Lake Whitefish Research Articles

Effect of elevated embryonic incubation temperature on the temperature preference of juvenile lake (Coregonus clupeaformis) and round whitefish (Prosopium cylindraceum).

Anthropogenic impacts can lead to increased temperatures in freshwater environments through thermal effluent and climate change. Thermal preference of aquatic organisms can be modulated by abiotic and biotic factors including environmental temperature. Whether increased temperature during embryogenesis can lead to long-term alterations in thermal preference has not been explicitly tested in native freshwater species. Lake (Coregonus clupeaformis) and round (Prosopium cylindraceum) whitefish were incubated at natural and elevated temperatures until hatching, following which, all groups were moved to common garden conditions (15°C) during the post-hatching stage. Temperature preference was determined at 8months (Lake whitefish only) and 12months of age (both species) using a shuttle box system. Round whitefish preferred a cooler temperature when incubated at 2 and 6°C compared with 0.5°C. Lake whitefish had similar temperature preferences regardless of age, weight and incubation temperature. These results reveal that temperature preference in freshwater fish can be programmed during early development, and that round whitefish may be more sensitive to incubation temperature. This study highlights the effects that small increases in temperature caused by anthropogenic impacts may have on cold-adapted freshwater fish.

Can scale cortisol concentration be quantified non-lethally in wild fish species?

Cortisol, the primary glucocorticoid in fishes, is secreted into the bloodstream in response to stress. Circulating cortisol accumulates in scales, a durable calcified structure that can be easily sampled from many fish species. As such, the use of scale cortisol concentration (SCC) is currently being explored as a means of chronic stress biomonitoring in wild fishes. Scales serve an important role in fish physiology and thus the number of scales required for reliable cortisol analysis is a limiting factor in the non-lethal collection of such samples. To date, scale cortisol quantification has also only been performed non-lethally in captive fishes and due to differences in stress responsiveness SCCs likely differ in wild species. As such, this study aimed to (1) apply our fish scale processing and analysis protocol to wild fish species and (2) apply it to five north temperate fish species to provide information useful to future non-lethal scale sampling regimes. Cortisol was successfully measured in scales collected from wild northern pike (Esox lucius), walleye (Sander vitreus), whitefish (Coregonus clupeaformis), white sucker (Catostomus commersonii) and captive rainbow trout (Oncorhynchus mykiss). SCCs were significantly different between species and thus the sample mass required for reliable cortisol analysis differed as well. In addition to the size of the fish and the mass of their scales this is an important consideration for future scale cortisol analyses as these factors could make SCC an attainable non-lethal sample matrix in some species of fish but impractical in others.

Energy Density of Three Prosopium Fish Species Endemic to Bear Lake, Utah–Idaho

Abstract We used bomb calorimetry to quantify the energy density of three Prosopium fish species endemic to Bear Lake, Utah–Idaho, that we collected in 2020–2021: Bear Lake Whitefish Prosopium abyssicola, Bonneville Whitefish Prosopium spilonotus, and Bonneville Cisco Prosopium gemmifer. We found that mean ± standard deviation wet weight energy densities were 6,312 ± 760 J/g for Bear Lake Whitefish; 5,301 ± 778 J/g for Bonneville Whitefish; and 4,743 ± 443 J/g for Bonneville Cisco. We built linear mixed models and found relationships between energy density and dry matter ratio (i.e., ratio of dried weight to wet weight of a fish) for all three species, suggesting that the energy density of future samples collected in Bear Lake could potentially be determined from comparisons between the dried and wet weight of fishes belonging to these species. Our results are useful for future bioenergetics modeling with these three Bear Lake endemic species and potentially with others species in related genera that share similar feeding, behavior, and life-history traits.

