Study Plan & Objectives
The Middle Fork John Day IMW was established to help meet the need for effectiveness monitoring of restoration programs and projects as outlined in the Oregon Plan for Salmon and Watersheds. This project will be linked with the work undertaken by sister states Washington and Idaho through the Collaborative System-wide Monitoring and Evaluation Project (CSMEP), Integrated Status and Effectiveness Monitoring Project (ISEMP), and Pacific Northwest Aquatic Monitoring Partnership (PNAMP).
Oregon presently has a number of Intensively Monitored Watershed programs and studies throughout the state. Most of these are located in western Oregon with a particular focus on coastal systems and species. A clear need exists in other eco-regions of Oregon where listed salmonids are located to complement the restoration and monitoring efforts for these species and for overall watershed health.
The Middle Fork John Day represents an opportunity for a variety of collaborators from both the public and private sectors already working to implement restoration and monitoring programs. In addition to past projects, the Middle Fork IMW area also contains plans and programs for significant restoration actions over the next several years. Collaborative funding is presently provided from the Bonneville Power Administration, Bureau of Reclamation, Oregon Watershed Enhancement Board, National Marine Fisheries Service, The Nature Conservancy, U.S. Forest Service, and others for both restoration and monitoring. These factors all build a foundation for a high likelihood of success.
The following criteria had a significant bearing on the selection of the Middle Fork John Day IMW and assisted in the formulation of the monitoring tasks found within this proposal:
Limiting Factors to be addressed
Spring Chinook salmon and summer steelhead are the predominate salmonids inhabiting the watershed, although bull trout Salvelinus confluentus are also found in tributaries with limited seasonal use of mainstem habitats by fluvial adults. Both steelhead and bull trout are listed as threatened species. Spring Chinook salmon are not currently listed. Steelhead are the most widely distributed salmonid species, occupying most tributaries and mainstem habitats. Chinook distribution is slightly more confined to mainstem habitats and larger tributaries, although juvenile Chinook often migrate into cool-water tributaries during warm summer periods. Bull trout distribution is limited by their temperature tolerance. Chinook and steelhead have similar temperature tolerances, but recent evidence from the John Day River basin suggests that steelhead parr may have a greater tolerance for warmer temperatures. Given the similar distribution but slightly lower tolerance for warm temperatures, Chinook parr would be a suitable complementary species to monitor along with listed steelhead.
Water quality in the Middle Fork John Day Subbasin generally exhibits satisfactory chemical, physical, and biological quality as compared to Oregon Department of Environmental Quality (DEQ) water quality standards. But Middle Fork mainstem channel has elevated summer temperatures, along with most of its major tributaries.
Temperature has been identified as a limiting factor for salmonid production in the watershed. The recent development of stock-recruitment curves has suggested that freshwater rearing habitat is limiting Chinook production in the John Day River basin. Further, juvenile surveys have indicated that much of the Middle Fork habitat is vacated during warm summer months and much of the watershed is listed as impaired by summer temperatures. Sediment has also been identified as a factor limiting salmonid production and survival. The limiting factors form a basis for the type and extent of monitoring planned in this IMW.
Steelhead and Chinook Monitoring
Objective 1: Estimate spawner escapement of summer steelhead and spring Chinook.
Spawner escapement for Chinook is measured with a complete census of spawning grounds by counting redds and carcasses. This effort is funded through other sources. Currently there is not a complementary redd count for steelhead in the watershed nor is a complete census count practical. Therefore it is proposed to conduct steelhead redd surveys using a spatially explicit approach by implementing the EMAP sampling framework, a statistically based and spatially explicit sampling design, to quantify the status and trends in the abundance of steelhead redds. This approach is currently implemented in the John Day River basin at the entire basin scale. We propose to implement a complementary effort at the Middle Fork Watershed scale. The South Fork watershed will be similarly monitored as a reference basin for steelhead. Some as yet undetermined number of spatially balanced, randomly selected reaches will be sampled repeatedly and steelhead redds quantified in each watershed annually. These surveys will provide the added benefit of better defining the distribution of steelhead spawning habitat in the Middle Fork watershed.
Objective 2: Estimate freshwater productivity (smolts/redd) of spring Chinook and summer steelhead populations.
