Lacustrine growth of juvenile pink salmon and a comparison with sympatric sockeye salmon

The growth rates of naturally sympatric juvenile pink Oncorhynchus gorbuscha and sockeye Oncorhynchus nerka salmon were compared in a common lacustrine environment in south‐west Alsaka, an unusual opportunity given the normal disparity in freshwater residence time of these two species. Fork length ( L _F) frequency distributions of juvenile pink salmon caught in the lake during the summer in 1991 and 1999–2003 indicated a growth rate of 0·54 mm day⁻¹, 54% greater than the estimated growth rate of juvenile sockeye salmon sampled from 1958 to 2003 (0·35 mm day⁻¹). Examination of daily growth rings on otoliths indicated that pink salmon in Lake Aleknagik grew an average of 1·34 mm day⁻¹ in 2003 but sockeye salmon grew only 0·63 mm day⁻¹(average specific growth rates were 3·0 and 1·8% day⁻¹, respectively). Pink salmon increased from c . 32 mm L _F and 0·2 g at emergence to 78 mm L _F and 3·0 g within 3–4 weeks. After experiencing these rapid growth rates, the pink salmon appeared to leave the lake by late July in most years. The diets of pink and sockeye salmon in the littoral zone of the lake were very similar; >80% of the stomach contents consisted of adult and pupal insects and the remainder was zooplankton. This high degree of diet overlap suggested that the observed differences in growth rate were not attributable to variation in prey composition.     

Linking climate change projections for an Alaskan watershed to future coho salmon production

Climate change is predicted to dramatically change hydrologic processes across Alaska, but estimates of how these impacts will influence specific watersheds and aquatic species are lacking. Here, we linked climate, hydrology, and habitat models within a coho salmon (Oncorhynchus kisutch) population model to assess how projected climate change could affect survival at each freshwater life stage and, in turn, production of coho salmon smolts in three subwatersheds of the Chuitna (Chuit) River watershed, Alaska. Based on future climate scenarios and projections from a three‐dimensional hydrology model, we simulated coho smolt production over a 20‐year span at the end of the century (2080–2100). The direction (i.e., positive vs. negative) and magnitude of changes in smolt production varied substantially by climate scenario and subwatershed. Projected smolt production decreased in all three subwatersheds under the minimum air temperature and maximum precipitation scenario due to elevated peak flows and a resulting 98% reduction in egg‐to‐fry survival. In contrast, the maximum air temperature and minimum precipitation scenario led to an increase in smolt production in all three subwatersheds through an increase in fry survival. Other climate change scenarios led to mixed responses, with projected smolt production increasing and decreasing in different subwatersheds. Our analysis highlights the complexity inherent in predicting climate‐change‐related impacts to salmon populations and demonstrates that population effects may depend on interactions between the relative magnitude of hydrologic and thermal changes and their interactions with features of the local habitat.     

Reduced growth in wild juvenile sockeye salmon Oncorhynchus nerka infected with sea lice

Daily growth rings were examined in the otoliths of wild juvenile sockeye salmon Oncorhynchus nerka to determine whether infection by ectoparasitic sea lice Caligus clemensi and Lepeophtheirus salmonis was associated with reduced host body growth, an important determinant of survival. Over 98% of the sea lice proved to be C. clemensi and the fish that were highly infected grew more slowly than uninfected individuals. Larger fish also grew faster than smaller fish. Finally, there was evidence of an interaction between body size and infection status, indicating the potential for parasite‐mediated growth divergence.     

