Discovery and characterization of single nucleotide polymorphisms in coho salmon,Oncorhynchus kisutch

Molecular population genetic analyses have become an integral part of ecological investigation and population monitoring for conservation and management. Microsatellites have been the molecular marker of choice for such applications over the last several decades, but single nucleotide polymorphism (SNP) markers are rapidly expanding beyond model organisms. Coho salmon (Oncorhynchus kisutch) is native to the north Pacific Ocean and its tributaries, where it is the focus of intensive fishery and conservation activities. As it is an anadromous species, coho salmon typically migrate across multiple jurisdictional boundaries, complicating management and requiring shared data collection methods. Here, we describe the discovery and validation of a suite of novel SNPs and associated genotyping assays which can be used in the genetic analyses of this species. These assays include 91 that are polymorphic in the species and one that discriminates it from a sister species, Chinook salmon. We demonstrate the utility of these SNPs for population assignment and phylogeographic analyses, and map them against the draft trout genome. The markers constitute a large majority of all SNP markers described for coho salmon and will enable both population‐ and pedigree‐based analyses across the southern part of the species native range.     

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.     

Rearing environment affects spatial learning in juvenile Chinook salmon Oncorhynchus tshawytscha

We tested the prediction that a complex physical rearing environment would enhance short-term spatial memory as assessed by learning ability in a spatial navigation task in juvenile Chinook salmon Oncorhynchus tshawytscha. We reared fish in two low-density treatments, where fish were either in bare fiberglass tanks (bare) or in tanks with physical structure (complex). We also tested conventionally reared high-density hatchery fish to compare with these other experimental treatments. Our reason for including this third hatchery treatment is that the two low-density treatments, aside from the manipulation of structure, followed a rearing programme that is designed to produce fish with more wild-like characteristics. We tested individually marked fish for seven consecutive days and recorded movement and time to exit a testing maze. Stimulus conspecific fish outside the exit of the maze provided positive reinforcement for test fish. Fish from the bare treatment were less likely to exit the start box compared with fish in the complex and hatchery treatments. However, fish in the hatchery treatment were significantly more likely to exit the maze on their own compared with both the bare and complex treatments. Hatchery fish effectively learned the task as shown by a decrease in the number of mistakes over time, but the number of mistakes was significantly greater on the first day of trials. Increasing habitat complexity with structure may not necessarily promote spatial learning ability, but differences between hatchery and experimental treatments in rearing density and motivation to be near conspecifics likely led to observed behavioural differences.     

Coronary ligation reduces maximum sustained swimming speed in Chinook salmon, Oncorhynchus tshawytscha

The maximum aerobic swimming speed of Chinook salmon (Oncorhynchus tshawytscha) was measured before and after ligation of the coronary artery. Coronary artery ligation prevented blood flow to the compact layer of the ventricular myocardium, which represents 30% of the ventricular mass, and produced a statistically significant 35.5% reduction in maximum swimming speed. We conclude that the coronary circulation is important for maximum aerobic swimming and implicit in this conclusion is that maximum cardiac performance is probably necessary for maximum aerobic swimming performance.     

Linking marine and freshwater growth in western Alaska Chinook salmon Oncorhynchus tshawytscha

The hypothesis that growth in Pacific salmon Oncorhynchus spp. is dependent on previous growth was tested using annual scale growth measurements of wild Chinook salmon Oncorhynchus tshawytscha returning to the Yukon and Kuskokwim Rivers, Alaska, from 1964 to 2004. First-year marine growth in individual O. tshawytscha was significantly correlated with growth in fresh water. Furthermore, growth during each of 3 or 4 years at sea was related to growth during the previous year. The magnitude of the growth response to the previous year's growth was greater when mean year-class growth during the previous year was relatively low. Length (eye to tail fork, L _ETF) of adult O. tshawytscha was correlated with cumulative scale growth after the first year at sea. Adult L _ETF was also weakly correlated with scale growth that occurred during freshwater residence 4 to 5 years earlier, indicating the importance of growth in fresh water. Positive growth response to previous growth in O. tshawytscha was probably related to piscivorous diet and foraging benefits of large body size. Faster growth among O. tshawytscha year classes that initially grew slowly may reflect high mortality in slow growing fish and subsequent compensatory growth in survivors. Oncorhynchus tshawytscha in this study exhibited complex growth patterns showing a positive relationship with previous growth and a possible compensatory response to environmental factors affecting growth of the age class.     

