Landscape heterogeneity and local adaptation define the spatial genetic structure of Pacific salmon in a pristine environment

Identifying the spatial distribution of genetic variation across the landscape is an essential step in informing species conservation. Comparison of closely related and geographically overlapping species can be particularly useful in cases where landscape may similarly influence genetic structure. Congruent patterns among species highlight the importance that landscape heterogeneity plays in determining genetic structure whereas contrasting patterns emphasize differences in species-specific ecology and life-history or the importance of species-specific adaptation to local environments. We examined the interacting roles of demography and adaptation in determining spatial genetic structure in two closely related and geographically overlapping species in a pristine environment. Using single nucleotide polymorphism (SNP) loci exhibiting both neutral and putative adaptive variation, we evaluated the genetic structure of sockeye salmon in the Copper River, Alaska; these data were compared to existing data for Chinook salmon from the same region. Overall, both species exhibited patterns of isolation by distance; the spatial distribution of populations largely determined the distribution of genetic variation across the landscape. Further, both species exhibited largely congruent patterns of within- and among-population genetic diversity, highlighting the role that landscape heterogeneity and historical processes play in determining spatial genetic structure. Potential adaptive differences among geographically proximate sockeye salmon populations were observed when high F_ST outlier SNPs were evaluated in a landscape genetics context. Results were evaluated in the context of conservation efforts with an emphasis on reproductive isolation, historical processes, and local adaptation.     

Heterosis in crosses between lines of Drosophila melanogaster selected for adaptation to different environments

Summary Experiments were designed to examine whether heterosis would occur in crosses of Drosophila melanogaster populations adapted to 18 °C or 28 °C environments. Crosses were examined in parental environments, an intermediate environment (23 °C) and a mixed environment (alternating 18°/28°C). Parental populations did not show divergence for larval viability, cold shock or high temperature mortalities when tested in a common environment. However, the 28 °C population was less fecund than the 18 °C population, but had higher larval competitive ability and higher adult longevity. Heterosis for viability, cold shock mortality and high temperature mortality occurred in crosses between a population adapted to 18 °C and another adapted to 28 °C, but not in crosses between two populations adapted to the same temperature. The results suggest that, in the absence of drift, heterosis is expected in crosses between lines or populations with different histories of selection but not between lines with the same selection histories.     

Recent local adaptation of sockeye salmon to glacial spawning habitats

Salmonids spawn in highly diverse habitats, exhibit strong genetic population structuring, and can quickly colonize newly created habitats with few founders. Spawning traits often differ among populations, but it is largely unknown if these differences are adaptive or due to genetic drift. To test if sockeye salmon (Oncorhynchus nerka) populations are adapted to glacial, beach, and tributary spawning habitats, we examined variation in heritable phenotypic traits associated with spawning in 13 populations of wild sockeye salmon in Lake Clark, Alaska. These populations were commonly founded between 100 and 400 hundred sockeye salmon generations ago and exhibit low genetic divergence at 11 microsatellite loci (F _ST < 0.024) that is uncorrelated with spawning habitat type. We found that mean P _ST (phenotypic divergence among populations) exceeded neutral F _ST for most phenotypic traits measured, indicating that phenotypic differences among populations could not be explained by genetic drift alone. Phenotypic divergence among populations was associated with spawning habitat differences, but not with neutral genetic divergence. For example, female body color was lighter and egg color was darker in glacial than non-glacial habitats. This may be due to reduced sexual selection for red spawning color in glacial habitats and an apparent trade-off in carotenoid allocation to body and egg color in females. Phenotypic plasticity is an unlikely source of phenotypic differences because Lake Clark sockeye salmon spend nearly all their lives in a common environment. Our data suggest that Lake Clark sockeye salmon populations are adapted to spawning in glacial, beach and tributary habitats and provide the first evidence of a glacial spawning ecotype in salmonids. Glacial spawning habitats are often young (i.e., <200 years old) and ephemeral. Thus, local adaptation of sockeye salmon to glacial habitats appears to have occurred recently.     

