Salmon Oncorhynchus Research Articles

ЭКОЛОГИЯ ПИТАНИЯ СИВУЧА С РЕПРОДУКТИВНОГО ЛЕЖБИЩА НА МЫСЕ КОЗЛОВА (ВОСТОЧНАЯ КАМЧАТКА)

We studied the Steller's sea lion Eumetopias jubatus feeding ecology based on undigested food items found in feces at the Kozlova Cape rookery, Eastern coast of Kamchatka Peninsula, in summers (2004 through 2008). Atka mackerel Pleurogrammus monopterygius and walleye pollock Theragra chalcogramma were dominant in a sea lion diet hauled out at Kozlova Cape rookery in terms of frequency of occurrence. Less frequently occurred were Pacific sand lance Ammodytes hexapterus, Threespine stickleback Gasterosteus aculaeatus, Smelt Osmerus mordax, Sculpins Cottidae, Pacific sandfish Trichodon trichodon, Flatfishes Pleuronectidae, Salmon Oncorhynchus sp., Pacific cod Gadus macrocephalus, and Squid and Octopus Cephalopoda. The contribution of the other food items was not significant. Diet diversity median during sea lion single foraging trip was two prey items, range being one to nine Atka mackerel and Walleye pollock as the major prey objects. Most of sea lion food items were referred to species featuring a marked seasonal presence near the shore or on the shelf. Sea lions feed near the rookery close to the shore on seasonal food aggregations common to the area. Seasonal prey aggregations can be extremely important for breeding animals due to increasing the efficiency of food search and capture, which in turn can affect the reproductive success of animals and their survival. In this regard, the stability of the food resource near Kozlova Cape Rookery may influence sea lion population status there.

Acoustic Classification of Juvenile Pacific Salmon (Oncorhynchus spp) and Pacific Herring (Clupea pallasii) Schools Using Random Forests

Acoustic surveys are the standard approach for evaluating many fish stocks around the world. The analysis of such survey data requires the accurate echo-classification of target species. This classification is often challenging as many organisms exhibit overlapping characteristics in terms of shape, acoustic amplitude, and behavior. In this study, a random forest approach was used to distinguish juvenile Pacific salmon (Oncorhynchus spp) from Pacific herring (Clupea pallasii) aggregations using the acoustic and morphological characteristics of their echo traces. The acoustic data was collected with an autonomous, multi-frequency echosounder deployed on the seafloor in the Discovery Islands, British Columbia from May to September 2015. The model was able to differentiate juvenile Pacific salmon from Pacific herring with a 98% accuracy. School depth and school mean volume backscattering strength were the most important predictors in determining the school classification. This study supports other publications suggesting that random forests represent a promising approach to acoustic target classification in fisheries science.

Strontium signal lag in otoliths of juvenile sockeye salmon (<i> Oncorhynchus nerka</i>) during transition from the freshwater to marine environments

The shift in strontium (Sr) concentrations in fish otoliths is a commonly used proxy for identification of marine environment entry during diadromous migrations. However, there is still controversy about the appearance of the Sr-based sea entry mark relative to the true point of entry. In this study, the Sr signal lag was assessed in otoliths of juvenile sockeye salmon (Oncorhynchus nerka) under experimental conditions replicating the transition to seawater during juveniles’ seaward migration. A Sr signal delay was observed to average at 8.2 (SD = 5.1) days for fish with a body length of 140–170 mm (and a weight of 30–70 g). This lag may be species-specific and should be taken into consideration when estimating marine entry timing and marine residence duration of juvenile salmon.

Escape from the heat: thermal stratification in a well-mixed estuary and implications for fish species facing a changing climate

Climate change may cause organisms to seek thermal refuge from rising temperatures, either by shifting their ranges or seeking microrefugia within their existing ranges. We evaluate the potential for thermal stratification to provide refuge for two fish species in the San Francisco Estuary (Estuary): Chinook Salmon (Oncorhynchus tshawytscha Walbaum, 1792) and Delta Smelt (Hypomesus transpacificus McAllister, 1963). We compiled water temperature data from multiple monitoring programs to evaluate spatial, daily, hourly, intra-annual, and inter-annual trends in stratification using generalized additive models. We used our models to predict the locations and periods of time that the bottom of the water column could function as thermal refuge for salmon and smelt. Periods in which the bottom was cooler than surface primarily occurred during the peak of summer and during the afternoons, with more prominent stratification during warmer years. Although the Estuary is often exceedingly warm for fish species and well-mixed overall, we identified potential thermal refugia in a long and deep terminal channel for Delta Smelt, and in the periods bordering summer for Chinook Salmon. Thermal stratification may increase as the climate warms, and pockets of cooler water at depth, though limited, may become more important for at-risk fishes in the future.

