Microhabitat contributes to microgeographic divergence in threespine stickleback

Since the New Synthesis, most migration-selection balance theory has predicted that there should be negligible differentiation over small spatial scales (relative to dispersal), because gene flow should erode any effect of divergent selection. Nevertheless, there are classic examples of microgeographic divergence, which theory suggests can arise under specific conditions: exceptionally strong selection, phenotypic plasticity in philopatric individuals, or nonrandom dispersal. Here, we present evidence of microgeographic morphological variation within lake and stream populations of threespine stickleback (Gasterosteus aculeatus). It seems reasonable to assume that a given lake or stream population of fish is well-mixed. However, we found this assumption to be untenable. We examined trap-to-trap variation in 34 morphological traits measured on stickleback from 16 lakes and 16 streams. Most traits varied appreciably among traps within populations. Both between-trap distance and microhabitat characteristics such as depth and substrate explained some of the within-population morphological variance. Microhabitat was also associated with genotype at particular loci but there was no genetic isolation by distance, implying that heritable habitat preferences may contribute to microgeographic variation. Our study adds to growing evidence that microgeographic divergence can occur across small spatial scales within individuals’ daily dispersal neighborhood where gene flow is expected to be strong.     

Parallels,nonparallels, and plasticity in population differentiation of threespine stickleback within a lake

The frequent occurrence of parallel phenotypic divergence in similar habitats is often evoked when emphasizing the role of ecology in adaptive radiation and speciation. However, because phenotypic plasticity can contribute to the observed pattern of divergence, confirmation of divergence at loci underlying phenotypic traits is important for confirming adaptive divergence. In the present study, we examine parallel morphological, neutral, and potentially adaptive genetic divergence of threespine stickleback inhabiting different habitats within a lake. Three genetic clusters best explained the neutral genetic structure within the lake; however, morphological differences were only weakly connected to genetic clusters and there was considerable phenotypic variation within clusters. Among the factors that could contribute to the observed pattern of morphological and genetic divergence are phenotypic plasticity, selective mortality of hybrids, and habitat choice based on morphology. Several loci are identified as outliers indicating divergent selection between the morphs and some parallels in morphological and adaptive genetic divergence are found in stickleback spawning at two lava sites. However, neutral genetic structure indicates considerable genetic connectivity among the two lava sites, and the parallels in morphology may therefore represent selective distribution of phenotypes rather than parallel divergence. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98 , 803–813.     

Differences in rheotactic responses contribute to divergent habitat use between parapatric lake and stream threespine stickleback

Migration among populations is widely thought to undermine adaptive divergence, assuming gene flow arises from random movement of individuals. If individuals instead differ in dispersal behavior, phenotype‐dependent dispersal can reduce the effective rate of gene flow or even facilitate divergence. For example, parapatric populations of lake and stream stickleback tend to actively avoid dispersing into the adjoining habitat. However, the behavioral basis of this nonrandom dispersal was previously unknown. Here, we show that lake and stream stickleback exhibit divergent rheotactic responses (behavioral response to currents). During the breeding season, wild‐caught inlet stream stickleback were better than lake fish at maintaining position in currents, faced upstream more, and spent more time in low‐current areas. As a result, stream fish expended significantly less energy in currents than did lake fish. These divergent rheotactic responses likely contribute to divergent habitat use by lake and stream stickleback. Although rheotactic differences were absent in nonbreeding fish, divergent behavior of breeding‐season fish may suffice for assortative mating by breeding location. The resulting reproductive isolation between lake and stream fish may explain the fine‐scale evolutionary differentiation in parapatric stickleback populations.     

