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Groups of sympatric taxa with low interspecific genetic differentiation, but considerable ecological differences, offer great opportunities to study the dynamics of divergence and speciation. This is the case of ciscoes (Coregonus spp.) in the Laurentian Great Lakes, which are characterized by a complex evolutionary history and are commonly described as having undergone an adaptive radiation. In this study, morphometrics, stable isotopes and transcriptome sequencing were used to study the relationships within the Coregonus artedi complex in western Lake Superior. We observed general concordance for morphological, ecological and genomic variation, but the last was more taxonomically informative as it showed less overlap among species in multivariate space. Low levels of genetic differentiation were observed between individuals morphologically identified as Coregonus hoyi and C. zenithicus, which could be evidence of incomplete lineage sorting or recent hybridization between the two groups. Transcriptome-based single nucleotide polymorphisms exhibited significant divergence for genes associated with vision, development, metabolism and immunity among species that occupy different habitats. This study highlights the importance of using an integrative approach when studying groups of taxa with a complex evolutionary history, as individual-level analyses of multiple independent data sets can provide a clearer picture of the patterns and processes associated with the origins of biodiversity.

Hydroacoustic surveys using hull-mounted down-looking transducers are useful for estimating pelagic fish densities; however, this method may miss shallow fish owing to the acoustic surface dead zone and vessel avoidance. Our objective was to compare pelagic fish density estimates acquired by a traditional down-looking acoustic survey to estimates obtained by a new multi-directional-towed sled capable of sampling the entire water column using upward-, sideways-, and downward-aimed transducers simultaneously. We deployed both systems concurrently in the western arm of Lake Superior during a period of stable stratification. We found the two survey approaches provided significantly different estimates of fish density in the upper water column layer (~4–9 m below the lake surface) with the sled up-looking transducer providing 56 times higher densities compared to the traditional ship down-looking method. Densities also varied significantly in the 9–14 m layer where densities were 6.2 times higher in the sled survey. Midwater trawl sampling indicated that cisco (Coregonus artedi) and rainbow smelt (Osmerus mordax) were the predominant species occupying the uppermost 14 m of the water column. The two acoustic approaches provided similar results at water column depths >14 m where rainbow smelt and kiyi (Coregonus kiyi) were predominant. Overall, the sled-based method estimates were, on average, 2.5 times higher for the whole water column. Our findings show that the new sled can reduce bias by better sampling the surface dead zone leading to more accurate estimation of pelagic fish densities for both management and research.

Prey fish abundances in the Great Lakes are a driver for several agencies’ commitments to the Council of Lake Committees to support fisheries management. These management decisions have profound economic and social impacts within the Great Lakes region. Fisheries estimates done by echosounders or trawling may be biased due to the propagated noise from large fisheries vessels. In the first two years of a four-year collaborative study, crewed fisheries vessels and uncrewed Saildrone vessels were used to compare abundance estimates between “loud” and “quiet” vessels. To quantify the effects of ship noise on prey fish abundance estimates, a mobile ship noise measurement system was designed and deployed to measure radiated acoustic signatures of several ships in the Great Lakes. This talk will discuss the deployment of a mobile underwater acoustic test range and show results of ship noise measurements from the first two years of the program. In addition, plans for future data generation, analysis, and comparison between crewed and autonomous systems will be discussed and an overview of the effects of ship noise on fish avoidance will be discussed in the proceeding talk.

Acoustic surveys of fish are a foundational component of many fisheries monitoring programs, including surveys in the Great Lakes. These surveys are conducted with traditional crewed and motorized vessels, but fish avoidance of these types of platforms has been reported in multiple studies, potentially biasing estimates. A quiet uncrewed surface vessel, Saildrone, was equipped with a 120 kHz Simrad EK80 transducer and deployed in Lakes Huron, Michigan, and Superior in the summers of 2021 and 2022. The drone was then overtaken by numerous motorized vessels using transducers with the same frequency. The average target depth, target strength, and nautical area scattering during overtakes were compared. We looked for a fish behavioral response with General Additive Models using distance from the Saildrone to the vessel as the predictor. We also compared the effectiveness of acoustic surveys from each platform with analyses of variances over 2 km sections of the overtake. Fish showed a limited response to approaching vessels, and acoustic estimates of fisheries relevant measures were similar between Saildrone and motorized vessels. Findings from this work will inform interpretation of acoustic data in the Great Lakes and provide the largest scale testing of fish avoidance to acoustic surveys to date.

