On the Origins of Phenotypic Parallelism in Benthic and Limnetic Stickleback.

Rapid evolution of similar phenotypes in similar environments, giving rise to in situ parallel adaptation, is an important hallmark of ecological speciation. However, what appears to be in situ adaptation can also arise by dispersal of divergent lineages from elsewhere. We test whether two contrasting phenotypes repeatedly evolved in parallel, or have a single origin, in an archetypal example of ecological adaptive radiation: benthic-limnetic three-spined stickleback (Gasterosteus aculeatus) across species pair and solitary lakes in British Columbia. We identify two genomic clusters across freshwater populations, which differ in benthic-limnetic divergent phenotypic traits and separate benthic from limnetic individuals in species pair lakes. Phylogenetic reconstruction and niche evolution modeling both suggest a single evolutionary origin for each of these clusters. We detected strong phylogenetic signal in benthic-limnetic divergent traits, suggesting that they are ancestrally retained. Accounting for ancestral state retention, we identify local adaptation of body armor due to the presence of an intraguild predator, the sculpin (Cottus asper), and environmental effects of lake depth and pH on body size. Taken together, our results imply a predominant role for retention of ancestral characteristics in driving trait distribution, with further selection imposed on some traits by environmental factors.

Reproductive isolation in a three-way contact zone.

Contact zones between divergent forms within a species provide insight into the role of gene flow in adaptation and speciation. Previous work has focused on contact zones involving only two divergent forms, but in nature, many more than two populations may overlap simultaneously and experience gene flow. Patterns of introgression in wild populations are, therefore, likely much more complicated than is often assumed. We begin to address this gap in current knowledge by investigating patterns of divergence and introgression across a complex natural contact zone. We use phenotypic and genomic data to confirm the existence of a three-way contact zone among divergent freshwater resident, saltwater resident and saltwater migratory three-spined stickleback (Gasterosteus aculeatus) on the island of North Uist, Scottish Western Isles. We find evidence for hybridization, mostly between saltwater resident and saltwater migratory forms. Despite hybridization, genomic analyses reveal pairwise islands of divergence between all forms that are maintained across the contact zone. Genomic cline analyses also provide evidence for selection and/or hybrid incompatibilities in divergent regions. Divergent genomic regions occur across multiple chromosomes and involve many known adaptive loci and several chromosomal inversions. We also identify distinct immune gene expression profiles between forms, but no evidence for transgressive expression in hybrids. Our results suggest that reproductive isolation is maintained in this three-way contact zone, despite some hybridization, and that reduced recombination in chromosomal inversions may play an important role in maintaining this isolation.

The maintenance of standing genetic variation: Gene flow vs. selective neutrality in Atlantic stickleback fish.

Adaptation to derived habitats often occurs from standing genetic variation. The maintenance within ancestral populations of genetic variants favourable in derived habitats is commonly ascribed to long-term antagonism between purifying selection and gene flow resulting from hybridization across habitats. A largely unexplored alternative idea based on quantitative genetic models of polygenic adaptation is that variants favoured in derived habitats are neutral in ancestral populations when their frequency is relatively low. To explore the latter, we first identify genetic variants important to the adaptation of threespine stickleback fish (Gasterosteus aculeatus) to a rare derived habitat-nutrient-depleted acidic lakes-based on whole-genome sequence data. Sequencing marine stickleback from six locations across the Atlantic Ocean then allows us to infer that the frequency of these derived variants in the ancestral habitat is unrelated to the likely opportunity for gene flow of these variants from acidic-adapted populations. This result is consistent with the selective neutrality of derived variants within the ancestor. Our study thus supports an underappreciated explanation for the maintenance of standing genetic variation, and calls for a better understanding of the fitness consequences of adaptive variation across habitats and genomic backgrounds.

Admixture between Ancient Lineages, Selection, and the Formation of Sympatric Stickleback Species-Pairs.