Cryptic genetic variation and body size evolution in threespine stickleback

The role of environment as a selective agent is well-established. Environment might also influence evolution by altering the expression of genetic variation associated with phenotypes under selection. Far less is known about this phenomenon, particularly its contribution to evolution in novel environments. We investigated how environment affected the evolvability of body size in the threespine stickleback (Gasterosteus aculeatus). Gasterosteus aculeatus is well suited to addressing this question due to the rapid evolution of smaller size in the numerous freshwater populations established following the colonization of new freshwater habitats by an oceanic ancestor. The repeated, rapid evolution of size following colonization contrasts with the general observation of low phenotypic variation in oceanic stickleback. We reared an oceanic population of stickleback under high and low salinity conditions, mimicking a key component of the ancestral environment, and freshwater colonization, respectively. There was low genetic variation for body size under high salinity, but this variance increased significantly when fish were reared under low salinity. We therefore conclude that oceanic populations harbor the standing genetic variation necessary for the evolution of body size, but that this variation only becomes available to selection upon colonization of a new habitat.     

Twelve years of contemporary armor evolution in a threespine stickleback population

Abstract —Loberg Lake, Alaska was colonized by sea-run Gasterosteus aculeatus between 1983 and 1988, after the original stickleback population was exterminated. Annual samples from 1990 to 2001 reveal substantial evolution of lateral plate (armor) phenotypes. The 1990 sample was nearly monomorphic for the complete plate morph, which is monomorphic in local sea-run populations; the low plate morph, which is usually monomorphic in local freshwater populations, was absent. By 2001, the frequency of completes had declined to 11%, and lows had increased to 75%. The partial plate morph and two unusual intermediate plate phenotypes were generally rare, but occurrence of the intermediates was unexpected. These intermediate phenotypes rarely occur in other, presumably older, polymorphic populations. When low morphs first appeared, they averaged 6.8 plates per side, indicating that the ancestral plate number of low morphs is high, and their mean has subsequently declined. Contemporary evolution in this population indicates that threespine stickleback adapt to freshwater habitats within decades after invasion from the ocean, and thus phenotypes in most populations are adapted to current conditions.     

Evolutionary diversification of opercle shape in Cook Inlet threespine stickleback

We investigated the evolution of a large facial bone, the opercle (OP), in lake populations of the threespine stickleback that were founded by anadromous ancestors, in Cook Inlet, Alaska. Recent studies characterized OP variation among marine and lake populations and mapped a quantitative trait locus with a large influence on OP shape. Using populations from diverse environments and independent evolutionary histories, we examined divergence of OP shape from that of the anadromous ancestor. We report preliminary evidence for divergence between benthic and generalist lake ecotypes, necessitating further investigation. Furthermore, rapid divergence of OP shape has occurred in a lake population that was founded by anadromous stickleback in the 1980s, which is consistent with divergence of other phenotypic traits and with OP diversification in other lake populations. By contrast, there has been limited evolution of OP shape in a second lake population that may have experienced a genetic bottleneck early in its history and lacks genetic variation for OP divergence. Taken together, the results obtained from these two populations are consistent with studies of other stickleback phenotypic traits that implicate ancestral variation in postglacial adaptive radiation of threespine stickleback in fresh water.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 832–844.     

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.     

Evolution and assessment of colour patterns in stream-resident and anadromous male threespine stickleback Gasterosteus aculeatus from three regions

We compared the colour patterns of free swimming, reproductively active male threespine stickleback Gasterosteus aculeatus of the anadromous and stream ecotypes from three geographically distinct regions. Consistent with the hypothesis of environmentally mediated selection, our results indicate ecologically replicated differences in G. aculeatus coloration between anadromous and stream-resident populations, and that G. aculeatus probably have the visual acuity to discriminate colour pattern differences between anadromous and stream-resident fish.     

Intraspecific variation of spectral sensitivity in threespine stickleback (Gasterosteus aculeatus) from different photic regimes

To examine the influence of the spectral characteristics of underwater light on spectral sensitivity of the ON and OFF visual pathways, compound action potential recordings were made from retinal ganglion cells of threespine stickleback from different photic regimes. In fish from a red-shifted photic regime (P₅₀ 680 nm for downwelling light at 1m), peak sensitivity of both the ON and OFF pathways was limited to long wavelength light (_max 600–620). In contrast, the ON pathway of fish from a comparatively blue-shifted (P₅₀ 566 nm) photic regime exhibited sensitivity to medium (_max 540–560) and long (_max 600 nm) wavelengths, while the OFF pathway exhibited peak sensitivity to only medium (_max 540 nm) wavelength light. In a third population, where the the ambient light is moderately red-shifted (P₅₀ 629 nm), the ON pathway once again exhibited only a long wavelength sensitivity peak at 620 nm, while the OFF pathway exhibited sensitivity to both medium (_max 560 nm) and long (_max 600–620 nm) wavelength light. These findings suggest that the photic environment plays an integral role in shaping spectral sensitivity of the ON and OFF pathways.     