Ecosystem-based management relies on understanding how perturbations influence ecosystem structure and function (e.g., invasive species, exploitation, abiotic changes). However, data on unimpacted systems are scarce, therefore, we often rely on impacted systems to make inferences about ‘natural states.’ Among the Laurentian Great Lakes, Lake Superior provides a unique case study to address non-native species impacts because the food web is dominated by native species. Additionally, Lake Superior is both vertically (benthic versus pelagic) and horizontally (nearshore versus offshore) structured by depth, providing an opportunity to compare the function of these sub-food webs. We developed an updated Lake Superior EcoPath model using data from the 2005/2006 lake-wide multi-agency surveys covering multiple trophic levels. We then compared trophic transfer efficiency (TTE) to previously published EcoPath models. Finally, we compared ecosystem function of the 2005/2006 ecosystem to that with non-native linkages removed and compared native versus non-native species-specific approximations of TTE and trophic flow. Lake Superior was relatively efficient (TTE = 0.14) compared to systems reported in a global review (average TTE = 0.09) and the microbial loop was highly efficient (TTE > 0.20). Non-native species represented a very small proportion (

Groups of sympatric taxa with low inter-specific genetic differentiation, but considerable ecological differences, offer great opportunities to study the dynamics of divergence and speciation. This is the case of ciscoes (Coregonus spp.) in the Laurentian Great Lakes, which are characterized by a complex evolutionary history and are commonly described as having undergone an adaptive radiation. In this study, morphometrics, stable isotopes and transcriptome sequencing were used to study the relationships within the Coregonus artedi complex in western Lake Superior. We observed general concordance for morphological, ecological and genomic variation, but the latter was more taxonomically informative as it showed less overlap among species in multivariate space. Low levels of genetic differentiation were observed between individuals morphologically identified as C. hoyi and C. zenithicus, and we hypothesize this could be associated with recent hybridization between the two species. Transcriptome-based single nucleotide polymorphisms exhibited significant divergence for genes associated with vision, development, metabolism and immunity, among species that occupy different habitats. This study highlights the importance of using an integrative approach when studying groups of taxa with a complex evolutionary history, as individual-level analyses of multiple independent datasets can provide a clearer picture of the patterns and processes associated with the origins of biodiversity.

Local adaptation can drive diversification of closely related species across environmental gradients and promote convergence of distantly related taxa that experience similar conditions. We examined a potential case of adaptation to novel visual environments in a species flock (Great Lakes salmonids, genus Coregonus) using a new amplicon genotyping protocol on the Oxford Nanopore Flongle and MinION. We sequenced five visual opsin genes for individuals of Coregonus artedi, Coregonus hoyi, Coregonus kiyi, and Coregonus zenithicus. Comparisons revealed species-specific differences in a key spectral tuning amino acid in rhodopsin (Tyr261Phe substitution), suggesting local adaptation of C. kiyi to the blue-shifted depths of Lake Superior. Ancestral state reconstruction demonstrates that parallel evolution and “toggling” at this amino acid residue has occurred several times across the fish tree of life, resulting in identical changes to the visual systems of distantly related taxa across replicated environmental gradients. Our results suggest that ecological differences and local adaptation to distinct visual environments are strong drivers of both evolutionary parallelism and diversification.

Stock assessments are critical to modern fisheries management, supporting the calculation of key reference variables used to make informed management decisions. However, there is still considerable uncertainty as to which class of assessment models is appropriate to use under different circumstances. A common class of models used when age data are available are statistical catch-at-age assessment (SCAA) models, which track annual cohorts through time. When age data are unavailable, as is often the case in invertebrate fisheries where the lack of a bony structure such as otoliths makes aging difficult, statistical catch-at-size assessment (SCSA) models are more often employed, tracking fish or invertebrates through time by size-classes rather than ages. Do SCAA models actually perform better than SCSA models when age data are available, or is this just an assumption we make in fisheries research and management? We examined this question by evaluating the effectiveness of both SCAA and SCSA models in characterizing cisco, Coregonus artedi, population dynamics in Thunder Bay, Ontario. Both models were fit using an integrated framework with multiple sources of data including hydroacoustic estimates of spawning stock, fishery-dependent and -independent age/length compositions, and harvest data. Our results suggest that for cisco in Thunder Bay, data-limitations related to lack of size-composition data over the size range for which cisco growth is rapid resulted in difficulty estimating relative year-class strength within a SCSA. This led to parameter confounding and ultimately the inability to estimate natural mortality within a SCSA. This hampered the utility of a SCSA model in comparison with a SCAA model when age-composition data were available.

We examined the spatial scale of recruitment variability for disparate cisco (Coregonus artedi) populations in the Great Lakes (n = 8) and Minnesota inland lakes (n = 4). We found that the scale of synchrony was approximately 400 km when all available data were utilized; much greater than the 50-km scale suggested for freshwater fish populations in an earlier global analysis. The presence of recruitment synchrony between Great Lakes and inland lake cisco populations supports the hypothesis that synchronicity is driven by climate and not dispersal. We also found synchrony in larval densities among three Lake Superior populations separated by 25–275 km, which further supports the hypothesis that broad-scale climatic factors are the cause of spatial synchrony. Among several candidate climate variables measured during the period of larval cisco emergence, maximum wind speeds exhibited the most similar spatial scale of synchrony to that observed for cisco. Other factors, such as average water temperatures, exhibited synchrony on broader spatial scales, which suggests they could also be contributing to recruitment synchrony. Our results provide evidence that abiotic factors can induce synchronous patterns of recruitment for populations of cisco inhabiting waters across a broad geographic range, and show that broad-scale synchrony of recruitment can occur in freshwater fish populations as well as those from marine systems.

