Lake Whitefish Stocks Research Articles

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.

Defining the Need for Genetic Stock Assignment when Describing Stock Demographics and Dynamics: an Example using Lake Whitefish in Lake Michigan

AbstractGenetic stock assignment is not routinely used when describing the dynamics and demographics of individual stocks supporting mixed‐stock fisheries, and capture location and timing are often used as alternative assignment methods. However, variation in stock demographics and dynamics may not be accounted for if stock assignments based on capture location or timing do not accurately reflect genetic assignments. We used Lake Whitefish Coregonus clupeaformis in Lake Michigan as a model fishery to determine whether stock mixing could undermine efforts to describe stock status when using October capture location as a proxy for genetic stock assignment. Accuracy of stock assignments based on October capture location ranged from 54% to 100% among management zones. Metrics describing length and age distributions, weight at length, fecundity, and growth varied among genetic stocks. Stock‐specific metrics were typically similar between stock assignment methods (capture location versus genetics) because only one or two genetic stocks were collected in most locations and the majority of those fish were from spatially proximal stocks with similar metrics. However, more extensive mixing of Lake Whitefish stocks has been documented; thus, using capture location for stock assignment could result in incorrect conclusions regarding stock status and harvest management depending on stock composition. Ambiguity in genetic stock assignments was a problem in two management zones, where between 23% and 42% of Lake Whitefish did not assign to a specific stock with a probability of at least 0.70. In the future, using genomic techniques rather than microsatellites may provide different conclusions regarding genetic stock structure; these differences could affect the accuracy of using capture location for stock assignment. Use of capture location as a proxy for genetic stock assignment may not be warranted for all mixed‐stock fisheries but may be appropriate when stock mixing is limited or is restricted to stocks with consistently similar characteristics.

Lake whitefish ( Coregonus clupeaformis ) energy and nutrient partitioning in lakes Michigan, Erie and Superior

A concurrent decrease in lake whitefish (Coregonus clupeaformis) condition and Diporeia spp. abundance in Lake Michigan has spurred investigations into possible links between the two phenomena. We examined female lake whitefish δ13C and δ15N stable isotopes, growth, reproductive investment, dorsal muscle total lipid and docosahexaenoic acid (DHA) contents from lakes Erie, Michigan and Superior to determine whether differences in food source were correlated with measures of stock success. Stocks with higher somatic growth rates and mean reproductive potential had higher energy stores in terms of percent total lipid. Stocks with low muscle lipid concentration also had smaller egg sizes as egg number increased. Diet varied among stocks as evidenced by δ13C and δ15N stable isotope analyses; however, muscle total lipid and DHA were not correlated to apparent Diporeia spp. prey use. When compared to stocks from lakes Erie and Superior, Lake Michigan stocks had lower growth, reproduction, and lipid stores. While stocks in Lake Michigan with access to declining Diporeia spp. populations may still feed on the amphipod, it appears that they are unable to consume the quantities necessary to maintain historical growth and reproduction. Stable isotope analyses of lakes Erie and Superior stocks, with higher growth rates and lipid values, indicated different feeding strategies with no indication of reliance on Diporeia spp. While differences in prey resources may have an effect on lake whitefish stocks, differences in Diporeia spp. abundance alone cannot explain differences in lake whitefish condition observed among the Great Lakes included in this study.

Measures of larval lake whitefish length and abundance as early predictors of year-class strength in Lake Michigan

Many lake whitefish stocks in Lake Michigan have experienced substantial declines in growth and condition since the 1990s. Reduced growth and condition could result in reduced quality or quantity of eggs produced by spawning females, which in turn could negatively impact recruitment. We evaluated the potential for reduced recruitment by measuring early life stage density and length, and we discuss the utility of these measures as early indicators of lake whitefish year-class strength. Overall, mean larval density (number per 1000 m 3 ± SE) in Lake Michigan was greater in 2006 (373.7 ± 28.3) than in 2005 (16.6 ± 24.8); whereas, mean length (mm ± SE) of larval lake whitefish was smaller in 2006 (12.87 ± 0.07) than in 2005 (14.38 ± 0.13). The ratio of zooplankton to fish density did not show an expected relationship with larval fish density or length. Rather, variation in larval density was best explained by a multiple-regression model that included larval length, spring wind intensity, and adult stock density as predictor variables. Our results suggest that the density of larval lake whitefish is not directly regulated by temperature or zooplankton density at the time of emergence, but that a potential for density-dependent regulation exists when larval emergence rates are high. We conclude that the observed declines in growth and condition of adult lake whitefish are not resulting in substantial reductions in recruitment.

