Defining marine habitat of juvenile Chinook salmon, <Emphasis Type="Italic">Oncorhynchus tshawytscha</Emphasis>, and coho salmon, <Emphasis Type="Italic">O. kisutch</Emphasis>, in the northern California Current System

We investigated habitat use by juvenile Chinook salmon (Oncorhynchus tshawytscha) and coho salmon (O. kisutch) to identify environmental characteristics that may define their optimal marine habitat. We utilized physical and biological data from four cruises in the northern California Current system from Newport, Oregon, to Crescent City, California, in June and August 2000 and 2002. A non-parametric statistical method was used to analyze and select environmental parameters that best defined ocean habitat for each species. Regression trees were generated for all cruises combined to select the most important habitat variables. Chlorophyll a concentration best defined habitat of yearling Chinook salmon, while decapod larvae, salinity, and neuston biovolume defined habitat of yearling coho salmon. Using criteria from the regression tree analysis, GIS maps were produced to show that the habitat of yearling Chinook salmon was widespread over the continental shelf and the habitat of yearling coho salmon was variable and mainly north of Cape Blanco.     

Amino acid cues emanating from Pacific salmon eggs and ovarian fluid

The eggs of salmonid fishes are an important food source for many aquatic predators that detect eggs using olfaction. Moreover, chemicals from eggs and ovarian fluid aid sperm cells in detecting and locating eggs for fertilization, and ovarian fluid is attractive to conspecific males. Thus chemicals from eggs and ovarian fluid may facilitate reproduction but may also attract egg predators. The authors sampled mature females of three Pacific salmon species – Chinook (Oncorhynchus tshawytscha), coho (Oncorhynchus kisutch) and sockeye (Oncorhynchus nerka) – and determined the proportional representation of amino acids, potent fish odorants, from their eggs and ovarian fluid (Chinook and coho salmon only). They then tested juvenile coho salmon, an egg predator, for responses to ovarian fluid and egg odours using the electro-olfactogram (EOG) recording technique. The amino acid compositions of the salmon species were significantly and positively correlated with each other, and the interspecific differences were comparable to those between individuals of the same species. The egg water samples were, on average, dominated by lysine, alanine and glutamine (12.6%, 12.4% and 10.9%, respectively). The ovarian fluid samples were dominated by lysine (20.5%), followed by threonine (9.7%), glycine (9.2%) and arginine (8.8%). EOG recordings demonstrated the ability of juvenile coho salmon to detect the chemical traces of eggs and ovarian fluid. It is concluded that salmon eggs are a potent source of odours for potential predators but likely not highly differentiated among salmon species.     

Ontogenetic variations in the type and size of prey consumed by juvenile coho,Oncorhynchus kisutch,and chinook,O. tshawytscha,salmon

Synopsis Stomach contents of juvenile coho,Oncorhynchus kisutch, and chinook,O. tshawytscha, salmon collected in purse seines off the coast of Washington and Oregon were examined for variations related to predator size. There was a general trend toward increasing consumption of fish with increasing body size, due mainly to the increase in northern anchovy biomass consumed by the larger salmon. Most of the major prey taxa showed significant differences among the size classes examined for both salmon species. There was a direct relationship between predator and prey size for both coho and chinook, but considerable variation was found in prey length consumed within each size class. Prey width did not provide as good a fit as prey length for either species. In general, coho consumed larger fish prey in relation to their body length than chinook but there were substantial differences by month or year of collection.     

Warming Ocean Conditions Relate to Increased Trophic Requirements of Threatened and Endangered Salmon