Within/between population crosses reveal genetic basis for siring success in Silene latifolia (Caryophyllaceae)

Divergence at reproductive traits can generate barriers among populations, and may result from several mechanisms, including drift, local selection and co-adaptation between the sexes. Intersexual co-adaptation can arise through sexually antagonistic co-evolution, a timely hypothesis addressed in animals but, to our knowledge, not yet in flowering plants. We investigated whether male and female population of origin affected pollen competition success, offspring fitness and sex ratio in crosses within/between six genetically differentiated populations of the white campion, Silene latifolia. Each female was crossed with pollen from one focus male from the same population, and pollen from two focus males from two distinct populations, both as single-donor and two-donor crosses against a fixed tester male with a 2-h interpollination interval (n = 288 crosses). We analysed paternity with microsatellite DNA. Male populations of origin significantly differed for siring success and in vitro pollen germination rates. In vitro pollen germination rate was heritable. Siring success also depended on sex ratio in the female family of origin, but only in between-population crosses. In some female populations, two-donor crosses produced less female-biased sex ratios compared with single-donor crosses, yet in other female populations the reverse was true. Offspring sex ratio varied with donor number, depending on the female population. Within/between population crosses did not differ significantly in seed set or offspring fitness, nor were siring success and offspring fitness significantly correlated. Altogether this suggests reproductive divergence for traits affecting pollen competition in S. latifolia.     

Use of population viability analysis models for Atlantic and Pacific salmon recovery planning

Uncertainty and risk abound in making natural resource management decisions. Population viability analysis (PVA) includes a variety of qualitative or quantitative analyses to predict the future status of a population or collection of populations and to predict the risk of extinction (or quasi-extinction) over time given some assumptions of the factors driving population dynamics. In this paper, we review the various PVA models applied to Atlantic and Pacific salmon for determination of listing under the Endangered Species Act and in planning recovery actions. We also review the numerous cautions involved in developing PVA models and in interpreting their results. There have been a larger number of PVA models applied to Pacific salmon compared to Atlantic salmon due to the greater geographic range and number of species of Pacific salmon. Models for both Atlantic and Pacific salmon have ranged from simple models that view populations as simply a number of organisms to complex age- or stage-structured models depending on the purpose of the model and available data for model parameterization. The real value of PVA models to salmon conservation is not in making absolute predictions of the risk of extinction, but rather in evaluating relative effects of management alternatives on extinction risk and informing decision making within an adaptive management framework. As computing power, quantitative techniques, and knowledge of mechanistic linkages between terrestrial, freshwater, and marine environments advance, PVA models will become an even more powerful tool in conservation planning for salmon species.     

Considerations of a method of analyzing diallel crosses of atlantic salmon.

Inferences derived from a proposed mixed model analysis of a diallel cross involving four stocks of Atlantic salmon (Salmo salar) are illustrated with growth data on weight and length. Variation between stocks was more apparent when samples represented dams as opposed to sires, thus stressing the relative importance of maternal effects. However, the ranking of stocks was not altered when either the means of sire sources or the means of dam sources were considered. No heterotic effects were found for the growth traits studied.     

Temporal change in genetic integrity suggests loss of local adaptation in a wild Atlantic salmon (Salmo salar) population following introgression by farmed escapees

