Subyearling chinook salmon use of the Lower Willamette River. proposal 200728500

FY07-09 proposal 200728500

Section 1. Administrative

Proposal title	Subyearling chinook salmon use of the Lower Willamette River.
Proposal ID	200728500
Organization	City of Portland
Short description	This study will investigate racial composition, habitat use and migration/residence time of subyearling chinook salmon in the Lower Willamette River.
Information transfer	Information generated by this study will be available through annual reports, peer-review manuscripts, workshops, and technical presentations. This information will help the City of Portland with meeting regulatory obligations under the Endangered Species Act. It will provide habitat restoration guidance that will be useful for a variety of planning processes, including the Army Corps of Engineer' Water Resources Damage Assessment (WRDA) and the City's River Renaissance Vision. The Corps' feasibility study under WRDA will require this information for identifying habitat restoration actions and evaluating their potential benefits, The study will also help the goal developed by the Oregon Department of Fish and wildlife of maintaining optimum populations and distribution of the basin's fish resources to provide the greatest recreational, commercial, economic, and nonconsumptive benefits to present and furture generations of Oregon citizens.
Proposal contact person or principal investigator

Contacts

Contact	Organization	Email
Form submitter
Tim Dalton	Oregon Department of Fish and Wildlife	tim.dalton@state.or.us
All assigned contacts
Cynthia Baker	Ducks Unlimited, Inc	cbaker2@ducks.org
Tim Dalton	Oregon Department of Fish and Wildlife	tim.dalton@state.or.us
Tim Dalton	Oregon Department of Fish and Wildlife	tim.dalton@state.or.us
Jim Middaugh	City of Portland	jimm@bes.ci.portland.or.us
Dave Ward	Oregon Department of Fish & Wildlife	david.l.ward@state.or.us

Section 2. Locations

Province / subbasin: Lower Columbia / Willamette

Latitude	Longitude	Waterbody	Description
N45.64631	W122.76769	Lower Willamette River	Kelly Point Park
N45.45908	W122.6641	Lower Willamette River	Power's Marine Park
N45.5538	W122.69926	Lower Willamette River	East Shore of Terminal 2
N45.60630	W122.78776	Lower Willamette River	River mile 4
45o36'54.09"	122o44'32.94"	Lower Willamette River	Smith and Bybee
45o38'36.54"	122o46'2.14"	Lower Willamette River	Columbia Slough and Ramsey Lake
45o39'27.25"	122o50'54.65"	Lower Willamette River	enyart bottoms
45o41'22.82"	122o52'6.93"	Lower Willamette River	multnomah north
N45.57446	W122.74774	Lower Willamette River	Ship Skeleton
N45.37255	W122.61569	Lower Willamette River	Goat Island

Section 3. Focal species

primary: Chinook Upper Willamette River ESU
secondary: Chinook Lower Columbia River ESU

Section 4. Past accomplishments

Year	Accomplishments

Section 5. Relationships to other projects

Funding source	Related ID	Related title	Relationship
BPA	200303600	CBFWA Monitor/Eval Program	We will inform CSMEP of our efforts
BPA	200400200	PNAMP Funding	We will inform PNAMP of our efforts
BPA	200301100	Columbia R/Estuary Habitat	We will inform this group of our activities which will be useful in setting habitat target criteria for subyearling Chinook
Other: Corps	TPE-W-06-02	Alternative Smolt Transportation Methods	We may catch their tagged fish in our study.
Other: Corps	EST-P-02-01	Juvenile Salmon Survival in the Estuary	We may capture their tagged fish at lower sites in the Willamette River.
Other: ODFW	10800203000-10	Spring Chinook Salmon in the Willamette and Sandy Rivers	We may catch their PIT tagged Chinook from the upper Willamette River at our lower Willamette River sites.