The trophic habits, size and condition of yearling Chinook salmon (Oncorhynchus tshawytscha) caught early in their marine residence were examined during 19 survey years (1981–1985; 1998–2011). Juvenile salmon consumed distinct highly piscivorous diets in cold and warm ocean regimes with major differences between ocean regimes driven by changes in consumption of juvenile rockfishes, followed by several other fish prey, adult euphausiids and decapod larvae. Notable, Chinook salmon consumed 30% more food in the warm versus cold ocean regime in both May and June. Additionally, there were about 30% fewer empty stomachs in the warm ocean regime in May, and 10% fewer in warm June periods. The total prey energy density consumed during the warmer ocean regime was also significantly higher than in cold. Chinook salmon had lower condition factor and were smaller in fork length during the warm ocean regime, and were longer and heavier for their size during the cold ocean regime. The significant increase in foraging during the warm ocean regime occurred concurrently with lower available prey biomass. Adult return rates of juvenile Chinook salmon that entered the ocean during a warm ocean regime were lower. Notably, our long term data set contradicts the long held assertion that juvenile salmon eat less in a warm ocean regime when low growth and survival is observed, and when available prey are reduced. Comparing diet changes between decades under variable ocean conditions may assist us in understanding the effects of projected warming ocean regimes on juvenile Chinook salmon and their survival in the ocean environment. Bioenergetically, the salmon appear to require more food resources during warm ocean regimes.     

Diet,feeding patterns,and prey selection of subyearling Atlantic salmon (Salmo salar) and subyearling chinook salmon (Oncorhynchus tshawytscha) in a tributary of Lake Ontario

Since juvenile Atlantic salmon (Salmo salar) and Chinook salmon (Oncorhynchus tshawytscha) occupy a similar habitat in Lake Ontario tributaries, we sought to determine the degree of diet similarity between these species in order to assess the potential for interspecific competition. Atlantic salmon, an historically important but currently extirpated component of the Lake Ontario fish community, are the focus of a bi‐national restoration effort. Presently this effort includes the release of hatchery produced juvenile Atlantic salmon in Lake Ontario tributaries. These same tributaries support substantial numbers of naturally reproduced juvenile Pacific salmonids including Chinook salmon. Subyearling Atlantic salmon and subyearling Chinook salmon had significantly different diets during each of the three time periods examined. Atlantic salmon fed slightly more from the benthos than from the drift and consumed mainly chirononmids (47.0%) and ephemeropterans (21.1%). The diet of subyearling Chinook salmon was more closely associated with the drift and consisted mainly of chironomids (60.2%) and terrestrial invertebrates (16.0%). Low diet similarity between subyearling Atlantic salmon and subyearling Chinook salmon likely minimizes competitive interactions for food between these species in Lake Ontario tributaries. However, the availability of small prey such as chironomids which comprise over 50% of the diet of each species, soon after emergence, could constitute a short term resource limitation. To our knowledge this is the first study of interspecific diet associations between these two important salmonid species.     

Interspecific habitat associations of juvenile salmonids in Lake Ontario tributaries: implications for Atlantic salmon restoration

Diel variation in habitat use of subyearling Chinook salmon (Oncorhynchus tshawytscha), subyearling coho salmon (O. kisutch), yearling steelhead (O. mykiss), and yearling Atlantic salmon (Salmo salar) was examined during the spring in two tributaries of Lake Ontario. A total of 1318 habitat observations were made on juvenile salmonids including 367 on steelhead, 351 on Chinook salmon, 333 on Atlantic salmon, and 261 on coho salmon. Steelhead exhibited the most diel variation in habitat use and Chinook the least. Juvenile salmonids were generally associated with more cover and larger substrate during the day in both streams. Interspecific differences in habitat use in both streams occurred with Atlantic salmon (fast velocities) and coho salmon (pools) using the least similar habitat. Chinook salmon and Atlantic salmon used similar habitat in both streams. These findings should help guide future management actions specific to habitat protection and restoration of Atlantic salmon in Lake Ontario tributaries.     

Estimation of a Killer Whale (Orcinus orca) Population’s Diet Using Sequencing Analysis of DNA from Feces

