Download Molecular data have provided valuable insight into mating

STUDY PERFORMANCE REPORT
State: Michigan
Project No.: F-81-R-11
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, 2009 to September 30, 2010
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 were scheduled for 2009-10, and progress is reported below.
Job 1. Title: Review literature.–A large body of literature was reviewed in several areas in support
of Fisheries Division management, research, and hatchery programs. Details are provided below
is each of several major areas.
1. This year a large amount of time was devoted to review of literature in the general area of
landscape ecology and landscape genetics. Syntheses of literature pertaining to
methodologies for developing cost surfaces reflecting the degree of permeability of
habitats to dispersal were developed. Literature pertaining to considerations of temporal
and spatial scales for landscape genetic studies were developed. Literature reviewed has
provided information to develop sampling designs that would establish predictive
relationships between land-use/land-cover features, and fish population variables such as
population size, habitat occupancy, or dispersal. This information will provide important
insight into biological processes and future population responses to human changes to
Michigan’s rivers. Given that landscape features affects the survival of hatchery fish
stocked into inland lakes and streams, significant effort was devoted to review of
literature on stream hydrogeomorphology related to stocking prescriptions. Materials
synthesized as part of this review were used in four publications (Spear et al. 2010,
Epperson et al. 2010, Manel et al. 2010, Anderson et al. 2010) that were published as part
of a special issue on Landscape Genetics in the journal Molecular Ecology.
2. A considerable amount of time was devoted to reviews of literature on genetic analyses
of stock mixtures. This literature was used for ongoing research and Great Lakes stock
assessment work associated with sturgeon (e.g., Homola et al. 2010 in Lake Superior)
and ongoing work in open-water, near-shore and river mouth regions in Lake Michigan.
Literature was also used for ongoing research in cooperation with the Michigan State
1
F-81-R-11, Study 230723
University Quantitative Fisheries Center associated with simultaneously assessment of
stock composition and recruitment based on collections of individuals from numerous
stocks or hatchery strains in the Great Lakes.
3. A literature review was conducted in areas related to use of parentage analyses to
estimate recruitment in fish populations. This work was used in part to direct efforts
associated with ongoing lake sturgeon hatchery and recruitment studies and was used in
publications by Duong, Crossman and others referenced below that are either in press or
submitted. We also developed an analytical approach to estimate the number of adults
contributing offspring based on analysis of multi-locus genotypes that is being used in
ongoing project of lake sturgeon and black bass based on literature reviewed in this area.
4. A considerable amount of literature has been reviewed in areas of phenotypic and
behavioral plasticity and the role of plasticity in evolvability of natural fish populations.
When faced with changing environments, fish have the ability to physiologically and
behaviorally respond to accommodate new environmental conditions that affect their
ability to survive and reproduce. The ubiquity of this process contrasts with our ignorance
of its evolutionary significance or importance to understanding recruitment dynamics.
While within generation accommodation of novel environmental inputs has clear fitness
consequences that ultimately affect stock recruitment, current evolutionary theory cannot
easily link function importance and inheritance of novel accommodations. This is
particularly true in anthropogenically altered environments where natural linkages are
being disrupted, and where the rate of change seasonally within a year and among years
has been accelerated. Anthropogenically altered systems may disproportionally impact
organisms exhibiting complicated life histories where functional response at different
stages may be conditional on environmental characteristics at both current and former
periods. Long-lived organisms with long generation intervals are particularly at risk.
5. A large body of literature has been reviewed associated with the use of genetic markers to
estimate effective population size and how estimates can be used to guide fisheries
supplementation programs. Background information is being integrated into genetic
assessment methodology to predict the effects of variability in environmental parameters
on stock recruitment. Variability in adult reproductive success is related to levels of
genetic diversity in larvae recruited from different segments of the spawning adult
population each year and in different cohorts across years. Effective population size (Ne)
is an important parameter describing evolutionary processes of finite populations, and
therefore has been an important conceptual focus in the conservation and management of
fish populations. Ne allows predictions of generational rates of change in allele
frequencies and of inbreeding occurring in a finite population due to genetic drift and
interactive effects of drift with mutation, migration, recombination and selection.