Allometric relationships in morphological traits associated with foraging,swimming ability,and predator defense reveal adaptations toward brackish and freshwater environments in the threespine stickleback

Freshwater colonization by threespine stickleback has led to divergence in morphology between ancestral marine and derived freshwater populations, making them ideal for studying natural selection on phenotypes. In an open brackish–freshwater system, we previously discovered two genetically distinct stickleback populations that also differ in geometric shape: one mainly found in the brackish water lagoon and one throughout the freshwater system. As shape and size are not perfectly correlated, the aim of this study was to identify the morphological trait(s) that separated the populations in geometric shape. We measured 23 phenotypes likely to be important for foraging, swimming capacity, and defense against predation. The lateral plate morphs in freshwater displayed few significant changes in trait sizes, but the low plated expressed feeding traits more associated with benthic habitats. When comparing the completely plated genetically assigned populations, the freshwater, the hybrids, the migrants and the lagoon fish, many of the linear traits had different slopes and intercepts in trait‐size regressions, precluding our ability to directly compare all traits simultaneously, which most likely results from low variation in body length for the lagoon and migrant population. We found the lagoon stickleback population to be more specialized toward the littoral zone, displaying benthic traits such as large, deep bodies with smaller eyes compared to the freshwater completely plated morph. Further, the lagoon and migrant fish had an overall higher body coverage of lateral plates compared to freshwater fish, and the dorsal and pelvic spines were longer. Evolutionary constraints due to allometric scaling relationships could explain the observed, overall restricted, differences in morphology between the sticklebacks in this study, as most traits have diversified in common allometric trajectories. The observed differences in foraging and antipredation traits between the fish with a lagoon and freshwater genetic signature are likely a result of genetic or plastic adaptations toward brackish and freshwater environments.     

SSCP analysis of Mhc class IIB genes in the threespine stickleback

Due to its universality, speed, sensitivity, precision and reproducibility, PCR followed by fluorescence SSCP analysis represents an attractive tool for the characterization of Mhc class II B genotypes and the estimation of DNA sequence variability of Mhc genes in natural stickleback Gasterosteus aculeatus populations.     

Postglacial intra-lacustrine divergence of Icelandic threespine stickleback morphs in three neovolcanic lakes

The geographical context of divergence and local adaptation of lacustrine fish is controversial. Despite recent theoretical support for sympatric and parapatric divergence, empirical studies providing unequivocal support for this remain scant. An important component of such a case would be where multiple lakes have different morphs and a range of markers, both mitochondrial and nuclear, show monophyly within lakes. Here we describe such a situation for threespine sticklebacks in three lakes in Iceland. By analysing the variation at nuclear and mitochondrial markers in several freshwater and marine populations as well as three pairs of intra-lacustrine morphs we infer their phylogenetic relationships and colonization pattern. There were high levels of microsatellite variation in all populations and no evidence was found for either repeated colonization of marine fish or colonization from distinct glacial refugia. Intra-lacustrine threespine stickleback morphs in all three lakes show significant genetic divergence probably indicating restricted gene flow.     

Historical and ecological correlates of body shape in the brook stickleback, Culaea inconstans

Using geometric morphometric methods, we evaluated the correlation between phenotypic variation and available historical and habitat information for two genetically differentiated, allopatric lineages of a widespread North American species, the brook stickleback ( Culaea inconstans ). The results obtained revealed strong patterns of structured phenotypic differentiation across the species range with extreme phenotypes occurring at the northwest and southeast range boundaries. Shape variation was broadly congruent with the distribution of two mitochondrial DNA lineages; a deep-bodied eastern form (Atlantic refugium) and a slim-bodied western form (Mississippian refugium); however, the two forms were not lineage-specific and phenotypic cladistic diversification is likely to be an artefact of underlying clinal variation associated with longitudinal and latitudinal gradients. In addition, we found little evidence of diagnosable lake and river forms across North America. Taken together, large-scale patterns of phenotypic diversity observed in C. inconstans suggest that relatively recent factors, such as continually varying natural selection across the range and/or potential local gene flow, may substantially mitigate the effects of historical separation or a generalized adaptive response to alternative habitats.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 769–783.     