Consumption of Pacific salmon (Oncorhynchus spp.) by California sea lions (Zalophus californianus) and Steller sea lions (Eumetopias jubatus) in northwest Washington during 2010–2013: supplementary table 4

Consumption of Pacific salmon (Oncorhynchus spp.) by California sea lions (Zalophus californianus) and Steller sea lions (Eumetopias jubatus) in northwest Washington during 2010–2013: supplementary table 4

Consumption of Pacific salmon (Oncorhynchus spp.) by California sea lions (Zalophus californianus) and Steller sea lions (Eumetopias jubatus) in northwest Washington during 2010–2013: supplementary table 3

Consumption of Pacific salmon (Oncorhynchus spp.) by California sea lions (Zalophus californianus) and Steller sea lions (Eumetopias jubatus) in northwest Washington during 2010–2013: supplementary table 3

Consumption of Pacific salmon (Oncorhynchus spp.) by California sea lions (Zalophus californianus) and Steller sea lions (Eumetopias jubatus) in northwest Washington during 2010–2013: supplementary table 2

Consumption of Pacific salmon (Oncorhynchus spp.) by California sea lions (Zalophus californianus) and Steller sea lions (Eumetopias jubatus) in northwest Washington during 2010–2013: supplementary table 2

Consumption of Pacific salmon (Oncorhynchus spp.) by California sea lions (Zalophus californianus) and Steller sea lions (Eumetopias jubatus) in northwest Washington during 2010–2013: supplementary table 1

Consumption of Pacific salmon (Oncorhynchus spp.) by California sea lions (Zalophus californianus) and Steller sea lions (Eumetopias jubatus) in northwest Washington during 2010–2013: supplementary table 1

Transduction of Brain Neurons in Juvenile Chum Salmon (Oncorhynchus keta) with Recombinant Adeno-Associated Hippocampal Virus Injected into the Cerebellum during Long-Term Monitoring.

Corpus cerebelli in juvenile chum salmon is a multiprojective region of the brain connected via afferent and efferent projections with the higher regions of the brainstem and synencephalon, as well as with multiprojection regions of the medulla oblongata and spinal cord. During the postembryonic development of the cerebellum in chum salmon, Oncorhynchus keta, the lateral part of the juvenile cerebellum gives rise to the caudomedial part of the definitive cerebellum, which is consistent with the data reported for zebrafish and mouse cerebellum. Thus, the topographic organization of the cerebellum and its efferents are similar between fish (chum salmon and zebrafish) and mammals, including mice and humans. The distributions of recombinant adeno-associated viral vectors (rAAVs) after an injection of the base vector into the cerebellum have shown highly specific patterns of transgene expression in bipolar neurons in the latero-caudal lobe of the juvenile chum tectum opticum. The distribution of rAAVs in the dorsal thalamus, epithalamus, nucleus rotundus, and pretectal complex indicates the targeted distribution of the transgene via the thalamo-cerebellar projections. The detection of GFP expression in the cells of the epiphysis and posterior tubercle of juvenile chum salmon is associated with the transgene’s distribution and with the cerebrospinal fluid flow, the brain ventricles and its outer surface. The direct delivery of the rAAV into the central nervous system by intracerebroventricular administration allows it to spread widely in the brain. Thus, the presence of special projection areas in the juvenile chum salmon cerebellum, as well as outside it, and the identification of the transgene’s expression in them confirm the potential ability of rAAVs to distribute in both intracerebellar and afferent and efferent extracerebellar projections of the cerebellum.

A novel ND1 mitochondrial DNA mutation is maternally inherited in growth hormone transgenesis in amago salmon (Oncorhynchus masou ishikawae)

Growth hormone (GH) transgenesis can be used to manipulate the growth performance of fish and mammals. In this study, homozygous and hemizygous GH-transgenic amago salmon (Oncorhynchus masou ishikawae) derived from a single female exhibited hypoglycemia. Proteomic and signal network analyses using iTRAQ indicated a decreased NAD+/NADH ratio in transgenic fish, indicative of reduced mitochondrial ND1 function and ROS levels. Mitochondrial DNA sequencing revealed that approximately 28% of the deletion mutations in the GH homozygous- and hemizygous-female-derived mitochondrial DNA occurred in ND1. These fish also displayed decreased ROS levels. Our results indicate that GH transgenesis in amago salmon may induce specific deletion mutations that are maternally inherited over generations and alter energy production.