Quantifying temporal variation in effective population size and the relationship between
Ne and adult census size (N) is important to predict genetic changes in small and isolated
populations.
6. Literature was reviewed on the effects of hydroelectric operations or other human-related
disruption of aquatic systems on behavioral and phenotypic traits of fishes during early
life stages. Normally, cues in the natural environment of an organism elicit a
corresponding behavioral response that is associated predictably with an adaptive
outcome. Traps (ecological or evolutionary) can arise in either of two ways. First, the
environmental conditions experienced by the organism has been altered such that,
although the original cue still occurs and elicits its normal behavioral response, there no
longer is a match between the behavior and the environment. Second, the altered
2
F-81-R-11, Study 230723
environment contains a novel element that mimics the original cue closely enough to
elicit the original behavior, but in an inappropriate context. Nearly all rivers that support
large and economically important fish species in the Great Lakes are dammed. The
ecological consequences of altered timing and magnitude of flow, changes of temperature
and oxygen regimes have not been evaluated for critical early life stages of aquatic
species. Nothing is known of the direct effects of important dam-related environmental
influences on the behavior of aquatic species and direct effects on embryo and larval
growth, behavior, and survival. Effects of river flow on timing of spawning and survival
during early development will provide critical linkages between conditions resulting from
dam operations, larval behavior, morphology, growth and survival. Results will provide
agencies and industry with information that can be used to delineate maximal allowable
deviance in natural river regimes during important pre-spawning egg maturation,
incubation, and early post-hatch life stages. Knowledge gained will also allow greater
prediction of the effects of natural variation in environmental conditions on embryo and
larval traits.
7. 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).
8. Literature was reviewed in the area of climate change and anticipated effects of genetic
diversity and future adaptive potential.
9. 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.–Members of my research group and I worked 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 oral talks, reports, and
summaries.
1. Genetic guidelines were prepared for lake sturgeon culture in the Great Lakes region. The
document (Welch et al. 2010) summarizes information pertaining to stock structure and
use of stocks for collection of gametes or larvae. The document also outlines gamete take
and fertilization scenarios, as well as rearing and stocking recommendations.
2. Genetic analyses were preformed to confirm species and strain of a potential world
record brown trout and Atlantic salmon. In conjunction with this work we have
established a DNA-barcoding set of PCR primers that are capable of identifying species
of origin for all Great Lakes fish species.
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 in the form of reports and oral presentations made at the national American
Fisheries Society meeting, at lake technical committees, and at the Lake Michigan lake
sturgeon task group meeting. 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 coincident with a basin-wide tagging data base. Through
consultation with contributors and agency biologists we have parameterized models that
3
F-81-R-11, Study 230723
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 and the
Lake Michigan lake sturgeon task group 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 programs 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 reduced levels of
coancestry in offspring while increasing the effective number of breeders. Differences
between hatchery rearing environments have the ability to influence the genetic variation
observed in the progeny.
5. I have provided expert opinion and literature and I have met with DNRE staff biologists
and lawyers working with e-DNA and carp in the Great Lakes
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. We developed an electronic database of all genetic collections of fishes supplied by Great
Lakes cooperators over the past 13 years. The database includes information pertaining to
phenotype, age, and characteristics of the water bodies samples were collected from. 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.
4
F-81-R-11, Study 230723
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 fishes in Michigan and across the Great Lakes. Additional work has been
focused on hatchery protocols associated with stream-side rearing of cultured lake sturgeon.
1. We have collected samples from adults from all broodstocks and wild-caught adults at
weirs. We have collected samples from portions of all progeny produced 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. These samples were archived for evaluation of the impact changes in gamete
collection regimes have had on the genetic diversity of progeny released. An electronic
dataset 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 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 developed covering
all aspects of sturgeon gamete collection, culture, and release.
