Using parentage analysis to estimate rates of straying and homing in Chinook salmon (Oncorhynchus tshawytscha)

We used parentage analysis based on microsatellite genotypes to measure rates of homing and straying of Chinook salmon (Oncorhynchus tshawytscha) among five major spawning tributaries within the Wenatchee River, Washington. On the basis of analysis of 2248 natural‐origin and 11594 hatchery‐origin fish, we estimated that the rate of homing to natal tributaries by natural‐origin fish ranged from 0% to 99% depending on the tributary. Hatchery‐origin fish released in one of the five tributaries homed to that tributary at a far lower rate than the natural‐origin fish (71% compared to 96%). For hatchery‐released fish, stray rates based on parentage analysis were consistent with rates estimated using physical tag recoveries. Stray rates among major spawning tributaries were generally higher than stray rates of tagged fish to areas outside of the Wenatchee River watershed. Within the Wenatchee watershed, rates of straying by natural‐origin fish were significantly affected by spawning tributary and by parental origin: progeny of naturally spawning hatchery‐produced fish strayed at significantly higher rates than progeny whose parents were themselves of natural origin. Notably, none of the 170 offspring that were products of mating by two natural‐origin fish strayed from their natal tributary. Indirect estimates of gene flow based on F_ST statistics were correlated with but higher than the estimates from the parentage data. Tributary‐specific estimates of effective population size were also correlated with the number of spawners in each tributary.     

Elevated incubation temperature improves later-life swimming endurance in juvenile Chinook salmon,Oncorhynchus tshawytscha

The effect of incubation and rearing temperature on muscle development and swimming endurance under a high-intensity swimming test was investigated in juvenile Chinook salmon (Oncorhynchus tshawytscha) in a hatchery experiment. After controlling for the effects of fork length (L_F) and parental identity, times to fatigue of fish were higher when fish were incubated or reared at warmer temperatures. Significant differences among combinations of pre- and post-emergence temperatures conformed to 15–15°C > 15–9°C > 9–9°C > 7–9°C > 7–7°C in 2011 when swimming tests were conducted at 300 accumulated temperature units post-emergence and 15–9°C > (7–9°C = 7–7°C) in 2012 when swimming tests were conducted at an L_F of c. 40 mm. The combination of pre- and post-emergence temperatures also affected the number and size of muscle fibres, with differences among temperature treatments in mean fibre cross-sectional area persisting after controlling for L_F and parental effects. Nonetheless, neither fibre number nor fibre size accounted for significant variation in swimming endurance. Thus, thermal carryover effects on swimming endurance were not mediated by thermal imprinting of muscle structure. This is the first study to test how temperature, body size and muscle structure interact to affect swimming endurance during early development in salmon.     

Effect of parental mate choice and semi‐natural early rearing environment on the growth performance and seawater tolerance of Chinook salmon Oncorhynchus tshawytscha

To assess whether parental mate choice and early rearing in a semi‐natural spawning channel may benefit the culture of Chinook salmon Oncorhynchus tshawytscha, 90 day growth trials were conducted using hatchery O. tshawytscha (hatchery), mate choice O. tshawytscha (i.e. the offspring of parents allowed to choose their own mate) that spent 6 months in a spawning channel prior to hatchery rearing (channel) and mate choice O. tshawytscha transferred to the hatchery as fertilized eggs (transfer). During the growth trials, all O. tshawytscha stocks were reared separately or in either mixed channel and hatchery or transfer and hatchery groups for comparison of performance to traditional practices. After 60 days in fresh water, all O. tshawytscha were transferred to seawater for an additional 30 days. Reared separately, all stocks grew c. 4·5 fold over 90 days but specific growth rate (G) and food conversion efficiency were higher in fresh water than after seawater transfer on day 60. In contrast, hatchery O. tshawytscha from mixed hatchery and channel and hatchery and transfer growth trials had a larger mass and length gain than their counterparts on day 60, but reduced G in seawater. In general, plasma levels of growth hormone, insulin‐like growth factor I and cortisol did not differ among any O. tshawytscha groups in either the separate or mixed growth trials. Despite some differences in gill Na⁺,K⁺‐ATPase activity, all O. tshawytscha had a high degree of seawater tolerance and experienced virtually no perturbation in plasma chloride following seawater transfer. Overall, all O. tshawytscha exhibited similar growth and seawater performance under traditional hatchery conditions and any benefit derived from either parental mate choice or semi‐natural early rearing environment was only observed in the presence of mutual competition with hatchery O. tshawytscha.     

