FY 2003 Mainstem/Systemwide proposal 199900301

Section 1. General administrative information
Section 2. Past accomplishments
Section 3. Relationships to other projects
Section 4. Budgets for planning/design phase
Section 5. Budgets for construction/implementation phase
Section 6. Budgets for operations/maintenance phase
Section 7. Budgets for monitoring/evaluation phase
Section 8. Budget summary

Reviews and Recommendations

Additional documents

Title	Type
199900301 Narrative	Narrative
199900301 Powerpoint Presentation	Powerpoint Presentation
199900301 Sponsor Response to the ISRP	Response
FY 2005 Powerpoint Presentation Update for Project 199900301	Powerpoint Presentation
FY 2005 Powerpoint Presentation Update for Project 199900301	Powerpoint Presentation
FY 2005 Powerpoint Presentation Update for Project 199900301 - Attached Animation File	Powerpoint Presentation Attached File

Section 1. Administrative

Proposal title	Evaluate Spawning of Fall Chinook and Chum Salmon Just Below the Four Lowermost Mainstem Dams
Proposal ID	199900301
Organization	Pacific States Marine Fisheries Commission, Oregon Department of Fish and Wildlife, U.S. Fish and Wildlife Service, U.S. Geological Survey, Pacific Northwest National Laboratory (PSMFC/ODFW/USFWS/PNNL)
Proposal contact person or principal investigator
Name	Joe Hymer
Mailing address	2108 Grand Blvd. Vancouver, WA 98661
Phone / email	3609066740 / hymerjah@dfw.wa.gov
Manager authorizing this project	Joe Hymer, Pat Frazier, Don Anglin
Review cycle	Mainstem/Systemwide
Province / Subbasin	Mainstem/Systemwide /
Short description	Monitor, protect, and enhance the spawning populations of fall chinook and chum below Bonneville Dam. Search for evidence of fall chinook spawning below The Dalles, John Day, and McNary dams.
Target species	Fall Chinook (Oncorhynchus tshawytscha) and Chum (Oncorhynchus keta) Salmon

Project location

Latitude	Longitude	Description
		The mainstem Columbia and its tributaries from McNary Dam (River Mile 293) downstream.
45.93	-119.32	McNary Study Site
45.71	-120.72	John Day Study Site
45.61	-121.14	The Dalles Study Site
45.62	-122	Bonneville Study Site

Reasonable and Prudent Alternatives (RPAs)

Sponsor-reported:

RPA
155
156
157
199 1058
NMFS RPA 2001

Relevant RPAs based on NMFS/BPA review:

Reviewing agency	Action #	BiOp Agency	Description
NMFS/BPA	Action 199	NMFS	The Action Agencies shall implement the specific research/monitoring actions outlined in Appendix H.
NMFS	Action 199	NMFS	The Action Agencies shall implement the specific research/monitoring actions outlined in Appendix H.
NMFS	Action 155	NMFS	BPA, working with BOR, the Corps, EPA, and USGS, shall develop a program to 1) identify mainstem habitat sampling reaches, survey conditions, describe cause-and- effect relationships, and identify research needs; 2) develop improvement plans for all mainstem reaches; and 3) initiate improvements in three mainstem reaches. Results shall be reported annually.
NMFS/BPA	Action 155	NMFS	BPA, working with BOR, the Corps, EPA, and USGS, shall develop a program to 1) identify mainstem habitat sampling reaches, survey conditions, describe cause-and- effect relationships, and identify research needs; 2) develop improvement plans for all mainstem reaches; and 3) initiate improvements in three mainstem reaches. Results shall be reported annually.
NMFS	Action 157	NMFS	BPA shall fund actions to improve and restore tributary and mainstem habitat for CR chum salmon in the reach between The Dalles Dam and the mouth of the Columbia River.
NMFS/BPA	Action 156	NMFS	The Action Agencies and NMFS shall study the feasibility (including both biological benefits and ecological risks) of habitat modification to improve spawning conditions for chum salmon in the Ives Island area.
NMFS/BPA	Action 157	NMFS	BPA shall fund actions to improve and restore tributary and mainstem habitat for CR chum salmon in the reach between The Dalles Dam and the mouth of the Columbia River.

