Salmon Oncorhynchus Research Articles

Foraging ecology of walleye and brown trout in a Great Lakes tributary

Abstract The role of alternative prey on predator diet selection and survival of juvenile (parr) Chinook salmon ( Oncorhynchus tshawytscha ) is not well understood in the Laurentian Great Lakes. Therefore, measures of predator foraging ecology (prey species and size selection), prey densities, and functional response relationships were determined for adult walleye ( Sander vitreus ) and brown trout ( Salmo trutta ) (hatchery-reared) feeding on parr and alternate prey in the Muskegon River, a tributary of Lake Michigan, USA, from 2004 to 2007. Walleye selected for smaller than average brown trout and rainbow trout (hatchery-reared) but walleye prey size (within-prey) was independent of predator size. In general, walleye showed neutral selection for all prey species but, in some years, showed positive selection for rainbow trout and negative selection for parr. Hatchery-reared brown trout selected the smallest parr in the environment although prey size was independent of predator size. Parr were positively selected by brown trout only in April. Functional response curves were fit to describe the consumption of parr and other prey types by walleye (type II) and brown trout (type I). Interactions among rainbow trout, walleye, and brown trout favored parr survival, i.e. the presence of alternate prey (rainbow trout) significantly influenced walleye predation on parr, while brown trout appeared to become quickly limited by size or escape ability of parr. Our results should enhance understanding of food web dynamics in Great Lakes tributary habitats.

Seasonal Rearing Habitat in a Large Mediterranean-Climate River: Management Implications at the Southern Extent of Pacific Salmon (Oncorhynchusspp.)

Pacific salmon (Oncorhynchus) use a variety of rearing environments prior to seaward migration, yet large river habitats and their use have not been well defined, particularly at the southernmost salmon range where major landscape-level alterations have occurred. We explored juvenile Chinook salmon (Oncorhynchus tshawytscha) and steelhead (Oncorhynchus mykiss) presence along the river continuum and in main-channel and off-channel habitats of a regulated California Mediterranean-climate river. Over an 8-year period, off-channels of the lower Mokelumne River exhibited slower and warmer water than the main-channel. Probability of salmonid presence varied by stream reach and habitat types. Steelhead and Chinook salmon both demonstrated transitional responses to the dry season, with juveniles leaving off-channels by midsummer. This corresponded to flow recession, increasing water temperatures, salmonid growth and end of emigration period. Main-channel steelhead observations continued until the following storm season, which brought cool flood flows to reconnect off-channels and the next juvenile cohort of both species to the river. Within arid climates, low-gradient off-channels appear more transiently used than in cooler and more northern humid climate systems. Within a highly regulated Mediterranean-climate river, off-channel habitats become increasingly scarce, disconnected or temperature limiting in low-gradient reaches both seasonally and due to anthropogenic modifications. These observations may provide guidance for future management within large salmon streams. Copyright © 2015 John Wiley & Sons, Ltd.

Ecomorphological plasticity of juvenile fall-run chinook salmon (Oncorhynchus tshawytscha) in perennial and ephemeral streams

In the Central Valley of California, environmental characteristics differ between perennial and ephemeral stream types and therefore present different challenges for rearing salmonids with respect to water discharge, water temperature, food availability, and habitat complexity. Body shape of juvenile fall-run Chinook salmon (Oncorhynchus tshawytscha) reared in a perennial stream environment was compared to juveniles reared in an ephemeral stream environment. Using geometric morphometrics and multivariate analyses, this study presents morphological differences of rearing juvenile Chinook salmon both within and between ephemeral and perennial stream types. We found that shape differences between stream types were primarily associated with expansion of the mid-body region relative to differences in body length. Specifically, juvenile Chinook salmon reared in the ephemeral stream expressed increased body depth dominated by dorsal-ventral elongation of the dorsal, adipose, and anal fins. Eye position and gill opercula-body insertion points also were anteriorly shifted in the juvenile body shape of the ephemeral stream. Our findings support that juvenile Chinook salmon are morphologically flexible and can express habitat-specific developmental differences.