Evaluating Chinook salmon (Oncorhynchus tshawytscha) response to artificial light in support of bycatch mitigation

In commercial trawl fisheries in the North Pacific and US West Coast, fishermen and scientists are evaluating if artificial lights facilitate escapement of bycaught Chinook salmon (Oncorhynchus tshawytscha) from the trawl by attracting them to an opening provided by a bycatch reduction device. Inconsistent behaviour and escapement rates when lights were used in the trawl led us to conduct a laboratory study to evaluate the role of light properties (intensity, colour, and strobe) on marine Chinook salmon behaviour. Results from this study suggest a negative phototactic response. Light colour and strobe, and the interaction between them, differentially affected behavioural response with regard to mean swimming speed and distance from and habituation to the light. White light intensity had limited influence on response; however, the range of trialed intensities was limited. While behaviour is contextual and responses in a laboratory setting cannot be directly extrapolated to responses in fishing gear, this study highlights the significant role of light properties when trying to affect behaviour for bycatch mitigation and the importance of distinguishing between a response to light and to illuminated surroundings.

Gene expression levels of synaptic exocytosis regulator synaptophysin in the brain and the olfactory organ of anadromous salmon.

Anadromous Pacific salmon (genus Oncorhynchus) are known for their homing behavior based on olfactory imprinting, which is formed during their seaward migration. Soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE/Snare) complex is a minimum unit of vesicle exocytosis from the pre-synaptic membrane. Its component genes (synaptosome-associated protein 25, syntaxin 1, and vesicle-associated membrane protein 2) are more strongly expressed in the olfactory nervous system (olfactory epithelium, olfactory bulb, and telencephalon) at the migration stages related to olfactory imprinting and/or retrieval in salmon. This study focused on the mRNA synthesis of synaptophysin (Syp), one of the Snare regulatory factors. syp is strongly expressed in chum salmon (Oncorhynchus keta) olfactory nervous system during the seaward migration and temporarily increased during the homeward migration. In reference to our previous studies, these expression changes were similar to the snare genes in the chum salmon. Therefore, syp and Snare component genes were synchronously expressed reflecting the development and short-term plasticity of the olfactory nervous system that is essential for olfactory imprinting.

Counting the Parts to Understand the Whole: Rethinking Monitoring of Steelhead in California’s Central Valley

Steelhead (Oncorhynchus mykiss expressing an anadromous life history) in the Sacramento and San Joaquin rivers and their tributaries in California’s Central Valley (CCV) belong to a Distinct Population Segment (DPS) that is listed as threatened under the US Endangered Species Act. Although contemporary management and recovery plans include numerous planned and ongoing efforts seeking to aid in DPS recovery—such as gravel augmentation, manipulation of spring flows, and restoration of rearing and spawning habitat—a paucity of data precludes the possibility of evaluating the effect of these actions on populations of Steelhead in CCV streams. Knowledge gaps relating to historic and current abundance, population-specific ratios of resident and anadromous life-history expression, and the influence of hatchery-reared fish remain largely unaddressed. This is partly a result of aspects of Steelhead biology that make them difficult to monitor, including the multitude of factors that contribute to the expression of anadromy, polymorphic populations, and migration periods that coincide with challenging field conditions. However, these gaps in understanding are also partly the result of an institutional focus on Chinook Salmon (Oncorhynchus tshawytscha) and a pervasive notion that actions benefiting Chinook populations will also benefit Steelhead populations. To evaluate these gaps and to suggest approaches for assessing DPS recovery actions, we review available data and existing monitoring efforts, and consider the actions necessary to inform the development of targeted O. mykiss monitoring programs. Current management and recovery goals focus on abundance estimates of Steelhead only, yet current monitoring is insufficient for reliable estimates. We argue that a reallocation of monitoring resources to better understand the interaction between resident O. mykiss and Steelhead would provide better data to estimate the vital rates needed to evaluate the effects of recovery actions.

