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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
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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
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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
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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
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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
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