For the measurement of recovery of listed fish species, NMFS is primarily interested in estimates of fish production or survival which relate directly to their recovery. Estimating smolts/redd is the most direct approach we currently have to estimate production and current efforts for monitoring Chinook allow for estimates of their freshwater production (smolts/redd) within the Middle Fork watershed. Spring Chinook redds are counted by conducting a repeated, census survey of all utilized spawning habitat and this effort is currently funded through other grants. Objective 1 will enumerate steelhead redds. These surveys will provide us an estimate of the number of redds and spawners within the Middle Fork watershed. A rotary screw trap (RST) is also currently operated using BPA funds and is located near Ritter at the proposed downstream extent of our IMW. This trapping effort provides a measure of the abundance of Chinook and steelhead smolts migrating out of the watershed. A complementary trap is operated on the South Fork John Day River and can act as a reference site. By combining redd counts and smolt abundance of each species, we can provide annual estimates of freshwater productivity (smolts/redd).
Objective 3: Estimate parr-to-smolt survival of spring Chinook and summer steelhead.
While snorkel surveys of habitat utilized by rearing parr will provide a measure of distribution of parr, it will not provide any measure of the quality of the habitat for parr rearing. Parr to smolt survival will be estimated by PIT tagging parr in various habitat areas and detecting tagged fish in our RST as they migrate out of the basin as smolts. This tagging effort would be coordinated with distribution surveys. A representative number of parr in several tributaries of varying temperatures would be PIT tagged and scale samples would be taken to age fish. Survival to emigration could then be compared among tributaries to determine if survival rates differ among tributaries. Tributaries would be selected to provide a wide range of rearing temperatures. An additional benefit of this effort would be to provide a basin-wide parr-to-smolt survival rate.
Objective 4: Delineate seasonal parr rearing habitat.
Regional managers have requested a comprehensive study of the summer distribution of Chinook parr in the watershed. We currently have information indicating that parr vacate warmer reaches of mainstem habitats and enter cooler tributaries. This suggests that temperature is limiting smolt production in the basin. Using snorkel surveys, we propose to conduct a comprehensive presence/absence census of all habitat used by parr during summer months (July, August). This information will enable us to estimate the amount of habitat not currently used by rearing juveniles during the critical summer period. This in turn will allow a measure of the potential for increasing freshwater production of salmonids and could be used to direct the placement of water temperature recorders.
Identify potential tributaries for parr rearing based on current knowledge.
Conduct presence/absence snorkel surveys.
Update GIS coverage using collected data.
Objective 5: Provide additional measures of the factors limiting freshwater production.
Temperature has been identified as a limiting factor for salmonid production in the watershed but we still do not have a comprehensive view of temperature in the basin as it relates to salmonids. Past fish surveys have shown that many locations within the proposed IMW are not utilized for juvenile salmonid rearing during warm summer months. Coordinated with the above parr surveys, water temperature loggers will be placed at the downstream extent of observed parr distribution in the mainstem Middle Fork and its tributaries. Temperature loggers will be deployed and monitored throughout the parr rearing seasons. Data from loggers will be incorporated into a database including a GIS coverage.
Identify locations for deploying and deploy loggers.
Incorporate data into database and GIS layer
Coordination
Coordination is one of the most important tasks during implementation of the project. The IMW coordinator is the key contact and is responsible for data management and administrative duties.
Project outcome
To successfully establish baseline steelhead and Chinook population data requires at least one complete life cycle or approximately 5 years. Monitoring of Chinook redds and trapping of emigrating Chinook and steelhead smolts is currently ongoing. Once parr are tagged during the summer of 2008, it will take two additional years before all steelhead smolts will emigrate from the basin and therefore provide data for freshwater survival. Production, measured as smolts/redd, will take two years for Chinook and three years for steelhead. Our ability to measure and demonstrate positive affects relating to restoration activities will depend on the magnitude of the restoration activities and their resultant impact on fish populations. It is expected that trends in production and survival data will have a greater probability of detecting positive outcomes compared to simple status during a given year.
The desired outcome will be a detectable change in the productivity or survival of the monitored species when compared to the reference population. Productivity estimates for Chinook will be available during the initial year. Similar estimates for steelhead will take three years from the first redd surveys for this species. Parr-to-smolt survival estimates will be available 1-2 years after project initiation. Data on the distribution of parr will be available during the first year after the initial sampling season.
Oregon presently has a number of Intensively Monitored Watershed programs and studies throughout the state. Most of these are located in western Oregon with a particular focus on coastal systems and species. A clear need exists in other eco-regions of Oregon where listed salmonids are located to complement the restoration and monitoring efforts for these species and for overall watershed health.
