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Networks - The assessment of marine reserve networks: Guidelines for ecological evaluation

As marine ecosystems are plagued by an ever-increasing suite of threats including climate change, pollution, habitat degradation, and fisheries impacts (Roessig et al ., 2004; Lotze et al ., 2006; Jackson, 2008), there are now no ocean areas that are exempt from anthropogenic impacts (Halpern et al ., 2008). In order to preserve marine biodiversity, ecosystem function, and the goods and services provided by resistant and/or resilient systems, marine reserves have been increasingly recommended as part of an ecosystem-based approach to management (Browman and Stergiou, 2004; Levin et al ., 2009). Marine reserves are defined as “areas of the ocean completely protected from all extractive and destructive activities” (Lubchenco et al ., 2003) and can be experimental controls for evaluating the impact of these activities on marine ecosystems. Growing scientific information has shown consistent increases in species density, biomass, size, and diversity in response to full protection inside reserves of varying sizes and ages located in diverse regions (Claudet et al ., 2008; Lester et al ., 2009; Molloy et al ., 2009). However, most of these data are from individual marine reserves and therefore have inherently limited transferability to networks of marine reserves, which when properly designed can outperform single marine reserves for a variety of ecological, economic, and social management goals (Roberts et al ., 2003; Almany et al ., 2009; Gaines et al ., 2010). The concept of marine reserve networks grew out of a desire to achieve both conservation and fishery management goals by minimizing the potential negative economic, social, and cultural impacts of a single large reserve while still producing similar or even greater ecological and economic returns (Murray et al ., 1999; Gaines et al ., 2010). In addition, reserves networks can provide insurance by protecting areas across a region and spreading the risk that these sites may be impacted by localized catastrophes such as hurricanes or oil spills (Allison et al ., 2003). The World Conservation Union's Marine Programme defines a network as “a collection of individual marine protected areas (MPAs) or reserves operating co-operatively and synergistically, at various spatial scales and with a range of protection levels that are designed to meet objectives that a single reserve cannot achieve” (IUCN–WCPA, 2008). However, general terms such as “co-operatively” and “synergistically” can have myriad meanings. Without a clear definition of a network, it becomes difficult to identify attainable management goals and design a process for evaluating whether the network achieves those goals. Besides, different management goals may in turn result in the need for different types of networks. The use of MPAs with varying protection levels together with no-take zones in multiple-zoning schemes adds another layer of complexity to network design and evaluation; however, partially protected areas are generally used to manage coastal uses and avoid conflicts (rather than for strict ecological purposes) and are therefore a function of the local social, economic, and cultural context. As we are here interested in the ecological effects of networks, for the purposes of this chapter, we focus on marine reserves because these areas are no-take and therefore offer greater ecological benefits than other types of MPAs that allow some forms of extraction (Lester and Halpern, 2008).

Book chapter↗

Effects of climate and land-use changes on fish catches across lakes at a global scale

Globally, our knowledge on lake fisheries is still limited despite their importance to food security and livelihoods. Here we show that fish catches can respond either positively or negatively to climate and land-use changes, by analyzing time-series data (1970–2014) for 31 lakes across five continents. We find that effects of a climate or land-use driver (e.g., air temperature) on lake environment could be relatively consistent in directions, but consequential changes in a lake-environmental factor (e.g., water temperature) could result in either increases or decreases in fish catch in a given lake. A subsequent correlation analysis indicates that reductions in fish catch was less likely to occur in response to potential climate and land-use changes if a lake is located in a region with greater access to clean water. This finding suggests that adequate investments for water-quality protection and water-use efficiency can provide additional benefits to lake fisheries and food security.