Mortality threshold for juvenile Chinook salmon Oncorhynchus tshawytscha in an epidemiological model of Ceratomyxa shasta

The myxozoan parasite Ceratomyxa shasta is a significant pathogen of juvenile Chinook salmon Oncorhynchus tshawytscha in the Klamath River, California, USA. This parasite requires 2 hosts to complete its life cycle: a freshwater polychaete (Manayunkia speciosa) and a salmonid. The complex life cycle and large geographic area where infection occurs make it difficult to monitor and manage ceratomyxosis. We present a model for ceratomyxosis-induced mortality in O. tshawytscha, from which parameters important to the persistence of C. shasta are identified. We also experimentally quantify specific parameters from the model and identify a mortality threshold (a critical parameter), by naturally exposing native O. tshawytscha to C. shasta in the Klamath River. The average percent mortality that resulted from these experimental challenges ranged from 2.5 to 98.5% over an exposure dose of 4.4 to 612 x 10(6) parasites. This experiment identified a non-linear mortality threshold of 7.7 +/- 2.1 x 10(4) actinospores fish(-1) for Chinook salmon from the Iron Gate Hatchery on the Klamath River. Below this threshold no mortality occurred and above it mortality increased dramatically, thus providing a target by which to reduce parasitism in emigrating juvenile O. tshawytscha.     

Gauging resource exploitation by juvenile Chinook salmon (Oncorhynchus tshawytscha) in restoring estuarine habitat

In the context of delta restoration and its impact on salmonid rearing, success is best evaluated based on whether out‐migrating juvenile salmon can access and benefit from suitable estuarine habitat. Here, we integrated 3 years of post‐restoration monitoring data including habitat availability, invertebrate prey biomass, and juvenile Chinook salmon (Oncorhynchus tshawytscha) physiological condition to determine whether individuals profited from the addition of 364 ha of delta habitat in South Puget Sound, Washington, United States. Productivity in the restored mudflat was comparable to reference sites 3 years after dike removal, surpassing a mean total of 6 million kJ energy from invertebrate prey. This resulted from the development of a complex network of tidal channels and a resurgence in dipteran biomass that was unique to the restoration area. Consequently, a notable shift in invertebrate consumption occurred between 2010 and 2011, whereby individuals switched from eating primarily amphipods to dipteran flies; however, dietary similarity to the surrounding habitat did not change from year to year, suggesting that this shift was a result of a change in the surrounding prey communities. Growth rates did not differ between restored and reference sites, but catch weight was positively correlated with prey biomass, where greater prey productivity appeared to offset potential density‐dependent effects. These results demonstrate how the realized function of restoring estuarine habitat is functionally dependent. High prey productivity in areas with greater connectivity may support healthy juvenile salmon that are more likely to reach the critical size class for offshore survival.     

Prevalence and analysis of Renibacterium salmoninarum infection among juvenile Chinook salmon Oncorhynchus tshawytscha in North Puget Sound

Renibacterium salmoninarum causes bacterial kidney disease (BKD), a chronic and sometimes fatal disease of salmon and trout that could lower fitness in populations with high prevalences of infection. Prevalence of R. salmoninarum infection among juvenile Chinook salmon Oncorhynchus tshawytscha inhabiting neritic marine habitats in North Puget Sound, Washington, USA, was assessed in 2002 and 2003. Fish were collected by monthly surface trawl at 32 sites within 4 bays, and kidney infections were detected by a quantitative fluorescent antibody technique (qFAT). The sensitivity of the qFAT was within an order of magnitude of the quantitative real-time PCR (qPCR) sensitivity. Prevalence of infection was classified by fish origin (marked/hatchery vs. unmarked/likely natural spawn), month of capture, capture location and stock origin. The highest percentages of infected fish (63.5 to 63.8%) and the greatest infection severity were observed for fish collected in Bellingham Bay. The lowest percentages were found in Skagit Bay (11.4 to 13.5%); however, there was no difference in prevalence between marked and unmarked fish among the capture locations. The optimal logistic regression model of infection probabilities identified the capture location of Bellingham Bay as the strongest effect, and analysis of coded wire tagged (CWT) fish revealed that prevalence of infection was associated with the capture location and not with the originating stock. These results suggest that infections can occur during the early marine life stages of Chinook salmon that may be due to common reservoirs of infection or horizontal transmission among fish stocks.     

