BPA Project Number:  1999-003-01
BPA Project Title: Evaluate spawning of fall Chinook and chum salmon just below the four lowermost Columbia River mainstem dams.
Contract Number: CR-66578
Contract Title:  Evaluate spawning of fall Chinook and chum salmon just below the four lowermost Columbia River mainstem dams.
Performance/Budget Period: October 1, 2005 through September 30, 2006

Contract Background Section:
Introduction
The Northwest Power Planning Council's Independent Advisory Board and the salmon managers have placed a high priority on the protection and enhancement of naturally spawning populations including fall Chinook and chum salmon spawning in the mainstem Columbia River. Spawning of fall Chinook and chum salmon in the mainstem Columbia River has been documented just below Bonneville Dam and may also be occurring just below The Dalles, John Day, and McNary dams.  Very little was known about the existence and/or size of these populations and their associated genetic composition, spawning timing, emergence timing, juvenile rearing duration, and juvenile to adult survival rates. Additionally, little was known about the habitat requirements for these populations and the effect changing flows and water temperatures have on spawning location and success (measured by outmigrating juveniles and returning adults).  

The purpose of this project is fourfold:  (l) Document the existence of fall Chinook salmon populations spawning just below Bonneville, The Dalles, John Day, and McNary dams;  (2) profile stocks for important population characteristics; including spawning time, emergence timing, emigration size and timing, and juvenile to adult survival rates, and relate these population characteristics to river flows and water temperatures; (3) determine habitat requirements that are necessary for successful fall Chinook and chum salmon spawning and rearing in the mainstem Columbia River; and (4) conduct chum salmon spawning ground surveys from The Dalles Dam downstream.  The primary goal of this project is to collect data concerning fall Chinook and chum salmon spawning just below the four lowermost Columbia River mainstem dams so that the hydrosystem can be managed in a manner to protect and enhance these spawning populations.

Background

Historically, fall Chinook salmon were known to spawn in the mainstem Columbia River where adequate habitat existed; however, with the development of the region, hydroelectric facilities that were built along the length of the Columbia River inundated the majority of the spawning habitat in the mainstem Columbia River.  Currently the free flowing stretch of river between McNary and Priest Rapids dams contain the vast majority of the remaining mainstem spawning habitat in the Columbia River.  A significant self-sustaining wild population of fall Chinook salmon does use and depend on this stretch of the Columbia River for spawning and rearing purposes.  Similar type habitat may exist below other mainstem Columbia dams and self-sustaining populations may exist in these areas also.  There had been little effort to determine if fall Chinook salmon are spawning in the mainstem Columbia River below McNary Dam.  However, fall Chinook salmon spawning in the mainstem Columbia River just below Bonneville Dam was documented in recent years.  Limited spawning ground surveys were conducted in the area around Ives and Pierce Islands during 1994-1997 and based on these surveys it is believed that fall Chinook and chum salmon were successfully spawning in this area.  Through 1997, limited sampling of adult carcasses had occurred but were inadequate for estimating spawning population sizes.  Additionally, no data had been collected concerning juvenile production or habitat characteristics of these spawning locations.  

It has also become apparent that fluctuating flows may be negatively impacting these populations through redd dewatering, lack of access to prime spawning areas, and possible stranding of juveniles.  In addition, fall Chinook salmon fisheries management under the ESA requires accountability of all fall Chinook salmon stocks returning to the Columbia River.

The federal agencies that operate or market power from the Federal Columbia River Power System (FCRPS), namely BPA, the U.S. Army Corps of Engineers, and the U.S. Bureau of Reclamation reinitiated consultation to consider the effects of the Federal Columbia River Power System on the six species listed during 1999.  Those species listed under the Endangered Species Act at that time included Lower Columbia River Chinook salmon (listed as threatened on March 24, 1999) and Columbia River chum salmon (listed as threatened on March 25, 1999).  The objective of this consultation was to determine whether the operation of the FCRPS is likely to jeopardize the continued existence of any newly listed species or likely to destroy or adversely modify designated critical habitat.

