Strong gene flow and lack of stable population structure in the face of rapid adaptation to local temperature in a spring-spawning salmonid, the European grayling (Thymallus thymallus)

The population genomics of repeated freshwater colonizations by Gulf pipefish

How organisms adapt to the novel challenges imposed by the colonization of a new habitat has long been a central question in evolutionary biology. When multiple populations of the same species independently adapt to similar environmental challenges, the question becomes whether the populations have arrived at their adaptations through the same genetic mechanisms. In recent years, genetic techniques have been used to tackle these questions by investigating the genome-level changes underlying local adaptation. Here, we present a genomic analysis of colonization of freshwater habitats by a primarily marine fish, the Gulf pipefish (Syngnathus scovelli). We sample pipefish from four geographically distinct freshwater locations and use double-digest restriction site associated DNA sequencing to compare them to 12 previously studied saltwater populations. The two most geographically distant and isolated freshwater populations are the most genetically distinct, although demographic analysis suggests that these populations are experiencing ongoing migration with their saltwater neighbours. Additionally, outlier regions were found genome-wide, showing parallelism across ecotype pairs. We conclude that these multiple freshwater colonizations involve similar genomic regions, despite the large geographical distances and different underlying mechanisms. These similar patterns are probably facilitated by the interacting effects of intrinsic barriers, gene flow among populations and ecological selection in the Gulf pipefish.

Cytosine methylation patterns suggest a role of methylation in plastic and adaptive responses to temperature in European grayling (Thymallus thymallus) populations

Temperature is a key environmental parameter affecting both the phenotypes and distributions of organisms, particularly ectotherms. Rapid organismal responses to thermal environmental changes have been described for several ectotherms; however, the underlying molecular mechanisms often remain unclear. Here, we studied whole genome cytosine methylation patterns of European grayling (Thymallus thymallus) embryos from five populations with contemporary adaptations of early life history traits at either 'colder' or 'warmer' spawning grounds. We reared fish embryos in a common garden experiment using two temperatures that resembled the 'colder' and 'warmer' conditions of the natal natural environments. Genome-wide methylation patterns were similar in populations originating from colder thermal origin subpopulations, whereas single nucleotide polymorphisms uncovered from the same data identified strong population structure among isolated populations, but limited structure among interconnected populations. This was surprising because the previously studied gene expression response among populations was mostly plastic, and mainly influenced by the developmental temperature. These findings support the hypothesis of the magnified role of epigenetic mechanisms in modulating plasticity. The abundance of consistently changing methylation loci between two warmer-to-colder thermal origin population pairs suggests that local adaptation has shaped the observed methylation patterns. The dynamic nature of the methylomes was further highlighted by genome-wide and site-specific plastic responses. Our findings support both the presence of a plastic response in a subset of CpG loci, and the evolutionary role of methylation divergence between populations adapting to contrasting thermal environments.

Rapid evolution of genetic and phenotypic divergence in Atlantic salmon following the colonisation of two new branches of a watercourse

BACKGROUND

Selection acts strongly on individuals that colonise a habitat and have phenotypic traits that deviate from the local optima. Our objective was to investigate the evolutionary rates in Atlantic salmon (Salmo salar) in a river system (the Vefsna watershed in Norway), fewer than 15 generations after colonisation of two new branches of the watercourse for spawning, which were made available by construction of fish ladders in 1889.

METHODS

Differences in age and size were analysed using scale samples collected by anglers. Age and size of recaptures from a tagging experiment were compared between the three branches. Furthermore, genetic analyses of scale samples collected in the three river branches during two periods were performed to evaluate whether observed differences evolved by genetic divergence over this short period, or were the result of phenotypic plasticity.

RESULTS

We demonstrate that evolution can be rapid when fish populations are subjected to strong selection, in spite of sympatry with their ancestral group, no physical barriers to hybridisation, and natal homing as the only reproductive isolating barrier. After fewer than 15 generations, there was evidence of genetic isolation between the two branches based on genetic variation at 96 single nucleotide polymorphism loci, and significant differences in several life history traits, including size and age at maturity. Selection against large size at maturity appears to have occurred, since large individuals were reluctant to ascend the branch with less abundant water. The estimated evolutionary rate of change in life history traits is within the upper 3 to 7% reported in other fish studies on microevolutionary rates.

CONCLUSIONS

These findings suggest that with sufficient genetic diversity, Atlantic salmon can rapidly colonise and evolve to new accessible habitats. This has profound implications for conservation and restoration of populations and habitats in order to meet evolutionary challenges, including alterations in water regime, whether altered by climate change or anthropogenic factors.