Ecological speciation has become a popular model for the development and maintenance of reproductive isolation in closely related sympatric pairs of species or ecotypes. An implicit assumption has been that such pairs originate (possibly with gene flow) from a recent, genetically homogeneous ancestor. However, recent genomic data have revealed that currently sympatric taxa are often a result of secondary contact between ancestrally allopatric lineages. This has sparked an interest in the importance of initial hybridization upon secondary contact, with genomic reanalysis of classic examples of ecological speciation often implicating admixture in speciation. We describe a novel occurrence of unusually well-developed reproductive isolation in a model system for ecological speciation: the three-spined stickleback (Gasterosteus aculeatus), breeding sympatrically in multiple lagoons on the Scottish island of North Uist. Using morphological data, targeted genotyping, and genome-wide single-nucleotide polymorphism data, we show that lagoon resident and anadromous ecotypes are strongly reproductively isolated with an estimated hybridization rate of only ∼1%. We use palaeoecological and genetic data to test three hypotheses to explain the existence of these species-pairs. Our results suggest that recent, purely ecological speciation from a genetically homogeneous ancestor is probably not solely responsible for the evolution of species-pairs. Instead, we reveal a complex colonization history with multiple ancestral lineages contributing to the genetic composition of species-pairs, alongside strong disruptive selection. Our results imply a role for admixture upon secondary contact and are consistent with the recent suggestion that the genomic underpinning of ecological speciation often has an older, allopatric origin.

Prior exposure to long-day photoperiods alters immune responses and increases susceptibility to parasitic infection in stickleback.

Seasonal disease and parasitic infection are common across organisms, including humans, and there is increasing evidence for intrinsic seasonal variation in immune systems. Changes are orchestrated through organisms' physiological clocks using cues such as day length. Ample research in diverse taxa has demonstrated multiple immune responses are modulated by photoperiod, but to date, there have been few experimental demonstrations that photoperiod cues alter susceptibility to infection. We investigated the interactions among photoperiod history, immunity and susceptibility in laboratory-bred three-spined stickleback (a long-day breeding fish) and its external, directly reproducing monogenean parasite Gyrodactylus gasterostei. We demonstrate that previous exposure to long-day photoperiods (PLD) increases susceptibility to infection relative to previous exposure to short days (PSD), and modifies the response to infection for the mucin gene muc2 and Treg cytokine foxp3a in skin tissues in an intermediate 12 L : 12 D photoperiod experimental trial. Expression of skin muc2 is reduced in PLD fish, and negatively associated with parasite abundance. We also observe inflammatory gene expression variation associated with natural inter-population variation in resistance, but find that photoperiod modulation of susceptibility is consistent across host populations. Thus, photoperiod modulation of the response to infection is important for host susceptibility, highlighting new mechanisms affecting seasonality of host-parasite interactions.

A genetics-based approach confirms immune associations with life history across multiple populations of an aquatic vertebrate (Gasterosteus aculeatus).

Understanding how wild immune variation covaries with other traits can reveal how costs and trade-offs shape immune evolution in the wild. Divergent life history strategies may increase or alleviate immune costs, helping shape immune variation in a consistent, testable way. Contrasting hypotheses suggest that shorter life histories may alleviate costs by offsetting them against increased mortality, or increase the effect of costs if immune responses are traded off against development or reproduction. We investigated the evolutionary relationship between life history and immune responses within an island radiation of three-spined stickleback, with discrete populations of varying life histories and parasitism. We sampled two short-lived, two long-lived and an anadromous population using qPCR to quantify current immune profile and RAD-seq data to study the distribution of immune variants within our assay genes and across the genome. Short-lived populations exhibited significantly increased expression of all assay genes, which was accompanied by a strong association with population-level variation in local alleles and divergence in a gene that may be involved in complement pathways. In addition, divergence around the eda gene in anadromous fish is likely associated with increased inflammation. A wider analysis of 15 populations across the island revealed that immune genes across the genome show evidence of having diverged alongside life history strategies. Parasitism and reproductive investment were also important sources of variation for expression, highlighting the caution required when assaying immune responses in the wild. These results provide strong, gene-based support for current hypotheses linking life history and immune variation across multiple populations of a vertebrate model.

Otolith development in wild populations of stickleback: Jones & Hynes method does not apply to most populations.