Building trust through the Two-Eyed Seeing approach to joint fisheries research

The Saugeen Ojibway Nation (SON) and the Ontario Ministry of Natural Resources and Forestry (MNRF) collaboratively govern the commercial fishery within the SON's traditional territory situated in Lake Huron’s main basin and Georgian Bay of the North American Great Lakes. Prior to the application of a Two-Eyed Seeing approach (Etuaptmumk), the two groups often operated in separate silos and relied on external experts to aid communication, which contributed to a sense of mistrust regarding the legitimacy of science that was being used to inform management. A breakthrough occurred when MNRF and SON began using the Two-Eyed Seeing approach to collaborate and jointly conduct research on fish populations in Lake Huron. In this article, we share how we used Two-Eyed Seeing to jointly develop a research proposal that is guided by both SON’s ecological knowledge and Western science. Our research involves addressing the role that lake trout (namegos; Salvelinus namaycush) have played in declines in lake whitefish (dikameg; Coregonus clupeaformis) abundance in Lake Huron, a priority identified by SON members. We share the challenges and lessons learned while reflecting on the ethical knowledge co-production framework we developed. Our goal is to provide a useful example of how Two-Eyed Seeing can be applied to foster relationship-building between government agencies and First Nations in the pivotal early stages of co-developing a research project. The Two-Eyed Seeing approach is foundational to building more equitable partnerships between Indigenous and non-Indigenous communities and for supporting healthy Great Lakes ecosystems and fisheries.

Morphoecological and Genetic Differentiation among Sympatric Morphs of Whitefish in Lake Kuetsjärvi (River Pasvik Basin, Murmansk Oblast)

Morphoecological and Genetic Differentiation among Sympatric Morphs of Whitefish in Lake Kuetsjärvi (River Pasvik Basin, Murmansk Oblast)

The seafood basket: Application of zero-inflated model to fish count purchase

The study analyzed demand for fish in the United States by the number of species purchased from a basket of species, rather than the usual approach focusing on one single species. The basket includes largemouth bass, hybrid striped bass, bluegill, walleye, yellow perch, rainbow trout, Great Lakes whitefish, lake trout, barramundi, and tilapia. These results largely confirm that consumers purchase different fish species or a combination of them from time to time and that consumers pay little attention to green factors such as sustainability, 3rd party certification and hormone-free when purchasing seafood. It appears that the effects of green credence attributes may not apply generically to a collection of fish or that the utility of green characteristics to seafood demand may be declining. As for production systems, although a higher percentage of consumers indicated preference for wild-caught fish, the importance of farmed fish to them was found to increase fish purchased.

Estimates, spatial variability, and environmental drivers of mercury biomagnification rates through lake food webs in the Canadian subarctic

Biomagnification of mercury (Hg) through lake food webs is understudied in rapidly changing northern regions, where wild-caught subsistence fish are critical to food security. We investigated estimates and among-lake variability of Hg biomagnification rates (BMR), relationships between Hg BMR and Hg levels in subsistence fish, and environmental drivers of Hg BMR in ten remote subarctic lakes in Northwest Territories, Canada. Lake-specific linear regressions between Hg concentrations (total Hg ([THg]) in fish and methyl Hg ([MeHg]) in primary consumers) and baseline-adjusted δ15N ratios were significant (p < 0.001, r2 = 0.58–0.88), indicating biomagnification of Hg through food webs of all studied lakes. Quantified using the slope of Hg-δ15N regressions, Hg BMR ranged from 0.16 to 0.25, with mean ± standard deviation of 0.20 ± 0.03). Using fish [MeHg] rather than [THg] lowered estimates of Hg BMR by ∼10%, suggesting that the use of [THg] as a proxy for [MeHg] in fish can influence estimates of Hg BMR. Among-lake variability of size-standardized [THg] in resident fish species from different trophic guilds, namely Lake Whitefish (Coregonus clupeaformis) and Northern Pike (Esox lucius), was not significantly explained by among-lake variability in Hg BMR. Stepwise multiple regressions indicated that among-lake variability of Hg BMR was best explained by a positive relationship with catchment forest cover (p = 0.009, r2 = 0.59), likely reflecting effects of forest cover on water chemistry of downstream lakes and ultimately, concentrations of biomagnifying MeHg (and percent MeHg of total Hg) in resident biota. These findings improve our understanding of Hg biomagnification in remote subarctic lakes.

Saugeen Ojibway Nation community input and action: Initiating a two-eyed seeing approach for dikameg (Coregonus clupeaformis) in Lake Huron

