Demographic patterns of walleye (Sander vitreus) reproductive success in a Wisconsin population

Harvest in walleye Sander vitreus fisheries is size-selective and could influence phenotypic traits of spawners; however, contributions of individual spawners to recruitment are unknown. We used parentage analyses using single nucleotide polymorphisms to test whether parental traits were related to the probability of offspring survival in Escanaba Lake, Wisconsin. From 2017 to 2020, 1339 adults and 1138 juveniles were genotyped and 66% of the offspring were assigned to at least one parent. Logistic regression indicated the probability of reproductive success (survival of age-0 to first fall) was positively (but weakly) related to total length and growth rate in females, but not age. No traits analyzed were related to reproductive success for males. Our analysis identified the model with the predictors' growth rate and year for females and the models with year and age and year for males as the most likely models to explain variation in reproductive success. Our findings indicate that interannual variation (i.e., environmental conditions) likely plays a key role in determining the probability of reproductive success in this population and provide limited support that female age, length, and growth rate influence recruitment.

Shrinking body size and climate warming: Many freshwater salmonids do not follow the rule

Declining body size is believed to be a universal response to climate warming and has been documented in numerous studies of marine and anadromous fishes. The Salmonidae are a family of coldwater fishes considered to be among the most sensitive species to climate warming; however, whether the shrinking body size response holds true for freshwater salmonids has yet to be examined at a broad spatial scale. We compiled observations of individual fish lengths from long-term surveys across the Northern Hemisphere for 12 species of freshwater salmonids and used linear mixed models to test for spatial and temporal trends in body size (fish length) spanning recent decades. Contrary to expectations, we found a significant increase in length overall but with high variability in trends among populations and species. More than two-thirds of the populations we examined increased in length over time. Secondary regressions revealed larger-bodied populations are experiencing greater increases in length than smaller-bodied populations. Mean water temperature was weakly predictive of changes in body length but overall minimal influences of environmental variables suggest that it is difficult to predict an organism's response to changing temperatures by solely looking at climatic factors. Our results suggest that declining body size is not universal, and the response of fishes to climate change may be largely influenced by local factors. It is important to know that we cannot assume the effects of climate change are predictable and negative at a large spatial scale.

Genomic and environmental influences on resilience in a cold-water fish near the edge of its range

Small, isolated populations present a challenge for conservation. The dueling effects of selection and drift in a limited pool of genetic diversity make the responses of small populations to environmental perturbations erratic and difficult to predict. This is particularly true at the edge of a species range, where populations often persist at the limits of their environmental tolerances. Populations of cisco, Coregonus artedi, in inland lakes have experienced numerous extirpations along the southern edge of their range in recent decades, which are thought to result from environmental degradation and loss of cold, well-oxygenated habitat as lakes warm. Yet, cisco extirpations do not show a clear latitudinal pattern, suggesting that local environmental factors and potentially local adaptation may influence resilience. Here, we used genomic tools to investigate the nature of this pattern of resilience. We used restriction site-associated DNA capture (Rapture) sequencing to survey genomic diversity and differentiation in southern inland lake cisco populations and compared the frequency of deleterious mutations that potentially influence fitness across lakes. We also examined haplotype diversity in a region of the major histocompatibility complex involved in stress and immune system response. We correlated these metrics to spatial and environmental factors including latitude, lake size, and measures of oxythermal habitat and found significant relationships between genetic metrics and broad and local factors. High levels of genetic differentiation among populations were punctuated by a phylogeographic break and residual patterns of isolation-by-distance. Although the prevalence of deleterious mutations and inbreeding coefficients was significantly correlated with latitude, neutral and non-neutral genetic diversity were most strongly correlated with lake surface area. Notably, differences among lakes in the availability of estimated oxythermal habitat left no clear population genomic signature. Our results shed light on the complex dynamics influencing these isolated populations and provide valuable information for their conservation.