Testing for Local Adaptation to Spawning Habitat in Sympatric Subpopulations of Pike by Reciprocal Translocation of Embryos

We tested for local adaption in early life-history traits by performing a reciprocal translocation experiment with approximately 2,500 embryos of pike (Esox lucius) divided in paired split-family batches. The experiment indicated local adaptation in one of the two subpopulations manifested as enhanced hatching success of eggs in the native habitat, both when compared to siblings transferred to a non-native habitat, and when compared to immigrant genotypes from the other subpopulation. Gene-by-environment effects on viability of eggs and larvae were evident in both subpopulations, showing that there existed genetic variation allowing for evolutionary responses to divergent selection, and indicating a capacity for plastic responses to environmental change. Next, we tested for differences in female life-history traits. Results uncovered that females from one population invested more resources into reproduction and also produced more (but smaller) eggs in relation to their body size compared to females from the other population. We suggest that these females have adjusted their reproductive strategies as a counter-adaptation because a high amount of sedimentation on the eggs in that subpopulations spawning habitat might benefit smaller eggs. Collectively, our findings point to adaptive divergence among sympatric subpopulations that are physically separated only for a short period during reproduction and early development-which is rare. These results illustrate how combinations of translocation experiments and field studies of life-history traits might infer about local adaptation and evolutionary divergence among populations. Local adaptations in subdivided populations are important to consider in management and conservation of biodiversity, because they may otherwise be negatively affected by harvesting, supplementation, and reintroduction efforts targeted at endangered populations.

Isolation by distance and non-identical patterns of gene flow within two river populations of the freshwater fish Rutilus rutilus (L. 1758)

The spatial distribution of organisms is maintained by a combination of in situ reproduction and dispersal of conspecifics from elsewhere within its habitable range. The determination of dispersal origin and sub-population connectivity has a vital role to play in forming effective management policies. The common roach (Rutilus rutilus) is an important component of the economically and socially valuable recreational fishery and represents a well-studied member of the Cyprinidae. Microsatellite allele data were used to investigate hypothetically variant levels of microevolutionary structuring and isolation-by-distance (IBD) in in the Rivers Stour and Thames. A strong signal of IBD was found in the Stour, probably due to the limited capacity for unrestricted bidirectional dispersal in this river compared with the Thames. A weak inference of IBD in the Thames is likely erroneous and effected by a strong localised genetic signal from a recent stocking event. Whilst we found significantly genetically divergent upstream areas in the River Stour, a strong signal of IBD remained when the headwater sub-population was removed, suggesting that that the signal is not biased by non-equilibrium conditions in upstream reaches. We discuss these results with reference to the management of aquatic bioresources and emphasise the idiosyncrasy that aquatic biota and hydrological complexity may imprint upon patterns of biodiversity within any given system.

Genetic parentage analysis confirms a polygynandrous breeding system in the European grayling (Thymallus thymallus)

Knowing the breeding system of a species is important in order to understand individual variation in reproductive success. Large variation in reproductive success and thus reproductive skew strongly impacts on the effective number of breeders and thus the long-term effective population size (Ne). Fishes, in particular species belonging to the salmonid family, exhibit a wide diversity of breeding systems. In general, however, breeding systems are rarely studied in detail in the wild. Here we examine the breeding system of the spring-spawning European grayling Thymallus thymallus from a small Norwegian stream using parentage assignment based on the genotyping of 19 polymorphic microsatellite loci. In total 895 individual grayling fry and 154 mature grayling (57 females and 97 males) were genotyped. A total of 466 offspring were assigned a father, a mother, or a parent pair with a confidence of 90% or higher. Successfully reproducing males had on average 11.9 ± 13.3 (SD) offspring with on average 2.1 ± 1.2 partners, whereas successful females had on average 9.5 ± 12.8 offspring and 2.3 ± 1.5 partners. Parents with more partners also produced more offspring. Thus the grayling breeding system within this small stream revealed a polygynandrous breeding system, similar to what has been observed for many other salmonid fish species. The present study thus unambiguously corroborates a polygynadrous breeding system in the European grayling. This knowledge is critical for managing populations of this species, which has suffered significant local population declines throughout its range over the last several decades.

