First isolation of Flavobacterium psychrophilum from wild adult Great Lakes lake whitefish (Coregonus clupeaformis).

Lake whitefish (Coregonus clupeaformis; LWF) is an economically and ecologically valuable native species to the Great Lakes, but recent declines in their recruitment have generated significant concern about their future viability. Although studies have sought to identify factors contributing to declining recruitment, the potential role(s) of infectious diseases has not been thoroughly investigated. In 2018 and 2019, adult LWF were collected from Lakes Superior, Michigan, and Huron for clinical examination and bacteriological analyses. Herein, we describe the first isolation of Flavobacterium psychrophilum, aetiological agent of bacterial coldwater disease (BCWD) and rainbow trout fry syndrome (RTFS), from systemically infected adult LWF. Bacterial isolates were yellow-orange, Gram-negative, filamentous bacilli that were oxidase and catalase positive, and produced a flexirubin-type pigment in 3% potassium hydroxide. Isolate identity was confirmed via F. psychrophilum-specific PCR, and multilocus sequence typing revealed three new singleton sequence types (STs) that were distinct from all previously described F. psychrophilum STs. The prevalence of F. psychrophilum infections was 3.3, 1.7, and 0.0% in Lakes Superior, Michigan and Huron respectively. Findings illustrate the potential for F. psychrophilum to cause systemic infections in adult LWF and highlight the need for future studies to investigate the bacterium's potential role in declining LWF recruitment.

Thermal acclimation alters both basal heat shock protein gene expression and the heat shock response in juvenile lake whitefish (Coregonus clupeaformis).

Long-term temperature shifts associated with seasonal variability are common in temperate regions. However, these natural shifts could place significant strain on thermal stress responses of fishes when combined with mean increases in water temperatures predicted by climate change models. We examined the relationship between thermal acclimation, basal expression of heat shock protein (hsp) genes and the activation of the heat shock response (HSR) in lake whitefish (LWF; Coregonus clupeaformis), a cold water species of cultural and commercial significance. Juveniles were acclimated to either 6, 12, or 18°C water for several months prior to the quantification of hsp mRNA levels in the presence or absence of acute heat shock (HS). Acclimation to 18°C increased basal mRNA levels of hsp70 and hsp47, but not hsc70 or hsp90ß in gill, liver and white muscle, while 6°C acclimation had no effect on basal hsp transcription. Fish in all acclimation groups were capable of eliciting a robust HSR following acute HS, as indicated by the upregulation of hsp70 and hsp47. An increase of only 2°C above the 18°C acclimation temperature was required to trigger these transcriptional changes, suggesting that the HSR may be frequently initiated in LWF populations living at mildly elevated temperatures. Collectively, these expression profiles show that environmental temperature influences both basal hsp levels and the HSR in LWF, and indicate that these fish may have a greater physiological and ecological susceptibility to elevated temperatures than to cooler temperatures.

Factors affecting year-class strength and growth of lake whitefish (Coregonus clupeaformis) in impounded lakes as revealed by otolith chronologies.

Recruitment and growth rates for lake whitefish (Coregonus clupeaformis) inhabiting the Smallwood Reservoir, Labrador, Canada, were influenced by facets of its creation and the temporal variability in water levels associated with its operation. Filling of the reservoir between 1971 and 1974 created a concurrent increase in lake whitefish recruitment above long-term averages. In addition, recruitment was influenced by winter drawdown levels: higher water levels during February enhanced recruitment, accounting for an additional 10% of the long-term variation in recruitment. Using otolith increments as a growth index, the authors determined that growth was influenced by reservoir creation. Growth rates during the initial period of flooding (1971-1975) exceeded long-term averages and were greater than those in any other 5-year period between 1965 and 1995. Growth rate increases were attributed to a simultaneous zooplankton bloom. After exceptional growth, lake whitefish showed a period (1976-1980) when growth rates decreased. The authors developed a quantitative technique using otoliths as an index to establish chronologies of fish growth rates. The index can be used to quantify and assess the impacts of reservoir hydrology on fish populations.

