Extent of QTL Reuse During Repeated Phenotypic Divergence of Sympatric Threespine Stickleback

How predictable is the genetic basis of phenotypic adaptation? Answering this question begins by estimating the repeatability of adaptation at the genetic level. Here, we provide a comprehensive estimate of the repeatability of the genetic basis of adaptive phenotypic evolution in a natural system. We used quantitative trait locus (QTL) mapping to discover genomic regions controlling a large number of morphological traits that have diverged in parallel between pairs of threespine stickleback (Gasterosteus aculeatus species complex) in Paxton and Priest lakes, British Columbia. We found that nearly half of QTL affected the same traits in the same direction in both species pairs. Another 40% influenced a parallel phenotypic trait in one lake but not the other. The remaining 10% of QTL had phenotypic effects in opposite directions in the two species pairs. Similarity in the proportional contributions of all QTL to parallel trait differences was about 0.4. Surprisingly, QTL reuse was unrelated to phenotypic effect size. Our results indicate that repeated use of the same genomic regions is a pervasive feature of parallel phenotypic adaptation, at least in sticklebacks. Identifying the causes of this pattern would aid prediction of the genetic basis of phenotypic evolution.     

Determinants of Variation in Antipredator Behavior of Territorial Male Threespine Stickleback in the Wild

Although antipredator behavior of threespine stickleback has been extensively studied in the laboratory, interactions between stickleback and their predators in nature have never been described. This paper describes interactions between territorial male stickleback and four predators on males or on the young they guard. Two of the predators, cutthroat trout and a hemipteran nymph (Belostomatidae), prey on males but not on young. Another, the roughskin newt, is a potential predator of young but does not pose a threat to males. Prickly sculpin prey both on the males and on offspring that males guard. Differences in behavior toward the four predators indicate that males are capable of rapid discrimination among predators and the threats they pose. Males also discriminate among size classes of sculpin that present different predation risks, but not among size classes of trout large enough to pose a threat. The difference in response to these predators probably reflects the difference in risk to offspring and the amount of time each predator typically stays in the territory of a male. Trout pass through rapidly, whereas sculpin, which are ambush predators, can remain within a territory for a long period of time if not chased out. The presence of young in the nest had no apparent effect on the response of males to these predators. This could, however, be due to a masking effect of uncontrolled variation in natural encounters. Responses to newts were similar to those directed toward sculpin too small to attack the male. They involved rapid chases and bites, often directed at the head, a part of the body that was typically avoided in encounters with larger sculpin. Males watch and avoid the belostomatid nymphs, but do not attack them.     

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

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

Genomics of Rapid Incipient Speciation in Sympatric Threespine Stickleback

Ecological speciation is the process by which reproductively isolated populations emerge as a consequence of divergent natural or ecologically-mediated sexual selection. Most genomic studies of ecological speciation have investigated allopatric populations, making it difficult to infer reproductive isolation. The few studies on sympatric ecotypes have focused on advanced stages of the speciation process after thousands of generations of divergence. As a consequence, we still do not know what genomic signatures of the early onset of ecological speciation look like. Here, we examined genomic differentiation among migratory lake and resident stream ecotypes of threespine stickleback reproducing in sympatry in one stream, and in parapatry in another stream. Importantly, these ecotypes started diverging less than 150 years ago. We obtained 34,756 SNPs with restriction-site associated DNA sequencing and identified genomic islands of differentiation using a Hidden Markov Model approach. Consistent with incipient ecological speciation, we found significant genomic differentiation between ecotypes both in sympatry and parapatry. Of 19 islands of differentiation resisting gene flow in sympatry, all were also differentiated in parapatry and were thus likely driven by divergent selection among habitats. These islands clustered in quantitative trait loci controlling divergent traits among the ecotypes, many of them concentrated in one region with low to intermediate recombination. Our findings suggest that adaptive genomic differentiation at many genetic loci can arise and persist in sympatry at the very early stage of ecotype divergence, and that the genomic architecture of adaptation may facilitate this.     