Nature Communications↗

Expanding our view of the cold-water coral niche and accounting of the ecosystem services of the reef habitat

Coral reefs are iconic ecosystems that support diverse, productive communities in both shallow and deep waters. However, our incomplete knowledge of cold-water coral (CWC) niche space limits our understanding of their distribution and precludes a complete accounting of the ecosystem services they provide. Here, we present the results of recent surveys of the CWC mound province on the Blake Plateau off the U.S. east coast, an area of intense human activity including fisheries and naval operations, and potentially energy and mineral extraction. At one site, CWC mounds are arranged in lines that total over 150 km in length, making this one of the largest reef complexes discovered in the deep ocean. This site experiences rapid and extreme shifts in temperature between 4.3 and 10.7 °C, and currents approaching 1 m s −1 . Carbon is transported to depth by mesopelagic micronekton and nutrient cycling on the reef results in some of the highest nitrate concentrations recorded in the region. Predictive models reveal expanded areas of highly suitable habitat that currently remain unexplored. Multidisciplinary exploration of this new site has expanded understanding of the cold-water coral niche, improved our accounting of the ecosystem services of the reef habitat, and emphasizes the importance of properly managing these systems.

Scientific Reports↗

Critical assessment and ramifications of a purported marine trophic cascade

When identifying potential trophic cascades, it is important to clearly establish the trophic linkages between predators and prey with respect to temporal abundance, demographics, distribution, and diet. In the northwest Atlantic Ocean, the depletion of large coastal sharks was thought to trigger a trophic cascade whereby predation release resulted in increased cownose ray abundance, which then caused increased predation on and subsequent collapse of commercial bivalve stocks. These claims were used to justify the development of a predator-control fishery for cownose rays, the “Save the Bay, Eat a Ray” fishery, to reduce predation on commercial bivalves. A reexamination of data suggests declines in large coastal sharks did not coincide with purported rapid increases in cownose ray abundance. Likewise, the increase in cownose ray abundance did not coincide with declines in commercial bivalves. The lack of temporal correlations coupled with published diet data suggest the purported trophic cascade is lacking the empirical linkages required of a trophic cascade. Furthermore, the life history parameters of cownose rays suggest they have low reproductive potential and their populations are incapable of rapid increases. Hypothesized trophic cascades should be closely scrutinized as spurious conclusions may negatively influence conservation and management decisions.

Connecticut, Delaware, Maryland, Massachusetts, Ne↗

Genetic origins of a resurging lake whitefish, Coregonus clupeaformis, population in the Detroit River, Laurentian Great Lakes

The Detroit River connects Lake Huron and Lake Erie of the Laurentian Great Lakes. The river once supported a substantial lake whitefish ( Coregonus clupeaformis ) fishery until the early 1900s, when habitat loss, pollution, and overfishing contributed to the collapse of the fishery and loss of spawning populations in the river. In the early 1970s, efforts were initiated to improve water and habitat quality, and in December 2005 a spawning male lake whitefish and viable eggs were collected; the first documented evidence of spawning since 1916. Researchers have tracked the spawning magnitude of the lake whitefish population in the Detroit River since 2005 by assessing the number of eggs deposited on egg mats. Genetic analysis of larval fish hatched from eggs collected in the field between 2005 and 2018 was used to determine the relative contributions of Lake Erie and Lake Huron to the resurging population. Over 80% of the hatched larvae had parents originating from Lake Erie in all the years sampled. The estimated number of full-sibling families sampled at Belle Isle was the same in 2010 and 2014 and varied between 2009 and 2016 at Fighting Island. The estimated number of lake whitefish parents at Fighting Island decreased in the most recent collections possibly due to loss of habitat on spawning reefs due to sedimentation. Our results provide additional evidence that restored spawning habitat in the Detroit River is again being used by lake whitefish and continued reproduction at these sites may improve the Great Lakes portfolio of ecological and genetic diversity.