Two-Eyed Seeing (Etuaptmumk in Mi’kmaw) involves seeing with the strengths of Indigenous ways of knowing through one eye, that of Western ways through the other, and using both eyes together to benefit all. Originating from Mi’kmaw Elder Dr. Albert Marshall, its benefits have been demonstrated across a broad array of disciplines, including fisheries research and management. We initiate a Two-Eyed Seeing approach to inform research priorities and explore solutions for the co-managed Saugeen Ojibway Nation lake whitefish (dikameg in Anishinaabemowin) fishery, in light of recent declines that remain poorly understood. We held interviews with harvesters and community members from the Chippewas of Nawash Unceded First Nation and the Chippewas of Saugeen First Nation through focus groups in each community, in addition to surveys that were completed at a community celebration in Nawash, to draw from the communities’ knowledge related to causes of dikameg declines, actions that could be taken to address them, and the future of the fishery in Lake Huron. Participants identified 19 themes, of which the most frequently mentioned were: 1) Harvesting, 2) Non-indigenous and invasive species, 3) Stocking of other fish species, 4) Habitat and water quality, 5) Assisting dikameg reproduction, 6) People and the community, 7) Ecological effects, and 8) Aquaculture and hatcheries for dikameg. Herein, we describe the communities’ concerns and demonstrate how these have formed the foundations of collaborative and community-based research initiatives aimed at applying Indigenous and Western scientific-based knowledge systems to better understand dikameg and their recent declines in Lake Huron.

Diet composition and overlap for adult walleye, lake whitefish, and yellow perch in Green Bay, Lake Michigan

Interspecific interactions among walleye Sander vitreus, lake whitefish Coregonus clupeaformis, and yellow perch Perca flavescens in Green Bay could influence the population status of each species, but potential trophic interactions are poorly understood. Our objectives were to determine if diet assemblages for each species and diet overlap among species varied spatially and temporally within Green Bay. Adult walleye (≥381 mm total length (TL); N = 981), lake whitefish (≥432 mm TL; N = 1507), and yellow perch (≥150 mm TL; N = 1174) were collected during May-October of 2018 and 2019 from multiple locations in southern and northern Green Bay. Diet assemblages of each species varied between northern and southern Green Bay, but walleye diets were more temporally variable (among months within zones and between years) than diets of lake whitefish or yellow perch. Lake whitefish represented a seasonally important prey item for walleye in southern Green Bay, composing 10 % and 41 % of walleye diets by weight in May and June, respectively. Yellow perch generally composed <15 % of walleye diets by weight but were consumed at a broader spatiotemporal scale than lake whitefish. Diet overlap between walleye and both lake whitefish and yellow perch was generally weak or moderate, whereas diet overlap between whitefish and perch was generally strong. Our assessment of adult trophic interactions suggests that changes in the population status of one species could influence fisheries for all three, and we identify additional research questions to address potential population-level effects of these trophic interactions.

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.

Invasive Species Appearance and Climate Change Correspond with Dramatic Regime Shift in Thermal Guild Composition of Lake Huron Beach Fish Assemblages

Lake Huron has undergone dramatic and well-documented lake-wide food web changes as a result of non-native species introductions. Coastal beaches, which serve as nursery habitats for native and introduced species, are, however, relatively poorly studied. Our objective was to assess fish assemblages of beach habitats in western Lake Huron and compare species composition pre- (1993) and post-invasion (2012) of dreissenid mussels and round goby (Neogobius melanostomus). Nearshore beach fish assemblages were sampled by nighttime beach seining during spring and summer in 1993 and 2012 in the western basin of Lake Huron along the Michigan shoreline. Catch rates were considerably higher, but there were fewer species present in 2012 than in 1993. The composition of species changed dramatically from a cold- and cool-water species assemblage in 1993 (dominated by alewife (Alosa pseudoharengus), spottail shiner (Notropis hudsonius), and lake whitefish (Coregonus clupeaformis), as well as Chinook salmon (Oncorhynchus tshawytscha) and rainbow smelt (Osmerus mordax)) to a cool- and warm-water species assemblage in 2012 (dominated by cyprinids, round goby (Nogobius melanstomus), and yellow perch (Perca flavescens)). The observed rise in catch rate and shift in species composition appears related to the introduction of invasive species as well as an on-going warming pattern in nearshore waters.

Challenges in fish aging: the role of otolith preparation technique and experience level in aging lake whitefish (Coregonus clupeaformis)

Lake whitefish ( Coregonus clupeaformis (Mitchill, 1818)) is an important commercial and recreational species in the Great Lakes. Precise age estimates are important for management, and two widely used techniques for otolith preparation are thin-section and crack-and-burn, which have not been compared for lake whitefish. Sagittal otoliths were collected from 92 lake whitefish in Green Bay and Lake Michigan and aged using thin-section and crack-and-burn techniques. Otoliths were aged independently by three individuals (two novices and one expert) to assess repeatability in estimated ages. Our investigation highlights the inherent difficulty of aging lake whitefish, where thin-section produced significantly older estimated ages (6–30 years) compared to crack-and-burn (5–26 years). Percent agreement of estimated ages between preparation techniques was low for all readers within ±0 years but increased when tolerance buffers were applied. Mean coefficient of variation values from both experience levels (&gt;10.8%) exceeded the acceptable range reported in the literature (5%–7%); however, species longevity and nature of the structure must be considered when establishing target values. Variation in estimated ages is attributed to the experience level and interpretation of structural features. Species-specific training and establishing an objective framework to identify annuli will improve precision metrics.

