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Data from: Population and individual identification of Coho Salmon in British Columbia through parentage-based tagging and genetic stock identification: an alternative to coded-wire tags
Beacham, Terry D.; Wallace, Colin G.; MacConnachie, Cathy; Jonsen, Kim; McIntosh, Brenda; Candy, John R.; Devlin, Robert H.; Withler, Ruth E.; Wallace, Colin — 2018-06-12 Parentage-based tagging (PBT) and genetic stock identification (GSI) were used to identify individual coho salmon (Oncorhynchus kisutch) to specific populations and brood years. In total, 20 242 individuals from 117 populations were genotyped at 304 single nucleotide polymorphisms (SNPs) via direct sequencing of amplicons. Coho salmon from 15 populations were assigned via parentage analysis that required the genotypes of both parents. The overall accuracy of assignment for 1939 coho salmon to the correct population was 100%, and to correct brood year within population was also 100%. Inclusion of individuals requiring only a single parental genotype for identification resulted in assignments of 2101 individuals, with an accuracy of 99.95% (2000–2001) to population and 100.0% to age. With 23 regions defined by the coded-wire tag (CWT) program, and individuals displaying an assignment probability <0.85 excluded from the analysis, mean regional assignment accuracy of individuals via GSI was 98.4% over all 23 regions. A PBT–GSI or PBT system of identification will provide an alternate method of identification in the assessment and management of Canadian-origin coho salmon relative to the existing CWT program.
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Data from: Predation, metabolic priming and early life-history rearing environment affect the swimming capabilities of growth hormone transgenic rainbow trout
Crossin, Glenn T.; Devlin, Robert H. — 2017-08-17 The period of first feeding, when young salmonid fishes emerge from natal stream beds, is one fraught with predation risk. Experiments conducted in semi-natural stream mesocosms have shown that growth hormone transgenic salmonids are at greater risk of predation than their non-transgenic siblings, due partly to the higher metabolic demands associated with transgenesis, which force risky foraging behaviours. This raises questions as to whether there are differences in the swim-performance of transgenic and non-transgenic fishes surviving predation experiments. We tested this hypothesis in wild-origin rainbow trout (Oncorhynchus mykiss) that were reared from first feeding in semi-natural stream mesocosms characterized by complex hydrodynamics, the presence of predators and oligotrophic conditions. Using an open-flume raceway, we swam fish and measured their capacity for burst-swimming against a sustained flow. We found a significant genotype effect on burst-performance, with transgenic fish sustaining performance longer than their wild-type siblings, both in predator and predator-free stream segments. Importantly, this effect occurred before differences in growth were discernable. We also found that mesocosm-reared fish had greater burst-performance than fish reared in the controlled hatchery environment, despite the latter being unexposed to predators and having abundant food. Our results suggest a potential interaction between predation and metabolic priming, which leads to greater burst capacity in transgenic trout.
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Data from: Red and white Chinook salmon: genetic divergence and mate choice
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Lehnert, Sarah J.; Pitcher, Trevor E.; Devlin, Robert H.; Heath, Daniel D. — 2016-01-25 Chinook salmon (Oncorhynchus tshawytscha) exhibit extreme differences in coloration of skin, eggs and flesh due to genetic polymorphisms affecting carotenoid deposition, where colour can range from white to bright red. A sympatric population of red and white Chinook salmon occurs in the Quesnel River, British Columbia, where frequencies of each phenotype are relatively equal. In our study, we examined evolutionary mechanisms responsible for the maintenance of the morphs, where we first tested whether morphs were reproductively isolated using microsatellite genotyping, and second, using breeding trials in seminatural spawning channels, we tested whether colour assortative mate choice could be operating to maintain the polymorphism in nature. Next, given extreme difference in carotenoid assimilation and the importance of carotenoids to immune function, we examined mate choice and selection between colour morphs at immune genes (major histocompatibility complex genes: MHC I-A1 and MHC II-B1). In our study, red and white individuals were found to interbreed, and under seminatural conditions, some degree of colour assortative mate choice (71% of matings) was observed. We found significant genetic differences at both MHC genes between morphs, but no evidence of MHC II-B1-based mate choice. White individuals were more heterozygous at MHC II-B1 compared with red individuals, and morphs showed significant allele frequency differences at MHC I-A1. Although colour assortative mate choice is likely not a primary mechanism maintaining the polymorphisms in the population, our results suggest that selection is operating differentially at immune genes in red and white Chinook salmon, possibly due to differences in carotenoid utilization.