Detroit River↗

Emerging viral diseases of fish and shrimp

The rise of aquaculture has been one of the most profound changes in global food production of the past 100 years. Driven by population growth, rising demand for seafood and a levelling of production from capture fisheries, the practice of farming aquatic animals has expanded rapidly to become a major global industry. Aquaculture is now integral to the economies of many countries. It has provided employment and been a major driver of socio-economic development in poor rural and coastal communities, particularly in Asia, and has relieved pressure on the sustainability of the natural harvest from our rivers, lakes and oceans. However, the rapid growth of aquaculture has also been the source of anthropogenic change on a massive scale. Aquatic animals have been displaced from their natural environment, cultured in high density, exposed to environmental stress, provided artificial or unnatural feeds, and a prolific global trade has developed in both live aquatic animals and their products. At the same time, over-exploitation of fisheries and anthropogenic stress on aquatic ecosystems has placed pressure on wild fish populations. Not surprisingly, the consequence has been the emergence and spread of an increasing array of new diseases. This review examines the rise and characteristics of aquaculture, the major viral pathogens of fish and shrimp and their impacts, and the particular characteristics of disease emergence in an aquatic, rather than terrestrial, context. It also considers the potential for future disease emergence in aquatic animals as aquaculture continues to expand and faces the challenges presented by climate change.

Veterinary Research↗

Including long-term biological index performance in a multi-criteria Decision Support System

A Decision Support System (DSS) was developed for the reservoirs operated by the U.S. Bureau of Reclamation that incorporates biological resources in a palette of decision variables. A scoring technique was developed for the DSS to help to evaluate the long-term effects of proposed reservoir system operations on those variables. The biological component of the DSS was developed to help Bureau of Reclamation reservoir operators evaluate the effects of different scenarios of reservoir operations on a variety of water-related biological resources. In this DSS, Reclamation's Reservoir Operations Modeling System (ROMS) is linked to modules evaluating power production, flood control benefits, irrigation water deliveries, municipal and industrial water supplies, habitat for endemic fish communities, tailwater fisheries, nesting habitat for shorebirds, reservoir recreation, reservoir fisheries, and regeneration of riparian cottonwood forests. Operation scenarios generated in ROMS are scored for each decision variable by comparison to a target range of a decision variable for a reference location and time period. The score for a variable is calculated based on the ratio between the percent of time that target conditions are met under alternative operating conditions and under the reference condition, respectively. A scoring technique was developed that recognizes that under either natural or highly managed conditions the reference target is not met at all times. Higher scores are achieved for environmental decision variables by operations scenarios that approach natural seasonal and annual variability in habitat availability.

Conference Paper↗

Pelagic habitat visualization: the need for a third (and fourth) dimension: HabitatSpace

Habitat in open water is not simply a 2-D to 2.5-D surface such as the ocean bottom or the air-water interface. Rather, pelagic habitat is a 3-D volume of water that can change over time, leading us to the term habitat space. Visualization and analysis in 2-D is well supported with GIS tools, but a new tool was needed for visualization and analysis in four dimensions. Observational data (cruise profiles (x<sub>o</sub>, y<sub>o</sub>, z, t<sub>o</sub>)), numerical circulation model fields (x,y,z,t), and trajectories (larval fish, 4-D line) need to be merged together in a meaningful way for visualization and analysis. As a first step toward this new framework, UNIDATA&rsquo;s Integrated Data Viewer (IDV) has been used to create a set of tools for habitat analysis in 4-D. IDV was designed for 3-D+time geospatial data in the meteorological community. NetCDF Java<sup>TM</sup> libraries allow the tool to read many file formats including remotely located data (e.g. data available via OPeNDAP ). With this project, IDV has been adapted for use in delineating habitat space for multiple fish species in the ocean. The ability to define and visualize boundaries of a water mass, which meets specific biologically relevant criteria (e.g., volume, connectedness, and inter-annual variability) based on model results and observational data, will allow managers to investigate the survival of individual year classes of commercially important fisheries. Better understanding of the survival of these year classes will lead to improved forecasting of fisheries recruitment.

Conference Paper↗

Seasonal and diel effects on acoustic fish biomass estimates: application to a shallow reservoir with untargeted common carp ( Cyprinus carpio )

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&ndash;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 < 0.001) from autumn to winter. Based on our autumn night-time survey, overall fish biomass in the Bir-Mcherga Reservoir was high (mean (&plusmn; s.d.) 185 &plusmn; 98 tonnes (Mg)), but annual fishery exploitation is low (19.3&ndash;24.1 Mg) because the fish biomass is likely dominated by invasive carp not targeted by fishers. The results suggest that controlling carp would help improve the fishery.

