Using otolith microstructure and microchemistry to delineate growth patterns and spatial structure of Snake River Fall Chinook salmon proposal 200716800

FY07-09 proposal 200716800

Section 1. Administrative

Proposal title	Using otolith microstructure and microchemistry to delineate growth patterns and spatial structure of Snake River Fall Chinook salmon
Proposal ID	200716800
Organization	National Oceanic & Atmospheric Administration (NOAA)
Short description	We will conduct microstructural and microchemical analyses of otoliths from Snake River Fall Chinook salmon to examine how growth patterns vary with juvenile migration timing and residence times in different habitats along their migration routes.
Information transfer	Findings will be published in a peer-reviewed journal, and presentations will be made to regional stakeholders and other scientists at professional conferences. Reports will be made available on the internet or upon request within six months of the completion of the project.
Proposal contact person or principal investigator

Contacts

Contact	Organization	Email
Form submitter
Richard Zabel	NOAA Fisheries	rich.zabel@noaa.gov
All assigned contacts
William Connor	U.S. Fish & Wildlife Service	william_connor@fws.gov
Brian Kennedy	University of Idaho	kennedy@uidaho.edu
Mark Scheuerell	NOAA Fisheries	mark.scheuerell@noaa.gov
Kenneth Tiffan	U.S. Geological Survey	ken_tiffan@usgs.gov
Richard Zabel	NOAA Fisheries	rich.zabel@noaa.gov

Section 2. Locations

Province / subbasin: Mainstem/Systemwide / Systemwide

Latitude	Longitude	Waterbody	Description
			spatial domain of the Snake River Fall Chinook ESU

Section 3. Focal species

primary: Chinook Snake River Fall ESU

Section 4. Past accomplishments

Year	Accomplishments

Section 5. Relationships to other projects

Funding source	Related ID	Related title	Relationship
BPA	198335003	Nez Perce Tribal Hatchery M&E	This project aims to identify an appropriate suite of performance variables which, when monitored over time and space, will provide the information necessary to resolve key uncertainties in the relative success of hatchery fall Chinook salmon and enable informed decision-making. This project assigned highest priority to demographic, life history, and genetic variables. Our project will fill in some of the current data gaps in demographic and life-history attributes that describe differences among groups of fall Chinook in the Columbia River basin.
BPA	199102900	Post-Release Survival of Fall	This project is assessing fall Chinook juvenile life history characteristics, emigration timing and survival in the mainstem Snake River and Columbia Rivers. Project cooperation includes: describing juvenile life history characteristics of wild and Lyons Ferry Hatchery supplemented fall Chinook, emigration survival as it relates to environmental conditions, and conducting fall Chinook aerial redd surveys and documenting hatchery fish contributions to the natural spawning population.
BPA	199403400	Upper Clearwater - Assessing S	The goal of this project is to collect life history and survival information on wild Snake River fall Chinook and to evaluate supplementation strategies that would be favorable for the recovery and restoration of summer and fall Chinook in the last remaining mainstem habitats in the Snake River basin above Lower Granite Dam. This study looked at emigration timing, growth, and survival using Lyons Ferry Hatchery fall Chinook subyearlings as surrogates for wild fall Chinook in the Clearwater River. Our study will expand upon this project by comparing differences among populations of fall Chinook across a much larger spatial area.
BPA	199801004	M&E Snake R. Fall Ch Spawning	This project measures pre-release condition, post-release survival and emigration behavior to evaluate the effectiveness of Lyons Ferry Hatchery yearling releases to enhance natural fall Chinook production (the goal of Project 199801005). We will work in cooperation on adult return monitoring through radio telemetry, redd surveys, and carcass collection to determine subyearling and yearling hatchery contributions to natural production. Our results will assist in the greater effort to understand the causes and consequences of the varying life-history types observed among fall Chinook salmon in the Snake River.
BPA	200306000	Eval Repro Success Snake Rvr C	This project is developing a genetic admixture model for assessing the relative productivity of wild and hatchery stocks of fall Chinook salmon. The results of our study will allow for similar investigations for varying life-histories of fall Chinook (reservoir-type vs. ocean-type) and compare the genetic evidence to inferred growth rates and spatial location.
BPA	200310700	Eval of Salmonid Growth	This project is investigating the effects of changing water temperature and sediment load on growth of juvenile salmonids. Because the two life-history types consider here potentially experience very different thermal regimes during their juvenile life stage, our results will inform other within-species comparisons in addition to comparisons among species.

Section 6. Biological objectives

Biological objectives	Full description	Associated subbasin plan	Strategy
1. Collect otliths and water samples	Obtain necessary fish and water samples for the chemical and structural analyses	None	[Strategy left blank]
2. Analyze microstructure of otoliths	Obtain estimates of daily growth rates by examining the microstructure of fish otoliths	None	[Strategy left blank]
3. Develop otolith & fish size relationships	Develop necessary relationship between the size of otoliths and fish sizes to use in growth rate projections	None	[Strategy left blank]
4. Analyze chemical signatures of otoliths & water	Derive chemical concentrations of Sr stable isotopes and other trace elements in otoliths and water samples	None	[Strategy left blank]
5. Determine effective spatial scale	Evaluate the effective spatial scale for assigning fish rearing locations based on their chemical signatures	None	[Strategy left blank]
6. Communicate results	Disseminate findings through written reports, peer-reviewed publications, and oral presentations	None	[Strategy left blank]
I. Mitigation across the basin	One of the Council's four overarching biological objectives is mitigation across the basin for the adverse effects caused by development of the hydrosystem.	None	[Strategy left blank]
II. Increase total adult salmon runs	One of the Council's three regional objectives for anadromous fish is to increase total adult salmon runs above Bonneville by 2025 in a manner that supports tribal and non-tribal harvest. They also aim to achieve sustainable populations in 100 years, representing full mitigation for losses of anadromous fish.	None	[Strategy left blank]