Angler and environmental influences on walleye Sander vitreus and muskellunge Esox masquinongy angler catch in Escanaba Lake, Wisconsin 2003-2015

Angler trip success and catch rates are dependent upon a fishes' vulnerability to angling. Angling vulnerability can be influenced by angler-specific attributes (i.e., bait choice, lure size, use of a guide), and individual fish traits (i.e., boldness, aggression, stress responsiveness, and memory retention). The mechanisms that function in a fishes' angling vulnerability, and contribute to catch rate, are likely correlated with environmental factors however, the influence of environmental factors on angling vulnerability are not well understood. We used the long-term (1946 -present) compulsory creel dataset from Escanaba Lake, WI, USA to test for interactions between angling vulnerability (i.e., angler trip success and catch rates) and environmental factors to better understand these dynamics in recreational fisheries. Our objective was to test for the influence of angler associated variables and environmental factors on open water angler trip success (i.e., catch ≥ one fish) and catch rate of walleye Sander vitreus and muskellunge Esox masquinongy during 2003-2015 using a hurdle model approach. Fishing trip success and catch rates for both species were most strongly influenced by angler-related variables (i.e., guide status, bait type, the proportion of the fish population previously caught). Environmental factors associated with lower light intensity (i.e., diel period, mean daily solar radiation, solar-Julian day interaction) had a positive influence on walleye vulnerability. Lower air temperatures and lunar position (moon overhead or underfoot) and phase (gibbous' and full moon) also had a positive effect on walleye angling. Muskellunge trip success and catch rate were positively influenced by light metrics (i.e., diel period and mean daily solar radiation) and increased with air temperature. Lunar variables (position and phase), as well as wind speed and direction also influenced muskellunge angling vulnerability. A better understanding of the influence of environmental factors on angling vulnerability is an important component of fisheries management as management goals focus on balancing fish populations and creating satisfactory catch rates to enhance the angling experience. Our results suggest that angler-specific variables, light, temperature, lunar, and weather conditions influenced species-specific angling vulnerability for walleye and muskellunge.

The ghosts of propagation past: haplotype information clarifies the relative influence of stocking history and phylogeographic processes on contemporary population structure of walleye (Sander vitreus)

Stocking of fish is an important tool for maintaining fisheries but can also significantly alter population genetic structure and erode the portfolio of within-species diversity that is important for promoting resilience and adaptability. Walleye (Sander vitreus) are a highly valued sportfish in the midwestern United States, a region characterized by postglacial recolonization from multiple lineages and an extensive history of stocking. We leveraged genomic data and recently developed analytical approaches to explore the population structure of walleye from two midwestern states, Minnesota and Wisconsin. We genotyped 954 walleye from 23 populations at ~20,000 loci using genotyping by sequencing and tested for patterns of population structure with single-SNP and microhaplotype data. Populations from Minnesota and Wisconsin were highly differentiated from each other, with additional substructure found in each state. Population structure did not consistently adhere to drainage boundaries, as cases of high intra-drainage and low inter-drainage differentiation were observed. Low genetic structure was observed between populations from the upper Wisconsin and upper Chippewa river watersheds, which are found as few as 50 km apart and were likely homogenized through historical stocking. Nevertheless, we were able to differentiate these populations using microhaplotype-based co-ancestry analysis, providing increased resolution over previous microsatellite studies and our other single SNP-based analyses. Although our results illustrate that walleye population structure has been influenced by past stocking practices, native ancestry still exists in most populations and walleye populations may be able to purge non-native alleles and haplotypes in the absence of stocking. Our study is one of the first to use genomic tools to investigate the influence of stocking on population structure in a nonsalmonid fish and outlines a workflow leveraging recently developed analytical methods to improve resolution of complex population structure that will be highly applicable in many species and systems.