Influence of Wood and Other Habitat Characteristics on the Distribution and Abundance of Coho Salmon in a Relatively Large River

Abstract The influences of wood and other habitat variables on juvenile coho salmon (Oncorhynchus kisutch) summer distribution and relative abundance, which has rarely been studied in relatively large river channels (> 15 m wide), were assessed in a relatively large river channel in Washington State (summer wetted width 15–30 m). The influence of wood and habitat variables including water depth, velocity, and substrate on juvenile coho salmon summer relative abundance was assessed by snorkelling areas with introduced (generally 2–3 evergreen trees from the riparian zone), natural, and no wood. Juvenile coho salmon relative densities were compared at stations with introduced, natural, and no wood and their distribution (presence) assessed at natural wood stations using logistic regression. Relative densities of coho salmon were greatest at stations with introduced wood and were greater at introduced and natural wood stations than stations lacking wood, where juvenile coho salmon were generally absent. Wood...

Functional gene diversity and migration timing in reintroduced Chinook salmon

Reintroductions are used to reestablish populations to historical habitats from which they were extirpated. The long-term success of these efforts will depend on genetic diversity and the ability of reintroduced individuals to adapt to ecological change. We examined variation at circadian clock (OtsClock1b and OmyFbxw11) and reproductive timing (Ots515NWFSC)—associated genes in two threatened spring-run Chinook salmon (Oncorhynchus tshawytscha) populations that are undergoing restoration to historical habitats above dams. We also tested for an association between the genes and individual variation in arrival time to the spawning grounds. Our findings indicate that levels of genetic diversity in reintroduced individuals are similar to those found in previously studied spring, summer, fall and winter-run Chinook salmon populations. Captive-rearing programs established following dam construction and the more recent reintroduction efforts thus appear to have maintained diversity at these genes. We observed temporal (between run-years) and spatial (between populations) patterns of genetic differentiation, but little evidence that selection underlies these differences. However, there was a relationship between the circadian-associated gene, OmyFbxw11, and arrival time to the spawning grounds, and in one year of the study, “early” and “late” arrivers to the spawning grounds were more differentiated at the gene than at neutral markers. Taken together, these findings suggest that reintroduced salmon may be capable of an evolutionary response to ecological shifts that alter the adaptive landscape between fitness and arrival timing to the spawning grounds.

Chum salmon (Oncorhynchus keta) growth and temperature indices as indicators of the year-class strength of age-1 walleye pollock (Gadus chalcogrammus) in the eastern Bering Sea

Ecosystem-based fisheries management requires the development of physical and biological time series that index ocean productivity for stock assessment and recruitment forecasts for commercially important species. As recruitment in marine fish is related to ocean condition, we developed proxies for ocean conditions based on sea surface temperature (SST) and biometric measurements of chum salmon (Oncorhynchus keta) captured in the walleye pollock (Gadus chalcogrammus) fishery in the eastern Bering Sea in three periods (July 16–30, September 1–15 and September 16–30). The main purpose of this paper was to evaluate Pacific salmon (Oncorhynchus spp.) growth as a possible indicator of ocean conditions that, in turn, may affect age-1 walleye pollock recruitment. Marine growth rates of Pacific salmon are the result of a complex interplay of physical, biological and population-based factors that fish experience as they range through oceanic habitats. These growth rates can, therefore, be viewed as indicators of recent ocean productivity. Thus, our hypothesis was that estimated intra-annual growth in body weight of immature and maturing age-4 male and female chum salmon may be used as a biological indicator of variations in rearing conditions also experienced by age-0 walleye pollock; consequently, they may be used to predict the recruitment to age-1 in walleye pollock. Summer SSTs and chum salmon growth at the end of July and September explained the largest amount of variability in walleye pollock recruitment indicating that physical and biological indices of ocean productivity can index fish recruitment.