Temporal population genetic instability in range-edge western toads, Anaxyrus boreas

In this article, we address the temporal stability of population genetic structure in a range-edge population that is undergoing continual, short-distance colonization events. We sampled western toad, Anaxyrus boreas, breeding populations over 2 seasons near their northern range limit in southeast Alaska. We sampled 20 ponds each during the summers of 2008 and 2009, with 14 ponds sampled in both summers. We found considerable turnover in the population genetic relationships among ponds in those 2 seasons, as well as biologically meaningful genetic differentiation between years within some ponds. We found relatively consistent relationships between major population centers, whereas the relationships between the central ponds and smaller, outlying populations differed year to year. This finding indicates that multiple years of genetic sampling may be important for understanding the genetic landscape of some populations.

AFLPs and mitochondrial haplotypes reveal local adaptation to extreme thermal environments in a freshwater gastropod

The way environmental variation shapes neutral and adaptive genetic variation in natural populations is a key issue in evolutionary biology. Genome scans allow the identification of the genetic basis of local adaptation without previous knowledge of genetic variation or traits under selection. Candidate loci for divergent adaptation are expected to show higher F_ST than neutral loci influenced solely by random genetic drift, migration and mutation. The comparison of spatial patterns of neutral markers and loci under selection may help disentangle the effects of gene flow, genetic drift and selection among populations living in contrasting environments. Using the gastropod Radix balthica as a system, we analyzed 376 AFLP markers and 25 mtDNA COI haplotypes for candidate loci and associations with local adaptation among contrasting thermal environments in Lake Mývatn, a volcanic lake in northern Iceland. We found that 2% of the analysed AFLP markers were under directional selection and 12% of the mitochondrial haplotypes correlated with differing thermal habitats. The genetic networks were concordant for AFLP markers and mitochondrial haplotypes, depicting distinct topologies at neutral and candidate loci. Neutral topologies were characterized by intense gene flow revealed by dense nets with edges connecting contrasting thermal habitats, whereas the connections at candidate loci were mostly restricted to populations within each thermal habitat and the number of edges decreased with temperature. Our results suggest microgeographic adaptation within Lake Mývatn and highlight the utility of genome scans in detecting adaptive divergence.

Gene pleiotropy constrains gene expression changes in fish adapted to different thermal conditions

Understanding the factors that shape the evolution of gene expression is a central goal in biology, but the molecular mechanisms behind this remain controversial. A related major goal is ascertaining how such factors may affect the adaptive potential of a species or population. Here we demonstrate that temperature-driven gene expression changes in fish adapted to differing thermal environments are constrained by the level of gene pleiotropy estimated by either the number of protein interactions or gene biological processes. Genes with low pleiotropy levels were the main drivers of both plastic and evolutionary global expression profile changes, while highly pleiotropic genes had limited expression response to temperature treatment. Our study provides critical insights into the molecular mechanisms by which natural populations can adapt to changing environments. In addition to having important implications for climate change adaptation, these results suggest that gene pleiotropy should be considered more carefully when interpreting expression profiling data.

The factors that shape the evolution of gene expression and their role in adaptation are poorly understood. Here, Papakostas et al. show that gene pleiotropy constrains protein expression evolution in freshwater salmonids adapted to different temperatures.

Parental influences on pathogen resistance in brown trout embryos and effects of outcrossing within a river network

Phenotypic plasticity can increase tolerance to heterogeneous environments but the elevations and slopes of reaction norms are often population specific. Disruption of locally adapted reaction norms through outcrossing can lower individual viability. Here, we sampled five genetically distinct populations of brown trout (Salmo trutta) from within a river network, crossed them in a full-factorial design, and challenged the embryos with the opportunistic pathogen Pseudomonas fluorescens. By virtue of our design, we were able to disentangle effects of genetic crossing distance from sire and dam effects on early life-history traits. While pathogen infection did not increase mortality, it was associated with delayed hatching of smaller larvae with reduced yolk sac reserves. We found no evidence of a relationship between genetic distance (W, FST) and the expression of early-life history traits. Moreover, hybrids did not differ in phenotypic means or reaction norms in comparison to offspring from within-population crosses. Heritable variation in early life-history traits was found to remain stable across the control and pathogen environments. Our findings show that outcrossing within a rather narrow geographical scale can have neutral effects on F1 hybrid viability at the embryonic stage, i.e. at a stage when environmental and genetic effects on phenotypes are usually large.

