Lake trout reproduction has increased in Lake Michigan since the 2000 s. Previous genetic studies reported that the strains of stocked adults did not contribute equally to wild recruits. Consequently, reproductive potential of spawning biomass estimated in stock assessments will depend upon strain composition, complicating comparisons across time and space. We integrated data from a stock assessment with genetic data to estimate an effective lake trout spawning biomass that accounts for strain-specific reproductive efficiency. A reproductive power index (RPI) was developed for six strains of hatchery-reared lake trout using genetic data from lakes Michigan and Huron. The RPI is the ratio of the observed to expected genetic contribution of a strain to wild recruits. The Seneca Lake strain had the highest RPI, followed by Lake Manitou, Lewis Lake, Green Lake, Lake Superior, and Lake Huron strains. The RPI in southern Lake Michigan was 2.56 for Seneca Lake, 0.74 for Lake Superior, 0.50 for Lewis Lake, and 0.32 for Green Lake strains. Strain-specific effective spawning biomass in southern Lake Michigan was estimated using numbers stocked, population demographics from a stock assessment, and RPI to develop an annual effective spawning biomass index (ESBI) as a measure of reproductive potential. After 1996, ESBI increased faster than spawning biomass, and continued to increase when spawning biomass leveled off, reflecting the shift toward lake trout strains with higher RPI. The contribution to the ESBI after 2010 was 46 % Seneca Lake, 34 % wild adults, 12 % Lake Superior, and 4 % for the Lewis Lake and Green Lake strains.

ObjectiveThis purpose of this paper is to describe the characteristics of recovered Lake Trout Salvelinus namaycush populations in Lake Superior by describing its population dynamics, ecology, and recent research and management activities since 1993, when Lake Trout were declared rehabilitated.MethodsData from commercial fisheries, recreational fisheries, agency stocking reports, and natural resource agency fishery-independent survey data along with published research findings on lean Lake Trout in Lake Superior between 1993 and 2022 were synthesized and reported.ResultCurrently, Lake Trout populations are self-sustaining and lightly exploited with only a few areas with elevated total mortality rates. The total annual mortality has been far below the target maximum range of 42-45%. Furthermore, stocking of hatchery Lake Trout is no longer necessary.ConclusionWe have learned from research and management experience that the regulatory role of Lake Trout in the Great Lakes is critical to proper ecosystem function. Thus, continued commitment from natural resource agencies to cooperate and implement effective management actions is required to preserve the accomplishments of lakewide recovery of Lake Trout populations. Impact statement The Lake Trout is the keystone predator in deepwater areas of the Great Lakes, and its successful recovery in Lake Superior has restored ecosystem stability and valued fisheries. This paper synthesizes information that describes the status of a highly managed species after restoration objectives have been achieved and maintained.

Objective: Overfishing and Sea Lamprey Petromyzon marinus predation led to extirpation of Lake Trout Salvelinus namaycush from Lake Michigan in the 1950s. Large populations of hatchery-reared fish were developed by the 1970s, but natural reproduction was limited until the early 2000s when it began to increase in the southern main basin. Hypothesizing that the relatively low mortality of spawning-aged fish contributed to this reproductive success, we estimated the total annual mortality rate for this population. Methods: We used catch curves to estimate the total instantaneous mortality rate Z using coded wire tags, which provided definitive ages. We made separate estimates from fish collected in three on-going surveys: a spring gill-net survey, a fall gill-net spawning survey, and a sport fishery survey. Result: Our estimates of Z +/- SE were 0.297 +/- 0.019, 0.239 +/- 0.009, and 0.205 +/- 0.007 for the spring, spawning, and sport fishery surveys, respectively. We suggest that the mean Z +/- SE of all survey estimates of 0.247 +/- 0.027 would be a reasonable estimate for this population, which equates to a total annual mortality of 22 +/- 3%. This estimate is in the low range of rates reported for the species and is in the same range as other populations in the Great Lakes with well-established natural reproduction. Conclusion: We concluded that these low total mortality rates contributed to the reproductive success in southern Lake Michigan through increasing spawning stock density and age structure and that previous estimates of another important population parameter, the instantaneous natural mortality rate M, were too high. Estimates of M ranged from 0.210 to 0.240 and were based on the Pauly equation, a growth- and temperature-based estimator. We suggest maximum-age-based estimators of M are more appropriate for Lake Trout. Several alternative maximum-age-based estimators produced estimates for M of 0.132-0.058, all of which are more compatible with our estimate of Z.

