Biology subjects

Jeffries, K. M.

Publications and source records attributed to Jeffries, K. M..

17 recordsLinked to original sources

bioRxiv2026

Gene transcriptional profiling to assess Chinook salmon osmoregulatory resilience to salinity challenges

Given unprecedented environmental change, Pacific salmonids are becoming increasingly threatened; however, genomic technologies provide an opportunity to assess Pacific salmonid resilience to on-going environmental change. Also, given increasing conservation and animal welfare concerns, non-lethal tissue sampling is emerging for assessing the physiological status of wild species. Relatively few studies, however, have compared the transcriptomic response of fish sampled non-lethally versus lethally for fish health and stress quantification. Here, we conducted a comparative gene transcriptional profiling study using 28 qPCR assays on the OpenArray platform as an osmoregulatory stress transcriptional profiling chip. We sampled both non-lethal (gill biopsies, skin swabs, and water [eRNA]) and lethal (whole gill and liver) tissue samples from Chinook salmon (Oncorhynchus tshawytscha) smolts exposed for 0 h, 24 h, and 72 h to freshwater (0 PSU), brackish water (15 PSU) or seawater (30 PSU). We observed that most assays showed higher qPCR amplification success in both non-lethal gill biopsies and lethal gill tissues, compared to other tissues. We found more significant differences in transcript abundance in traditional lethal tissues compared to non-lethal tissues. With increasing duration of salinity exposure, gene transcript levels were typically upregulated in seawater samples compared to freshwater samples for both non-lethal and lethal tissues. The targeted genes for both non-lethal and lethal tissues were significantly and positively correlated across time points. Our findings support the use of non-lethal tissue sampling to improve Chinook salmon hatchery rearing, inform hatchery release timing, and facilitate future field application for the conservation of wild stocks.

genomics↗

bioRxiv2026

Long-term effects of early-life thermal fluctuations on the cellular stress response and CTmax of zebrafish, Danio rerio

Temperatures in aquatic ecosystems have been affected by anthropogenic activities such as agricultural and industrial water use, and climate change caused by greenhouse gas emissions. Changes in water temperature directly affect the cellular and organismal physiology of fishes because most fishes are ectotherms. These effects can take different forms, such as increased cellular stress and reactive oxygen species (ROS) production. However, the type and magnitude of response depend on the duration and the frequency of the exposure to elevated water temperature. In this study, we investigated the long-term effects of exposure to daily thermal fluctuations occurring during early-life stages of zebrafish, Danio rerio, on gene expression and CTmax in later developmental stages. To do so, wild-type zebrafish were exposed daily to a + 5{degrees}C fluctuation in temperature from ambient (28 {degrees}C) to 33 {degrees}C over the first 30 days post fertilization (dpf), before being held until 90 dpf at ambient temperature. The fish that experienced daily thermal fluctuation were compared to a control group that was kept at 28 {degrees}C throughout the experiment and sampled at the same timepoints. Samples were collected at 18 (larval), 30, 60 (juvenile), and 90 (adult) dpf to study the expression of heat shock proteins and oxidative stress genes. The thermotolerance of fish was tested using CTmax trials at 60 and 90 dpf. Daily thermal fluctuation over the first 30 dpf led to a significant increase in the expression of hsp47, gstp1a, sod1, and sod2 genes at 60 dpf, and hsp47, hsp90aa1, hsp90ab1, cat, glulb, gstp1a, sod1, and sod2 genes at 90 dpf. The only significant increase detected during the larval stage was glulb at 18 dpf. Fish that experienced thermal fluctuation also had a higher CTmax at 60 dpf, but this increased thermotolerance significantly decreased from 60 to 90 dpf, where it was not different between treatments. Overall, our study demonstrates that early-life thermal stress increased cellular stress responses and thermotolerance in zebrafish into later ontological stages.

physiology↗

bioRxiv2025

High-throughput multispecies qPCR assays to study the effects of acute thermal stress in three species of Acipenser sturgeon

In this study, we developed a multispecies OpenArray qPCR "chip" to measure the effects of acute thermal stress on the mRNA response of Acipenser sturgeons. The qPCR chips were then tested on three species: Acipenser fulvescens, Acipenser oxyrinchus oxyrinchus, and Acipenser brevirostrum. The A. fulvescens were from two genetically distinct populations (Burntwood River and Winnipeg River, Manitoba, Canada) that were acclimated to three different temperatures (16, 20, and 24 {degrees}C) to quantify the effects of genetic background and acclimation temperatures on the transcriptomic response to acute thermal stress. Additionally, juvenile A. oxyrinchus oxyrinchus and A. brevirostrum were acclimated to 10 {degrees}C and then experienced acute thermal stress. All three species were sampled for gill and liver before and after experiencing acute thermal stress, which was applied using a CTmax test. The expression of 52 genes of interest was quantified using the multispecies qPCR chip for all three species, along with 4 reference genes. We showed that acute thermal stress affected the mRNA expression of 17-26 of the thermal metabolic stress genes that were assayed using the chip, depending on the species. However, the mRNA patterns varied between species and genetically distinct populations.

