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STUDY PERFORMANCE REPORT State: Michigan Project No.: F-81-R-10 Study No.: 230723 Title: Genetic diversity of fish populations in Michigan: Effects of environmental and anthropogenic factors on recruitment and apportionment of phenotypic and genetic diversity of fish populations in inland and Great Lakes habitats Period Covered: October 1, 2008 to September 30, 2009 Study Objectives: To use molecular markers and population genetics theory to investigate demographic, ecological, and genetic stock relationships within and among native and naturalized fish species of importance in Michigan. We will monitor recruitment, assess variation in life history traits, estimate degree of stock structure, and the effects environmental and anthropogenic factors on population and meta-population levels of genetic diversity. Summary: Research is ongoing in each of the main focus areas, related to factors affecting the genetic diversity and viability of fisheries in Michigan waters. Studies involve numerous native species of economic and ecological importance that are intensively managed. This project seeks to provide information to better understand how recent management practices and environmental factors have affected the genetic diversity and long-term sustainability of Michigan’s fisheries. Findings: Jobs 1–6 and 8 were scheduled for 2008-09, and progress is reported below. Job 1. Title: Review literature.–This year a large amount of time was devoted to review of literature in the general area of landscape ecology and landscape genetics. Michigan Department of Natural Resources (MDNR) fisheries managers require information on population demographic characteristics of, and degree of connectivity among populations of economically and ecologically important fish species as well as species of conservation concern. The manner in which multi-scale environmental controls influence populations is a major issue affecting the timing and direction of management actions. Knowledge of current and the ability to predict future species diversity, abundance, and movements through different watersheds and basins of the state is key for effective management in the face of increasing anthropogenic changes to Michigan’s riverscapes. Literature reviewed suggest that land-use/land-cover change including urban development, agriculture, and deforestation are common throughout the state, yet their influence on stream fish populations, along with effects of natural environmental factors, likely varies regionally. Understanding these influences on biodiversity within and across drainage basins is critical for improved protection and restoration of Michigan’s fluvial fisheries. Study proposals are being developed based on part on the literature reviewed and Division research needs. 1. Predicting effects of stream and adjoining landscape features and anticipated changes in these features to species abundance, recruitment, and movements at population, watershed, and basin scales necessitates that managers be able to identify factors that affect degree of population connectivity across multiple spatial scales, from stream catchments, to riparian zones, to stream reaches. Habitat complexity, degradation, and fragmentation can affect the relative abundance within and dispersal among populations and are critical areas of conservation research. This literature review provided a means to develop sampling designs that would establish predictive relationships between land1 F-81-R-10, Study 230723 use/land-cover features, and population variables such as population size, habitat occupancy, or dispersal that can provide important insight into biological processes and future population responses to human changes to Michigan’s riverscapes. 2. The effects of landscape features also likely affects the survival of hatchery fish stocked into inland lakes and streams. Accordingly, significant effort was devoted to review of literature on stream hydrogeomorphology related to stocking prescriptions. Approximately 40% of all recreational fishing in the state of Michigan depends on stocked fish. The Fisheries Division alone stocks approximately 9 million fish of 10 different species (including 18 genetically-distinct strains) at hundreds of locations throughout the state. Although the annual financial commitment required to raise and release these fish costs millions of dollars, comparatively little effort is expended to determine whether stocked fish survive following release. Therefore, fisheries managers lack critical information that is needed to conclude when and where stocking is necessary and most successful. 3. A significant amount of time was devoted to review of literature on brook trout, particularly in regards to heritability of life history traits and basis for adaptations, including resident vs podadromous life histories. This literature was used for work conducted under other jobs related to consultation with partner agencies (Job 2), landscape genetic studies (Job 3), and effects of stocking (Job 4) 4. Literature was reviewed pertaining to use of genetic data in the area of stock recruitment. Critical data are needed to direct corrective action to enhance natural reproduction, survival through critical early life stages, and recruitment. Part of the difficulty in identifying environmental or biological impediments to recruitment is that there often is disconnects between how recruitment is measured and how factors likely affect to recruitment are integrated into statistical