INTEGRATION OF MOLECULAR GENOMIC AND ECOLOGICAL METHODOLOGY AND THEORY TO ENHANCE SUSTAINABILITY OF MICHIGAN AQUATIC COMMUNITIES

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: NEW
• Funding Source: HATCH
• Reporting Frequency: Annual
• Accession No.: 1018022
• Project No.: MICL02587
• Project Start Date: Jan 1, 2019
• Project End Date: Dec 31, 2023

Project Director
Scribner, K.

Recipient Organization
MICHIGAN STATE UNIV
(N/A)
EAST LANSING,MI 48824

Performing Department
Fisheries & Wildlife

Non Technical Summary
Natural fish stocks are declining for several reasons including habitat loss, contaminants,excessive harvests, and emergence of aquatic invasive species. To thesesomewhat localized pressures we must now add the specter of global climate change. For this reason, understanding how fish adapt to different climate-induced changes in environmental conditions in natural and manipulated aquatic agroecosystems is essential. Our previous research has established the need to investigate the effects of anthropogenic activities, principallychanges in stream flow and temperature on reproduction, survival and growth during all fish life stages. We expand the suite of molecular methods and analytical framework to investigate issues of associated with the conservation and management of regional aquatic resources.Findings will improve scientific knowledge to foster an expanding aquatic conservation and commercial aquaculture presence in the Great Lakes region.

Animal Health Component

10%

Research Effort Categories

Basic

50%

Applied

45%

Developmental

5%

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
136	0210	1070	100%

Knowledge Area
136 - Conservation of Biological Diversity;

Subject Of Investigation
0210 - Water resources;

Field Of Science
1070 - Ecology;

Keywords

fisheries

recruitment

aquatic invasive species

aquaculture

anthropogenic change

genetics

Goals / Objectives
GRA-1.1The overall goal of this component of the project is to use existing large-scale, regional data of Great Lakes tributaries to identify lake sturgeon habitat conditions that facilitate estimates of the abundance of alternative prey (i.e., specific macroinvertebrate taxa) that we hypothesize mediates predation on dispersing larval sturgeon. Specific objectives are: (1) To quantify associations between 'coarse' landscape and hydrological data from regional data bases with 'fine-scale' stream substrate and invertebrate data from Great Lakes tributaries. (2) To develop and validate hierarchical models that predict sturgeon larval predation risk using regionally available landscape, hydrologic and fish community data ('course-scale') with stream reach habitat characteristics and macroinvertebrate abundance and diversity ('fine-scale').GR-1.2The overall objective of this component of the proposed work to quantify reproductive 'effort' in terms of reproductive activity in a given year of males of different age and prior reproductive histories, and quantify whether male reproductive success in a given year is predicted by current year effort and whether effort in a given year is predictive of inter-spawning interval (e.g., there is a trade-off between current effort and the timing of and success in future reproductive events).Effects of current year environmental conditions on offspring phenotype and survival may be counter to reproductive allocation decisions. Therefore, environmental conditions that vary in such a way that environmental cues for spawning (and investment in current year reproductive) are not predictive of subsequent conditions affecting larval vigor and survival can lead to ecological and evolutionary consequences (Schlaepfer et al. 2002) for males.GRA-2.1The objective of this component of the proposal is to evaluate a series of models of the aquatic invasive species invasion around the Lower Peninsula of Michigan, as well as within three inland river basins that are fragmented by one or more impoundments. All events occurred within a few dozen generations of the initial Great Lakes founding event. Commonalities and differences associated with Great Lakes expansion and inland invasions of multiple and ecologically different species and into environmentally different Great Lakes tributaries will be evaluated. Our analyses will provide information on likely source populations and mechanisms associated with inland invasions. We further characterize demographic parameters associated with range expansion event, including estimates of bottleneck severity and effective population size of inland and Great Lakes populations.GRA-2.2The objectives of this component of the proposal are to: (1) develop genomics tools and data from lake trout hatchery strains and wild recruits of different ages collected from multiple management units, at different time points, and from different environments within the Great Lakes, with emphasis on understanding the genetic basis of emergence of wild recruitment in Lake Huron; (2) quantify the relative importance of inter-strain hybridization and potential for domestication selection in hatchery strains, 3) quantify evidence of selection and whether alleles at the same loci are disproportionally (and consistently) represented at high frequency in wild fish across locations, sampling periods, and, 4) quantify associations between lake physical features (e.g., near shore shallow vs off-shore deeper reef environments) with genetic variation at adaptive and neutral loci genome-wide.GRA-3The objectives of this component of the proposed project are (1) to develop eDNA metabarcoding methods for species of different ecological guilds (aquatic plants, arthropods, and mollusks) in addition to fish that co-occur in different lake habitats, (2) To develop baselines of DNA sequence data for Michigan natives and AIS from each taxonomic group, (3) To evaluate whether surface or benthic sampling or sampling early or late in the summer would result in different numbers of species across different taxa.

