Recent local adaptation of sockeye salmon to glacial spawning habitats

Does egg carotenoid improve larval quality in Arctic charr ( Salvelinus alpinus )?

Females in mutually ornamented species are often less conspicuously ornamented than their male conspecifics. It has been hypothesized that offspring quality may decrease if females invest more resources into ornaments at the expense of resources in eggs. An experiment was carried out to test whether natural variation in carotenoid in the eggs from a wild population of Arctic charr (Salvelinus alpinus) was associated with survival and growth of their offspring until hatching. Wild Arctic charr were caught at a spawning ground during the spawning period. Eggs from two different females, one female with yellowish carotenoid‐rich eggs and one with paler eggs, were fertilized by sperm from the same male. This was repeated until gametes were collected from 42 females and 21 males, giving a total of 21 groups. After fertilization, the zygotes from each of the two females were reared in four replicated groups. These 168 groups were reared separately until hatching when the surviving larvae were counted and their body length measured. For the two response variables survival and body length at hatching, no effect was demonstrated of any of the predictors (i) amount of carotenoid in the unfertilized eggs, (ii) the mothers' body condition, or (iii) ornament intensity of their red carotenoid‐based abdominal ornament. Thus, this study gives no support for the hypothesis that females investing less carotenoid into their eggs suffer from decreased offspring quality until hatching. This lack of association between female ornament intensity and their fitness is not as expected if female ornaments evolved due to direct sexual selection from males on the more ornamented females (“direct selection hypothesis”).

Life histories and ecotype conservation in an adaptive vertebrate: Genetic constitution of piscivorous brown trout covaries with habitat stability

Ecotype variation in species exhibiting different life history strategies may reflect heritable adaptations to optimize reproductive success, and potential for speciation. Traditionally, ecotypes have, however, been defined by morphometrics and life history characteristics, which may be confounded with individual plasticity. Here, we use the widely distributed and polytypic freshwater fish species brown trout (Salmo trutta) as a model to study piscivorous life history and its genetic characteristics in environmentally contrasting habitats; a large lake ecosystem with one major large and stable tributary, and several small tributaries. Data from 550 fish and 13 polymorphic microsatellites (He = 0.67) indicated ecotype-specific genetic differentiation (θ = 0.0170, p < .0001) among Bayesian assigned small riverine resident and large, lake migrating brown trout (>35 cm), but only in the large tributary. In contrast, large trout did not constitute a distinct genetic group in small tributaries, or across riverine sites. Whereas life history data suggest a small, river resident and a large migratory piscivorous ecotype in all studied tributaries, genetic data indicated that a genetically distinct piscivorous ecotype is more likely to evolve in the large and relatively more stable river habitat. In the smaller tributaries, ecotypes apparently resulted from individual plasticity. Whether different life histories and ecotypes result from individual plasticity or define different genetic types, have important consequence for conservation strategies.

Associations of stream geomorphic conditions and prevalence of alternative reproductive tactics among sockeye salmon populations

In many species, males may exhibit alternative life histories to circumvent the costs of intrasexual competition and female courtship. While the evolution and underlying genetic and physiological mechanisms behind alternative reproductive tactics are well studied, there has been less consideration of the ecological factors that regulate their prevalence. Here, we examine six decades of age composition records from thirty-six populations of sockeye salmon (Oncorhynchus nerka) to quantify associations between spawning habitat characteristics and the prevalence of precocious sneakers known as 'jacks'. Jack prevalence was independent of neutral genetic structure among stream populations, but varied among habitat types and as a function of continuous geomorphic characteristics. Jacks were more common in streams relative to beaches and rivers, and their prevalence was negatively associated with stream width, depth, elevation, slope and area, but positively related to bank cover. Behavioural observations showed that jacks made greater use of banks, wood and shallows than guard males, indicating that their reproductive success depends on the availability of such refuges. Our results emphasize the role of the physical habitat in shaping reproductive tactic frequencies among populations, likely through local adaptation in response to variable fitness expectations under different geomorphic conditions.

The evolutionary consequences of habitat fragmentation: Body morphology and coloration differentiation among brook trout populations of varying size

A reduction in population size due to habitat fragmentation can alter the relative roles of different evolutionary mechanisms in phenotypic trait differentiation. While deterministic (selection) and stochastic (genetic drift) mechanisms are expected to affect trait evolution, genetic drift may be more important than selection in small populations. We examined relationships between mature adult traits and ecological (abiotic and biotic) variables among 14 populations of brook trout. These naturally fragmented populations have shared ancestry but currently exhibit considerable variability in habitat characteristics and population size (49 < N_c < 10,032; 3 < N_b < 567). Body size, shape, and coloration differed among populations, with a tendency for more variation among small populations in both trait means and CV when compared to large populations. Phenotypic differences were more frequently and directly linked to habitat variation or operational sex ratio than to population size, suggesting that selection may overcome genetic drift at small population size. Phenotype-environment associations were also stronger in females than males, suggesting that natural selection due to abiotic conditions may act more strongly on females than males. Our results suggest that natural and sexual-selective pressures on phenotypic traits change during the process of habitat fragmentation, and that these changes are largely contingent upon existing habitat conditions within isolated fragments. Our study provides an improved understanding of the ecological and evolutionary consequences of habitat fragmentation and lends insight into the ability of some small populations to respond to selection and environmental change.

Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout

Rapid adaptation to novel environments may drive changes in genomic regions through natural selection. Such changes may be population-specific or, alternatively, may involve parallel evolution of the same genomic region in multiple populations, if that region contains genes or co-adapted gene complexes affecting the selected trait(s). Both quantitative and population genetic approaches have identified associations between specific genomic regions and the anadromous (steelhead) and resident (rainbow trout) life-history strategies of Oncorhynchus mykiss. Here, we use genotype data from 95 single nucleotide polymorphisms and show that the distribution of variation in a large region of one chromosome, Omy5, is strongly associated with life-history differentiation in multiple above-barrier populations of rainbow trout and their anadromous steelhead ancestors. The associated loci are in strong linkage disequilibrium, suggesting the presence of a chromosomal inversion or other rearrangement limiting recombination. These results provide the first evidence of a common genomic basis for life-history variation in O. mykiss in a geographically diverse set of populations and extend our knowledge of the heritable basis of rapid adaptation of complex traits in novel habitats.

Experimental tests for heritable morphological color plasticity in non-native brown trout (Salmo trutta) populations

The success of invasive species is frequently attributed to phenotypic plasticity, which facilitates persistence in novel environments. Here we report on experimental tests to determine whether the intensity of cryptic coloration patterns in a global invader (brown trout, Salmo trutta) was primarily the result of plasticity or heritable variation. Juvenile F₁ offspring were created through experimental crosses of wild-caught parents and reared for 30 days in the laboratory in a split-brood design on either light or dark-colored gravel substrate. Skin and fin coloration quantified with digital photography and image analysis indicated strong plastic effects in response to substrate color; individuals reared on dark substrate had both darker melanin-based skin color and carotenoid-based fin colors than other members of their population reared on light substrate. Slopes of skin and fin color reaction norms were parallel between environments, which is not consistent with heritable population-level plasticity to substrate color. Similarly, we observed weak differences in population-level color within an environment, again suggesting little genetic control on the intensity of skin and fin colors. Taken as whole, our results are consistent with the hypothesis that phenotypic plasticity may have facilitated the success of brown trout invasions and suggests that plasticity is the most likely explanation for the variation in color intensity observed among these populations in nature.

Ecological speciation in postglacial European whitefish: rapid adaptive radiations into the littoral, pelagic, and profundal lake habitats

Understanding how a monophyletic lineage of a species diverges into several adaptive forms has received increased attention in recent years, but the underlying mechanisms in this process are still under debate. Postglacial fishes are excellent model organisms for exploring this process, especially the initial stages of ecological speciation, as postglacial lakes represent replicated discrete environments with variation in available niches. Here, we combine data of niche utilization, trophic morphology, and 17 microsatellite loci to investigate the diversification process of three sympatric European whitefish morphs from three northern Fennoscandian lakes. The morphological divergence in the gill raker number among the whitefish morphs was related to the utilization of different trophic niches and was associated with reproductive isolation within and across lakes. The intralacustrine comparison of whitefish morphs showed that these systems represent two levels of adaptive divergence: (1) a consistent littoral–pelagic resource axis; and (2) a more variable littoral–profundal resource axis. The results also indicate that the profundal whitefish morph has diverged repeatedly from the ancestral littoral whitefish morph in sympatry in two different watercourses. In contrast, all the analyses performed revealed clustering of the pelagic whitefish morphs across lakes suggesting parallel postglacial immigration with the littoral whitefish morph into each lake. Finally, the analyses strongly suggested that the trophic adaptive trait, number of gill rakers, was under diversifying selection in the different whitefish morphs. Together, the results support a complex evolutionary scenario where ecological speciation acts, but where both allopatric (colonization history) and sympatric (within watercourse divergence) processes are involved.

How does coarse gravel augmentation affect early-stage Chinook salmon Oncorhynchus tshawytscha embryonic survivorship?

Early-stage Chinook salmon Oncorhynchus tshawytscha embryos were incubated in artificial redds that mimicked hyporheic conditions in gravel-augmented habitat to assess survivorship. Two complementary experiments were conducted where units varied along gradients of (1) increasing interstitial flow velocity (0·05-2·50 cm s⁻¹) in a uniformly coarse (particles ≥22 mm) sediment mixture and (2) increasing sediment porosity with interstitial flow velocity held constant. Embryonic survivorship increased moderately along a gradient of interstitial flow velocity, while survivorship among units with varying sediment porosities was consistent. No evidence for flow-induced agitation and mortality was observed. Results suggest that high interstitial flow velocities may confer a moderate advantage for incubating salmonid embryos when conditions that typically reduce embryonic mortality (i.e. low concentrations of fine particles) are ideal.