Genomic islands of divergence linked to ecotypic variation in sockeye salmon

Regions of the genome displaying elevated differentiation (genomic islands of divergence) are thought to play an important role in local adaptation, especially in populations experiencing high gene flow. However, the characteristics of these islands as well as the functional significance of genes located within them remain largely unknown. Here, we used data from thousands of SNPs aligned to a linkage map to investigate genomic islands of divergence in three ecotypes of sockeye salmon (Oncorhynchus nerka) from a single drainage in southwestern Alaska. We found ten islands displaying high differentiation among ecotypes. Conversely, neutral structure observed throughout the rest of the genome was low and not partitioned by ecotype. One island on linkage group So13 was particularly large and contained six SNPs with F_ST > 0.14 (average F_ST of neutral SNPs = 0.01). Functional annotation revealed that the peak of this island contained a nonsynonymous mutation in a gene involved in growth in other species (TULP4). The islands that we discovered were relatively small (80–402 Kb), loci found in islands did not show reduced levels of diversity, and loci in islands displayed slightly elevated linkage disequilibrium. These attributes suggest that the islands discovered here were likely generated by divergence hitchhiking; however, we cannot rule out the possibility that other mechanisms may have produced them. Our results suggest that islands of divergence serve an important role in local adaptation with gene flow and represent a significant advance towards understanding the genetic basis of ecotypic differentiation.     

Temporal and spatial variation in growth of juvenile Atlantic salmon

Spatial and temporal variation in length‐at‐age and environmental factors affecting variation in growth rate of juvenile Atlantic salmon Salmo salar were studied using data from a long‐term study in the River Stjørdalselva, central Norway. Mean annual instantaneous growth rate among 1+ and 2+year juvenile Atlantic salmon varied between 0·59 and 1·50 g g⁻¹ year⁻¹ and mean instantaneous daily growth rate of young‐of‐the‐year (YOY) varied between 0·013 and 0·033 g g⁻¹ day⁻¹. Between year variation in growth was larger than the within year intra‐watercourse spatial variation. For YOY and 1+year Atlantic salmon, a major part of the observed between year variation in growth rates was explained by variation in mean daily water discharge and spring temperature. For 2+year juvenile Atlantic salmon, mean daily water discharge and cohort density were the only variables to significantly explain variation in growth rates. A large part of the within water‐course spatial variation could not be explained by temperature variations and juvenile Atlantic salmon in the uppermost areas of the river, experiencing the lowest ambient temperatures during the growth period, displayed the highest growth rates. Within the baselines set by temperature, biotic and abiotic factors connected to water flow regime and variation in food availability are suggested to be a major determinants of the temporal and spatial variation in juvenile Atlantic salmon growth rates.     

Sea louse infection of juvenile sockeye salmon in relation to marine salmon farms on Canada's west coast

Background

Pathogens are growing threats to wildlife. The rapid growth of marine salmon farms over the past two decades has increased host abundance for pathogenic sea lice in coastal waters, and wild juvenile salmon swimming past farms are frequently infected with lice. Here we report the first investigation of the potential role of salmon farms in transmitting sea lice to juvenile sockeye salmon (Oncorhynchus nerka).

Methodology/Principal Findings

We used genetic analyses to determine the origin of sockeye from Canada''s two most important salmon rivers, the Fraser and Skeena; Fraser sockeye migrate through a region with salmon farms, and Skeena sockeye do not. We compared lice levels between Fraser and Skeena juvenile sockeye, and within the salmon farm region we compared lice levels on wild fish either before or after migration past farms. We matched the latter data on wild juveniles with sea lice data concurrently gathered on farms. Fraser River sockeye migrating through a region with salmon farms hosted an order of magnitude more sea lice than Skeena River populations, where there are no farms. Lice abundances on juvenile sockeye in the salmon farm region were substantially higher downstream of farms than upstream of farms for the two common species of lice: Caligus clemensi and Lepeophtheirus salmonis, and changes in their proportions between two years matched changes on the fish farms. Mixed-effects models show that position relative to salmon farms best explained C. clemensi abundance on sockeye, while migration year combined with position relative to salmon farms and temperature was one of two top models to explain L. salmonis abundance.

Conclusions/Significance

This is the first study to demonstrate a potential role of salmon farms in sea lice transmission to juvenile sockeye salmon during their critical early marine migration. Moreover, it demonstrates a major migration corridor past farms for sockeye that originated in the Fraser River, a complex of populations that are the subject of conservation concern.     