The Middle Fork John Day represents an opportunity for a variety of collaborators from both the public and private sectors already working to implement restoration and monitoring programs. In addition to past projects, the Middle Fork IMW area also contains plans and programs for significant restoration actions over the next several years. Collaborative funding is presently provided from the Bonneville Power Administration, Bureau of Reclamation, Oregon Watershed Enhancement Board, National Marine Fisheries Service, The Nature Conservancy, U.S. Forest Service, and others for both restoration and monitoring. These factors all build a foundation for a high likelihood of success.
The following criteria had a significant bearing on the selection of the Middle Fork John Day IMW and assisted in the formulation of the monitoring tasks found within this proposal:
- Confirming population limiting factors and determining the extent to which restoration actions treat them.
- Aligning the frequency and distribution of restoration actions with likely population level responses.
- Establishment of a robust and statistically rigorous design linking restoration actions and the collection of monitoring data with appropriate analyses.
- The specific roles and capabilities of the partner organizations that could be linked to outcomes to ensure successful implementation.
Limiting Factors to be addressed
Spring Chinook salmon and summer steelhead are the predominate salmonids inhabiting the watershed, although bull trout Salvelinus confluentus are also found in tributaries with limited seasonal use of mainstem habitats by fluvial adults. Both steelhead and bull trout are listed as threatened species. Spring Chinook salmon are not currently listed. Steelhead are the most widely distributed salmonid species, occupying most tributaries and mainstem habitats. Chinook distribution is slightly more confined to mainstem habitats and larger tributaries, although juvenile Chinook often migrate into cool-water tributaries during warm summer periods. Bull trout distribution is limited by their temperature tolerance. Chinook and steelhead have similar temperature tolerances, but recent evidence from the John Day River basin suggests that steelhead parr may have a greater tolerance for warmer temperatures. Given the similar distribution but slightly lower tolerance for warm temperatures, Chinook parr would be a suitable complementary species to monitor along with listed steelhead.
Water quality in the Middle Fork John Day Subbasin generally exhibits satisfactory chemical, physical, and biological quality as compared to Oregon Department of Environmental Quality (DEQ) water quality standards. But Middle Fork mainstem channel has elevated summer temperatures, along with most of its major tributaries.
Temperature has been identified as a limiting factor for salmonid production in the watershed. The recent development of stock-recruitment curves has suggested that freshwater rearing habitat is limiting Chinook production in the John Day River basin. Further, juvenile surveys have indicated that much of the Middle Fork habitat is vacated during warm summer months and much of the watershed is listed as impaired by summer temperatures. Sediment has also been identified as a factor limiting salmonid production and survival. The limiting factors form a basis for the type and extent of monitoring planned in this IMW.
Steelhead and Chinook Monitoring
Objective 1: Estimate spawner escapement of summer steelhead and spring Chinook.
Spawner escapement for Chinook is measured with a complete census of spawning grounds by counting redds and carcasses. This effort is funded through other sources. Currently there is not a complementary redd count for steelhead in the watershed nor is a complete census count practical. Therefore it is proposed to conduct steelhead redd surveys using a spatially explicit approach by implementing the EMAP sampling framework, a statistically based and spatially explicit sampling design, to quantify the status and trends in the abundance of steelhead redds. This approach is currently implemented in the John Day River basin at the entire basin scale. We propose to implement a complementary effort at the Middle Fork Watershed scale. The South Fork watershed will be similarly monitored as a reference basin for steelhead. Some as yet undetermined number of spatially balanced, randomly selected reaches will be sampled repeatedly and steelhead redds quantified in each watershed annually. These surveys will provide the added benefit of better defining the distribution of steelhead spawning habitat in the Middle Fork watershed.
- Using EMAP approach, delineate summer steelhead habitat and draw representative sample for survey site selection.
- Census spring Chinook redds in watershed (funded by other sources).
- Survey randomly drawn 2-km reaches for steelhead in MFJD watershed.
- Survey randomly drawn 2-km reaches for steelhead in SFJD watershed.
- Develop GIS data base for redd distributions.
- Provide redd and spawner abundance estimates.
Objective 2: Estimate freshwater productivity (smolts/redd) of spring Chinook and summer steelhead populations.