Prespawning Movements and Spawning Distribution of Sockeye Salmon in an Urbanizing Alaskan Lake

Abstract The efficacy of fish habitat conservation in land planning processes in Alaska is often constrained by the extent of current knowledge of fish distributions and habitat use. In response to requests for information from land and salmon resource management stakeholders regarding Auke Lake sockeye salmon (Oncorhynchus nerka) status and life history, we examined the prespawning movements and spawning distribution of adult sockeye salmon to provide ecological information needed for Auke Lake watershed management. We used radiotelemetry to track the movements of 80 fish in the Auke Lake watershed during 2012. The prespawning distribution of the fish was not random, indicating five spatially and temporally distinct high-use staging areas within the lake. The Auke Lake sockeye salmon population was dominated by stream-spawning fish (98.5%), with minimal lakeshore spawning (1.5%) observed in association with a small intermittent tributary of the lake. The prespawning distribution patterns identified in this study corroborate observations from Auke Lake 20 y ago, indicating consistent habitat use patterns by sockeye salmon in the lake. Telemetry data also indicate 12% of sockeye salmon expired in Auke Lake without spawning and that 14% of stream-spawning fish were preyed upon by black bear (Usrus americanus). The prespawning and spawning behavior by Auke Lake sockeye salmon suggest that discrete lake staging areas and stream spawning beds are important candidate habitats for protection during the land planning process for shoreline development surrounding the lake.

Validation of Daily Increment Formation in Otoliths from Spring Chinook Salmon

Abstract Increments of a fish otolith are commonly used to estimate age and somatic growth; yet the accuracy of such estimates first requires an understanding of the periodicity with which increments are formed. We conducted a rearing experiment to evaluate daily formation of increments in otoliths from spring Chinook salmon (Oncorhynchus tshawytscha), an anadromous fish from the Yakima River, Washington. Specifically, we compared the known number of post-emergence days that fish were alive to the number of otolith increments formed after an emergence check. Our results indicated daily formation of otolith increments, thus corroborating previous studies and supporting the use of otolith increments to estimate age and somatic growth of individual Chinook salmon. Given the positive relationship between body size and survival to adulthood, continued use of otolith microstructure to quantify age and growth will help identify factors critical for the recovery of listed Chinook salmon populations.

English

doi: http://dx.doi.org/10.15447/sfews.2014v12iss4art3 California’s Feather River Hatchery (FRH) propagates two runs of Chinook salmon (Oncorhynchus tshawytscha): spring run and fall run. Loss of spawning habitat and historical hatchery practices have led to introgression of these runs. Recent efforts to reform hatchery operations at the FRH are focused on reducing introgression and increasing the proportion of natural-origin spawners in the broodstock. Implementing these reforms, however, requires a means of distinguishing FRH fish from natural-origin fish, and FRH spring-run fish from FRH fall-run fish. Coded-wire tagging and parentage-based genetic tagging can be used for this purpose, but are labor-intensive and expensive. Otolith thermal marking (OTM) is a 100% marking technique widely used in the Pacific Northwest, Alaska, and Russia that can be effective and relatively inexpensive. We initiated an OTM program at the FRH in 2005 to determine its viability as a 100% marking tool for a hatchery with an annual production goal of 10 million smolts. Our analysis of otoliths collected from returning adults at the FRH demonstrated that OTM could be successfully applied to identify the origin (FRH or natural) and, for FRH fish, the run type (spring run or fall run). Otoliths collected between 2009 and 2011 show run-type mixing between 12% to 20% in both spring-run and fall-run FRH broodstock. Additionally, results suggest natural-spawner contribution to hatchery broodstock is very low (<1% to 10%). OTM may provide another way to reduce the rate of introgression between FRH spring-run and fall-run Chinook salmon, and increasing the proportion of natural origin spawners in hatchery broodstock, both of which should improve the long-term viability of FRH spring-run and fall-run Chinook salmon.