Sympatric and Allopatric Divergence of MHC Genes in Threespine Stickleback

Parasites can strongly affect the evolution of their hosts, but their effects on host diversification are less clear. In theory, contrasting parasite communities in different foraging habitats could generate divergent selection on hosts and promote ecological speciation. Immune systems are costly to maintain, adaptable, and an important component of individual fitness. As a result, immune system genes, such as those of the Major Histocompatability Complex (MHC), can change rapidly in response to parasite-mediated selection. In threespine stickleback (Gasterosteus aculeatus), as well as in other vertebrates, MHC genes have been linked with female mating preference, suggesting that divergent selection acting on MHC genes might influence speciation. Here, we examined genetic variation at MHC Class II loci of sticklebacks from two lakes with a limnetic and benthic species pair, and two lakes with a single species. In both lakes with species pairs, limnetics and benthics differed in their composition of MHC alleles, and limnetics had fewer MHC alleles per individual than benthics. Similar to the limnetics, the allopatric population with a pelagic phenotype had few MHC alleles per individual, suggesting a correlation between MHC genotype and foraging habitat. Using a simulation model we show that the diversity and composition of MHC alleles in a sympatric species pair depends on the amount of assortative mating and on the strength of parasite-mediated selection in adjacent foraging habitats. Our results indicate parallel divergence in the number of MHC alleles between sympatric stickleback species, possibly resulting from the contrasting parasite communities in littoral and pelagic habitats of lakes.     

Femme Fatale — the Case of the Threespine Stickleback

In addition to courting females, male threespine sticklebacks must guard their nests from attacks on the eggs by female cannibals. We hypothesized that the presence of females in high densities in tide pools adversely affects a male's health and reproductive success. In the laboratory males housed with conspecific females during the breeding season were in poorer physical condition and died sooner than solitary males and males housed with conspecific males or with heterospecific females.     

Chromosomal Fusions Facilitate Adaptation to Divergent Environments in Threespine Stickleback

Chromosomal fusions are hypothesized to facilitate adaptation to divergent environments, both by bringing together previously unlinked adaptive alleles and by creating regions of low recombination that facilitate the linkage of adaptive alleles; but, there is little empirical evidence to support this hypothesis. Here, we address this knowledge gap by studying threespine stickleback (Gasterosteus aculeatus), in which ancestral marine fish have repeatedly adapted to freshwater across the northern hemisphere. By comparing the threespine and ninespine stickleback (Pungitius pungitius) genomes to a de novo assembly of the fourspine stickleback (Apeltes quadracus) and an outgroup species, we find two chromosomal fusion events involving the same chromosomes have occurred independently in the threespine and ninespine stickleback lineages. On the fused chromosomes in threespine stickleback, we find an enrichment of quantitative trait loci underlying traits that contribute to marine versus freshwater adaptation. By comparing whole-genome sequences of freshwater and marine threespine stickleback populations, we also find an enrichment of regions under divergent selection on these two fused chromosomes. There is elevated genetic diversity within regions under selection in the freshwater population, consistent with a simulation study showing that gene flow can increase diversity in genomic regions associated with local adaptation and our demographic models showing gene flow between the marine and freshwater populations. Integrating our results with previous studies, we propose that these fusions created regions of low recombination that enabled the formation of adaptative clusters, thereby facilitating freshwater adaptation in the face of recurrent gene flow between marine and freshwater threespine sticklebacks.     

Phenotypic Plasticity and Population Differentiation in an Ongoing Species Invasion

The ability to succeed in diverse conditions is a key factor allowing introduced species to successfully invade and spread across new areas. Two non-exclusive factors have been suggested to promote this ability: adaptive phenotypic plasticity of individuals, and the evolution of locally adapted populations in the new range. We investigated these individual and population-level factors in Polygonum cespitosum, an Asian annual that has recently become invasive in northeastern North America. We characterized individual fitness, life-history, and functional plasticity in response to two contrasting glasshouse habitat treatments (full sun/dry soil and understory shade/moist soil) in 165 genotypes sampled from nine geographically separate populations representing the range of light and soil moisture conditions the species inhabits in this region. Polygonum cespitosum genotypes from these introduced-range populations expressed broadly similar plasticity patterns. In response to full sun, dry conditions, genotypes from all populations increased photosynthetic rate, water use efficiency, and allocation to root tissues, dramatically increasing reproductive fitness compared to phenotypes expressed in simulated understory shade. Although there were subtle among-population differences in mean trait values as well as in the slope of plastic responses, these population differences did not reflect local adaptation to environmental conditions measured at the population sites of origin. Instead, certain populations expressed higher fitness in both glasshouse habitat treatments. We also compared the introduced-range populations to a single population from the native Asian range, and found that the native population had delayed phenology, limited functional plasticity, and lower fitness in both experimental environments compared with the introduced-range populations. Our results indicate that the future spread of P. cespitosum in its introduced range will likely be fueled by populations consisting of individuals able to express high fitness across diverse light and moisture conditions, rather than by the evolution of locally specialized populations.     