Season and species influence stable isotope ratios between lethally and non-lethally sampled tissues in freshwater fish.

The field of stable isotope ecology is moving away from lethal sampling (internal organs and muscle) towards non-lethal sampling (fins, scales and epidermal mucus). Lethally and non-lethally sampled tissues often differ in their stable isotope ratios due to differences in metabolic turnover rate and isotopic routing. If not accounted for when using non-lethal tissues, these differences may result in inaccurate estimates of resource use and trophic position derived from stable isotopes. To address this, the authors tested whether tissue type, season and their interaction influence the carbon and nitrogen stable isotope ratios of fishes and whether estimates of species trophic position and resource use are affected by tissue type, season and their interaction. This study developed linear conversion relationships between two fin types and dorsal muscle, accounting for seasonal variation. The authors focused on three common temperate freshwater fishes: northern pike Esox lucius, yellow perch Perca flavescens and lake whitefish Coregonus clupeaformis. They found that fins were enriched in 13 C and depleted in 15 N compared to muscle in all three species, but the effect of season and the interaction between tissue type and season were species and isotope dependent. The estimates of littoral resource use based on fin isotope ratios were between 13% and 36% greater than those based on muscle across species. Season affected this difference for some species, suggesting the potential importance of using season-specific conversions when working with non-lethal tissues. Fin and muscle stable isotopes produced similar estimates of trophic position for northern pike and yellow perch, but fin-based estimates were 0.2-0.4 trophic positions higher than muscle-based estimates for lake whitefish. The effect of season was negligible for estimates of trophic position in all species. Strong correlations existed between fin and muscle δ13 C and δ15 N values for all three species; thus, linear conversion relationships were developed. The results of this study support the use of non-lethal sampling in stable isotope studies of fishes. The authors suggest that researchers use tissue conversion relationships and account for seasonal variation in these relationships when differences between non-lethal tissues and muscle, and seasonal effects on those differences, are large relative to the scale of isotope values under investigation and/or the trophic discrimination factors under use.

The heat shock response shows plasticity in embryonic lake whitefish (Coregonus clupeaformis) exposed to repeated thermal stress.

We examined the impact of repeated thermal stress on the heat shock response (HSR) of thermally sensitive lake whitefish (Coregonus clupeaformis) embryos. Our treatments were designed to mimic temperature fluctuations in the vicinity of industrial thermal effluents. Embryos were either maintained at control temperatures (3 oC) or exposed to a repeated thermal stress (TS) of 3 or 6 oC above control temperature every 3 or 6 days throughout embryonic development. At 82 days post-fertilisation, repeated TS treatments were stopped and embryos received either a high level TS of 12, 15, or 18 oC above ambient temperature for 1 or 4 h, or no additional TS. These treatments were carried out after a 6 h recovery from the last repeated TS. Embryos in the no repeated TS group responded, as expected, with increases in hsp70 mRNA in response to 12, 15 and 18 oC high-level TS. However, exposure to repeated TS of 3 or 6 °C every 6 days also resulted in a significant upregulation of hsp70 mRNA relative to the controls. Importantly, these repeated TS events and the associated elevations in hsp70 attenuated the upregulation of hsp70 in response to a 1 h, high-level TS of 12 oC above ambient, but not to either longer (4 h) or higher (15 or 18 oC) TS events. Conversely, hsp90α mRNA levels were not consistently elevated in the no repeated TS groups exposed to high-level TS. In some instances, hsp90α levels appeared to decrease in embryos exposed to repeated TS followed by a high-level TS. The observed attenuation of the HSR in lake whitefish embryos demonstrates that embryos of this species have plasticity in their HSR and repeated TS may protect against high-level TS, but the response differs based on repeated TS treatment, high-level TS temperature and duration, and the gene of interest.

Hypoxia affects the ontogeny of the hypothalamus-pituitary-interrenal axis functioning in the lake whitefish (Coregonus clupeaformis).