Swimming behavior of emigrating Chinook Salmon smolts

Swimming behavior of Chinook Salmon (Oncorhynchus tshawytscha) smolts affects transit time, route selection and survival in complex aquatic ecosystems. Behavior quantified at the river reach and junction scale is of particular importance for route selection and predator avoidance, though few studies have developed field-based approaches for quantifying swimming behavior of juvenile migratory fishes at this fine spatial scale. Two-dimensional acoustic fish telemetry at a river junction was combined with a three-dimensional hydrodynamic model to estimate in situ emigration swimming behavior of federally-threatened juvenile Chinook salmon smolts. Fish velocity over ground was estimated from telemetry, while the hydrodynamic model supplied simultaneous, colocated water velocities, with swimming velocity defined by the vector difference of the two velocities. Resulting swimming speeds were centered around 2 body lengths/second, and included distinct behaviors of positive rheotaxis, negative rheotaxis, lateral swimming, and passive transport. Lateral movement increased during the day, and positive rheotaxis increased in response to local hydrodynamic velocities. Swim velocity estimates were sensitive to the combination of vertical shear in water velocities and vertical distribution of fish.

Genotyping-in-Thousands by sequencing panel development and application for high-resolution monitoring of introgressive hybridization within sockeye salmon

Stocking programs have been widely implemented to re-establish extirpated fish species to their historical ranges; when employed in species with complex life histories, such management activities should include careful consideration of resulting hybridization dynamics with resident stocks and corresponding outcomes on recovery initiatives. Genetic monitoring can be instrumental for quantifying the extent of introgression over time, however conventional markers typically have limited power for the identification of advanced hybrid classes, especially at the intra-specific level. Here, we demonstrate a workflow for developing, evaluating and deploying a Genotyping-in-Thousands by Sequencing (GT-seq) SNP panel with the power to detect advanced hybrid classes to assess the extent and trajectory of intra-specific hybridization, using the sockeye salmon (Oncorhynchus nerka) stocking program in Skaha Lake, British Columbia as a case study. Previous analyses detected significant levels of hybridization between the anadromous (sockeye) and freshwater resident (kokanee) forms of O. nerka, but were restricted to assigning individuals to pure-stock or “hybrid”. Simulation analyses indicated our GT-seq panel had high accuracy, efficiency and power (> 94.5%) of assignment to pure-stock sockeye salmon/kokanee, F1, F2, and B2 backcross-sockeye/kokanee. Re-analysis of 2016/2017 spawners previously analyzed using TaqMan® assays and otolith microchemistry revealed shifts in assignment of some hybrids to adjacent pure-stock or B2 backcross classes, while new assignment of 2019 spawners revealed hybrids comprised 31% of the population, ~ 74% of which were B2 backcross or F2. Overall, the GT-seq panel development workflow presented here could be applied to virtually any system where genetic stock identification and intra-specific hybridization are important management parameters.

Data on the diets of Salish Sea harbour seals from DNA metabarcoding

Marine trophic ecology data are in high demand as natural resource agencies increasingly adopt ecosystem-based management strategies that account for complex species interactions. Harbour seal (Phoca vitulina) diet data are of particular interest because the species is an abundant predator in the northeast Pacific Ocean and Salish Sea ecosystem that consumes Pacific salmon (Oncorhynchus spp.). A multi-agency effort was therefore undertaken to produce harbour seal diet data on an ecosystem scale using, 1) a standardized set of scat collection and analysis methods, and 2) a newly developed DNA metabarcoding diet analysis technique designed to identify prey species and quantify their relative proportions in seal diets. The DNA-based dataset described herein contains records from 4,625 harbour seal scats representing 52 haulout sites, 7 years, 12 calendar months, and a total of 11,641 prey identifications. Prey morphological hard parts analyses were conducted alongside, resulting in corresponding hard parts data for 92% of the scat DNA samples. A custom-built prey DNA sequence database containing 201 species (192 fishes, 9 cephalopods) is also provided.

At-Sea Habitat Use of Rhinoceros Auklets Breeding in the Shelf Region of Eastern Hokkaido.

At-sea habitat use of breeding seabirds is strongly influenced by marine environmental features that vary over space and time. The use of bio-loggers allows researchers to track fine-scale movements of seabirds and provides opportunities to identify the primary factors affecting their area use for foraging. Using GPS loggers, we tracked chick-rearing rhinoceros auklets (Cerorhinca monocerata), which are wing-propelled divers, at Daikoku Island, eastern Hokkaido, Japan. The central phase for foraging activity on birds' trips was determined using a multiple change points model. To examine environmental factors explaining the distribution of the foraging phase, a generalized additive model was used where sea surface temperature, chlorophyll a concentration, bathymetry, and distance from the colony were explanatory variables. To obtain information supporting the behavioral tracking, prey items in the bill-loads of adult auklets were collected. We found that auklets foraged over the continental shelf shallower than the 200-m isobath and that distance from the colony was related to the area use. Adult auklets predominately brought back age-0 chum salmon (Oncorhynchus keta), which was abundant in coastal waters along southeast Hokkaido during the study period. Our findings indicate that rhinoceros auklets rearing chicks, hence visiting nests frequently, on Daikoku Island can find suitable feeding grounds nearby.