models. Recruitment is typically estimated as a function of spawner abundance through one of several stock-recruitment models (e.g., Ricker, Beverton-Holt, or Cushing models). Literature reviewed allowed development of prototypes of protocols for future research and monitoring. Specifically, environmental factors and biological interactions can be added to stock-recruitment models as covariates, causing yearly predicted levels of recruitment to deviate from the mean conditional relationship between recruits and spawner abundance. Environmental factors such as climatic variables including temperature and rainfall are typically measured at large (i.e., basin-level) scales. These variables are highly spatially autocorrelated and fail to quantify environmental heterogeneity or heterogeneity in species composition and abundance among or within tributaries that likely contribute greatly to spatial and temporal variation in recruitment. Based on an extensive literature review, a more robust approach to measuring impediments to recruitment can be developed using genetic markers and genetic determination of parentage in the context of ongoing research on lake sturgeon in the Black Lake system. This site can be a prototype for future and more wide-spread application. The system is amenable to measurement of variables that affect recruitment at an individual level. The number of recruits produced by individual is affected by large-scale features, by habitat and hydrogeomorphological features where spawning takes place, and by the phenotype, age, and condition of parents at the time of spawning. The effects of parental attributes on individual reproductive success and concomitantly to annual recruitment can be especially important for populations that are supplemented by hatcheries because of perceived disparities in reproductive success between younger adults (likely of hatchery origin) and older adults (residual wild fish). Recruitment can also vary in space and time as a function of the composition and abundance of predators and alternative prey. Individual-based assessments of recruitment 2 F-81-R-10, Study 230723 in species that display other forms of spawning behavior, such as broadcast spawners (e.g. lake sturgeon) is challenging and requires a system such as Black Lake where researchers have complete access to all adults, eggs, and larvae. Stock requirement models also require extensive data collected over multiple years and ranges of response and predictor variables. 5. Literature was reviewed in the area of climate change and anticipated effects of genetic diversity and future adaptive potential. 6. Literature was reviewed in areas of microbial ecology and community genetics, focusing on effects of microbes as a selective agent affecting levels of mortality at the egg stage and on indirect effects on larval phenotype, growth, and survival. Job 2. Title: Consultation.–Considerable effort was made to work with personnel from Hatchery, Management, and Research Sections within Fisheries Division to obtain information, coordinate research activities, and to communicate results. Information was conveyed to Division personnel and to other agency and citizen groups in the form of reports and summaries. 1. Issues arose this year with regards to proposed changes in hatchery practices associated with a new strain of brown trout in development. Managers were seeking information about the concerns from a genetics perspective regarding proposed photoperiod manipulation of broodstock. A white paper was prepared for the Fisheries Division Trout Committee that outlined the issues associated with selection in the hatchery and potential for loss of genetic variation in increases in degree of domestication. 2. Information was synthesized and conveyed to Hatchery Section personnel regarding recent initiatives in areas of genetic policy and hatchery reform from the Pacific Northwest. 3. Information regarding landscape-genetic analyses of open-water and nearshore distributions of lake sturgeon sub-adults and adults was conveyed to agency cooperators and managers. We have worked extensively with cooperators in federal and state agencies in Michigan and Wisconsin to develop a spatially explicit lake sturgeon genetic data base. Through consultation with contributors and agency biologists we have parameterized models that will be used to predict occupancy of openwater habitats during different seasons and by different age classes and by members of different genetic stocks. 4. Information has been communicated to Fisheries Division’s Hatchery Section regarding the effects of hatchery rearing on genetic diversity of lake sturgeon. Methods and results described in research by our group (Crossman et al. references below) provide a framework for evaluating alternative strategies for managers designing and implementing conservation programs for lake sturgeon and other long-lived iteroparous species. To ensure high levels of genetic diversity in offspring supplemented into natural populations, programs should focus on developing collection methods that incorporate aspects of the species reproductive ecology to ensure they adequately capture the genetic diversity of the adult breeding population. Populations are composed of a mixture of individuals that reproduce at different times and in different locations. Collection of gametes from adults captured from a finite number of locations and times will limit the diversity represented in offspring, including traits adapted to environmental conditions where and when adults reproduce. For lake sturgeon, a species that has undergone significant reductions in abundance, conservation programs should be designed based on rigorous evaluations of the most effective methods required to collect, rear, and stock progeny back into the natural environment. We found that collecting dispersing larvae downstream of the 3 F-81-R-10, Study 230723 spawning grounds minimized estimates of coancestry while at the same time increased the effective number of breeders. Differences between hatchery rearing environments have the ability to influence the genetic variation observed in the progeny. Job 3. Title: Conduct studies including the effects of landscape features.