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Chronic exposure to high temperatures may leave freshwater fishes vulnerable to opportunistic pathogens, particularly during early life stages. Lake sturgeon, Acipenser fulvescens, populations within the northern expanse of their range in Manitoba, Canada, may be susceptible to high temperature stress and pathogenic infection. We acclimated developing lake sturgeon for 22 days to two ecologically relevant, summer temperatures (16 and 20°C). Individuals from both acclimation treatments were then exposed to 0, 30 and 60 µg ml−1 bacterial lipopolysaccharides (endotoxins), as an immune stimulus, for 48 h and sampled 4 and 48 h during trial exposures and following a 7 day recovery period. We then measured whole-body transcriptional (mRNA) responses involved in the innate immune, stress and fatty acid responses following acute exposure to the bacterial endotoxins. Data revealed that overall levels of mRNA transcript abundance were higher in 20°C-reared sturgeon under control conditions. However, following exposure to a bacterial stimulus, lake sturgeon acclimated to 16°C produced a more robust and persistent transcriptional response with higher mRNA transcript abundance across innate immune, stress and fatty acid responses than their 20°C-acclimated counterparts. Additional whole-animal performance metrics (critical thermal maximum, metabolic rate, cortisol concentration and whole-body and mucosal lysozyme activity) demonstrated acclimation-specific responses, indicating compromised metabolic, stress and enzymatic capacity following the initiation of immune-related responses. Our study showed that acclimation to 20°C during early development impaired the immune capacity of developing lake sturgeon as well as the activation of molecular pathways involved in the immune, stress and fatty acid responses. The present study highlights the effects of ecologically relevant, chronic thermal stress on seasonal pathogen susceptibility in this endangered species.

Rising mean and variance in temperatures elevate threats to endangered freshwater species such as lake sturgeon,Acipenser fulvescens. Previous research demonstrated that higher temperatures during development result in physiological consequences for lake sturgeon populations throughout Manitoba, Canada, with alteration of metabolic rate, thermal tolerance, transcriptional responses, growth, and mortality. We acclimated lake sturgeon (30 – 60 days post fertilization, a period of high mortality) from northern and southern populations (56° 02′ 46.5″ N, 96° 54′ 18.6″ W and 50° 17′ 52″ N, 95° 32′ 51″ W respectively, separated by approximately 650 km) within Manitoba to current (summer highs of 20-23°C) and future projected (+2-3°C) environmental temperatures of 16, 20, and 24°C for 30 days, and measured gill transcriptional responses using RNAseq. Transcripts revealed SNPs consistent with genetically distinct populations and transcriptional responses altered by acclimation temperature. There were a higher number of differentially expressed transcripts observed in the southern, compared to the northern, population as temperatures increased, indicating enhanced transcriptional plasticity. Both lake sturgeon populations responded to elevated acclimation temperatures by downregulating the transcription of genes involved in protein synthesis and energy production. Further, there were population-specific thresholds for the downregulation of processes promoting transcriptional plasticity as well as mitochondrial function as the northern population showed decreases at 20°C, while this capacity was not diminished until 24°C in the southern population. These transcriptional responses highlight the molecular impacts of increasing temperatures for divergent lake sturgeon populations during vulnerable developmental periods and the critical influence of transcriptome plasticity on acclimation capacity.

Municipal wastewater is a large source of pollution to Canadian waters, yet its effects on Arctic marine ecosystems remains relatively unknown. We characterized the impacts of municipal wastewater from a growing northern community, Iqaluit, Nunavut, on the Arctic truncate soft-shell clam, Mya truncata. Clams were sampled from six locations that varied in proximity to the wastewater treatment plant, and shell biogeochemical analysis revealed that clams nearest the wastewater treatment plant had slower growth rates, lower carbon and oxygen stable isotope ratios, and elevated concentrations of copper and lead. A parallel analysis on mRNA expression profiles characterized M. truncata’s physiological response to wastewater effluent. Clams nearest the wastewater treatment plant had significantly lower mRNA expression of genes associated with metabolism, antioxidants, molecular chaperones, and phase I and II detoxification, but had heightened mRNA expression in genes coding for enzymes that bind and remove contaminants. These results demonstrated a biological response to Iqaluit’s wastewater effluent and highlight M. truncata’s potential to act as a biomonitor of municipal wastewater along Arctic coastlines in Canada.

Effective management of freshwater fish habitat is essential to supporting healthy aquatic ecosystems and sustainable fisheries. In Canada, recent changes to the Fisheries Act enhanced the protection of fish habitat, but application of those provisions relies on sound scientific evidence. We employed collaborative research prioritization methods to identify scientific research questions that, if addressed, would significantly advance the management of freshwater fish habitat in Canada. This list was generated by a diverse group of freshwater fish experts, including substantial contributions from practitioners who administer provisions of the Fisheries Act. The research questions generated in this study identify priority topics for future research, while highlighting issues that could be addressed with different funding models. As a result, this study should support evidence-based management of Canada’s aquatic resources by identifying scientific knowledge gaps faced by practitioners, and suggesting mechanisms to address them. Given the important contribution of Canadian freshwater systems to global ecosystem values, and the similar scientific challenges facing fish habitat managers in other jurisdictions, this study is likely to have broad applicability.

In Manitoba, Canada, wild lake sturgeon (Acipenser fulvescens) populations exist along a latitudinal gradient and are reared in hatcheries to bolster threatened populations. We reared two populations of lake sturgeon, one from each of the northern and southern ends of Manitoba and examined the effects of typical hatchery temperatures (16°C) as well as 60-day acclimation to elevated rearing temperatures (20°C) on mortality, growth and condition throughout early development. Additionally, we examined the cold shock response, which may be induced during stocking, through the hepatic mRNA expression of genes involved in the response to cold stress and homeoviscous adaptation (HSP70, HSP90a, HSP90b, CIRP and SCD). Sturgeon were sampled after 1 day and 1 week following stocking into temperatures of 8, 6 and 4°C in a controlled laboratory environment. The southern population showed lower condition and higher mortality during early life than the northern population while increased rearing temperature impacted the growth and condition of developing northern sturgeon. During the cold shock, HSP70 and HSP90a mRNA expression increased in all sturgeon treatments as stocking temperature decreased, with higher expression observed in the southern population. Expression of HSP90b, CIRP and SCD increased as stocking temperature decreased in northern sturgeon with early acclimation to 20°C. Correlation analyses indicated the strongest molecular relationships were in the expression of HSP90b, CIRP and SCD, across all treatments, with a correlation between HSP90b and body condition in northern sturgeon with early acclimation to 20°C. Together, these observations highlight the importance of population and rearing environment throughout early development and on later cellular responses induced by cold stocking temperatures.