In some wild Atlantic salmon populations, rapid declines in numbers of wild returning adults has been associated with an increase in the prevalence of farmed salmon. Studies of phenotypic variation have shown that interbreeding between farmed and wild salmon may lead to loss of local adaptation. Yet, few studies have attempted to assess the impact of interbreeding at the genome level, especially among North American populations. Here, we document temporal changes in the genetic makeup of the severely threatened Magaguadavic River salmon population (Bay of Fundy, Canada), a population that might have been impacted by interbreeding with farmed salmon for nearly 20 years. Wild and farmed individuals caught entering the river from 1980 to 2005 were genotyped at 112 single-nucleotide polymorphisms (SNPs), and/or eight microsatellite loci, to scan for potential shifts in adaptive genetic variation. No significant temporal change in microsatellite-based estimates of allele richness or gene diversity was detected in the wild population, despite its precipitous decline in numbers over the last two decades. This might reflect the effect of introgression from farmed salmon, which was corroborated by temporal change in linkage-disequilibrium. Moreover, SNP genome scans identified a temporal decrease in candidate loci potentially under directional selection. Of particular interest was a SNP previously shown to be strongly associated with an important quantitative trait locus for parr mark number, which retained its genetic distinctiveness between farmed and wild fish longer than other outliers. Overall, these results indicate that farmed escapees have introgressed with wild Magaguadavic salmon resulting in significant alteration of the genetic integrity of the native population, including possible loss of adaptation to wild conditions.     

Inference of parasite local adaptation using two different fitness components

Estimating parasite fitness is central to studies aiming to understand parasite evolution. Theoretical models generally use the basic reproductive rate R(0) to express fitness, yet it is very difficult to quantify R(0) empirically and experimental studies often use fitness components such as infection intensity or infectivity as substitutes. These surrogate measures may be biased in several ways. We assessed local adaptation of the microsporidium Ordospora colligata to its host, the crustacean Daphnia magna using two different parasite fitness components: infection persistence over several host generations in experimental populations and infection intensity in individual hosts. We argue that infection persistence is a close estimator of R(0), whereas infection intensity measures only a component of it. Both measures show a pattern that is consistent with parasite local adaptation and they correlate positively. However, several inconsistencies between them suggest that infection intensity may at times provide an inadequate estimate of parasite fitness.     

Genetic variability and population structure of sockeye salmon from the Asian Coast of Pacific Ocean

Variability of six microsatellite loci and 45 single nucleotide polymorphism (SNP) loci was analyzed in 17 samples of sockeye salmon from 10 major spawning watersheds on the Asian coast of the Pacific Ocean. On the basis of the analysis of SNP loci variability of sockeye salmon in the examined part of the range, five population groups were identified, including local stocks from the Palana, Okhota, and Kamchatka rivers, as well as the population groups of Southwestern Kamchatka, and Northeastern Kamchatka and Chukotka. Rather different pattern of samples differentiation was obtained by estimating variability of six microsatellite DNA loci. Regional complexes of the eastern and western coasts of Kamchatka were identified. Moreover, sockeye salmon from the Palana River fell into the cluster of Western Kamchatka populations, while the population from the Okhota River and Meynypilgin lake–river system (Chukotka), confined to the subperiphery of the range, where the most differentiated from the others. The possible reasons for the discrepancies and high divergence of the Palana River and the Okhota River sockeye salmon populations, inferred from the SNP markers analysis, are discussed.     

Diverse foraging opportunities drive the functional response of local and landscape-scale bear predation on Pacific salmon

The relationship between prey abundance and predation is often examined in single habitat units or populations, but predators may occupy landscapes with diverse habitats and foraging opportunities. The vulnerability of prey within populations may depend on habitat features that hinder predation, and increased density of conspecifics in both the immediate vicinity and the broader landscape. We evaluated the relative effects of physical habitat, local, and neighborhood prey density on predation by brown bears on sockeye salmon in a suite of 27 streams using hierarchical Bayesian functional response models. Stream depth and width were inversely related to the maximum proportion of salmon killed, but not the asymptotic limit on total number killed. Interannual variation in predation was density dependent; the number of salmon killed increased with fish density in each stream towards an asymptote. Seven streams in two geographical groups with ≥23 years of data in common were then analyzed for neighborhood density effects. In most (12 of 18) cases predation in a stream was reduced by increasing salmon abundance in neighboring streams. The uncertainty in the estimates for these neighborhood effects may have resulted from interactions between salmon abundance and habitat that influenced foraging by bears, and from bear behavior (e.g., competitive exclusion) and abundance. Taken together, the results indicated that predator–prey interactions depend on density at multiple spatial scales, and on habitat features of the surrounding landscape. Explicit consideration of this context dependency should lead to improved understanding of the ecological impacts of predation across ecosystems and taxa.     

