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Information regarding site occupancy of fish that migrate long distances during nonspawning periods together with estimates of recruitment trends for individual populations can be informative for management, especially when individuals from different spawning populations intermix and are sampled or harvested together. Tendencies for individuals from different populations to preferentially occupy specific regions increases vulnerability to anthropogenic and natural disturbances. Using mixed stock analysis (MSA), we estimated population-specific occupancy of lake sturgeon (Acipenser fulvescens) in open-water and nearshore regions of Lake Michigan across a hierarchy of spatial scales. Open-water mixture composition differed between Lake Michigan’s eastern and western basins. Significant heterogeneity in habitat occupancy was also observed at microgeographic scales throughout open-water regions of Green Bay, indicating nonrandom occupancy to regions proximal to natal streams. Estimates of relative recruitment levels determined from MSA extensions indicated increasing recruitment trends for spawning populations associated with Wisconsin tributaries (Oconto–Peshtigo, Fox, and Menominee rivers). Our lake sturgeon results demonstrate the utility of genetic data for informing management efforts for spatially structured, highly migratory species. Similar analyses could prove beneficial for species with similar characteristics.

Fish population structure in previously glaciated regions is often influenced by natural colonization processes and human-mediated dispersal, including fish stocking. Endemic populations are of conservation interest because they may contain rare and unique genetic variation. While coregonines are native to certain Michigan inland lakes, some were stocked with fish from Great Lakes sources, calling into question the origin of extant populations. While most stocking targeted lake whitefish (Coregonus clupeaformis), cisco (C. artedi) were also stocked from the Great Lakes to inland waterbodies. We used population genetic data (microsatellite genotypes and mitochondrial (mt)DNA sequences), coalescent modeling, and approximate Bayesian computation to investigate the origins of 12 inland Michigan cisco populations. The spatial distribution of mtDNA haplotypes suggests Michigan is an introgression zone for two ancestral cisco lineages associated with separate glacial refugia. Low levels of genetic diversity and high levels of genetic divergence were observed for populations located well inland of the Great Lakes relative to populations occupying waterbodies near the Great Lakes. Estimates of recent Great Lakes gene flow ranged from 27 to 48% for populations near the Great Lakes shoreline but were substantially lower (under 8%) for populations further inland. Inland lakes with elevated recent gene flow estimates may have been recipients of stocked coregonine fry, including cisco. Low levels of genetic diversity paired with a high likelihood of endemism as indicated by strong genetic divergence and low Great Lakes population inputs suggest the analyzed cisco populations occupying southern Michigan kettle lakes are of elevated conservation interest.

Populations of stream organisms across trophic levels, including microbial taxa, are adapted to physical and biotic stream features, and are sentinels of geological and hydrological landscape processes and anthropogenic disturbance. Stream bacterial diversity and composition can have profound effects on resident and migratory species in Great Lakes tributaries. Study objectives were to characterize and compare the taxonomic composition and diversity of bacterial communities in 18 rivers of the Lake Michigan basin during April and June 2019 and to quantify associations with stream and watershed physical features and dominant landuse practices. River water was filtered, and genomic DNA was extracted from filtrate using antiseptic techniques. We performed high-throughput amplicon sequencing using the highly variable V4 region of the 16S rRNA gene to characterize microbial community composition and diversity. Effects of landscape-scale landuse, environmental variables and dispersal predictors (e.g., inter-stream distance) on community compositional differences were quantified. Greater than 90% of variation in bacterial relative abundance between rivers and time were attributed to 11 phyla representing 10,800 operational taxonomic units. Inter-stream geographic distance, stream hydrology, and variation in stream properties that were tied to patterns of watershed landuse were significantly associated with differences in bacterial community composition among streams at both sampling time periods. based on Bray-Curtis distances. Understanding how environmental characteristics and watershed-scale landuse influence lower trophic level stream communities such as bacteria will inform managers as biological indicators of ecosystem health, sources of disturbance, and current and future bottom-up trophic changes in coupled tributary-Great Lakes ecosystems.