The invasive rainbow smelt (Osmerus mordax) was an abundant food source for Lake Winnipeg walleye (Sander vitreus), especially in the north basin of the lake, until the smelt’s collapse in approximately 2013. We quantified changing length-at-age (≈ growth rates) and relative mass (≈ body condition) in Lake Winnipeg walleye caught for a gillnet index data set. Here, walleye showed smaller length-at-age, particularly young fish in the north basin, over time. This approach to assessing growth suggests a constraint in the north basin fish, possibly a nutritional limitation between 2017 and 2018, that was not present in the south. We then analyzed a separate group of walleye (≥452 mm in fork length) sampled in 2017 as part of a large-scale tracking study, which had a similar slope in length-mass relationship to large walleye caught in that year for the gillnet index data. A panel of metabolites in whole blood samples associated with amino acid metabolism and protein turnover was compared. These metabolites revealed elevated essential amino acids in fish caught in the Dauphin River, and suggest that protein degradation may be elevated in north basin walleye. Therefore, based on both growth estimates and metabolites associated with protein balance, we suggest there were spatially distinct separations affecting Lake Winnipeg walleye with decreased nutritional status of walleye in the north basin of Lake Winnipeg being of particular concern.

Transcriptomics provides a mechanistic understanding of an organism’s response to environmental challenges such as increasing temperatures, which can provide key insights into the threats posed by thermal challenges associated with urbanization and climate change. Differential gene expression and alternative splicing are two elements of the transcriptomic stress response that may work in tandem, but relatively few studies have investigated these interactions in fishes of conservation concern. We studied the imperilled redside dace (Clinostomus elongatus) as thermal stress is hypothesised to be an important cause of population declines. We tested the hypothesis that gene expression-splicing interactions contribute to the thermal stress response. Wild fish exposed to acute thermal stress were compared with both handling controls and fish sampled directly from a river. Liver tissue was sampled to study the transcriptomic stress response. Thermally stressed fish showed a prominent transcriptional response (estimated with mRNA transcript abundance) related to transcription regulation and responses to unfolded proteins, and prominent alternatively spliced genes related to gene expression regulation and metabolism. One splicing factor, prpf38b, was upregulated in the thermally stressed group compared to the other treatments. This splicing factor may have a role in the Jun/AP-1 cellular stress response, a pathway with wide-ranging and context-dependent effects. Given large gene interaction networks and the context-dependent nature of transcriptional responses, our results highlight the importance of understanding interactions between gene expression and splicing for understanding transcriptomic responses to thermal stress. Our results also reveal transcriptional pathways that can inform conservation breeding, translocation, and reintroduction programs for redside dace and other imperilled species by identifying appropriate source populations.SUMMARY STATEMENTGene expression and alternative splicing interact in response to thermal stress in an imperilled fish, with implications for conservation and mechanisms of thermal tolerance in vertebrate ectotherms.

Despite the promising applications of genome-wide information to conservation, the field of conservation genomics remains hindered by a research-practice gap. Identifying the benefits from genomics in relation to fish conservation planning and decision-making could contribute to bridging this gap. The goals of our study were twofold. First, we reviewed the fish conservation genomic literature to determine how genomic information has been used to inform conservation decision making; and second, we examined how genomic information can be linked to an existing conservation decision framework. Our review showed that, as fish conservation genomics studies accumulate over time, collaborations between researchers and conservation practitioners are becoming increasingly frequent. While the field is dominated by studies of economically important families (e.g. salmonids, acipenserids) in first-world countries (North America, Europe), it has a broad taxonomic coverage where species of both local and global conservation concern are well represented. We also show that genomic information can readily be harnessed to guide decisions within existing conservation decision frameworks, from the conceptualization (identification of conservation targets and threats) to the implementation and the monitoring of conservation actions. In addition, our review identifies some limitations related to genomic inferences for conservation and proposes solutions to address these uncertainties and improve communication between conservation genomic scientists and practitioners. For genomic researchers, we outline how conservation decisions are made; for practitioners, we illustrate how genomic information can inform decision-making.

Blood sampling through the caudal vasculature is a widely used technique in fish biology for investigating organismal health and physiology. In live fishes, it can provide a quick, easy and relatively non-invasive method for obtaining a blood sample (cf. cannulation and cardiac puncture). Here, a general set of recommendations are provided for optimizing the blood sampling protocol that reflects best practices in animal welfare and sample integrity. This includes selecting appropriate use of anaesthetics for blood sampling as well as restraint techniques for situations where sedation is not used. In addition, ideal sampling environments where the fish can freely ventilate and strategies for minimizing handling time are discussed. This study summarizes the techniques used for extracting blood from the caudal vasculature in live fishes, highlighting the phlebotomy itself, the timing of sampling events and acceptable blood sample volumes. This study further discuss considerations for selecting appropriate physiological metrics when sampling in the caudal region and the potential benefits that this technique provides with respect to long-term biological assessments. Although general guidelines for blood sampling are provided here, it should be recognized that contextual considerations (e.g., taxonomic diversity, legal matters, environmental constraints) may influence the approach to blood sampling. Overall, it can be concluded that when done properly, blood sampling live fishes through the caudal vasculature is quick, efficient and minimally invasive, thus promoting conditions where live release of focal animals is possible.

Multiple stressors are commonly encountered by wild animals, but their cumulative effects are poorly understood, especially regarding infection development. We conducted a holding study with repeated gill and blood sampling to characterize the effects of cumulative stressors on infection development in adult coho salmon. Treatments included chronic thermal stress (15°C vs. 10°C) and acute gill net entanglement with an air exposure (simulating fisheries bycatch release). The potential loadings of 35 infectious agents and the expression of 17 host immune genes were quantified using high-throughput quantitative polymerase chain reaction, while host physiology was characterized with chemical analysis of blood. Temporal increases in infectious agent richness and loads were concurrent with decreased expression of immune genes in fish sampled in the river. In the laboratory, mortality was minimal in cool water regardless of fishery treatment ( 1 wk) and enhanced mortality associated with handling and biopsy (∼40% both sexes). Experimental gillnetting at high temperature further enhanced female mortality (73%). Fish held at high temperature demonstrated heavier infectious agent loads, osmoregulatory impairment, suppressed female maturation, and upregulation of inflammatory and extracellular immune genes. At high temperature, heavy Parvicapsula minibicornis loads were associated with premature mortality. Females exhibited physiological impairment from both stressors after 1 wk, and infection burdens correlated poorly with immune gene regulation compared with males. Cumulative effects of multiple stressors on female mortality are likely a function of physiological impairment and enhanced infections at high temperature.