Section 6. Biological objectives

Biological objectives	Full description	Associated subbasin plan	Strategy
1. Quantify subyearling Chinook habitiat use	Quantitatively associate subyearling Chinook salmon habitat use with specific measurable parameters previously identified as important in classifying shoreline areas. Key variables (predictors) then can be used to predict juvenile Chinook salmon relative abundance or density (response variable) at other areas.	Willamette	Provides measures of biological performance of habitat benefits for focal species. Use EDT or other modeling.
2. Measure migration/residence time and growth	Measure migration/residence times and growth rates of subyearling Chinook salmon in the main stem river and floodplain wetlands. Fish tagged at the Sullivan facility at Willamette falls will be recaptured at multiple sites between the facility and the mouth of the river, February-June.	Willamette	Providing for conservation and recovery planning.
3.Protect ESA-listed species	Assess the genetic composition of subyearling Chinook salmon in the lower Willamette River to determine the proportions that are of the spring-run or of the fall-run race. Frequency ratios of fall-run and spring-run subyearlings will be determined and compared over various spatial and temporal strata.	Willamette	Consider focal species and habitat first. "For both conservation and restoration, first consider opportunities for this plan's focal habitat types and species....highest priority should be accorded to those that are federally listed"
4. Determine habitat use/migration of individuals	Determine movements and habitat use of individual subyearling Chinook salmon during emigration through the lower Willamette River. Radio-telemetry will be employed.	Willamette	Providing for conservation and recovery planning.
5. Assess use of food resources by rearing Chinook	Analyze diet of sub-yearling Chinook salmon collected at main stem and floodplain wetland sites and at the PGE Sullivan Hydroelectric Facility at Willamette Falls. A modification of the graphical Costello method (Amundsen et al. 1996) based on a two-dimensional representation of prey-specific abundance and frequency of occurrence of the different prey types in the diet is proposed for the analysis of stomach contents data.	Willamette	Provides measures of biological performance of habitat benefits for focal species.

Section 7. Work elements (coming back to this)