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 ~8.5Mb 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.

A 90-year record of lake whitefish Coregonus clupeaformis abundances in Michigan waters of the upper Laurentian Great Lakes

Fishery managers throughout the upper Laurentian Great Lakes are currently faced with a two-decade decline in abundance and harvest of lake whitefish Coregonus clupeaformis stocks. We used multivariate auto-regressive state-space (MARSS) models to develop long-term (90-year; 1929–2018) time-series of lake whitefish relative abundance based on commercial catch-per-effort (CPE) data for 13 statistical districts in State of Michigan waters, including 1836 and 1842 Treaty ceded waters, of Lakes Superior, Michigan, and Huron. CPE time-series were used to estimate historical baseline conditions, which were compared to more recent conditions, specifically with reference to select regulatory, environmental, and ecological conditions in each lake and fishing intensity. Population growth rates suggested that lake whitefish stocks responded: (1) negatively to high levels of harvest and expansion of sea lamprey Petromyzon marinus populations during the early-1900s; (2) positively to commercial fishery regulation and sea lamprey control during the late-1950s and early-1960s; and (3) negatively to establishment of dreissenid mussels Dreissena spp. in Lakes Michigan and Huron by 2005 and the recent period of low productivity in all three lakes since the mid- to late-2000s. When placed in a historical context, the most recent (2011–2018) lake whitefish abundances are low, intermediate, and high in 31 %, 46 %, and 23 % of all districts examined. Although environmental and ecological conditions likely drove recent declines, correlation analysis suggested that higher levels of fishing intensity were associated with greater district-specific declines in abundance during the last two decades (1999–2016), a period characterized by lower overall productivity and limited recruitment in most lake whitefish stocks.

Predicting physical and geomorphic habitat associated with historical lake whitefish and cisco spawning locations in Lakes Erie and Ontario

The Great Lakes basin was historically populated by multiple, coevolved coregonine species, but much of that diversity has been lost. In Lakes Erie and Ontario, both lake whitefish (Coregonus clupeaformis) and cisco (Coregonus artedi) occurred in high numbers before habitat degradation, overfishing, invasive species, and other factors caused significant declines. There is growing interest in restoring these populations, and suggested actions include restoration of critical habitats such as spawning habitat. Unfortunately, our current understanding of lake whitefish and cisco spawning habitat characteristics and locations in these lakes is limited. To highlight areas of potential importance for conservation and restoration, we used random forest models and data on historical spawning locations to predict lake whitefish and cisco spawning habitats based on hypothesized key factors including wind fetch, ice cover duration, distance from 1st and 6th order tributaries, and lake bottom substrate. Our model accurately predicted spawning habitat locations for 71% and 54% of cases for lake whitefish and cisco, respectively. Fetch was the most important variable in the lake whitefish model, with spawning habitats being most likely to occur in regions of low to moderate fetch. Cisco spawning habitats were most likely to occur in areas of relatively low fetch near a 1st order stream. We used these models to predict spawning habitat locations for both species across Lakes Erie, Ontario, and St. Clair. Our results improve our understanding of lake whitefish and cisco spawning habitat characteristics and will aid in the spatial prioritization of actions to restore these native fishes.

Juvenile-to-adult transition invariances in fishes: Perspectives on proximate and ultimate causation.

To bridge physiological and evolutionary perspectives on size at maturity in fishes, the authors focus on the approximately invariant ratio between the estimated oxygen supply at size at maturity (Qm ) relative to that at asymptotic size (Q∞ ) among species within a taxonomic group, and show how two important theories related to this phenomenon complement each other. Gill-oxygen limitation theory proposes a mechanistic basis for a universal oxygen supply-based threshold for maturation, which applies among and within species. On the contrary, the authors show that a generalisation of life-history theory for the invariance of size at maturity (Lm ) relative to asymptotic size (L∞ ) can provide an evolutionary rationale for an oxygen-limited maturation threshold (Qm /Q∞ ). Extending previous inter- and intraspecific analyses, the authors show that maturation invariances also occur in lake whitefish Coregonus clupeaformis (Mitchill 1818), but at both scales, theory seems to underestimate the value of the maturation threshold. They highlight some key uncertainties in the model that should be addressed to help resolve the mismatch.

