U.S. Fish & Wildlife Service Grant for Atlantic Salmon Restoration in Lake Champlain

Take an integrative approach to restoring Atlantic salmon to Lake Champlain complementing existing research undertaken in the system. The focus is understanding what stocking and release strategies generate the highest survival to the subadult and adult life stages in Lake Champlain, what selective factors within the lake or its tributaries influence success in early juvenile, subadult and adult stages, and whether and how artificially selecting more fit individual genotypes can demographically boost reintroduced populations following controlled experiments. This work will combine genetic approaches like parentage using microsatellite DNA loci, genome wide surveys of molecular variation under selection, using an Atlantic salmon array, habitat and creel surveys, and controlled experiments in the wild. The work will comprise two graduate student projects. The two students will work collaboratively in the field to complete project objectives.

Funds under this cooperative agreement award are to be used to
Use adaptive management and applied research methods to identify stocking, release and management propagation strategies that generate Atlantic salmon with the highest survival and success in Lake Champlain for the purposes of restoring river-runs and naturally reproducing populations of the species.

The project will evaluate survival and performance of hatchery-origin landlocked Atlantic salmon reared and released using experimental and standard procedures. All hatchery fish will be reared at the U.S. Fish and Wildlife Service D.D. Eisenhower National Fish Hatchery. Survival and performance of hatchery origin fish will be quantified at the subadult stage in Lake Champlain and adult stage, returning spawners, in the Bouquet River and Winooski River, tributaries of the lake.

A variety of approaches will be combined to assess performance, including DNA based parentage methods, genome scans, using large numbers of single nucleotide polymorphisms, controlled releases of juveniles, and habitat/creel surveys.

Spawning and juvenile rearing habitat for landlocked salmon will be characterized and quantified in the Boquet River. These results will be used to guide habitat restoration in the watershed to increase quality and quantity of salmon habitat in the Boquet River.
The project will comprise two graduate student projects, conducted by a Doctoral and a Masters candidate. It will be a collaborative research effort between the U.S. Fish and Wildlife Service, Essex Junction, VT, and Concordia University, Montreal, Quebec, Canada.

Objectives
The first objective is to use DNA based parentage methods to determine what stocking and release strategies, including strain and life stage stocked, numbers, dates, locations, and sizes, generate the highest survival to the subadult and adult stages in Lake Champlain and adult returns to the Boquet River and Winooski River. The second objective is to characterize spawning and rearing habitat in the Bouquet River, a river adjacent to the Canadian border with a small annual returning run of Atlantic salmon, and relate juvenile densities to habitat characteristics. And the last objective is to use controlled releases of salmon in the natural environment, coupled with genome scans of large numbers of single nucleotide polymorphisms, to determine optimal genotypes for demographically boosting a reintroduced population in the lake.

Tasks

To accomplish the above objectives, Concordia University will, the first is to develop a parental based tagging database using multilocus genotype data at a minimum of 10 microsatellite loci for all salmon parents used to generate individuals for stocking in the Boquet River and Winooski River. A total of 1,800 parents will be used for three brood years, including 2010, 2011, and 2012. These parental based tags will allow for identification of life stage stocked, date and location of stocking, and hatchery rearing protocols for all progeny stocked into the Boquet River and Winooski River. The second task is to use the parental based database developed in Task 1 to assign parentage to hatchery origin juvenile, subadult, and adult fish sampled from Lake Champlain, Bouquet River, and Winooski River, 1200 fish will be sampled. These DNA based parentage results be used to determine what stocking and release strategies, including strain and life stage stocked, numbers, dates, locations, sizes, generate the highest survival in these locations. The third task is to quantify several spawning and rearing habitat characteristics in the Bouquet River, including water temperature, drift abundance, current velocity, depth, and substrate, and relate these to performance of juveniles, survival, growth. This work will include identification of salmon spawning locations in the Boquet River in the fall of 2013 and electrofishing and/or snorkeling of the Bouquet River in the summer of 2014. And, last, use a SNP chip, minimum 16,000 SNPs, to relate salmon genotypes having the highest performance in Lake Champlain at different stages, including 400 juvenile and subadults to specific selective agents, including abiotic and biotic factors, in the lake.