Project Methods
?GRA-1.1Data on stream gradient, temperature, and fish community composition will be provided by the Great Lakes Aquatic Habitat Framework and from partners Riseng and Wehrly, and following methods described in Brenden et al. (2006). Fine-scale estimates of stream depth, substrate size, and flow and estimates of benthic macroinvertebrate community composition, richness and diversity will be estimated at multiple locations within each of several sampled lake sturgeon streams. Estimates of predator fish taxonomic composition and relative abundance will be determined using electrofishing. Nightly drift sampling will associate fish diets with drifting co-occurring macroinvertebrate and larval fish prey. Fish dietary composition will be quantified using DNA metabarcoding (Waraniak et al. 2018a, 2018b). We will use structural equation hierarchical models and generalized linear models using Akaike's information criteria using geo-referenced stream habitat features to quantify predictability of levels of sturgeon predation.GRA-1.2The work will be conducted on the Black River population of lake sturgeon in Cheboygan Co., Michigan. Reproductive 'effort' will be measured by the duration of time spent on the spawning areas and the number of migration events. Male body size (length weight) will be measured. Measures sperm quality including sperm counts, velocity, and duration of motility will be recorded using a hemocytometer and compound microscope. Sperm quality will be analysed using a general linear model as a function of male size, inter-spawning interval (yrs) and number of migration bouts. Estimates of male reproductive success will be determined using genetic determination of parentage from larvae dispersing from spawning areas. Larvae will be collected nightly using D-frame nets (Auer and Baker, 2002). DNA will be extracted from larval fin clips using DNeasy(R) extraction kits. Polymerase chain reaction and genotyping will be conducted using methods described in Duong et al. (2011). Genotypic data will be used to assign parentage using program COLONY 2.0.5.8 (Jones and Wang, 2010a). Generalized linear models will be used to determine how male reproductive success varies as a function of biological, demographic, and abiotic factors.GRA-2.1We will studyfour aquatic invasive species (AIS) comprising three ecologically different taxonomic and trophic groups that we hypothesize can be transported from Great Lakes to inland water bodies by different vectors and during different life stages - the Round Goby, Zebra Mussel, and Rusty Crayfish, and Red Swamp Crayfish. Specimens will be sampled from locations in the lower peninsula of Michigan using seines, fishing gear, traps, or backpack electrofishing. Three river basins will be chosen because they vary in recreational use, distance from populated areas, and number or type of human-constructed barriers that impede natural upstream movement, which are important factors associated with the secondary spread of aquatic invasive species (Drake and Mandrake 2010, Drake and Mandrake 2014).Sequencing-DNA will be extracted from tissue samples collected at each location using Qiagen DNeasy kits. Libraries for each species will be prepared for sequencing using the 'BEST RAD' protocol (Ali et al., 2016). Libraries will be sequenced on two paired-end 150 base-pair lanes of a HiSeq 2500 at Michigan State University's Research Technology Support Facility.Bioinformatics-Sequencing data for all libraries will be processed using STACKS v. 1.44 (Catchen et al. 2011, Catchen et al. 2013) on the High Performance Computing Cluster (HPCC) at Michigan State University's Institute for Cyber Enabled Research.Statistical Analysis-We will calculate summary statistics that include information on the size and genetic diversity of populations, as well as the divergence among populations. All statistics were calculated in the R statistical computing