Work element name	Work element title	Description	Start date	End date	Est budget
Analyze/Interpret Data	Analyze and describe migration patterns, residence time and growth rates	Migration periods from dates of tagging to dates of recapture will be examined for subyearling Chinook salmon, as well as coho salmon, first for the separate size groups and individual tag release groups, then for these considered together. Migration periods can be estimated within ranges as short as the time between individual sampling events, and migration rates can be calculated based on the river-kilometer distance to the site of recapture. For recaptures at the mainstem and wetland sites near the mouth of the river, migration periods give direct minimum estimates of residence periods in the study area. For marked fish recaptured at sites nearer the middle of the study area, residence period can be extrapolated from migration period, distance traveled, and distance remaining to the mouth, assuming migration rate of the fish remains relatively constant. The temporal sequence of recaptures among the sites may provide for reasonable estimates of migration/residence periods for the subyearling Chinook salmon population as a whole. Growth of recaptured fish will be estimated by comparison of their lengths and weights to the averages for the tag release group as a whole. Growth can also be assessed by comparison of average lengths and weights for all juveniles captured at individual sites, particularly upstream sites compared to downstream sites.	7/1/2009	9/30/2009	$43,373
Biological objectives 2. Measure migration/residence time and growth			Metrics
Analyze/Interpret Data	Analyze radio tracking data	Data will be analyzed to describe behavior of radio tagged subyearling Chinook salmon in the lower Willamette River. Migration rates (km/d) will be calculated based on travel time from the initial release point to subsequent downstream relocation points (Ward et al. 1994). Field relocations will be verified by plotting GPS waypoints with GIS software, and residence time calculated by multiplying the overall migration rate for each fish by the study area distance. These migration rates and residence times will be compared to data collected from VIE-marked fish. We will also compare migration rates and residence times among metrics (e.g. year, body size, study area section) using nonparametric multiple comparison tests. Factors that could influence migration rates, including river flow, temperature, release day, and fish size (fork length) will be assessed using simple and multiple linear regressions. We will use distributions of radio telemetry relocations across the river channel to determine if radio tagged fish are closely associated with nearshore areas, and are therefore likely to encounter different nearshore habitat types. We will analyze river channel distributions using the chi-square test. Similar procedures will be used to determine if nearshore relocations among habitat types are distributed differently than the availability of the habitats, which could indicate selection or avoidance.	7/1/2009	9/30/2009	$65,060
Biological objectives 4. Determine habitat use/migration of individuals			Metrics
Analyze/Interpret Data	Construct subyearling Chinook salmon habitat use model by environmental variable	A model each for main stem and floodplain sites to relate fish densities or relative abundances to measured environmental variables will be constructed. This information will provide resource managers with target habitat crieteria for protection and restoration.	7/1/2009	9/30/2009	$21,687
Biological objectives 1. Quantify subyearling Chinook habitiat use			Metrics
Analyze/Interpret Data	Summarize and compare diet of subyearling Chinook across sites, through time and with other nearby studies	A modification of the graphical Costello method (Amundsen et al. 1996) is proposed for the analysis of stomach contents data. The new method allows prey importance, feeding strategy and the inter- and intra-individual components of niche width to be explored using graphical presentation. The analysis is based on a two-dimensional representation of prey-specific abundance and frequency of occurrence of the different prey types in the diet.	7/1/2009	9/30/2009	$21,687
Biological objectives 5. Assess use of food resources by rearing Chinook			Metrics
Analyze/Interpret Data	Test for significant differences in proportion of fall- and spring-run Chinook among and between three sampling strata	Frequency ratios of fall-run (fall) and spring-run (spring) subyearlings will be tested by chi-square analysis for differences between and among the three collection strata on a monthly and an overall season basis. With the data from the dam we will make monthly and seasonal frequency ratio composition estimates of fall and spring subyearlings of the Lower Willamette River. These frequency ratios will be statistically compared to those among the samples from the main stem and floodplain sampling sites individually and in various spatial and temporal strata. Spatial strata will include upper main stem sites, lower main stem sites, Multnomah channel sites, and Columbia slough sites, or combinations of these (e.g., all sites, all mainstem sites, all floodplain sites, lower main stem plus floodplain sites).	7/1/2009	9/30/2009	$21,687
Biological objectives 3.Protect ESA-listed species			Metrics