Beavers (Castor canadensis) influence habitat for juvenile salmon in a large Alaskan river floodplain

Our aim was to determine how beavers affect habitats and food resources for juvenile salmon in the Kwethluk River in western Alaska.

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Inter-annual variation in responses of water chemistry and epilithon to Pacific salmon spawners in an Alaskan stream

1. Pacific salmon (Oncorhynchus spp.) deliver salmon‐derived nutrients (SDN) to the streams in which they spawn. However, many stream parameters, such as discharge and spawner abundance, can vary from year to year, which could alter the quantity and flux of SDN. 2. Over six consecutive years, we studied responses in streamwater chemistry and epilithon (i.e. the microbial community on submerged rocks) to salmon spawners in Fish Creek, southeastern Alaska, U.S.A. The lower reach of Fish Creek receives spawners of several salmon species, while the upper reach does not receive spawners because of an intervening waterfall. 3. We estimated salmon spawner biomass, analysed water chemistry [ammonium, nitrate, soluble reactive phosphorus (SRP) and dissolved organic carbon (DOC)], and measured epilithon abundance [as chlorophyll a (chl a) and ash‐free dry mass (AFDM)] in Fish Creek. Measurements were made in both the upper and lower reaches, before, during and after the major salmon runs. 4. Absolute values and relative differences indicated that the presence of salmon spawners consistently increased dissolved ammonium (by 58 μg L⁻¹ on average, 41× over background), SRP (by 6 μg L⁻¹, 14×), epilithon chl a (by 35 mg m⁻², 16×), and epilithon AFDM (by 3 g m⁻², 8×). Salmon spawners did not increase nitrate or DOC in either absolute or relative amounts. The persistence and magnitude of spawner effects varied among years and appeared to reflect weather‐driven hydrology as well as spawner biomass. 5. Salmon‐derived nutrients can stimulate the growth of primary producers by increasing streamwater nutrient concentrations, but this positive influence may be modulated by other factors, such as water temperature and discharge. To better assess the ecological influence of SDN on stream biota, future studies should explicitly consider the role of key environmental factors and their temporal and spatial dynamics in stream ecosystems.     

Lake‐specific variation in growth,migration timing and survival of juvenile sockeye salmon Oncorhynchus nerka: separating environmental from genetic influences

Time series on juvenile life‐history traits obtained from sockeye salmon Oncorhynchus nerka were analysed to assess lake‐specific environmental influences on juvenile migration timing, size and survival of fish from a common gene pool. Every year for the past two decades, O. nerka have been spawned at a hatchery facility, and the progeny released into two lakes that differ in average summer temperatures, limnological attributes and growth opportunities. Juveniles reared in the warmer, more productive Crosswind Lake were larger and heavier as smolts compared to those from the cooler, less productive Summit Lake and had higher in‐lake and subsequent marine survival. Crosswind Lake smolts migrated from the lake to sea slightly earlier in the season but the migration timing distributions overlapped considerably across years. Fry stocking density had a negative effect on smolt length for both lakes, and a negative effect on in‐lake survival in Summit Lake. Taken together, the results revealed a strong effect of lake‐rearing environment on the expression of life‐history variation in O. nerka. The stocking of these lakes each year with juveniles from a single mixed‐source population provided a large‐scale reverse common‐garden experiment, where the same gene pool was exposed to different environments, rather than the different gene pools in the same environment approach typical of evolutionary ecology studies. Other researchers are encouraged to seek and exploit similar serendipitous situations, which might allow environmental and genetic influences on ecologically important traits to be distinguished in natural or semi‐natural settings.     

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.     