The Effects of Relaxed and Reversed Selection by Predators on the Antipredator Behavior of the Threespine Stickleback, Gasterosteus aculeatus

Isolation from predators can lead to the reduction or loss of ancestral behavioral defenses in prey, but does not always do so. Predators introduced to populations that have experienced relaxed selection from some ancestral predators can favor the evolution of antipredator behavior that has been lost. We examined these possibilities by eliciting antipredator behavior in three populations of threespine stickleback fish, Gasterosteus aculeatus : an oceanic population thought to resemble the ancestral form, and two populations historically (up to 20 000 yr) devoid of piscine predators (relaxed selection), one of which has been stocked with salmonids for nearly 25 yr (reversed selection). We used three kinds of predator models: a sculpin (ambush predator), a rainbow trout (chasing predator), and an overhead silhouette of an arctic tern. Stickleback reacted differently to the three models, indicating that they distinguished among them. Individuals from all populations responded similarly to the tern model. The ancestral population showed the weakest response to the sculpin model despite being the only population that encounters these predators naturally. Stickleback from the trout-free population displayed slightly reduced responses to the trout model, and recovery times like those in the ancestral population providing only weak evidence for loss of the ancestral antipredator repertoire. Fish from the reverse-selected population exhibited fascinating, elevated responses to both the trout and sculpin models relative to the other two populations. These findings offer initial evidence of (1) a partial alteration of the ancestral behavioral repertoire during a long period of relaxed selection from piscine predators, and (2) rapid acquisition of extreme responses to piscine predators under reverse selection.     

Climate‐driven habitat change causes evolution in Threespine Stickleback

Climate change can shape evolution directly by altering abiotic conditions or indirectly by modifying habitats, yet few studies have investigated the effects of climate‐driven habitat change on contemporary evolution. We resampled populations of Threespine Stickleback (Gasterosteus aculeatus) along a latitudinal gradient in California bar‐built estuaries to examine their evolution in response to changing climate and habitat. We took advantage of the strong association between stickleback lateral plate phenotypes and Ectodysplasin A (Eda) genotypes to infer changes in allele frequencies over time. Our results show that over time the frequency of low‐plated alleles has generally increased and heterozygosity has decreased. Latitudinal patterns in stickleback plate phenotypes suggest that evolution at Eda is a response to climate‐driven habitat transformation rather than a direct consequence of climate. As climate change has reduced precipitation and increased temperature and drought, bar‐built estuaries have transitioned from lotic (flowing‐water) to lentic (still‐water) habitats, where the low‐plated allele is favoured. The low‐plated allele has achieved fixation at the driest, hottest southernmost sites, a trend that is progressing northward with climate change. Climate‐driven habitat change is therefore causing a reduction in genetic variation that may hinder future adaptation for populations facing multiple threats.     

Population-Specific Covariation between Immune Function and Color of Nesting Male Threespine Stickleback

Multiple biological processes can generate sexual selection on male visual signals such as color. For example, females may prefer colorful males because those males are more readily detected (perceptual bias), or because male color conveys information about male quality and associated direct or indirect benefits to females. For example, male threespine stickleback often exhibit red throat coloration, which females prefer both because red is more visible in certain environments, and red color is correlated with male immune function and parasite load. However, not all light environments favor red nuptial coloration: more tannin-stained water tends to favor the evolution of a melanic male phenotype. Do such population differences in stickleback male color, driven by divergent light environments, lead to changes in the relationship between color and immunity? Here, we show that, within stickleback populations, multiple components of male color (brightness and hue of four body parts) are correlated with multiple immune variables (ROS production, phagocytosis rates, and lymphocyte:leukocyte ratios). Some of these color-immune associations persist across stickleback populations with very different male color patterns, whereas other color-immune associations are population-specific. Overall, lakes with red males exhibit stronger color-immune covariance while melanic male populations exhibit weak if any color-immune associations. Our finding that color-immunity relationships are labile implies that any evolution of male color traits (e.g., due to female perceptual bias in a given light environment), can alter the utility of color as an indicator of male quality.     