In estuary and coastal systems, human demand for freshwater, climate change‐driven precipitation variability, and extreme weather impact salinity levels, reducing connectivity between mesohaline coastal fish populations and potentially contributing to genomic divergence. We examined gill transcriptome responses to salinity in wild‐caught juveniles from two populations of Sacramento splittail (Pogonichthys macrolepidotus), a species of conservation concern that is endemic to the San Francisco Estuary, USA, and the lower reaches of its tributaries. Recent extreme droughts have led to salinities above the tolerance limits for this species, creating a migration barrier between these populations, which potentially contributed to population divergence. We identified transcripts involved in a conserved response to salinity; however, the more salinity‐tolerant San Pablo population had greater transcriptome plasticity (3.6‐fold more transcripts responded than the Central Valley population) and a response consistent with gill remodeling after 168 hr of exposure to elevated salinity. The reorganization of the gill in response to changing osmotic gradients is a process critical for acclimation and would facilitate enhanced salinity tolerance. We detected an upregulation of receptors that control the Wnt (wingless‐type) cell signaling pathway that may be required for an adaptive response to increases in salinity, patterns not observed in the relatively salinity‐sensitive Central Valley population. We detected 62 single nucleotide polymorphisms (SNPs) in coding regions of 26 transcripts that differed between the populations. Eight transcripts that contained SNPs were associated with immune responses, highlighting the importance of diversity in immune gene sequences as a defining characteristic of genomic divergence between these populations. Our data demonstrate that these populations have divergent transcriptomic responses to salinity, which is consistent with observed physiological differences in salinity tolerance.

Background Messenger RNA sequencing is becoming more common in studies of non-model species and is most often used for gene expression-based investigations. However, the method holds potential for numerous other applications as well—including analyses of alternative splicing, population structure, and signatures of selection. To maximize the utility of mRNA data sets, distinct analyses may be combined such as by exploring dynamics between gene expression with signatures of selection in the context of population structure. Here, we compare two published data sets describing two populations of a minnow species endemic to the San Francisco Estuary (Sacramento splittail, Pogonichthys macrolepidotus): a microsatellite data set showing population structure, and an mRNA whole transcriptome data set obtained after the two populations were exposed to a salinity challenge. We compared measures of population structure and genetic variation using single nucleotide polymorphisms (SNPs) called from mRNA from the whole transcriptome sequencing study with those patterns determined from microsatellites. For investigating plasticity and evolution, intra- and inter-population transcriptome plasticity was investigated with differential gene expression, differential exon usage, and gene expression variation. Outlier SNP analysis was also performed on the mRNA data set and signatures of selection and phenotypic plasticity were investigated on an individual-gene basis. Results We found that mRNA sequencing revealed patterns of population structure consistent with those found with microsatellites, but with lower magnitudes of genetic variation and population differentiation consistent with widespread purifying selection expected when using mRNA. In addition, within individual genes, phenotypic plasticity or signatures of selection were found in almost mutual exclusion (except heatr6, nfu1, slc22a6, sya, and mmp13). Conclusions These results show that an mRNA sequencing data set may have multiple uses, including describing population structure and for investigating the mechanistic interplay of evolution and plasticity in adaptation. MRNA sequencing thus complements traditional sequencing methods used for population genetics, in addition to its utility for describing phenotypic plasticity.

Municipal wastewater is a large source of pollution to Canadian waters, yet its effects on Arctic marine ecosystems remains relatively unknown. We characterized the impacts of municipal wastewater from a growing northern community, Iqaluit, Nunavut on the Arctic truncate soft-shell clam, Mya truncata. Clams were sampled from six locations that varied in proximity to the wastewater treatment plant and shell biogeochemical analysis revealed that clams nearest the wastewater treatment plant had slower growth rates, lower carbon and oxygen stable isotope ratios, and elevated concentrations of copper and lead. A parallel analysis on mRNA expression profiles characterized M. truncata’s physiological response to wastewater effluent. Clams nearest the wastewater treatment plant had significantly lower mRNA expression of genes associated with metabolism, antioxidants, molecular chaperones, and phase I and II detoxification, but had heightened mRNA expression in genes coding for enzymes that bind and remove contaminants. These results demonstrated a biological response to Iqaluit’s wastewater effluent and highlight M. truncata’s potential to act as a biomonitor of municipal wastewater along Canadian Arctic coastlines.

Brook trout (Salvelinus fontinalis) populations are at risk of exposure to high water temperatures in the species’ native range in eastern North America. We quantified the physiological and molecular responses of juvenile brook trout to six acclimation temperatures that span the thermal distribution of the species (5, 10, 15, 20, 23, and 25°C). Using quantitative PCR (qPCR), we measured the mRNA transcript abundance of temperature-induced cellular stress genes to identify a potential sub-lethal temperature threshold for brook trout between 20–23°C. Brook trout exhibited an upregulation of stress-related genes (heat shock protein 90-beta;heat shock cognate 71 kDa protein;glutathione peroxidase 1) and a downregulation of transcription factors and osmoregulation-related genes (Na+/K+/2Cl−co-transporter-1-a;nuclear protein 1) at temperatures ≥20°C. We also used respirometry to assess the effects of the acclimation temperatures on oxygen consumption. Standard metabolic rate results indicated that energy expenditure was higher at temperatures ≥20°C. We then examined the effects of acclimation temperature on metabolic rate and blood plasma parameters in fish exposed to an acute exhaustive exercise and air exposure stress. Fish acclimated to temperatures ≥20°C exhibited elevated levels of plasma cortisol, muscle lactate, and plasma glucose after exposure to the acute stressors. After 24 h of recovery, fish showed longer metabolic recovery times at 15 and 20°C and cortisol levels remaining elevated at temperatures ≥20°C. Our findings suggest that brook trout may have a limited ability to acclimate to temperatures >20°C and increases in temperatures beyond 20°C may impact brook trout populations.