environment, using a combination of functions from the 'strataG' R package (Archer et al. 2016).Approximate Bayesian Computation (ABC) model development-We will test hypotheses to explain how each AIS colonized each the three sampled drainage systems in an ABC framework to assess if there were consistent patterns in secondary invasions from the Great Lakes to inland systems. ABC analyses will then be conducted using the R packages 'abc' (Csilléry et al. 2012) and 'abcrf' (Marin et al. 2017). Model selection analyses will be carried out using neural network (Blum and François 2010) and random forest (Pudlo et al. 2015) methods.GRA-2.2We will use samples and data from our existing collections of wild lake trout from Lake Huron, and from different time periods including historical samples (pre-crash) and hatchery strains. To identify thousands of genetic markers (SNPs) genome-wide and in functional genes and gene regions, we will use RAD-seq (restriction site associated DNA sequencing). Analysis of SNP genotype data will document effects of demographic and selective processes across the genome using established computational approaches to identify the genes and chromosomal regions associated with SNPs. We will test whether emergence of natural recruitment is associated with inter-strain mating (e.g., hybrid vigor) and/or emergence of adaptive novel multi-gene complexes.GRA-3Field sampling-We will expand ongoing eDNA sampling to 20 Michigan inland lakes. One liter water samples were filtered on site using Smith Root's ANDe backpack filtration system (Thomas et al. in press). All filtered water samples will be stored in 95% ethanol in the field and returned to the laboratory.Taxonomic database developmentFish-eDNA samples will be interrogated for fish species using the 12S_fish and 16S_fish PCR primers slightly modified from Riaz et al. (2011) and Deagle et al. (2009)..Crayfish-We will amplify a 350 base pair (bp) product (containing the 16S locus) with primers developed by Crandall et al. (1996).Gastropods and Bivalves-Klymus et al. (2017) developed a 16S metabarcoding assay to identify invasive bivalves and gastropods in the Great Lakes, hereafter 16S_BG, which we intended to use to survey eDNA samples for species within these taxa that may reside in Michigan waterways.Plants-We will use an assay developed for plant diet analysis (Valentini et al. 2009) which amplifies suitably sized (50-135 bp) fragments of the tRNA-Leu p6 loop region (Taberlet et al. 2006).DNA library preparation-Filters will be allowed to dry overnight in a closed UV sterilized hood. We will extract eDNAs from each filter using a protocol developed by Laramie et al. (2015), using the Qiagen DNeasy Blood and Tissue Kit supplemented with a Qiagen QIAshredder column, followed by treatment of the extracted DNA with a Zymo OneStep PCR Inhibitor Removal column.Analysis of eDNA multi-community data-We will sequence ~200 bp dual-indexed 12S_fish, 16S_fish, 16S_crayfish, 16S_BM, and tRNA-L PCR products on five independent MiSeq v2 flow cell paired-end 150 base pair lanes at the Michigan State University RTSF.We will process the metabarcoding sequence data using Mothur v1.39.5 (Schloss et al. 2009), a commonly used microbial metabarcoding sequence data analysis program, on Michigan State University's high performance computing cluster (HPCC).Lake differences in community composition will be quantified by calculating Bray-Curtis dissimilarity matrices and plotting differences in non-metric multidimensional scaling (NMDS) space. All community matrix analyses will be conducted in R v3.3.4 using the packages vegan (Oksanen et al. 2017) and tidyverse (Wickham 2017). Statistical significance was assessed at α = 0.05 and multiple tests were false-discovery rate (FDR) corrected (Benjamini and Hochberg 1995). We will report AIS detections for each assay. For each lake, sampling event, and assay, we enumerated species richness per sample (S).

