Integrated Status & Effectiveness Monitoring Program
Project # 2003-017-00
PI: Dr. Chris Jordan, NOAA Fisheries, NWFSC
Statement of Work:
Expansion of Existing Smolt Trapping Program and Steelhead Spawner Surveys by Washington Department of Fish and Wildlife

Principal Investigator for WDFW:
Andrew Murdoch
Washington Department of Fish and Wildlife
3515 Chelan Highway Wenatchee, WA 98801
Telephone: 509 664-3148
Email murdoarm@dfw.wa.gov
Administrative Contact for WDFW:  
Ted Nelson
Washington Department of Fish and Wildlife
600 Capitol Way N.
Olympia, WA. 98501-1091
Telephone (360) 902-2401
FAX:  (360) 902-2941

Project # 2003-017-00 Period:  2004 - 2007
Current SOW Period:  1 March 2005 - 28 February 2006
PROJECT PURPOSE/JUSTIFICATION
Project #2003-017-00 (Project) seeks to develop two novel monitoring and evaluation programs: (i) subbasin-scale pilot status and trend monitoring efforts for anadromous salmonids and their habitat in the Wenatchee, John Day and South Fork Salmon River subbasins, and (ii) effectiveness monitoring for suites of habitat restoration projects in selected watersheds within the three target subbasins.  This work - critical for implementing the 2000 NMFS FCRPS Biological Opinion (RPA Actions 180, 181, and 183) (BiOp) - builds on current status and trend monitoring programs within each of these subbasins.  Several regional and local organizations are funding and implementing these programs.  In short, this project will integrate existing and new monitoring and evaluation activities in three pilot subbasins to help ensure that provisions of the BiOp are satisfied.
This Scope of Work (SOW) will enable the Bonneville Power Administration (Bonneville) to implement the Project in the Wenatchee Subbasin.  Specifically, within this SOW, Washington Department of Fish and Wildlife (WDFW) will 1) estimate the total number of steelhead redds in selected streams within the Wenatchee Subbasin by conducting index spawning ground counts, and will 2) estimate the smolt production of spring chinook salmon and steelhead for the Wenatchee Subbasin.  
Both of these work elements expand upon previous and current monitoring work being conducted by WDFW and are key components of the two monitoring and evaluation programs developed by Project.  These work elements are interrelated with other Project components including: 1) steelhead spawning surveys at randomized locations, 2) smolt production estimates of other species and/or at other locations, and 3) several habitat and water quality studies.  While the completion of work elements within this SOW is not dependent on the implementation of interrelated Project components, the completion of this SOW will provide the context for, and facilitate the interpretation of, data collected in other Project components.  
Background Details:  Steelhead Spawning Ground Surveys
Steelhead spawning surveys were initiated in the Wenatchee Subbasin by WDFW in 2000.  The objective of these surveys was to determine the efficacy of a supplementation program that was begun in 1998 after the stock was listed as endangered.  Chelan County Public Utility District (PUD) currently funds these activities.  The scope of the project was limited to selected tributaries in the Wenatchee Subbasin.  This Project would expand the scope of the surveys to include all tributaries in the Wenatchee Subbasin with significant steelhead spawning populations.
In addition to the funds to be spent on spawning ground surveys as part of this BPA-funded Project, WDFW commits approximately $44,000 annually to steelhead spawning ground surveys.
Current methodology involving the use of index sites has been determined to provide reliable and accurate estimates of those spawning populations (e.g., status/trend monitoring).  The extent of steelhead spawning outside those identified spawning populations is unknown.  The proposed probabilistic sampling of small order streams (see related SOW for USFS) should provide data to answer this question.  Data generated from both index and probabilistic surveys will be used in estimating the spawning escapement of major tributaries and the entire subbasin.  These data will not only be used in determining the effect of supplementation programs on increasing spawner abundance and estimating egg deposition for ongoing smolt monitoring but will also be used by fishery managers to monitor recovery efforts.  Steelhead redd location data obtained from GPS-based georeferencing of each redd, to be generated from both index and probabilistic surveys, will be used to elucidate variability in the distribution of steelhead within the Wenatchee Subbasin.  Changes in spawning distribution may interact with variable habitat quality to affect overall steelhead production.
Background Details:  Smolt Production Monitoring
Smolt production monitoring in the Wenatchee Subbasin began in 1993.  Chelan County PUD currently funds a smolt monitoring project on the Chiwawa River to determine the efficacy of a spring chinook supplementation program.  In 1997, Chelan County PUD began funding a similar project on the upper Wenatchee River (0.5 km below Lake Wenatchee) to determine the efficacy of a sockeye supplementation program.   The Washington State Salmon Recovery Funding Board (SRFB) began a Wenatchee Subbasin smolt monitoring program in 2000.  The objective of this program is to estimate smolt production of anadromous species in the Wenatchee Subbasin.  Chelan County PUD also provides logistical support and funds all necessary repairs.  The WDFW currently operates and conduct data analysis of all these projects.  
In addition to the funds to be spent on smolt trapping operations as part of this BPA-funded Project, WDFW commits approximately $88,000 annually to the smolt monitoring activities at the upper and lower Wenatchee traps.
The limited scope of the upper Wenatchee smolt monitoring program (i.e., sockeye) prohibits estimating smolt production of other species (e.g. spring chinook and steelhead) that spawn in the Little Wenatchee and White River watersheds (tributaries of Lake Wenatchee).  The trapping period of the lower Wenatchee trap is sufficient to meet the objectives of this Project.  
However, the trap efficiency at both locations is inadequate to provide smolt production estimates of steelhead and spring chinook with the desired level of precision.  An additional trap operated under this Project at each location would increase the capture efficiency and provide a higher level of precision.  In addition to the second additional trap, funding for the necessary personnel to operate two traps simultaneously.
A second eight-foot trap is needed at the lower Wenatchee river location.  The cone and livebox will be purchased from the vendor, while Chelan PUD will construct the trap.  During the trapping period it is likely that the cone will become damaged.  Extra cones have been previously purchased for this trap location that can be installed immediately, minimizing the time period the trap is out of operation.  A second five-foot trap is needed at the upper Wenatchee river location.  The water depth during the proposed trapping period (March - November) is typically too shallow for the operation of eight-foot cones.  No extra cones are available for this trap and will need to be purchased to complete this Project.
Table 1.  Current and future smolt trap locations in the Wenatchee Subbasin.
Trap Location River km Year started Funding Agency
Lower Wenatchee - 2 traps 9.6 2000 & 2005* SRFB & CCPUD; BPA*
Upper Wenatchee - 2 traps 89.7 1997 & 2005* CCPUD; BPA*
Chiwawa River 1.0 1993 CCPUD
Nason Creek 2001 YN & BPA**
Peshastin Creek 2004** BPA**
Icicle Creek 2004** BPA**
* Funded under this contact.                                                                                                             ** Proposed under this project but different contracts.
Technical methodologies for all work conducted under this SOW will follow protocols specified in the following document unless Upper Columbia Regional Technical Team and WDFW mutually agree to changes to these methodologies:
Hillman, T.W.  2004.  Monitoring strategy for the Upper Columbia Basin: Draft report February 1, 2004.  Prepared for Upper Columbia Regional Technical Team, Wenatchee, Washington.