Larval lake sturgeon, Acipenser fulvescens, reared in hatcheries for stock enhancement of wild populations may be susceptible to early opportunistic bacterial infection. Thus, we examined survival and whole-body mRNA expression of both stress- and immune-related genes (MyD88, IL-1β, StAR, GR1, and HSP70) in 30 days post fertilization larval lake sturgeon following immune challenge with lipopolysaccharides (LPS). Larval sturgeon were exposed to 0, 25, 50, 100, 150, and 200 μg ml−1 LPS and sampled after 30 min, 4 h, and 48 h. Mortality was zero in 0 and 25 μg ml−1 LPS; 37.5% in 50 μg ml−1 LPS and 100% in the higher concentrations. Expression of MyD88 and StAR mRNA were positively correlated and increased with time in the 50 μg ml−1 LPS treatment. There was an influence of both treatment and time on IL-1β mRNA, with expression 10-fold higher than controls after 4 h. Expression of HSP70 mRNA was suppressed within 30 min of 50 μg ml−1 LPS exposure and remained so throughout the time course. Correlated mRNA expression of GR1 with MyD88, StAR and IL-1β suggests a potential relationship between the innate immune and glucocorticoid responses of larval lake sturgeon during this early developmental stage. Data presented suggest that larval lake sturgeon largely responded with predicted changes in gene expression of immune related and stress response genes following LPS challenge. This study provides a foundation for future research examining the effects of hatchery and naturally occurring stressors on the immune responses of larval lake sturgeon.

The climate change has the potential to dramatically affect species' thermal physiology and may change the ecology and evolution of species' lineages. In this work, we investigated the transition of dynamics in the heat shock response when the thermal stress approaches the upper thermal limits of species to understand how the climate change may affect the heat shock responses in ectotherms and endotherms. The heat shock protein 70, HSP70, prevents protein denaturation or misfolding under thermal stresses. When thermal stress increases, the number of misfolded proteins increases, which leads to high levels of HSP70 protein. However, when temperatures approach limits of thermal tolerance (i.e., the critical thermal maximum, CTmax, for ectotherms and the superior critical temperature, SCT, for endotherms), levels of HSP70 protein synthesis start to decrease. Thus, we hypothesized that the temperature at the first reduction of HSP abundance indicates the thermal limits of the species. In this work, we provide a mathematical model to investigate the behavior of the heat shock responses related to HSP70 protein. This model captures the dynamics of HSP70 protein and Hsp70 mRNA, in HeLa cells (i.e., representative for endotherms) and multiple species of fishes (i.e., representative for ectotherms) with different acclimation histories. Based on our hypothesis of the relationship between the HSP70 protein level and CTmax/SCT, our model provides three methods to predict the CTmax of fishes with varying acclimation temperature and the SCT of HeLa cells. The CTmax increases as the acclimation temperature increases in fishes, however the CTmax plateaus when the acclimation temperature is higher than 20°C in brook trout, a representative cool water salmonid. Our model also captures the situation that the heat shock reaction in fish is more sensitive to the heat shock temperature than HeLa cells, when the heat shock temperature is lower than the upper thermal tolerance. However, both fish and HeLa cells are sensitive to the heat shock temperature when the temperature reaches the thermal tolerance limits. Additionally, our sensitive analysis result indicates that the status of some components in the heat shock reaction changes when the temperature reaches the thermal tolerance resulting in failure in protein refolding in fish and speeding up the refolding process in HeLa cells. Mathematical analysis is also applied on a simplified mathematical model to investigate the detailed dynamics of the model, such as the steady states of the substrate, Hsp70 mRNA, and HSP70 protein, at different thermal stresses. The comparison between the original model and simplified model shows that the inhibition on HSP70 protein transcription by thermal stresses leads to the reduction in HSP70 protein at extreme temperatures.

The invasive rainbow smelt (Osmerus mordax) was an abundant food source for Lake Winnipeg walleye (Sander vitreus), especially in the north basin of the lake, until the smelt’s collapse in approximately 2013. We quantified changing length-at-age (≈ growth rates) and relative mass (≈ body condition) in Lake Winnipeg walleye caught for a gillnet index data set. Here, walleye showed smaller length-at-age, particularly in the north basin with young fish, over time. This approach to assessing growth suggests a constraint in the north basin fish, possibly a nutritional limitation between 2017 and 2018, that was not present in the south. We then analyzed a separate group of walleye (≥452 mm in fork length) sampled in 2017 as part of a large-scale tracking study, which had a similar slope in length-mass relationship to large walleye caught in that year for the gillnet index data. A panel of metabolites associated with amino acid metabolism and protein turnover was compared in whole blood. These metabolites revealed elevated essential amino acids and suggest protein degradation may be elevated in north basin walleye. Therefore, based on both growth estimates and metabolites associated with protein balance, we suggest there were spatially distinct separations affecting Lake Winnipeg walleye with decreased nutritional status of walleye in the north basin of Lake Winnipeg being of particular concern.

Our understanding of the importance of cortisol in the development of fishes largely stems from teleosts and in particular the zebrafish, Danio rerio. However, studies examining the ontogeny of the cortisol endocrine axis in acipenseriformes (sturgeon and paddlefish) have demonstrated similar general patterns during early development. Beginning with maternal deposition of cortisol in the egg, followed by development of de novo synthesis, a hypo-responsive period, and finally the ability of the fish to appropriately increase whole-body levels of cortisol in response to a stressor. In the present study, we demonstrate a similar pattern of ontogeny in the cortisol response in lake sturgeon over two-year classes. Whole-body levels of cortisol were examined over two cohorts and found to be different in both concentration and timing of endogenous production. The 2016 cohort were found to have relatively high levels of cortisol and developed to first feeding approximately six days faster than the 2017 cohort with lower levels of cortisol. In the 2017 cohort, mRNA expression of steroidogenic acute regulatory protein (StAR) and glucocorticoid receptor 1 (GR1) increased just prior to the increase in cortisol and associated onset of exogenous feeding. Treatment in metyrapone, an inhibitor of 11β-hydroxylase, significantly inhibited cortisol production and resulted in the inability of the fish to appropriately transition to exogenous feeding. Data suggest a potential key role for cortisol in lake sturgeon as they transition between diets during early life history.