Early life stages are sensitive to environmental insults and changes during critical developmental periods; this can often result in altered adult behaviour and physiology. Examining the development of the hypothalamus-pituitary-interrenal (HPI) axis and its responsiveness, or lack thereof, during development are important for understanding the short- and long-term impacts of stressors on embryonic and larval fish. We examined the ontogeny of the HPI axis in embryonic (21, 38, 63, 83 and 103 days post-fertilisation (dpf)) and larval (1, 2, 3 and 4 weeks post-hatch (wph)) lake whitefish (Coregonus clupeaformis) by quantifying changes in mRNA levels of several genes associated with HPI axis functioning and whole animal cortisol levels throughout development and in response to a severe or mild hypoxic stress. Cortisol, and crh, crhbp1, pomc and star transcripts were detected from the earliest embryonic age studied. Cortisol levels in control embryos decreased between 21 and 63 dpf, suggesting the utilisation of maternal cortisol deposits. However, by 83 dpf (70% developed) endogenous de novo synthesis had generated a 4.5-fold increase in whole embryo cortisol. Importantly, we provide novel data showing that the HPI axis can be activated even earlier. Whole body cortisol increased in eyed lake whitefish embryos (38 dpf; ~32% developed) in response to hypoxia stress. Coincident with this hypoxia-induced increase in cortisol in 38 dpf embryos were corresponding increases in crh, crhbp1, pomc and star transcript levels. Beyond 38 dpf, the HPI axis in lake whitefish embryos was hyporesponsive to hypoxia stress at all embryonic ages examined (63, 83 and 103 dpf; 54, 72 and 85% developed, respectively). Post-hatch, larvae responded to hypoxia with an increase in cortisol levels and HPI axis genes at 1 wph, but this response was lost and larvae appeared hyporesponsive at subsequent ages (2, 3 and 4 wph). Collectively our work demonstrates that during fish embryogenesis and the larval stage there are windows where the HPI axis is responsive and windows where it is truly hyporesponsive; both could be beneficial in ensuring undisrupted development particularly in the face of increasing environmental changes.

Modifying effects of a cobble substrate on thermal environments and implications for embryonic development in lake whitefish (Coregonus clupeaformis).

A laboratory flume was constructed to examine substrate effects on aquatic development. The flume was designed as a once-through system with a submerged cobble-filled corebox. Lake whitefish (Coregonus clupeaformis) embryos and temperature probes were deployed at multiple sites within the cobble and in the open water channel. Embryos were incubated in the flume for two different experimental periods: one to examine substrate impacts during natural lake cooling (37 days: 5 December 2016 to 10 January 2017) and the second to investigate substrate effects while administering a twice weekly 1 h heat shock (51 days: 11 January to 2 March 2017). During incubation, no significant difference was found in the average temperature between locations; however, temperatures were more stable within the cobble. Following both incubation periods, embryos retrieved from the cobble were significantly smaller in both dry mass and body length by up to 20%. These results demonstrate differences between embryos submerged in a cobble substrate and in the open water column, highlighting the need to consider the physical influences from the incubation environment when assessing development effects as part of any scientific study or environmental assessment.

Expression and activity of lipid and oxidative metabolism enzymes following elevated temperature exposure and thyroid hormone manipulation in juvenile lake whitefish (Coregonus clupeaformis).