Management of a widely distributed species can be a challenge when management priorities, resource status, and assessment methods vary across jurisdictions. For example, restoration and preservation of coregonine species diversity is a goal of management agencies across the Laurentian Great Lakes. However, management goals and the amount of information available varies across management units, making the focus for management efforts challenging to determine. Genetic data provide a spatially consistent means to assess diversity. Therefore, we examined the genetic stock structure of cisco (Coregonus artedi) in the Great Lakes where the species is still extant. Using genotype data from 17 microsatellite DNA loci, we observed low levels of population structure among collections with most contributions to overall diversity occurring among lakes. Cisco from lakes Superior, Michigan, Ontario, and the St. Marys River could be considered single genetic populations while distinct genetic populations were observed among samples from northern Lake Huron. Significant within-lake diversity in Lake Huron is supported by populations found in embayments in northern Lake Huron. The Grand Traverse Bay population in Lake Michigan represents a distinct population with reduced levels of genetic variation when compared to other lakes. The different levels of within lake population structure we observed will be important to consider as future lake-specific management plans are developed.

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.

We estimated total mortality using catch curves based on relative return rates (RRs) of coded wire tagged lake trout (Salvelinus namaycush) in US waters of Lake Huron. RR was calculated as age-specific CPUE per million of fish stocked. Annual mortality for the late 1990s through early 2000s was estimated as 38% from the 1991–1995 year classes, with an effective age range of 5–10 years, and then was estimated as 24% for the post-2000 period from the 1996–2009 year classes. The two estimates from simple catch curve regressions based on average RR at age values were the same as from a mixed model with individual RR values from all stocking events. These two estimates were also comparable to the findings from statistical catch-at-age assessments with fundamentally different assumptions. Our approach is not constrained by the assumption that the expected recruitment is a constant over time and thus has the advantage to use multiple observations on each age from multiple cohorts. Our approach has broad applicability to aquatic ecosystems in which multiple mark-and-release events of fish stocking have been implemented.

In response to invasive species, the course of action taken by management agencies often evolves over a range of options from a do-nothing approach to suppression to complete eradication. As a case study of suppression targets, we explore the history of approaches used by the Great Lakes Fishery Commission in response to the invasion of the Laurentian Great Lakes by sea lampreys (Petromyzon marinus). With the early realization that eradication was not possible using available techniques, focus shifted to suppression of sea lampreys to support fish community objectives for the lakes. As a surrogate for damage to the fishery, a suppression target was defined for the maximum acceptable marking rate, indicated by the average number of sea lamprey wounds observed on every 100 large lake trout (Salvelinus namaycush) surveyed. Historic marking rates were used to delineate time periods of acceptable sea lamprey predation levels as an approximate measure of sea lamprey-induced mortality. A second target, independent of lake trout population status, was based on the average sea lamprey abundance estimated during the specified time periods. These intuitive targets have served as suppression benchmarks for the Sea Lamprey Control Program in the Great Lakes, allowing decision makers to gauge progress towards targets, refine control strategies and prioritize geographic areas for increased control effort. Here we document the development and subsequent changes to targets, summarize the methods used to implement these changes, and provide considerations for the future.

Fecundity of fish is influenced by several factors, including body length, condition, population density, and environmental conditions. It follows that fecundity of fish populations can exhibit spatiotemporal variability; thus, periodic quantification of length-fecundity relationships is important for management. We hypothesized that average fecundity of CiscoCoregonus artediin the upper Laurentian Great Lakes would be lower in Lake Superior than in Lakes Huron and Michigan. The trophic status of these lakes recently converged, but Lakes Huron and Michigan currently support lower Cisco densities; thus, we expected that they would reach larger sizes and have greater fecundity owing to lower intraspecific competition. Ovaries were collected from prespawn Cisco during 2008-2010 to test this hypothesis. We also compared length-fecundity relationships for 2008-2010 to those of precollapse (1930s-1950s) populations to explore how relationships have changed. Average fecundity of Cisco during 2008-2010 was lower in Lake Superior compared to Lakes Huron and Michigan; length-fecundity relationships in the latter two lakes did not vary significantly, so they were combined. Body condition was highest in Lakes Huron and Michigan. We used otoliths to determine age and found that body condition was domed shaped with respect to age in Lakes Huron and Superior. There were no females older than age 5 in our samples from Lake Michigan because that population was just beginning to recover from very low levels. Females of intermediate age had the highest fecundities in both Lake Huron (ages 7-13) and Lake Superior (ages 8-18). We hypothesize that differences in body morphometry may also influence fecundity, with deeper-bodiedC. artedi albus, the predominant form in Lakes Michigan and Huron, having greater fecundity than shallower-bodiedC. artedi artediin Lake Superior. Moreover, varying Cisco diets and seasonal movement patterns across lakes may have also contributed to differences. Females in Lakes Superior and Michigan are currently more fecund than their precollapse counterparts.

