BackgroundPacific salmon (Oncorhynchus spp.) serve as good biological indicators of the breadth of climate warming effects on fish because their anadromous life cycle exposes them to environmental challenges in both marine and freshwater environments. Our study sought to mine the extensive functional genomic studies in fishes to identify robust thermally-responsive biomarkers that could monitor molecular physiological signatures of chronic thermal stress in fish using non-lethal sampling of gill tissue.ResultsCandidate thermal stress biomarkers for gill tissue were identified using comparisons among microarray datasets produced in the Molecular Genetics Laboratory, Pacific Biological Station, Nanaimo, BC, six external, published microarray studies on chronic and acute temperature stress in salmon, and a comparison of significant genes across published studies in multiple fishes using deep literature mining. Eighty-two microarray features related to 39 unique gene IDs were selected as candidate chronic thermal stress biomarkers. Most of these genes were identified both in the meta-analysis of salmon microarray data and in the literature mining for thermal stress markers in salmonids and other fishes. Quantitative reverse transcription PCR (qRT-PCR) assays for 32 unique genes with good efficiencies across salmon species were developed, and their activity in response to thermally challenged sockeye salmon (O. nerka) and Chinook salmon (O. tshawytscha) (cool, 13–14 °C and warm temperatures 18–19 °C) over 5–7 days was assessed. Eight genes, including two transcripts of each SERPINH1 and HSP90AA1, FKBP10, MAP3K14, SFRS2, and EEF2 showed strong and robust chronic temperature stress response consistently in the discovery analysis and both sockeye and Chinook salmon validation studies.ConclusionsThe results of both discovery analysis and gene expression showed that a panel of genes involved in chaperoning and protein rescue, oxidative stress, and protein biosynthesis were differentially activated in gill tissue of Pacific salmon in response to elevated temperatures. While individually, some of these biomarkers may also respond to other stressors or biological processes, when expressed in concert, we argue that a biomarker panel comprised of some or all of these genes could provide a reliable means to specifically detect thermal stress in field-caught salmon.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5108-9) contains supplementary material, which is available to authorized users.

An organism's ability to respond effectively to environmental change is critical to its survival. Yet, life stage and overall condition can dictate tolerance thresholds to heightened environmental stressors, such that stress may not be equally felt across individuals and at all times. Also, the transcriptional responses induced by environmental changes can reflect both generalized responses as well as others that are highly specific to the type of change being experienced. Thus, if transcriptional biomarkers specific to a stressor, even under multi-stressor conditions, can be identified, the biomarkers could then be applied in natural environments to determine when and where an individual experiences such a stressor. Here, we experimentally challenged juvenile Chinook salmon ( Oncorhynchus tshawytscha ) to validate candidate gill gene expression biomarkers. A sophisticated experimental design manipulated salinity (freshwater, brackish water and seawater), temperature (10, 14 and 18°C) and dissolved oxygen (normoxia and hypoxia) in all 18 possible combinations for 6 days using separate trials for three smolt statuses (pre-smolt, smolt and de-smolt). In addition, changes in juvenile behaviour, plasma variables, gill Na + /K + -ATPase activity, body size, body morphology and skin pigmentation supplemented the gene expression responses. We identified biomarkers specific to salinity and temperature that transcended the multiple stressors, smolt status and mortality (live, dead and moribund). Similar biomarkers for dissolved oxygen were not identified. This work demonstrates the unique power of gene expression biomarkers to identify a specific stressor even under multi-stressor conditions, and we discuss our next steps for hypoxia biomarkers using an RNA-seq study.