–Predicting effects of aquatic and adjoining terrestrial landscape features and anticipated changes in these features to fish species abundance, recruitment, and movements at population, watershed, and basin scales necessitates that managers be able to identify factors that affect degree of population connectivity across multiple spatial scales, from stream catchments, to riparian zones, to stream reaches. 1. I worked with Michigan State University cooperators and Division Fisheries managers and research biologists to synthesize information from the fish inventory system and stream valley segment data base to develop a study plan to integrate genetic data as a predictive variable to characterize movements and provide surrogate measures of abundance in heterogeneous river habitats. Habitat complexity, degradation, and fragmentation can affect the relative abundance within and dispersal among populations and are critical areas of conservation research. Predictive relationships between land-use/land-cover features, and population variables such as population size, habitat occupancy, or dispersal can provide important insight into biological processes and future population responses to human changes to Michigan’s riverscapes. Preliminary findings are being used to develop research proposals for future collaborative university-Fish Division research. 2. We have developed a landscape model based on stream environmental covariates to predict spawning site selection, patterns of egg deposition, and egg survival for lake sturgeon on the upper Black River. We are developing the statistical architecture using this well-studied system in the hopes of generalizing the approach with other fish species. Data revealed that adult lake sturgeon preferred to aggregate and spawn in relatively deep river segments immediately upstream of long segments characterized by high water velocity and shallow water depth. Despite the consistency in spawning site selection, quantified features associated with egg deposition and during incubation including substrate size, water depth and water velocity differed significantly among the primary spawning locations. Specifically, sites differed significantly in overall mean value for water velocity, average substrate size, and maximum substrate size but not in water depth Environmental covariates exhibited spatial heterogeneity within and among locations largely depending on channel morphology. Job 4. Title: Design hatchery monitoring protocols and examine effects of stocking. – Research findings from several past and ongoing projects have been integrated into hatchery culture and stocking protocols for Michigan fishes. Findings also established the need for an integrated ecological and ecological electronic data base. 1. We have implemented collection regimes for all species, strains, and year classes in the Michigan DNR hatchery system. Samples were collected at each of the broodstock weirs to evaluate the potential genetic implications of stocking practices. Samples were collected from northern musky from broodstock lakes. These samples were archived for evaluation at a later date. An electronic data set and metadata were established to track receipt of all DNR samples, record biological data accompanying samples, cross-reference field and archival locations, and track associated genetic data collected from individual samples. 2. Standard operating procedures (SOPs) were developed collaboratively and were summarized and provided to Hatchery Section personnel along with copies of all manuscripts that provide the scientific basis for development of recommendations and protocols. The SOPs that were 4 F-81-R-10, Study 230723 developed governed all aspects of sturgeon gamete collection, culture, and release. Protocols included: (1) collection of gametes, (2) methods of fertilization, (3) egg incubation, (4) treatment for environmental pathogens, (5) feeding, (5) hatchery enrichment, (6) disease screening and treatment, (7) tagging, and (8) release. 3. During 2009 a stream-side lake sturgeon hatchery was completed on the upper Black River. Based on research conducted by our group, we worked with Michigan DNR staff to design the facility, tailor SOPs to the facility, and implement lake sturgeon research recommendations developed in the context to Crossman et al. research (detailed under Job 8). 