Section 2. Past accomplishments

Year	Accomplishment
2002	Geist, D.R., T.P. Hanrahan, E.V. Arntzen, G.A. McMichael, C.J. Murray, and Y. Chien. In press. Physicochemical characteristics of the hyporheic zone affect redd sites of chum salmon and fall chinook salmon in the Columbia River. N.A. J. Fish. Mgt.
2002	Initiated 2-D Hydrodynamic Model for the John Day study Site
2002	Completed GIS based Habitat/Hydraulic Model for adult Fall Chinook and Chum salmon for the Bonneville Study Site
2001	Completed a Logistic Regression analysis for Spawning Chum and Chinook Salmon
2001	Provided in-season hydrosystem management recommendations to salmon managers and hydrosystem operators regarding spawning habitat conditions and flows required for chum salmon to complete incubation and emergence.
2001	Maintained real time emperical data and analyses availablity on the Fish Passage Center web site.
2001	Applied CWTs to 10,000 juvenile fall chinook captured in the Ivs/Pierce island complex.
2001	Based on allozyme analysis, it was determined the Ives/Pierce island complex and Wood's Landing/Rivershore chum populations are genetically similar to each other and most closely related to the chum population in Hardy and Hamilton creeks.
2001	Completed 2-D Hydrodynamic model for the Bonneville Study Site
2000	Incorporated data collected from piezometers to estimate emergence timing for chinook and chum in the Ives/Pierce island complex.
2000	Documented evidence of fall chinook spawning below John Day Dam.
2000	Produced population estimates for fall chinook and chum in the Ives/Pierce island complex.
2000	Documented and mapped over 100 fall chinook redds spawning in deep water near Ives and Pierce Islands, characterized the general substrate type at redds, and collected velocity measurements at selected redds.
2000	Successfully installed piezometers within the study area; collected long-term temperature data that demonstrate a temperature gradient between the hyporheic zone and the river.
2000	Maintained real time empirical data and analyses availability on the Fish Passage Center web site.
2000	Initial pilot work to collect information pertaining to the physical and biological aspects of chum/chinook stranding/entrapment in the Ives/Pierce island complex. This information will be used as a guide for the FY 2001 studies.
2000	Verification that both chum and chinook fry were stranded in the Ives/Pierce island complex as a result of river flow fluctuations.
1999	FACT SHEET provided to FPAC, BPA, and NMFS for discussions on Bonneville Dam flow requirements for fall chinook and chum spawning and rearing.
1999	Determined emergence timing for chinook and chum in the Ives/Pierce island complex and verified accuracy of preseason estimates.
1999	Estimated emergence timing for chinook and chum in the Ives/Pierce island complex.
1999	Documentation of earlier spawning fall chinook is found in the Ives/Pierce island complex.
1999	Observations of both chum and chinook fry stranding events in the Ives/Pierce island complex as a result of reductions.
1999	Evidence of fall chinook spawning below The Dalles and John Day dams and chum below Bonneville Dam is documented.
1999	Developed population estimates for fall chinook and chum spawning below Bonneville Dam for the 1999 return.
1999	Conducted extensive in-season analysis to determine spawning and incubation flows and to recommend flows to protect alevins and juveniles from elevated total dissolved gas levels and stranding.
1999	Measured microhabitat parameters for fall chinook and chum and recorded geographic locations of some important hydraulic features.
1999	Deep water redds are found below Bonneville Dam.
1999	Installed two water level recorders in the island complex and mainstem Columbia for 2-dimensional model.
1999	Location of shallow and deep water redds for the 1999 return are recorded on GPS and map of general known spawning area is developed
1999	Installed two water level recorders/thermistors with remote communication from spawning and rearing areas below Bonneville Dam.
1998	Coursery observations reveal some stranding and entrapment of juvenile chinook and chum below Bonneville Dam.
1998	Model developed to provide spawning and incubation flows for fall chinook and chum salmon below Boneville Dam.
1998	Reached goal of 100 samples for genetic testing of bright stock fall chinook spawning below Bonneville Dam