Heritability of DNA methylation in threespine stickleback (Gasterosteus aculeatus)

Epigenetic mechanisms underlying phenotypic change are hypothesized to contribute to population persistence and adaptation in the face of environmental change. To date, few studies have explored the heritability of intergenerationally stable methylation levels in natural populations, and little is known about the relative contribution of cis- and trans-regulatory changes to methylation variation. Here, we explore the heritability of DNA methylation, and conduct methylation quantitative trait loci (meQTLs) analysis to investigate the genetic architecture underlying methylation variation between marine and freshwater ecotypes of threespine stickleback (Gasterosteus aculeatus). We quantitatively measured genome-wide DNA methylation in fin tissue using reduced representation bisulfite sequencing of F1 and F2 crosses, and their marine and freshwater source populations. We identified cytosines (CpG sites) that exhibited stable methylation levels across generations. We found that additive genetic variance explained an average of 24–35% of the methylation variance, with a number of CpG sites possibly autonomous from genetic control. We also detected both cis- and trans-meQTLs, with only trans-meQTLs overlapping with previously identified genomic regions of high differentiation between marine and freshwater ecotypes. Finally, we identified the genetic architecture underlying two key CpG sites that were differentially methylated between ecotypes. These findings demonstrate a potential role for DNA methylation in facilitating adaptation to divergent environments and improve our understanding of the heritable basis of population epigenomic variation.     

Ecological causes of sex-biased parasitism in threespine stickleback

Males and females can differ in levels of parasitism and such differences may be mediated by the costs of sexual selection or by ecological differences between the genders. In threespine stickleback, Gasterosteus aculeatus , males exhibit paternal care and territorial nest defence and the costs of reproduction may be particularly high for males relative to females. We monitored levels of parasitism for 15 years in a population of stickleback infected by four different parasite species. Consistent with general predictions, overall parasite prevalence (total parasitism) was greater in males than in females. However, this excess did not occur for each species of parasite. Males had higher prevalence of a cestode Cyathocephalus truncatus and a trematode Bunodera sp. relative to females, while females had higher prevalence of a cestode Schistocephalus solidus and nematodes. This suggested ecological sources to differences in parasitism rather than reproductive costs and therefore we examined diet of unparasitized stickleback, predicting that differences in dietary niche would influence relative parasitism. This was partially confirmed and showed that female stomach contents had increased frequency of pelagic items, the major habitat for the primary host of S. solidus whereas males exhibited increased frequency of benthic items, the dominant habitat of C. truncatus and Bunodera. Temporal shifts in the extent and direction of differential parasitism among years between the sexes were associated with temporal shifts in dietary differences. Our results, combined with those in the literature, suggest that ecological differences between genders could be a more important component to patterns of parasitic infection in natural populations than currently appreciated.     

Microgeographical diversification of threespine stickleback: body shape–habitat correlations in a small, ecologically diverse Alaskan drainage

Adaptive radiations are a major source of evolutionary diversity in nature, and understanding how they originate and how organisms diversify during the early stages of adaptive radiation is a major problem in evolutionary biology. The relationship between habitat type and body shape variation was investigated in a postglacial radiation of threespine stickleback in the upper Fish Creek drainage of Cook Inlet, Alaska. Although small, the upper Fish Creek drainage includes ecologically diverse lakes and streams in close proximity to one another that harbour abundant stickleback. Specimens from ancestral anadromous and derived resident freshwater populations differed substantially and could be distinguished by body shape alone, suggesting that the initial stages of adaptation contribute disproportionately to evolutionary divergence. Body shape divergence among resident freshwater populations was also considerable, and phenotypic distances among samples from freshwater populations were associated with habitat type but not geographical distance. As expected, stream stickleback from slow-moving, structurally complex environments tended to have the deepest bodies, stickleback from lakes with a mostly benthic habitat were similar but less extreme, and stickleback from lakes with a mostly limnetic habitat were the most shallow-bodied, elongate fish. Beyond adapting rapidly to conditions in freshwater environments, stickleback can diversify rapidly over small geographical scales in freshwater systems despite opportunities for gene flow. This study highlights the importance of ecological heterogeneity over small geographical scales for evolutionary diversification during the early stages of adaptive radiation, and lays the foundation for future research on this ecologically diverse, postglacial system.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 139–151.     