Marine and Freshwater Research↗

Expanding freshwater biologger studies to view fish as environmental sensing platforms

While recording fish habitat use by electronic sensors, biologgers can also be viewed as autonomous environmental monitoring systems with the organism as a vehicle. This dual perspective has provided novel results from marine ecosystems, but has not been applied to freshwater ecosystems. To understand limitations in fresh water, we evaluated miniature depth and temperature recorders as aquatic monitoring systems in a Laurentian Great Lake: Erie. As part of an acoustic telemetry study, biologgers were opportunistically implanted in a subsample of walleye Sander vitreus . Biologgers recorded temperature and depth at half-hour intervals for up to 1 year. Recaptures provided six biologgers for analysis of seasonal temperature patterns and lake stratification, key variables for understanding dimictic lakes. Depth-resolved temperature patterns showed close correspondence with independent weather buoy measurements. Because the buoy was deployed late in the season, biologger data provided improved estimates of the start of stratification, which had important implications for understanding development of hypoxia in the hypolimnion. Drawbacks to biologger data included imprecise knowledge of fish location and reliance on tag recoveries from the fishery. Optimistically, our results show how biologgers could be part of a monitoring approach that integrates limnological surveys with fisheries science.

Marine and Freshwater Research↗

A new water temperature modeling approach to predict thermal habitat suitability for nonnative cichlids in Florida rivers

As global temperatures increase, the spatiotemporal arrangement of thermal habitats in Florida rivers may shift, creating the potential for greater dispersal and establishment of nonnative tropical freshwater fishes. To understand how water temperature changes may affect the spatial distribution of these nonnative species, more effective water temperature prediction models are necessary. Currently, most models employ either a generalized air–water temperature relationship or require expensive and complicated tools to measure hydrometeorological factors (e.g. groundwater input). Thus, we developed a novel modeling approach that is accurate, accessible, and cost-effective in allowing fisheries managers to project water temperatures in rivers across Central and North Florida. To characterize the potential for nonnative fishes to spread northward, we evaluated two hardy and abundant species currently found primarily in South Florida: Mayan Cichlid ( Mayaheros urophthalmus ) and Oscar ( Astronotus ocellatus ). Our results show an increase in thermally suitable winter days for both species in 10 of 11 rivers studied, consistent with predicted water temperature warming under 16 climate-change scenarios spanning different levels of air temperature warming (+1 °C, +2 °C, +3 °C, +4 °C) and precipitation/groundwater thermal sensitivity (0, 0.33, 0.66, 1). Considering resource limitations, fisheries managers can use our water temperature modeling approach to predict effects of climate change on Mayan Cichlid and Oscar survival, growth, and dispersal and take actions to manage potential northward movement of these species.

Florida↗

Potential threats facing a globally important population of the magnificent frigatebird Fregata magnificens

Tracking of seabirds has been used to identify foraging hotspots, migratory routes and to assess at-sea threats facing populations. One such threat is the potential negative interaction between seabirds and fisheries through incidental by-catch. In 2012, 60 magnificent frigatebirds Fregata magnificens were found dead, entangled in fishing line, at the globally important breeding site in the British Virgin Islands (BVI). To assess the potential relationship between foraging behaviour and fishing activity, data loggers were deployed on breeding magnificent frigatebirds to record foraging movements. In addition, a survey of local fishers was conducted to assess the scale of incidental by-catch. We recorded 28 complete foraging trips from GPS and GPS-GSM loggers, and 1758 PTT locations. Birds travelled up to 3.3–1067 km from their breeding colony and entered the waters of 10 neighbouring territories. A high percentage of fishers (93% n = 28) reported catching at least one seabird annually, of which the most common were magnificent frigatebirds and brown boobies Sula leucogaster . There are estimated to be at least 1112 vessels in the recreational and artisanal fishing fleets of BVI and its neighbouring islands. Thus, this substantial fishery may have potentially profound effects on seabird populations in the region.

