent reduction in body size and fecundity in stream fish relative to lake fish. Stomach content analysis suggests that life history divergence might reflect a genetic or plastic response to pelagic versus benthic foraging modes in the lake and the streams. Microsatellite and mitochondrial markers further reveal that life history shifts in the different streams have occurred independently following the colonization by Lake Constance stickleback, and indicate the presence of strong barriers to gene flow across at least some of the lake-stream habitat transitions. Given that body size is known to strongly influence stickleback mating behavior, these barriers might well be related to life history divergence.

Parallel and nonparallel ecological, morphological and genetic divergence in lake-stream stickleback from a single catchment

Parallel phenotypic evolution in similar environments has been well studied in evolutionary biology; however, comparatively little is known about the influence of determinism and historical contingency on the nature, extent and generality of this divergence. Taking advantage of a novel system containing multiple lake-stream stickleback populations, we examined the extent of ecological, morphological and genetic divergence between three-spined stickleback present in parapatric environments. Consistent with other lake-stream studies, we found a shift towards a deeper body and shorter gill rakers in stream fish. Morphological shifts were concurrent with changes in diet, indicated by both stable isotope and stomach contents analysis. Performing a multivariate test for shared and unique components of evolutionary response to the distance gradient from the lake, we found a strong signature of parallel adaptation. Nonparallel divergence was also present, attributable mainly to differences between river locations. We additionally found evidence of genetic substructuring across five lake-stream transitions, indicating that some level of reproductive isolation occurs between populations in these habitats. Strong correlations between pairwise measures of morphological, ecological and genetic distance between lake and stream populations supports the hypothesis that divergent natural selection between habitats drives adaptive divergence and reproductive isolation. Lake-stream stickleback divergence in Lough Neagh provides evidence for the deterministic role of selection and supports the hypothesis that parallel selection in similar environments may initiate parallel speciation.

Genome divergence during evolutionary diversification as revealed in replicate lake-stream stickleback population pairs

Evolutionary diversification is often initiated by adaptive divergence between populations occupying ecologically distinct environments while still exchanging genes. The genetic foundations of this divergence process are largely unknown and are here explored through genome scans in multiple independent lake-stream population pairs of threespine stickleback. We find that across the pairs, overall genomic divergence is associated with the magnitude of divergence in phenotypes known to be under divergent selection. Along this same axis of increasing diversification, genomic divergence becomes increasingly biased towards the centre of chromosomes as opposed to the peripheries. We explain this pattern by within-chromosome variation in the physical extent of hitchhiking, as recombination is greatly reduced in chromosome centres. Correcting for this effect suggests that a great number of genes distributed widely across the genome are involved in the divergence into lake vs. stream habitats. Analyzing additional allopatric population pairs, however, reveals that strong divergence in some genomic regions has been driven by selection unrelated to lake-stream ecology. Our study highlights a major contribution of large-scale variation in recombination rate to generating heterogeneous genomic divergence and indicates that elucidating the genetic basis of adaptive divergence might be more challenging than currently recognized.

Parallel and nonparallel aspects of ecological, phenotypic, and genetic divergence across replicate population pairs of lake and stream stickleback

Parallel (or convergent) evolution provides strong evidence for a deterministic role of natural selection: similar phenotypes evolve when independent populations colonize similar environments. In reality, however, independent populations in similar environments always show some differences: some nonparallel evolution is present. It is therefore important to explicitly quantify the parallel and nonparallel aspects of trait variation, and to investigate the ecological and genetic explanations for each. We performed such an analysis for threespine stickleback (Gasterosteus aculeatus) populations inhabiting lake and stream habitats in six independent watersheds. Morphological traits differed in the degree to which lake-stream divergence was parallel across watersheds. Some aspects of this variation were correlated with ecological variables related to diet, presumably reflecting the strength and specifics of divergent selection. Furthermore, a genetic scan revealed some markers that diverged between lakes and streams in many of the watersheds and some that diverged in only a few watersheds. Moreover, some of the lake-stream divergence in genetic markers was associated within some of the lake-stream divergence in morphological traits. Our results suggest that parallel evolution, and deviations from it, are primarily the result of natural selection, which corresponds in only some respects to the dichotomous habitat classifications frequently used in such studies.

Sympatric Speciation in Threespine Stickleback: Why Not?

Numerous theoretical models suggest that sympatric speciation is possible when frequency-dependent interactions such as intraspecific competition drive disruptive selection on a trait that is also subject to assortative mating. Here, I review recent evidence that both conditions are met in lake populations of threespine stickleback (Gasterosteus aculeatus). Nonetheless, sympatric speciation appears to be rare or absent in stickleback. If stickleback qualitatively fit the theoretical requirements for sympatric speciation, why do they not undergo sympatric speciation? I present simulations showing that disruptive selection and assortative mating in stickleback, though present, are too weak to drive speciation. Furthermore, I summarize empirical evidence that disruptive selection in stickleback drives other forms of evolutionary diversification (plasticity, increased trait variance, and sexual dimorphism) instead of speciation. In conclusion, core assumptions of sympatric speciation theory seem to be qualitatively reasonable for stickleback, but speciation may nevertheless fail because of (i) quantitative mismatches with theory and (ii) alternative evolutionary outcomes.