This project is primarily composed of four closely related activities. Each agency is responsible for completing one activity with Pacific States Marine Fisheries Commission leading the adult portion, Oregon Department of Fish and Wildlife leading the juvenile portion, and the U.S. Fish and Wildlife Service leading the habitat portion of this project.  Oregon Department of Fish and Wildlife and Pacific States Marine Fisheries Commission will be conducting chum salmon spawning ground surveys from The Dalles Dam downstream.  All four portions of the project are designed to work together to achieve the purposes of this project and each agency took the lead on an objective based on their special skills and/or knowledge in those areas.  Study results from PNNL's work contribute to all three tasks.

The primary function of the adult sampling portion of this project is to profile and estimate the fall Chinook and chum salmon spawning populations in the mainstem Columbia below Bonneville Dam.  Surveys for live fish and carcasses will be the basis for determining the size of that population.  Spawning ground surveys, which consist of fish and redd counts, will also be used to determine time and location of spawning and redd locations will be recorded using a GPS.  In conjunction with the spawning ground surveys, carcasses will be examined for the purpose of determining genetic heritage, spawning success, sex ratios, and age composition.

Oregon Department of Fish and Wildlife and Pacific States Marine Fisheries Commission will perform stream surveys for chum salmon on Columbia River tributaries from The Dalles Dam downstream.   Streams that historically supported chum salmon runs but are no longer surveyed will be primarily targeted.  In addition, streams that currently support fish will also be surveyed.  Surveys would begin in mid-October and last through December.  Multiple surveys to count live and dead fish plus redds will be made.  Population estimates will be calculated based on the proportion of marked carcasses recovered.  Spawning locations will be recorded on a GPS and mapped with GIS.  Water temperatures will be taken at the spawning sites to determine if spring sources are present.  Scale samples taken will provide data necessary to determine age composition on the natural spawning population.  DNA and otolith samples will be taken for future analysis to profile the genetic heritage of the naturally spawning chum salmon populations.    

The primary purpose of the juvenile sampling portion of this project is to determine emergence timing and emigration size and timing and relate these indices to flow and water temperature.  Spawning areas identified in the adult sampling objective will be sampled for emergence timing and monitored for possible dewatering.  In conjunction with this work stranding of juvenile fall Chinook and chum salmon in the study area will be noted.  Additionally, CWT's will be applied to juvenile fall Chinook salmon for the purposes of determining juvenile to adult survival rates and relating production and recruitment of the stocks to flow and temperature experienced during juvenile stages of life.

The primary purpose of the habitat sampling portion of this project is to accurately describe the kind of mainstem Columbia River habitat fall Chinook and chum salmon prefer to spawn in and how different flow levels impact spawning and rearing habitat.  Habitat will be mapped for the purpose of developing hydraulic models for fall Chinook and chum salmon spawning and rearing areas.  Spawning and rearing habitat descriptions will include a description of type of substrates and the associated water velocities and depth.  The effects of elevated flows on the spawning behavior and redd-site selection of chum salmon will be investigated using a two-dimensional acoustic array to obtain a continuous record of the locations of fish fitted with acoustic transmitters.  Experimental flows from Bonneville Dam will be requested to determine the flows and velocities that alter spawning behavior, and to determine if fish spawn at higher riverbed elevations under higher flows.

The adult, juvenile, and habitat sampling objectives will be concentrated just below Bonneville Dam.  The adult sampling objective will determine where populations currently exist, begin a monitoring program for existing populations, and determine which populations would benefit from additional study.  The juvenile and habitat sampling crews will perfect their sampling designs in the area just below Bonneville Dam, specifically near Ives and Pierce Islands, and will branch out into other areas as additional populations are identified.

This project has four primary objectives.  Work elements and milestones have been organized to adhere to this original structure as outlined in the 2004-2005 Statement of Work.  The ODFW will work on Objectives 1-3 in coordination with PSMFC and PNNL.  The USGS, USFWS, and PNNL will conduct work toward Objective 4.  All Coordinating agencies will work to complete Objective 5.

OBJECTIVE 1 - Adult Sampling:  Search for evidence of fall Chinook and chum salmon spawning in the mainstem Columbia below Bonneville Dam. Collect genetic and biological data to profile the stock and determine possible stock origin.

