Holding behavior of Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss) smolts, as influenced by habitat features of levee banks, in the highly modified lower Sacramento River, California

Using acoustic telemetry methods on large numbers of tagged fish, we studied how the holding behavior of Chinook salmon and steelhead smolts could be related to habitat features and spatial and temporal variables on a highly altered section of the Sacramento River. We viewed downstream migration as a process in which fish transition between moving and holding states, and used a binomial and negative binomial Generalized Linear Model to analyze two aspects of holding: 1) probability of holding, and 2) holding time. For Chinook salmon, the probability of holding increased as wood size and fine substrates increased; holding time increased as overhead shade increased. For steelhead, holding behavior was only weakly related to habitat variables, in contrast to the strong relationships with spatial and temporal variables. For both species, the probability of holding increased when distance from the release location decreased and instream flows decreased. We found support for three main findings: 1) spatial and temporal factors have considerably greater influence on Chinook salmon and steelhead smolt holding behavior than nearshore habitat features; 2) holding behaviors of Chinook salmon smolts are influenced more strongly by habitat features than steelhead smolts; and 3) incorporation of habitat features such as large woody material and overhead shade should be considered when conducting nearshore bank rehabilitation projects to increase cover from predators and provide velocity refuge, improving holding habitat during downstream migration.     

Multigenerational outbreeding effects in Chinook salmon (Oncorhynchus tshawytscha)

Outbreeding, mating between genetically divergent individuals, may result in negative fitness consequences for offspring via outbreeding depression. Outbreeding effects are of notable concern in salmonid research as outbreeding can have major implications for salmon aquaculture and conservation management. We therefore quantified outbreeding effects in two generations (F₁ hybrids and F₂ backcrossed hybrids) of Chinook salmon (Oncorhynchus tshawytscha) derived from captively-reared purebred lines that had been selectively bred for differential performance based on disease resistance and growth rate. Parental lines were crossed in 2009 to create purebred and reciprocal hybrid crosses (n = 53 families), and in 2010 parental and hybrid crosses were crossed to create purebred and backcrossed hybrid crosses (n = 66 families). Although we found significant genetic divergence between the parental lines (F_ST = 0.130), reciprocal F₁ hybrids showed no evidence of outbreeding depression (hybrid breakdown) or favorable heterosis for weight, length, condition or survival. The F₂ backcrossed hybrids showed no outbreeding depression for a suite of fitness related traits measured from egg to sexually mature adult life stages. Our study contributes to the current knowledge of outbreeding effects in salmonids and supports the need for more research to better comprehend the mechanisms driving outbreeding depression.     

Cardiovascular responses of Chinook salmon (Oncorhynchus tshawytscha) during rapid anaesthetic induction and recovery

The effects of three anaesthetics on induction and recovery were compared in Chinook salmon (Oncorhynchus tshawytscha). Heart rate (HR), cardiac output (Q), dorsal aortic pressure (DAP) and stroke volume (SV) were measured in minimally disturbed salmon during 5 min anaesthetic inductions with approximately equi-potent concentrations of MS222 (100 ppm), metomidate (6-10 ppm) and AQUI-S (60 ppm). MS222 induction caused a steady decline in DAP only, while metomidate induction did not affect any cardiovascular variable. AQUI-S caused a biphasic response, and within 2 min had depressed HR, Q, DAP and SV by between 20 and 50%. In the final 3 min HR returned to pre-anaesthesia levels, and Q and SV climbed to greater than pre-anaesthesia levels. Blood samples taken pre- and post-anaesthesia showed all inductions caused hypoxaemia (oxygen partial pressure of dorsal aortic blood (PaO2): MS222 47 mmHg, metomidate 35 mmHg, AQUI-S 21 mmHg). Haematocrit and plasma adrenaline and noradrenaline levels increased slightly in AQUI-S treated fish only. Recovery was monitored for 6 h post-anaesthesia, and was similar for each anaesthetic. All cardiovascular variables had returned to control levels within 5 min with the exception of DAP, which was initially slightly elevated (up to 20%) but returned to control values within 30 min. Anaesthesia is usually preceded by handling. Netting prior to anaesthesia caused significant increases in HR, Q and SV, which masked any anaesthetic dependent effects. Recovery from anaesthesia combined with surgery was also generally anaesthetic independent and recovery was prolonged, compared to anaesthesia alone. These data suggest limiting fish handling/manipulation is more important in minimising cardiovascular disturbance than the choice of anaesthetic.     