Female ornaments revisited - are they correlated with offspring quality?

The evolution and signalling content of female ornamentation has remained an enduring challenge to evolutionary biologists, despite the fact that secondary sexual characters are widespread in females. While females usually invest significant amounts of their resources, including carotenoids, in offspring, all the resources allocated to elaborate ornamentation reduce resources available for other purposes. This may in turn constrain female fitness leading to dishonest female signalling. We review the literature for empirical studies on mutually ornamented species with conventional sex roles, by focusing on the association between female ornaments and quality of their offspring. We found 43 papers where 33 (77%) are bird-studies, nine (21%) are on fishes, and one (2%) is a lizard-study. Nine of these report negative, 14 non-existing, and 20 positive associations between female ornament and offspring quality. Eighteen of the bird studies (55%) show a positive association between the two traits investigated, whereas five (15%) of the studies report a negative association. The number of fish studies, although few, is skewed in the opposite direction with two (22%) and four (44%) studies supporting positive and negative association, respectively. A minority of studies on carotenoids-based ornaments reports a positive association (4 of 18 studies, or 22%) between the traits, which is low compared to studies on non-carotenoids-based ornaments (16 of 25 studies, or 64%). The above-mentioned relative large number of studies with negative association, especially common in studies on fishes and in carotenoids-based-ornaments, challenges the generality of the direct selection hypothesis to account for female fineries. This is important because this hypothesis seems to have strong support in recent literature on the topic. In the present paper, we also propose possible explanations for the observed differences between taxa and suggest directions and ideas for future research on the evolution of female ornamentation.

Detection of outlier loci and their utility for fisheries management

Genetics-based approaches have informed fisheries management for decades, yet remain challenging to implement within systems involving recently diverged stocks or where gene flow persists. In such cases, genetic markers exhibiting locus-specific (‘outlier’) effects associated with divergent selection may provide promising alternatives to loci that reflect genome-wide (‘neutral’) effects for guiding fisheries management. Okanagan Lake kokanee (Oncorhynchus nerka), a fishery of conservation concern, exhibits two sympatric ecotypes adapted to different reproductive environments; however, previous research demonstrated the limited utility of neutral microsatellites for assigning individuals. Here, we investigated the efficacy of an outlier-based approach to fisheries management by screening >11 000 expressed sequence tags for linked microsatellites and conducting genomic scans for kokanee sampled across seven spawning sites. We identified eight outliers among 52 polymorphic loci that detected ecotype-level divergence, whereas there was no evidence of divergence at neutral loci. Outlier loci exhibited the highest self-assignment accuracy to ecotype (92.1%), substantially outperforming 44 neutral loci (71.8%). Results were robust among-sampling years, with assignment and mixed composition estimates for individuals sampled in 2010 mirroring baseline results. Overall, outlier loci constitute promising alternatives for informing fisheries management involving recently diverged stocks, with potential applications for designating management units across a broad range of taxa.

Single nucleotide polymorphisms unravel hierarchical divergence and signatures of selection among Alaskan sockeye salmon (Oncorhynchus nerka) populations

Background

Disentangling the roles of geography and ecology driving population divergence and distinguishing adaptive from neutral evolution at the molecular level have been common goals among evolutionary and conservation biologists. Using single nucleotide polymorphism (SNP) multilocus genotypes for 31 sockeye salmon (Oncorhynchus nerka) populations from the Kvichak River, Alaska, we assessed the relative roles of geography (discrete boundaries or continuous distance) and ecology (spawning habitat and timing) driving genetic divergence in this species at varying spatial scales within the drainage. We also evaluated two outlier detection methods to characterize candidate SNPs responding to environmental selection, emphasizing which mechanism(s) may maintain the genetic variation of outlier loci.

Results

For the entire drainage, Mantel tests suggested a greater role of geographic distance on population divergence than differences in spawn timing when each variable was correlated with pairwise genetic distances. Clustering and hierarchical analyses of molecular variance indicated that the largest genetic differentiation occurred between populations from distinct lakes or subdrainages. Within one population-rich lake, however, Mantel tests suggested a greater role of spawn timing than geographic distance on population divergence when each variable was correlated with pairwise genetic distances. Variable spawn timing among populations was linked to specific spawning habitats as revealed by principal coordinate analyses. We additionally identified two outlier SNPs located in the major histocompatibility complex (MHC) class II that appeared robust to violations of demographic assumptions from an initial pool of eight candidates for selection.

Conclusions

First, our results suggest that geography and ecology have influenced genetic divergence between Alaskan sockeye salmon populations in a hierarchical manner depending on the spatial scale. Second, we found consistent evidence for diversifying selection in two loci located in the MHC class II by means of outlier detection methods; yet, alternative scenarios for the evolution of these loci were also evaluated. Both conclusions argue that historical contingency and contemporary adaptation have likely driven differentiation between Kvichak River sockeye salmon populations, as revealed by a suite of SNPs. Our findings highlight the need for conservation of complex population structure, because it provides resilience in the face of environmental change, both natural and anthropogenic.