Molecular techniques have been increasingly used in a conservation physiology framework to provide valuable information regarding the mechanisms underlying responses of wild organisms to environmental and anthropogenic stressors. In the present study, we developed a reference gill transcriptome for walleye (Sander vitreus) allowing us to pair a gene-suite approach with multivariate statistics to examine the physiological status of wild-caught walleye. For molecular analyses of wild fish, the gill is a useful target for conservation studies, not only because of its importance as an indicator of the physiological status of fish but also because it can be biopsied non-lethally. Walleye were non-lethally sampled following short- (∼1.5 month) and long-term (∼3.5 month) holding in the Delta Marsh, that is located south of Lake Manitoba in Manitoba, Canada. Large-bodied walleye are held in the Delta Marsh from late April to early August by exclusion screens used to protect the marsh from invasive common carp (Cyprinus carpio), exposing fish to potentially stressful water quality conditions. Principal components analysis (PCA) revealed patterns of transcript abundance consistent with exposure of fish to increasingly high temperature and low oxygen conditions with longer holding in the marsh. For example, longer-term holding in the marsh was associated with increases in the mRNA levels of heat shock proteins and a shift in the mRNA abundance of aerobic to anaerobic metabolic genes. Overall, the results of the present study suggest that walleye held in the Delta Marsh may be exhibiting sub-lethal responses to high temperature and low oxygen conditions and provides valuable information for managers invested in mediating these impacts to a local species of conservation concern. More broadly, we highlight the usefulness of pairing transcriptomic techniques with multivariate statistics to address potential confounding factors that can affect measured physiological responses of wild-caught fish.Lay summaryNon-lethal molecular techniques were used to assess the physiological status of wild-caught walleye confined in the Delta Marsh, Manitoba, Canada, because of common carp exclusion screens. Walleye sampled during the warmest months of the year exhibited responses to elevated temperature and low oxygen conditions, suggesting sub-lethal effects of local conditions.

RNA sequencing is an effective approach for studying an aquatic species with little prior molecular information available, yielding both physiological and genomic data, but its genetic applications are not well-characterized. We investigate this possible role for RNA sequencing for population genomics in Lake Winnipeg, Manitoba, Canada, walleye (Sander vitreus). Lake Winnipeg walleye represent the largest component of the second-largest freshwater fishery in Canada. In the present study, large female walleye were sampled via nonlethal gill biopsy over two years at three spawning sites representing a latitudinal gradient in the lake. Genetic variation from sequenced messenger RNA was analyzed for neutral and adaptive markers to investigate population structure and possible adaptive variation. We find low population divergence (FST= 0.0095), possible northward gene flow, and outlier loci that vary latitudinally in transcripts associated with cell membrane proteins and cytoskeletal function. These results indicate that Lake Winnipeg walleye may be effectively managed as a single demographically connected metapopulation with contributing subpopulations, and suggest genomic differences possibly underlying observed phenotypic differences. Because RNA sequencing data can yield physiological in addition to genetic information discussed here, we argue that it is useful for addressing diverse molecular questions in the conservation of freshwater species.

Understanding physiological limits and the ability to acclimatize to changing conditions will determine whether species will be able to cope with further increases in water temperature. Changes in temperature may be considered to become stressful for an ectotherm when it results in reduced performance, which can lead to fitness level consequences. The relative intensity of the stressor as well as the duration of the exposure to the stressor will determine the response observed. Transcriptomic responses can potentially indicate thresholds where physiological performance begins to decline. An understanding of the cellular shifts throughout the temperature range that an organism experiences in the wild is often lacking, especially for species of conservation concern such as the delta smelt (Hypomesus transpacificus). We examined the expression of 15 genes that represented cellular responses related to stress, growth, cell proliferation and osmoregulation to show how the response patterns change to acute increases in temperatures that occur throughout the thermal distribution of the species. Several genes showed U-shaped or inverted U-shaped response patterns suggesting the presence of sub-lethal thresholds as temperatures increase. We also highlight the importance of including a temporal component to exposure studies as several genes showed a delay in the recovery to control levels at extreme temperatures. We propose that the non-linear response patterns represent sub-lethal thermal thresholds that can predict the severity of the response to thermal stressors. Identifying these sub-lethal thresholds can help differentiate between responses to routine increases in water temperature and responses that can lead to longer-term fitness impacts.

Fishes respond to different abiotic and biotic stressors through changes in gene expression as a part of an integrated physiological response. Transcriptomics approaches have been used to quantify gene expression patterns as a reductionist approach to understand responses to environmental stressors in animal physiology and have become more commonly used to study wild fishes. We argue that non-lethal sampling for transcriptomics should become the norm for assessing the physiological status of wild fishes, especially when there are conservation implications. Processes at the level of the transcriptome provide a “snapshot” of the cellular conditions at a given time; however, by using a non-lethal sampling protocol, researchers can connect the transcriptome profile with fitness-relevant ecological endpoints such as reproduction, movement patterns and survival. Furthermore, telemetry is a widely used approach in fisheries to understand movement patterns in the wild, and when combined with transcriptional profiling, provides arguably the most powerful use of non-lethal sampling for transcriptomics in wild fishes. In this review, we discuss the different tissues that can be successfully incorporated into non-lethal sampling strategies, which is particularly useful in the context of the emerging field of conservation transcriptomics. We briefly describe different methods for transcriptional profiling in fishes from high-throughput qPCR to whole transcriptome approaches. Further, we discuss strategies and the limitations of using transcriptomics for non-lethally studying fishes. Lastly, as ‘omics’ technology continues to advance, transcriptomics paired with different omics approaches to study wild fishes will provide insight into the factors that regulate phenotypic variation and the physiological responses to changing environmental conditions in the future.