Progress 10/01/19 to 09/30/20

Outputs
Target Audience:The target audience for the research produced include colleagues in academic and federal and state natural resource professionals in allied conservation, resource management, and genetic disciplines. Research findings are also targeting stakeholder groups, students at university graduate and undergraduate levels and K-12 students and educators. A portion of our research is also targeting Agriculture and Natural Resource outreach professionals. Changes/Problems:No problems have been encountered. There will be no changes in the coming reporting period. What opportunities for training and professional development has the project provided?Training was provided through research experience for undergraduate students (N=3). Five graduate students received training through research activities. Two post doctoral researchers received training through research activities. Professional development opportunities were provided for two technical staff to increase proficiency in writing and computational training. How have the results been disseminated to communities of interest?Results have been disseminated in the form of scientific peer review literature published and through papers presented at professional conferences. PI Scribner participates on several agency science advisory committees and results have been disseminated at these venues. Research outcomes have also been communicated to stakeholders through collaborations with Michigan State University Extension and the Michigan Sea Grant program. What do you plan to do during the next reporting period to accomplish the goals?Research will continue in each topical area in the next year. All objectives of this project are multi-year in scope. Progress in the next year will build upon knowledge gained during the past reporting period.

Impacts
What was accomplished under these goals? Accomplishments under GRA-1.1 We collated and analyzed a 10 year data set on stream dispersing macro-invertebrates and lake sturgeon larvae to quantify inter-relationship between timing of dispersal of co-distributed prey. We also quantified spatial variation in prey community composition and relationships between prey diversity and abundance and stream physical characteristic. Two manuscripts are in review for publication Doretto, Alberto, Joseph Receveur, M. Eric Benbow, Edward A. Baker, and Kim T. Scribner. Macroinvertebrate community assembly along a river continuum: the role of spatial scale and local habitat Assembly. Aquatic Sciences. In review. Receveur, J., A. Doretto, E. Baker, D. Larson, J. Bauman, R. Walquist, E. Benbow, and Kim T. Scribner. Drift Communities During Larval Fish Dispersal Over Multiple Recruitment Years Freshwater Biology. In review. An additional paper that quantifies predator-prey relationships in an experimental context is also in review. Riedy, Joseph J. and Kim T. Scribner. Experimental evidence for the role of evening light conditions to lake larval sturgeon predation by stream fish predators. Journal of Freshwater Ecology. In review. Accomplishments under GRA-1.2 During this reporting period we completed a project and published a paper quantifying tradeoffs in current year male reproductive success with inter-breeding interval. The paper is accepted for publication -- reference below. Larson, Douglas L., Jacob G. Kimmel,, Jonathan Hegna, Joseph Riedy, Edward A. Baker, and Kim T. Scribner. 2020. Male migratory behavior is associated with Lake Sturgeon (Acipenser fulvescens) intra-annual variability in sperm quality and reproductive success. Canadian Journal of Fisheries and Aquatic Sciences. https://doi.org/10.1139/cjfas-2020-0124. Accomplishments under GRA-2.1 and GRA-3 We completed a Grant during the past reporting period entitled "Using genomic approaches for assessing community composition and relative abundance: an application for the early detection of invasive plants, invertebrates, and fishes in Michigan's aquatic systems". In the grant we used environmental (e)DNA metabarcoding to quantify community taxomonic composition for 22 inland Michigan lakes for fish, plants, and arthropods. Several publications from this work are being prepared. We are collaborating on the genome project for an invasive aquatic fish the Round Goby. We will complete genomic interrogration that describes spatial and temporal variation during and following the initial colonization process in the Great Lakes. We have also developed geomorphometic analytical methods for Round Goby and a paper is in review describing this work. Lorencen, Bailey M., Jared J. Homola, John D. Robinson, Kim T. Scribner. Effects of ethanol preservation on round goby through time. Journal of Fish Biology. In review. Accomplishments under GRA-2.2 We have completed a lake trout linkage map that was published during this reporting period (reference below).. We are also nearly ready to complete and submit a publication describing the lake trout genome. Work continues regarding other objectives. Smith, Seth R., Stephen J. Amish, Louis Bernatchez, Jeremy Le Luyer, Chris Wilson, Olivia Boeberitz, Gordon Luikart, Kim T. Scribner. 2020. A high-density linkage and centromere map for lake trout enables mapping of ecologically relevant traits. Genes, Genomes, Genetics (G3). 10:1929-1947.