4. We finalized analyses for lake sturgeon overwinter survival. Knowledge of age specific survivorship is critical when developing management prescriptions for imperiled species such as the lake sturgeon (Acipenser fulvescens). Management has focused on population restoration through hatchery supplementation, largely in the absence of data about relationships between hatchery rearing conditions, size/age at release, and estimates of overwinter survival for stocked age-0 lake sturgeon. We reared young of the year lake sturgeon from egg to age three months in two separate hatchery environments, a streamside hatchery on the natal Upper Black River, Michigan, and a traditional hatchery environment. From age 3-6 months all fish were reared in the traditional hatchery. Fish (n=20) originating from each rearing environment were surgically implanted with ultrasonic transmitters at 6 months of age (mean total length: 31.4cm; mean weight: 106.4g) and released into Black Lake in December of 2005. Tracking using manual and automated hydrophones was conducted during April and May of 2006 to estimate overwinter survival and to test for differences in survival of fish reared in different hatchery environments. Eighteen fish (45%) were detected, 16 (40%) of which survived the winter (range of distance traveled between observations of surviving fish was 0.09 to 0.55km). The remaining fish were not detected. No significant differences in survival were documented due to rearing environment or size at release. This study represents the first quantified estimate of overwinter survival for stocked age-0 lake sturgeon. Our minimum estimate of 40% survival through the first winter is encouraging for hatchery programs, and will aid development of management prescriptions for this species. Job 5. Title: Estimate effects of environmental pathogens.– 1. Understanding mechanisms underlying adaptation to different environmental conditions that affect retention of biological diversity in natural ecosystems during the current era of global environmental degradation is both challenging and essential. We initiated studies on lake sturgeon (Acipenser fulvescens) using our Black Lake site as a model system to investigate interactions between microbial communities and developmental processes during critical life stages. The studies were developed around the concept that the interaction of the developing sturgeon egg with the microbial community is a critical point of reference for studies of developmental evolution, for development of predictive models of consequences of changes in land-use, damning of rivers, and global warming, and for conservation. Our focus is on reproductive traits of the sturgeon that interact both positively and negatively with the microbial populations of streams. Traits can co-evolve based on the degree of covariance between the selected traits and environmental variables tied to locations and timing of reproduction. Lake sturgeon represent an example of adaptation to temporal variation in environmental conditions within a breeding season that is common to many ecologically important fish species in Michigan. We’ve shown that stream environmental conditions including temperature and microbial communities vary temporally within a season and spatially over different scales, and affect embryonic development and juvenile traits at hatch. Our long term 5 F-81-R-10, Study 230723 goals are to understand how microbes and temperature affect multivariate selection during embryogenesis and early larval life stages in lake sturgeon, and to understand how temporal and spatial variation in these agents of selection affect the evolution of complex phenotypes. Preliminary data reveal that the probability of egg survival was significantly affected by the incubation temperature and whether or not microbes were present. The allocation of yolk resources to embryo growth and potentially to immunological responses to microbe infection significantly altered larval phenotypes at hatch and significantly decreased available yolk resources of post-hatch development, which may affect probabilities of post-hatch survival. Survival during these early life stages represents a substantial component of variation in the lifetime fitness and, therefore, represents a high opportunity for selection during these life stages. The outcomes of this ongoing research will have important implications for hatchery culture practices for all species and will serve to develop predictive models incorporating microbes as a biotic factor affecting natural stock recruitment. Job 6. Title: Prepare annual report and communicate results.–Findings of activities are communicated in this document and to Michigan DNR and regional fisheries biologists via oral communications at meetings, professional meetings, and written reports. Job 8. Title: Publish reports.–The following manuscripts were submitted for publication or were published during the reporting period. Bott, K., K. T. Scribner, G. Kornely, M. Donofrio, and R. F. Elliott. In press. Mixed-stock analysis of lake sturgeon harvest mixtures and from adjoining open waters of western Lake Michigan. North American Journal of Fisheries Management. Bruggeman, D. J. M. L. Jones, K. T. Scribner, and F. Lupi. In press. Relating tradable credits for biodiversity to sustainability criteria at a landscape-scale. Landscape Ecology. Crossman, J. A., P. S. Forsythe, E. A. Baker, and K. T. Scribner. 2009. Over-winter survival of stocked age-0 lake sturgeon reared in natal and non-natal environments. Journal of Applied Ichthyology 25:516-521. Dawson, H. A., M. L. Jones, K.T. Scribner, and S.A. Gilmore. 2009. An assessment of age determination methods for Great Lakes larval sea lampreys (Petromyzon marinus). North American Journal of Fisheries Management 29:914-927. Welsh, A., B. May, C. Krueger, K. T. Scribner, R. Elliott, and H. Quinlan. In press. Genetic Guidelines for the Stocking of Lake Sturgeon (Acipenser fulvescens) in the Great Lakes Basin. Great Lakes Fishery Commission, Special Publication. Prepared by: Kim Scribner Date: September 30, 2009 6