Theory predicts that hybrid fitness should decrease as population divergence increases. This suggests that the effects of human-induced hybridization might be adequately predicted from the known divergence among parental populations. We tested this prediction by quantifying trait differentiation between multigenerational crosses of farmed Atlantic salmon (Salmo salar) and divergent wild populations from the Northwest Atlantic; the former escape repeatedly into the wild, while the latter are severely depleted. Under common environmental conditions and at the spatiotemporal scale considered (340 km, 12 000 years of divergence), substantial cross differentiation had a largely additive genetic basis at behavioral, life history, and morphological traits. Wild backcrossing did not completely restore hybrid trait distributions to presumably more optimal wild states. Consistent with theory, the degree to which hybrids deviated in absolute terms from their parental populations increased with increasing parental divergence (i.e., the collective environmental and life history differentiation, genetic divergence, and geographic distance between parents). Nevertheless, while these differences were predictable, their implications for risk assessment were not: wild populations that were equally divergent from farmed salmon in the total amount of divergence differed in the specific traits at which this divergence occurred. Combined with ecological data on the rate of farmed escapes and wild population trends, we thus suggest that the greatest utility of hybridization data for risk assessment may be through their incorporation into demographic modeling of the short- and long-term consequences to wild population persistence. In this regard, our work demonstrates that detailed hybridization data are essential to account for life-stage-specific changes in phenotype or fitness within divergent but interrelated groups of wild populations. The approach employed here will be relevant to risk assessments in a range of wild species where hybridization with domesticated relatives is a concern, especially where the conservation status of the wild species may preclude direct fitness comparisons in the wild.

Cultured organisms undergo genetically-based behavioural changes that may reduce their ability to survive in the wild. This has raised concerns that interbreeding between escaped cultured and wild organisms will generate hybrids exhibiting maladaptive behaviours which may ultimately reduce the fitness of the wild counterpart. We compared anti-predator responses in Atlantic salmon (Salmo salar) from two wild North American populations, the major farmed strain used in regional aquaculture, and their wild-farmed hybrids (F 1 , F 2 , and wild backcross). Anti-predator responses of fry (age 0? parr) were measured under common environmental conditions, using a model of a natural predator (belted kingfisher, Ceryle alcyon). Farmed fry exhibited significantly reduced antipredator responses relative to fry from both wild populations. The anti-predator responses of wild-farmed hybrid fry were intermediate to those of the parental populations (pure farmed or wild). The magnitude by which wildfarmed hybrids differed in anti-predator responses from pure wild fish also depended on the wild population. These results suggest that: (1) the observed behavioural differences have a genetic basis; (2) wild-farmed hybrids have, on average, reduced anti-predator responses relative to wild fish; and that (3) the effects of wild-farmed interbreeding on anti-predator responses will differ between wild populations. Our study is consistent with the general hypothesis that continual farmed-wild interbreeding may have detrimental effects on the fitness of wild organisms.

Only a quarter of reintroduction programs succeed in restoring a self-sustaining population of an extirpated species. Optimal source population selection for restoration efforts can increase the fitness of translocated individuals and improve reintroduction success. Here, we describe the support for two strategies for selecting source populations: pre-existing adaptation and adaptive potential. The pre-existing adaptation strategy focuses on source populations with a high frequency of genotypes that confer adaptations, and within this strategy we detail the ancestry matching approach and environment matching approach. The adaptive potential strategy focuses on source populations with high heritable genetic variation that confer the potential to adapt, and within this strategy we detail the single source population approach and multiple source population approach. We review empirical tests of the different approaches, and find stronger support for the pre-existing adaptation strategy than the adaptive potential strategy. We provide a framework for source population selection based on the two strategies, highlighting the importance of gathering information on key environment features in the source and restoration locations, as well as detail the knowledge gaps. Filling these knowledge gaps is important for validating and potentially revising our proposed framework, and ultimately improving the success rate of restoring extirpated populations.