Publications

• Type: Journal Articles Status: Published Year Published: 2020 Citation: Califf, Katy J., David S Green, Aaron P Wagner, Kim T. Scribner, Karen Beatty, Meredith E Wagner, Kay E Holekamp. 2020. Genetic relatedness and space use in two populations of striped hyenas (Hyaena hyaena). Journal of Mammalogy. 101:361372.
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Weise, Ellen M., Nicholas M. Sard, Lauren Stanchek, Andrew Nehfer, Kim T. Scribner. 2020. Adaptive genetic management: assessing the efficacy of translocations. Conservation Genetics. 21: 277-287.
• Type: Book Chapters Status: Accepted Year Published: 2020 Citation: Scribner, Kim T., N. Sard, M. Kardos, G. Luikart, and R.S. Waples. 2020. Application of Genetic Data and Theory in Fisheries Management. In. C. Guy, J. Brown, and T. Brenden (eds). Analysis and Interpretation of Freshwater Fisheries Data" 2nd ed. American Fisheries Society Special Publication. In press.
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Hegna, Jonathan, Kim T. Scribner, Edward Baker. 2020. Movement and habitat use characteristics of juvenile lake sturgeon in a small hydroelectric reservoir system. Canadian Journal of Fisheries and Aquatic Sciences. 77:611624.
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Abdul Razak, S.A. and Kim T. Scribner. 2020. Ecological and Ontogenetic Components of Larval Lake Sturgeon Gut Microbiota Assembly, Successional Dynamics, and Ecological Evaluation Of Neutral Community Processes. Journal of Applied and Environmental Microbiology. DOI: 10.1128/AEM.02662-19
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Hunter, R., E. Roseman, R. DeBrunye, N. Sard, J. Wang, and Kim T. Scribner. 2020. Using pedigree analysis to characterized use of artificial spawning reefs by lake sturgeon (Acipenser fulvescens) in the St. Clair-Detroit River system. Transactions American Fisheries Society. 149:266-283. DOI: 10.1002/tafs.10225.
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Hunter, R., E. Roseman, R. DeBrunye, N. Sard, D. Hayes, T. Brenden, and Kim T. Scribner. 2020. Assessing potential bias in sample collection methods for use with genetic pedigree analysis: a lake sturgeon (Acipencer fulvescens) large river example. North American Journal of Fisheries Management 40:307-319. DOI: 10.1002/nafm.
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Heinle, Kadie, Douglas L. Larson, Andrew M. Lockwood, Edward A. Baker, and Kim T. Scribner. 2020. Predation during early ontogenetic stages of Lake Sturgeon (Acipenser fulvescens, Rafinesque, 1817) by Rainbow Darter (Etheostoma caeruleum, Storer, 1845). Journal of Applied Ichthyology. 36:151158.
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Smith, Seth R., Stephen J. Amish, Louis Bernatchez, Jeremy Le Luyer, Chris Wilson, Olivia Boeberitz, Gordon Luikart, Kim T. Scribner. 2020. A high-density linkage and centromere map for lake trout enables mapping of ecologically relevant traits. Genes, Genomes, Genetics (G3). 10:1929-1947.
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Wassink, L., B. Huerta, W. Li, and Kim T. Scribner. 2020. Stressors experienced by mothers and offspring interact to influence behavior and physiology in lake sturgeon. Animal Behaviour. 161:49-59.
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Sard, Nicholas, Seth Smith, Jared Homola, Jeannette Kanefsky, Gale Bravener, Jean Adams, Chris Holbrook, Peter Hrodey, Kevin Tallon, Kim T. Scribner. 2020. Rapture (RAD capture) panel facilitates analyses characterizing sea lamprey reproductive ecology and movement dynamics. Ecology and Evolution. 10:1469-1488.
