Kenneth M. Jeffries

Understanding the roles of philopatry and geography in determining genetic population structure is an important part of managing species characterized by metapopulations. In this study, we examined population structure, kinship, and runs of homozygosity in walleye (Sander vitreus) from Lake Champlain, a large, fragmented lake with four main spawning tributaries that form a metapopulation. Using microsatellite genotyping at 12 loci, we investigated population genetic structure among the four tributaries to examine how spawning site fidelity influenced pairwise genetic distances. Using a high-density Rapture dataset containing thousands of reference-aligned SNP genotypes, we estimated evidence of inbreeding based on runs of homozygosity (ROH) in Lake Champlain and compared findings to four other large walleye populations in North America. The Lamoille and Poultney Rivers were genetically distinct from the Missisquoi and Winooski Rivers, despite evidence of 10% straying among rivers. Within-site kinship and the number of runs of homozygosity (ROH) in the Lamoille and Poultney Rivers were elevated compared to Missisquoi and Winooski Rivers, suggesting ongoing or recent inbreeding at these locations. Comparisons with other large-lake walleye populations revealed that the elevated number of ROHs in Lake Champlain was specific to the Lamoille and Poultney Rivers. We suggest that this inbreeding may be driven by demographic bottlenecks and small effective population sizes (<50 based on microsatellite data) that were potentially facilitated by hatchery practices. Our findings indicate that when combined with other factors, philopatry can have powerful impacts on fine-scale population structure and genomic diversity. We emphasize that metapopulations composed of philopatric sub-populations may be more vulnerable to localized inbreeding than systems with more random dispersal. Our results demonstrate how genetic data can inform conservation strategies, particularly in the face of habitat fragmentation and declining population sizes.

Fishes experience thermal stress in their natural environment that can be caused by natural or anthropogenic factors and can directly affect their physiology. In this study, we developed a multispecies OpenArray™ qPCR (quantitative polymerase chain reaction) ‘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 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°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°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 CT _max test. The expression of 52 genes of interest was quantified using the multispecies qPCR chip for all three species, along with four 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, suggesting differences in cellular responses to thermal stress that can lead to different susceptibilities to thermal stress in their natural habitats.

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 °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 °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., CT _max ). Transcriptional profiles were assessed in the gill, liver, and and epidermal mucus. Generally, fish acclimated to the greatest combined stressor (18 °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.

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, sub-lethal cellular thresholds occur at similar temperatures to other physiological or behavioural changes, or at temperatures associated with common physiological endpoints measured in fishes to estimate thermal tolerance. To test this, we estimated temperature preference (15.1±1.1°C, mean±s.d.) using a shuttle box, agitation temperature (22.0±1.4°C), defined as the point where a fish exhibits a behavioural avoidance response, and the upper thermal limit (CTmax, 28.2±0.4°C) for 1 year old brook trout (Salvelinus fontinalis) acclimated to 10°C. We then acutely exposed a different subset of fish to the mean temperatures associated with the pre-determined physiological endpoints and sampled tissues when they reached the target temperature or after 60 min of recovery at 10°C for transcriptomic analysis. 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 once the agitation temperature was reached, which may identify a possible link between the cellular stress response and the behavioural avoidance response.

Rivers, lakes, and wetlands are facing threats that continue to grow in intensity and frequency from climate change, habitat fragmentation, invasive species, changes in food availability, natural disasters, various forms of pollution (e.g., trace metals, light, noise), and emerging infectious diseases. These disruptions to freshwater environments are driving population declines in freshwater fishes as well as threatening migratory species that need freshwater habitats to complete their life cycle. To improve freshwater fish conservation efforts, it is essential to understand the magnitude and nature of the threats fish are currently facing. Here, we present a series of case studies that illustrate the utility of employing physiological methods to assess both the threats facing freshwater fishes, and the conservation efforts being used to help preserve freshwater biodiversity. We present an array of physiological tools that can be used across multiple levels of biological organization, from molecular to population-level, to address a variety of questions. Finally, we share what we view to be pressing questions in freshwater fish conservation physiology and highlight strategies to help bridge gaps across different user groups.