Genome-wide genetic diversity may help identify fine-scale genetic structure among lake whitefish spawning groups in Lake Erie

In Lake Erie, lake whitefish Coregonus clupeaformis supported lucrative fisheries before populations were decimated by overfishing and water quality degradation. In recent years, there has been a renewed interest in lake whitefish and management of the fishery they support. Lake whitefish spawn on several reefs throughout Lake Erie, but the relative recruitment dynamics and contributions of spawning groups to the fishery are not well understood. Modern high-throughput sequencing approaches offer new opportunities to census population diversity and to identify subtle differences among closely related populations. We used high-throughput sequencing data to evaluate the genetic structure and diversity of lake whitefish collected opportunistically across broad spatial scales in Lake Erie. Using RAD-capture (Rapture), we sequenced and genotyped individuals (N = 88) from the west, central, and east basin of Lake Erie at 120,268 single nucleotide polymorphisms (SNPs). Lake whitefish from Niagara and Crib Reefs (west basin) diverged from the three collections. Interestingly, these were the only lake whitefish collected during the act of spawning (late November), and all other fish were collected pre-spawn (August-early November). These results suggest that some lake whitefish spawning reefs may be reproductively isolated, though definition of these groups into stocks will require more intentional sampling during the act of spawning.

Seventy years of food-web change in South Bay, Lake Huron

Though aquatic ecosystems (and the Laurentian Great Lakes in particular) have faced many stressors over the past century, including fisheries collapses and species invasions, rarely are data available to evaluate the long-term impacts of these stressors on food web structure. Stable isotopes of fish scales from the 1940s to the 2010s in South Bay, Lake Huron were used to quantify trophic position and resource utilization for fishes from offshore (alewife, cisco, lake trout, lake whitefish, rainbow smelt) and nearshore (rock bass, smallmouth bass, white sucker, yellow perch) habitats, providing one of the longest continuous characterizations of food webs in the Laurentian Great Lakes. Mean δ15N and δ13C values for each species were compared across twenty-year time periods. Using directional statistics, no significant community-wide changes were detected between time periods from 1947 to 1999. In contrast, a significant change was detected between 1980-1999 and 2000–2017, with all species showing increased reliance on nearshore resources. The increase in nearshore resource reliance for lake whitefish between these time periods was the greatest in magnitude compared with any other species between any two adjacent time periods. Besides lake whitefish, the increased reliance on nearshore resources was more pronounced for nearshore compared to offshore species. The timing of these shifts coincided with the invasion of dreissenid mussels and round goby, and declines in offshore productivity and prey densities. These results show the unprecedented magnitude of recent food-web change in Lake Huron after 50 years of relative stability.

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.

Genome assembly, structural variants, and genetic differentiation between lake whitefish young species pairs (Coregonus sp.) with long and short reads.

Nascent pairs of ecologically differentiated species offer an opportunity to get a better glimpse at the genetic architecture of speciation. Of particular interest is our recent ability to consider a wider range of genomic variants, not only single-nucleotide polymorphisms (SNPs), thanks to long-read sequencing technology. We can now identify structural variants (SVs) such as insertions, deletions and other rearrangements, allowing further insights into the genetic architecture of speciation and how different types of variants are involved in species differentiation. Here, we investigated genomic patterns of differentiation between sympatric species pairs (Dwarf and Normal) belonging to the lake whitefish (Coregonus clupeaformis) species complex. We assembled the first reference genomes for both C. clupeaformis sp. Normal and C. clupeaformis sp. Dwarf, annotated the transposable elements and analysed the genomes in the light of related coregonid species. Next, we used a combination of long- and short-read sequencing to characterize SVs and genotype them at the population scale using genome-graph approaches, showing that SVs cover five times more of the genome than SNPs. We then integrated both SNPs and SVs to investigate the genetic architecture of species differentiation in two different lakes and highlighted an excess of shared outliers of differentiation. In particular, a large fraction of SVs differentiating the two species correspond to insertions or deletions of transposable elements (TEs), suggesting that TE accumulation may represent a key component of genetic divergence between the Dwarf and Normal species. Together, our results suggest that SVs may play an important role in speciation and that, by combining second- and third-generation sequencing, we now have the ability to integrate SVs into speciation genomics.