Lake sturgeon populations in the Laurentian Great Lakes experience two age-specific mortality sources influenced by the sea lamprey Petromyzon marinus control program: lampricide (TFM) exposure-induced mortality on age-0 fish and sea lamprey predation on sub-adults (ages 7–24). We used a generic age-structured population model to show that although lampricide-induced mortality on age-0 lake sturgeon can limit attainable population abundance, sea lamprey predation on sub-adult lake sturgeon may have a greater influence. Under base conditions, adult lake sturgeon populations increased by 5.7% in the absence of TFM toxicity if there was no change in predation; whereas, a 13% increase in predation removed this effect, and a doubling of sea lamprey predation led to a 32% decrease in adult lake sturgeon. Our estimates of lake sturgeon abundance were highly dependent on the values of life history and mortality parameters, but the relative impacts of ceasing TFM treatment and increasing predation were robust given a status quo level of predation. The status quo predation was based on sea lamprey wounding on lake sturgeon, and improvements in this information would help better define tradeoffs between the mortality sources for specific systems. Reduction or elimination of TFM toxicity on larval lake sturgeon, while maintaining TFM toxicity on larval sea lamprey, can promote lake sturgeon restoration and minimize negative impacts on other fish community members.

Spatially separated fish populations may display synchrony in annual recruitment if the factors that drive recruitment success, particularly abiotic factors such as temperature, are synchronised across broad spatial scales. We examined inter-annual variation in recruitment among lake whitefish (Coregonus clupeaformis) populations in lakes Huron, Michigan and Superior using fishery-dependent and -independent data from 1971 to 2014. Relative year-class strength (RYCS) was calculated from catch-curve residuals for each year class across multiple sampling years. Pairwise comparison of RYCS among datasets revealed no significant associations either within or between lakes, suggesting that recruitment of lake whitefish is spatially asynchronous. There was no consistent correlation between pairwise agreement and the distance between datasets, and models to estimate the spatial scale of recruitment synchrony did not fit well to these data. This suggests that inter-annual recruitment variation of lake whitefish is asynchronous across broad spatial scales in the Great Lakes. While our method primarily evaluated year-to-year recruitment variation, it is plausible that recruitment of lake whitefish varies at coarser temporal scales (e.g. decadal). Nonetheless, our findings differ from research on some other Coregonus species and suggest that local biotic or density-dependent factors may contribute strongly to lake whitefish recruitment rather than inter-annual variability in broad-scale abiotic factors.

Movement ecology is an important component of life history and population dynamics, and consequently its understanding can inform successful fishery management decision-making. While lake trout populations in Lake Huron have shown signs of recovery from near extinction in recent years, knowledge of their movement behavior remains incomplete. We used acoustic telemetry to describe and compare movement patterns of two Lake Huron lake trout populations: Drummond Island and Thunder Bay. Both populations showed high spawning site fidelity, with no evidence of co-mingling during non-spawning season. Detections between spawning periods were mainly limited to receivers within 100km of spawning locations, and suggested that the two populations likely remained segregated throughout the year. Drummond Island fish, which spawn inside the Drummond Island Refuge, primarily dispersed east into Canadian waters of Lake Huron, with 79–92% of fish being detected annually on receivers outside the refuge. In contrast, Thunder Bay fish tended to disperse south towards Saginaw Bay. Large proportions (i.e., >80%) of both populations were available to fisheries outside the management zone containing their spawning location. Thunder Bay fish moved relatively quickly to overwinter habitat after spawning, and tended to repeat the same post-spawning movement behavior each year. The consistent, predictable movement of both populations across management zones highlights the importance of understanding population dynamics to effective management of Lake Huron lake trout.