Linking marine and freshwater growth in western Alaska Chinook salmon Oncorhynchus tshawytscha

The hypothesis that growth in Pacific salmon Oncorhynchus spp. is dependent on previous growth was tested using annual scale growth measurements of wild Chinook salmon Oncorhynchus tshawytscha returning to the Yukon and Kuskokwim Rivers, Alaska, from 1964 to 2004. First-year marine growth in individual O. tshawytscha was significantly correlated with growth in fresh water. Furthermore, growth during each of 3 or 4 years at sea was related to growth during the previous year. The magnitude of the growth response to the previous year's growth was greater when mean year-class growth during the previous year was relatively low. Length (eye to tail fork, L _ETF) of adult O. tshawytscha was correlated with cumulative scale growth after the first year at sea. Adult L _ETF was also weakly correlated with scale growth that occurred during freshwater residence 4 to 5 years earlier, indicating the importance of growth in fresh water. Positive growth response to previous growth in O. tshawytscha was probably related to piscivorous diet and foraging benefits of large body size. Faster growth among O. tshawytscha year classes that initially grew slowly may reflect high mortality in slow growing fish and subsequent compensatory growth in survivors. Oncorhynchus tshawytscha in this study exhibited complex growth patterns showing a positive relationship with previous growth and a possible compensatory response to environmental factors affecting growth of the age class.     

Using otolith chemical and structural analysis to investigate reservoir habitat use by juvenile Chinook salmon Oncorhynchus tshawytscha

Isotopic composition of ⁸⁷Sr:⁸⁶Sr and natural elemental tracers (Sr, Ba, Mg, Mn and Ca) were quantified from otoliths in juvenile and adult Chinook salmon Oncorhynchus tshawytscha to assess the ability of otolith microchemistry and microstructure to reconstruct juvenile O. tshawytscha rearing habitat and growth. Daily increments were measured to assess relative growth between natal rearing habitats. Otolith microchemistry was able to resolve juvenile habitat use between reservoir and natal tributary rearing habitats (within headwater basins), but not among catchments. Results suggest that 90% (n = 18) of sampled non‐hatchery adults returning to the Middle Fork Willamette River were reared in a reservoir and 10% (n = 2) in natal tributary habitat upstream from the reservoir. Juveniles collected in reservoirs had higher growth rates than juveniles reared in natal streams. The results demonstrate the utility of otolith microchemistry and microstructure to distinguish among rearing habitats, including habitats in highly altered systems.     

Tactic‐specific benefits of polyandry in Chinook salmon Oncorhynchus tshawytscha

This study examined whether polyandrous female Chinook salmon Oncorhynchus tshawytscha obtain benefits compared with monandrous females through an increase in hatching success. Both of the alternative reproductive tactics present in male O. tshawytscha (large hooknoses and small, precocious jacks) were used, such that eggs were either fertilized by a single male (from each tactic) or multiple males (using two males from the same or different tactics). The results show that fertilized eggs from the polyandrous treatments had a significantly higher hatching success than those from the monandrous treatments. It is also shown that sperm speed was positively related with offspring hatching success. Finally, there were tactic‐specific effects on the benefits females received. The inclusion of jacks in any cross resulted in offspring with higher hatching success, with the cross that involved a male from each tactic providing offspring with the highest hatching success than any other cross. This study has important implications for the evolution of multiple mating and why it is so prevalent across taxa, while also providing knowledge on the evolution of mating systems, specifically those with alternative reproductive tactics.     