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Data from: Redder isn’t always better: cost of carotenoids in Chinook salmon eggs
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Lehnert, Sarah J.; Devlin, Robert H.; Pitcher, Trevor E.; Semeniuk, Christina A.D.; Heath, Daniel D. — 2016-11-30 Carotenoids provide animals with many fitness benefits through increased mating success, immune function, gamete quality, and antioxidant capacity. Despite these benefits, carotenoids are not utilized equally by all animals, implying trade-offs associated with the pigments; although, few studies have quantified fitness costs of carotenoid pigmentation. Salmon are known for their conspicuous red coloration; however, amongst Chinook salmon (Oncorhynchus tshawytscha), a natural genetic color polymorphism exists (red and white morphs) which results in carotenoid-based color differences in eggs and other tissues. Although the fitness benefit of egg carotenoid content on egg incubation survival has been demonstrated, carotenoid pigmentation also results in highly visible eggs vulnerable to predation. Therefore, although white Chinook salmon eggs experience costs in terms of viability, a potential benefit in terms of reduced predation could help explain the maintenance of the polymorphism. Here, using red and white eggs from wild Chinook salmon, we show that increased carotenoid content of salmon eggs leads to greater predation risk. We found that 2 populations of wild-type rainbow trout (O. mykiss; an ecologically relevant predator) showed a significant bias for red eggs over white eggs under choice experiments, where red eggs were consumed first twice as often and significantly faster than white eggs. Our study suggests that trade-offs between red and white Chinook salmon during the egg stage provide an evolutionary mechanism promoting the maintenance of the unique Chinook salmon color polymorphism in nature, while also, for the first time, demonstrating a direct fitness cost of carotenoids in salmon.
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Data from: Significant differences in maternal carotenoid provisioning and effects on offspring fitness in Chinook salmon colour morphs
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Lehnert, Sarah J.; Garver, Kyle A.; Richard, Jon; Devlin, Robert H.; Lajoie, Celine; Pitcher, Trevor E.; Heath, Daniel D. — 2018-10-02 In oviparous species, maternal carotenoid provisioning can deliver diverse fitness benefits to offspring via increased survival, growth, and immune function. Despite demonstrated advantages of carotenoids, large intra‐ and interspecific variation in carotenoid utilization exists, suggesting trade‐offs associated with carotenoids. In Chinook salmon (Oncorhynchus tshawytscha), extreme variation in carotenoid utilization delineates two colour morphs (red and white) that differ genetically in their ability to deposit carotenoids into tissues. Here, we take advantage of this natural variation to examine how large differences in maternal carotenoid provisioning influence offspring fitness. Using a full‐factorial breeding design crossing morphs and common‐garden rearing, we measured differences in a suite of fitness‐related traits, including survival, growth, viral susceptibility, and host response, in offspring of red (carotenoid‐rich eggs) and white (carotenoid‐poor eggs) females. Eggs of red females had significantly higher carotenoid content than those of white females (6X more); however, this did not translate into measurable differences in offspring fitness. Given that white Chinook salmon may have evolved to counteract their maternal carotenoid deficiency, we also examined the relationship between egg carotenoid content and offspring fitness within each morph separately. Egg carotenoids only had a positive effect within the red morph on survival to eyed‐egg (earliest measured trait), but not within the white morph. While previous work shows that white females benefit from reduced egg predation, our study also supports a hypothesis that white Chinook salmon have evolved additional mechanisms to improve egg survival despite low carotenoids, providing novel insight into evolutionary mechanisms that maintain this stable polymorphism.
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Data from: Influence of a growth hormone transgene on the genetic architecture of growth-related traits: a comparative analysis between transgenic and wild-type coho salmon
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Kodama, Miyako; Naish, Kerry A.; Devlin, Robert H. — 2018-08-08 Genetic engineering has been increasingly applied to many commercially important plant and animal species, generating phenotypic changes that are not observed in natural populations and creating genetic interactions that have not experienced natural selection. The degree to and way in which such human-induced genetic variation interacts with the rest of the genome is currently largely unknown. Integrating such information into ecological and risk assessment frameworks is crucial to understand the potential effects of genetically modified organisms in natural environments. Here, we performed QTL mapping to investigate the genetic architecture of growth-related traits in non-transgenic (NT) and growth hormone transgenic (T) coho salmon with large changes in growth and related physiology, with the aim of identifying how an inserted transgene might influence the opportunity for selection. These fish shared the same parental genetic background, thus allowing us to determine whether the same or different loci influence these traits within the two groups. The use of over 1700 loci, derived from Restriction site Associated DNA Sequencing, revealed that different genomic regions were linked with growth over time between the two groups. Additionally, the effect sizes of detected QTL appear to have been influenced by the transgene. Direct comparison of QTL between the T and NT fish during two size-matched periods identified little overlap in their location. Taken together, the results showed that the transgene altered the genetic basis of growth-related traits in this species. The study has important implications for effective conservation and management of wild populations experiencing introduction of transgenes. Evolutionary changes and their ecological consequences may occur at different rates and in different directions in NT versus T individuals in response to selection. Thus assessments of phenotypic change, and hence ecological risk, should be determined periodically to evaluate whether initial estimates made with founder strains remain valid.

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(Author: Devlin, Robert H.)

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