Understanding fish movement patterns is vital for stock assessment and fishery management. We used a variable selection procedure in a Bayesian framework to understand what factors most likely affect the net movement distance of individual fish based on a conventional tag-recovery study of lake whitefish populations in Lake Huron during 2003–2011, where fish of this species with spawning site fidelity were tagged during the spawning season and recovered throughout the year. We found that fish with greater total length, and those that were tagged and released from tagging sites near Cheboygan and Alpena, Michigan, moved longer net distances than fish from other tagging sites. Habitat conditions also had a profound effect on net movement distance. We found that shorter movement distances by lake whitefish can be expected if the relative density of the benthic amphipod Diporeia spp. was higher near the tagging site during the recovery year. We also found evidence that lake whitefish may start their annual spawning migration runs earlier during warmer years. More generally, our Bayesian framework for analysis of conventional tagging data has potential for wide applicability, and model details and our code are provided to facilitate this.

We evaluated the ecosystem regime shift in the main basin of Lake Huron that was indicated by the 2003 collapse of alewives (Alosa pseudoharengus) and dramatic declines in Chinook salmon (Oncorhynchus tshawytscha) abundance thereafter. We found that the period of 1995–2002 should be considered as the early phase of the final regime shift. We developed two Bayesian hierarchical models to describe time-varying growth based on the von Bertalanffy growth function and the length–mass relationship. We used asymptotic length as an index of growth potential and predicted body mass at a given length as an index of body condition. Modeling fits to length and body mass at age of lake trout (Salvelinus namaycush), Chinook salmon, and walleye (Sander vitreus) were excellent. Based on posterior distributions, we evaluated the shifts in among-year geometric means of the growth potential and body condition. For a given top piscivore, one of the two indices responded to the regime shift much earlier than the 2003 collapse of alewives, the other corresponded to the 2003 changes, and which index provided the early signal differed among the three top piscivores.

Catch-at-age or catch-at-size stock assessment models require specification of an effective sample size (ESS) as a weighting component for multinomial composition data. ESS weights these data relative to other data that are fit, and is not an estimable parameter within a model that uses a multinomial likelihood. The ESS is typically less than the actual sample size (the number of fish) because of factors such as sampling groups of fish (clusters) that are caught together. A common approach for specifying ESS is to iteratively re-fit the model, estimating ESS after each fit so that the standardized residual variance is “correct,” until ESS converges. We survey iterative methods for determining ESS for a multinomial likelihood and apply them to two Great Lakes whitefish stocks. We also propose an extension of such methods: (the Generalized Mean Approach – GMA) for the case where ESS is based on mean age (or length) to account for correlation structures among proportions. Our extension allows for greater flexibility in the relationship between ESS and sampling intensity. Our results show that the choice of ESS estimation method can impact assessment model results. Simulations (in the absence of correlation structures) showed that all the approaches to calculating effective sample size could provide reasonable results on average, however methods that estimated annual ESS independently across years were highly imprecise. In our simulations and application, methods: that did account for correlation structure in annual proportions produced lower ESS than those that did not and suggested that these methods are adjusting for a deviation from the multinomial correlation structure. We recommend using methods that adjust for correlation structures in the proportions, and either assuming a constant ESS or, when there is substantial inter-annual variation in sampling levels, assuming ESS is related to sampling intensity and using the GMA or a similar approach to estimate that relationship.

We determined whole-fish Hg concentrations of 26 female and 34 male adult lake whitefish (Coregonus clupeaformis) from northern Lake Huron captured during November 2010. Subsampling from these 60 fish, Hg concentration was also determined in both somatic tissue and ovaries (n = 5), while methylmercury (MeHg) concentration was determined in whole fish (n = 18). Bioenergetics modeling was used to assess the growth dilution effect on the difference in Hg concentrations between the sexes. Mean whole-fish Hg concentration in females (59.9 ng/g) was not significantly different from mean whole-fish Hg concentration in males (54.4 ng/g). MeHg accounted for 91% of the mercury found in the lake whitefish. Bioenergetics modeling results indicated that the growth dilution effect did not contribute to the difference in Hg concentrations between the sexes. We estimated that females increased in Hg concentration by 17.9%, on average, immediately after spawning due to release of eggs. Using polychlorinated biphenyl (PCB) data for the same 60 lake whitefish from a previous study, we detected a significant interaction between sex and contaminant type (Hg or PCBs), which was attributable to males being significantly higher in PCB concentration than females. Males may be eliminating Hg at a faster rate than females.