Section 3. Relationships to other projects

Project ID	Title	Description
200001200	Evaluate factors limiting Columbia River gorge chum salmon populations	Data/technology exchange, information used to predict run timing, emergence, and population dynamics
198810804	Stream Net	This project will provide data to the anadromous fish data base. Data provided will be used to annually update and enhance information in the stock summary reports.
199801003	Spawning distribution of fall chinook salmon in the Snake River	Both projects examine naturally spawning fall chinook salmon in the basin.
199406900	Estimate production potential of fall chinook salmon in the Hanford Reach of the Columbia River	The methods for the physical habitat modeling proposed by this project have been adapted from this project.
199102900	Life history of fall chinook salmon in the Columbia River basin	The methods for the physical habitat modeling proposed by this project have been adapted from this project.
200105300	Re-Introduction of Columbia River Chum Salmon Into Duncan Creek	The level of chum brood stock collection for the Duncan Creek Project depends upon general abundance and distribution found during spawning ground surveys on this project.
199403400	Assessing summer and fall chinook salmon restoration in the upper Clearwater and principal tributaries	Both projects examine naturally spawning fall chinook salmon in the basin.

Section 4. Budget for Planning and Design phase

Task-based budget

Objective	Task	Duration in FYs	Estimated 2003 cost	Subcontractor

Outyear objectives-based budget

Objective	Starting FY	Ending FY	Estimated cost

Outyear budgets for Planning and Design phase

Section 5. Budget for Construction and Implementation phase

Task-based budget

Objective	Task	Duration in FYs	Estimated 2003 cost	Subcontractor

Outyear objectives-based budget

Objective	Starting FY	Ending FY	Estimated cost

Outyear budgets for Construction and Implementation phase

Section 6. Budget for Operations and Maintenance phase

Task-based budget

Objective	Task	Duration in FYs	Estimated 2003 cost	Subcontractor

Outyear objectives-based budget

Objective	Starting FY	Ending FY	Estimated cost

Outyear budgets for Operations and Maintenance phase

Section 7. Budget for Monitoring and Evaluation phase

Task-based budget

Objective	Task	Duration in FYs	Estimated 2003 cost
1. Determine locations of fall chinook and chum salmon spawning below Bonneville Dam and collect biological and physical data to profile stock origins and habitat use	a. Document evidence and success of fall chinook and chum spawning in the mainstem Columbia River below Bonneville Dam and estimate the number of fall chinook and chum spawning in shallow water habitat just below Bonneville Dam (PSMFC, ODFW, PNNL).	On-going	$113,932
	b. Document evidence of chum salmon spawning in the mainstem Columbia River outside the Ives/Pierce island complex plus Washington and Oregon tributaries downstream of Bonneville Dam. (PSMFC, ODFW).	On-going	$196,906
	c. Collect biological and genetic data to profile fall chinook and chum spawners below Bonneville Dam (PSMFC, ODFW).	On-going	$36,503
	d. Refine chum spawning habitat suitability model with ground water-surface water interactions, hyporheic physicochemical characteristics, and/or substrate quality (PNNL, USGS, USFWS).	On-going	$129,356
2. Determine the biological and physical characteristics affecting production of juvenile fall chinook and chum populations rearing in the mainstem Columbia below Bonneville Dam..	a. Estimate emergence timing of juvenile fall chinook and chum spawning below Bonneville Dam (PNNL, PSMFC, ODFW).	On-going	$125,310
	b. Determine emergence timing, size at emigration, and time of emigration for juvenile fall chinook and chum rearing below Bonneville Dam (PSMFC, ODFW).	On-going	$50,160
	c. Begin feasibility study to enumerate juvenile chum salmon production from the mainstem Columbia in the Ives/Pierce island area. (PSMFC, USFWS).	FY 03-05	$91,305