Control of invasive sea lamprey (Petromyzon marinus) in the Laurentian Great Lakes includes widespread application of lampricides which consist of two active compounds, 3-trifluoromethyl-4-nitrophenol (TFM) & niclosamide. The toxicological action of these lampricides is thought to result from inhibition of aerobic energy synthesis, with TFM having a relatively selective action against lampreys. While toxicity (i.e. lethal concentrations [LC]) has been reported for a wide range of aquatic species and the physiological effects of TFM characterized, the impacts associated with exposure to niclosamide and TFM;niclosamide mixtures are poorly characterized in non-target fishes despite being an important consideration for management and conservation. Therefore, focusing on responses associated with energy metabolism, we quantified and compared the physiological responses of larval sea lamprey and bluegill (Lepomis macrochirus), a non-target, native species. Both species were subjected to each lampricide alone (TFM at species-specific 24 h LC10; niclosamide at 1.5% of [TFM]) or to a mixture of the two (sea lamprey at TFM 24 h LC10 + 1.5% niclosamide; bluegill at sea lamprey's TFM 24 h LC99.9 + 1.5% niclosamide) for 24 h. Tissues (brain, skeletal muscle, and liver) were sampled at 6, 12, and 24 h of exposure and assayed for whole tissue [ATP], [phosphocreatine (PCr)], [glycogen], [lactate], and [glucose]. In sea lamprey, TFM had little effect on brain and skeletal muscle, but niclosamide resulted in a depletion of high energy substrates in both tissues (brain ATP, PCr, glycogen, lactate, & glucose; muscle ATP, & glycogen). Sea lamprey exposed to the mixture showed general depletion of high energy substrates (brain ATP & glycogen; muscle ATP, PCr, & glycogen), accumulation of lactate, and high mortality rates. Bluegill were largely unaffected by exposure to either toxicant, alone or together, for the response endpoints measured. Our results indicate that lampricide toxicity in sea lamprey is mediated through a depletion of high energy substrates because of impaired aerobic ATP synthesis. We also confirmed that non-target bluegill show high tolerance to lampricide exposure, an effect potentially mediated through a high detoxification capacity relative to lampreys.

Fish health can be affected by many environmental factors including infection with pathogens. Infectious disease can lead to high mortality in wild populations and in aquaculture, resulting in significant economic losses. Teleost fishes share a highly conserved response to pathogen infections, starting with an immediate activation of the innate immune response before shifting to an adaptive immune response. Fishes also show altered transcriptomic expression in stress-related genes during acute and chronic infections. The ciliate Ichthyophthirius multifiliis ( Ich ) is one of the most widely distributed ectoparasites for freshwater fish, providing the possibility to identify infection severity via phenotypical assessments. Molecular markers are increasingly incorporated in health assessments and to determine sublethal physiological responses to stressors. We evaluated the effects of an infection with Ich using the pelagic fish species delta smelt ( Hypomesus transpacificus ) as a model. We investigated transcriptional changes of ten genes belonging to the innate immune response and five heat shock genes related to thermal and general stress response. Molecular assessments were conducted in three tissues (gill, spleen and kidney), and collected from fish with different infection intensities. The combination of molecular markers, including immune and stress-related genes, resulted in significant differentiation between infection levels in all tissue types. The strongest results were observed in gill and kidney, however, the detection of infection severity was most effective when combining the transcriptomic results from all tissues. Chemokine cxcb was the most responsive gene in all tissues and provided significant upregulation in fish with visible Ich -infection. The identification of molecular markers targeting fundamental host responses associated with infections is contributing to the establishment of techniques to assess fish health in natural habitats and in aquaculture.

The upper thermal tolerance of brook trout Salvelinus fontinalis was estimated using critical thermal maxima (CTmax ) experiments on fish acclimated to temperatures that span the species' thermal range (5-25°C). The CTmax increased with acclimation temperature but plateaued in fish acclimated to 20, 23 and 25°C. Plasma lactate was highest, and the hepato-somatic index (IH ) was lowest at 23 and 25°C, which suggests additional metabolic costs at those acclimation temperatures. The results suggest that there is a sub-lethal threshold between 20 and 23°C, beyond which the fish experience reduced physiological performance.

The Sacramento splittail (Pogonichthys macrolepidotus) is a species of special concern that is native to the San Francisco Estuary, USA. Two genetically distinct populations exist and differ in maximal salinity tolerances. We examined the expression of 12 genes representative of osmoregulatory functions in the gill over a 14 day time course at two different salinities [11 or 14 PSU (Practical Salinity Units)] and revealed that each population showed distinct patterns of gene expression consistent with population differences in response to osmotic regimes. The relatively more salinity-tolerant San Pablo population significantly upregulated nine out of the 12 transcripts investigated on day 1 of 11 PSU salinity exposure in comparison to the day zero freshwater control. Three transcripts (nka1a, nka1b, and mmp13) were differentially expressed between the populations at 7 and 14 days of salinity exposure, suggesting a reduced ability of the relatively salinity-intolerant Central Valley population to recover. Additionally, a phylogenetic analysis of several Sacramento splittail Na+/K+-ATPase α1 sequences resulted in grouping by proposed paralog rather than species, suggesting that different paralogs of this gene may exist. These findings, together with prior research conducted on the Sacramento splittail, suggest that the San Pablo population may be able to preferentially regulate select osmoregulatory genes, including different Na+/K+-ATPase α1 paralogs, to better cope with salinity challenges.

Silver carp (Hypophthalmichthys molitrix) are invasive to North America, and their range has expanded within the Mississippi River Basin, seemingly unchecked, since their introduction in the late 1970s, with the exception of the upper reaches of the Illinois River. With the imminent threat of their movement into the Great Lakes, the goal of the present study was to assess whether differences in the physiological status between silver carp at the leading edge of their invasion front and core population sites could explain their lack of expansion upstream toward Lake Michigan over the past decade. A transcriptomic approach using RNA sequencing and analysis of plasma variables were used to quantify differences among fish at the leading edge and two downstream core population sites. Leading-edge fish exhibited upregulation of genes associated with xenobiotic defense (e.g., ATP-binding cassette C1 [abcc1], abcc2, abcc6), decreased cell integrity (i.e., macroautophagy and apoptosis; autophagy-related protein 9A [atg9a], caspase 3b [casp3b]), and cholesterol metabolism (e.g., abca1, apolipoprotein A1 [apoa1], sterol O-acyltransferase [soat1]) and downregulation of genes associated with DNA repair (e.g., tumor suppressor p53-binding protein 1 [tp53bp1]) compared to core population sites. Transcriptomic profiles of leading-edge fish were consistent with fish inhabiting a polluted environment and suggest that poorer water quality conditions upstream of the leading edge may represent a non-permanent barrier to silver carp range expansion. The present study provides potential molecular targets for monitoring the physiological status of silver carp over time and in response to future improvements in water quality upstream of their leading edge.