3. Research has been conducted in several areas to investigate the effects of temperature,
flow, and feeding regime on larval sturgeon growth and survival. We have found that
periods of rapid increases in temperature result in elevated levels of mortality. Variable
flow regimes appear to alter the duration of incubation and the time of day in which hatch
occurs. Use of filtered and UV treated water greatly increase egg survival to hatch.
4. Work was summarized and published (Crossman et al. 2010) showing that post-stocking
survival of lake sturgeon increased significantly within increasing age/size at release.
Survival of released lake sturgeon was higher for stream-side reared juveniles compared
to juveniles reared in a traditional hatchery.
5. Work was summarized and published (Crossman et al. in press) showing that several
measures of genetic diversity for juvenile lake sturgeon were significantly higher in
larvae collected from streams and naturally produced eggs collected from streams than
for juveniles reared from eggs collected directly from females. Levels of genetic diversity
in juveniles reared in a stream-side hatchery were significantly higher than juveniles
reared in a traditional hatchery, due primarily to higher variance in survival of eggs and
larvae in the traditional hatchery compared to the stream-side hatchery.
Job 5. Title: Estimate effects of environmental pathogens.–
1. We are emphasizing studies on lake sturgeon (Acipenser fulvescens) using our Black
Lake site as a model system to investigate effects of microbial colonization and
proliferation on egg surfaces, egg survival and post-hatch larval development. We
hypothesize knowledge of the interactions of the developing sturgeon egg with the
microbial community is critical to understand direct and indirect effects on survival
during critical early life stages. Preliminary findings show that methods that reduce the
number and taxonomic diversity of microbes on the egg surface at the time of fertilization
greatly increase egg survival. Eggs incubated in water treated to reduce the number of
taxonomic diversity of microbes produced larvae that had significantly larger amounts of
yolk reserve at hatch than did larvae incubating in untreated stream water. The outcomes
of this ongoing research will have important implications for hatchery culture practices
5
F-81-R-11, Study 230723
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 DNRE and regional fisheries biologists via oral
communications at meetings, professional meetings, and written reports. Results were also
communicated through the peer-reviewed literature. The following papers were completed and
published at the time this report was prepared. In addition four other manuscripts have been
accepted for publication, and six more have been submitted to journals and are now in the peerreview process.
Published Papers
Anderson, C., B.K. Epperson, M.-J. Fortin, R. Holderegger, P. James, M. Rosenberg, K.T.
Scribner, and S. Spear. 2010. Consideration of scale in landscape genetics can improve
predictive relationships between measures of spatial genetic structure and landscape
pattern. Molecular Ecology. 19: 3565-3574.
Crossman, J.A., Patrick S. Forsythe, Edward A. Baker, K. T. Scribner. 2010. Experimental
releases of lake sturgeon. Fisheries Management and Ecology. In press.
Epperson, B.K., B. McRae, K.T. Scribner, S. Cushman, M. S. Rosenberg, M.-J. Fortin, P.
James, M. Murphy, S. Manel, P. Legendre, and M. Dale. 2010. Utility of computer
simulations in landscape genetics. Molecular Ecology. 19: 3549-3565.
Homola, J.J., K.T. Scribner, E.A. Baker, N.A. Auer. Genetic assessment of straying rates of
wild and hatchery reared lake sturgeon (Acipenser fulvescens) in Lake Superior
tributaries. Journal of Great Lakes Research. In press.
Manel, S, S. Joost, B. K. Epperson, R. Holderegger, A. Storfer, M. S. Rosenberg, K.T.
Scribner, A. Bonin and M-J Fortin. 2010. Perspectives on the use of geo-environmental
data in landscape genetics in the face of global change. Molecular Ecology. 19: 37733788.
Spear, S.F., N. Balkenhol, M.-J. Fortin, B. McRae, and K.T. Scribner. 2010. Use of cost
surfaces for landscape genetic studies: Considerations for parameterization and analysis.
Molecular Ecology. 19: 3576–3591.
Prepared by: Kim Scribner
Date: September 30, 2010
6