physiology↗

bioRxiv2025

Cumulative effects of high temperature and low dissolved oxygen alter the acute thermal tolerance and cellular stress response in lake trout

Lake trout (Salvelinus namaycush) is an important food fish in Northern communities, inhabiting cool, well-oxygenated water. Yet, climate change is reducing available habitat with extended summer stratification of lakes creating an upper thermal barrier ([~]15 {degrees}C) and lower dissolved oxygen (DO) boundary (4-7 mg L-1). Together, these environmental factors can influence tolerance thresholds and climate change may lead to abiotic factors exceeding these physiological thresholds in lake trout habitats. Thresholds can shift with environmental acclimation in lake trout populations, but the functional basis of this shift has yet to be examined. The abundance of mRNA transcripts offers insight into underlying cellular responses to environmental stressors that can provide an early warning of fitness consequences. Here, we used a stress-response transcriptional profiling chip to investigate a suite of genes involved in thermal and general stress in lake trout acclimated to a range of temperatures (6-18 {degrees}C) and DO (normoxia: > 8.5 mg L-1 or hypoxia: 5.5-6.5 mg L-1), as well as following an acute thermal stress (i.e., CTmax). Transcriptional profiles were assessed in the gill, liver, and and epidermal mucus. Generally, fish acclimated to the greatest combined stressor (18 {degrees}C and hypoxia) had the largest transcriptional response, suggestive of a transition from a routine stress response to an extreme survival response. A noted temperature dependence occurred in liver tissue, which was not evident in gill or mucus tissues. Further, transcriptional responses in the gill and mucus were highly correlated (r = 0.74-0.87), highlighting the potential use of these tissues for non-lethal sampling methods to enhance management and conservation strategies for lake trout across their distribution.

physiology↗

bioRxiv2024

Transcriptional profiling provides insights on sublethal thermal stress thresholds in juvenile bull trout

Bull trout (Salvelinus confluentus) inhabit mainly cold-water streams in their Western North American range. Multiple anthropogenic stressors, including climate change, have caused population declines and range reduction, leading to classification of bull trout as threatened. Characterizing how fish respond to increasing temperature can identify key thresholds beyond which fish health is impacted, which is useful for developing species recovery strategies. Juvenile bull trout were acclimated to a range of relevant temperatures (6-21 {degrees}C), after which mRNA transcripts involved in responding to thermal stress were measured using high- throughput qPCR, and their upper thermal tolerance (critical thermal maximum, CTmax) was determined. Beyond 18 {degrees}C appears to be a critical sublethal threshold for bull trout: capacity to increase CTmax through acclimation was lost, growth and survival decreased, and transcriptional data suggest widespread activation of cellular stress and growth suppression. Below 18 {degrees}C, transcriptional data suggest subtler metabolic adjustments in response to acclimation temperature, preceding changes in whole-animal performance. Altogether, these data provide insight into thermal responses in bull trout, and their capacity to cope with climate-change related warming.

physiology↗

bioRxiv2024

Development of multi-species qPCR assays for a stress transcriptional profiling (STP) Chip to assess the resilience of salmonids to changing environments

Ecologically and socio-economically important salmonid fishes in Canada are threatened by diverse environmental stressors. However, predicting species responses to environmental change requires understanding the underlying molecular mechanisms governing environmental stress tolerance. Developing advanced molecular genetic tools will provide opportunities to predict how salmonid fishes will respond to environmental stressors and assess their adaptive potential and vulnerability into the future. Here, we developed a panel of Taqman quantitative PCR (qPCR) assays designed to measure mRNA transcript abundance at selected candidate loci for use across salmonids. We designed and applied those assays for use in a high-throughput nanofluidic OpenArray Stress Transcriptional Profiling Chip (STP-Chip) capable of 2688 simultaneous qPCR at multiple gene loci (112 targets for 12 samples in duplicate). Using the nanofluidic STP-Chip, we tested these 112 multi-species qPCR assays using gill, liver and muscle tissue from eight species of salmonids across four genera. Of the selected 112 assays, 69 assays showed amplification in gill, 64 in liver, and 67 in muscle across all eight salmonid species. The percentage of assays that showed amplification across three tissues varied between genera: In general, Salmo, Oncorhynchus, and Salvelinus species showed a higher success rate than Coregonus species. Stress, circadian rhythm, apoptosis, growth-metabolism, and detoxification-relevant assays showed high success rates for amplification across all salmonid species for all three tissues. In contrast, neural plasticity, appetite regulation, osmoregulation, immune function, endocrine disruption, and hypoxia-relevant assays showed low success. Not surprisingly, we observed tissue-specific variation among qPCR amplification patterns. There were significant differences in mRNA transcript abundance among species across the four genera, but we did not see variation between species from the same genus. These qPCR assays can be used to design custom STP-Chips that can be used for quantifying stress in salmonid fish, improving health through more accurate diagnostic tests for disease, and monitoring adaptation to accelerated climate change regionally and globally.