Endocrine changes during onset of puberty in male spring Chinook salmon,Oncorhynchus tshawytscha

In male salmonids, the age of maturation varies from 1 to 6 years and is influenced by growth during critical periods of the life cycle. The endocrine mechanisms controlling spermatogenesis and how growth affects this process are poorly understood. Recent research has indicated that gonadotropins, 11-ketotestosterone, and insulin-like growth factor I play roles in spermatogenesis in fish. To expand our understanding of the roles of these endocrine factors in onset of puberty, male spring chinook salmon (Oncorhynchus tshawytscha) were sampled at monthly intervals 14 mo prior to spermiation. This sampling regime encompassed two hypothesized critical periods when growth influences the initiation and completion of puberty for this species. Approximately 80% of the males matured during the experimental period, at age 2 in September 1999. An initial decline in the ratio of primary A to transitional spermatogonia was observed from July to December 1998, and during this period plasma levels of 11-ketotestosterone and pituitary levels of FSH increased. From January 1999 onward, males with low plasma 11-ketotestosterone levels (<1 ng/ml) had low pituitary and plasma FSH levels and no advanced development of germ cells. Conversely, from January through September 1999, males with high plasma 11-ketotestosterone levels (>1 ng/ml) had testes with progressively more advanced germ cell stages along with elevated pituitary and plasma FSH. Plasma levels of insulin-like growth factor I increased during maturation. These data provide the first physiological evidence for activation of the pituitary-testis axis during the fall critical period when maturation is initiated for the following year.     

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.     

Environmental rearing conditions produce forebrain differences in wild Chinook salmon Oncorhynchus tshawytscha

Recent studies suggest that hatchery-reared fish can have smaller brain-to-body size ratios than wild fish. It is unclear, however, whether these differences are due to artificial selection or instead reflect differences in rearing environment during development. Here we explore how rearing conditions influence the development of two forebrain structures, the olfactory bulb and the telencephalon, in juvenile Chinook salmon (Oncorhynchus tshawytscha) spawned from wild-caught adults. First, we compared the sizes of the olfactory bulb and telencephalon between salmon reared in a wild stream vs. a conventional hatchery. We next compared the sizes of forebrain structures between fish reared in an enriched NATURES hatchery and fish reared in a conventional hatchery. All fish were size-matched and from the same genetic cohort. We found that olfactory bulb and telencephalon volumes relative to body size were significantly larger in wild fish compared to hatchery-reared fish. However, we found no differences between fish reared in enriched and conventional hatchery treatments. Our results suggest that significant differences in the volume of the olfactory bulb and telencephalon between hatchery and wild-reared fish can occur within a single generation.     

Elevated incubation temperature improves later-life swimming endurance in juvenile Chinook salmon,Oncorhynchus tshawytscha

The effect of incubation and rearing temperature on muscle development and swimming endurance under a high-intensity swimming test was investigated in juvenile Chinook salmon (Oncorhynchus tshawytscha) in a hatchery experiment. After controlling for the effects of fork length (L_F) and parental identity, times to fatigue of fish were higher when fish were incubated or reared at warmer temperatures. Significant differences among combinations of pre- and post-emergence temperatures conformed to 15–15°C > 15–9°C > 9–9°C > 7–9°C > 7–7°C in 2011 when swimming tests were conducted at 300 accumulated temperature units post-emergence and 15–9°C > (7–9°C = 7–7°C) in 2012 when swimming tests were conducted at an L_F of c. 40 mm. The combination of pre- and post-emergence temperatures also affected the number and size of muscle fibres, with differences among temperature treatments in mean fibre cross-sectional area persisting after controlling for L_F and parental effects. Nonetheless, neither fibre number nor fibre size accounted for significant variation in swimming endurance. Thus, thermal carryover effects on swimming endurance were not mediated by thermal imprinting of muscle structure. This is the first study to test how temperature, body size and muscle structure interact to affect swimming endurance during early development in salmon.     

The complete sequence of the mitochondrial genome of the Chinook salmon, Oncorhynchus tshawytscha

The complete sequence of the mitochondrial genome of Chinook salmon, Oncorhynchus tshawytscha, has been determined. The circular genome consisting of 16,644 base pairs encodes thirteen proteins, the 12S and 16S ribosomal RNAs, and 22 transfer RNAs. These genes are ordered in the same way as most other vertebrates. The nucleotide and amino acid sequences of the ribosomal RNAs and the thirteen protein-coding genes were compared with those of other salmonids such as Oncorhynchus mykiss, Salmo salar, Salvelinus fontinalis, Salvelinus alpinus and Coregonus lavaretus. The sequence features of the control region (D-loop), the origin of L-strand replication and a putative peptide codified by the 16S mitochondrial RNA are described and discussed.     