Biofilm nutrient limitation, metabolism, and standing crop responses to experimental application of salmon carcass analog in Idaho streams

Dramatic declines of Pacific salmon (Oncorhynchus spp.) populations have decreased delivery of marine-derived material to Pacific Northwest streams where juvenile salmon reside. Managers use artificial nutrient additions to increase juvenile salmon growth and survival and typically assume nutrient-driven increases in biofilm production are an important pathway by which nutrients become available to higher trophic levels. To evaluate how biofilms respond to additions of salmon carcass analog, a pasteurized, processed form of nutrient mitigation materials, we quantified biofilm nutrient limitation, benthic and whole-stream metabolism, and biofilm standing crops before and following experimental additions in tributaries of the Salmon River, Idaho, USA. Biofilm nutrient limitation did not change and standing crop did not increase in response to analog additions at two different levels (low, 30 g·m−2; or high, 150 g·m−2) within 1 month of addition. In contrast, whole-stream and benthic primary productivity and respiration increased in a high-analog treated segment, but did not increase in a low-analog treated segment. Together, our results suggest that metabolism may be a more appropriate tool for assessing the ecosystem effects of nutrient additions than biofilm standing crop or nutrient limitation, which are constrained by a variety of abiotic and biotic factors like hydrology and grazing.

Assessment of radiocaesium accumulation by hatchery-reared salmonids after the Fukushima nuclear accident

To understand the process of radiocaesium uptake in salmonids after the Fukushima Dai-ichi Nuclear Power Plant accident, a lake caging experiment and two captive-rearing experiments with controlled radiocaesium concentrations of water and feed were conducted in and around Lake Chuzenji, central Honshu Island, Japan (160 km from the station). Substantial accumulations of radiocaesium were confirmed in muscle of hatchery-reared kokanee (Oncorhynchus nerka) and masu salmon (Oncorhynchus masou) after release into the cages, indicating that radionuclide contamination of fish is an ongoing process, 1.5 years after the nuclear accident. Two captive experiments, controlling water and feed radiocaesium levels, showed that direct radiocaesium transfer from water (43 mBq·L–1) in Lake Chuzenji to muscle tissue was undetected, at least during the ∼90-day experimental period, whereas a rapid increase in radiocaesium levels was observed when fish were cultured using radiocaesium-contaminated pellets. The results revealed that radiocaesium contamination in salmonids is mainly via the food chain and that direct intake from water via the skin, gut, and (or) gills has no major direct impact on muscle tissue concentrations.

Habitat connectivity, complexity, and quality: predicting adult coho salmon occupancy and abundance

The distribution, quality, and connectivity of instream habitat can influence adult salmon occupancy and abundance patterns and alter population dynamics. In this study, we evaluated the relationships between adult coho salmon (Oncorhynchus kisutch) occupancy and abundance with instream habitat conditions, including measures of spawning gravel, habitat complexity, and juvenile rearing habitat. We used corresponding adult salmon spawning and instream habitat data collected within coastal Oregon watersheds as part of a long-term monitoring program. We modeled two processes as a function of habitat characteristics: the number of coho salmon when they were present and the occupancy probabilities of coho salmon. The results from both submodels were then combined into an estimate of total abundance at each site. Adult coho salmon occupancy was best predicted by the capacity of the habitat to support parr during the winter, complex pools, percent bedrock, and site distance to the ocean. Although lacking the predictive capacity of the occupancy model, increases in adult coho counts at sites were also influenced by the site distance to the ocean, and there is evidence that both percent gravel and complex pools may also be valuable predictors. By taking advantage of long-term datasets with broad spatial range, using an integrative approach across coho salmon life stages, and utilizing innovative Bayesian modeling techniques, this study is a unique approach to understanding a complicated ecological narrative. Combined, our results indicate the spatial distribution and proximity of spawning and rearing habitats may maximize productivity for coho salmon in coastal Oregon watersheds.

Isolation and characterization of eighteen polymorphic microsatellite DNA loci from masu salmon (Oncorhynchus masou) using next-generation sequencing and cross-species amplification

A total of 18 novel microsatellite markers in masu salmon, an important fisheries resource around the Far East, were isolated using a next-generation sequencing approach. The number of alleles and expected heterozygosity per locus ranged 5–15 and 0.55847–0.92944, respectively. Four loci also were polymorphic in three other salmonid species after cross-species amplification. These newly isolated loci will provide important information for the sustainable adaptive management of masu salmon.