This paper critiques Jones & Hynes (1950) findings by analysing sequential samples of otoliths from three wild populations of Gasterosteus aculeatus from North Uist, Scotland and Nottingham, England. Contrary to Jones & Hynes (1950), but coincident with the finding of later researchers, our results showed that no true translucent ring formed in the otolith of G. aculeatus during their first summer. The first translucent ring was probably starting to be formed by the end of summer and was completed by the end of their first winter. There was no second opaque ring in the otoliths of G. aculeatus before they passed their first winter. The second opaque ring was just starting to appear by early April of the second year in the southern population i.e. Nottingham, but later, by May, in the northern populations i.e. North Uist. Formation of the opaque ring in G. aculeatus mostly occurs in spring and summer, with younger fish starting earlier. In contrast, the formation of translucent rings is mostly during autumn and winter, but can be more widespread through the year, possibly as a result of reproductive investment.

What Are the Environmental Determinants of Phenotypic Selection? A Meta-analysis of Experimental Studies.

Although many selection estimates have been published, the environmental factors that cause selection to vary in space and time have rarely been identified. One way to identify these factors is by experimentally manipulating the environment and measuring selection in each treatment. We compiled and analyzed selection estimates from experimental studies. First, we tested whether the effect of manipulating the environment on selection gradients depends on taxon, trait type, or fitness component. We found that the effect of manipulating the environment was larger when selection was measured on life-history traits or via survival. Second, we tested two predictions about the environmental factors that cause variation in selection. We found support for the prediction that variation in selection is more likely to be caused by environmental factors that have a large effect on mean fitness but not for the prediction that variation is more likely to be caused by biotic factors. Third, we compared selection gradients from experimental and observational studies. We found that selection varied more among treatments in experimental studies than among spatial and temporal replicates in observational studies, suggesting that experimental studies can detect relationships between environmental factors and selection that would not be apparent in observational studies.

No evidence of local adaptation of immune responses to Gyrodactylus in three-spined stickleback (Gasterosteus aculeatus).

Parasitism represents one of the most widespread lifestyles in the animal kingdom, with the potential to drive coevolutionary dynamics with their host population. Where hosts and parasites evolve together, we may find local adaptation. As one of the main host defences against infection, there is the potential for the immune response to be adapted to local parasites. In this study, we used the three-spined stickleback and its Gyrodactylus parasites to examine the extent of local adaptation of parasite infection dynamics and the immune response to infection. We took two geographically isolated host populations infected with two distinct Gyrodactylus species and performed a reciprocal cross-infection experiment in controlled laboratory conditions. Parasite burdens were monitored over the course of the infection, and individuals were sampled at multiple time points for immune gene expression analysis. We found large differences in virulence between parasite species, irrespective of host, and maladaptation of parasites to their sympatric host. The immune system responded to infection, with a decrease in expression of innate and Th1-type adaptive response genes in fish infected with the less virulent parasite, representing a marker of a possible resistance mechanism. There was no evidence of local adaptation in immune gene expression levels. Our results add to the growing understanding of the extent of host-parasite local adaptation, and demonstrate a systemic immune response during infection with a common ectoparasite. Further immunological studies using the stickleback-Gyrodactylus system can continue to contribute to our understanding of the function of the immune response in natural populations.

Spatial and temporal variation in macroparasite communities of three-spined stickleback.

Patterns in parasite community structure are often observed in natural systems and an important question in parasite ecology is whether such patterns are repeatable across time and space. Field studies commonly look at spatial or temporal repeatability of patterns, but they are rarely investigated in conjunction. We use a large dataset on the macroparasites of the three-spined stickleback, Gasterosteus aculeatus L., collected from 14 locations on North Uist, Scotland over an 8-year period to investigate: (1) repeatability of patterns in parasite communities among populations and whether variation is consistent across years, (2) whether variation between years can be explained by climatic variation and progression of the season and (3) whether variation in habitat characteristics explain population differences. Differences in relative abundance and prevalence across populations were observed in a number of parasites investigated indicating a lack of consistency across years in numerous parasite community measures; however, differences between populations in the prevalence and abundance of some parasites were consistent throughout the study. Average temperature did not affect parasite community, and progression of the season was only significant for two of 13 community measures. Two of the six habitat characteristics investigated (pH and calcium concentration) significantly affected parasite presence.

Parasites contribute to ecologically dependent postmating isolation in the adaptive radiation of three-spined stickleback.