Correlated contemporary evolution of life history traits in New Zealand Chinook salmon, Oncorhynchus tshawytscha

Size at age and age at maturity are important life history traits, affecting individual fitness and population demography. In salmon and other organisms, size and growth rate are commonly considered cues for maturation and thus age at maturity may or may not evolve independently of these features. Recent concerns surrounding the potential phenotypic and demographic responses of populations facing anthropogenic disturbances, such as climate change and harvest, place a premium on understanding the evolutionary genetic basis for evolution in size at age and age at maturity. In this study, we present the findings from a set of common-garden rearing experiments that empirically assess the heritable basis of phenotypic divergence in size at age and age at maturity in Chinook salmon (Oncorhynchus tshawytscha) populations introduced to New Zealand. We found consistent evidence of heritable differences among populations in both size at age and age at maturity, often corresponding to patterns observed in the wild. Populations diverged in size and growth profiles, even when accounting for eventual age at maturation. By contrast, most, but not all, cases of divergence in age at maturity were driven by the differences in size or growth rate rather than differences in the threshold relationship linking growth rate and probability of maturation. These findings help us understand how life histories may evolve through trait interactions in populations exposed to natural and anthropogenic disturbances, and how we might best detect such evolution.     

Dietary carotenoid levels affect carotenoid and retinoid allocation in female Chinook salmon Oncorhynchus tshawytscha

This study examined the effect of dietary carotenoid availability on carotenoid and retinoid concentrations in the flesh, plasma, skin and eggs of female Chinook salmon Oncorhynchus tshawytscha. Carotenoid concentrations in all tissues were closely related to dietary availability. Early in the breeding season, carotenoids were stored primarily in the muscle, with a flesh carotenoid concentration of 9·9 µg g^?1 in fish fed a high carotenoid diet compared with 1·9 µg g^?1 in fish fed a low carotenoid diet. During the breeding season, carotenoid reserves were mobilized predominantly to the eggs and also to the skin. By the end of the breeding season, carotenoid concentrations in the eggs were 17·9 µg g^?1 in fish fed a high carotenoid diet and 3·9 µg g^?1 in fish fed a low carotenoid diet. Conversely, egg retinoid concentrations were only c. 20% lower in fish fed a low v. high carotenoid diet, which suggests that retinoid concentrations were not limited by the availability of carotenoid precursors. Egg carotenoid concentrations were not correlated with either skin carotenoid concentration or colouration, which suggests that female carotenoid displays are not a reliable signal that males can use to evaluate egg carotenoid resources.     

Discovery,validation and characterization of 1039 cattle single nucleotide polymorphisms

We identified ～13 000 putative single nucleotide polymorphisms (SNPs) by comparison of repeat‐masked BAC‐end sequences from the cattle RPCI‐42 BAC library with whole‐genome shotgun contigs of cattle genome assembly Btau 1.0. Genotyping of a subset of these SNPs was performed on a panel containing 186 DNA samples from 18 cattle breeds including 43 trios. Of 1039 SNPs confirmed as polymorphic in the panel, 998 had minor allele frequency ≥0.25 among unrelated individuals of at least one breed. When Btau 4.0 became available, 974 of these validated SNPs were assigned in silico to known cattle chromosomes, while 41 SNPs were mapped to unassigned sequence scaffolds, yielding one SNP every ～3 Mbp on average. Twenty‐four SNPs identified in Btau 1.0 were not mapped to Btau 4.0. Of the 1015 SNPs mapped to Btau 4.0, 959 SNPs had nucleotide bases identical in Btau 4.0 and Btau 1.0 contigs, whereas 56 bases were changed, resulting in the loss of the in silico SNP in Btau 4.0. Because these 1039 SNPs were all directly confirmed by genotyping on the multi‐breed panel, it is likely that the original polymorphisms were correctly identified. The 1039 validated SNPs identified in this study represent a new and useful resource for genome‐wide association studies and applications in animal breeding.     

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.     

Recovery of barotrauma injuries in Chinook salmon, Oncorhynchus tshawytscha from exposure to pile driving sound

Juvenile Chinook salmon, Oncorhynchus tshawytscha, were exposed to simulated high intensity pile driving signals to evaluate their ability to recover from barotrauma injuries. Fish were exposed to one of two cumulative sound exposure levels for 960 pile strikes (217 or 210 dB re 1 μPa(2)·s SEL(cum); single strike sound exposure levels of 187 or 180 dB re 1 μPa(2)?s SEL(ss) respectively). This was followed by an immediate assessment of injuries, or assessment 2, 5, or 10 days post-exposure. There were no observed mortalities from the pile driving sound exposure. Fish exposed to 217 dB re 1 μPa(2)·s SEL(cum) displayed evidence of healing from injuries as post-exposure time increased. Fish exposed to 210 dB re 1 μPa(2)·s SEL(cum) sustained minimal injuries that were not significantly different from control fish at days 0, 2, and 10. The exposure to 210 dB re 1 μPa(2)·s SEL(cum) replicated the findings in a previous study that defined this level as the threshold for onset of injury. Furthermore, these data support the hypothesis that one or two Mild injuries resulting from pile driving exposure are unlikely to affect the survival of the exposed animals, at least in a laboratory environment.     