	d. Collect fish abundance and size data pertaining to stranding of juvenile chinook and chum in the Ives Island area. Also enumerate dewatered redds.	On-going	$25,261
	(PSMFC, PNNL)		$0
	e. Juvenile fall chinook captured below Bonneville Dam will be marked with CWTs to determine juvenile to adult survival rate.	On-going	$124,875
3. Describe physical habitat use and requirements for fall chinook in the Columbia River downstream from The Dalles, John Day, and McNary dams by determining the relationship between river discharge and location and quantity of spawning and rearing	a. Expand the 2-dimensional hydraulic model beyond the baseline modeling conducted in FY 02 to predict the physical conditions in potential fall chinook spawning and rearing areas downstream from John Day and evaluate the need for similar work downstream	On-going	$27,000
habitat.	from McNary and The Dalles dams based on new salmon observations (USFWS, USGS).		$0
	b. Conduct use surveys and analysis describing habitat used in terms of depth, velocity, lateral slope, substrate, cover, and temperatures below John Day Dam. Work performed below The Dalles and McNary dams will continue at FY 02 reconnaissance levels	On-going	$58,011
	only (USFWS, USGS).		$0
	c. Quantify fall chinook spawning and rearing habitat as a function of river discharge and downstream pool elevation below John Day Dam (USFWS, USGS).	On-going	$10,000
4. Provide habitat and in-season management data to fisheries management agencies, e.g., information on water levels, temperatures, and habitat availability in the Ives Island area.	a. Maintain remote, recording water level and temperature monitors in index fall chinook and chum spawning areas downstream from Bonneville Dam. Maintaining a recording water level monitor near the former USGS gaging station site at Warrendale, Oregon	On-going	$10,500
	downstream from the Ives/Pierce/Hamilton islands complex (USFWS).		$0
	b.Maintain internet-based data access (ODFW, USFWS).	On-going	$13,286

Outyear objectives-based budget

Objective	Starting FY	Ending FY	Estimated cost
Objective 1 – Determine locations of fall chinook and chum salmon spawning below Bonneville Dam, and collect biological and physical data to profile stock, determine stock origins, and habitat use.	2004	2007	$2,157,355
Objective 2 – Determine the biological and physical characteristics affecting production of juvenile fall chinook and chum populations rearing below Bonneville Dam, specifically near Ives and Pierce islands.	2004	2007	$1,886,786
Objective 3 – Describe physical habitat use & requirements for fall chinook in the Columbia River downstream from The Dalles, John Day, & McNary dams by determining the relationship btwn river discharge & location & quantity of spawning & rearing habitat	2004	2007	$429,985
Objective 4 – Provide habitat and in-season management data to the fisheries management agencies, e.g., information on water levels, temperatures, and habitat availability in the Ives Island area.	2004	2007	$107,646

Outyear budgets for Monitoring and Evaluation phase

FY 2004	FY 2005	FY 2006	FY 2007
$1,063,025	$1,116,177	$1,171,985	$1,230,585

Section 8. Estimated budget summary

Itemized budget

Item	Note	FY 2003 cost
Personnel	FTE: 3.4 PSMFC $157,083 4.0 ODFW $122,785 0.92 USFWS $45,800 0.92 USGS $28,358 1.1 PNNL $67,691	$421,717
Fringe	PSMFC $48,849 ODFW $44,203 USFWS $11,400 USGS $ 4,793 PNNL $21,957	$131,202
Supplies	PSMFC $25,350 ODFW $34,150 USFWS $8,400 USGS $3,400 PNNL $18,479	$89,779
Travel	PSMFC $4,928 ODFW $9,800 USFWS $7,200 USGS $0 PNNL $9,746	$31,674
Indirect	PSMFC $36,234 ODFW $51,679 USFWS 17,700 USGS $14,460 PNNL $121,612	$241,685
Capital	PSMFC $0 ODFW $0 USFWS $0 USGS $0 PNNL $44,127	$44,127
NEPA		$0
PIT tags	# of tags: 0	$0
Subcontractor	WDFW $40,146 PNNL $5,575	$45,721
Other	Equipment rental (USFWS $5,000), Boat operation (USGS $1,500)	$6,500
		$1,012,405