Widespread infection of lake whitefish Coregonus clupeaformis with the swimbladder nematode Cystidicola farionis in northern lakes Michigan and Huron

We estimated the prevalence, intensity, and abundance of swimbladder nematode infection in 1281 lake whitefish ( Coregonus clupeaformis) collected from four sites in northern lakes Huron (Cheboygan and DeTour Village) and Michigan (Big Bay de Noc and Naubinway) from fall 2003 through summer 2006. Morphological examination of nematode egg, larval, and mature stages through light and scanning electron microscopy revealed characteristics consistent with that of Cystidicola farionis Fischer 1798. Total C. farionis prevalence was 26.94%, while the mean intensity and abundance of infection was 26.72 and 7.21 nematodes/fish, respectively. Although we detected C. farionis in all four stocks that were examined, Lake Huron stocks generally had higher prevalence, intensity, and abundance of infection than Lake Michigan stocks. A distinct seasonal fluctuation in prevalence, abundance, and intensity of C. farionis was observed, which does not coincide with reported C. farionis development in other fish species. Lake whitefish that were heavily infected with C. farionis were found to have thickened swimbladder walls with deteriorated mucosa lining, which could affect swimbladder function. Whether C. farionis infection may be negatively impacting lake whitefish stocks in the Great Lakes is unclear; continued monitoring of C. farionis infection should be conducted to measure responses of lake whitefish stocks to infection levels.

Estimates of fishing and natural mortality rates for four Lake Whitefish stocks in Northern Lakes Huron and Michigan

We analyzed tag-recovery data to estimate instantaneous fishing ( F) and natural mortality ( M) rates of four lake whitefish stocks in lakes Michigan and Huron during 2004–2007. We tagged and released 22,452 adult lake whitefish of which 8.7% were subsequently recovered. Annual tag-reporting rates ranged from 17.8% to 56.2%. Tag retention was high for the first 5–6 months after tagging, but tag loss increased substantially thereafter. Nine tag-recovery models were evaluated with respect to whether F and/or M varied among stocks, lakes, or years. There was support for three models based on Akaike information criteria. The best model had yearly and stock-specific estimates of F of 0.03 to 0.79 and lake-specific estimates of M of 0.35 for Lake Michigan and 0.60 for Lake Huron. The second best model had yearly and stock-specific estimates of F of 0.04 to 0.71 and a constant estimate for M of 0.52. The third model had yearly and stock-specific estimates of F of 0.04 to 0.85 and stock-specific estimates of M of 0.32 to 0.67. Model-averaged estimates of F ranged from 0.04 to 0.78 and were substantially different than statistical catch-at-age estimates of F. Model-averaged estimates of M ranged from 0.40 to 0.59 and were greater than estimates obtained from prediction equations, possibly due to sea lamprey-induced mortality. We recommend that tag-recovery estimates of F and M be used as Bayesian priors in future lake whitefish stock assessments to help refine mortality estimates for the stocks.

Infection of Lake Whitefish ( Coregonus clupeaformis) with motile Aeromonas spp. in the Laurentian Great Lakes

Infections with motile Aeromonas species were detected in lake whitefish collected over a one-year period from four stocks within lakes Michigan and Huron, USA. Sixty-nine isolates were recovered from the kidneys and swim-bladders of sixty-four infected fish. Representative isolates were Gram-negative bacilli that produced cytochrome oxidase, grew in the absence of salt, were facultative anaerobes, and were resistant to the vibriostatic agent 2,4-diamino,6,7-di-isopropylpteridine. Phenotypic characterization placed twenty-two isolates into the A. hydrophila complex, twelve into the A. sobria complex, and one into the A. caviae complex, while six isolates were characterized as A. allosaccharophila, two as A. veronii bv. veronii, and one as A. popoffi. The prevalence of infection by motile aeromonads varied by site and season, with lake whitefish sampled in the summer having a significantly higher prevalence. Clinical signs in lake whitefish infected only with Aeromonas spp. included congestion and hemorrhaging in the fins and musculature; generalized pallor; congestion, hemorrhaging, and multifocal necrotic foci within the liver; moderate to severe splenomegaly; congestion and swelling of the kidneys; ascites within the peritoneal cavity; and hemorrhagic enteritis. This study provides evidence on the wide spread prevalence of motile aeromonad infections in lake whitefish stocks inhabiting northern lakes Michigan and Huron.

