Salmonid Productivity, Status, and Trend Monitoring in the John Day River Basin
Statement of Work and Budget FY2016
BPA Project Number:  1998-016-00
Contract Number: 289767
Performance/Budget Period: 1 Feb. 2016 to 31 Jan. 2017

The John Day River subbasin supports some of the last remaining wild populations of spring Chinook salmon and summer steelhead in the Columbia River Basin.  These populations, however, remain depressed relative to historic levels.  In consideration of these two factors, NOAA Fisheries has specifically identified the John Day as a priority subbasin for habitat and species recovery in 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.  Mid-Columbia spring Chinook are not a federally listed DPS.  However, because the John Day River populations are not supplemented with hatchery releases and pass only three dams on the Columbia River, they are relied upon as a reference for comparisons to listed stocks and for assessing the effects of alternative future management actions on salmon stocks in the Columbia Basin.

Numerous habitat protection and rehabilitation projects to improve salmonid freshwater production and survival have been implemented in the basin.  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.  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.  

To meet data needs as reference stocks, assess the long-term effectiveness of habitat projects, and to differentiate freshwater and ocean survival, annual estimates of spawner escapement, age structure, smolt-to-adult ratios (SAR), and egg-to-smolt survival are needed.  Additional sampling and analyses to meet these goals include an estimate of smolt abundance and SAR rates.  Hence, this project focuses on estimating adult abundance (via a GRTS design for redd surveys), estimating juvenile abundance (at a subset of sites sampled for redds), estimating smolt abundance (via rotary screw traps), and estimating SAR through the PIT tagging of 8,000 smolts each year (4,000 Chinook and 4,000 steelhead).  Age sampling is conducted at each monitoring step so that productivity can be measured on a brood year basis.

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 to 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.

Data from this project has thus far been incorporated into both recovery plans and peer-reviewed scientific literature (see selected references below) describing the status and ecological aspects of John Day River salmonid populations.  During future years, we will continue these data applications, and also characterize the steelhead population structure in the John Day River basin using a suite of nuclear DNA markers, including microsatellite loci (variable-number simple-sequence repeats) assayed via restriction enzyme analysis.  Current stock structure will be used to guide conservation and management measures.  We will also continue to develop fish-habitat relationships for the John Day River basin using CHaMP data which will provide a vehicle for evaluating habitat limiting factors and restoration effects.

While these monitoring efforts will not specifically measure the effectiveness of any individual habitat project, they provide data for assessing the effectiveness of restoration projects at a sub-basin scale.  This work is coordinated with restoration efforts in the John Day River basin through periodic meetings (John Day Basin partnership).  Our efforts provide nearly all of the status and trend monitoring, and some of the effectiveness monitoring, for the RM&E projects.  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.  This project is a high priority based on the emphasis the NWPPC Fish and Wildlife Program, Subbasin Summaries, NOAA Fisheries, 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.

Selected References:

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.

Lindsay, R.B., and five co-authors. 1986. Study of wild spring chinook salmon in the John Day River System. Oregon Department of Fish and Wildlife, Portland, OR. Final Report to Bonneville Power Administration. Project No. 79-004-00.  https://efw.bpa.gov/Environment/EW/EWP/DOCS/REPORTS/HABITAT/H39796-1.pdf

Tattam, I.A., J.R. Ruzycki, P. B. Bayley, H. W. Li, and G. R. Giannico.  2013.  The Influence of Release Strategy and Migration History on Capture Rate of Oncorhynchus mykiss in a Rotary Screw Trap.  North American Journal of Fisheries Management 33:237–244.

Tattam, I.A., J.R. Ruzycki, H. W. Li, and G. R. Giannico.  2013.  Body size and growth rate influence emigration timing of Oncorhynchus mykiss.  Transactions of the American Fisheries Society 142:1406–1414.

Tattam, I.A., J.R. Ruzycki, J.L. McCormick, and R.W. Carmichael.  2015.  Length and condition of wild Chinook Salmon smolts influence age at maturity.  Transactions of the American Fisheries Society 144:1237–1248.