Temperature has unequivocal effects on several aspects of fish physiology, but the full extent of its interaction with key endocrine signaling systems to influence metabolic function remains unknown. The aim of the current study was to assess the individual and combined effects of elevated temperature and hyperthyroidism on hepatic metabolism in juvenile lake whitefish by quantifying mRNA abundance and activity of key metabolic enzymes. Fish were exposed to 13 (control), 17 or 21 °C for 0, 4, 8 or 24 days in the presence or absence of low-T4 (1 µg × g body weight-1) or high-T4 (10 µg × g body weight-1) treatment. Our results demonstrate moderate sensitivity to elevated temperature in this species, characterized by short-term changes in mRNA abundance of several metabolic enzymes and long-term declines in citrate synthase (CS) and cytochrome c oxidase (COX) activities. T4-induced hyperthyroidism also had several short-term effects on mRNA abundance of metabolic transcripts, including depressions in acetyl-coA carboxylase ß (accß) and carnitine palmitoyltransferase 1ß (cpt1ß), and stabilization of cs mRNA levels; however, these effects were primarily limited to elevated temperature groups, indicating temperature-dependent effects of exogenous T4 treatment in this species. In contrast, maximal CS and COX activities were not altered by hyperthyroidism at any temperature. Collectively, our data suggest that temperature has the potential to manipulate thyroid hormone physiology in juvenile lake whitefish and, under warm-conditions, hyperthyroidism may suppress certain elements of the ß-oxidation pathway without substantial impacts on overall cellular oxidative capacity.

Hypoxia alters the expression of hif-1a mRNA and downstream HIF-1 response genes in embryonic and larval lake whitefish (Coregonus clupeaformis).

Lake whitefish (Coregonus clupeaformis) embryos and larvae were exposed to hypoxia at different developmental ages to determine when the cellular response to hypoxia could be initiated. mRNA levels of hypoxia-inducible factor 1α (hif-1α), hsp70, and several HIF-1 target genes were quantified in embryos at 21, 38, 63, 83- and 103-days post fertilisation (dpf) and in larvae at 1, 2, 3- and 4-weeks post hatch (wph) following a 6-hour hypoxia exposure. hsp70 mRNA levels were increased in response to hypoxia at all embryonic ages. By comparison, the first observed change in hif-1α mRNA in response to hypoxia was at 38 dpf, where it was down-regulated from high basal levels, with this response persisting through to 83 dpf. Interestingly, this decrease in hif-1α mRNA coincided with increases in the mRNA levels of the HIF-1 target genes: vegfa (vascular endothelial growth factor A), igfbp1 (insulin-like growth factor binding protein 1), ldha (lactate dehydrogenase a), gapdh (glyceraldehyde-3-phosphate dehydrogenase) and epo (erythropoietin) at select ages. Collectively, this suggests a possible HIF-1-mediated response to hypoxia despite a decrease in hif-1α mRNA. Coinciding with a decrease in basal levels, increases in hif-1α were measured in response to hypoxia at 103 dpf and in larval fish at 1, 2 and 3 wph but there were no consistent increases in HIF-1 target genes at these ages. Overall, our findings indicate that lake whitefish can mount a response to hypoxia early in embryogenesis which may mitigate some of the damaging effects of exposure to low oxygen levels at these critical life history stages.

Exogenous thyroid hormones regulate the activity of citrate synthase and cytochrome c oxidase in warm- but not cold-acclimated lake whitefish (Coregonus clupeaformis).

Thermal acclimation is known to elicit metabolic adjustments in ectotherms, but the cellular mechanisms and endocrine control of these shifts have not been fully elucidated. Here we examined the relationship between thermal acclimation, thyroid hormones and oxidative metabolism in juvenile lake whitefish. Impacts of thermal acclimation above (19°C) or below (8°C) the thermal optimum (13°C) and exposure to exogenous thyroid hormone (60µg T4/g body weight) were assessed by quantifying citrate synthase and cytochrome c oxidase activities in liver, red muscle, white muscle and heart. Warm acclimation decreased citrate synthase activity in liver and elevated both citrate synthase and cytochrome c oxidase activities in red muscle. In contrast, induction of hyperthyroidism in warm-acclimated fish stimulated a significant increase in liver citrate synthase and heart cytochrome c oxidase activities, and a decrease in the activity of both enzymes in red muscle. No change in citrate synthase or cytochrome c oxidase activities was observed following cold acclimation in either the presence or absence of exogenous thyroid hormones. Collectively, our results indicate that thyroid hormones influence the activity of oxidative enzymes more strongly in warm-acclimated than in cold-acclimated lake whitefish, and they may play a role in mediating metabolic adjustments observed during thermal acclimation.