The number of fall Chinook and chum spawning in the mainstem Columbia below Bonneville Dam will be estimated based on counts of live/dead fish and redds observed.  Carcasses will be examined for biological data (i.e. length, sex, scales, etc.) to profile stock for age composition, size at return, and gender ratios.  Carcasses will also be examined for spawning success (egg retention).  Possible origins of fall Chinook will be determined based on CWT recoveries.  Genetic samples will be collected from live adult chum collected at the Bonneville Dam trap.  Chum redds and fall Chinook spawning areas will be recorded on a GPS.  Radio tags will be placed in chum trapped at Bonneville Dam and their migration and spawning areas traced.  

Work Elements: A-E, H-K.

OBJECTIVE 2 - Spawning ground surveys for Columbia River chum salmon in tributaries from The Dalles Dam downstream.

We will conduct extensive spawning ground surveys for chum salmon in Washington and Oregon tributaries from The Dalles Dam downstream.   The spawning ground surveys will be conducted in areas that historically supported Columbia River chum salmon and are not always annually surveyed.  In addition, stream surveys will be conducted in areas that currently support fish.  If possible, spawning populations will be estimated.  Spawning locations will be mapped and general habitat parameters will be collected.  We will collect biological and genetic data to profile these stocks.    

Multiple surveys to count live and dead fish plus redds will be made on each stream.  Determine whether rough population estimates using live fish counts from spawning ground surveys can be reliably made using an Area Under the Curve method.  Redd locations will be recorded on a GPS and mapped on a GIS.  Carcasses from spawning ground surveys will be examined for biological data (i.e. length, gender, scales, egg retention, etc) to profile the stocks for size and age at return, gender ratio, and spawning success.  Collect DNA and otolith samples from carcasses for future use to determine genetic heritage.  Water temperatures and stream types will be taken at the spawning sites to determine if spring sources are present and possible stream type preference.  We will document possible physical stream blockages.  

Work Elements: A-E, H-K.

OBJECTIVE 3 - Naturally produced juvenile fall Chinook and chum in the mainstem Columbia below Bonneville Dam will be sampled to determine emergence timing and size and time of emigration from local rearing areas and rearing distribution.  Naturally produced juvenile fall Chinook will be coded-wire tagged to determine eventual juvenile to adult survival rates.  

Location of spawning areas will be identified using GPS waypoints. Rearing areas will be seined weekly to determine emergence timing, plus size and time of emigration.  Flow and temperature recorders will be installed on selected redds and in select rearing areas to relate emergence timing and emigration size and time to flow and temperature data.  Naturally produced juvenile fall Chinook will be collected and coded-wire tagged for the purpose of providing data necessary for estimating juvenile to adult survival rates.

Work Elements: F, G, L-N.

OBJECTIVE 4 - Describe physical habitat use and requirements for fall Chinook salmon in the Columbia River downstream from The Dalles, John Day, and McNary dams and for chum salmon downstream from Bonneville Dam by determining the relationship between river discharge and the location and quantity of spawning and rearing habitat.

The purpose of this project is to evaluate spawning below the four mainstem dams on the lower Columbia River.  Efforts have been concentrated at Ives/Pierce Islands downstream from Bonneville Dam because it is an important area for both fall Chinook and ESA listed chum salmon.  The other dams have received little attention because any spawning that might be occurring is probably in deep water that cannot be documented by visual observations during boat surveys.  Surveys conducted from 2001 to 2004 documented significant spawning activity in each year below John Day Dam.  Work conducted below the Dalles and McNary dams will be aimed at describing the level of spawning. Therefore, the primary purposes of this objective are to accurately describe the kind of mainstem Columbia River habitat fall Chinook prefer to spawn in below John Day and how different dam operations impact spawning and rearing habitat.  Habitat will be mapped for the purpose of developing hydraulic models for fall Chinook spawning and rearing areas.

Spawning and rearing habitat evaluations will include a description of the types of substrates and the depths and water velocities available.  The ultimate goal of the project is to maximize the amount of suitable habitat available to spawning and rearing fall Chinook and chum salmon for any given water year.  In providing the best available habitat, we hope to maximize the numbers of naturally producing populations of salmon.

These objectives are addressed in work plans for other cooperators.

OBJECTIVE 5 - Reports

Report findings to BPA on a quarterly and annual basis to document progress toward accomplishing project objectives. Quarterly reports will summarize findings occurring during that work period while annual report will summarize findings to date for that project.

Work Elements: P, Q.