Varying herbivore population structure correlates with lack of local adaptation in a geographic variable plant-herbivore interaction

Local adaptation of parasites to their hosts due to coevolution is a central prediction of many theories in evolutionary biology. However, empirical studies looking for parasite local adaptation show great variation in outcomes, and the reasons for such variation are largely unknown. In a previous study, we showed adaptive differentiation in the arctiid moth Utetheisa ornatrix to its host plant, the pyrrolizidine alkaloid-bearing legume Crotalaria pallida, at the continental scale, but found no differentiation at the regional scale. In the present study, we sampled the same sites to investigate factors that may contribute to the lack of differentiation at the regional scale. We performed field observations that show that specialist and non-specialist polyphagous herbivore incidence varies among populations at both scales. With a series of common-garden experiments we show that some plant traits that may affect herbivory (pyrrolizidine alkaloids and extrafloral nectaries) vary at the regional scale, while other traits (trichomes and nitrogen content) just vary at the continental scale. These results, combined with our previous evidence for plant population differentiation based on larval performance on fresh fruits, suggest that U. ornatrix is subjected to divergent selection even at the regional scale. Finally, with a microsatellite study we investigated population structure of U. ornatrix. We found that population structure is not stable over time: we found population differentiation at the regional scale in the first year of sampling, but not in the second year. Unstable population structure of the herbivore is the most likely cause of the lack of regional adaptation.     

Spatial scale of local adaptation and population genetic structure in a miniature succulent, Argyroderma pearsonii

Explicit understanding of the spatial scale of evolutionary processes is required in order to set targets for their effective conservation. Here, we explore the spatial context of neutral and adaptive divergence in the species-rich Knersvlakte region of South Africa. Specifically, we aimed to assess the importance of erosional drainage basins as spatial units of evolutionary process. We used amplified fragment length polymorphism (AFLP) and reciprocal transplants to investigate genetic differentiation in Argyroderma pearsonii, sampled from sparse and dense quartz habitats within each of three drainage basins. This design allowed assessment of differentiation at two distinct spatial scales; between habitats within basins, and between basins. We found near-perfect concordance between genetic clusters and basin occupancy, suggesting restricted interbasin gene flow. In addition, transplants reveal adaptive divergence between basins on the dense quartz habitat. We have shown that neutral and adaptive differentiation occurs between basins, but not between habitats within basins, suggesting that conservation plans aimed at conserving multiple interconnected drainage basins will capture an important axis of evolutionary process on the Knersvlakte.     

A meta-analysis of factors affecting local adaptation between interacting species

Adaptive divergence among populations can result in local adaptation, whereby genotypes in native environments exhibit greater fitness than genotypes in novel environments. A body of theory has developed that predicts how different species traits, such as rates of gene flow and generation times, influence local adaptation in coevolutionary species interactions. We used a meta-analysis of local-adaptation studies across a broad range of host-parasite interactions to evaluate predictions about the effect of species traits on local adaptation. We also evaluated how experimental design influences the outcome of local adaptation experiments. In reciprocally designed experiments, the relative gene flow rate of hosts versus parasites was the strongest predictor of local adaptation, with significant parasite local adaptation only in the studies in which parasites had greater gene flow rates than their hosts. When nonreciprocal studies were included in analyses, species traits did not explain significant variation in local adaptation, although the overall level of local adaptation observed was lower in the nonreciprocal than in the reciprocal studies. This formal meta-analysis across a diversity of host-parasite systems lends insight into the role of both biology (species traits) and biologists (experimental design) in detecting local adaptation in coevolving species interactions.     