Lipid content and fatty acid profile during lake whitefish embryonic development at different incubation temperatures.

Lipids serve as energy sources, structural components, and signaling molecules during fish embryonic development, and utilization of lipids may vary with temperature. Embryonic energy utilization under different temperatures is an important area of research in light of the changing global climate. Therefore, we examined percent lipid content and fatty acid profiles of lake whitefish (Coregonus clupeaformis) throughout embryonic development at three incubation temperatures. We sampled fertilized eggs and embryos at gastrulation, eyed and fin flutter stages following chronic incubation at temperatures of 1.8, 4.9 and 8.0°C. Hatchlings were also sampled following incubation at temperatures of 3.3, 4.9 and 8.0°C. Fertilized eggs had an initial high percentage of dry mass composed of lipid (percent lipid content; ~29%) consisting of ~20% saturated fatty acids (SFA), ~32% monounsaturated fatty acids (MUFA), ~44% polyunsaturated fatty acids (PUFA), and 4% unidentified. The most abundant fatty acids were 16:0, 16:1, 18:1(n-9c), 20:4(n-6), 20:5(n-3) and 22:6(n-3). This lipid profile matches that of other cold-water fish species. Percent lipid content increased during embryonic development, suggesting protein or other yolk components were preferentially used for energy. Total percentage of MUFA decreased during development, which indicated MUFA were the primary lipid catabolized for energy during embryonic development. Total percentage of PUFA increased during development, driven largely by an increase in 22:6(n-3). Temperature did not influence percent lipid content or percent MUFA at any development stage, and had inconsistent effects on percent SFA and percent PUFA during development. Thus, lake whitefish embryos appear to be highly adapted to low temperatures, and do not alter lipids in response to temperature within their natural incubation conditions.

The effects of fluctuating temperature regimes on the embryonic development of lake whitefish (Coregonus clupeaformis).

Fluctuating incubation temperatures may have significant effects on fish embryogenesis; yet most laboratory-based studies use constant temperatures. For species that experience large, natural seasonal temperature changes during embryogenesis, such as lake whitefish (Coregonus clupeaformis), seasonal temperature regimes are likely optimal for development. Anthropogenic activities can increase average and/or variability of natural incubation temperatures over large (e.g. through climate change) or smaller (e.g. thermal effluent discharge) geographic scales. To investigate this, we incubated lake whitefish embryos under constant (2, 5, or 8°C) and fluctuating temperature regimes. Fluctuating temperature regimes had a base temperature of 2°C with: 1) seasonal temperature changes that modeled natural declines/inclines; 2) tri-weekly +3°C, 1h temperature spikes; or 3) both seasonal temperature changes and temperature spikes. We compared mortality to hatch, morphometrics, and heart rate at three developmental stages. Mortality rate was similar for embryos incubated at constant 2°C, constant 5°C, or with seasonal temperatures, but was significantly greater at constant 8°C. Embryos incubated constantly at >2°C had reduced body growth and yolk consumption compared to embryos incubated with seasonal temperature changes. When measured at the common base temperature of 2°C, embryos incubated at constant 2°C had lower heart rates than embryos incubated with both seasonal temperature changes and temperature spikes. Our study suggests that incubating lake whitefish embryos with constant temperatures may significantly alter development, growth, and heart rate compared to incubating with seasonal temperature changes, emphasizing the need to include seasonal temperature changes in laboratory-based studies.

Development of the embryonic heat shock response and the impact of repeated thermal stress in early stage lake whitefish (Coregonus clupeaformis) embryos.