Estimating diet composition is important for understanding interactions between predators and prey and thus illuminating ecosystem function. The diet of many species, however, is difficult to observe directly. Genetic analysis of fecal material collected in the field is therefore a useful tool for gaining insight into wild animal diets. In this study, we used high-throughput DNA sequencing to quantitatively estimate the diet composition of an endangered population of wild killer whales (Orcinus orca) in their summer range in the Salish Sea. We combined 175 fecal samples collected between May and September from five years between 2006 and 2011 into 13 sample groups. Two known DNA composition control groups were also created. Each group was sequenced at a ~330bp segment of the 16s gene in the mitochondrial genome using an Illumina MiSeq sequencing system. After several quality controls steps, 4,987,107 individual sequences were aligned to a custom sequence database containing 19 potential fish prey species and the most likely species of each fecal-derived sequence was determined. Based on these alignments, salmonids made up >98.6% of the total sequences and thus of the inferred diet. Of the six salmonid species, Chinook salmon made up 79.5% of the sequences, followed by coho salmon (15%). Over all years, a clear pattern emerged with Chinook salmon dominating the estimated diet early in the summer, and coho salmon contributing an average of >40% of the diet in late summer. Sockeye salmon appeared to be occasionally important, at >18% in some sample groups. Non-salmonids were rarely observed. Our results are consistent with earlier results based on surface prey remains, and confirm the importance of Chinook salmon in this population’s summer diet.     

Effects of species, culture history, size and residency on relative competitive ability of salmonids

The relative competitive ability of juvenile farm and wild salmonids was investigated to provide insight into the potential effects of introduction of cultured salmon on wild Pacific salmonid ( Oncorhynchus ) species. Aquarium experiments involving equal contests ( i.e. size matched, simultaneously introduced individuals) indicated that two wild coho salmon Oncorhynchus kisutch populations were competitively equal to a farm coho salmon population. In equal contests between farm Atlantic salmon Salmo salar (Mowi strain) and these wild coho salmon populations or coastal cutthroat trout Oncorhynchus clarki clarki , Atlantic salmon were subordinate in all cases. When Atlantic salmon were given a residence advantage, however, they were competitively equal to both wild coho salmon populations, but remained subordinate to coastal cutthroat trout. When Atlantic salmon were given a 10–30% length advantage, they were competitively equal to one wild coho salmon population but remained subordinate to the other. In equal contests in semi-natural stream channels, both wild coho and farm Atlantic salmon grew significantly more in the presence of the other species than when alone. It appears that coho salmon obtain additional food ration by out competing Atlantic salmon, whereas Atlantic salmon were stimulated to feed more in the presence of coho salmon competitors. These results suggest that wild coho salmon and cutthroat trout should out compete farm Atlantic salmon of a similar size in nature. As the relative competitive ability of Atlantic salmon improves when they have a size and residence advantage, should feral populations become established, they may exist on a more equal competitive footing owing to the long freshwater residence of Atlantic salmon.     

Inorganic pyrophosphatase: a new polymorphic allozyme locus in Pacific salmon

Genetic polymorphism of inorganic pyrophosphatase was investigated in 2799 individuals in four species of Pacific salmon: chinook salmon (Oncorhynchus tshawytscha), coho salmon (O. kisutch), kokanee (O. nerka), and steelhead (O. mykiss), using horizontal starch gel electrophoresis. This enzyme system appears to be an isolocus system with electrophoretically indistinguishable allozymes encoded by two loci (PP-1,2*) expressed in retinal tissue. Mendelian inheritance was observed with a breeding study in three family crosses. Population variability in four species was characterized in 44 populations from the U.S. Pacific coast. Three alleles were found in chinook salmon; two alleles each were found in coho salmon, kokanee, and steelhead. Chinook salmon and kokanee populations differed enough with respect to PP-1,2* frequencies that this isolocus is useful for genetic stock identification in these species.     

Common relationships among proximate composition components in fishes

Relationships between the various body proximate components and dry matter content were examined for five species of fishes, representing anadromous, marine and freshwater species: chum salmon Oncorhynchus keta, Chinook salmon Oncorhynchus tshawytscha, brook trout Salvelinus fontinalis, bluefish Pomatomus saltatrix and striped bass Morone saxatilis. The dry matter content or per cent dry mass of these fishes can be used to reliably predict the per cent composition of the other components. Therefore, with validation it is possible to estimate fat, protein and ash content of fishes from per cent dry mass information, reducing the need for costly and time‐consuming laboratory proximate analysis. This approach coupled with new methods of non‐lethal estimation of per cent dry mass, such as from bioelectrical impedance analysis, can provide non‐destructive measurements of proximate composition of fishes.     