• Type: Journal Articles Status: Awaiting Publication Year Published: 2020 Citation: Draheim, Hope M., Jennifer A. Moore, Scott Winterstein, Kim T. Scribner. 2020. Spatial genetic structure and landscape connectivity in black bears: Investigating the significance of using different land cover data sets in landscape genetics analyses. Ecology and Evolution. In Press.
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Tucker, Stefan., Angela N. Grimm, James A. Crossman, Kim T. Scribner and Patrick S. Forsythe. 2020. Milt volume influences the probability of egg fertilization in lake sturgeon (Acipenser fulvescens, Rafinesque, 1817). Journal of Applied Ichthyology. 36:282-287. DOI: 10.1111/jai.14031.
• Type: Journal Articles Status: Accepted Year Published: 2020 Citation: Larson, D., M. Faisal, R. Tempelman, and Kim T. Scribner. 2020. Effects of density, handling, and nutrition experiment on probability of RS infection. Journal of Aquatic Animal Health. https://doi-org.proxy2.cl.msu.edu/10.1002/aah.10103
• Type: Journal Articles Status: Accepted Year Published: 2020 Citation: Byford, Greg J., Mohamed Faisal, Robert Tempelman, and Kim T. Scribner. 2020. Prevalence of Renibacterium salmoninarum in non-salmonine fishes from Great Lakes and inland habitats: indicators of environmental reservoirs. Journal of Great Lakes Research. In press.
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Osborne, M.J., T.E. Dowling, Kim T. Scribner, and T.F. Turner. 2020. Wild@heart: incorporating elements of the wild life cycle into conservation hatchery programs. Biological Conservation. DOI: 10.1016/j.biocon.2020.108768
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Jay, Kathleen J., James A. Crossman, and Kim T. Scribner. 2020. Effects of temperature on yolk-sac larval development in White Sturgeon Acipenser transmontanus. Environmental Biology of Fishes. DOI 10.1007/s10641-020-01007-1.
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Larson, Douglas L., Jacob G. Kimmel,, Jonathan Hegna, Joseph Riedy, Edward A. Baker, and Kim T. Scribner. 2020. Male migratory behavior is associated with Lake Sturgeon (Acipenser fulvescens) intra-annual variability in sperm quality and reproductive success. Canadian Journal of Fisheries and Aquatic Sciences. https://doi.org/10.1139/cjfas-2020-0124.
• Type: Theses/Dissertations Status: Published Year Published: 2020 Citation: Wassink, L. 2020. Investigations into effects of environmental stressors on Lake Sturgeon physiology, behavior, and survival during early ontogeny. PhD Dissertation, Michigan State University.
• Type: Journal Articles Status: Accepted Year Published: 2020 Citation: Dammerman, K.J., J.P. Steibel, and Kim T. Scribner. 2020. Shifts in the influence of microhabitat incubation conditions and genetic parentage effects on offspring traits during early ontogeny in lake sturgeon (Acipenser fulvescens). Environmental Biology of Fishes. In Press.
• Type: Journal Articles Status: Accepted Year Published: 2020 Citation: Fujimoto, M., T. Marsh, and Kim T. Scribner. 2020. Effects of filtration and temperature on microbial colonization of lake sturgeon eggs, survival, and development in aquaculture. North American Journal of Aquaculture. DOI: 10.1002/naaq.10169.
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Ye, D., L. Bapu, M.M. Cavalcante, Kim T. Scribner, and T.L. Marsh. 2020. Exogenous protein as an environmental stimulus of biofilm formation in select bacterial strains. Advances in Microbiology 10:123-144.
• Type: Journal Articles Status: Accepted Year Published: 2020 Citation: Wassink, L., B. Huerta, W. Li, and Kim T. Scribner. 2020. Hatchery and wild larval lake sturgeon experience effects of captivity on stress reactivity, behavior, and predation risk. Conservation Physiology. In Press.