For the measurement of recovery of listed fish species, NMFS is primarily interested in estimates of fish production or survival which relate directly to their recovery. Estimating smolts/redd is the most direct approach we currently have to estimate production and current efforts for monitoring Chinook allow for estimates of their freshwater production (smolts/redd) within the Middle Fork watershed. Spring Chinook redds are counted by conducting a repeated, census survey of all utilized spawning habitat and this effort is currently funded through other grants. Objective 1 will enumerate steelhead redds. These surveys will provide us an estimate of the number of redds and spawners within the Middle Fork watershed. A rotary screw trap (RST) is also currently operated using BPA funds and is located near Ritter at the proposed downstream extent of our IMW. This trapping effort provides a measure of the abundance of Chinook and steelhead smolts migrating out of the watershed. A complementary trap is operated on the South Fork John Day River and can act as a reference site. By combining redd counts and smolt abundance of each species, we can provide annual estimates of freshwater productivity (smolts/redd).
- Operate rotary screw trap (RST) on MFJD to estimate abundance of salmonid smolts emigrating from IMW (funded by BPA).
- Operate rotary screw trap (RST) on SFJD to estimate abundance of salmonid smolts emigrating from IMW (funded by BPA).
- Use redd counts and smolt abundances to estimate smolts/redd for each species.
Objective 3: Estimate parr-to-smolt survival of spring Chinook and summer steelhead.
While snorkel surveys of habitat utilized by rearing parr will provide a measure of distribution of parr, it will not provide any measure of the quality of the habitat for parr rearing. Parr to smolt survival will be estimated by PIT tagging parr in various habitat areas and detecting tagged fish in our RST as they migrate out of the basin as smolts. This tagging effort would be coordinated with distribution surveys. A representative number of parr in several tributaries of varying temperatures would be PIT tagged and scale samples would be taken to age fish. Survival to emigration could then be compared among tributaries to determine if survival rates differ among tributaries. Tributaries would be selected to provide a wide range of rearing temperatures. An additional benefit of this effort would be to provide a basin-wide parr-to-smolt survival rate.
- PIT tag representative sample of steelhead and Chinook parr.
- Monitor temperatures of tributaries where parr are collected.
- Trap and record PIT tagged smolts in RST.
Objective 4: Delineate seasonal parr rearing habitat.
Regional managers have requested a comprehensive study of the summer distribution of Chinook parr in the watershed. We currently have information indicating that parr vacate warmer reaches of mainstem habitats and enter cooler tributaries. This suggests that temperature is limiting smolt production in the basin. Using snorkel surveys, we propose to conduct a comprehensive presence/absence census of all habitat used by parr during summer months (July, August). This information will enable us to estimate the amount of habitat not currently used by rearing juveniles during the critical summer period. This in turn will allow a measure of the potential for increasing freshwater production of salmonids and could be used to direct the placement of water temperature recorders.
Identify potential tributaries for parr rearing based on current knowledge.
Conduct presence/absence snorkel surveys.
Update GIS coverage using collected data.
Objective 5: Provide additional measures of the factors limiting freshwater production.
Temperature has been identified as a limiting factor for salmonid production in the watershed but we still do not have a comprehensive view of temperature in the basin as it relates to salmonids. Past fish surveys have shown that many locations within the proposed IMW are not utilized for juvenile salmonid rearing during warm summer months. Coordinated with the above parr surveys, water temperature loggers will be placed at the downstream extent of observed parr distribution in the mainstem Middle Fork and its tributaries. Temperature loggers will be deployed and monitored throughout the parr rearing seasons. Data from loggers will be incorporated into a database including a GIS coverage.
Identify locations for deploying and deploy loggers.
Incorporate data into database and GIS layer
Coordination
Coordination is one of the most important tasks during implementation of the project. The IMW coordinator is the key contact and is responsible for data management and administrative duties.
Project outcome
To successfully establish baseline steelhead and Chinook population data requires at least one complete life cycle or approximately 5 years. Monitoring of Chinook redds and trapping of emigrating Chinook and steelhead smolts is currently ongoing. Once parr are tagged during the summer of 2008, it will take two additional years before all steelhead smolts will emigrate from the basin and therefore provide data for freshwater survival. Production, measured as smolts/redd, will take two years for Chinook and three years for steelhead. Our ability to measure and demonstrate positive affects relating to restoration activities will depend on the magnitude of the restoration activities and their resultant impact on fish populations. It is expected that trends in production and survival data will have a greater probability of detecting positive outcomes compared to simple status during a given year.
The desired outcome will be a detectable change in the productivity or survival of the monitored species when compared to the reference population. Productivity estimates for Chinook will be available during the initial year. Similar estimates for steelhead will take three years from the first redd surveys for this species. Parr-to-smolt survival estimates will be available 1-2 years after project initiation. Data on the distribution of parr will be available during the first year after the initial sampling season.