Use of seasonal freshwater wetlands by fishes in a temperate river floodplain

This study examined the use of freshwater wetland restoration and enhancement projects ( i.e . non-estuarine wetlands subject to seasonal drying) by fish populations. To quantify fish use of freshwater emergent wetlands and assess the effect of wetland enhancement ( i.e . addition of water control structures), two enhanced and two unenhanced emergent wetlands were compared, as well as two oxbow habitats within the Chehalis River floodplain. Eighteen fish species were captured using fyke nets and emigrant traps from January to the beginning of June, with the most abundant being three-spined stickleback Gasterosteus aculeatus and Olympic mudminnow Novumbra hubbsi . Coho salmon Oncorhynchus kisutch was the dominant salmonid at all sites. Enhanced wetlands, with their extended hydroperiods, had significantly higher abundances of yearling coho salmon than unenhanced wetlands. Both enhanced and unenhanced emergent wetlands yielded higher abundances of non-game native fishes than oxbow habitats. Oxbow habitats, however, were dominated by coho salmon. Fish survival in the wetland habitats was dependent on emigration to the river before dissolved oxygen concentrations decreased and wetlands became isolated and stranding occurred. This study suggests that wetland enhancement projects with an outlet to the river channel appear to provide fishes with important temporary habitats if they have the opportunity to leave the wetland as dissolved oxygen levels deteriorate.     

Can non-native smallmouth bass, <Emphasis Type="Italic">Micropterus dolomieu</Emphasis>, be swamped by hatchery fish releases to increase juvenile Chinook salmon, <Emphasis Type="Italic">Oncorhynchus tshawytscha</Emphasis>, survival?

One of the strategies that can be used to reduce predation impacts to valued fish species is by swamping predators with more prey than they can eat. We examined whether this approach was viable by calculating the maximum bioenergetic consumption potential of non-native smallmouth bass Micropterus dolomieu on fall Chinook salmon Oncorhynchus tshawytscha juveniles in the Yakima River throughout the spring between 1998 and 2002 and comparing those estimates to previously published estimates of fall Chinook salmon consumption. We found that the smallmouth bass population consumed fall Chinook salmon well below their bioenergetic potential. However, individual smallmouth bass that were piscivorous were eating other food items at a level near satiation. Furthermore, the maximum consumption potential was relatively low prior to mid-April, and then increased substantially to a peak in May. Predation mortality to hatchery fall Chinook salmon could be reduced within a year by releasing hatchery fall Chinook salmon that will emigrate quickly prior to mid-April, when predation potential is still very low. However, attempting to swamp predators with hatchery Chinook salmon to benefit naturally produced Chinook salmon poses uncertain benefits to natural origin fish and likely unacceptable costs to hatchery fish. Considerable swamping is occurring by other naturally produced fish species in the Yakima River such as dace Rhinichthys spp., mountain whitefish Prosopium williamsoni, and crayfish Pacificastus spp. Therefore, it is important to consider impacts to these non-target species because they could have indirect predation impacts on Chinook salmon.     

Identification of the sex chromosome pair in coho salmon (Oncorhynchus kisutch): lack of conservation of the sex linkage group with chinook salmon (Oncorhynchus tshawytscha)

Fluorescence in situ hybridization (FISH) using a probe to the male-specific GH-Y (growth hormone pseudogene) was used to identify the Y chromosome in coho salmon (Oncorhynchus kisutch). The sex chromosome pair is morphologically similar to chinook salmon (Oncorhynchus tshawytscha) with the GH-Y localized to the small short arm of the largest subtelocentric chromosome pair. FISH experiments with probes containing sex-linked genes in rainbow trout (Oncorhynchus mykiss) (SCAR163) and chinook salmon (Omy7INRA) showed that the coho sex linkage group is different from chinook and rainbow trout and this was confirmed by segregation analysis for the Omy7INRA locus. The telomeric location of the SEX locus, the presence of shared male-specific markers in coho and chinook salmon, and the lack of conservation of sex-linkage groups suggest that transposition of a small male-specific region may have occurred repeatedly in salmonid fishes of the genus Oncorhynchus.     