Demographic data including characterizations of population sex and age composition are of fundamental importance for effective management, especially for numerically depressed Great Lakes populations of imperiled species such as lake sturgeon (Acipenser fulvescens). The goal of this paper was to extend a recently reported Acipenserid-derived PCR-based genotyping test to determine sex of lake sturgeon. We demonstrate that the recently reported AllWSex2 primers amplified the female sex-specific region in lake sturgeon of known sex, consistent with a ZZ/ZW mode of inheritance. Sanger sequencing of female lake sturgeon PCR products matched published sequences from female sterlet (Acipenser ruthenus), showing 100% query cover and 98% (63/64) identity. The ability to provide a rapid, cost-effective, and unambiguous determination of sex for lake sturgeon will allow managers to determine compositional estimates of sex ratios during any season, and for individuals at any age or size, which is of great utility for species characterized by delayed sexual maturity and lacking external sexual dimorphisms.

Genomic tools are lacking for invasive and native populations of sea lamprey (Petromyzon marinus). Our objective was to discover single nucleotide polymorphism (SNP) loci to conduct pedigree analyses to quantify reproductive contributions of adult sea lampreys and dispersion of sibling larval sea lampreys of different ages in Great Lakes tributaries. Additional applications of data were explored using additional geographically expansive samples. We used restriction site‐associated DNA sequencing (RAD‐Seq) to discover genetic variation in Duffins Creek (DC), Ontario, Canada, and the St. Clair River (SCR), Michigan, USA. We subsequently developed RAD capture baits to genotype 3,446 RAD loci that contained 11,970 SNPs. Based on RAD capture assays, estimates of variance in SNP allele frequency among five Great Lakes tributary populations (mean F ST 0.008; range 0.00–0.018) were concordant with previous microsatellite‐based studies; however, outlier loci were identified that contributed substantially to spatial population genetic structure. At finer scales within streams, simulations indicated that accuracy in genetic pedigree reconstruction was high when 200 or 500 independent loci were used, even in situations of high spawner abundance (e.g., 1,000 adults). Based on empirical collections of larval sea lamprey genotypes, we found that age‐1 and age‐2 families of full and half‐siblings were widely but nonrandomly distributed within stream reaches sampled. Using the genomic scale set of SNP loci developed in this study, biologists can rapidly genotype sea lamprey in non‐native and native ranges to investigate questions pertaining to population structuring and reproductive ecology at previously unattainable scales., We developed a single nucleotide polymorphism (SNP) panel for pedigree analyses for larval sea lamprey to characterize levels of diversity within and among populations (mean interpopulation F ST range 0.001–0.020). Genome‐wide annotation based on the sea lamprey genome facilitated the identification of putative functions of outlier loci (range of interpopulation F ST 0.205–0.374). Simulation and empirical analyses demonstrated accuracy in pedigree assignment, and facilitated estimation of effective breeding population size, aspects of the species reproductive ecology, and extent of larval dispersal.

The Lake Michigan brown trout (Salmo trutta) fishery is sustained by the stocking of five hatchery strains by four state natural resource agencies. In the absence of exhaustive marking programs, strain-specific measures of stocking success are lacking for brown trout in Lake Michigan. We used microsatellite-based genetic assignment testing and genetic stock identification (GSI) to determine the strain of 122 angler-caught brown trout from four northeastern Lake Michigan ports. We compared strain composition estimates for sportfishing harvest to expected proportions of each brown trout strain in Lake Michigan at the time of harvest using stocking records corrected for age-specific mortality rates. Reassignment rates of individuals from baseline strains averaged 92.1% (range: 84.1–98.0%). Assignment testing and GSI analyses consistently found Wild Rose strain brown trout represented approximately 89% of the northeastern Lake Michigan sportfishing harvest, while only comprising 43.8% of the expected stock. Of the Michigan angler harvest of Wild Rose strain brown trout, approximately half were estimated to have originated from Wisconsin hatcheries, demonstrating a propensity for lake-wide movements. Continued assessments will improve understanding of strain relative contributions to angler harvests that can direct future stocking efforts.