A GT-seq panel for walleye (Sander vitreus) provides important insights for efficient development and implementation of amplicon panels in non-model organisms

Targeted amplicon sequencing methods, such as genotyping-in-thousands by sequencing (GT-seq), facilitate rapid, accurate, and cost-effective analysis of hundreds of genetic loci in thousands of individuals. Development of GT-seq panels is nontrivial, but studies describing trade-offs associated with different steps of GT-seq panel development are rare. Here, we construct a dual-purpose GT-seq panel for walleye (Sander vitreus), discuss trade-offs associated with different development and genotyping approaches, and provide suggestions for researchers constructing their own GT-seq panels. Our GT-seq panel was developed using an ascertainment set consisting of restriction site-associated DNA data from 954 individuals sampled from 23 populations in Minnesota and Wisconsin, USA. We conducted simulations to test the utility of all loci for parentage analysis and genetic stock identification and designed 600 primer pairs to maximize joint accuracy for these analyses. We then performed three rounds of primer optimization to remove loci that overamplified and our final panel consisted of 436 loci. We also explored different approaches for DNA extraction, multiplexed polymerase chain reaction (PCR) amplification, and cleanup steps during the GT-seq process and discovered the following: (i) inexpensive Chelex extractions performed well for genotyping; (ii) the exonuclease I and shrimp alkaline phosphatase (ExoSAP) procedure included in some current protocols did not improve results substantially and was probably unnecessary; and (iii) it was possible to PCR amplify panels separately and combine them prior to adapter ligation. Well-optimized GT-seq panels are valuable resources for conservation genetics and our findings and suggestions should aid in their construction in myriad taxa.

Body condition (Wr ) and reproductive potential of bighead and silver carp hybrids: Postzygotic selection in the Mississippi River Basin

Invasive bighead (Hypophthalmichthys nobilis) and silver carp (H. molitrix) are reproductively isolated in their native range, but form a bimodal, multigenerational hybrid swarm within the Mississippi River Basin (MRB). Despite observed F1 hybrid superiority in experimental settings, effects of postzygotic selection on bighead and silver carp hybrids have not been tested in a natural system. Individual parent and hybrid genotypes were resolved at 57 species-specific loci and used to evaluate postzygotic selection for body condition (Wr ) and female reproductive potential (presence of spawning stage gonads and gonadosomatic index [GSI]) in the MRB during 2009-2011. Body condition in the Marseilles Reach, Illinois River declined with a decrease in species-specific allele frequency from 1.0 to 0.4 for each species and early generation hybrids (F1, F2, and first-generation backcross) had lower mean Wr than late generation hybrids (2nd+ generation backcrosses) and parentals. Proportions of stage IV and stage V (spawning stage) female gonads differed between bighead and silver carp, but not among parentals and their early and late generation hybrids within the MRB. Mean GSI values did not differ between parentals and hybrids. Because reproductive potential did not differ between hybrids and parentals, our results suggest that early generation hybrids occur in low frequency either as a factor of poor condition (Wr ) and postreproductive survival, infrequent reproductive encounters by parental bighead and silver carp, or selection pressures acting on juvenile or immature life stages. Our results suggest that a combination of genetic and environmental factors may contribute to the postzygotic success of bighead and silver carp hybrids in the Mississippi River Basin.

Interspecific and Spatial Comparisons of Perfluorinated Compounds in Bighead and Silver Carp in the Illinois River, Illinois, USA

We examined perfluoroalkyl compounds (PFC) in bighead (BHCP; Hypophthalmichthys nobilis) and silver (SVCP; H. molitrix) carp from the Illinois River, Illinois, USA. Summed PFC concentrations in whole fish did not differ by species or river reach. Perfluorooctanesulfonate (PFOS) concentrations were much greater in whole fish (16.4 ng/g) than in fillets (3.4 ng/g). PFOS concentrations represented 35%-51% of total measured PFC concentrations in whole fish, and in fillets were weakly associated with carcass mass (R2=0.17, p=0.01) and % carcass lipid (R2=0.16, p=0.01). No such relationship was observed in whole fish. The relationship between concentrations of individual PFC congeners in whole fish and carcass mass or % lipid content varied by species. Our study demonstrated that filter-feeders such as BHCP and SVCP can accumulate measureable concentrations of PFC and these results are important for understanding the fate of these compounds in large river systems.