An Evaluation of Age Estimation Structures for Lake Whitefish in Lake Michigan: Selecting an Aging Method Based on Precision and a Decision Analysis

AbstractDeclines in growth and condition of lake whitefish Coregonus clupeaformis in Lakes Huron and Michigan have led to increased mean age in the harvest and greater difficulty in scale age interpretation. We evaluated the precision and efficiency of scale acetate impressions, transverse pectoral fin ray sections, and transverse sagittal otolith sections for three lake whitefish stocks (Bailey's Harbor, Naubinway, and Saugatuck) that were sampled in Lake Michigan during 2004 and 2005. We conducted a decision matrix analysis that incorporated capital, production, and personnel costs and precision of age estimates to determine the best aging method given current management priorities. For the Bailey's Harbor stock, age estimates were systematically lower based on scales (mean = 7.85 years) than based on fin rays (8.44 years) or otoliths (8.78 years); fin ray and otolith estimates did not differ significantly. Similar results were observed for both Naubinway and Saugatuck stocks. For Bailey's Harbor lake whitefish, greater precision in age estimates was achieved by use of fin rays (median coefficient of variation [CV] = 4.88%) than by use of scales (5.44%) or otoliths (5.44%). For the Saugatuck stock, age estimates were more precise when obtained from pectoral fin rays (median CV = 4.96%) than from scales, but precision did not differ between fin ray and sagittal otolith ages. Differences between scale and pectoral fin ray age estimates began at age 5 for the Bailey's Harbor stock and at age 6 for the Naubinway and Saugatuck stocks. Differences between scale and sagittal otolith age estimates began at age 5 for the Bailey's Harbor and Saugatuck stocks and at age 8 for the Naubinway stock. Based on the decision matrix analysis, pectoral fin rays provided more‐precise estimates and their use involved lower costs than use of the other methods; therefore, pectoral fin rays were deemed the best method for aging lake whitefish in Lake Michigan under current conditions.

Population Dynamics and Management of Lake Whitefish Stocks in Grand Traverse Bay, Lake Michigan

The population parameters and movement patterns of lake whitefish Coregonus clupeaformis in Grand Traverse Bay, Lake Michigan, were investigated in response to an expanding commercial fishery. Tagging data indicated that distinct spawning populations exist in West, Outer, and East bays. Little mixing was observed during the fishing season between the West Bay and East Bay populations, but both contributed to the Outer Bay fishery. The West Bay population was predominantly localized and characterized by a broad age distribution and low exploitation rates. The East Bay population was characterized by a younger age distribution and higher exploitation rates. The Outer Bay fishery mainly consisted offish 4–6 years of age, with intermediate growth and exploitation rates. Biomass in the fishery decreased by 39%, from 439,000 kg in 1986 to 268,000 kg in 1987, because of a combination of increased exploitation and decreased recruitment. Catch quotas (total allowable catch, TAC) for Grand Traverse Bay stocks are dependent upon estimates of recruitment, which is unstable and unpredictable, Calculations of TAC that have resulted, if realized as true harvest levels, could jeopardize the integrity of these lake whitefish stocks. Calculations of TAC can be improved by including an index of the strength of the recruiting year-class.