The establishment and spread of aquatic invasive species are ecologically and economically harmful and a source of conservation concern internationally. Processes of species invasion have traditionally been inferred from observational data of species presence/absence and relative abundance. However, genetic‐based approaches can provide valuable sources of inference. Restriction site‐associated DNA sequencing was used to identify and genotype single nucleotide polymorphism (SNP) loci for Round Gobies (Neogobius melanostomus) (N = 440) from 18 sampling locations in the Great Lakes and in three Michigan, USA, drainages (Flint, Au Sable, and Cheboygan River basins). Sampled rivers differed in size, accessibility, and physical characteristics including man‐made dispersal barriers. Population levels of genetic diversity and interpopulation variance in SNP allele frequency were used in coalescence‐based approximate Bayesian computation (ABC) to statistically compare models representing competing hypotheses regarding source population, postcolonization dispersal, and demographic history in the Great Lakes and inland waters. Results indicate different patterns of colonization across the three drainages. In the Flint River, models indicate a strong population bottleneck (

Predictive relationships between estimates of functional population connectivity and physical and biotic landscape features can provide important insights into present and future population responses to human-mediated landscape change. Quantification of associations between landscape features and dispersal or genetic surrogates such as gene flow among areas can be particularly challenging for continuously distributed and highly mobile wildlife species. We assessed the relative influence of natural and human- altered landscape features on white-tailed deer (Odocoileus virginianus) spatial genetic structure (SGS) in southern Michigan (USA) using 7 microsatellite markers assayed for 326 adult individuals from 21 contiguous counties (33,284km 2 ). We used previously collected telemetry data to quantify probabilities of habitat occupancy and seasonal movements that allowed selection and weighting of landscape features to create habitat suitability indices (HSI). We assigned individuals to groups (n ¼13) for statistical analyses quantifying relationships between measures of SGS (response variable) with Euclidean distance, least cost distances parameterized using HSI, and presence of natural (rivers) and man-made (roads) barriers to dispersal.Over theentirestudy area,geneticdifferentiationwassignificant (meanFst ¼0.019,P

Natural rates of straying are difficult to quantify over large spatial scales using direct observations, particularly for long-lived fish species characterized by delayed sexual maturity and long interspawning intervals. Using multilocus microsatellite genotypes and likelihood-based statistical methods, we quantified rates of immigration and emigration for six genetically differentiated (mean F ST = 0.041) lake sturgeon Acipenser fulvescens populations in Lake Michigan based on adults (n = 437) captured in tributaries during the spawning season. Estimated rates of straying were high (mean = 0.105), asymmetrical, and highly variable across populations. We found no significant association between the total length (a surrogate measure of age) of individuals that strayed and those that did not. Linear distance between streams was more predictive of straying rates and F ST than least-cost distances estimated based on lakescape features (bathymetry and lake current patterns). Historical rates of gene f...

Genetic differentiation among brook trout ( Salvelinus fontinalis ) of different life history forms and populations can result from reproductive isolation imposed by natural or anthropogenically derived barriers to gene flow, behavioral incompatibilities, or differential exposure to environmental cues. We used multi-locus microsatellite genotypes and likelihood and Bayesian-based analyses to characterize the degree of genetic differentiation and evidence of introgression among stream resident brook trout above a natural barrier, and putative stream residents and adfluvial (coaster) brook trout from below the barrier in the Salmon Trout River (STR); the sole tributary along the southern shore of Lake Superior known to be inhabited by a viable remnant population of coaster brook trout. Two genetically differentiated populations were identified, generally associated with individuals inhabiting sections of the STR above and below the falls. No evidence of differentiation was found between a priori classified resident and coaster brook trout from below the falls. Gene flow from individuals above the falls was detected based on evidence of interbreeding between upper river individuals and coasters below the falls. We collected only a relatively small number of individuals that we a priori classified as being stream residents below the falls, and these individuals had a high probability of having ancestry originating from the population above the barrier, which suggests that the stream-resident life history may be exceptionally rare or absent in the lower Salmon Trout River.

