Columbia Basin Fish and Wildlife Program Columbia Basin Fish and Wildlife Program
SOW Report
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Escapement and Productivity of Spring Chinook and Steelhead
Province Subbasin %
Columbia Plateau John Day 100.00%
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A coordinated approach to the monitoring and evaluation of status and trends in anadromous and resident salmonid populations and their habitats is needed to support restoration efforts in the Columbia River basin. Currently in the John Day River subbasin, independent research projects and some monitoring activities are conducted by various state and federal agencies, tribes, and to some extent by watershed councils or landowners, but there is no overall framework for coordination of efforts or for interpretation and synthesis of results. This project extends the structure and methods employed by the Oregon Plan for Salmon and Watersheds Monitoring Program to the John Day River subbasin of the Columbia Plateau Province. This approach, successfully implemented in Oregon's coastal watersheds, applies a rigorous, Tier-2 sampling design to answer key monitoring questions, provides integration of sampling efforts, and has greatly improved coordination among state, federal, and tribal governments, along with local watershed groups. This project is high priority based on the high level of emphasis the NWPPC Fish and Wildlife Program, Subbasin Summaries, NMFS, and the Oregon Plan for Salmon and Watersheds have placed on monitoring and evaluation to provide the real-time data to guide restoration and adaptive management in the region.

The John Day River Basin is a pilot study subbasin and information derived from this project will quantify the current status and future trends in fish populations in this important basin.  Further, NOAA Fisheries has specifically identified the Upper John Day as a priority subbasin to receive immediate attention for habitat and species recovery for the Mid-Columbia steelhead distinct population segment (DPS).  The John Day River, together with its anadromous fish populations is also an important reference subbasin for comparisons to other anadromous stocks in more highly impacted subbasins of the Columbia River (Schaller et al. 1999, 2007). Mid-Columbia spring Chinook are not a federally listed DPS. However, the population(s) in the John Day River are not supplemented with hatchery releases, have a long history of monitoring, and are relied upon as a reference for comparisons to listed stocks.

There is near universal support in the scientific and regulatory community regarding the critical role of monitoring to assure accountability, adaptive learning, and the credibility of recovery efforts for native salmonids and the watersheds that support them.  When the Oregon Plan for Salmon and Watersheds was developed for coastal watersheds, monitoring was one of the four primary elements of the Plan. The conceptual framework and the programs that support the Oregon Plan Monitoring Program were critically reviewed and strongly supported by State, Federal, Tribal, and Non-Governmental experts, along with the State of Oregon’s Independent Multidisciplinary Scientific Team prior to implementation.  The Plan received high marks for the comprehensive, integrated, and coordinated approach the State has taken to monitoring the effectiveness of the Oregon Plan.

The program described in this contract is consistent with and supports the monitoring needs specified by the amended NWPPC’s Columbia Basin Fish and Wildlife Program and Subbasin Summaries, NMFS 2000/04 FCRPS Biological Opinion(s), and the Oregon Plan for Salmon and Watersheds.  The Fish and Wildlife Program (Chapter 9) calls for monitoring and evaluation of biological and environmental conditions at the scale of provinces and subbasins.  The John Day subbasin plan calls for a framework for the coordination and integration of monitoring efforts, increased monitoring of the status trends in anadromous and resident fish populations and habitats, and a process to prioritize how and where restoration and protection efforts are focused.  This monitoring program will provide a framework for improved coordination and integration of monitoring efforts.  ODFW will monitor and evaluate the status and trends in fish populations (abundance and distribution) and habitat (quantity and quality) at the subbasin and population scales.  The purpose of the monitoring and evaluation program is to assure that the effects of actions taken under subbasin plans are measured, that these measurements are analyzed so that we have better knowledge of the effects of the action, and that this improved knowledge is used to choose future actions. ODFW will implement a watershed prioritization process to delineate priority watersheds for increased habitat protection and/or accelerated habitat restoration. The probabilistic (GRTS) sampling described in this proposal is strongly supported by recent ISRP reviews.

The proportion of hatchery-origin stray (PHOS) steelhead spawners in the John Day River basin is of increasing concern for regional managers (Carmichael & Taylor 2009).  The proportion of out-of-basin strays in a mixed spawning aggregation with natural-origin fish has been shown to be detrimental to population productivity in steelhead populations in Oregon (Chilcote 2003). Recent observations on spawning grounds have indicated that up to 30-50% of spawners in some tributaries of the John Day are composed of hatchery origin strays. Similarly, information from an in-stream PIT tag antenna array on the John Day River indicates similar proportions of hatchery-origin steelhead entering the subbasin. This data suggests a considerable proportion of some John Day populations may be composed of hatchery-origin adults potentially reducing productivity through genetic introgression and/or reproductive interference.  An objective of this study is therefore, to collect genetic data that allows an objective determination of the population(s) structure of steelhead within the basin together with a measure of introgression from out-of-basin strays.  After consultation with NOAA geneticists, we will sample representative age-0 O. mykiss from randomly selected reaches in each of the five currently identified population segments. Juveniles will be collected by electrofishing from a minimum of four cohorts and by collecting non-lethal fin tissue for DNA analysis.  Populations will be characterized using a suite of nuclear DNA markers, including microsatellite loci (variable-number simple-sequence repeats) assayed via restriction enzyme analysis.  Endemic stock structure, based on this genetic information, will be used to guide the development of conservation measures.