Few estimates of migration rates or descriptions of behavior or survival exist for wild populations of out-migrating Pacific salmon smolts from natal freshwater rearing areas to the ocean. Using acoustic transmitters and fixed receiver arrays across four years (2010-2013), we tracked the migration of > 1850 wild sockeye salmon (Oncorhynchus nerka) smolts from Chilko Lake, British Columbia, to the coastal Pacific Ocean (> 1000 km distance). Cumulative survival to the ocean ranged 3-10% among years, although this may be slightly underestimated due to technical limitations at the final receiver array. Distinct spatial patterns in both behavior and survival were observed through all years. In small, clear, upper-river reaches, downstream migration largely occurred at night at speeds up to 50 km/d and coincided with poor survival. Among years, only 57-78% of smolts survived the first 80 km. Parallel laboratory experiments revealed excellent short-term survival and unhindered swimming performance of dummy-tagged smolts, suggesting that predators rather than tagging effects were responsible for the initial high mortality of acoustic-tagged smolts. Migration speeds increased in the Fraser River mainstem (~220 km/d in some years), diel movement patterns ceased, and smolt survival generally exceeded 90% in this segment. Marine movement rates and survival were variable across years, with among-year segment-specific survival being the most variable and lowest (19-61%) during the final (and longest, 240 km) marine migration segment. Osmoregulatory preparedness was not expected to influence marine survival, as smolts could maintain normal levels of plasma chloride when experimentally exposed to saltwater (30 ppt) immediately upon commencing their migration from Chilko Lake. Transportation of smolts downstream generally increased survival to the farthest marine array. The act of tagging may have affected smolts in the marine environment in some years as dummy-tagged fish had poorer survival than control fish when transitioned to saltwater in laboratory-based experiments. Current fisheries models for forecasting the number of adult sockeye returning to spawn have been inaccurate in recent years and generally do not incorporate juvenile or smolt survival information. Our results highlight significant potential for early migration conditions to influence adult recruitment.

Pyrethroid pesticides are a class of insecticides found to have endocrine disrupting properties in vertebrates such as fishes and in human cell lines. Endocrine disrupting chemicals (EDCs) are environmental contaminants that mimic or alter the process of hormone signaling. In particular, EDCs that alter estrogen and androgen signaling pathways are of major concern for fishes because these EDCs may alter reproductive physiology, behavior, and ultimately sex ratio. Bifenthrin, a pyrethroid with escalating usage, is confirmed to disrupt estrogen signaling in several species of fish, including Menidia beryllina (inland silverside), an Atherinid recently established as a euryhaline model. Our main objective was to broadly assess the molecular and physiological responses of M. beryllina to the ng/L concentrations of bifenthrin typically found in the environment, with a focus on endocrine-related effects, and to discern links between different tiers of the biological hierarchy. As such, we evaluated the response of juvenile Menidia to bifenthrin using a Menidia-specific microarray, quantitative real-time polymerase chain reaction (qPCR) on specific endocrine-related genes of interest, and a Menidia-specific ELISA to the egg-coat protein choriogenin, to evaluate a multitude of molecular-level responses that would inform mechanisms of toxicity and any underlying causes of change at higher biological levels of organization. The sublethal nominal concentrations tested (0.5, 5 and 50ng/L) were chosen to represent the range of concentrations observed in the environment and to provide coverage of a variety of potential responses. We then employed a 21-day reproductive assay to evaluate reproductive responses to bifenthrin (at 0.5ng/L) in a separate group of adult M. beryllina. The microarray analysis indicated that bifenthrin influences a diverse suite of molecular pathways, from baseline metabolic processes to carcinogenesis. A more targeted examination of gene expression via qPCR demonstrated that bifenthrin downregulates a number of estrogen-related transcripts, particularly at the lowest exposure level. Choriogenin protein also decreased with exposure to increasing concentrations of bifenthrin, and adult M. beryllina exposed to 0.5ng/L had significantly reduced reproductive output (fertilized eggs per female). This reduction in fecundity is consistent with observed changes in endocrine-related gene expression and choriogenin production. Taken together, our results demonstrate that environmental concentrations of bifenthrin have potential to interfere with metabolic processes, endocrine signaling, and to decrease reproductive output.

Social buffering is a phenomenon where the presence of conspecifics reduces an animal's stress response. Well known in mammals, social buffering was recently described in fishes exhibiting pronounced social hierarchies. Lake sturgeon (Acipenser fulvescens) are a gregarious rather than hierarchical fish. Therefore, we tested their capacity for social buffering following exposure to an acute thermal stress. Isolated or grouped (three or six similarly sized conspecifics) age-0 lake sturgeon were exposed to a critical thermal maximum (CTmax) test. We measured the endocrine and cellular response to acute thermal shock by assessing whole body cortisol concentration and mRNA expression of steroidogenic acute regulatory protein (StAR) and heat shock proteins (hsp90a, hsp90b, and hsp70) during recovery from the CTmax test. Isolation or grouping had no effect on CTmax. Whole body cortisol concentrations in isolated fish were approximately three-fold higher than in grouped fish 1 h post-CTmax and two-fold higher than grouped fish 20 h post-CTmax. Similarly, 1 h post-CTmax, mRNA expression of StAR, hsp90a, hsp90b and hsp70 were three to four-fold higher in isolated fish compared to groups of three and six fish. At 20 h post-CTmax, expression of StAR was approximately two-fold higher in isolated fish, but expression of hsp90a, hsp90b, and hsp70 was not significantly different between isolated and grouped fish. While conspecific presence had no effect on CTmax, the significant reduction of endocrine and cellular stress markers post-CTmax in grouped fish strongly suggests that lake sturgeon may use social buffering to combat potential deleterious effects of exposure to heat stress.

Sturgeon, one of the most endangered families of vertebrates, are of high conservation concern with population restoration efforts worldwide. Sturgeon species are often raised in conservation hatcheries to supplement wild populations with little understanding of effects of hatchery-related stressors on early development. Lake Sturgeon hatcheries deviate from natural conditions by coating adhesive embryos in clay to prevent clumping, embryos are then added to tumbling jars, colloquially referred to as McDonald Jars; a cone or cylinder-shaped container with constant flow, causing the embryos to roll and move throughout the water column. In the wild, Lake Sturgeon embryos adhere to substrate in fast-flowing rivers, where orientation is maintained throughout embryogenesis. In this study, we examined the effects of hatchery early-rearing environment, i.e. the use of tumbling jars, on gene expression, endogenous cortisol production, growth, and survival in larval Lake Sturgeon. We compared pre- and post-hatch tumbled larvae to non-tumbled larvae that were allowed to adhere to substrate throughout embryogenesis. We hypothesized that deviating from natural rearing conditions, with the use of tumbling jars, would result in changes to cortisol production, growth and mortality in post-hatch, tumbled larvae. Endogenous cortisol production was delayed one week for fish in the tumbled treatment (two-factor ANOVA; P

Background Pacific 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. Results Candidate 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. Conclusions The 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 material The online version of this article (10.1186/s12864-018-5108-9) contains supplementary material, which is available to authorized users.