Rapid Morphological Changes in Threespine Stickleback, Gasterosteus aculeatus, in Freshwater

Synopsis Freshwater and marine threespine stickleback, Gasterosteus aculeatus, differ remarkably in armour plate number and body shape, although differences in other morphological characters are also common. Most freshwater populations have apparently evolved after isolation of marine sticklebacks in freshwater. After colonisation of freshwater habitats, they show rapid morphological changes and associated genetic isolation within as few as eight generations. I transferred fish from marine tide pools to two isolated freshwater ponds, differing in habitat characteristics, at the beginning of the breeding season, when females had ripe ovaries and males had breeding coloration. The first generation fish that I sampled from the ponds had significantly fewer armour plates than their marine ancestors and differed in shape. I also found some significant differences between fish sampled from the larger pond and those from a smaller, adjacent pond. This extremely rapid morphological divergence suggests that either the marine sticklebacks were highly phenotypically plastic or that there was very strong natural selection acting on the first generation within freshwater habitats.     

Landscape Genetics of Schistocephalus solidus Parasites in Threespine Stickleback (Gasterosteus aculeatus) from Alaska

The nature of gene flow in parasites with complex life cycles is poorly understood, particularly when intermediate and definitive hosts have contrasting movement potential. We examined whether the fine-scale population genetic structure of the diphyllobothriidean cestode Schistocephalus solidus reflects the habits of intermediate threespine stickleback hosts or those of its definitive hosts, semi-aquatic piscivorous birds, to better understand complex host-parasite interactions. Seventeen lakes in the Cook Inlet region of south-central Alaska were sampled, including ten in the Matanuska-Susitna Valley, five on the Kenai Peninsula, and two in the Bristol Bay drainage. We analyzed sequence variation across a 759 bp region of the mitochondrial DNA (mtDNA) cytochrome oxidase I region for 1,026 S. solidus individuals sampled from 2009-2012. We also analyzed allelic variation at 8 microsatellite loci for 1,243 individuals. Analysis of mtDNA haplotype and microsatellite genotype variation recovered evidence of significant population genetic structure within S. solidus. Host, location, and year were factors in structuring observed genetic variation. Pairwise measures revealed significant differentiation among lakes, including a pattern of isolation-by-distance. Bayesian analysis identified three distinct genotypic clusters in the study region, little admixture within hosts and lakes, and a shift in genotype frequencies over time. Evidence of fine-scale population structure in S. solidus indicates that movement of its vagile, definitive avian hosts has less influence on gene flow than expected based solely on movement potential. Observed patterns of genetic variation may reflect genetic drift, behaviors of definitive hosts that constrain dispersal, life history of intermediate hosts, and adaptive specificity of S. solidus to intermediate host genotype.     

Geographical and Temporal FA Variation in Threespine Stickleback Populations from Galicia (NW Spain)

Subtle departures from bilateral symmetry (FA) in morphological traits has been used as a measure of developmental stability in populations subjected to genetic and environmental processes as inbreeding, pollution or parasitic infection. Geographic variation of FA was assessed in 19 threespine stickleback (Gasterosteus aculeatus) populations from Miño and Limia rivers, from Galicia (NW Spain). This variation was evaluated using four FA indices on five meristic and one morphometric traits. Temporal variation of FA was also assessed using several samples through time in only one population. Significant geographical variation was detected for pectoral fin rays, lateral forks, lateral plates and spine length. Lateral plates, upper gillrakers, pectoral fin rays and spine length showed significant variation through the time. The variation of FA through the time showed a common performance for all characters during the period considered: a slight increase in the intermediate months with a decrease at the end of the period. Symmetric and asymmetric sticklebacks exhibited similar infection, with one exception: symmetric sticklebacks for lower gillrakers of Antela populations exhibited increased parasite infection relative to asymmetric ones. Sticklebacks with extreme phenotypes exhibited much higher levels of asymmetry than modal ones in all samples for all traits.     

Divergent Macroparasite Infections in Parapatric Swiss Lake-Stream Pairs of Threespine Stickleback (Gasterosteus aculeatus)

Spatial heterogeneity in diversity and intensity of parasitism is a typical feature of most host-parasite interactions, but understanding of the evolutionary implications of such variation is limited. One possible outcome of infection heterogeneities is parasite-mediated divergent selection between host populations, ecotypes or species which may facilitate the process of ecological speciation. However, very few studies have described infections in population-pairs along the speciation continuum from low to moderate or high degree of genetic differentiation that would address the possibility of parasite-mediated divergent selection in the early stages of the speciation process. Here we provide an example of divergent parasitism in freshwater fish ecotypes by examining macroparasite infections in threespine stickleback (Gasterosteus aculeatus) of four Swiss lake systems each harbouring parapatric lake-stream ecotype pairs. We demonstrate significant differences in infections within and between the pairs that are driven particularly by the parasite taxa transmitted to fish from benthic invertebrates. The magnitude of the differences tended to correlate positively with the extent of neutral genetic differentiation between the parapatric lake and stream populations of stickleback, whereas no such correlation was found among allopatric populations from similar or contrasting habitats. This suggests that genetic differentiation is unrelated to the magnitude of parasite infection contrasts when gene flow is constrained by geographical barriers while in the absence of physical barriers, genetic differentiation and the magnitude of differences in infections tend to be positively correlated.     