Lake whitefish (Coregonus clupeaformis) embryos were exposed to thermal stress (TS) at different developmental stages to determine when the heat shock response (HSR) can be initiated and if it is altered by exposure to repeated TS. First, embryos were subject to one of three different TS temperatures (6, 9, or 12°C above control) at 4 points in development (21, 38, 60 and 70 days post-fertilisation (dpf)) for 2h followed by a 2h recovery to understand the ontogeny of the HSR. A second experiment explored the effects of repeated TS on the HSR in embryos from 15 to 75 dpf. Embryos were subjected to one of two TS regimes; +6°C TS for 1h every 6 days or +9°C TS for 1h every 6 days. Following a 2h recovery, a subset of embryos was sampled. Our results show that embryos could initiate a HSR via upregulation of heat shock protein 70 (hsp70) mRNA at all developmental ages studied, but that this response varied with age and was only observed with a TS of +9 or +12°C. In comparison, when embryos received multiple TS treatments, hsp70 was not induced in response to the 1h TS and 2h recovery, and a downregulation was observed at 39 dpf. Downregulation of hsp47 and hsp90α mRNA was also observed in early age embryos. Collectively, these data suggest that embryos are capable of initiating a HSR at early age and throughout embryogenesis, but that repeated TS can alter the HSR, and may result in either reduced responsiveness or a downregulation of inducible hsps. Our findings warrant further investigation into both the short- and long-term effects of repeated TS on lake whitefish development.

Thermal stress and the heat shock response in embryonic and young of the year juvenile lake whitefish.

We investigated the effects of thermal stress on embryonic (fin flutter, vitelline circulation stage) and young of the year (YOY) juvenile lake whitefish by characterizing the kinetics of the heat shock response (HSR). Lake whitefish were subjected to one of three different heat shock (HS) temperatures (3, 6, or 9 °C above control) for six different lengths of time (0.25, 0.50, 1, 2, 3, or 4h) followed by a 2h recovery period at the control temperature of 2 °C or 14 °C for embryos and YOY juveniles, respectively. The duration of the HSR was examined by allowing the fish to recover for 1, 2, 4, 8, 12, 16, 24, 36, or 48 h following a 2h HS. In embryos, at the fin flutter stage, only hsp70 mRNA levels were upregulated in response to the various HS treatments. By comparison, all three typically inducible hsps, hsp90α, hsp70 and hsp47, were upregulated in the YOY juveniles. In both instances the HSR was long lasting, but much more so in embryos where hsp70 mRNA levels continued to increase for 48 h after a 2h HS and remained significantly higher than untreated controls. Collectively our data indicate that both embryo and YOY juvenile lake whitefish have a robust HSR which permits them to survive a 4h, 9 °C HS. Moreover, both life history stages are capable of triggering a HSR following a moderate 3 °C HS which is likely an important protective mechanism against environmental stressors during embryogenesis and early life history stages of lake whitefish.

Targeted sequence capture and resequencing implies a predominant role of regulatory regions in the divergence of a sympatric lake whitefish species pair (Coregonus clupeaformis).

Latest technological developments in evolutionary biology bring new challenges in documenting the intricate genetic architecture of species in the process of divergence. Sympatric populations of lake whitefish represent one of the key systems to investigate this issue. Despite the value of random genotype-by-sequencing methods and decreasing cost of sequencing technologies, it remains challenging to investigate variation in coding regions, especially in the case of recently duplicated genomes as in salmonids, as this greatly complicates whole genome resequencing. We thus designed a sequence capture array targeting 2773 annotated genes to document the nature and the extent of genomic divergence between sympatric dwarf and normal whitefish. Among the 2728 genes successfully captured, a total of 2182 coding and 10,415 noncoding putative single-nucleotide polymorphisms (SNPs) were identified after applying a first set of basic filters. A genome scan with a quality-refined selection of 2203 SNPs identified 267 outlier SNPs in 210 candidate genes located in genomic regions potentially involved in whitefish divergence and reproductive isolation. We found highly heterogeneous FST estimates among SNP loci. There was an overall low level of coding polymorphism, with a predominance of noncoding mutations among outliers. The heterogeneous patterns of divergence among loci confirm the porous nature of genomes during speciation with gene flow. Considering that few protein-coding mutations were identified as highly divergent, our results, along with previous transcriptomic studies, imply that changes in regulatory regions most likely had a greater role in the process of whitefish population divergence than protein-coding mutations. This study is the first to demonstrate the efficiency of large-scale targeted resequencing for a nonmodel species with such a large and unsequenced genome.