Section 7. Work elements (coming back to this)

Work element name	Work element title	Description	Start date	End date	Est budget
Produce Environmental Compliance Documentation	Obtain neccesary permits	Obtain necessary federal (ESA) and state fish handling permits as needed, submit required reports of take activities as required.	10/1/2006	2/28/2007	$52,385
Biological objectives 1. Collect otliths and water samples I. Mitigation across the basin II. Increase total adult salmon runs			Metrics
Manage and Administer Projects	Prepare SOW, and Budget, and Attend Meetings.	Prepare SOW, and Budget, and Attend Meetings.	1/1/2007	9/30/2009	$58,435
Biological objectives 6. Communicate results I. Mitigation across the basin II. Increase total adult salmon runs			Metrics
Produce/Submit Scientific Findings Report	Produce status reports.	Produce status reports.	1/1/2007	9/30/2009	$104,799
Biological objectives 6. Communicate results I. Mitigation across the basin II. Increase total adult salmon runs			Metrics
Analyze/Interpret Data	Conduct discriminant-function analyses.	Conduct discriminant-function analyses with results from the chemical analyses to determine whether specific regions of the river systems segregate based on chemical signatures. Use the results of these analyses to address hypotheses concerning site and duration of residence for juveniles migrating through the hydrosytem.	10/1/2006	9/30/2009	$120,253
Biological objectives 5. Determine effective spatial scale I. Mitigation across the basin II. Increase total adult salmon runs			Metrics
Analyze/Interpret Data	Develop growth models to back-calculate juvenile growth rates and trajectories for adult fish.	Use growth models to back-calculate juvenile growth rates and trajectories for adult fish with known life-history types (ocean-type and reservoir type).	10/1/2006	9/30/2009	$89,344
Biological objectives 3. Develop otolith & fish size relationships I. Mitigation across the basin II. Increase total adult salmon runs			Metrics
Collect/Generate/Validate Field and Lab Data	Collect otoliths from juveniles and adults and collect water samples	Collect otoliths from juveniles and adults and collect water samples	3/1/2007	9/30/2009	$60,908
Biological objectives 1. Collect otliths and water samples I. Mitigation across the basin II. Increase total adult salmon runs			Metrics
Collect/Generate/Validate Field and Lab Data	Prepare otoliths for chemical analyses.	Prepare otoliths for chemical analyses.	10/1/2006	9/30/2009	$572,747
Biological objectives 4. Analyze chemical signatures of otoliths & water I. Mitigation across the basin II. Increase total adult salmon runs			Metrics
Collect/Generate/Validate Field and Lab Data	Process otoliths for analysis of microstructure and develop growth models.	Process otoliths for analysis of microstructure and develop growth models.	9/1/2007	9/30/2009	$309,212
Biological objectives 2. Analyze microstructure of otoliths I. Mitigation across the basin II. Increase total adult salmon runs			Metrics

Section 8. Budgets

Itemized estimated budget

Item	Note	FY07	FY08	FY09
Personnel	[blank]	$72,049	$74,211	$76,438
Fringe Benefits	[blank]	$19,093	$19,666	$20,256
Supplies	[blank]	$12,365	$12,736	$13,118
Travel	[blank]	$16,530	$17,026	$17,537
Capital Equipment	[blank]	$25,000	$0	$0
Overhead	[blank]	$47,913	$49,351	$50,831
Other	direct contract to U of Idaho	$115,000	$118,450	$122,004
Other	direct contract to U of Washington	$100,000	$103,000	$106,090
Other	laboratory fees	$51,577	$53,124	$54,718
Totals		$459,527	$447,564	$460,992

Total estimated FY 2007-2009 budgets

Total itemized budget:	$1,368,083
Total work element budget:	$1,368,083

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
Totals		$0	$0	$0

Section 9. Project future

FY 2010 estimated budget: $507,603
FY 2011 estimated budget: $507,603

Comments: [Outyear comment field left blank]

Future O&M costs:

Termination date: 9/30/2009
Comments:

Final deliverables: Annual synthesis reports to BPA. Peer-reviewed publications.

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	Basinwide	Do Not Fund
NPCC DRAFT FUNDING RECOMMENDATIONS (Sep 15, 2006) [full Council recs]
$0	$0	$0	$0		Basinwide

ISRP PRELIMINARY REVIEW (Jun 2, 2006)

Recommendation: Fundable

NPCC comments: The authors propose to use otolith microstructure and microchemistry to study growth patterns and spatial structure of Snake River fall Chinook salmon with a specific objective of gaining understanding of the reservoir-type migrants. They hope to learn when and where these migrants spend their time during downstream migration. The proposal identifies the importance of the recently detected "reservoir" life history type of Snake River fall Chinook and provides a logical reasoning to refining when and where these fish reside and migrate within the Columbia River hydrosystem. An enormous commitment has been made to understanding how flow, spill, temperature, sediment, load following, and transport affect the viability of the fall Chinook ESU, which has precarious status. This project will provide additional insight into the adaptation of fall Chinook to the modified Columbia River ecosystem. The proposal suggests using recent advances in microchemistry along with standard microscopy to evaluate where in the hydrosystem fall Chinook were residing and growing prior to ocean entry, and then estimate food consumption rates. The methods are innovative (but used elsewhere with notable success) and have a potential to provide insights into the life cycle of fall Chinook unavailable traditionally.

ISRP FINAL REVIEW (Aug 31, 2006)

Recommendation: Fundable