Characterization of sixteen polymorphic microsatellite DNA loci in the chum salmon (Oncorhynchus keta) isolated by next-generation sequencing

Chum salmon (Oncorhynchus keta) is an important fisheries resource around the North Pacific region. However, the genetic characteristics of this species mostly remain to be elucidated with competent molecular genetic markers for their effective resource management and sustainable use. A total of sixteen novel microsatellite markers in chum salmon were isolated using a next-generation sequencing approach. All loci were polymorphic with 6–21 alleles, with the observed and expected heterozygosities of 0.41667–0.97917 and 0.66184–0.92434, respectively. These new loci will provide a tool for examining the genetic diversity and population structure of chum salmon, which are an important information for the adaptive management of this species.

Stock identification and life history interpretation using trace element signatures in salmon otoliths

Chum salmon (Oncorhynchus keta) in the North Pacific Ocean are anadromous fish, and spend most of their life in the sea until spawning in natal streams. To identify the stock and habitat characteristics of chum salmon, the composition of chemical elements (Ca, Mn, Sr, Zn, and Ba) in otolith was examined using laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS). Two main types of analytical work have been carried out; discrete spot analysis and line scan analysis of otolith sections. Salmon otoliths were obtained from the eastern (Canada and USA) and western (Japan and Korea) North Pacific during 1997–1999 spawning seasons. Spot analysis of otolith cores demonstrated significant differences in the element concentration among countries (p = 0.003). Line scanning from the core to the margin showed that Sr concentrations were elevated at the core of the otoliths, decreased during the freshwater stage, increased suddenly at a certain point, and oscillated periodically towards the margin matching with year-ring. The elevated Sr concentration at the core may reflect the maternal contribution to the egg, and the oscillations toward the margin may reflect salinity gradients between onshore/offshore or north/south migrations. The Zn profiles also oscillated and corresponded to the annual ring of the otolith. However, the profiles of Sr and Zn oscillated oppositely after salmon migrated to saline water and the Zn uptake declined toward the rim of the otolith while Sr uptake increased.

Can intense predation by bears exert a depensatory effect on recruitment in a Pacific salmon population?

It has long been recognized that, as populations increase in density, ecological processes affecting growth and survival reduce per capita recruitment in the next generation. In contrast to the evidence for such "compensatory" density dependence, the alternative "depensatory" process (reduced per capita recruitment at low density) has proven more difficult to demonstrate in the field. To test for such depensation, we measured the spawner-recruit relationship over five decades for a sockeye salmon (Oncorhynchus nerka) population in Alaska breeding in high-quality, unaltered habitat. Twenty-five years of detailed estimates of predation by brown bears, Ursus arctos, revealed strong density dependence in predation rate; the bears killed ca. 80% of the salmon in years of low salmon spawning abundance. Nevertheless, the reconstructed spawner-recruit relationship, adjusted to include salmon intercepted in the commercial fishery, provided no evidence of demographic depensation. That is, in years when few salmon returned and the great majority were killed by bears, the few that spawned were successful enough that the population remained highly productive, even when those killed by bears were included as potential spawners. We conclude that the high quality of breeding habitat at this site and the productive nature of semelparous Pacific salmon allowed this population to avoid the hypothesized depressed recruitment from depensatory processes expected at low density. The observed lack of demographic depensation is encouraging from a conservation standpoint because it implies that depleted populations may have the potential to rebound successfully given suitable spawning and rearing habitat, even in the presence of strong predation pressure.

Habitat influences Pacific salmon (Oncorhynchus spp.) tissue decomposition in riparian and stream ecosystems