Prey naivety in the behavioural responses of juvenile Chinook salmon (Oncorhynchus tshawytscha) to an invasive predator

1. Non‐native predators might inflict proportionally higher mortality on prey that have no previous experience of them, compared to species that have coexisted with the predator for some time. 2. We tested whether juvenile Chinook salmon (Oncorhynchus tshawytscha) were less able to recognise a non‐native than a native predator, by investigating behavioural responses to the chemical cues of the invasive smallmouth bass (Micropterus dolomieu) and the native northern pikeminnow (Ptychocheilus oregonensis) in both laboratory and field experiments. 3. Laboratory results demonstrated strong innate antipredator responses of individual juvenile Chinook salmon to northern pikeminnow; fish spent 70% of time motionless and exhibited 100% greater panic response than in controls. By contrast, antipredator responses to the chemical cues of smallmouth bass did not differ from controls. 4. These results were supported by similar differences in recognition of these predator odours by groups of juvenile Chinook salmon in fully natural conditions, though responses reflected a greater range of antipredator behaviours by individuals. In field trials, responses to northern pikeminnow odour resulted in increased flight or absence, reductions in swimming and foraging, and increased time spent near the substratum, compared to smallmouth bass odour. 5. Given that survival of juvenile fish is facilitated by predator recognition, our results support the hypothesis that naivety may be an important factor determining the effect of non‐native predators on prey populations. Efforts to manage the effect of native and non‐native predators may benefit by considering complex behavioural interactions, such as these at the individual and group levels.     

Spatial and temporal patterns of growth and consumption by juvenile spring/summer Chinook salmon Oncorhynchus tshawytscha

Somatic growth is often used as a metric of habitat quality, but such an approach has limitations because growth results from complex interactions between abiotic and biotic factors. In this study, we derived estimates of weekly growth (based on otolith growth increments) across several months for four populations of threatened Chinook salmon, Oncorhynchus tshawytscha, from the Salmon River Basin, Idaho, USA. Although mean stream temperature varied by 2–5 °C across populations, growth across the season did not vary significantly by population. To investigate this further, we applied a bioenergetics model that produced estimates of consumption rates. We then examined how growth and consumption rates varied according to rearing stream and day in the season. Using generalized least squares models, somatic growth (g?day^?1) was best explained by stream and date, yet a model with only date had moderate support, and thus indicated limited support for stream effects. Specific consumption rate (g?g^?1?day^?1 and J?g^?1?day^?1) was best explained using a model that included main effects of stream and date. These findings are consistent with the hypothesis that higher temperatures confer higher metabolic costs that require greater consumption to produce similar growth rates in cooler streams. This highlights that similarity in growth rate among streams may mask changes in individual behavior and/or energetic acquisition associated with differences in temperatures among streams. Results of this study represent the first steps towards identifying factors that underlie important population level and habitat quality differences.     

Environmental correlates of life-history variation in juvenile chinook salmon, Oncorhynchus tshawytscha (Walbaum)

Throughout its native North Pacific, the chinook salmon, Oncorhynchus tshawytscha (Walbaum), exists as twolife-history types that aredistinguished by the age at which juvenile salmon migrate to sea as smolts. 'Stream-type' chinook migrate seaward after I or more years of feeding in fresh water, whereas 'ocean-type' fish migrate to sea as newly emerged fry or after 2–3 months in fresh water. Stream-type chinook predominate in populations distant from the sea south of 56° N, and in both inland and coastal populations north of this point. By contrast, ocean-type chinook predominate in coastal populations south of 56° N, but are rare in populations in more northerly latitudes. Stream-type populations are associated with areas of low 'growth opportunity' (as measured by temperature and photoperiod regimes) and/or areas distant from the sea compared to ocean-type. Geographic variability in juvenile life history is suggested to result, in part, from environmental modulation of smolting timing via differences in growth opportunity among geo-graphic areas. In addition, differences in migration distance and temperature regime may result in selection for different sizes at migration among populations which, through differences in growth opportunity, might promote geographic variability in age at seaward migration.     

Preliminary examination of oxidative stress in juvenile spring Chinook salmon Oncorhynchus tshawytscha of wild origin sampled from transport barges

Migrating juvenile wild Chinook salmon Oncorhynchus tshawytscha, collected and loaded onto transport barges at Lower Granite Dam on the Snake River, were sampled from barges at John Day Dam, 348 km downstream, at 5 day intervals beginning in late April and ending in late May. An increase in lipid peroxidation and decrease in vitamin E in liver were observed from early to late in the barge transportation season. These changes seemed unrelated to changes in plasma cortisol or corresponding glucose levels, which declined from early to late in the season, or the concentration of n‐3 highly unsaturated fatty acid (HUFA) concentrations in tissue but may be related to water temperature, which increased during the transport season, or other changes associated with the parr–smolt transformation.     