Density of the waterborne parasite Ceratomyxa shasta and its biological effects on salmon

The myxozoan parasite Ceratomyxa shasta is a significant pathogen of juvenile salmonids in the Pacific Northwest of North America and is limiting recovery of Chinook (Oncorhynchus tshawytscha) and coho (O. kisutch) salmon populations in the Klamath River. We conducted a 5-year monitoring program that comprised concurrent sentinel fish exposures and water sampling across 212 river kilometers of the Klamath River. We used percent mortality and degree-days to death to measure disease severity in fish. We analyzed water samples using quantitative PCR and Sanger sequencing, to determine total parasite density and relative abundance of C. shasta genotypes, which differ in their pathogenicity to salmonids. We detected the parasite throughout the study zone, but parasite density and genetic composition fluctuated spatially and temporally. Chinook and coho mortality increased with density of their specific parasite genotype, but mortality-density thresholds and time to death differed. A lethality threshold of 40% mortality was reached with 10 spores liter(-1) for Chinook but only 5 spores liter(-1) for coho. Parasite density did not affect degree-days to death for Chinook but was negatively correlated for coho, and there was wider variation among coho individuals. These differences likely reflect the different life histories and genetic heterogeneity of the salmon populations. Direct quantification of the density of host-specific parasite genotypes in water samples offers a management tool for predicting host population-level impacts.     

Predictability of multispecies competitive interactions in three populations of Atlantic salmon Salmo salar

Juvenile Atlantic salmon Salmo salar from three allopatric populations (LaHave, Sebago and Saint‐Jean) were placed into artificial streams with combinations of four non‐native salmonids: brown trout Salmo trutta, rainbow trout Oncorhynchus mykiss, Chinook salmon Oncorhynchus tshawytscha and coho salmon Oncorhynchus kisutch. Non‐additive effects, as evidenced by lower performance than predicted from weighted summed two‐species competition trials, were detected for S. salar fork length (L_F) and mass, but not for survival, condition factor or riffle use. These data support emerging theory on niche overlap and species richness as factors that can lead to non‐additive competition effects.     

Relationship between temperature and Ceratomyxa shasta -induced mortality in Klamath River salmonids

Water temperature influences almost every biological and physiological process of salmon, including disease resistance. In the Klamath River (California), current thermal conditions are considered sub-optimal for juvenile salmon. In addition to borderline temperatures, these fish must contend with the myxozoan parasite Ceratomyxa shasta , a significant cause of juvenile salmonid mortality in this system. This paper presents 2 studies, conducted from 2007 to 2010, that examine thermal effects on C. shasta -induced mortality in native Klamath River Chinook ( Oncorhynchus tshawytscha ) and coho ( Oncorhynchus kisutch ) salmon. In each study, fish were exposed to C. shasta in the Klamath River for 72 hr and then reared in the laboratory under temperature-controlled conditions. The first study analyzed data collected from a multi-year monitoring project to asses the influence of elevated temperatures on parasite-induced mortality during the spring/summer migration period. The second study compared disease progression in both species at 4 temperatures (13, 15, 18, and 21 C) representative of spring/summer migration conditions. Both studies demonstrated that elevated water temperatures consistently resulted in higher mortality and faster mean days to death. However, analysis of data from the multi-year monitoring showed that the magnitude of this effect varied among years and was more closely associated with parasite density than with temperature. Also, there was a difference in the timing of peak mortality between species; Chinook incurred high mortalities in 2008 and 2009, whereas coho was greatest in 2007 and 2008. As neither temperature nor parasite density can be easily manipulated, management strategies should focus on disrupting the overlap of this parasite and its obligate hosts to improve emigration success and survival of juvenile salmon in the Klamath River.     

Development of 54 novel single-nucleotide polymorphism (SNP) assays for sockeye and coho salmon and assessment of available SNPs to differentiate stocks within the Columbia River