Tropical Zoology↗

Ten lessons for controlling invasive species: Wisdom from the long-standing sea lamprey control program on the Laurentian Great Lakes

Sea lamprey ( Petromyzon marinus ) control in the Laurentian Great Lakes of North America is among the largest and most successful control programs of an invasive species anywhere on the planet. The effort began more than 75 years ago; it unites multiple nations, states, and provinces with the common goal of controlling this invasive species and protecting a valuable fishery. The science-based control program is administered by the Great Lakes Fishery Commission (GLFC), a body arising from a treaty signed by the United States and Canada. In the present article, we share 10 lessons learned from decades of successful sea lamprey control with the hopes of informing ongoing and future control programs targeting biological invasions. The 10 lessons we identified are to act boldly in times of crisis, to maintain the social license, to invest in capacity building, to break down the silos, to support fundamental science, to diversify your portfolio of control measures, to strive for continuous improvement, to confront the trade-off between information and action, to keep your foot on the gas, and to keep your eyes on the prize. The GLFC has long fostered a framework that uses some military strategy and verbiage that extends across the lessons (e.g., know your enemy). Other lessons are more nascent as the GLFC reenvisions its relationship with Indigenous peoples and governments in a path to reconciliation where two-eyed seeing is being embraced. Through adaptive management, horizon scanning methods, and embracing implementation science, the lessons learned about sea lamprey control will continue to evolve, which is itself a lesson. We submit that the lessons shared in the present article will help guide invasive species control programs spanning taxa, ecosystems, and regions.

Laurentian Great Lakes↗

Dynamics of lake trout production in the main basin of Lake Huron

To inform lake trout (Salvelinus namaycush) fishery management in Lake Huron that has undergone rapid ecosystem changes, we quantified lake trout production dynamics by coupling age-structured stock assessment and fish bioenergetics models. Our approach revealed the connection between piscivore production and prey consumption, included growth compensation to reproduction losses, and allowed comparisons between long-term dynamics of fishery harvests and fish production. We found that despite the collapse of alewives, a major non-native pelagic prey fish, lake trout production appeared to be sustainable. To a certain degree, the effect of recent recruitment declines on lake trout production was offset by release of harvest pressure from subadult lake trout, and reduction of fishing and sea lamprey induced mortality on adult lake trout. Evidence for sustainability also included the finding that no changes in average ratios of annual production to beginning-of-the-year biomass. Juvenile P:B ratio remained as high as 2.1. The effect of growth declines on adult and subadult production was offset by reduction in population mortality. Body growth and condition did not continue to decline when lake trout became more and more reliant on round goby as food, and the dynamics of total consumption of prey fish continued to be recipient controlled.

Lake Huron↗

Accounting for spatiotemporal sampling variation in joint species distribution models

Estimating relative abundance is critical for informing conservation and management efforts and for making inferences about the effects of environmental change on populations. Freshwater fisheries span large geographic regions, occupy diverse habitats and consist of varying species assemblages. Monitoring schemes used to sample these diverse populations often result in populations being sampled at different times and under different environmental conditions. Varying sampling conditions can bias estimates of abundance when compared across time, location and species, and properly accounting for these biases is critical for making inferences. We develop a joint species distribution model (JSDM) that accounts for varying sampling conditions due to the environment and time of sampling when estimating relative abundance. The novelty of our JSDM is that we explicitly model sampling effort as the product of known quantities based on time and gear type and an unknown functional relationship to capture seasonal variation in species life history. We use the model to study relative abundance of six freshwater fish species across the state of Minnesota, USA. Our model enables estimates of relative abundance to be compared both within and across species and lakes, and captures the inconsistent sampling present in the data. We discuss how gear type, water temperature and day of the year impact catchability for each species at the lake level and throughout a year. We compare our estimates of relative abundance to those obtained from a model that assumes constant catchability to highlight important differences within and across lakes and species. Synthesis and applications : Our method illustrates that assumptions relating indices of abundance to observed catch data can greatly impact model inferences derived from JSDMs. Specifically, not accounting for varying sampling conditions can bias inference of relative abundance, restricting our ability to detect responses to management interventions and environmental change. While our focus is on freshwater fisheries, this model architecture can be adopted to other systems where catchability may vary as a function of space, time and species.