Major histocompatibility complex heterozygote advantage and widespread bacterial infections in populations of Chinook salmon (Oncorhynchus tshawytscha)

Despite growing evidence for parasite-mediated selection on the vertebrate major histocompatibility complex (MHC), little is known about variation in the bacterial parasite community within and among host populations or its influence on MHC evolution. In this study, we characterize variation in the parasitic bacterial community associated with Chinook salmon ( Oncorhynchus tshawytscha ) fry in five populations in British Columbia (BC), Canada across 2 years, and examine whether bacterial infections are a potential source of selection on the MHC. We found an unprecedented diversity of bacteria infecting fry with a total of 55 unique bacteria identified. Bacterial infection rates varied from 9% to 29% among populations and there was a significant isolation by distance relationship in bacterial community phylogenetic similarity across the populations. Spatial variation in the frequency of infections and in the phylogenetic similarity of bacterial communities may result in differential parasite-mediated selection at the MHC across populations. Across all populations, we found evidence of a heterozygote advantage at the MHC class II, which may be a source of balancing selection on this locus. Interestingly, a co-inertia analysis indicated only susceptibility associations between a few of the MHC class I and II alleles and specific bacterial parasites; there was no evidence that any of the alleles provided resistance to the bacteria. Our results reveal a complex bacterial community infecting populations of a fish and underscore the importance of considering the role of multiple pathogens in the evolution of host adaptations.     

Dietary carotenoid levels affect carotenoid and retinoid allocation in female Chinook salmon Oncorhynchus tshawytscha

This study examined the effect of dietary carotenoid availability on carotenoid and retinoid concentrations in the flesh, plasma, skin and eggs of female Chinook salmon Oncorhynchus tshawytscha. Carotenoid concentrations in all tissues were closely related to dietary availability. Early in the breeding season, carotenoids were stored primarily in the muscle, with a flesh carotenoid concentration of 9·9 µg g^?1 in fish fed a high carotenoid diet compared with 1·9 µg g^?1 in fish fed a low carotenoid diet. During the breeding season, carotenoid reserves were mobilized predominantly to the eggs and also to the skin. By the end of the breeding season, carotenoid concentrations in the eggs were 17·9 µg g^?1 in fish fed a high carotenoid diet and 3·9 µg g^?1 in fish fed a low carotenoid diet. Conversely, egg retinoid concentrations were only c. 20% lower in fish fed a low v. high carotenoid diet, which suggests that retinoid concentrations were not limited by the availability of carotenoid precursors. Egg carotenoid concentrations were not correlated with either skin carotenoid concentration or colouration, which suggests that female carotenoid displays are not a reliable signal that males can use to evaluate egg carotenoid resources.     

Environmental adaptation in Chinook salmon (Oncorhynchus tshawytscha) throughout their North American range

Landscape genomics is a rapidly growing field with recent advances in both genotyping efficiency and statistical analyses that provide insight towards local adaptation of populations under varying environmental and selective pressure. Chinook salmon (Oncorhynchus tshawytscha) are a broadly distributed Pacific salmon species, occupying a diversity of habitats throughout the northeastern Pacific with pronounced variation in environmental and climate features but little is understood regarding local adaptation in this species. We used a multivariate method, redundancy analysis (RDA), to identify polygenic correlations between 19 703 SNP loci and a suite of environmental variables in 46 collections of Chinook salmon (1956 total individuals) distributed throughout much of its North American range. Models in RDA were conducted on both rangewide and regional scales by hierarchical partitioning of the populations into three distinct genetic lineages. Our results indicate that between 5.8 and 21.8% of genomic variation can be accounted for by environmental features, and 566 putatively adaptive loci were identified as targets of environmental adaptation. The most influential drivers of adaptive divergence included precipitation in the driest quarter of the year (Rangewide and North Coastal Lineage, anova P = 0.002 and 0.01, respectively), precipitation in the wettest quarter of the year (Interior Columbia River Stream‐Type Lineage, anova P = 0.03), variation in mean diurnal range in temperature (South Coastal Lineage, anova P = 0.005), and migration distance (Rangewide, anova P = 0.001). Our results indicate that environmental features are strong drivers of adaptive genomic divergence in this species, and provide a foundation to investigate how Chinook salmon might respond to global environmental change.     