Factors Affecting the Recruitment of Lake Whitefish in Two Areas of Northern Lake Michigan

Stock-recruitment and integrated recruitment models incorporating biotic and abiotic factors were developed for lake whitefish populations in northern Green Bay and the North Shore areas of Lake Michigan. Abundance and recruitment indices were calculated for the 1961-1985 year classes based on lake whitefish catch and effort data from the commercial fishery in each area. Previous research indicates that spawning stock abundance, winter ice cover, and spring temperatures are important in determining the egg and larval abundance and survival of lake whitefish. Therefore, spawning stock abundance, ice cover, winter wind velocity, and spring water and air temperature variables were used as model inputs in regression modeling. The biotic/abiotic recruitment model for northern Green Bay hindcasted lake whitefish recruitment as a function of spawning stock abundance and the number of days that ice cover exceeded 40% during egg incubation. This regression model (R 2 = 0.62) demonstrated improved hindcasting ability of historic recruitment when compared to the Beverton-Holt (R 2 = 0.37) or the Ricker (R 2 = 0.33) stock-recruitment models for the 1961-1985 cohorts. The biotic/abiotic recruitment model for the North Shore hindcasted lake whitefish recruitment as a function of average air temperature in May after larval emergence, the number of days that ice concentration exceeded 70% during egg incubation, and spawning stock abundance. The regression model (R 2 = 0.57) also demonstrated improved hindcasting ability of historical recruitment when compared with Beverton-Holt (R 2 = 0.09) or the Ricker (R 2 = 0.13) stock-recruitment models. Results of this study indicate that biotic/abiotic recruitment models were more successful in hindcasting recruitment than solely biologically based stock-recruitment relationships. Consideration of significant abiotic variables will be useful in the management of lake whitefish stocks in the Great Lakes by improving forecasts of recruitment.

Population Dynamics and Stock Differentiation of Lake Whitefish in Northeastern Lake Michigan with Implications for their Management

Lake whitefish (Coregonus clupeaformis) were tagged and the commercial trap-net catch was sampled in northeastern Lake Michigan to differentiate discrete stocks and determine their vital statistics. Distribution of tag returns and statistical comparisons of certain population parameters suggested the existence of at least three discrete stocks in the study area. The stock inhabiting the North Shore area of eastern Lake Michigan was considerably larger in both numbers and biomass than the stock fished near Leland, Michigan. The Leland catch had a broader age composition and contained larger fish than the North Shore and Beaver Island samples. Exploitation and total mortality rates were similar in the North Shore and in the Leland fisheries. The more abundant North Shore stock showed slower back-calculated and instantaneous growth than the Leland stock. In terms of management, statistics of abundance, growth, and mortality clearly varied between different lake whitefish stocks within Lake Michigan, indicating stock-by-stock management programs would be more likely to succeed than a lakewide program.

Population Statistics, Yield Estimates, and Management Considerations for Two Lake Whitefish Stocks in Lake Michigan

Lake whitefish (Coregonus clupeaformis) were tagged at North and Moonlight bays (NMB), Wisconsin and Big Bay de Noc (BBN), Michigan, and commercial catches were sampled in 1975-1980 to determine discreteness, distribution, biological statistics, and equilibrium yield per recruit for lake whitefish stocks in Green Bay and northern Lake Michigan. Discrete stocks were associated with the spawning grounds at NMB and BBN and fish from the NMB stock were migratory, whereas fish from the BBN stock were not. Age-3 lake whitefish dominated the commercial harvest from the BBN stock, but ages 3-5 comprised the majority of the harvest from the NMB stock. The 1972 and 1975 year classes were more abundant than other year classes in the 1975-1980 harvest from the NMB stock, whereas the 1976 year class was more abundant in the 1979-1980 harvest from the BBN stock. Mortality rates were higher for fish from the BBN stock (84%) than for fish from the NMB stock (65%), and fish of Age-7 and older experienced lower mortality rates than younger ages. Fishing caused a larger proportion of the total mortality in the BBN stock than in the NMB stock. The population size of the NMB stock was roughly 3-4 times larger than the BBN stock. Estimated yield per recruit was greater for the BBN stock than for the NMB stock and indicated that increasing the minimum size limit would reduce yield per recruit for both stocks but would increase the biomass of spawners and spawning frequency - substantially so in BBN. We concluded that management steps to delay age at recruitment to the fishery and increase the biomass would benefit the BBN stock but possibly not the NMB stock. Increased fishing effort on either population would not be beneficial for the stocks.