Integrated population models reveal local weather conditions are the key drivers of population dynamics in an aerial insectivore

Changes to weather patterns under a warming climate are complex: while warmer temperatures are expected virtually worldwide, decreased mean precipitation is expected at mid-latitudes. Migratory birds depend on broad-scale weather patterns to inform timing of movements, but may be more susceptible to local weather patterns during sedentary periods. We constructed Bayesian integrated population models (IPMs) to assess whether continental or local weather effects best explained population dynamics in an environmentally sensitive aerial insectivorous bird, the tree swallow (Tachycineta bicolor), along a transcontinental gradient from British Columbia to Saskatchewan to New York, and tested whether population dynamics were synchronous among sites. Little consistency existed among sites in the demographic rates most affecting population growth rate or in correlations among rates. Juvenile apparent survival at all sites was stable over time and greatest in New York, whereas adult apparent survival was more variable among years and sites, and greatest in British Columbia and Saskatchewan. Fledging success was greatest in Saskatchewan. Local weather conditions explained significant variation in adult survival in Saskatchewan and fledging success in New York, corroborating the hypothesis that local more than continental weather drives the population dynamics of this species and, therefore, demographic synchrony measured at three sites was limited. Nonetheless, multi-population IPMs can be a powerful tool for identifying correlated population trajectories caused by synchronous demographic rates, and can pinpoint the scale at which environmental drivers are responsible for changes. We caution against applying uniform conservation actions for populations where synchrony does not occur or is not fully understood.     

Evolutionary-physiological aspects of adaptation of the Pacific salmon fry of the Oncorhynchus genus to migration to the sea water

A complex of adaptive changes occurring in the Pacific salmon fry in the process of migration to the sea is described, including behavior, ion content in carcasses, and morphological changes in Stannius bodies, gill epithelium, and nephron tubular epithelium. Participating in experiments with transfer from fresh water into a two-layer aquarium (the lower layer - sea water, the upper layer - fresh water) were smolts of chum salmon and underyearlings of masu salmon as well as the trachurus and leiurus forms of the three-spined stickleback Casterosteus aculeatus. All fish, regardless of their salt preference, at once after placement into the two-layer aquarium, occupied the sea water zone, at the very bottom of the aquarium. After 1 h, there started brief excursions of masu salmon and chum salmon to the upper, fresh water layer; however, both forms of the three-spined stickleback did not participate in these excursions. After 12 h, the chum salmon settled down in the lower, sea water layer, while the masu salmon - in the upper, fresh water layer. Both forms of the three-spined stickleback never left the sea water layer and felt quite comfortably on the aquarium bottom. It seems that the high tolerance of the both stickleback forms to wide salinity limits allows them to choose the convenient position regardless of the water salt composition. By analyzing the material obtained for three years (2001-2003) on structure and functions of the gill epithelium chloride cells (CC), we have come to the conclusion that the fresh water fry of two salmon species, chum and masu salmons, caught at the same time and practically in the same water reservoirs can be divided into three groups. The underyearlings of the masu salmon as a rule are characterized by the thickened epithelium of secondary gill lamellae, but by a very small number of CC. In smolts of chum salmon, on the contrary, the epithelium is sufficiently thin, but enriched in the CC that demonstrate an active structure in the very beginning of migration to sea. However, with approaching the sea (and with an increase of terms of migration) the CC activity drops, but their amount does not change. And only after migration to the sea the CC activity rises again, although their amount seems to remain unchanged. The described peculiarities of behavior and of the ion composition regulation in the migrating salmon fry confirm the hypothesis that the salmons evolutionized in fresh water, that the Oncorhynchus genus appeared in large spaces of saltish waters, such as the Japan Sea at the period of the early Pleistocene, and that learning of fry of the Oncorhynchus genus (for instance, of O. gorbuscha and O. keta) is the most specialized in the salmons migrating to the sea, whereas the fresh water species of chars (Salvelinus) and of trouts (Salmo) are more primitive.     