Behavioural responses of a cold-water benthivore to loss of oxythermal habitat.

Climate-driven declines in oxythermal habitat in freshwater lakes can impose prolonged constraints on cold-water fishes sensitive to hypoxia. How fish cope with severe habitat limitations is not well understood, yet has implications for their persistence. Here, we use acoustic-positioning telemetry to assess seasonal habitat occupancy and activity patterns of lake whitefish (Coregonus clupeaformis), a cold-water benthivore, in a small boreal lake that regularly faces severe oxythermal constraints during summer stratification. During this stratified period, they rarely (< 15% of detections) occupied depths with water temperatures > 10 °C (interquartile range = 5.3-7.9 °C), which resulted in extensive use (> 90% of detections) of water with < 4 mg L-1 dissolved oxygen (DO; interquartile range = 0.3-5.3 mg L-1). Lake whitefish were least active in winter and spring, but much more active in summer, when only a small portion of the lake (1-10%) contained optimal oxythermal habitat (< 10 °C and > 4 mg L-1 DO), showing frequent vertical forays into low DO environments concurrent with extensive lateral movement (7649 m d-1). High rates of lateral movement (8392 m d-1) persisted in the complete absence of optimal oxythermal habitat, but without high rates of vertical forays. We found evidence that lake whitefish are more tolerant of hypoxia (< 2 mg L-1) than previously understood, with some individuals routinely occupying hypoxic habitat in winter (up to 93% of detections) despite the availability of higher DO habitat. The changes in movement patterns across the gradient of habitat availability indicate that the behavioural responses of lake whitefish to unfavourable conditions may lead to changes in foraging efficiency and exposure to physiological stress, with detrimental effects on their persistence. Supplementary Information: The online version contains supplementary material available at 10.1007/s10641-022-01335-4.

High-density genomic data reveal fine-scale population structure and pronounced islands of adaptive divergence in lake whitefish (Coregonus clupeaformis) from Lake Michigan.

Understanding patterns of genetic structure and adaptive variation in natural populations is crucial for informing conservation and management. Past genetic research using 11 microsatellite loci identified six genetic stocks of lake whitefish (Coregonus clupeaformis) within Lake Michigan, USA. However, ambiguity in genetic stock assignments suggested those neutral microsatellite markers did not provide adequate power for delineating lake whitefish stocks in this system, prompting calls for a genomics approach to investigate stock structure. Here, we generated a dense genomic dataset to characterize population structure and investigate patterns of neutral and adaptive genetic diversity among lake whitefish populations in Lake Michigan. Using Rapture sequencing, we genotyped 829 individuals collected from 17 baseline populations at 197,588 SNP markers after quality filtering. Although the overall pattern of genetic structure was similar to the previous microsatellite study, our genomic data provided several novel insights. Our results indicated a large genetic break between the northwestern and eastern sides of Lake Michigan, and we found a much greater level of population structure on the eastern side compared to the northwestern side. Collectively, we observed five genomic islands of adaptive divergence on five different chromosomes. Each island displayed a different pattern of population structure, suggesting that combinations of genotypes at these adaptive regions are facilitating local adaptation to spatially heterogenous selection pressures. Additionally, we identified a large linkage disequilibrium block of ~8.5 Mb on chromosome 20 that is suggestive of a putative inversion but with a low frequency of the minor haplotype. Our study provides a comprehensive assessment of population structure and adaptive variation that can help inform the management of Lake Michigan's lake whitefish fishery and highlights the utility of incorporating adaptive loci into fisheries management.

Correlation of Mercury Occurrence with Age, Elemental Composition, and Life History in Sea-Run Food Fish from the Canadian Arctic Archipelago's Lower Northwest Passage.