Journal of Applied Ecology↗

Characterization of a Y-specific duplication/insertion of the anti-Mullerian hormone type II receptor gene based on a chromosome-scale genome assembly of yellow perch, Perca flavescens

Yellow perch, Perca flavescens , is an ecologically and economically important species native to a large portion of the northern United States and southern Canada and is also a promising candidate species for aquaculture. However, no yellow perch reference genome has been available to facilitate improvements in both fisheries and aquaculture management practices. By combining Oxford Nanopore Technologies long-reads, 10X Genomics Illumina short linked reads and a chromosome contact map produced with Hi-C, we generated a high-continuity chromosome-scale yellow perch genome assembly of 877.4 Mb. It contains, in agreement with the known diploid chromosome yellow perch count, 24 chromosome-size scaffolds covering 98.8% of the complete assembly (N50 = 37.4 Mb, L50 = 11). We also provide a first characterization of the yellow perch sex determination locus that contains a male-specific duplicate of the anti-Mullerian hormone type II receptor gene ( amhr2by ) inserted at the proximal end of the Y chromosome (chromosome 9). Using this sex-specific information, we developed a simple PCR genotyping assay which accurately differentiates XY genetic males ( amhr2by + ) from XX genetic females ( amhr2by − ). Our high-quality genome assembly is an important genomic resource for future studies on yellow perch ecology, toxicology, fisheries and aquaculture research. In addition, characterization of the amhr2by gene as a candidate sex-determining gene in yellow perch provides a new example of the recurrent implication of the transforming growth factor beta pathway in fish sex determination, and highlights gene duplication as an important genomic mechanism for the emergence of new master sex determination genes.

Molecular Ecology Resources↗

Incomplete bioinformatic filtering and inadequate age and growth analysis lead to an incorrect inference of harvested-induced changes

Understanding the evolutionary impacts of harvest on fish populations is important for informing fisheries management and conservation and has become a growing research topic over the last decade. However, the dynamics of fish populations are highly complex, and phenotypes can be influenced by many biotic and abiotic factors. Therefore, it is vital to collect robust data and explore multiple alternative hypotheses before concluding that fish populations are influenced by harvest. In their recently published manuscript, Bowles et al, Evolutionary Applications, 13(6):1128 conducted age/growth and genomic analysis of walleye ( Sander vitreus ) populations sampled 13–15 years (1–2.5 generations) apart and hypothesized that observed phenotypic and genomic changes in this time period were likely due to harvest. Specifically, Bowles et al. (2020) documented differential declines in size-at-age in three exploited walleye populations compared to a separate, but presumably less-exploited, reference population. Additionally, they documented population genetic differentiation in one population pair, homogenization in another, and outlier loci putatively under selection across time points. Based on their phenotypic and genetic results, they hypothesized that selective harvest had led to fisheries-induced evolution (referred to as nascent changes) in the exploited populations in as little as 1–2.5 generations. We re-analyzed their data and found that (a) sizes declined across both exploited and reference populations during the time period studied and (b) observed genomic differentiation in their study was the result of inadequate data filtering, including retaining individuals with high amounts of missing data and retaining potentially undersplit and oversplit loci that created false signals of differentiation between time points. This re-analysis did not provide evidence for phenotypic or genetic changes attributable to harvest in any of the study populations, contrasting the hypotheses presented by Bowles et al. (2020). Our comment highlights the potential pitfalls associated with conducting age/growth analyses with low sample sizes and inadequately filtering genomic datasets.

Quebec↗

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

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

Michigan, Wisconsin↗