Total estimated budget

Total FY 2003 cost	$1,012,405
Amount anticipated from previously committed BPA funds	$0
Total FY 2003 budget request	$1,012,405
FY 2003 forecast from 2002	$626,000
% change from forecast	61.7%

Reason for change in estimated budget

Expand spawning ground surveys for chum salmon in the mainstem Columbia outside the Ives/Pierce island complex plus Washington and Oregon tributaries below Bonneville Dam. Expand deep water redd searches for chum spawning in the mainstem Columbia outside the Ives/Pierce island complex. Purchase equipment to provide real-time water temperature data of chum egg pockets in the mainstem Columbia. Begin feasibility study to enumerate juvenile chum production in the mainstem Columbia near the Ives/Pierce Island complex. Continue to develop and refine the chum habitat criteria model.

Reason for change in scope

Rather than a actual change of scope, the increase in the estimated budget is the result of efforts to determine distribution, biological and genetic makeup, and general abundance of Columbia River chum salmon. More intensive spawning ground surveys in the mainstem Columbia outside the Ives/Pierce island complex will aid in determining the actual relative importance of the Ives/Pierce island population. Developing a refined habitat suitability model will be useful to evaluate restoration options for chum in the tributaries and other mainstem locations. Salmon Managers voiced interest in a quantitative estimate for juvenile chum salmon. Without this number there is no way to document take (e.g., stranding of juveniles or dewatering of redds), potential egg-to-fry survival rates, and other important information. USFWS will provide technical assistance in designing a statistically rigorous sampling design.

Cost sharing

Organization	Item or service provided	Amount	Cash or in-kind

Reviews and recommendations

This information was not provided on the original proposals, but was generated during the review process.

REVIEW:
ISRP Preliminary Review (ISRP 2002-13)

Recommendation:
Fundable only if response is adequate

Date:
Aug 2, 2002

Comment:

A response is needed; this proposal is likely fundable in part. The proposal is aimed at obtaining information needed for management of chum salmon and chinook salmon spawning below Bonneville Dam.

There is insufficient justification of the need for the effort to determine the "feasibility" of estimating the juvenile chum salmon production from the mainstem Columbia in the Ives/Pierce Island area, as proposed under Objective 2, Task 2.b. Furthermore, the proposed method, to employ a mark recapture estimation procedure, would need to be described in more detail before it could be considered to be likely to succeed. The investigators need to give more thought to the problem of meeting the necessary assumptions in employing such methods, i.e. that emigration and immigration are negligible under the circumstances to be expected with chum salmon juveniles.

The response should address the following points:

The background statement should be enlarged to establish an understanding of the broader regional needs for flow and water management in the mainstem Columbia River. For example, it should be made clear that the investigators understand the tradeoffs that are involved in providing water to enhance spawning effectiveness in this area with use of water later to provide flow volumes to enhance outmigrations of upriver juvenile salmon.
An enlarged background statement would help identify the key questions that need to be answered and the tradeoffs that must be addressed as more and more salmon are observed to be adapting to the FCRPS.
It would seem to be appropriate to include in this proposal, either as background or as a specific task, exploration of the feasibility of opening up additional spawning area at the mouths of tributaries in the lower river.
Under Task 3.b Analysis, it is said that "Regression analysis will be used to determine in a statistically rigorous manner the extent to which each habitat metric plays in predicting habitat". This statement needs to be enlarged upon for clarification and to establish credibility.

Action Agency/NMFS RME Group Comments:

HYDRO SUBGROUP -- This proposal appears to be in direct response to RPA 199, RA-2001.

That RA (2001) calls for research to collect relevant information for lower Columbia fall chinook and chum salmon spawning populations. The tasks in this proposal appear to satisfy the information requested in that RA. The Willamette Lower Columbia TRT has been developing guidelines for delineating population structure of these species. Their finding would appear to have bearing on population sampling resolution that may be required to satisfy status monitoring requirements under the BO. Presumable that RME work group will treat that matter further.