Spatial variation in parasitic infections is common, and has the potential to drive population divergence and the reproductive isolation of hosts. However, despite support from theory and model laboratory systems, little strong evidence has been forthcoming from the wild. Here, we show that parasites are likely to cause reproductive isolation in the adaptive radiation of three-spined stickleback. Adjacent wild populations on the Scottish island of North Uist differ greatly and consistently in the occurrence of different parasites that have substantial effects on fitness. Laboratory-reared fish are more resistant to experimental infection by parasite species from their own population. Furthermore, hybrid backcrosses between the host populations are more resistant to parasites from the parental population to which they are more closely related. These patterns provide strong evidence that parasites can cause ecological speciation, by contributing to selection against migrants and ecologically dependent postmating isolation.

The ecology of an adaptive radiation of three-spined stickleback from North Uist, Scotland.

There has been a large focus on the genetics of traits involved in adaptation, but knowledge of the environmental variables leading to adaptive changes is surprisingly poor. Combined use of environmental data with morphological and genomic data should allow us to understand the extent to which patterns of phenotypic and genetic diversity within a species can be explained by the structure of the environment. Here, we analyse the variation of populations of three-spined stickleback from 27 freshwater lakes on North Uist, Scotland, that vary greatly in their environment, to understand how environmental and genetic constraints contribute to phenotypic divergence. We collected 35 individuals per population and 30 abiotic and biotic environmental parameters to characterize variation across lakes and analyse phenotype-environment associations. Additionally, we used RAD sequencing to estimate the genetic relationships among a subset of these populations. We found a large amount of phenotypic variation among populations, most prominently in armour and spine traits. Despite large variation in the abiotic environment, namely in ion composition, depth and dissolved organic Carbon, more phenotypic variation was explained by the biotic variables (presence of predators and density of predator and competitors), than by associated abiotic variables. Genetic structure among populations was partly geographic, with closer populations being more similar. Altogether, our results suggest that differences in body shape among stickleback populations are the result of both canalized genetic and plastic responses to environmental factors, which shape fish morphology in a predictable direction regardless of their genetic starting point.

Development of resident and migratory three-spined stickleback, Gasterosteus aculeatus.

The three-spined stickleback (Gasterosteus aculeatus) is a teleost fish and a model organism in evolutionary ecology, useful for both laboratory and natural experiments. It is especially valued for the substantial intraspecific variation in morphology, behaviour and genetics. Classic work of Swarup (1958) has described the development in the laboratory of embryos from a single freshwater population, but this was carried out at higher temperature than many stickleback would encounter in the wild and variation between populations was not addressed. Here we describe the development of embryos from two sympatric, saltwater ecotypes of stickleback from North Uist, Scotland raised at 14°C, the approximate temperature of North Uist lochs in the breeding season. The two ecotypes were (a) a large, migratory form in which the adults are completely plated with bony armour and (b) a smaller, low-plated form that is resident year-round in saltwater lagoons. By monitoring embryos every 24-hours post fertilisation, important characteristics of development were observed and photographed to provide a reference for North Uist ecotypes at this temperature. Hatching success was greater than 85% and did not differ between resident and migratory stickleback, but migratory eggs hatched significantly earlier than the resident ecotype. Our work provides a framework that can now be used to compare stickleback populations that may also grow in distinct environmental conditions, to help understand the breadth of normal developmental features and to characterise abnormal development.

The evolutionary ecology of dwarfism in three-spined sticklebacks.