The ability of fishery managers to quickly and effectively answer stakeholder questions using the best available science is crucial for successful management. The 2009 capture of a potential world record brown trout ( Salmo trutta ) and the 2010 capture of a potential world record land-locked Atlantic salmon ( S. salar ) in Michigan required managers to acquire genetic verification of the species identity. Given the variety of hatchery strains used to maintain Great Lakes fisheries for brown trout and in the absence of physical markings, managers also were interested to determine the strain of origin for information on assessing performance. DNA barcoding techniques using sequences from the mitochondrial (mt) DNA cytochrome c oxidase I (COI) gene and frequency-based analysis of species-specific microsatellite genotypes provided data to establish the species of both fish. The putative brown trout was confirmed to be a new world record specimen. Using individual assignment tests based on maximum likelihood estimators informed by multi-locus microsatellite genotypes, we determined the fish to be from the Seeforellen hatchery strain (p

Quantifying the spatial genetic structure of highly vagile species of birds is important in predicting their degree of population demographic and genetic independence during changing environmental conditions, and in assessing their abundance and distribution. In the western Arctic, Lesser Snow Geese (Chen caerulescens caerulescens) provide an example useful for evaluating spatial population genetic structure and the relative contribution of male and female philopatry to breeding and wintering locales. We analyzed biparentally inherited microsatellite loci and maternally inherited mtDNA sequences from geese breeding at Wrangel Island (Russia) and Banks Island (Canada) to estimate gene flow among populations whose geographic overlap during breeding and winter differ. Significant differences in the frequencies of mtDNA haplotypes contrast with the homogeneity of allele frequencies for microsatellite loci. Coalescence simulations revealed high variability and asymmetry between males and females in r...

Mortality that occurs during larval dispersal as a consequence of environmental, maternal, and genetic effects and their interactions can affect annual recruitment in fish populations. We studied larval lake sturgeon (Acipenser fulvescens) drift for two consecutive nights to examine whether larvae from different females exposed to the same environmental conditions during dispersal differed in relative levels of mortality. We estimated proportional contributions of females to larval collections and relative larval loss among females as larvae dispersed downstream between two sampling sites based on genetically determined parentage. Larval collections were composed of unequal proportions of offspring from different females that spawned at upstream and downstream locations (~0.8 km apart). Hourly dispersal patterns of larvae produced from females spawning at both locations were similar, with the largest number of larvae observed during 22:00–23:00 h. Estimated relative larval loss did not differ significantly among females as larvae were sampled at two sites approximately 0.15 and 1.5 km from the last section downstream of spawning locations. High inter- and intra-female variation in larval contributions and relative larval loss between nights may be a common feature of lake sturgeon and other migratory fish species, and likely is a source of inter-annual and intra-annual variation in fish recruitment.

Genetic stock identification analyses were conducted to determine spawning population contributions to the recreational fishery for Walleyes Sander vitreus in Saginaw Bay, Lake Huron. Two spawning population groups were considered: (1) the Tittabawassee River, which has been identified as the largest source of spawning Walleyes for Saginaw Bay; and (2) an aggregate of six spawning populations from Lake Erie and Lake St. Clair that were found to be genetically similar. Overall, the Lake Erie and Lake St. Clair spawning populations were estimated to comprise approximately 26% of the Walleye recreational harvest in Saginaw Bay during 2008–2009. Contribution levels were similar for the 2 years in which genetic samples were collected. Contributions from the Lake Erie and Lake St. Clair spawning populations to the harvest of age-5 and older Walleyes were greater during summer (31.8%; SE = 6.2%) than during late winter and spring (6.0%; SE = 3.7%). Conversely, contributions from the Lake Erie and Lake St. Clair spawning populations to the harvest of age-3 and age-4 fish were fairly similar between seasons (late winter and spring: 31.2%, SE = 6.7%; summer: 41.7%, SE = 5.6%), suggesting that younger Walleyes migrate earlier or reside in Saginaw Bay for extended periods. Our finding that one-quarter of the Saginaw Bay recreational harvest of Walleyes comprises fish from Lake Erie and Lake St. Clair has important management implications, as policies for one lake may have bearing on the other lake—one of the challenges associated with managing migratory fish species. Fisheries management in the Laurentian Great Lakes has a history of being highly coordinated and cooperative among the states and province bordering the individual lakes. Results from this study suggest that cooperation may need to be expanded to account for fish movement between lakes.Received October 28, 2014; accepted February 11, 2015