The effects of environmental factors on the migratory movement patterns of Sacramento River yearling late-fall run Chinook salmon (Oncorhynchus tshawytscha)

Understanding smolt migration dynamics is a critical step in the preservation and conservation of imperiled salmonids in California’s Sacramento River system. Late-fall run Chinook salmon yearling smolts were acoustically tagged and tracked during their outmigration through California’s Sacramento River and San Francisco Estuary during 2007–2009. Migration rates were 14.3 km·day^-1 (± 1.3 S.E.) to 23.5 km?day^-1 (± 3.6 S.E.), similar to rates published for other West Coast yearling Chinook salmon smolt emigrations. Region-specific movement rates were fastest through the upper river regions, and slowest in the Sacramento/San Joaquin River Delta. River travel times were recorded for smolts travelling through a series of ten monitor-delimited reaches. Using these, a smolt travel time model determined by two parameters (movement rate and rate of population spreading) was then used to determine the influence of different factors on the model’s fit, using model selection with Akaike’s Information Criterion. The model that allowed for both year and reach to be expressed additively for both travel time and population spreading rate estimates, while accounting for a “release” effect, was the best supported model. Finally, several models incorporated environmental data as a linear predictor of movement rates. The addition of the environmental variables, in order of importance, river width to depth ratio, river flow, water turbidity, river flow to mean river flow ratio, and water velocity all resulted in improved model fit. Water temperature did not improve model fit. These environmental associations are discussed and potential improvements on the travel time model are suggested.     

Diel movements of out-migrating Chinook salmon (Oncorhynchus tshawytscha) and steelhead trout (Oncorhynchus mykiss) smolts in the Sacramento/San Joaquin watershed

We used ultrasonic telemetry to describe the movement patterns of late-fall run Chinook salmon (Oncorhynchus tshawytscha) and steelhead trout (O. mykiss) smolts during their entire emigration down California’s Sacramento River, through the San Francisco Bay Estuary and into the Pacific Ocean. Yearling hatchery smolts were tagged via intracoelomic surgical implantation with coded ultrasonic tags. They were then released at four upriver locations in the Sacramento River during the winters of 2007 through 2010. Late-fall run Chinook salmon smolts exhibited a nocturnal pattern of migration after release in the upper river. This is likely because individuals remain within a confined area during the day, while they become active at night and migrate downstream. The ratio between night and day detections of Chinook salmon smolts decreased with distance traveled downriver. There was a significant preference for nocturnal migration in every reach of the river except the Estuary. In contrast, steelhead smolts, which reside upriver longer following release, exhibited a less pronounced diel pattern during their entire migration. In the middle river, Delta, and Estuary, steelhead exhibited a significant preference for daytime travel. In the ocean Chinook salmon preferred to travel at night, yet steelhead were detected on the monitors equally during the night and day. These data show that closely related Oncorhynchus species, with the same ontogenetic pattern of out-migrating as yearlings, vary in migration tactic.     

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.     

The effect of hatchery release strategy on marine migratory behaviour and apparent survival of Seymour River steelhead smolts (Oncorhynchus mykiss)

Early marine migratory behaviour and apparent survival of hatchery-reared Seymour River steelhead (Oncorhynchus mykiss) smolts was examined over a four year period (2006-2009) to assess the impact of various management strategies on improving early marine survival. Acoustically tagged smolts were released to measure their survival using estuary and coastal marine receivers forming components of the Pacific Ocean Shelf Tracking (POST) array. Early marine survival was statistically indistinguishable between releases of summer run and winter run steelhead races, night and day releases, and groups released 10 days apart. In 2009, the survival of summer run steelhead released into the river was again trialed against groups released directly into the ocean at a distance from the river mouth. Apparent survival was improved significantly for the ocean released groups. The health and physiological status of the various release groups were monitored in years 2007-2009, and results indicate that the fish were in good health, with no clinical signs of disease at the time of release. The possibility of a disease event contributing to early marine mortality was further examined in 2009 by vaccinating half of the released fish against common fish diseases (vibriosis, furunculosis). The results suggest that marine survival may be enhanced using this approach, although not to the extent observed when the smolts were transported away from the river mouth before release. In summary, direct experimental testing of different release strategies using the POST array to measure ocean survival accelerated the scientific process by allowing rapid collection of data which enabled the rejection of several existing theories and allowed tentative identification of several new alternative approaches that might improve early marine survival of Seymour River steelhead.     