1. Body size is a defining phenotypic trait, but the ecological causes of its evolution are poorly understood. Most studies have considered only a single putative causal agent and have failed to recognise that different environmental agents are often correlated. 2. Darwin suggested that although trait variation across populations is often associated with abiotic variation, evolution is more likely to be driven by biotic factors correlated with the abiotic variation. This hypothesis has received little explicit attention. 3. We use structural equation modelling to quantify the relative importance of abiotic (pH, metal concentrations) and biotic (competition, predation) factors in the evolution of body size in three-spined sticklebacks Gasterosteus aculeatus on the island of North Uist, Scotland. We combine phenotypic data from multiple isolated populations, detailed characterisation of their environment and a common garden experiment that establishes the genetic basis of size differences. 4. Three-spined sticklebacks on North Uist show almost unprecedented intraspecific evolution of body size that has taken place rapidly (<16,000 years). The smallest fish mature at only 7% of the mass of ancestral, anadromous fish. Dwarfism is associated with reduced abundance of a smaller competitor species, the nine-spined stickleback Pungitius pungitius, and with low pH indicative of poor resource conditions. Dwarfism also tends to occur where an important predator, the brown trout Salmo trutta, is also small. The abundance of P. pungitius and the size of S. trutta are themselves related to underlying abiotic environmental variation. 5. Despite the close association between abiotic and biotic factors across populations, our results support Darwin's hypothesis that biotic factors, associated with variation in the abiotic environment, are more important in explaining evolution than is abiotic variation per se. This study demonstrates the importance of considering the relationships between environmental variables before conclusions can be drawn about the causes of (body size) evolution on islands.

Ecological constraint, rather than opportunity, promotes adaptive radiation in three-spined stickleback (Gasterosteus aculeatus) on North Uist.

The context and cause of adaptive radiations have been widely described and explored but why rapid evolutionary diversification does not occur in related evolutionary lineages has yet to be understood. The standard answer is that evolutionary diversification is provoked by ecological opportunity and that some lineages do not encounter the opportunity. Three-spined sticklebacks on the Scottish island of North Uist show enormous diversification, which seems to be associated with the diversity of aquatic habitats. Sticklebacks on the neighboring island of South Uist have not been reported to show the same level of evolutionary diversity, despite levels of environmental variation that we might expect to be similar to North Uist. In this study, we compared patterns of morphological and environmental diversity on North and South Uist. Ancestral anadromous sticklebacks from both islands exhibited similar morphology including size and bony "armor." Resident sticklebacks showed significant variation in armor traits in relation to pH of water. However, North Uist sticklebacks exhibited greater diversity of morphological traits than South Uist and this was associated with greater diversity in pH of the waters of lochs on North Uist. Highly acidic and highly alkaline freshwater habitats are missing, or uncommon, on South Uist. Thus, pH appears to act as a causal factor driving the evolutionary diversification of stickleback in local adaptation in North and South Uist. This is consistent with diversification being more associated with ecological constraint than ecological opportunity.

Consistent differences in macroparasite community composition among populations of three-spined sticklebacks, Gasterosteus aculeatus L.

Parasite ecologists are often interested in the repeatability of patterns in parasite communities in space and/or time, because of implications for the dynamics of host-parasite interactions. Field studies usually examine temporal and spatial variation in isolation or limit themselves to a small number of host populations. Here, we studied the macroparasite communities of 12 populations of three-spined stickleback, Gasterosteus aculeatus L., on North Uist, Scotland, separated by small geographical distances, during the breeding season in 2 consecutive years (2007 and 2008) to determine: (1) the extent of spatial variation in macroparasite communities, (2) whether this variation is consistent across years, and (3) whether habitat characteristics can explain differences in macroparasite community composition among populations. We found substantial variation in parasite communities among populations. Generally, measures of parasite community composition were higher in 2008 than in 2007, but this effect of year was consistent across populations, such that the relative differences in these measures among populations changed little between years. These data suggest that there is short-term stability in the spatial variation in macroparasite communities of North Uist sticklebacks. However, none of the 5 habitat characteristics measured explained spatial variation in any measure of parasite community composition.

Courtship behavior, nesting microhabitat, and assortative mating in sympatric stickleback species pairs.

The maintenance of reproductive isolation in the face of gene flow is a particularly contentious topic, but differences in reproductive behavior may provide the key to explaining this phenomenon. However, we do not yet fully understand how behavior contributes to maintaining species boundaries. How important are behavioral differences during reproduction? To what extent does assortative mating maintain reproductive isolation in recently diverged populations and how important are "magic traits"? Assortative mating can arise as a by-product of accumulated differences between divergent populations as well as an adaptive response to contact between those populations, but this is often overlooked. Here we address these questions using recently described species pairs of three-spined stickleback (Gasterosteus aculeatus), from two separate locations and a phenotypically intermediate allopatric population on the island of North Uist, Scottish Western Isles. We identified stark differences in the preferred nesting substrate and courtship behavior of species pair males. We showed that all males selectively court females of their own ecotype and all females prefer males of the same ecotype, regardless of whether they are from species pairs or allopatric populations. We also showed that mate choice does not appear to be driven by body size differences (a potential "magic trait"). By explicitly comparing the strength of these mating preferences between species pairs and single-ecotype locations, we were able to show that present levels of assortative mating due to direct mate choice are likely a by-product of other adaptations between ecotypes, and not subject to obvious selection in species pairs. Our results suggest that ecological divergence in mating characteristics, particularly nesting microhabitat may be more important than direct mate choice in maintaining reproductive isolation in stickleback species pairs.