Another goal of this project is to further develop and implement a standard set of fish habitat monitoring methods in the John Day River subbasin.  We will cooperate with the Integrated Status and Effectiveness Monitoring (ISEMP) group to refine and implement these developing protocols. This fish habitat monitoring has been developed to capture habitat features that drive fish population biology and the 26 watersheds chosen throughout the Columbia River basin maximize the contrast in current habitat conditions and also represent a temporal gradient of expected change in condition through planned habitat actions.  The data from this project will be used to evaluate the quantity and quality of tributary fish habitat available to salmonids across the Columbia River basin.  When combined with parallel fish monitoring metrics from related projects, these data will also be used assess the impact of habitat management actions on fish population processes. The habitat status and trends monitoring proposed in the Columbia Habitat Monitoring Program (CHaMP) is a Columbia River basin wide habitat status and trends monitoring program built around a single habitat monitoring protocol (a protocol being a set of methods and associated metrics), with a program-wide approach to data collection and management.  This program will result in systematic habitat status and trends information that will be used to assess basin-wide habitat condition and correlated with biological response indicators to evaluate habitat management strategies.


Carmichael, R.W. and B.J. Taylor. 2009. Conservation and Recovery Plan for Oregon Steelhead Populations in the Middle Columbia River Steelhead Distinct Population Segment.

Chilcote, M.W. 2003. Relationship between natural productivity and the frequency of wild fish in mixed spawning populations of wild and hatchery steelhead (Oncorhynchus mykiss). Canadian Journal of Fisheries and Aquatic Sciences. 60:1057-1067.
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* Expenditures data includes accruals and are based on data through 31-Oct-2021.

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Viewing of Work Statement Elements

Deliverable Title WSE Sort Letter, Number, Title Start End Complete
NEPA/ESA Compliance B: 165. Provide ESA regulatory clearances to BPA 02/17/2012 10/14/2011
Steelhead Spawner Surveys C: 157. Steelhead spawner surveys 07/31/2012 07/01/2012
Fish Metrics Estimates D: 162. Estimate fish metrics 09/30/2012 09/25/2012
AFS Presentation E: 161. Professional presentations 05/31/2012 05/31/2012
Genetic Samples F: 157. Steelhead population genetics 09/30/2012 09/25/2012
Genetic characterization G: 162. Estimate genetic composition of steelhead populations 09/30/2012 09/25/2012
Contract documents for new performance period H: 119. SOW and Budget for FY 2013 07/16/2012
Final Annual Report I: 132. Annual technical report 02/29/2012 12/29/2011
Juvenile density J: 157. Juvenile steelhead density metrics 09/30/2012 09/25/2012
CHaMP habitat data from 40 sites in the John Day Subbasin K: 157. Steelhead habitat metrics using CHaMP habitat protocol 09/29/2012 09/25/2012
Metric Generation and End of Season Quality Assurance Review L: 159. Deliver habitat data to CHaMP Data System 09/30/2012 09/25/2012
Contribute to and review CHaMP Annual Lessons Learned/Synthesis Report M: 122. Contribute to and review CHaMP Annual Synthesis Report 09/30/2012 12/02/2011

Viewing of Implementation Metrics
Viewing of Environmental Metrics Customize

Primary Focal Species Work Statement Elements
Steelhead (O. mykiss) - Middle Columbia River DPS (Threatened)
  • 1 instance of WE 122 Provide Technical Review and Recommendation
  • 4 instances of WE 157 Collect/Generate/Validate Field and Lab Data
  • 1 instance of WE 159 Transfer/Consolidate Regionally Standardized Data
  • 1 instance of WE 161 Disseminate Raw/Summary Data and Results
  • 2 instances of WE 162 Analyze/Interpret Data

Sort WE ID WE Title NEPA NOAA USFWS NHPA Has Provisions Inadvertent Discovery Completed
A 185 Periodic Status Reports for BPA 10/01/2011
B 165 Provide ESA regulatory clearances to BPA 10/01/2011
C 157 Steelhead spawner surveys 11/29/2011
D 162 Estimate fish metrics 10/01/2011
E 161 Professional presentations 10/01/2011
F 157 Steelhead population genetics 04/16/2012
G 162 Estimate genetic composition of steelhead populations 10/01/2011
H 119 SOW and Budget for FY 2013 10/01/2011
I 132 Annual technical report 10/01/2011
J 157 Juvenile steelhead density metrics 04/16/2012
K 157 Steelhead habitat metrics using CHaMP habitat protocol 04/16/2012
L 159 Deliver habitat data to CHaMP Data System 10/01/2011
M 122 Contribute to and review CHaMP Annual Synthesis Report 10/01/2011