Differential survival of juvenile sockeye and coho salmon exposed to low dissolved oxygen during winter

Juvenile sockeye salmon (43–78 mm) survived 100% for 24 h in cages in ice–covered Black Lake, Alaska at oxygen saturations >65% (9 mg l^–1), but only 45% at 24% saturation (3·0–3·3 mg l^–1) and none at <17% saturation (2·3 mg l^–1). All juvenile coho (50–120 mm) survived 100% for 24 h down to 21% oxygen saturation (3·1 mg l^–1), and all 50 coho survived 4–5 days at 23–24% saturation (3·2–3·3 mg l^–1).     

Population dynamics of growth of young sockeye salmon in Lake Dalnee

Three periods sharply differing in the state of the ecosystem were observed in Lake Dalnee over the period of 30 years. 1. Different abundance of sockeye salmon, three-spined stickleback and predacious char; 2. Appearance and disappearance of a four-year periodicity in the abundance fluctuations; 3. Different proportions of one-, two- and three-year old fish migrating to sea and the number of residuals; (Changes in the first and second trophic levels and in biogenic content in the water took place. These features are associated with long-lasting changes. Disturbances in one link of the ecosystem resulted in serious long-term changes in the whole system. Such change of dynamic equilibrium may become irreversible.Read at the Limnological Congress in Leningrad, 1971.     

The influence of maternal condition on offspring performance in sockeye salmon Oncorhynchus nerka

Eggs were taken from adult sockeye salmon Oncorhynchus nerka that had reached their journey's end in spawn-ready and moribund condition, and fertilized by healthy males. Egg number, size, hatching success and offspring growth did not differ with maternal condition, which suggests the absence of any persisting physiological maternal effects. Differences were noted in the swimming behaviour and physiology of the offspring at parr stage. In a 30 min schooling test conducted using groups of five in a flume, parr from moribund females were more likely to fatigue, were not as tightly schooled, and had a diminished startle response, both in the per cent responding and the burst distance. In individual, confined swimming tests conducted within a tube, post-exercise plasma lactate concentration, which is an indicator of white muscle use, was greater for parr from moribund adult females. The moribund females also had elevated lactate following exercise (their migration), which suggests heritable differences may exist in muscle use. This study shows that juvenile O. nerka artificially propagated from females exhausted by their return migration can exhibit swimming performance differences, indicating that maternal condition may need to be considered in breeding programmes.     

Climate effects on inter‐annual variation in growth of the freshwater mussel (Anodonta beringiana) in an Alaskan lake

1. Warming trends are evident in many parts of the globe but are especially marked at higher latitudes, with complex effects on the biota that include direct effects on growth potential and indirect effects through food webs. 2. Air temperatures have been increasing over the past 50 years in southwestern Alaska, affecting the growth and population dynamics of many organisms, including a variety of aquatic species such as the freshwater mussel Anodonta beringiana. 3. We collected freshwater mussels from Iliamna Lake, in the Bristol Bay region of Alaska, and measured their shells to examine climatic effects on growth patterns. 4. Linear mixed effects models and ordinary least square linear regressions revealed strong positive correlations between local air temperatures (especially in May, October and the summer months) and inter‐annual variation in mussel growth. Slower mussel growth was also significantly correlated with later date of ice break‐up, which was linked to air temperatures in late spring.     

Aggression and growth depression in juvenile Atlantic salmon: the consequences of individual variation in standard metabolic rate

In aquaculture, competitive interactions for food are a major source of growth rate variation, since they result in aggressive individuals acquiring a disproportionate amount of food and growing faster. Consequently, such competition increases the variance and skew of the size distribution of fish. In Atlantic salmon Salmo salar acquaculture, rearing is often initiated with juveniles of uniform size. However, the initial factors allowing fish to out-compete others of the same size is unclear. This study shows that individual differences in standard metabolic rate (SMR) may contribute to differences in aggression between juvenile Atlantic salmon. Fish were segregated into three holding tanks on the basis of differences in relative SMR aggression was highest in the tank containing high SMR fish, and lowest in a low SMR group. However, there were no significant differences in mean growth between the three treatments, although the skew of the size distribution was much less in the low SMR group than in the high SMR group. Therefore, although mean growth was not improved in the low SMR group by excluding high SMR fish, their growth subsequently showed less variability, possibly as a consequence of fewer despotic individuals gaining disproportionate access to food.     