Species invading non‐native habitats can cause irreversible environmental damage and economic harm. Yet, how introduced species become widespread invaders remains poorly understood. Adaptation within native‐range habitats and rapid adaptation to new environments may both influence invasion success. Here, we examine these hypotheses using 7058 SNPs from 36 native, 40 introduced and 19 farmed populations of tench, a fish native to Eurasia. We examined genetic structure among these populations and accounted for long‐term evolutionary history within the native range to assess whether introduced populations exhibited lower genetic diversity than native populations. Subsequent to infer genotype–environment correlations within native‐range habitats, we assessed whether adaptation to native environments may have shaped the success of some introduced populations. At the broad scale, two glacial refugia contributed to the ancestry and genomic diversity of tench. However, native, introduced and farmed populations of admixed origin exhibited up to 10‐fold more genetic diversity (i.e., observed heterozygosity, expected heterozygosity and allelic richness) compared to populations with predominantly single‐source ancestry. The effects of introduction to a new location were also apparent as introduced populations exhibited fewer private alleles (mean = 9.9 and 18.9 private alleles in introduced and native populations, respectively) and higher population‐specific Fst compared to native populations, highlighting their distinctiveness relative to the pool of allelic frequencies across tench populations. Finally, introduced populations with varying levels of genetic variation and similar genetic compositions have become established and persisted under strikingly different climatic and ecological conditions. Our results suggest that lack of prior adaptation and low genetic variation may not consistently hinder the success of introduced populations for species with a demonstrated ability to expand their native range.

Atmospheric CO₂ and temperature are rising concurrently, and may have profound impacts on the transcriptional, physiological and behavioural responses of aquatic organisms. Further, spring snowmelt may cause transient increases of pCO₂ in many freshwater systems. We examined the behavioural, physiological and transcriptomic responses of an ancient fish, the lake sturgeon (Acipenser fulvescens) to projected levels of warming and pCO₂ during its most vulnerable period of life, the first year. Specifically, larval fish were raised in either low (16°C) or high (22°C) temperature, and/or low (1000 μatm) or high (2500 μatm) pCO₂ in a crossed experimental design over approximately 8 months. Following overwintering, lake sturgeon were exposed to a transient increase in pCO₂ of 10,000 μatm, simulating a spring melt based on data in freshwater systems. Transcriptional analyses revealed potential connections to otolith formation and reduced growth in fish exposed to high pCO₂ and temperature in combination. Network analyses of differential gene expression revealed different biological processes among the different treatments on the edges of transcriptional networks. Na⁺/K⁺‐ATPase activity increased in fish not exposed to elevated pCO₂ during development, and mRNA abundance of the β subunit was most strongly predictive of enzyme activity. Behavioural assays revealed 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 in lake sturgeon. Conserved elements of the cellular stress response across all organisms provide key information for how other freshwater organisms may respond to future climate change.

Many salmonid species are particularly susceptible to chronic and acute temperature changes caused by global warming. We aimed to study the differences in metabolic and transcriptomic responses of a chronic heat stress on a control and selected (absence of early sexual maturation and growth) line of brook charr Salvelinus fontinalis (Mitchill, 1814). We exposed individuals to different temperatures for 35 days (15, 17, and 19 °C). High temperature reduced the growth rate (in length) and the Fulton condition factor. Both maximal metabolic rate and the aerobic scope were higher in fish reared at 17 °C, while they decreased in fish maintained at 19 °C. The relative gene expression of cytochrome c oxidase was lower at 19 °C than at 15 °C. The relative gene expressions of both liver and gill hsp90 was higher at the highest temperature. The standard metabolic rate, while not affected by temperature, was higher for the control line over the selected line. Only in the control line, the relative expression of catalase and of receptor of insulin-like growth factor-1 increased at 19 °C. Our results showed that the selected line was able to cope more effectively with the oxidative stress caused by the rise in temperature.