Collect/Generate/Validate Field and Lab Data	Collect fish at PGE Sullilvan Hydroelectric Facility	Subyearling Chinook salmon will be collected in the PGE Sullivan Facility bypass four times per month from February-June of 2007-2009.	2/15/2007	6/30/2009	$10,843
Biological objectives 2. Measure migration/residence time and growth			Metrics
Collect/Generate/Validate Field and Lab Data	Collect stomach contents of subyearling Chinook at mainstem and floodplain wetland sites	Subsample 20 subyearling Chinook per month at mainstem and floodplain wetland sites for stomach contents (objective 1a). Specimens will be placed on ice to slow digestion and will be preserved in 70% ethanol within 8 hours. In the laboratory, samples will be filtered through a 500-µm sieve. All organisms will be identified to the lowest possible level, likely genus (Merritt and Cummins 1996; Smith 2001). Organisms of the same taxonomic group will be combined and weighed after excess water is blotted. A Mettler PM400 laboratory scale will be used to measure the wet weight of each food item to the nearest 0.1 mg.	2/15/2007	6/30/2009	$86,747
Biological objectives 5. Assess use of food resources by rearing Chinook			Metrics
Collect/Generate/Validate Field and Lab Data	Collect tissue samples from subyearling Chinook salmon	Fifty subyearling Chinook per month will be sub-sampled at the Sullivan Dam, main stem Willamette River and floodplain wetland sites in which small non-lethal fin clips will be taken. Tissue will be preserved in 70% ethanol. The protocol developed by collaboration with Genetic Analysis of Pacific Salmonids (GAPS) labs for the Columbia subset of Chinook salmon will be used to assay individual fish across 13 loci (Moran et al. 2005). Results from the microsatellite assay will be compared with the genetic baseline (Moran et al. 2005) to determine race (i.e., fall or spring) of individual fish.	7/1/2009	9/30/2009	$173,494
Biological objectives 3.Protect ESA-listed species			Metrics
Collect/Generate/Validate Field and Lab Data	Measure environmental variables	Measure environmental variables at each site where sampling takes place. There are up to 60 habitat variables that are to be measured, some of which include water temperature, water transparancy, vegetation cover, etc.	2/15/2007	6/30/2009	$43,373
Biological objectives 1. Quantify subyearling Chinook habitiat use			Metrics
Collect/Generate/Validate Field and Lab Data	Recapture marked fish at lower Willamette Rive mainstem and floodplain wetland sites	Marked fish will recaptured at mainstem and floodplain wetland sites downstream.	2/15/2007	6/30/2009	$173,494
Biological objectives 2. Measure migration/residence time and growth			Metrics
Collect/Generate/Validate Field and Lab Data	Sample lower Willamette River main stem and floodplain wetland sites for subyearling Chinook salmon	Sample subyearling Chinook salmon at lower Willamette River main stem and floodplain sites once per week from February through June.	2/15/2007	6/30/2009	$173,494
Biological objectives 1. Quantify subyearling Chinook habitiat use			Metrics
Collect/Generate/Validate Field and Lab Data	Track radiotagged subyearling Chinook salmon	We will employ mobile radio tracking to relocate radio tagged subyearling Chinook salmon in the lower Willamette River. Tracking efforts will begin about three hours after radio tagged fish are released. Tracking will be conducted from a boat using a single radio receiver and mounted or hand-held antennae (Friesen 2005). Crews will maneuver through the middle of the river channel above the Sellwood Bridge, and alternate between sides of the river below the Sellwood Bridge, where the river is wider. Upon locating a signal, crews will attempt to attempt to pinpoint the location of the fish using directional and submersible antennae. When power and gain readings indicate the fish is in close proximity, the crew will stop the boat and record the transmitter channel and code, gain and power readings, time, water depth and temperature, distance to the nearest shore, channel width, latitude and longitude, and river kilometer. Habitat type will be noted for fish relocated close to shore. Tracking will generally occur over 16 hours of a 24 hour period and will encompass both light and dark periods, and will occur for at least five consecutive days following a release of radio tagged fish. We will also employ a fixed receiver site to detect fish emigrating through the lower Columbia River. Three receivers will be placed at river kilometer 87, just downstream of Crims Island. One receiver will be placed on or near each shoreline, and one will be placed on a navigational marker between shores to ensure complete coverage of the channel. The fixed receivers will be downloaded once per week.	4/15/2007	6/30/2009	$216,867
Biological objectives 4. Determine habitat use/migration of individuals			Metrics
Mark/Tag Animals	Implant radio tags in subyearling Chinook salmon	We will surgically or gastrically implant radio tags (Lotek “nanotags” or equivalent) in up to 70 juvenile Chinook salmon <100 mm fork length (presumably subyearlings) collected from the juvenile fish trap of the Sullivan facility at Willamette Falls each spring.	4/15/2007	6/30/2009	$130,120
Biological objectives 4. Determine habitat use/migration of individuals			Metrics
Mark/Tag Animals	Mark/tag subyearling Chinook salmon and coho salmon at Sullivan Facility	Approximately 10,000 Chinook salmon and coho salmon as possible will be marked by either bismark brown dye or VIE, depending on the size of the fish.	2/15/2007	6/30/2009	$86,747
Biological objectives 2. Measure migration/residence time and growth			Metrics