He et al. (2015) described piscivory patterns in themain basin of Lake Huron for 1984–2010, during which there was also a pattern of stepwise declines in the abundance of dominant prey fish species. The approach of He et al. (2015) was to couple age-structured stock assessment and fish bioenergetics models to estimate prey fish consumption and to compare these patterns with prey fish biomass from a bottom trawl survey. Riley andDunlop (2016) were highly critical of themethods and conclusions reached byHe et al. (2015). They claimed that we incorrectly interpreted the bottom trawl survey data and did not account for uncertainty. We respond to these and other criticisms below, which we find do not undermine our findings.

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 400km 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 25–275km, 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.

We quantified piscivory patterns in the main basin of Lake Huron during 1984–2010 and found that the biomass transfer from prey fish to piscivores remained consistently high despite the rapid major trophic shift in the food webs. We coupled age-structured stock assessment models and fish bioenergetics models for lake trout (Salvelinus namaycush), Chinook salmon (Oncorhynchus tshawytscha), walleye (Sander vitreus), and lake whitefish (Coregonus clupeaformis). The model system also included time-varying parameters or variables of growth, length–mass relations, maturity schedules, energy density, and diets. These time-varying models reflected the dynamic connections that a fish cohort responded to year-to-year ecosystem changes at different ages and body sizes. We found that the ratio of annual predation by lake trout, Chinook salmon, and walleye combined with the biomass indices of age-1 and older alewives (Alosa pseudoharengus) and rainbow smelt (Osmerus mordax) increased more than tenfold during 1987–2010, and such increases in predation pressure were structured by relatively stable biomass of the three piscivores and stepwise declines in the biomass of alewives and rainbow smelt. The piscivore stability was supported by the use of alternative energy pathways and changes in relative composition of the three piscivores. In addition, lake whitefish became a new piscivore by feeding on round goby (Neogobius melanostomus). Their total fish consumption rivaled that of the other piscivores combined, although fish were still a modest proportion of their diet. Overall, the use of alternative energy pathways by piscivores allowed the increases in predation pressure on dominant diet species.

We determined whole-fish polychlorinated biphenyl (PCB) concentrations in 26 female lake whitefish (Coregonus clupeaformis) and 34 male lake whitefish from northern Lake Huron. In 5 of the 26 female lake whitefish, we also determined PCB concentrations in the somatic tissue and ovaries. In addition, bioenergetics modeling was used to determine the contribution of the growth dilution effect to the observed difference in PCB concentrations between the sexes. Whole-fish PCB concentrations for females and males averaged 60 ng/g and 80 ng/g, respectively; thus males were 34% higher in PCB concentration compared with females. Based on the PCB determinations in the somatic tissue and ovaries, we predicted that PCB concentration of females would increase by 2.5%, on average, immediately after spawning due to release of eggs. Thus, the change in PCB concentration due to release of eggs did not explain, to any degree, the higher PCB concentrations observed in males compared with females. Bioenergetics modeling results indicated that the growth dilution effect could account for males being only 0.7% higher in PCB concentration compared with females. Thus, the growth dilution effect contributed very little to the observed difference in PCB concentrations between the sexes. We conclude that males were higher than females in PCB concentration most likely due to a higher rate of energy expenditure, stemming from greater activity and a greater resting metabolic rate. A higher rate of energy expenditure leads to a higher rate of food consumption, which, in turn, leads to a higher PCB accumulation rate.

Recent observations of spawning lake trout Salvelinus namaycush near Drummond Island in northern Lake Huron indicate that lake trout use drumlins, landforms created in subglacial environments by the action of ice sheets, as a primary spawning habitat. From these observations, we generated a hypothesis that may in part explain locations chosen by lake trout for spawning. Most salmonines spawn in streams where they rely on streamflows to sort and clean sediments to create good spawning habitat. Flows sufficient to sort larger sediment sizes are generally lacking in lakes, but some glacial bedforms contain large pockets of sorted sediments that can provide the interstitial spaces necessary for lake trout egg incubation, particularly if these bedforms are situated such that lake currents can penetrate these sediments. We hypothesize that sediment inclusions from glacial scavenging and sediment sorting that occurred during the creation of bedforms such as drumlins, end moraines, and eskers create suitable conditions for lake trout egg incubation, particularly where these bedforms interact with lake currents to remove fine sediments. Further, these bedforms may provide high-quality lake trout spawning habitat at many locations in the Great Lakes and may be especially important along the southern edge of the range of the species. A better understanding of the role of glacially-derived bedforms in the creation of lake trout spawning habitat may help develop powerful predictors of lake trout spawning locations, provide insight into the evolution of unique spawning behaviors by lake trout, and aid in lake trout restoration in the Great Lakes.