Single-nucleotide polymorphisms (SNPs) have potential for broad application in population and conservation genetics, but availability of these markers is limited in many nonmodel species. In this study, genomic and expressed sequence tagged (EST) sequences from closely related salmonids (Chinook salmon and rainbow trout) were used to design primers for amplification and sequencing of sockeye (Oncorhynchus nerka) and coho (Oncorhynchus kisutch) salmon DNA for SNP discovery. One hundred and six primer sets were designed and tested for amplification in each species. An ascertainment panel of 32 diverse individuals from each species was used as template for PCR amplification and Sanger sequencing. In total, 21,647 bases of consensus sequence were screened in sockeye salmon and 20,784 bases in coho salmon with 93 and 149 SNP sites identified, respectively. Sixty-four SNP sites were chosen for assay development, and 54 of the assays were validated by comparison with genotype and sequence data (O. nerka = 23; O. kisutch = 31). These validated SNP assays along with 142 other available SNP assays [O. nerka = 103 (126 total); O. kisutch = 30 (61 total)] were used to genotype collections of O. nerka (N = 5) and O. kisutch (N = 4) from various sites in the Columbia River to evaluate the utility of these markers in this region. Results from factorial correspondence analysis indicate that these SNP markers are capable of distinguishing O. nerka populations, but O. kisutch collections were less distinct because of their common ancestry.     

DNA homologies between the rainbow trout, chum salmon and coho salmon

The thermal stabilities of hybrid duplexes between the DNAs from three salmonid fish species were monitored as measures of DNA homology. The chum salmon, Oncorhynchus keta, and coho salmon, Oncorhynchus kisutch, had more DNA homology with each other than either had with the rainbow trout, Salmo gairdnerii. Morphological, ecological and protein similarities between the coho salmon and the rainbow trout may be due to parallel or convergent evolution.     

Physiological and Behavioral Effects of Zinc and Temperature on Coho Salmon (Oncorhynchus kisutch)

Pacific salmon species including the U.S. federally endangered coho salmon (Oncorhynchus kisutch) and the U.S. federally threatened steelhead trout (Oncorhynchus mykiss) have declined at an alarming rate in the last 40 years. Two of the main causes for the decline in coastal coho populations include increases in temperature and contaminant loads in coastal watersheds. Zinc, in particular, is one of the most common contaminants in aquatic systems. Using an experimental mesocosm design, we examined physiological, biochemical, and behavioral responses of coho salmon to excess dietary zinc and increased temperatures, with the ultimate goal of relating results to wild populations of coho salmon and steelhead in the Navarro River, California. Fish were obtained from a hatchery and divided into four treatments: low water temperature-no dietary zinc, high temperature-no zinc, low temperature-zinc, and high temperature-zinc. Each treatment had four replicate tanks. Zinc concentrations in liver increased during exposure to a high zinc diet. Iron concentrations in liver increased during simultaneous exposure to high zinc diet and increased temperature, and growth was reduced in this experimental treatment. Expression of hsp-70 was not significantly different between treatments, but showed decreasing trends with high dietary zinc and high temperature. Feeding rate increased with exposure to a high zinc diet. Comparison with steelhead trout samples from the Navarro River, California, showed levels of zinc, iron, and hsp-70 greater than those found in the experimental Coho salmon. All comparisons between the hatchery coho salmon and wild steelhead should be viewed with caution due to the differences between species, the laboratory and natural environment, and the genetic differences between wild and hatchery fish.     

Understanding the behavior and ecology of Chinook salmon (Oncorhynchus tshawytscha) on an important feeding ground in the Gulf of Alaska

Population declines and demographic changes of Chinook salmon (Oncorhynchus tshawytscha), have been documented throughout this species’ range, though information on natural and anthropogenic mechanisms related to these changes are not fully understood. To provide insights into marine behaviors and survival of Chinook salmon, 40 pop-up satellite archival tags (PSATs), that collected environmental data, were attached to large (69–100 cm FL) Chinook salmon caught in the marine waters of Cook Inlet, Alaska. PSATs provided evidence of predation on tagged Chinook salmon by ectothermic and unconfirmed predators, and provided valuable information about the migratory characteristics and occupied depths and temperatures of this species while occupying Cook Inlet and the Gulf of Alaska. The results from this study suggest that late-marine mortality of Chinook salmon of a variety of stock-origins by apex predators is more common in Cook Inlet than previously thought, and may be used to improve our understanding this species’ population dynamics. Furthermore, results from this study adds to the existing knowledge of marine habitat use by Chinook Salmon and may be useful in assessing the vulnerability and interactions between this species and anthropogenic activities.