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

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

Tactic‐specific benefits of polyandry in Chinook salmon Oncorhynchus tshawytscha

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

Survival of captured and relocated adult spring-run Chinook salmon Oncorhynchus tshawytscha in a Sacramento River tributary after cessation of migration

We studied the efficacy of the process for capture and upstream relocation of 26 adult spring-run Chinook salmon in Butte Creek, California in 2009. These fish had ceased volitional upstream migration prior to reaching their summer holding habitat. The purpose of the relocation was to move fish upstream of two water diversion dams and release them in a part of the stream from which they could presumably swim to cool summer holding habitat, then spawn in the fall. Fish were netted, transported by truck, given an esophageal radio tag/temperature tag, and released. Radio tagging proved to be a useful technique for determining the survival and movement of relocated fish and temperature tags provide useful information to determine thermal exposure and time of death. Twenty-three tags (88 %) were recovered, compared with a 10 % tag recovery rate for an earlier study using fin clips. Most tags were recovered within 3.5 km upstream and 1 km downstream of the release site. A single tag was recovered 6 km upstream. No fish were determined to have survived to spawn. Temperature tag data indicate that most of the salmon died within 2–6 days after the relocation operation. After preventative measures have been exhausted, future relocations efforts, in any setting, should consider (1) intervention as soon as fish cease volitional migration but before they are exposed to further deleterious conditions (2) monitoring environmental conditions to choose appropriate release sites (3) evaluation of disease transmission risk, and (4) handling practices that minimize potential stress due to air immersion and thermal shock.     

Landscape features along migratory routes influence adaptive genomic variation in anadromous steelhead (Oncorhynchus mykiss)

Organisms typically show evidence of adaptation to features within their local environment. However, many species undergo long‐distance dispersal or migration across larger geographic regions that consist of highly heterogeneous habitats. Therefore, selection may influence adaptive genetic variation associated with landscape features at residing sites and along migration routes in migratory species. We tested for genomic adaptation to landscape features at natal spawning sites and along migration paths to the ocean of anadromous steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin. Results from multivariate ordination, gene–environment association and outlier analyses using 24,526 single nucleotide polymorphisms (SNPs) provided evidence that adaptive allele frequencies were more commonly associated with landscape features along migration paths than features at natal sites (91.8% vs. 8.2% of adaptive loci, respectively). Among the 45 landscape variables tested, migration distance to the ocean and mean annual precipitation along migration paths were significantly associated with adaptive genetic variation in three distinct genetic groups. Additionally, variables such as minimum migration water temperature and mean migration slope were significant only in inland stocks of steelhead that migrate up to 1,200 km farther than those near the coast, indicating regional differences in migratory selective pressures. This study provides novel approaches for investigating migratory corridors and some of the first evidence that environment along migration paths can lead to substantial divergent selection. Consequently, our approach to understand genetic adaptation to migration conditions can be applied to other migratory species when migration or dispersal paths are generally known.     

An integrated linkage map reveals candidate genes underlying adaptive variation in Chinook salmon (Oncorhynchus tshawytscha)

Salmonids are an important cultural and ecological resource exhibiting near worldwide distribution between their native and introduced range. Previous research has generated linkage maps and genomic resources for several species as well as genome assemblies for two species. We first leveraged improvements in mapping and genotyping methods to create a dense linkage map for Chinook salmon Oncorhynchus tshawytscha by assembling family data from different sources. We successfully mapped 14 620 SNP loci including 2336 paralogs in subtelomeric regions. This improved map was then used as a foundation to integrate genomic resources for gene annotation and population genomic analyses. We anchored a total of 286 scaffolds from the Atlantic salmon genome to the linkage map to provide a framework for the placement 11 728 Chinook salmon ESTs. Previously identified thermotolerance QTL were found to colocalize with several candidate genes including HSP70, a gene known to be involved in thermal response, as well as its inhibitor. Multiple regions of the genome with elevated divergence between populations were also identified, and annotation of ESTs in these regions identified candidate genes for fitness related traits such as stress response, growth and behaviour. Collectively, these results demonstrate the utility of combining genomic resources with linkage maps to enhance evolutionary inferences.     

Variation in reproductive success and effective number of breeders in a hatchery population of steelhead trout (Oncorhynchus mykiss): examination by microsatellite-based parentage analysis

Conservation programs that release captive-bred individuals into the wild to mix with naturally produced individuals are an increasingly common method of supporting or enhancing weak or reduced populations that otherwise may not be self-sustaining. Captive and supportive breeding can be important conservation tools for species with small or declining populations; however, in the case of hatcheries producing salmonid fishes, detailed evaluation of spawning programs is rare. We examined variation in reproductive success, measured by adult offspring production, from three parental generations of hatchery-bred steelhead trout (Oncorhynchus mykiss) using an exclusion-based method of genetic parentage assignment. Reproductive success varied greatly among individuals (especially males) and was correlated with fecundity and maternal spawning date. Estimates of egg to smolt survival for the population as a whole among years ranged from 64% to 95%, marine survival ranged from 0.32% to 2.30%, and the number of adults produced per female ranged from 0 to 18 and the number of adults produced per male ranged from 0 to 32. The effective number of breeders ranged from 11% to 31% of the census population size for that brood year. These ratios fell within estimates from estimates of Ne/N in chinook (O. tshawytscha) and rainbow trout (O. mykiss) hatchery populations.     