International audience; Fish species diversity can be lost through interacting stressors including habitat loss, stocking and overfishing. Although a multitude of stressors have played a role in the global decline of coregonid (Coregonus spp.) diversity, a number of contemporary studies have identified habitat loss stem-ming from eutrophication as the primary cause. Unfortunately, reconstructing the role of fishing and stocking practices can be difficult, because these records are incomplete or appear only in hard-to-access historic grey literature. Based on an illustrative set of historic and contemporary studies, we describe how fisheries management practices may have contributed to coregonid di-versity loss in European and North American lakes. We provide case studies examining how fish-ing and stocking may reduce coregonid diversity through demographic decline and introgressive hybridization. In some lakes, fisheries management practices may have led to a loss of coregonid diversity well before issues with habitat degradation manifested. Our review suggests that fish conservation policies could beneficially consider the relative importance of all stressors, including management practices, as potential drivers of diversity loss.

The ability of planktivorous fishes to exert top-down control on Bythotrephes potentially has far-reaching impacts on aquatic food-webs, given previously described effects of Bythotrephes on zooplankton communities. We estimated consumption of Bythotrephes by planktivorous and benthivorous fishes, using bioenergetics and daily ration models at nearshore (18 m), intermediate (46 m), and offshore (110 m) depths along one western Lake Superior transect (April, and September–November) and two northern Lake Michigan transects (April, July, and September). In Lake Superior, consumption (primarily by cisco Coregonus artedi ) exceeded Bythotrephes production at all offshore sites in September–November (up to 396% of production consumed) and at the intermediate site in November (842%) with no evidence of consumption nearshore. By comparing Bythotrephes biomass following months of excessive consumption, we conservatively concluded that top-down control was evident only at the offshore site during September–October. In Lake Michigan, consumption by fishes (primarily alewife Alosa pseudoharengus ) exceeded production at nearshore sites (up to 178%), but not in deeper sites ( Bythotrephes never subsequently declined. Using generalized additive models, temperature, and not fish consumption nor zooplankton prey density, best explained variability in Bythotrephes biomass. The non-linear pattern revealed Bythotrephes to increase with temperature up to 16 °C, and then decline between 16 and 23 °C. We discuss how temperature likely has direct negative impacts on Bythotrephes when temperatures near 23 °C, but speculate that predation also contributes to declining biomass when temperatures exceed 16 °C.

All examples of lake charr (Salvelinus namaycush) diversity occur within the largest, deepest lakes of North America (i.e. > 2000 km2). We report here Rush Lake (1.3 km2) as the first example of a small lake with two lake charr morphs (lean and huronicus). Morphology, diet, life history, and genetics were examined to demonstrate the existence of morphs and determine the potential influence of evolutionary processes that led to their formation or maintenance. Results showed that the huronicus morph, caught in deep-water, had a deeper body, smaller head and jaws, higher eye position, greater buoyancy, and deeper peduncle than the shallow-water lean morph. Huronicus grew slower to a smaller adult size, and had an older mean age than the lean morph. Genetic comparisons showed low genetic divergence between morphs, indicating incomplete reproductive isolation. Phenotypic plasticity and differences in habitat use between deep and shallow waters associated with variation in foraging opportunities seems to have been sufficient to maintain the two morphs, demonstrating their important roles in resource polymorphism. Rush Lake expands previous explanations for lake charr intraspecific diversity, from large to small lakes and from reproductive isolation to the presence of gene flow associated with strong ecological drivers.

The aim of the present study was to understand how seasonal fish distributions affect acoustically derived fish biomass estimates in a shallow reservoir in a semi-arid country (Tunisia). To that end, sampling events were performed during four seasons (spring (June), summer (September), autumn (December) and winter (March)) that included day and night surveys. A Simrad EK60 echosounder, equipped with two 120-kHz split-beam transducers for simultaneous horizontal and vertical beaming, was used to sample the entire water column. Surveys during spring and summer and daytime hours of winter were deemed unusable owing to high methane flux from the sediment, and during the day survey of autumn, fish were close to the reservoir bottom leading to low detectability. It follows that acoustic surveys should be conducted only at night during the cold season (December–March) for shallow reservoirs having carp Cyprinus carpio (L.) as the dominant species. Further, night-time biomass estimates during the cold season declined significantly (P