The disulfide bond pattern of salmon egg lectin 24K from the Chinook salmon Oncorhynchus tshawytscha

The disulfide bonds in the galactose-specific lectin SEL 24K from the egg of the Chinook salmon Oncorhynchus tshawytscha were determined by mass spectrometry. Four predictive in silico tools were used to determine the oxidation state of cysteines in the sequence and possible location of the disulfide bonds. A combination of tryptic digestion, HPLC separation, and chemical modifications were used to establish the location of seven disulfide bonds and one pair of free cysteines. After proteolysis, peptides containing one or two disulfide bonds were identified by reduction and mass spectral comparison. MALDI mass spectrometry was supported by chemical modification (iodoacetamide) and in silico digestion. The assignments of disulfide bonds were further confirmed by mass spectral fragmentation studies including in-source dissociation (ISD) and collision-induced dissociation (CID). The experimentally determined disulfide bonds and free Cys residues were only partially consistent with those generated by several automated public-domain algorithms.     

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.     

Environmental adaptation in Chinook salmon (Oncorhynchus tshawytscha) throughout their North American range

Landscape genomics is a rapidly growing field with recent advances in both genotyping efficiency and statistical analyses that provide insight towards local adaptation of populations under varying environmental and selective pressure. Chinook salmon (Oncorhynchus tshawytscha) are a broadly distributed Pacific salmon species, occupying a diversity of habitats throughout the northeastern Pacific with pronounced variation in environmental and climate features but little is understood regarding local adaptation in this species. We used a multivariate method, redundancy analysis (RDA), to identify polygenic correlations between 19 703 SNP loci and a suite of environmental variables in 46 collections of Chinook salmon (1956 total individuals) distributed throughout much of its North American range. Models in RDA were conducted on both rangewide and regional scales by hierarchical partitioning of the populations into three distinct genetic lineages. Our results indicate that between 5.8 and 21.8% of genomic variation can be accounted for by environmental features, and 566 putatively adaptive loci were identified as targets of environmental adaptation. The most influential drivers of adaptive divergence included precipitation in the driest quarter of the year (Rangewide and North Coastal Lineage, anova P = 0.002 and 0.01, respectively), precipitation in the wettest quarter of the year (Interior Columbia River Stream‐Type Lineage, anova P = 0.03), variation in mean diurnal range in temperature (South Coastal Lineage, anova P = 0.005), and migration distance (Rangewide, anova P = 0.001). Our results indicate that environmental features are strong drivers of adaptive genomic divergence in this species, and provide a foundation to investigate how Chinook salmon might respond to global environmental change.     

Juvenile Chinook salmon,Oncorhynchus tshawytscha,use of the Elwha river estuary prior to dam removal

The estuary of the Elwha River, on Washington’s Olympic Peninsula, has been degraded and simplified over the past century from sediment retention behind two large dams, levee construction, and channelization. With the removal of Elwha Dam and initiation of Glines Canyon Dam’s removal in fall 2011, sediment deposits will change the estuary and affect anadromous and nearshore marine fishes. Juvenile Chinook salmon commonly use estuaries and the river’s population is part of an Evolutionarily Significant Unit listed as Threatened under the U.S. Endangered Species Act. This study reports on monthly sampling in part of the river’s estuary from March 2007 through September 2011 to characterize the seasonal changes in relative abundance of yearlings and sub-yearlings, and size distributions prior to dam removal. Most (69 %) of the yearlings were caught in April, when this life history type was released from the hatchery, and to a lesser extent in May (28 %) and June (3 %). Yearlings caught in the estuary were smaller than those released from the hatchery (means: 153 mm?±?28 SD vs. 175 mm?±?5 SD), suggesting more rapid departure by larger fish. Sub-yearlings were much more abundant in the estuary, and were caught from March through November, increasing in mean fork length by 8.7 mm month^-1. The hatchery-origin sub-yearlings were not marked externally and so were not distinguishable from natural origin fish. However, 39 % of the sub-yearlings were caught prior to June, when sub-yearlings were released from the hatchery, indicating substantial use of the estuary by natural-origin fish. Thus, even in a reduced state after a century of dam operation, the highly modified estuary was used over many months by juvenile Chinook salmon. The information on juvenile Chinook salmon prior to dam removal provides a basis for comparison to patterns in the future, when the anticipated increase in estuarine complexity may further enhance habitat use by juvenile Chinook salmon.