Decomposition incorporates organic material delivered by Pacific salmon (Oncorhynchus spp.) into aquatic and terrestrial ecosystems of streams where salmon spawn. We hypothesized that salmon tissue decomposition would be faster, and macroinvertebrate abundance and biomass higher, in terrestrial compared to aquatic habitats, and this would be reflected in the nutritional quality of the tissue. Salmon tissue in coarse-mesh bags was placed in four habitats [terrestrial: riparian (RIP), gravel bars (GRA); aquatic: stream sediment surface (STR), buried in sediments (BUR)] in four southeast Alaska watersheds. After 2 (RIP, GRA) or 4 (STR, BUR) weeks of decomposition, tissue dry mass, macronutrient content, and macroinvertebrate colonizer abundance and biomass were determined. Overall, tissue decomposition was rapid (mean k = 0.088 day−1), while nutritional quality remained high based on elemental ratios (mean C:N = 4.9; C:P = 140; N:P = 30), and differed among habitats (Linear-mixed effects model p < 0.05). Macroinvertebrate assemblages colonizing carcasses were unique to each habitat, although Diptera generally dominated. In terrestrial habitats, the dominant macroinvertebrates were Sphaeroceridae (96 % of invertebrate abundance in RIP habitat) and Calliphoridae larvae (98 % in GRA habitat). In aquatic habitats, the dominant macroinvertebrates were Chironomidae (48 % in STR habitat) and Chloroperlidae (72 % in BUR habitat). Macroinvertebrate colonizer abundance and biomass were higher in RIP (mean 286 individuals and 22 mg g−1) than in other habitats (mean 4 individuals and 3 mg g−1) (Friedman p < 0.05). Rapid decomposition rates and high invertebrate biomass, combined with the high nutritional quality of tissue, suggest rapid incorporation of critical salmon nutrients and energy into both aquatic and terrestrial ecosystems.

Exploring cyclic dominance of sockeye salmon with a predator–prey model

We explain in an intuitive and detailed way a predator–prey model that generates cyclic dominance in Fraser River sockeye salmon. In contrast with usual predator–prey models, this model includes four distinct prey lines and thus a combination of continuous and discrete dynamics, reflecting the particular freshwater and marine life cycle features of sockeye salmon (Oncorhynchus nerka) populations. The predator–prey interaction causing the oscillations takes place in the rearing lakes, rather than in the ocean. The values of most parameters of this model can be estimated from empirical data that are available for the large salmon-rearing lakes in the Fraser River basin. The mechanism that produces the oscillations in this model is compared with other mechanisms that can generate population oscillations, and we argue that predator–prey dynamics is the most likely mechanism to produce the observed patterns. We explain why the period of the oscillation is exactly 4 years, and we explore how the dynamical pattern is affected by changes in external conditions or by management decisions.

Time-delayed subsidies: interspecies population effects in salmon.

Cross-boundary nutrient inputs can enhance and sustain populations of organisms in nutrient-poor recipient ecosystems. For example, Pacific salmon (Oncorhynchus spp.) can deliver large amounts of marine-derived nutrients to freshwater ecosystems through their eggs, excretion, or carcasses. This has led to the question of whether nutrients from one generation of salmon can benefit juvenile salmon from subsequent generations. In a study of 12 streams on the central coast of British Columbia, we found that the abundance of juvenile coho salmon was most closely correlated with the abundance of adult pink salmon from previous years. There was a secondary role for adult chum salmon and watershed size, followed by other physical characteristics of streams. Most of the coho sampled emerged in the spring, and had little to no direct contact with spawning salmon nutrients at the time of sampling in the summer and fall. A combination of techniques suggest that subsidies from spawning salmon can have a strong, positive, time-delayed influence on the productivity of salmon-bearing streams through indirect effects from previous spawning events. This is the first study on the impacts of nutrients from naturally-occurring spawning salmon on juvenile population abundance of other salmon species.

Dietary inclusion of salmon testes meal from Alaskan seafood processing byproducts: Effects on growth and immune function of rainbow trout, Oncorhynchus mykiss (Walbaum)

Abstract This study investigated the growth and immune function effects following partial replacement of fish meal with dried testes meal from pink salmon ( Oncorhynchus gorbuscha ) testes collected from Alaskan seafood processing byproducts. It was hypothesized that the dietary nucleotide content of testes meal may provide an immunostimulatory effect in rainbow trout ( Oncorhynchus mykiss ). Three diets were formulated and used for this study; a commercial type control diet, a Macrogard diet, and an experimental diet containing 50 g kg − 1 testes meal. Triplicate groups of juvenile rainbow trout (8.65 ± 0.13 g fish − 1 ) were fed each diet for 12 weeks, at which time they were challenged with Flavobacterium psychrophilum (the causative agent of coldwater disease). No significant differences in feed conversion ratio or specific growth rates were observed. Kidney macrophage (phagocytic) activity was significantly (P