genomics↗

bioRxiv2024

Behavioural responses to acute warming precede critical shifts in the cellular and physiological thermal stress responses in fish

From a conservation perspective, it is important to identify when sub-lethal temperatures begin to adversely impact an organism. However, it is unclear whether, during acute exposures, these cellular thresholds occur at similar temperatures to other physiological or behavioural changes. To test this, we estimated temperature preference (15.1 {+/-} 1.1 {degrees}C) using a shuttle box, thermal optima for aerobic scope (10-15 {degrees}C) using respirometry, agitation temperature (22.0 {+/-} 1.4 {degrees}C) as the point where a fish exhibits a behavioural avoidance response and the CTmax (28.2 {+/-} 0.4 {degrees}C) as the upper thermal limit for 1 yr old Brook Trout (Salvelinus fontinalis) acclimated to 10 {degrees}C. We then acutely exposed a different subset of fish to these temperatures and sampled tissues when they reached the target temperature or after 60 min of recovery at 10 {degrees}C. We used qPCR to estimate mRNA transcript levels of genes associated with heat shock proteins, oxidative stress, apoptosis, and inducible transcription factors. A major shift in the transcriptome response occurred near the agitation temperature, which may identify a link between the cellular stress response and the behavioural avoidance response.

physiology↗

bioRxiv2023

Integrated organismal responses induced by ecologically-relevant pCO2 and temperature exposures in developing lake sturgeon

Atmospheric CO2 and temperature are rising concurrently, and may have profound impacts on the transcriptional, physiological, and behavioral responses of aquatic organisms. Further, spring snow melt may cause transient increases of pCO2 in freshwater systems. Lake sturgeon (Acipenser fulvescens) groups were raised in current and projected levels of warming and pCO2. Following an overwintering period, lake sturgeon were exposed to a transient increase in pCO2, simulating a spring melt. Diverging transcriptional patterns were found in each group and metabolic rate was lower in the combined stressor group compared to others. Behavioral assays revealed no effect of environment on alarm cue responses or boldness, but there was a decrease in total activity following an acute CO2 exposure. These results demonstrate compensatory and compounding mechanisms of pCO2 and warming dependent on developmental conditions of a freshwater fish, and provide key information for responses to future climate change.

zoology↗

bioRxiv2022

Mercury contamination of an introduced generalist fish of intermediate trophic level

Mercury contamination is a global issue because mercury concentrations in aquatic systems are influenced by both natural and anthropogenic pathways, including the burning of fossil fuels and flooding during hydroelectric development. Mercury biomagnifies in aquatic ecosystems, leading to higher concentrations in piscivore fishes than those at lower trophic levels. Here, liver and muscle total mercury (THg) concentrations in black crappie Pomoxis nigromaculatus from three lakes in southeastern Manitoba, Canada were related to age, morphology and physiological traits to better understand the dynamics of mercury accumulation in an introduced generalist fish species. Black crappie liver and muscle samples from Big Whiteshell Lake (relatively large lake, 17.5 km2; n=30), Caddy Lake (small lake surrounded by wetlands, 3.1 km2; n=42) and Lac du Bonnet (river widening influenced by hydroelectric dams, 84.0 km2; n=29) were analyzed for THg content. These THg concentrations were then compared to black crappie mercury concentrations in other Canadian water bodies to assess within species relative contamination levels, as well as to mercury concentrations in other freshwater fishes to examine biomagnification. Age and size had strong positive correlations (r>0.60) with muscle mercury concentrations. No evidence of acute point source contamination was found in the study area when compared to black crappie muscle mercury concentrations in other water bodies, and tissue THg concentration was not correlated with a reduction in gonadosomatic index (GSI) or hepatosomatic index (HSI). Analysis of liver THg in addition to muscle THg revealed the possible impacts of seasonal and ontogenetic differences in diet on exposure. Furthermore, THg analysis of liver and muscle tissue showed how generalist foraging techniques of black crappie may curb the progressively greater mercury exposure and resultant physiological consequences expected from ontogenetic diet shifts from invertebrates to fishes. Although there appeared to be temporally varied levels of mercury exposure (i.e., liver THg) by sex, there was no sex effect observed in long-term accumulation in the muscle. Flood risk is believed to be a key driver of differences in black crappie THg concentrations between lakes in the region. Black crappie bioaccumulated less mercury at age than primary piscivore species in the region. These results will help foster a better understanding of mercury biomagnification in boreal shield lakes within a region impacted by legacy mercury.