Arteriosclerosis in steelhead trout, Oncorhynchus mykiss (Walbaum): a developmental analysis

Arteriosclerosis in Oncorhynchur mykiss has been examined histologically in parr, smolts, spawning adults and post-spawning adults captured during downstream migration. All stages of fish from the Clearwater River in Idaho are characterized by the presence of lesions in the main vessel on the bulbus arteriosus. The incidence is lowest in parr, increases significantly in smolts, and is present in 100% of spawning fish. Regression of lesions was not observed in either hatchery or wild fish after spawning.     

Captive rearing for Chinook salmon (Oncorhynchus tshawytscha) and Atlantic salmon (Salmo salar): the Idaho and Maine experiences

Captive rearing is a conservation strategy where juveniles are collected from the natural environment, reared to maturity in a hatchery environment, and then released back into the natural environment at maturity for volitional spawning. This strategy has been used to produce adult outplants for stock enhancement where natural escapement is poor or capture of adults is difficult. In both Idaho (Chinook salmon, Oncorhynchus tshawytscha) and Maine (Atlantic salmon, Salmo salar), captive rearing programs have been initiated as an experimental strategy to prevent cohort collapse and conserve genetic integrity of select depressed populations. In this paper, we provide an overview of these programs and describe some of the methods used to evaluate the effectiveness of this approach. Behaviors such as habitat selection, courting, and spawn timing were monitored. Data collected for both programs indicate that the captive fish display similar behaviors as their wild conspecifics in terms of habitat selection and spawning, although there were some differences in spawn timing. Evaluations of egg and fry production also indicate that captive-reared adults are successfully spawning and producing offspring. Each program is still waiting on final evaluations of reproductive success through genetic analyses of returning adults, but results so far indicate that this could be an additional captive propagation strategy for depressed populations.     

Discovery and characterization of single-nucleotide polymorphisms in steelhead/rainbow trout, Oncorhynchus mykiss

Single-nucleotide polymorphisms (SNPs) have several advantages over other genetic markers, including lower mutation and genotyping error rates, ease of inter-laboratory standardization, and the prospect of high-throughput, low-cost genotyping. Nevertheless, their development and use has only recently moved beyond model organisms to groups such as salmonid fishes. Oncorhynchus mykiss is a salmonid native to the North Pacific rim that has now been introduced throughout the world for fisheries and aquaculture. The anadromous form of the species is known as steelhead. Native steelhead populations on the west coast of the United States have declined and many now have protected status. The nonanadromous, or resident, form of the species is termed rainbow, redband or golden trout. Additional life history and morphological variation, and interactions between the forms, make the species challenging to study, monitor and evaluate. Here, we describe the discovery, characterization and assay development for 139 SNP loci in steelhead/rainbow trout. We used EST sequences from existing genomic databases to design primers for 480 genes. Sanger-sequencing products from these genes provided 130 KB of consensus sequence in which variation was surveyed for 22 individuals from steelhead, rainbow and redband trout groups. The resulting TaqMan assays were surveyed in five steelhead populations and three rainbow trout stocks, where they had a mean minor allele frequency of 0.15-0.26 and observed heterozygosity of 0.18-0.35. Mean F(ST) was 0.204. The development of SNPs for O. mykiss will help to provide highly informative genetic tools for individual and stock identification, pedigree reconstruction, phylogeography and ecological investigation.     