An assessment of hybridization potential between Atlantic and Pacific salmon

Salmonids possess straying abilities that allows them to exploit open territory and establish new populations. Atlantic salmon (Salmo salar) are expanding their distribution primarily as first-generation escapes from aquaculture, whereas Pacific salmon (Oncorhynchus spp.) are expanding their range in polar and temperate regions due to both anthropogenic and natural influences. Here we utilize artificial intergeneric reciprocal crosses to assess the ability of seven species of Pacific salmon to hybridize with Atlantic salmon. Most cross types were found to produce low numbers of hatched embryos, but none survived to sexual maturation. Survivors consisted of diploids and triploids containing both Atlantic and Pacific salmon parental genomes. Thus, introgression of DNA between Pacific and Atlantic salmon may occur to form F1 hybrids, but transmission to subsequent generations is expected to be rare and occur only over evolutionary time scales. Further, the low viability observed for the most part at early stages of development and in both reciprocal crosses indicates that intergeneric crosses in nature between Atlantic and Pacific salmon are expected to have severe fitness consequences for both dams and sires.

Size-dependent growth tactics of a partially migratory fish before migration.

In many migratory species, smaller migrants suffer higher mortality rates during the risky migration. To minimize the size-selective mortality, migrants with smaller body sizes would need to accelerate growth rates or delay migration timing to attain a large enough body size prior to migration. To test these predictions, we investigated size-dependent patterns of growth rates and migration timing of juvenile masu salmon (Oncorhynchus masou) before their oceanic migration. We tracked uniquely marked individuals in a study population consisted of oceanic migrants and river-dwelling residents using mark-recapture surveys and PIT-tag antenna-reader system. Data supported our predictions about size-dependent growth rates and migration timing. For approximately 6months before outmigration (i.e., between the decision of migration and the start of migration), eventual migrants grew more than residents if their initial size was smaller, but such a difference in growth rate diminished for fish with larger initial sizes. In addition, smaller eventual migrants delayed the timing of outmigration compared to larger individuals, to attain a larger body size in the river prior to migration. These results suggest that size-selective mortality during migration has shaped size-dependent patterns of the pre-migration growth in migratory masu salmon. Size-conditional changes in growth rate and duration of pre-migration period may be an adaptive tactic for the migratory animals.

Effectiveness monitoring of juvenile Chinook salmon restoration projects in south Lake Washington, Washington State

Tabor RA, Liermann MC, Gearns HA, Moore ZJ, Lynch KD, Kurko K, Crittenden J, Shoemaker ME. 2022. Effectiveness monitoring of juvenile Chinook salmon restoration projects in south Lake Washington, Washington State. Lake Reserv Manage. 38:180–196. We evaluated 4 large restoration projects in south Lake Washington that were designed to improve nearshore habitat for lake-rearing juvenile Chinook salmon (Oncorhynchus tshawytscha). Restoration projects included shoreline modification, substrate enhancement, addition of engineered log jams (ELJs), and nonnatal tributary improvements. For most projects, we used a BACI (before-after-control-impact) study design. Projects were evaluated by determining the nighttime abundance of juvenile Chinook salmon through visual observations (primarily snorkeling with some surface observations in small nonnatal tributaries). Juvenile Chinook salmon are typically concentrated in the south end of the lake near their natal stream, and the project that was the farthest away from the natal stream did not appear to be beneficial, likely because few Chinook salmon were present. The highest observed abundance of juvenile Chinook salmon was associated with ELJs, where the abundance in February to April was typically 2 to 5 times higher than along adjacent, open shorelines. From January to April, juvenile Chinook salmon were usually more abundant in a daylighted nonnatal tributary (i.e., reconfigured from an unusable underground culvert to a more natural stream channel at the surface) than in 2 reference sites. Overall, all 4 project types improved juvenile use of the restored area, with substrate enhancement generally having the weakest response and ELJs the strongest response. Although most restoration projects for salmonids in the Pacific Northwest have focused on lotic systems, our results suggest projects in lentic systems may also be beneficial and should be considered by land-use managers. Supplemental data for this article is available online at https://doi.org/10.1080/10402381.2022.2027054 .