Competitive interactions with non-native species can have negative impacts on the conservation of native species, resulting in chronic stress and reduced survival. Here, juvenile Atlantic salmon (Salmo salar) from two allopatric populations (Sebago and LaHave) that are being used for reintroduction into Lake Ontario were placed into semi-natural stream tanks with four non-native salmonid competitors that are established in Ontario streams: brown trout (S. trutta), rainbow trout (Oncorhynchus mykiss), Chinook salmon (O. tshawytscha) and coho salmon (O. kisutch). Brown trout and rainbow trout reduced the survival and fitness-related traits of Atlantic salmon, whereas Chinook salmon and coho salmon had no impact on these traits. These data support theories on ecological niche overlap and link differences in observed aggression levels with competitive outcomes. Measurements of circulating hormones indicated that the Atlantic salmon were not chronically stressed nor had a change in social status at the 10-month time point in the semi-natural stream tanks. Additionally, the Sebago population was better able to coexist with the non-native salmonids than the LaHave population. Certain populations of Atlantic salmon may thus be more suitable for some environments of the juvenile stream phase for the reintroduction into Lake Ontario.

Conservation biologists routinely face the dilemma of keeping small, fragmented populations isolated, wherein inbreeding depression may ensue, or mixing such populations, which may exacerbate population declines via outbreeding depression. The joint evaluation of inbreeding and outbreeding risks in the wild cannot be readily conducted in endangered species, so a suggested ‘safe’ strategy is to mix ecologically and genetically similar populations. To evaluate this strategy, we carried out a reciprocal transplant experiment involving three neighboring populations of endangered Atlantic salmon (Salmo salar) now bred in captivity and maintained in captive and wild environments. Pure, inbred, and outbred (first and second generation) cross types were released and recaptured in the wild to simultaneously test for local adaptation, inbreeding depression, and outbreeding depression. We found little evidence of inbreeding depression after one generation of inbreeding and little evidence of either heterosis or outbreeding depression via genetic incompatibilities after one or two generations of outbreeding. A trend for outbreeding depression via the loss of local adaptation was documented in one of three populations. The effects of inbreeding were not significantly different from the effects of outbreeding. Hence, at the geographic scale evaluated (34–50 km), inbreeding for one generation and outbreeding over two generations may have similar effects on the persistence of small populations. The results further suggested that outbreeding outcomes may be highly variable or unpredictable at small genetic distances. Our work highlights the necessity of evaluating the relative costs of inbreeding and outbreeding in the conservation and management of endangered species on a case-by-case basis.

Houde, A. S., Fraser, D. J., and Hutchings, J. A. 2010. Fitness-related consequences of competitive interactions between farmed and wild Atlantic salmon at different proportional representations of wild–farmed hybrids. – ICES Journal of Marine Science, 67: 657–667. Escaped farmed fish possess heritable characteristics that may give them and their wild–farmed hybrid offspring a competitive advantage over wild fish. Limited research has examined whether the results of wild vs. farmed pairwise behavioural contests can predict the change in fitness-related traits of wild fish when exposed to wild–farmed hybrids, or to different proportions of such hybrids, within stream environments. Pairwise aggression tests on North American Atlantic salmon (Salmo salar) revealed that regional farmed salmon and wild–farmed hybrids (F1, F2, and wild backcrosses) were more competitive than wild fish from two divergent populations. The ranking by which hybrids differed in competitive ability from wild fish also depended on the wild population. However, the magnitude of change in fitness-related traits of wild fish, such as mortality, size, and condition, from the same two populations could not be predicted from pairwise test results when replicate groups of wild fish were exposed to different proportions of hybrids (wild:hybrid ratios of 50:50, 70:30, and 85:15) in semi-natural stream environments. Notably, there was greater mortality of both wild and hybrid fish in treatments containing 30% hybrids for both populations; at a composition of 50% hybrids, the mortality of wild fish in one population increased more than it did in the other. The results suggest that for the life stage examined and provided the rate of farmed intrusion and wild–farmed interbreeding remains low (i.e. ≤15% hybrids), the effects of competitive interaction with their farmed counterparts may have comparatively little effect on the mortality of wild populations.