Acute stressors are commonly experienced by wild animals but their effects on fitness rarely are studied in the natural environment. Billions of fish are captured and released annually around the globe across all fishing sectors (e.g., recreational, commercial, subsistence). Whatever the motivation, release often occurs under the assumption of post-release survival. Yet, capture by fisheries (hereafter "fisheries-capture") is likely the most severe acute stressor experienced in the animal's lifetime, which makes the problem of physiological recovery and survival of relevance to biology and conservation. Indeed, fisheries managers require accurate estimates of mortality to better account for total mortality from fishing, while fishers desire guidance on strategies for reducing mortality and maintaining the welfare of released fish, to maximize current and future opportunities for fishing. In partnership with stakeholders, our team has extensively studied the effects of catch-and-release on Pacific salmon in both marine and freshwater environments, using biotelemetry and physiological assessments in a combined laboratory-based and field-based approach. The emergent theme is that post-release rates of mortality are consistently context-specific and can be affected by a suite of interacting biotic and abiotic factors. The fishing gear used, location of a fishery, water temperature, and handling techniques employed by fishers each can dramatically affect survival of the salmon they release. Variation among individuals, co-migrating populations, and between sexes all seem to play a role in the response of fish to capture and in their subsequent survival, potentially driven by pre-capture pathogen-load, maturation states, and inter-individual variation in responsiveness to stress. Although some of these findings are fascinating from a biological perspective, they all create unresolved challenges for managers. We summarize our findings by highlighting the patterns that have emerged most consistently, and point to areas of uncertainty that require further research.

Research into the effects of contaminants on fishes is often conducted on well- studied model test species, whose responses may be different than those of endangered species. We developed an oligonucleotide microarray consisting of 12 595 genes to examine the effects of the pesticide permethrin on an endangered fish in California, USA, the delta smelt Hypomesus transpacificus. The microarray was used in combination with quantitative PCR (qPCR) assess- ments. We exposed larval delta smelt to permethrin for 96 h at concentrations of 0.69, 1.37, 2.56, 4.84, 12.88 and 24.94 µg l �1 , and compared the responses to a control group. The 96 h 50% lethal concentration (LC50) was 4.07 µg l �1 , which is lower than those reported for model test species and similar to other endangered species. With increasing exposure concentration, we detected the dif- ferential expression of 3342 microarray features with elevated expression of genes involved in protein degradation and apoptosis, and decreased expression of immune function genes. Func- tional analysis indicated that genes involved in protein degradation, immune function, an unfolded protein response, meta bolism and cell signaling cascades were affected by exposure to permethrin. Many of the gene responses in the 0.69 µg l �1 treatment group differed in their direc- tional change in expression from those at higher exposure concentrations, suggesting a potential mechanistic threshold of sub-lethal toxicity at concentrations below the lowest observed effect concentration (LOEC) of 2.56 µg l �1 . These results are consistent with non-monotonic response patterns to contaminants, and demonstrate the effects on a sensitive fish species of a widely used pyrethroid pesticide at concentrations below those that affect model test species.

Ibuprofen is one of the most commonly detected pharmaceuticals in wastewater effluent; however, the effects of ibuprofen on aquatic organisms are poorly understood. This study presents the transcriptome-wide response of the inland silverside, Menidia beryllina, to chronic exposure to ibuprofen. At the lowest exposure concentration (0.0115 mg/L), we detected a downregulation of many genes involved in skeletal development, aerobic respiration, and immune function. At the highest exposure concentration (1.15 mg/L), we detected increased expression of regulatory genes in the arachidonic acid metabolism pathway and several immune genes involved in an inflammatory response. Additionally, there was differential expression of genes involved in oxidative stress responses and a downregulation of genes involved in osmoregulation. This study provides useful information for monitoring the effects of this common wastewater effluent contaminant in the environment and for the generation of biomarkers of exposure to ibuprofen that may be transferable to other fish species.

There is growing recognition of the need to understand the mechanisms underlying organismal resilience (i.e. tolerance, acclimatization) to environmental change to support the conservation management of sensitive and economically important species. Here, we discuss how functional genomics can be used in conservation biology to provide a cellular-level understanding of organismal responses to environmental conditions. In particular, the integration of transcriptomics with physiological and ecological research is increasingly playing an important role in identifying functional physiological thresholds predictive of compensatory responses and detrimental outcomes, transforming the way we can study issues in conservation biology. Notably, with technological advances in RNA sequencing, transcriptome-wide approaches can now be applied to species where no prior genomic sequence information is available to develop species-specific tools and investigate sublethal impacts that can contribute to population declines over generations and undermine prospects for long-term conservation success. Here, we examine the use of transcriptomics as a means of determining organismal responses to environmental stressors and use key study examples of conservation concern in fishes to highlight the added value of transcriptome-wide data to the identification of functional response pathways. Finally, we discuss the gaps between the core science and policy frameworks and how thresholds identified through transcriptomic evaluations provide evidence that can be more readily used by resource managers.

article i nfo Despite the common mechanisms that underlie vertebrate responses to exhaustive exercise stress, the magnitude and the timecourse of recovery can be context-specific. Here, we examine how wild, adult male and female pink (Oncorhynchus gorbuscha )a nd sockeye (Oncorhynchus nerka) salmon respond to and recover from an exhaustive exercise and air exposure stressor, designed to simulate fisheries capture and handling. We follow gill tissue gene expression for genes active in cellular stress, cell maintenance, and apoptosis as well as plasma osmoregulatory, stress, and reproductive indices. The stressor initiateda major stress response as indicatedby increasednormalised expression of two stress-responsive genes, Transcription Factor JUNB and cytochrome C (pink salmon only). The stressor resulted in increased plasma ion cortisol, lactate, and depressed estradiol (sockeye salmon only). Gene ex- pression and plasma variables showed a general recovery by 24 h post-stressor. Species- and sex-specifi cp atterns were observed in stress responseand recovery, withpinksalmonmountinga higher magnitude stress response for plasma variables and sockeye salmon exhibiting a higher and more variable gene expression profile. These results highlight species- and sex-specific responses of migrating Pacific salmon to simulated fisheries encounters, which contribute new knowledge towards understanding the consequences of fisheries capture-and-release.