Juvenile growth and aggression in diploid and triploid Chinook salmon Oncorhynchus tshawytscha (Walbaum)

Multilocus heterozygosity, aggressive and feeding behaviour, plasma cortisol levels and growth rate were evaluated among three groups of juvenile Chinook salmon Oncorhynchus tshawytscha : diploid, triploid and mixed groups of diploid and triploid fish. There was no difference between diploid and triploid fish in measurements of heterozygosity calculated using seven microsatellite loci, and these measurements did not correlate with performance measurements including feeding rate and growth rate. Aggression trials that examined small groups of fish revealed that after 4 days together in tanks, triploid fish were significantly less aggressive during feeding than diploid fish or fish in mixed groups. At the end of the trials, however, plasma cortisol levels did not differ among the three groups. Thirty-day growth trials in duplicate tanks of 60 fish revealed no difference in growth rate among diploid, triploid and mixed groups, but plasma cortisol levels were significantly lower in triploid fish than in either diploid fish or the mixed fish. Overall, independent of the above differences in aggressive behaviour and cortisol levels, these results suggest similar performance in diploid and triploid Chinook salmon, and thus provide support for the viability of triploid Chinook salmon culture in commercial aquaculture.     

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.     

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.     

Survival and movement patterns of central California coast native steelhead trout (Oncorhynchus mykiss) in the Napa River

Drawing on acoustic telemetry this study identifies and describes local and regional scale survival and movement patterns of Central California Coast steelhead (Oncorhynchus mykiss), including their potential utilization of newly restored tidal marsh habitats in the Napa River system. Between April 8th and May 5th of 2010, 20 steelhead smolts ranging in fork length from 164 to 305 mm were collected, tagged with acoustic transmitters, and released in the upper Napa River (above tidal influence). We found no effect of release date (P?<?0.001) or size (P?<?0.005) on survival estimates based on model likelihoods. Cumulative survival from smolt release location to the Golden Gate Bridge over approximately 77 river kilometers (RKM) was 0.60 (SE?=?0.16). Reach-specific survival was lowest in the initial 30 km reach (0.70 SE?=?0.1). Survival was higher in San Pablo Bay (0.89 SE?=?0.1) and San Francisco Bay (0.96 SE?=?0.2). Sixty percent of the fish that entered the ocean were detected on a line of acoustic monitors at Point Reyes approximately 60 km north of the Golden Gate. Average movement rates of smolts were highest in San Pablo Bay (36.6 km?d^-1 SE?=?3.3) and San Francisco Bay (28.9 km?d^-1 SE?=?6.6). Smolts migrated more slowly in the river (9.0 km?d^-1 SE?=?0.9) and ocean (4.1 km?d^-1 SE?=?1.2). However, smolt movement rates in the river were dependent on location. Average movement rates of smolts were greatest shortly before their exit from the Napa River (83 km?d^-1 SE?=?13.2). Fish were not detected within the recently reconnected former salt production ponds (North, Central, and South units) adjacent to the Napa River. Based on the detection patterns of fish throughout the study area, it appears that most fish were moving at relatively high rates and were not exploring off-channel habitat.     

Vascular reactivity of the coronary artery in steelhead trout (Oncorhynchus mykiss

1. The responses of vascular rings from the coronary artery in steelhead trout, Oncorhynchus mykiss, were measured using isometric force transducers.2. Coronary rings contracted with acetylcholine.3. Nitroglycerine and sodium nitroprusside relaxed coronary rings.4. Adenosine, ADP and ATP caused contractions.5. A comparison is made with the reactivity of the coronary artery in rainbow trout.     

Behavioural thermoregulation by subyearling fall (autumn) Chinook salmon Oncorhynchus tshawytscha in a reservoir

This study investigated behavioural thermoregulation by subyearling fall (autumn) Chinook salmon Oncorhynchus tshawytscha in a reservoir on the Snake River, Washington, U.S.A. During the summer, temperatures in the reservoir varied from 23° C on the surface to 11° C at 14 m depth. Subyearlings implanted with temperature-sensing radio transmitters were released at the surface at temperatures >20° C during three blocks of time in summer 2004. Vertical profiles were taken to measure temperature and depth use as the fish moved downstream over an average of 5·6–7·2 h and 6·0–13·8 km. The majority of the subyearlings maintained average body temperatures that differed from average vertical profile temperatures during most of the time they were tracked. The mean proportion of the time subyearlings tracked within the 16–20° C temperature range was larger than the proportion of time this range was available, which confirmed temperature selection opposed to random use. The subyearlings selected a depth and temperature combination that allowed them to increase their exposure to temperatures of 16–20° C when temperatures <16 and >20° C were available at lower and higher positions in the water column. A portion of the subyearlings that selected a temperature c. 17·0° C during the day, moved into warmer water at night coincident with an increase in downstream movement rate. Though subyearlings used temperatures outside of the 16–20° C range part of the time, behavioural thermoregulation probably reduced the effects of intermittent exposure to suboptimal temperatures. By doing so, it might enhance growth opportunity and life-history diversity in the population of subyearlings studied.     

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.