Restriction site-associated DNA sequencing generates high-quality single nucleotide polymorphisms for assessing hybridization between bighead and silver carp in the United States and China

Bighead carp (Hypophthalmichthys nobilis) and silver carp (H. molitrix) are invasive species and listed as US federally injurious species under the Lacy Act. They have established populations in much of the Mississippi River Basin (MRB; Mississippi, Illinois, and Missouri rivers) and are capable of producing fertile hybrids and complex introgression. Characterizing the composition of this admixture requires a large set of high-quality, evolutionarily conserved, diagnostic genetic markers to aid in the identification and management of these species in the midst of morphological ambiguity. Restriction site-associated DNA (RAD) sequencing of 45 barcoded bighead and silver carp from the United States and China produced reads that were aligned to the silver carp transcriptome yielded 261 candidate single nucleotide polymorphisms (SNPs) with fixed allelic differences between the two species. We selected the highest quality 112 SNP loci for validation using 194 putative pure-species and F1 hybrids from the MRB and putative bighead carp and silver carp pure species from China (Amur, Pearl and Yangtze rivers). Fifty SNPs were omitted due to design/amplification failure or lack of diagnostic utility. A total of 57 species-diagnostic SNPs conserved between carp species in US and Chinese rivers were identified; 32 were annotated to functional gene loci. Twenty-seven of the 181 (15%) putative pure species were identified as hybrid backcrosses after validation, including three backcrosses from the Amur River, where hybridization has not been documented previously. The 57 SNPs identified through RAD sequencing provide a diagnostic tool to detect population admixture and to identify hybrid and pure-species Asian carps in the United States and China.

Spatial and temporal influences on the physiological condition of invasive silver carp

We quantified nutritional and stress parameters (alkaline phosphatase, cholesterol, protein, triglycerides, cortisol, and glucose) in invasive silver carp (Hypophthalmichthys molitrix) inhabiting four large rivers throughout three distinct time periods in the Midwestern USA. Examining the basic biology and ecology of an invasive species is crucial to gain an understanding of the interaction between an organism and its environment. Analysis of the physiological condition of wild-caught silver carp across broad spatial and temporal scales is essential because stress and nutritional parameters can link individuals to their habitats and vary among populations across environments. During each time period, we collected blood samples from individual silver carp in the Illinois River and portions of the Mississippi, Ohio, and Wabash rivers in Illinois. We tested for relationships between silver carp nutrition and stress across rivers, reaches within rivers, and time periods. Principal component analyses separated physiological parameters into a stress component (cortisol and glucose) and two nutritional components representative of short-term feeding (alkaline phosphatase, protein, and triglycerides) and body energy reserves (cholesterol and protein). Akaike's information criterion suggested that time period had the greatest influence on stress. Stress levels were consistent in all four rivers, and declined across time periods. Akaike's information criterion also suggested that interactions of time period and river had the greatest influence on short-term feeding and body energy reserves. There was no specific pattern across time periods within each river, nor was there a pattern across rivers. Our results provide a better understanding of nutritional and stress conditions in invasive silver carp across a broad landscape and temporal scale, with implications for managing and predicting the spread of this species.

Human mercury toxicity and ice angler fish consumption: are people eating enough to cause health problems?

Mercury contamination of aquatic ecosystems is a global environmental concern. Bioaccumulation of mercury in fish exposes consumers to risk. We interviewed ice anglers on Monona Bay, Wisconsin during the 2001-2002 ice fishing season to determine risk associated with fish consumption and methyl mercury (MeHg) intake. The majority of anglers (95%) were not at risk of mercury toxicity because they ate less fish than would be required to create health problems. The remaining 5% of ice anglers barely exceeded the mercury toxicity threshold, with the exception of one angler who exceeded the threshold by 0.926 ppm. Anglers encountered were all male and predominantly Caucasian. Fish consumption by ice anglers was independent of awareness of consumption advisories, education, income, and age. This suggests that future awareness efforts should (1) identify groups of anglers most at risk and (2) create policies to effectively reach these audiences.