Evolutionary-physiological aspects of adaptation of the Pacific salmon fry of the oncorhynchus genus to migration to the sea water

A complex of adaptive changes occurring in the Pacific salmon fry in the process of migration to the sea is described, including behavior, ion content in carcasses, and morphological changes in Stannius bodies, gill epithelium, and nephron tubular epithelium. Participating in experiments with transfer from fresh water into a two-layer aquarium (the lower layer—sea water, the upper layer—fresh water) were smolts of chum salmon and underyearlings of cherry salmon as well as the trachurus and leiurus forms of the three-spined stickleback Casterosteus aculeatus. All fish, regardless of their salt preference, at once after placement into the two-layer aquarium, occupied the sea water zone, at the very bottom of the aquarium. After 1 h, there started brief excursions of cherry salmon and chum salmon to the upper, fresh water layer; however, both forms of the three-spined stickleback did not participate in these excursions. After 12 h, the chum salmon settled down in the lower, sea water layer, while the cherry salmon—in the upper, fresh water layer. Both forms of the three-spined stickleback never left the sea water layer and felt quite comfortably on the aquarium bottom. It seems that the high tolerance of the both stickleback forms to wide salinity limits allows them to choose the convenient position regardless of the water salt composition. By analyzing the material obtained for three years (2001–2003) on structure and functions of the gill epithelium chloride cells (CC), we have come to the conclusion that the fresh water fry of two salmon species, chum and cherry salmons, caught at the same time and practically in the same water reservoirs can be divided into three groups. The underyearlings of the cherry salmon as a rule are characterized by the thickened epithelium of secondary gill lamellae, but by a very small number of CC. In smolts of chum salmon, on the contrary, the epithelium is sufficiently thin, but enriched in the CC that demonstrate an active structure in the very beginning of migration to sea. However, with approaching the sea (and with an increase of terms of migration) the CC activity drops, but their amount does not change. And only after migration to the sea the CC activity rises again, although their amount seems to remain unchanged. The described peculiarities of behavior and of the ion composition regulation in the migrating salmon fry confirm the hypothesis that the salmons evolutionized in fresh water, that the Oncorhynchus genus appeared in large spaces of saltish waters, such as the Japan sea at the period of the early Pleistocene, and that learning of fry of the Oncorhynchus genus (for instance, of O. gorbuscha and O. keta) is the most specialized in the salmons migration to the sea, whereas the fresh water species of chars (Salvelinus) and of trouts (Salmo) are more primitive.     

Locking life-cycles onto seasons: Circle-map models of population dynamics and local adaptation

We have formulated a model describing the timing of maturity and reproduction in briefly semelparous organisms whose development rate is primarily controlled by environmental factors. The model is expressed as a circle-map relating time of year at maturation in successive generations. The properties of this map enable us to determine the degree of synchrony to be expected between the life-cycles of members of a population exposed to a regular seasonal environment. We have proved that organisms with a life-history composed of a contiguous series of stages, all with development driven by the same seasonal function, cannot phase-lock their life-cycles to the seasons. However if the organism exhibits facultative diapause induced by a critical time/critical development mechanism of the type proposed by Norling (1984a,b,c) then it will always succeed in phase-locking to a perfectly periodic driving function. Within the context of this circle-map model we have examined population extinctions caused by attempting to over-winter in an inappropriate life-history stage, or by attempting to reproduce at a time of year when this is impossible. We have shown that the possibility of such extinctions limits both the shortness of the post-critical stage, and the lateness of the critical time. We have examined the fitness of persistent cohorts as a function of critical time and development. We find that if the post-critical stage is riskier than the pre-critical then natural selection favors a short post-critical stage and a late critical time; the limitation of this process being dependent on the proportion of the growing season over which successful reproduction is possible. We have determined the variation with life-cycle length (and hence latitude or altitude) of the maturation pattern corresponding to optimal life-history parameters. We find that for organisms which can mature only over a small part of the growing season the majority of any latitudinal gradient exhibits a unimodal maturation pattern. Organisms which can mature and reproduce over the majority of the growing season exhibit more complex patterns, but still exhibit substantial ranges of latitude over which unimodal or bimodal patterns are optimal.