Progress 01/01/19 to 09/30/19

Outputs
Target Audience:Target audiences included science and management professionals. Oral presentations were made at several professional conferences including the following: Scribner, K.T. RAPTURE (RAD Capture) Panel facilitates characterization of aspects of sea lamprey reproductive ecology and movement dynamics. Great Lakes Fishery Commission, Sea Lamprey Research Board March 7, 2019 Scribner, K.T., L. Pukk, and J. Robinson. Great Lakes Interstate Prevention, Early Detection and Rapid Response Core Team Surveillance & Phase III Planning Meeting. March 21-22, 2019 Ann Arbor, MI Smith, S., G. Luikart, and K.T. Scribner. Discovery of adaptive genetic variation in recovering populations of lake trout in Lake Huron. International Association of Great Lakes Research. June 14-17, 2019. Brockport, NY. Nick Sard, Seth Smith, Jered Homola, and Kim T. Scribner. Sea lamprey RAPTURE baits enable efficient genotyping for population genomic and parentage studies. International Association of Great Lakes Research. June 14-17, 2019. Brockport, NY. Jered Homola, Nick Sard, John Robinson, and Kim T. Scribner. Patterns and processes associated with the round goby invasion of the Great Lakes basin. International Association of Great Lakes Research. June 14-17, 2019. Brockport, NY. Kim Scribner, Ryan Walquist, John Bauman, Justin Warraniak, and Terance Marsh. Molecular and developmental effects of invertebrate feeding groups on lake sturgeon eggs and larvae. International Association of Great Lakes Research. June 14-17, 2019. Brockport, NY. Lilian Pukk, John Robinson, and Kim T. Scribner. eDNA metabarcoding to detect aquatic invasive species and estimate community composition in lakes. International Association of Great Lakes Research. June 14-17, 2019. Brockport, NY. Alberto Doretto, Joseph Receveur, Edward Baker, Eric Benbow, and Kim T. Scribner.Variation of the near-bed conditions and diversity of macroinvertebrate communities along the river continuum. Italian Society of Ecology Meeting, April 22-24, 2019. Ferrara, Italy. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Our research has provided research opportunities for undergraduate students in the laboratory and in the field. Two post doctoral fellows are supported by projects associated with objectives of this proposal. Graduate students are receiving training in animal behavior, aquatic ecology, statistics, and genomics. How have the results been disseminated to communities of interest?Research associated with this project have been disseminated to academic and other agency professional audiences through publication of peer-reviewed papers and through presentations made at conferences. We have organized workshops with teachers. We provide place-based educational experiences at our field site. What do you plan to do during the next reporting period to accomplish the goals?During the next reporting period, research projected being conducted in areas allied with project objectives will continue in each area as proposed. We for see no changes in project scope.

Impacts
What was accomplished under these goals? We have expanded our work on fish microbiomes to include fungi. Collaborations have led to characterizations of fungal and oomycete taxonomic diversity and relative abundance on lake sturgeon egg surfaces. We have identified putative probiotic bacterial taxa that produce anti-fungal and anti-oomycete chemicals that retard fungal/oomycete growth. We have expanded fish microbiome research to investigate ontogenetic succession of microbial colonization of fish gastrointestinal tracts and effects of microbial communities in water sources and effects of feeding regimes on microbial community succession during early ontogenetic stages. We have expanded research on lake sturgeon reproductive allocation based on establishment of passive inducible transponder (PIT) tag recording stations in the Black River. We have expanded our research on components of male lake sturgeon reproductive success by developing and applying measures of sperm quality to assess effects of male reproductive allocation and sperm quality on male reproductive success. We have developed metabarcoding methods using next generation sequencing to determine diet of predatory stream fishes. We have expanded analyses of stream communities and relative abundance of stream prey invertebrates and fishes to quantify prey availability for analyses of prey selectivity based on metabarcoding diet analyses. We have expanded analyses of lake sturgeon stressors and effects on larval behavior and survival. We have characterized measures of genetic diversity and relatedness in offspring of Michigan cultured species as a means of assessing efficacy of hatchery management practices. We have developed rapid screening methods for SNP genotyping for multiple species including aquatic invasive species in the Great Lakes.