TECHNICAL TASKS
Task 1 - Conduct index spawning ground counts and estimate the total number of steelhead redds in selected streams within the Wenatchee Subbasin.
Description/Rationale:  Steelhead spawning escapement of selected tributaries will be estimated using index area redds counts within known core-spawning areas as described in Hillman (2004) with weekly index-reach surveys and a single survey of larger reference reaches, which can be comprised of one or more index-reaches.  BPA support for this monitoring beyond 2004 is conditioned, in part, upon BPA receiving an acceptable plan that clearly identifies the monitoring and analytical framework, timeframes (i.e., expected schedules across years), and collaborative contributions for data collection and analyses by partner entities.
Methods:   Comprehensive spawning ground surveys of index areas will be conducted weekly.  All redds within an index area will be individually flagged, georeferenced by GPS, and numbered sequentially.  
A final survey will be conducted of the entire reach(s) at the end or after peak spawning if poor water conditions are expected.  All redds in each reach will be counted.  Marking redds is not required during the final survey.  A different surveyor should survey within the index area and count only redds that are visible.  An index expansion factor (IF) will be calculated by dividing the number of visible redds in the index by the total number of redds in the index area.

The reach total (RT) will be calculated by expanding the redds in the non-index area by the proportion of visible redds in the index (i.e., index expansion factor) and adding the total number of redds found in the index area.


An estimate of the total number of redds (TR) in the tributary will be calculated by summing the reach totals.

The number of redds determined by probabilistic sampling for those tributaries within the subbasin would be added to the total number of redds to estimate the spawner escapement and egg deposition.