The disulfide bond pattern of salmon egg lectin 24K from the Chinook salmon Oncorhynchus tshawytscha

The disulfide bonds in the galactose-specific lectin SEL 24K from the egg of the Chinook salmon Oncorhynchus tshawytscha were determined by mass spectrometry. Four predictive in silico tools were used to determine the oxidation state of cysteines in the sequence and possible location of the disulfide bonds. A combination of tryptic digestion, HPLC separation, and chemical modifications were used to establish the location of seven disulfide bonds and one pair of free cysteines. After proteolysis, peptides containing one or two disulfide bonds were identified by reduction and mass spectral comparison. MALDI mass spectrometry was supported by chemical modification (iodoacetamide) and in silico digestion. The assignments of disulfide bonds were further confirmed by mass spectral fragmentation studies including in-source dissociation (ISD) and collision-induced dissociation (CID). The experimentally determined disulfide bonds and free Cys residues were only partially consistent with those generated by several automated public-domain algorithms.     

Candidate loci reveal genetic differentiation between temporally divergent migratory runs of Chinook salmon (Oncorhynchus tshawytscha)

Local adaptation is a dynamic process driven by selection that can vary both in space and time. One important temporal adaptation for migratory animals is the time at which individuals return to breeding sites. Chinook salmon (Oncorhynchus tshawytscha) are excellent subjects for studying the genetic basis of temporal adaptation because their high seasonal homing fidelity promotes reproductive isolation leading to the formation of local populations across diverse environments. We tested for adaptive genetic differentiation between seasonal runs of Chinook salmon using two candidate loci; the circadian rhythm gene, OtsClock1b, and Ots515NWFSC, a microsatellite locus showing sequence identity to three salmonid genes central to reproductive development. We found significant evidence for two genetically distinct migratory runs in the Feather River, California (OtsClock1b: F(ST)=0.042, P=0.02; Ots515NWFSC: F(ST)=0.058, P=0.003). In contrast, the fall and threatened spring runs are genetically homogenous based on neutral microsatellite data (F(ST)=-0.0002). Similarly, two temporally divergent migratory runs of Chinook salmon from New Zealand are genetically differentiated based on polymorphisms in the candidate loci (OtsClock1b: F(ST)=0.083, P-value=0.001; Ots515NWFSC: F(ST)=0.095, P-value=0.000). We used an individual-based assignment method to confirm that these recently diverged populations originated from a single source in California. Tests for selective neutrality indicate that OtsClock1b and Ots515NWFSC exhibit substantial departures from neutral expectations in both systems. The large F(ST )estimates could therefore be the result of directional selection. Evidence presented here suggests that OtsClock1b and Ots515NWFSC may influence migration and spawning timing of Chinook salmon in these river systems.     

The effects of depth and salinity on juvenile Chinook salmon Oncorhynchus tshawytscha (Walbaum) habitat choice in an artificial estuary

The energetic cost for juvenile Chinook salmon Oncorhynchus tshawytscha to forage in habitats of different salinity and depth was quantified using a behavioural titration based on ideal free distribution theory. When given a choice between freshwater habitats of different depths (>0·83 or <0·83 m), a greater proportion of fish used the deeper habitat. When the deeper habitat was saltwater, the proportion of fish using it increased. When food was added to both the shallow freshwater and deep saline habitats, however, fish distribution returned to that observed when both habitats were fresh water. This indicates that the preference for deep saline habitats during the stratified phase was driven by some benefit associated with residency in deeper water, rather than salinity. The low perceived cost of low salinity might be in part due to the fish's ability to minimize this cost by only making brief forays into the alternate freshwater habitat. When the food ration delivered to the more costly, shallow habitat was 50% greater than that delivered to the less costly, deep habitat, fish distributed themselves equally between the two habitats, presumably because of equal net benefits. This study demonstrates that juvenile Chinook salmon prefer deep saline habitat to shallow freshwater habitats but will make brief forays into the freshwater habitat if food availability is sufficiently high.