As mercury emissions continue and climate-mediated permafrost thaw increases the burden of this contaminant in northern waters, Inuit from a Northwest passage community in the Canadian Arctic Archipelago pressed for an assessment of their subsistence catches. Sea-run salmonids (n = 537) comprising Arctic char (Salvelinus alpinus), lake trout (S. namaycush), lake whitefish (Coregonus clupeaformis), and cisco (C. autumnalis, C. sardinella) were analyzed for muscle mercury. Methylmercury is a neurotoxin and bioaccumulated with fish age, but other factors including selenium and other elements, diet and trophic level as assessed by stable isotopes of nitrogen (δ15N) and carbon (δ13C), as well as growth rate, condition, and geographic origin, also contributed depending on the species, even though all the fish shared a similar anadromous or sea-run life history. Although mean mercury concentrations for most of the species were ~0.09 µg·g-1 wet weight (ww), below the levels described in several jurisdictions for subsistence fisheries (0.2 µg·g-1 ww), 70% of lake trout were above this guideline (0.35 µg·g-1 ww), and 19% exceeded the 2.5-fold higher levels for commercial sale. We thus urge the development of consumption advisories for lake trout for the protection of pregnant women and young children and that additionally, periodic community-based monitoring be initiated.

Identification of Arctic Food Fish Species for Anthropogenic Contaminant Testing Using Geography and Genetics.

The identification of food fish bearing anthropogenic contaminants is one of many priorities for Indigenous peoples living in the Arctic. Mercury (Hg), arsenic (As), and persistent organic pollutants including polychlorinated biphenyls (PCBs) are of concern, and these are reported, in some cases for the first time, for fish sampled in and around King William Island, located in Nunavut, Canada. More than 500 salmonids, comprising Arctic char, lake trout, lake whitefish, and ciscoes, were assayed for contaminants. The studied species are anadromous, migrating to the ocean to feed in the summers and returning to freshwater before sea ice formation in the autumn. Assessments of muscle Hg levels in salmonids from fishing sites on King William Island showed generally higher levels than from mainland sites, with mean concentrations generally below guidelines, except for lake trout. In contrast, mainland fish showed higher means for As, including non-toxic arsenobetaine, than island fish. Lake trout were highest in As and PCB levels, with salmonid PCB congener analysis showing signatures consistent with the legacy of cold-war distant early warning stations. After DNA-profiling, only 4-32 Arctic char single nucleotide polymorphisms were needed for successful population assignment. These results support our objective to demonstrate that genomic tools could facilitate efficient and cost-effective cluster assignment for contaminant analysis during ocean residency. We further suggest that routine pollutant testing during the current period of dramatic climate change would be helpful to safeguard the wellbeing of Inuit who depend on these fish as a staple input to their diet. Moreover, this strategy should be applicable elsewhere.

Trophic transfer of persistent organic pollutants through a pelagic food web: The case of Lake Como (Northern Italy).

Despite DDT and PCB having been banned for about 40 years, they are still detectable in the environment. In the present research we specifically investigated the trophic transfer of these organochlorine contaminants (OC) through a pelagic food web of a deep lake in Northern Italy (Lake Como) over time. Zooplankton and fish were sampled each season of a year and OC concentrations and the carbon and nitrogen isotopic ratios were measured. By using stable isotopes, the direct trophic relationship between pelagic zooplankton and zooplanktivorous fish was confirmed for Alosa agone only in summer. Based on this result, the biomagnification factor normalized on the trophic level (BMFTL) for organic contaminants was calculated. BMFTL values were within the range 0.9-1.9 for DDT isomers and 1.6-4.9 for some PCB congeners (PCB 95, PCB 101, PCB 149, PCB 153, PCB 138 - present both in zooplankton and in fish and representing >60% of the PCB contamination), confirming the biomagnification of these compounds in one of the two zooplanktivorous fish species of the lake.