Dosage effects on heritability and maternal effects in diploid and triploid Chinook salmon (Oncorhynchus tshawytscha)

Induced triploidy (3N) in salmon results from a blockage of maternal meiosis II, and hence provides a unique opportunity to study dosage effects on phenotypic variance. Chinook salmon families were bred using a paternal half-sib breeding design (62 females and 31 males) and half of each resulting family was treated to induce triploidy. The paired families were used to test for dosage effects (resulting from triploidy) on (1) the distribution and magnitude of phenotypic variation, (2) narrow-sense heritability and (3) maternal effects in fitness-related traits (i.e., survival, size-at-age, relative growth rate and serum lysozyme activity). Quantitative genetic analyses were performed separately for diploid and triploid family groups. Triploidization resulted in significantly higher levels of phenotypic variance and substantial differences in patterns of variance distribution for growth and survival-related traits, although the patterns were reversed for lysozyme activity. Triploids exhibited higher narrow sense heritability values relative to diploid Chinook salmon. However, maternal effects estimates were generally lower in triploids than in diploids. Thus, the dosage effects resulting from adding an extra set of chromosomes to the Chinook salmon genome are primarily additive. Somewhat counterintuitively, however, the relative magnitude of the combined effects of dominance, epistasis and maternal effects is not affected by dosage. Our results indicate that inheritance of fitness-related quantitative traits is profoundly affected by dosage effects associated with induced triploidy, and that triploidization can result in unpredictable performance and fitness outcomes.     

Postprandial intestinal blood flow, metabolic rates, and exercise in Chinook salmon (Oncorhynchus tshawytscha)

Following a relatively large meal (2% body mass of dry pellets), intestinal blood flow in chinook salmon (Oncorhynchus tshawytscha) increased significantly, up to 81%, between 14 and 29 h postprandially. Also, 15 h postprandially, oxygen consumption (M(2)) was elevated by 128% compared with a measurement of routine M(2) made after 1 wk of fasting. The postprandial increase in MO(2) (the heat increment) was 33 micromol O(2) min(-1) kg(-1). Because intestinal blood flow is known to decrease during swimming activity in fish, we therefore tested the hypothesis that swimming fish would have to make a trade-off between maximum swimming activity and digestive activity by comparing the swimming performance and metabolic rates of fed and fasted chinook salmon. As expected, MO(2) increased exponentially with swimming velocity in both fed and fasted fish. Moreover, the heat increment was irreducible during swimming, such that MO(2) remained approximately 39 micromol O(2) min(-1) kg(-1) higher in fed fish than in fasted fish at all comparable swimming speeds. However, maximum M dot o2 was unaffected by feeding and was identical in both fed and fasted fish (approximately 250 micromol O(2) min(-1) kg(-1)), and, as a result, the critical swimming speed (U(crit)) was 9% lower in the fed fish. Three days after the fish were fed and digestion was completed, MO(2) and U(crit) were not significantly different from those measured in fasted fish. The ability of salmonids to maintain feeding metabolism during prolonged swimming performance is discussed, and it is suggested that reduced swimming performance may be due to postprandial sparing of intestinal blood to support digestion, thereby limiting the allocation of blood flow to locomotory muscles.     

Discovery and characterization of single nucleotide polymorphisms in Chinook salmon, Oncorhynchus tshawytscha

Molecular population genetics of non-model organisms has been dominated by the use of microsatellite loci over the last two decades. The availability of extensive genomic resources for many species is contributing to a transition to the use of single nucleotide polymorphisms (SNPs) for the study of many natural populations. Here we describe the discovery of a large number of SNPs in Chinook salmon, one of the world's most important fishery species, through large-scale Sanger sequencing of expressed sequence tag (EST) regions. More than 3 Mb of sequence was collected in a survey of variation in almost 132 kb of unique genic regions, from 225 separate ESTs, in a diverse ascertainment panel of 24 salmon. This survey yielded 117 TaqMan (5' nuclease) assays, almost all from separate ESTs, which were validated in population samples from five major stocks of salmon from the three largest basins on the Pacific coast of the contiguous United States: the Sacramento, Klamath and Columbia Rivers. The proportion of these loci that was variable in each of these stocks ranged from 86.3% to 90.6% and the mean minor allele frequency ranged from 0.194 to 0.236. There was substantial differentiation between populations with these markers, with a mean F(ST) estimate of 0.107, and values for individual loci ranging from 0 to 0.592. This substantial polymorphism and population-specific differentiation indicates that these markers will be broadly useful, including for both pedigree reconstruction and genetic stock identification applications.     