Intercontinental genomic parallelism in multiple three-spined stickleback adaptive radiations.

Parallelism, the evolution of similar traits in populations diversifying in similar conditions, provides strong evidence of adaptation by natural selection. Many studies of parallelism focus on comparisons of different ecotypes or contrasting environments, defined a priori, which could upwardly bias the apparent prevalence of parallelism. Here, we estimated genomic parallelism associated with components of environmental and phenotypic variation at an intercontinental scale across four freshwater adaptive radiations (Alaska, British Columbia, Iceland and Scotland) of the three-spined stickleback (Gasterosteus aculeatus). We combined large-scale biological sampling and phenotyping with restriction site associated DNA sequencing (RAD-Seq) data from 73 freshwater lake populations and four marine ones (1,380 fish) to associate genome-wide allele frequencies with continuous distributions of environmental and phenotypic variation. Our three main findings demonstrate that (1) quantitative variation in phenotypes and environments can predict genomic parallelism; (2) genomic parallelism at the early stages of adaptive radiations, even at large geographic scales, is founded on standing variation; and (3) similar environments are a better predictor of genome-wide parallelism than similar phenotypes. Overall, this study validates the importance and predictive power of major phenotypic and environmental factors likely to influence the emergence of common patterns of genomic divergence, providing a clearer picture than analyses of dichotomous phenotypes and environments.

Relationships between immune gene expression and circulating cytokine levels in wild house mice.

Quantitative PCR (qPCR) has been commonly used to measure gene expression in a number of research contexts, but the measured RNA concentrations do not always represent the concentrations of active proteins which they encode. This can be due to transcriptional regulation or post-translational modifications, or localization of immune environments, as can occur during infection. However, in studies using free-living non-model species, such as in ecoimmunological research, qPCR may be the only available option to measure a parameter of interest, and so understanding the quantitative link between gene expression and associated effector protein levels is vital.Here, we use qPCR to measure concentrations of RNA from mesenteric lymph node (MLN) and spleen tissue, and multiplex ELISA of blood serum to measure circulating cytokine concentrations in a wild population of a model species, Mus musculus domesticus.Few significant correlations were found between gene expression levels and circulating cytokines of the same immune genes or proteins, or related functional groups. Where significant correlations were observed, these were most frequently within the measured tissue (i.e., the expression levels of genes measured from spleen tissue were more likely to correlate with each other rather than with genes measured from MLN tissue, or with cytokine concentrations measured from blood).Potential reasons for discrepancies between measures including differences in decay rates and transcriptional regulation networks are discussed. We highlight the relative usefulness of different measures under different research questions and consider what might be inferred from immune assays.

Internal embryonic development in a non-copulatory, egg-laying teleost, the three-spined stickleback, Gasterosteus aculeatus.

The switch from egg-laying to retaining and giving birth to live young is a major transition in the history of life. Despite its repeated evolution across the fishes, records of intermediate phenotypes are vanishingly rare, with only two known cases in existence of normally egg-laying fish species retaining embryos within the ovaries. We report the discovery of a third occurrence, in which well-developed embryos were found in the ovaries of a three-spined stickleback (Gasterosteus aculeatus), a non-copulatory, normally oviparous species. Extracted from the parent fish, these embryos hatched and grew to adulthood. Genetic and physiological examination of the parent fish and offspring ruled out development by parthenogenesis and hermaphroditism, therefore implicating internal fertilisation by a male stickleback. This extremely rare phenomenon may have been facilitated in this population by an unusual tendency for females to become egg-bound, and suggests that some major transitions may arise almost spontaneously.