Section 8. Budgets

Itemized estimated budget

Item	Note	FY07	FY08	FY09
Personnel	ODFW	$95,449	$98,312	$101,261
Fringe Benefits	ODFW	$60,055	$61,857	$63,713
Personnel	DU	$64,754	$64,754	$64,754
Other	genetic identification and report	$44,665	$44,665	$44,670
Travel	DU mileage	$1,613	$1,613	$1,612
Travel	DU conference	$0	$0	$560
Supplies	DU boat and nets	$5,376	$0	$0
Supplies	ODFW	$62,411	$54,411	$58,161
Overhead	ODFW	$79,571	$82,493	$83,157
Travel	ODFW	$8,666	$8,927	$9,194
Travel	ODFW-MEETING	$0	$1,000	$1,000
Totals		$422,560	$418,032	$428,082

Total estimated FY 2007-2009 budgets

Total itemized budget:	$1,268,674
Total work element budget:	$1,268,674

Cost sharing

Funding source/org	Item or service provided	FY 07 est value ($)	FY 08 est value ($)	FY 09 est value ($)	Cash or in-kind?	Status
City of Portland	Salary	$6,000	$6,000	$6,000	In-Kind	Confirmed
Ducks Unlimited	Equipment	$5,000	$5,000	$5,000	In-Kind	Confirmed
ODFW	Salary	$8,000	$8,000	$8,000	In-Kind	Confirmed
ODFW	Equipment	$10,000	$10,000	$10,000	In-Kind	Confirmed
Totals		$29,000	$29,000	$29,000

Section 9. Project future

FY 2010 estimated budget: $0
FY 2011 estimated budget: $0

Comments:

Future O&M costs:

Termination date: Sept. 2009
Comments:

Final deliverables: Final report, peer-review manuscripts, final workshop.

Section 10. Narrative and other documents

Reviews and recommendations

FY07 budget	FY08 budget	FY09 budget	Total budget	Type	Category	Recommendation
NPCC FINAL FUNDING RECOMMENDATIONS (Oct 23, 2006) [full Council recs]
$0	$0	$0	$0	Expense	ProvinceExpense	Do Not Fund
NPCC DRAFT FUNDING RECOMMENDATIONS (Sep 15, 2006) [full Council recs]
$0	$0	$0	$0		ProvinceExpense

ISRP PRELIMINARY REVIEW (Jun 2, 2006)

Recommendation: Fundable (Qualified)

NPCC comments: This proposal rated very high in all review criteria, and the ISRP found the project worthy of support. The ISRP is not requesting a response, but the proposal would be improved if the proponents provided a better justification for Objective 5. Specifically, a better description of how the diet data will be used to indicate the importance of certain habitat types in the lower Willamette (if prey availability data are also not collected). Other comments: Technical and scientific background: The proposal describes a research study to determine the habitat use of subyearling chinook and to examine if this habitat is limiting to survival and productivity (growth) of these juveniles. While it doesn't focus on a high priority problem it will provide information needed to understand the function and importance of the rather limited rearing habitat for subyearling chinook in the lower Willamette River. Rationale and significance to subbasin plans and regional programs: The proposal does a good job in relating its objectives to those in the Oregon Plan, the Willamette Subbasin Plan, and the US Army Corps of Engineers (USACE) Willamette Basin Floodplain Restoration Study. Relationships to other projects: A well-organized table summarizes relationships between this project and other projects funded by BPA, USACE, USFWS, and State of Oregon. The nature of the relationships between projects is described. Objectives: Objectives 1, 2, and 3 are linked to objectives in the Willamette Subbasin Plan and are very well justified. The rationale for the radio-telemetry (Objective 4) is located in the work element section 4c and could be moved up to follow the stated objective. The rationale for the food habits study (Objective 5) is weak, and the justification for these data needs further development. Tasks (work elements) and methods: Methods are described in detail, with text, maps and photos. Sampling procedures are extensively described, as are parameters to be measured and analytical procedures. Monitoring and evaluation: Monitoring of project implementation effectiveness is not a part of this proposal, but this project is collaborating with the Collaborative Systemwide Monitoring and Evaluation Program (CSMEP) and Pacific Northwest Aquatic Monitoring Partnership (PNAMP) on an "inform" basis. It isn't clear that these relationships will accomplish monitoring of this project. Information transfer: Information transfer will be accomplished through annual reports, peer reviewed publications, workshops, and technical presentations. The proponents also intend to provide habitat restoration guidance as an output of this project. Benefits to focal and non-focal species: Identification and significance of the lower Willamette rearing habitat for subyearling spring chinook may play an important role in the protection and restoration of this habitat over the long term.

ISRP FINAL REVIEW (Aug 31, 2006)

Recommendation: Fundable (Qualified)