Microsatellite DNA variation in sockeye salmon Oncorhynchus nerka (Walbaum, 1792) populations of eastern Kamchatka

The allelic variations of eight microsatellite loci (Ots107, Oki1a, Oki1b, One104, One109, OtsG68, OtsG85, and Oki6) were examined in sockeye salmon Oncorhynchus nerka (Walbaum) populations of eastern Kamchatka. Samples from river basins of the Karaginskiy and Olyutorskiy districts in the northern part of the investigated region are characterized by a smaller number of allelic variants and lower heterozygosity, compared to samples from the Kamchatka River basin. A fit to the Hardy-Weinberg distribution was found at most of the loci that were studied in all samples. The average differentiation between populations (st) over the eight loci was 2.93%, which corresponds to the statistical significance level. The most highly polymorphic loci proved to be the least differentiating between the analyzed samples.     

Signals of heterogeneous selection at an MHC locus in geographically proximate ecotypes of sockeye salmon

The genes of the major histocompatibility complex (MHC) are an important component of the vertebrate immune system and can provide insights into the role of pathogen‐mediated selection in wild populations. Here, we examined variation at the MHC class II peptide‐binding region in 27 populations of sockeye salmon (Oncorhynchus nerka), distributed among three distinct spawning ecotypes, from a complex of interconnected rivers and lakes in south‐western Alaska. We also obtained genotypes from 90 putatively neutral single nucleotide polymorphisms for each population to compare the relative roles of demography and selection in shaping the observed MHC variation. We found that MHC divergence was generally partitioned by spawning ecotype (lake beaches, rivers and streams) and was 30 times greater than variation at neutral markers. Additionally, we observed substantial differences in modes of selection and diversity among ecotypes, with beach populations displaying higher levels of directional selection and lower MHC diversity than the other two ecotypes. Finally, the level of MHC differentiation in our study system was comparable to that observed over much larger geographic ranges, suggesting that MHC variation does not necessarily increase with increasing spatial scale and may instead be driven by fine‐scale differences in pathogen communities or pathogen virulence. The low levels of neutral structure and spatial proximity of populations in our study system indicate that MHC differentiation can be maintained through strong selective pressure even when ample opportunities for gene flow exist.     

Mechanisms of drift-feeding behavior in juvenile Chinook salmon and the role of inedible debris in a clear-water Alaskan stream

Drift-feeding fish are challenged to discriminate between prey and similar-sized particles of debris, which are ubiquitous even in clear-water streams. Spending time and energy pursuing debris mistaken as prey could affect fish growth and the fitness potential of different foraging strategies. Our goal was to determine the extent to which debris influences drift-feeding fish in clear water under low-flow conditions when the distracting effect of debris should be at a minimum. We used high-definition video to measure the reactions of drift-feeding juvenile Chinook salmon (Oncorhynchus tshawytscha) to natural debris and prey in situ in the Chena River, Alaska. Among all potential food items fish pursued, 52 % were captured and quickly expelled from the mouth, 39 % were visually inspected but not captured, and only 9 % were ingested. Foraging attempt rate was only moderately correlated with ingestion rate (Kendall’s τ?=?0.55), raising concerns about the common use of foraging attempts as a presumed index of foraging success. The total time fish spent handling debris increased linearly with foraging attempt rate and ranged between 4 and 25 % of total foraging time among observed groups. Our results help motivate a revised theoretical view of drift feeding that emphasizes prey detection and discrimination, incorporating ideas from signal detection theory and the study of visual attention in cognitive ecology. We discuss how these ideas could lead to better explanations and predictions of the spatial behavior, prey selection, and energy intake of drift-feeding fish.