Publications

• Type: Journal Articles Status: Published Year Published: 2019 Citation: Abdul Razak, S, Griffin, M. J. Mischke, C. M., Bosworth, B. G. Waldbieser, G. C. Wise, D.J. Marsh. T. L., Scribner, K. T. 2018. Biotic and abiotic factors influencing channel catfish egg and gut microbiome dynamics during early life stages. Aquaculture 498:556-567.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Waraniak, Justin M., Terence Marsh, and Kim T. Scribner. 2019. 18S metabarcoding diet analysis of the predatory fish community in the Black River, Cheboygan County, MI, during and after the larval lake sturgeon drift period. Ecology and Evolution. DOI: 10.1002/ece3.4857
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Sard, N.M., J.D. Robinson, J. Kanefsky, S.J. Herbst, and Kim.T. Scribner. 2019. Testing coalescent models in an approximate Bayesian computation framework elucidates recent Round Goby colonization history in the Great Lakes. Evolutionary Applications. DOI:10.1111/eva.12779
• Type: Journal Articles Status: Accepted Year Published: 2019 Citation: Hegna, Jonathan, Kim T. Scribner, Edward Baker. Movement and habitat use characteristics of juvenile lake sturgeon in a small hydroelectric reservoir system. Canadian Journal of Fisheries and Aquatic Sciences. In press.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Hegna, J., K.T. Scribner and E.A. Baker. 2019. Evaluation of Optimal Surgical Incision Placement, Closure Methods, and Transmitter Burden on Surgical Outcomes for Intracoelomic Transmitter Implantation in Age-0 Lake Sturgeon. Fisheries Research. 218:198-208.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Dammerman, K., Webb, M., & Scribner, K. T. 2019. The influence of reproductive timing on female reproductive success and ovarian quality determined using plasma testosterone concentrations in lake sturgeon (Acipenser fulvescens). Canadian Journal of Fisheries and Aquatic Sciences. 76: 1147-1160.
• Type: Journal Articles Status: Accepted Year Published: 2019 Citation: Wassink, L., Ugo Bussy, Weiming Li, and Kim T. Scribner. Early life temperature stress in Lake Sturgeon (Acipenser fulvescens) causes cortisol and behavioral changes that increase predator survival. Animal Behavior. DOI.ORG/ 10.1016/j.anbehav.2019.09.005.
• Type: Journal Articles Status: Accepted Year Published: 2019 Citation: Hunter, R., E. Roseman, R. DeBrunye, N. Sard, and K.T. Scribner. Using pedigree analysis to characterized use of artificial spawning reefs by lake sturgeon (Acipenser fulvescens) in the St. Clair-Detroit River system. Transactions American Fisheries Society. In Press.
• Type: Journal Articles Status: Accepted Year Published: 2019 Citation: Homola, Jared, Alexander Samborski, Jeannette Kanefsky, and Kim T. Scribner. 2019. Genetic estimates of jurisdictional and strain contributions to the Lake Michigan brown trout sportfishing harvest. J. Great Lakes Research. In Press.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: McGuire, J.M., D. Bello-Deocampo, J. Bauman, E. Baker, and K.T. Scribner. Histological characterization of goanadal development of juvenile lake sturgeon (Acipenser fulvescens). Environmental Biology of Fishes. 102: 969-983.
• Type: Journal Articles Status: Accepted Year Published: 2019 Citation: Hunter, R., E. Roseman, R. DeBrunye, N. Sard, D. Hayes, T. Brenden, and K.T. Scribner. Assessing potential bias in sample collection methods for use with genetic pedigree analysis: a lake sturgeon (Acipencer fulvescens) large river example. North American Journal of Fisheries Management. In press.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Ye, Donna, Lekha Bapu, Mariane Mota Cavalcante, Jesse Kato, Maggie Sneideman, Frances Trail, Kim T. Scribner, Thomas Loch & Terence L. Marsh. Exogenous Protein as an Environmental Stimuli of Biofilm Formation in Select Bacterial Strains. BioRxiv.
• Type: Journal Articles Status: Accepted Year Published: 2019 Citation: Wassink, L., B. Huerta, W. Li, and K.T. Scribner. Stressors experienced by mothers and offspring interact to influence behavior and physiology in lake sturgeon. Animal Behaviour. In Press.
• Type: Journal Articles Status: Accepted Year Published: 2019 Citation: Sard, N. Seth J. Herbst, Genelle Uhri4, Jeannette Kanefsky John Robinson, and Kim T. Scribner. Environmental DNA metabarcoding methods are effective at detecting aquatic invasive species in complex fish communities. Environmental DNA. In Press.
• Type: Journal Articles Status: Accepted Year Published: 2019 Citation: Sard, Nicholas, Seth Smith, Jared Homola, Jeannette Kanefsky, Gale Bravener, Jean Adams, Chris Holbrook, Peter Hrodey, Kevin Tallon, Kim T. Scribner. Rapture (RAD capture) panel facilitates analyses characterizing sea lamprey reproductive ecology and movement dynamics. Ecology and Evolution. In press.