The proposal calls for the CWT implantation of Ives/Pierce Island fall chinook. It is not clear how these will be discriminate from other stocks that may move downstream and inhabit those locales. Clarifying this would be helpful.

ISRP Remarks on RME Group Comments:

The frequent use of the words "appear to" in the RME comments appear to hedge a bit. The RME technical comment on CWT implantation of fall chinook and the difficulty expected in discriminating from marked upstream stocks is a point that the proposers should address in their response.

REVIEW:
CBFWA Funding Recommendation

Recommendation:
Urgent

Date:
Oct 24, 2002

Comment:

New tasks have been added. Budget needs to be reviewed. This project meets RPAs 157 and 199 of the NMFS BiOp.

REVIEW:
CBFWA FY03 Budget Review Comments

Recommendation:
Urgent

Date:
Oct 24, 2002

Comment:

Modified Budget Reduction includes -$10,000 for chum genetic analysis, -$8,000 for airplane flights to count possible chum spawning in the mainstem Columbia downstream of the I-5 bridge. The new tasks for this project total approximately $164,000 in 2003, $172,000 in 2004, and $181,000 in 2005. If further reductions are required, please refer to the full response to CBFWA.

REVIEW:
ISRP Final Review (ISRP 2002-14)

Recommendation:
Fund

Date:
Nov 5, 2002

Comment:

Fundable. Agree with CBFWA's Urgent ranking. This is an ongoing proposal with some new tasks. The thorough and excellent response adequately addressed the ISRP questions. It appears that differences in timing of appearance of upstream chinook will make it possible to discriminate between them and the local stock. The proposed method, to employ a mark recapture estimation procedure, was described in adequate detail. The investigators gave more thought to the problem of meeting the necessary assumptions in employing such methods, i.e. that emigration and immigration are negligible under the circumstances to be expected with chum salmon juveniles. The background statement was enlarged and shows an understanding of the broader regional needs for flow and water management in the mainstem Columbia River. They identified the key questions that need to be answered and the tradeoffs that must be addressed as more and more salmon are observed to be adapting to the FCRPS. They also addressed the ISRP comments concerning exploration of the feasibility of opening up additional spawning area at the mouths of tributaries in the lower river. The regression analysis was clarified.

If funded, this project should be coordinated with other monitoring projects to ensure compatibility of objectives, common methods, and protocols. This coordination could be accomplished under the favorably reviewed CBFWA proposal #35033.

REVIEW:
NMFS Review

Recommendation:

Date:
Jan 21, 2003

Comment:

Statement of Potential Biological Benefit
The benefits are indirect. The proposal deals with over 90% of the spawning chum population. It would document existing size and range of the existing population.

Comments
This project has provided excellent information to date. Aspects of this project that provides information necessary to effectively manage this population are tasks 1a, 1b, and 2b. The costs of conducting these tasks is approximately $360,000. The added tasks which bring the project to $1 million need to be weighed against priorities in the overall budget.

Already ESA Required?
No

Biop?
Yes

REVIEW:
NWPPC Funding Recommendation

Recommendation:
Fund (Tier 1)

Date:
Jun 11, 2003

Comment:

Category:
1. Council Staff preferred projects that fit province allocation

Comments:
Budget revised by Council decision. Need management plan from NMFS.

REVIEW:
BPA Funding Decision

Recommendation:

Date:
Aug 4, 2003

Comment:

This is only project addressing mainstem spawning. Scope could be reduced to focus only on listed chum. May also be appropriate for potential funding by the Corps. Budget consistent with NPCC recommendation.

REVIEW:
Project Sponsor Request for FY04-05

Recommendation:

Date:
Sep 20, 2003

Comment:

The budget approved for FY 03 was $779,586.

REVIEW:
NW Power and Conservation Council's FY 2006 Project Funding Review

Funding category:
expense

Date:
May 2005

FY05 NPCC start of year:	FY06 NPCC staff preliminary:	FY06 NPCC July draft start of year:
$779,586	$779,586	$779,586

Sponsor comments: See comment at Council's website