Testing for local adaptation in brown trout using reciprocal transplants

BACKGROUND

Local adaptation can drive the divergence of populations but identification of the traits under selection remains a major challenge in evolutionary biology. Reciprocal transplant experiments are ideal tests of local adaptation, yet rarely used for higher vertebrates because of the mobility and potential invasiveness of non-native organisms. Here, we reciprocally transplanted 2500 brown trout (Salmo trutta) embryos from five populations to investigate local adaptation in early life history traits. Embryos were bred in a full-factorial design and raised in natural riverbeds until emergence. Customized egg capsules were used to simulate the natural redd environment and allowed tracking the fate of every individual until retrieval. We predicted that 1) within sites, native populations would outperform non-natives, and 2) across sites, populations would show higher performance at 'home' compared to 'away' sites.

RESULTS

There was no evidence for local adaptation but we found large differences in survival and hatching rates between sites, indicative of considerable variation in habitat quality. Survival was generally high across all populations (55% ± 3%), but ranged from 4% to 89% between sites. Average hatching rate was 25% ± 3% across populations ranging from 0% to 62% between sites.

CONCLUSION

This study provides rare empirical data on variation in early life history traits in a population network of a salmonid, and large-scale breeding and transplantation experiments like ours provide powerful tests for local adaptation. Despite the recently reported genetic and morphological differences between the populations in our study area, local adaptation at the embryo level is small, non-existent, or confined to ecological conditions that our experiment could not capture.

Contemporary divergence in early life history in grayling (Thymallus thymallus)

Background

Following colonization of new habitats and subsequent selection, adaptation to environmental conditions might be expected to be rapid. In a mountain lake in Norway, Lesjaskogsvatnet, more than 20 distinct spawning demes of grayling have been established since the lake was colonized, some 20-25 generations ago. The demes spawn in tributaries consistently exhibiting either colder or warmer temperature conditions during spawning in spring and subsequent early development during early summer. In order to explore the degree of temperature-related divergence in early development, a multi-temperature common-garden experiment was performed on embryos from four different demes experiencing different spring temperatures.

Results

Early developmental characters were measured to test if individuals from the four demes respond differently to the treatment temperatures. There was clear evidence of among-deme differences (genotype - environment interactions) in larval growth and yolk-to-body-size conversion efficiency. Under the cold treatment regime, larval growth rates were highest for individuals belonging to cold streams. Individuals from warm streams had the highest yolk-consumption rate under cold conditions. As a consequence, yolk-to-body-mass conversion efficiency was highest for cold-deme individuals under cold conditions. As we observed response parallelism between individuals from demes belonging to similar thermal groups for these traits, some of the differentiation seems likely to result from local adaptation

Conclusion

The observed differences in length at age during early larval development most likely have a genetic component, even though both directional and random processes are likely to have influenced evolutionary change in the demes under study.

Contemporary temperature-driven divergence in a Nordic freshwater fish under conditions commonly thought to hinder adaptation

Background

Evaluating the limits of adaptation to temperature is important given the IPCC-predicted rise in global temperatures. The rate and scope of evolutionary adaptation can be limited by low genetic diversity, gene flow, and costs associated with adaptive change. Freshwater organisms are physically confined to lakes and rivers, and must therefore deal directly with climate variation and change. In this study, we take advantage of a system characterised by low genetic variation, small population size, gene flow and between-trait trade-offs to study how such conditions affect the ability of a freshwater fish to adapt to climate change. We test for genetically-based differences in developmental traits indicating local adaptation, by conducting a common-garden experiment using embryos and larvae from replicate pairs of sympatric grayling demes that spawn and develop in natural cold and warm water, respectively. These demes have common ancestors from a colonization event 22 generations ago. Consequently, we explore if diversification may occur under severely constraining conditions.

Results

We found evidence for divergence in ontogenetic rates. The divergence pattern followed adaptation predictions as cold-deme individuals displayed higher growth rates and yolk conversion efficiency than warm-deme individuals at the same temperature. The cold-deme embryos had a higher rate of muscle mass development. Most of the growth- and development differences occurred prior to hatch. The divergence was probably not caused by genetic drift as there was a strong degree of parallelism in the divergence pattern and because phenotypic differentiation (Q_ST) was larger than estimated genetic drift levels (microsatellite F_ST) between demes from different temperature groups. We also document that these particular grayling populations cannot develop successfully at temperatures above 12°C, whereas other European populations can, and that increasing the muscle mass development rate comes at the cost of some skeletal trait development rates.

Conclusions

This study shows that genetically based phenotypic divergence can prevail even under conditions of low genetic variation and ongoing gene flow. Furthermore, population-specific maximum development temperatures along with musculoskeletal developmental trade-offs may constrain adaptation.