Expected Results

The anticipated characterization of ecological and genomic indicators of survival and success of juvenile, subadult and adult stages of Atlantic salmon in Lake Champlain will be used to improve stocking, release and management propagation strategies. Ultimately, such indicators will be useful towards restoring the species in Lake Champlain, by providing a novel means to demographically boost numbers of returning adults to Lake Champlain tributaries.

Roles and Responsibilities of Cooperators

The Primary Investigator from Concordia University is Dr. Dylan Fraser, principally, in collaboration with Dr. James Grant, both from the Department of Biology. They will work to address the three objectives outlined in this project description, as identified above. If any changes need to be made to these objectives or tasks, they will only be made following approval by the Service.

The Service will provide $170,274 to complete the work described above. Additionally, the Service will provide staff time and equipment to collect and conduct an angler creel survey within Lake Champlain, to culture fish, to transport fish from hatcheries to field release sites, as well as, if required, equipment and staff time to sample salmon within streams with the use of fish traps or ladders. The Service will also provide assistance with the translation of study findings into suggested management actions.

Timelines, Reports and Deliverables

Concordia University will provide a report by Jan. 25, 2014 detailing preliminary results for the salmon parent genotype database, another draft report will be provided by Jan. 25, 2015 detailing preliminary parentage results of wild caught subadults and control release juveniles in Lake Champlain, as well as preliminary results of the survey of spawning and rearing habitat in the Bouquet River, a third draft report will be provided by Jan. 25, 2016 detailing preliminary results linking individual genotypes with the highest performance to specific selective agents in Lake Champlain, and a final report will be provided to the Service by Aug. 25, 2016 summarizing all of the project¿s research findings, data, data analysis, and accomplishments. We also anticipate that work relating to the objectives outlined above will be submitted for publication in peer-reviewed journals in the years 2015 and 2016.

The performance and budget period of this award is February 4, 2013 through July 15, 2016.

This award is funded as follows

USFWS Matching
This obligation: $170,274 $102,000
Award Total: $170,274 $102,000

Detailed Budget

Laboratory work – $23,800
¿ Microsatellite genotyping supplies for 3000 individuals, total $19,800: DNA extractions and storage ($0.80/salmon), PCR amplification of multi-locus genotypes at ten microsatellite loci ($3.80/salmon, including primers and Taq polymerase, PCR plates etc.), and visualization of amplified loci on a Life Tech. 3500 Genetic Analyzer ($2.00/salmon)
¿ Lab equipment maintenance fees, total $4,000 (e.g. DNA sequencer, pipettors, thermocyclers, centrifuges) during completion of the project in years 1 and 2. Part of this amount will also be used to cover the project¿s postage, faxes and phone calls associated with the project.
Outsourcing genome-wide SNP genotyping – $36,000
¿ Minimum 16K (is presently expanding to 200K) SNP-array sequencing, total $36,000 (400 individuals @ $90/individual)

Field work – $21,960
¿ Transportation to-and-from field site, and for multiple meetings each year with the US Fish & Wildlife Service, total $9,460 (years 1 and 2: twenty-five return trips/year @ 400km/trip @ $0.43/km; year 3: five return trips)
¿ Accommodation (occasional camping or hotel) and associated meals, total $5,000
¿ Miscellaneous field supplies and gear, $7,500 (chiefly sample kits for anglers and creel surveys; notebooks, extra waders/boots; ≈ 500 PIT tags @ $5/tag)

Salaries – $71,000
¿ One PhD student, total $39,000 (years 1 and 2 with a TAship @ $10,500/year; year 3 without TAship @ $18,000)
¿ One MSc student, total $15,000 (years 1 and 2 with a TAship @ $7,500/year)
¿ Lab Technician, five months, total $17,000 (year 1, @$20/hr)

Concordia University Project Administration Fees – $17,514

In-kind contributions, Concordia University – $102,000
¿ Two years of TAship for a PhD student, total $15,000 (years 1 and 2)
¿ Two years of TAship for an MSc student, total $15,000 (years 1 and 2)
¿ Salary for the PhD Student for a fourth year ($18,000)
¿ Salary for Dr. Fraser, total $21,600 (10hrs/month @ $45/hr for four years)
¿ Salary for Dr. Grant, total $26,400 (10hrs/month @ $55/hr for four years)
¿ Travel/registration expenses for the two graduate students to attend a total of four national or international conferences over the course of the project, total $6,000
¿ Stream electrofisher use
¿ Tent/sleeping bags