Location:  Various sites in Wenatchee Subbasin
Table 2.  Wenatchee Subbasin survey reaches with index/reference areas - surveys conducted weekly from March through June.
Reach Index/reference area
Wenatchee River
Sleepy Hollow Br. to Lower Cashmere Br. (W2) Monitor boat ramp to Cashmere boat ramp
Leavenworth Bridge to Icicle Road Bridge (W6) Leavenworth boat ramp to Icicle River
Tumwater Bridge to Chiwawa River (W9) Tumwater Bridge to Plain Bridge
Chiwawa River to Lake Wenatchee (W10) Chiwawa pump station to Lake Wenatchee
Beaver Creek
Chiwawa loop road culvert to mouth (X1) Hwy culvert to mouth
Peshastin Creek
Mouth to Camas Creek (P1) 0.5 km below Kings Bridge to bridge 0.5km above Camas Ck
Camas Creek to mouth of Scotty Creek (P2) FR 7320 bridge to mouth of Shaser Cr.
Ingalls Creek
Trailhead to Wilderness Boundary rm 1.5 (D2) Trailhead to Wilderness Boundary rm 1.5
Chiwawa River
Mouth to Grouse Creek (C1) Mouth to Road 310 Bridge
Grouse Creek to Rock Creek (C2) Chikamin Creek to Log jam
Clear Creek
Mouth to HWY 22 (V1) Mouth to HWY 22
HWY 22 to Lower culvert rm 2.0 (V2) HWY 22 to Lower culvert
Nason Creek
Mouth to Kahler Creek Bridge (N1) Mouth to Swamp Creek
HWY 2 Bridge to Lower R.R. Bridge (N3) Highway 2 Bridge to Merrit Bridge
Lower R.R. Bridge to Whitepine Creek (N4) Rayrock to Church camp
Icicle River
Mouth to Hatchery (I1) Mouth to Hatchery
Little Wenatchee River
Mouth to Lost Creek (L2) Fish Weir to Lost Creek
Lost Creek to Rainy Creek Bridge (L3) Lost Creek to Rainy Creek Bridge
White River
Sears Cr. Bridge to Napeequa River (H2) Riprap bank to Napeequa River
Napeequa River to mouth of Panther Creek (H3) Napeequa River to Grasshopper Meadows.
Napeequa River
Mouth to rm 1.0 (Q1) Mouth to rm 1.0

Deliverables/Products/Schedule:  
Task Schedule Deliverable/Products
Subtask 1.1 - Field Surveys March 1 - June 15, 2005 Conduct surveys; Collect data
Subtask 1.2 - Data Entry March 15 - June 30, 2005 Quality controlled raw data in spread sheet format; Quality controlled, georeferenced, summarized data in spread sheet format

Task 2 - Estimate the smolt production of spring chinook salmon and steelhead for the Wenatchee Subbasin.
Description/Rationale:  Smolt production will be estimated for spring-chinook salmon and steelhead using data collected at rotary smolt traps to be operated at two trapping locations under this SOW.  Population estimates will be generated at Subbasin (e.g., at the lower Wenatchee River) and watershed scales (e.g., at the upper Wenatchee River below Lake Wenatchee).  
These traps will be part of a comprehensive trapping program consisting of six traps located throughout the Wenatchee Subbasin operated under other SOWs within the Project and/or by cooperating agencies funded outside of this Project.
Methods: Daily Captures:  Fish will be removed from the trap at a minimum every morning and placed in an anesthetic solution of MS-222.  Fish will be identified to species and counted.  Non-target species will be allowed to fully recover in fresh water prior to being released in an area of calm water downstream from the smolt trap.  Target species will be held in separate live boxes for use during mark/recapture efficiency trials conducted in the evening.
Methods: Length and Weight Analysis:  Fork length will be measured to the nearest millimeter and weight to the nearest 0.1 g.  A Fulton type condition factor (WH105/FL3) will be calculated for all target species.  The degree of smoltification (parr, transitional, or smolt) will be assessed by visual examination.  Juvenile spring chinook and steelhead O. mykiss will be classified as parr if parr marks are distinct, transitional if parr marks are not distinct, and smolts if parr marks were not visible and the fish exhibited a silvery appearance.
Methods: Efficiency Trials and Emigration Estimate:  Mark/recapture efficiency trials will be conducted throughout the trapping season.  The frequency of mark/recapture trials is dependent on the number of fish captured (no less than 100) and the river discharge.  These trials will be conducted over the widest range of discharge possible (interval depends on trap location).  Fish for the mark/recapture trials will be marked by clipping the tip of either the upper or lower lobe of the caudal fin.  Fish will be placed in a live pen to recover for at least 8 h before being transported to the release site at least 1 km upstream of the trap.  Marked fish will be distributed across the width of the river and along approximately 100 m of the bank in pools or in calm pockets of water around boulders.  In the case of the upper Wenatchee River trap, marked fish will be transported and released into Lake Wenatchee.  Fish will be released between 1800 h and 2000 h.  All recaptures of marked fish typically occur within 48 h after each trial.  
The number fish that could be marked and released may limit the frequency with which trap efficiency trials will be conducted.  Emigration estimates will be calculated using estimated daily trap efficiency derived from the regression formula using trap efficiency (dependent variable) and discharge (independent variable).  
Trap efficiency will be calculated using the following formula:
Trap efficiency, Ei=Ri/MI, where Ei is the trap efficiency during time period i; Mi is the number of marked fish released during time period i; and Ri is the number of marked fish recaptured during time period i.  
The number of fish captured will be expanded by the estimated daily trap efficiency (e) to estimate the daily number of fish migrating past the trap (Ni) using the following formula:
Estimated daily migration  =   where Ni is the estimated number of fish passing the trap during time period i; Ci is the number of unmarked fish captured during time period i; and ei is the estimated trap efficiency for time period i based on the regression equation.  
The variance for the total daily number of fish migrating past the trap will be calculated using the following formulas:
Variance of daily migration estimate =  
where Xi is the discharge for time period i, and n is the sample size.  If a relationship between discharge and trap efficiency was not present (i.e. P < 0.05; r2 . 0.5), a pooled trap efficiency was used to estimate daily emigration:

Pooled trap efficiency =   The daily emigration estimate will be calculated using the formula: Daily emigration estimate =  
The variance for daily emigration estimates using the pooled trap efficiency will be calculated using the formula:
Variance for daily emigration estimate =  
The total emigration estimate and confidence interval will be calculated using the following formulas:  Total emigration estimate =    95% confidence interval =  

Location:  Traps will be operated at lower Wenatchee River rkm 9.6 and upper Wenatchee River rkm 89.7 (Table 1).
Deliverables/Products/Schedule:  
Task Schedule Deliverable/Products
Subtask 2.1 - Smolt Trapping March 1 - Aug. 31, 2005 Operate smolt traps; Collect data
Subtask 2.2 - Data Entry March 1 - Nov. 30, 2005 Quality controlled raw data in spread sheet format; Quality controlled summarized data in spread sheet format
Subtask 2.3 - Population Estimation October 1 - December 31, 2005 Generate population estimates for each fish species for entire Wenatchee Subbasin and for the Lake Wenatchee watershed.

REPORTING:
Prepare quarterly, annual, and Biological Opinion progress reports.  Reports will be prepared in standard formats and submitted to the project's Principal Investigator, Dr. Chris Jordan, NOAA Fisheries, on a common schedule to allow compilation into overall progress reports for Project #2003-017-00.  
Progress Reports:

Progress reports will be submitted quarterly and will summarize the following information by objective:  
· Budget
o Funding originally budgeted:
o Estimate of expenditures during the reporting period:
o Funding remaining:
· Work completed
· Problems encountered/resolved, changes in work plan, or schedule deviations
· Activities planned for the next progress reporting period.  
Quarterly progress reports will be submitted within 15 days after the end of each federal fiscal quarter.

Annual Report:

A draft annual report will be submitted by January 15, 2006 and will be organized as follows:
· Abstract (limit 600 words)
· Introduction
· Description of project area
· Methods and materials by objective
· Results and discussion of results by objective
· Summary and conclusions
· Summary of expenditures, including a list of major property purchased during the contracting period
· Supplemental volume or appendices that contain detailed summaries of all data collected

A final annual report will be provided within one month of receiving BPA comments on the draft annual report.  The final report will be provided in electronic format consistent with the instructions for preparing and submitting electronic reports on BPA's Web site.  

BiOp Reporting:

Dr. Chris Jordan, NOAA Fisheries, the Principal Investigator for Project #2003-017-00, will compile a single BiOp report for all components of the Project.  BiOp reporting requirements for this SOW include contributing relevant elements to Dr. Jordan, under his direction, on or before December 15, 2005, to cover the previous Fiscal Year accomplishments and planned work in the current and future Fiscal years.  Specific relevant elements will be identified by Dr. Jordan during BiOp Report compilation and may include:
1. Concise summary of research, monitoring, or evaluation deliverables for the project (what was or is planned for the prior and future Fiscal Years)
2. Concise summary of research, monitoring, or evaluation accomplishments for the project (what was accomplished in the prior Fiscal Year)
3. The RPAs that the research, monitoring, or evaluation are believed to contribute to or accomplish.  The RPA Action Item for this project are 180, 181 and 183.  
4. The specific biological and physical metrics that were monitored (i.e. stream temperature, par densities, etc.  For more information on types of status and action effectiveness metrics and proposed protocols see Action Agency and NMFS FCRPS BiOp RME Plan https://efw.bpa.gov/cgi-bin/FW/welcome.cgi)
5. The spatial (GIS coordinates) and temporal characteristics of the monitoring (where, when, frequency, and/or duration)
6. The Endangered Species Unit(s) that are being monitored or for which habitat is being monitored (refer to list at https://efw.bpa.gov/cgi-bin/FW/welcome.cgi )
7. Where and how the associated data and meta-data are stored (i.e. personal Access database, Streamnet, etc.) and contact person or web site for access.
Budget Notes:
· Extended trapping at the Lake Wenatchee does not appear to be necessary (i.e., no fish captured during 2004).   Because two traps are operated at the lower Wenatchee and Lake Wenatchee sites additional funding may be required.
· Travel associated with this project is funded by existing projects.