Independent axes of genetic variation and parallel evolutionary divergence of opercle bone shape in threespine stickleback

Evolution of similar phenotypes in independent populations is often taken as evidence of adaptation to the same fitness optimum. However, the genetic architecture of traits might cause evolution to proceed more often toward particular phenotypes, and less often toward others, independently of the adaptive value of the traits. Freshwater populations of Alaskan threespine stickleback have repeatedly evolved the same distinctive opercle shape after divergence from an oceanic ancestor. Here we demonstrate that this pattern of parallel evolution is widespread, distinguishing oceanic and freshwater populations across the Pacific Coast of North America and Iceland. We test whether this parallel evolution reflects genetic bias by estimating the additive genetic variance-covariance matrix (G) of opercle shape in an Alaskan oceanic (putative ancestral) population. We find significant additive genetic variance for opercle shape and that G has the potential to be biasing, because of the existence of regions of phenotypic space with low additive genetic variation. However, evolution did not occur along major eigenvectors of G, rather it occurred repeatedly in the same directions of high evolvability. We conclude that the parallel opercle evolution is most likely due to selection during adaptation to freshwater habitats, rather than due to biasing effects of opercle genetic architecture.     

Evolutionary significance of fecundity reduction in threespine stickleback infected by the diphyllobothriidean cestode Schistocephalus solidus

Parasites may cause fecundity reduction in their hosts via life‐history strategies involving simple nutrient theft or manipulation of host energy allocation. Simple theft of nutrients incidentally reduces host energy allocation to reproduction, whereas manipulation is a parasite‐driven diversion of energy away from host reproduction. We aimed to determine whether the diphyllobothriidean cestode parasite Schistocephalus solidus causes loss of fecundity in the threespine stickleback fish (Gasterosteus aculeatus) through simple nutrient theft or the manipulation of host energy allocation. In one stickleback population (Walby Lake, Matanuska‐Susitna Valley, Alaska), there was no difference in the sizes and ages of infected and uninfected reproducing females. Lightly‐ and heavily‐infected females produced clutches of eggs, but increasingly smaller percentages of infected females produced clutches as the parasite‐to‐host biomass ratio (PI) increased. Infected, clutch‐bearing sticklebacks showed reductions in clutch size, egg mass, and clutch mass, which were related to increases in PI and reflected a reduction in reproductive parameters as growth in parasite mass occurs. The findings obtained for this population are consistent with the hypothesis of simple nutrient theft; however, populations of S. solidus in other regions may manipulate host energy allocation. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100 , 835–846.     

Twenty years of body shape evolution in a threespine stickleback population adapting to a lake environment

Analysis of contemporary evolution can provide important insights into the pattern and rate of phenotypic evolution. The threespine stickleback population in Loberg Lake was exterminated in 1982, and a new population was founded between 1983 and 1989 by anadromous stickleback. The body shape of the Loberg Lake population resembled that of anadromous populations in 1990, although it had diverged markedly by 1992. Between 1992 and 2009, the population evolved more slowly to resemble typical lake populations in the region, diverging approximately 68% of the distance separating its putative ancestor and the original native population by 2009. Temporal evolution is the main source of variation, although spatial heterogeneity, armour phenotype, and allometry contribute significant variation. There was no significant effect of ancestral phenotypic shape covariance on the evolutionary trajectory of this population. Temporal variation in the Loberg Lake population provides a rare glimpse into the evolutionary response of a complex trait to natural selection after a major habitat shift. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 817–831.