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.     

Effects of predator and flow manipulation on Chinook salmon (Oncorhynchus tshawytscha) survival in an imperiled estuary

We evaluated the effects of non-native, piscivorous fish removal and artificial flow manipulation on survival and migration speed of juvenile Chinook salmon, Oncorhynchus tshawytscha, emigrating through the eastern Sacramento-San Joaquin Delta of California (Delta) using a Before-After-Control-Impact study design. Acoustically-tagged salmon survival increased significantly after the first predator reduction in the impact reach. However, survival estimates returned to pre-impact levels after the second predator removal. When an upstream control gate opened (increasing flow and decreasing tidal effect) juvenile salmon emigration time decreased and survival increased significantly through the impact reach. Though a short-term, single season experiment, our results demonstrate that predator control and habitat manipulation in the Delta tidal transition zone can be effective management strategies to enhance salmon survival in this highly altered system.     

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.     

Fluvial rainbow trout contribute to the colonization of steelhead (Oncorhynchus mykiss) in a small stream

Life history polymorphisms provide ecological and genetic diversity important to the long term persistence of species responding to stochastic environments. Oncorhynchus mykiss have complex and overlapping life history strategies that are also sympatric with hatchery populations. Passive integrated transponder (PIT) tags and parentage analysis were used to identify the life history, origin (hatchery or wild) and reproductive success of migratory rainbow/steelhead for two brood years after barriers were removed from a small stream. The fluvial rainbow trout provided a source of wild genotypes to the colonizing population boosting the number of successful spawners. Significantly more parr offspring were produced by anadromous parents than expected in brood year 2005, whereas significantly more parr offspring were produced by fluvial parents than expected in brood year 2006. Although hatchery steelhead were prevalent in the Methow Basin, they produced only 2 parr and no returning adults in Beaver Creek. On average, individual wild steelhead produced more parr offspring than the fluvial or hatchery groups. Yet, the offspring that returned as adult steelhead were from parents that produced few parr offspring, indicating that high production of parr offspring may not be related to greater returns of adult offspring. These data in combination with other studies of sympatric life histories of O. mykiss indicate that fluvial rainbow trout are important to the conservation and recovery of steelhead and should be included in the management and recovery efforts.     

Circulatory limits to oxygen supply during an acute temperature increase in the Chinook salmon (Oncorhynchus tshawytscha)

This study was undertaken to provide a comprehensive set of data relevant to disclosing the physiological effects and possible oxygen transport limitations in the Chinook salmon (Oncorhynchus tshawytscha) during an acute temperature change. Fish were instrumented with a blood flow probe around the ventral aorta and catheters in the dorsal aorta and sinus venosus. Water temperature was progressively increased from 13 degrees C in steps of 4 degrees C up to 25 degrees C. Cardiac output increased from 29 to 56 ml.min(-1).kg(-1) between 13 and 25 degrees C through an increase in heart rate (58 to 105 beats/min). Systemic vascular resistance was reduced, causing a stable dorsal aortic blood pressure, yet central venous blood pressure increased significantly at 25 degrees C. Oxygen consumption rate increased from 3.4 to 8.7 mg.min(-1).kg(-1) during the temperature increase, although there were signs of anaerobic respiration at 25 degrees C in the form of increased blood lactate and decreased pH. Arterial oxygen partial pressure was maintained during the heat stress, although venous oxygen partial pressure (Pv(O(2))) and venous oxygen content were significantly reduced. Cardiac arrhythmias were prominent in three of the largest fish (>4 kg) at 25 degrees C. Given the switch to anaerobic metabolism and the observation of cardiac arrhythmias at 25 degrees C, we propose that the cascade of venous oxygen depletion results in a threshold value for Pv(O(2)) of around 1 kPa. At this point, the oxygen supply to systemic and cardiac tissues is compromised, such that the oxygen-deprived and acidotic myocardium becomes arrhythmic, and blood perfusion through the gills and to the tissues becomes compromised.