Phenotypic Plasticity in the Reproductive Behavior of Female Sand Tilefish, Malacanthus plumieri

Female sand tilefish (Malacanthus plumieri) inhabiting a deep channel in the fringing reef at Glover's Atoll, Belize (channel females) spawned planktonic eggs more frequently than those occupying the shallow sand‐rubble slopes adjacent to patch coral reefs inside the atoll lagoon (reef‐slope females). We tested five non‐exclusive hypotheses to explain habitat differences in female spawning frequency. We found no evidence that spawning frequency variation was a consequence of differences in food availability, variation in male fertility, or the intensity of predation on spawned eggs. On reef slopes, barracuda stalked tilefish near their benthic burrows, whereas these piscivores attacked channel tilefish by diving suddenly from higher in the water column. Differences in the hunting behavior of barracuda suggested that the behavior of tilefish females might be influenced by temporal variation in predation risk (risk allocation hypothesis). Consistent with this hypothesis, reef‐slope females had a much higher frequency of retreats to burrows in response to barracuda, spent more time burrowing and ventured less far from these refugia in response to a simulated predatory threat. As predicted by the risk allocation hypothesis, reef‐slope females also had lower and more variable frequencies of foraging bites, and shorter and more variable travel distances to forage than channel females. Estimated mortality from predation was over nine times higher in channel tilefish. Consistent with the hypothesis that investment in current vs. future reproduction is influenced by rates of adult mortality (mortality risk hypothesis), channel females invested more supplemental energy in egg production whereas reef‐slope females invested more in growth. Our results indicate that behavioral and life‐history traits of female tilefish show phenotypic plasticity depending upon the nature and intensity of localized predation risk.     

The Effects of Isolation on the Sensitization and Habituation of Aggression in the Threespine Stickleback (Gasterosteus aculeatus)

Our previous research showed that territorial threespine sticklebacks are more aggressive toward a male conspecific placed in their territory if they have been housed adjacent to a gravid female rather than a male or a nongravid female. This study replicated the condition of a territorial male with an adjacently housed male and compared the results with isolated territorial males. This permitted us to contrast explanations for the increased aggression when the neighbor was a gravid female. If the social context determines the level of aggression, then males with no neighbors (isolates) might be less aggressive because there would be no unique reproductive resource to protect nor any neighbor to protect resources from. Alternatively, if aggression is higher in the isolated group it might be because there was no male neighbor to redirect aggression toward. We found that isolated males were more aggressive toward an intruded male stimulus than males with a male neighbor. The study also provided evidence that sensitization produced by the appearance of an intruding male energizes other aggressive behavior, but not those related to feeding, nor does it cause increase in general activation as measured by increased locomotion.     

Synaptonemal Complex Analysis in Oocytes and Spermatocytes of Threespine Stickleback Gasterosteus Aculeatus (Teleostei, Gasterosteidae)

A surface-spreading synaptonemal complex (SC) technique was employed to analyze spermatocytes and oocytes of stickleback, Gasterosteus aculeatus, in order to visualize the process of chromosome synapsis. The mean SC length was 150±18m in three males and 143±12m in one female analyzed. A representative SC karyotype with 21bivalents was also presented. Each SC had lateral elements of equal length. No bivalent displaying the atypical synaptic behaviour which is often associated with heteromorphic sex chromosomes was observed neither in males nor in the female analyzed.     

Black Male Bellies and Red Female Throats: Color Changes with Breeding Status in a Threespine Stickleback

This paper provides the first report of black nuptial coloration on the ventral side for a population of threespine sticklebacks, Gasterosteus aculeatus, in Northern California. Black nuptial coloration was least intense during precourtship. Although the black coloration intensified during courtship, it was not a significant predictor of female choice and, unlike the red throat and blue eyes, was not inversely correlated with the number of female introductions necessary before spawning occurred. Black coloration was the most intense for males who successfully hatched embryos, supporting a parental-defense role late in the cycle. Unsuccessful fathers had more intensely colored red throats, blue eyes, and black bellies during most of the reproductive cycle than successful fathers. Some females in this study developed red coloration on their throat, although none to the intensity or distribution typical of a breeding male.