pharmacology and toxicology↗

bioRxiv2022

Tissue-specific transcriptomes reveal mechanisms of microbiome regulation in an ancient fish

The lake sturgeon (Acipenser fulvescens) is an ancient, octoploid fish faced with conservation challenges across its range in North America but a lack of genomic resources has hindered molecular research in the species. To support such research we aimed to provide a transcriptomic database from 13 tissues: brain, esophagus, gill, head kidney, heart, white muscle, liver, glandular stomach, muscular stomach, anterior intestine, pyloric cecum, spiral valve, and rectum. The transcriptomes for each tissue were sequenced and assembled individually from a mean of 98.3 million ({+/-}38.9 million std. dev.) reads each. In addition, an overall transcriptome was assembled and annotated with all data used for each tissue-specific transcriptome. All assembled transcriptomes and their annotations were made publicly available as a scientific resource. The non-gut transcriptomes provide important resources for many research avenues, however, the gut represents a compartmentalized organ system with compartmentalized functions and the sequenced gut tissues were from each of these portions. Therefore, we focused our analysis on mRNA transcribed in different tissues of the gut and explored evidence of microbiome regulation. Gene set enrichment analyses were used to reveal the presence of photoperiod and circadian-related transcripts in the pyloric caecum, which may support periodicity in lake sturgeon digestion. Similar analyses were used to identify different types of innate immune regulation across the gut, while analyses of unique transcripts annotated to microbes revealed heterogeneous genera and genes among different gut tissues. The present results provide a scientific resource and information about the mechanisms of compartmentalized function across gut tissues in a phylogenetically ancient vertebrate.

zoology↗

bioRxiv2022

Transcriptome-wide patterns reveal conserved and population-specific responses to increasing acclimation temperatures in developing lake sturgeon (Acipenser fulvescens)

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{degrees} 02' 46.5'' N, 96{degrees} 54' 18.6'' W and 50{degrees} 17' 52'' N, 95{degrees} 32' 51'' W respectively, separated by approximately 650 km) within Manitoba to current (summer highs of 20-23{degrees}C) and future projected (+2-3{degrees}C) environmental temperatures of 16, 20, and 24{degrees}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{degrees}C, while this capacity was not diminished until 24{degrees}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.

molecular biology↗

bioRxiv2022

Acute thermal stress elicits interactions between gene expression and alternative splicing in a fish of conservation concern

Transcriptomics provides a mechanistic understanding of an organisms 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.

physiology↗

bioRxiv2021

The truncate soft-shell clam, Mya truncata, as a biomonitor of municipal wastewater exposure and historical anthropogenic impacts in the Canadian Arctic.

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. truncatas 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 Iqaluits wastewater effluent and highlight M. truncatas potential to act as a biomonitor of municipal wastewater along Canadian Arctic coastlines.

pharmacology and toxicology↗

bioRxiv2020

Molecular and physiological responses predict acclimation limits in juvenile brook trout ( Salvelinus fontinalis )

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{degrees}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{degrees}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{degrees}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{degrees}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{degrees}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{degrees}C and cortisol levels remaining elevated at temperatures [≥]20{degrees}C. Our findings suggest that brook trout may have a limited ability to acclimate to temperatures >20{degrees}C and increases in temperatures beyond 20{degrees}C may impact brook trout populations.

physiology↗

bioRxiv2020

Morphology and Blood Metabolites Reflect Recent Spatial Differences Among Lake Winnipeg Walleye, Sander vitreus

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 smelts collapse in approximately 2013. We quantified changing length-at-age ({approx} growth rates) and relative mass ({approx} 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.

physiology↗

bioRxiv2020

Applying a gene-suite approach to examine the physiological status of wild-caught walleye (Sander vitreus)

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.

physiology↗

bioRxiv2020

Genomic signals found using RNA sequencing support conservation of walleye (Sander vitreus) in a large freshwater ecosystem.

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.

genomics↗