Salmonid Productivity, Status, and Trend Monitoring
in the John Day River Basin
Statement of Work and Budget FY2009

BPA Project Number:  1998-016-00
Performance/Budget Period: 1 Sep. 2009 to 30 Sep. 2010

INTRODUCTION

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 Plateau.  This project will focus on the Steelhead component of this need.  Currently, 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 SOW extends the structure and methods employed by the Oregon Plan for Salmon and Watersheds Monitoring Program (Nicholas, 1997a; 1997b; 1999) to the John Day subbasin of the Columbia Plateau. 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. Because the John Day subbasin populations of steelhead are part of the federally listed Mid-Columbia steelhead ESU status and trend monitoring needs to be integrated with ongoing projects in this subbasin. 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 sampling program described in this document fulfills critical monitoring needs for Council's Fish and Wildlife Program and help fulfill population and environmental monitoring requirements under the NMFS 2000 FCRPS Biological Opinion (Action 180).  The work under this statement of work will meet most of the BiOp requirements for Tier 1 and 2 monitoring throughout the John Day River subbasin.  Current population and environmental monitoring in the Province is based on a highly variable application of a combination of index surveys and periodic monitoring of some status and trend indicators.  For example, most adult steelhead monitoring is based on a small number of index sites relative to the number of streams steelhead use for spawning.  The index approach only allows us to draw inference about trends in adult abundance for the surveyed streams and provides little information on abundance (status) or distribution at the subbasin or plateau spatial scales.  This is due to the fact that index reaches are not randomly selected and represent an unknown proportion of the total population.  In addition, there are no systematic programs in place to collect information on the status, trends, and distribution of fish habitat/riparian conditions or juvenile salmonids.  

The ISRP, in their guidance on monitoring, strongly recommended that the region move away from index surveys and embrace probabilistic sampling for most population and habitat monitoring.  The ISRP stated "the Council's Fish and Wildlife Program calls for monitoring and evaluation of biological and environmental conditions at the scale of provinces and subbasins.  Tier 2-level monitoring is required to provide inductive inferences to entire provinces, subbasins, and many watersheds, because it is impossible to survey every square meter of every stream bottom, riparian zone, and uplands area in these large regions every month of every year for decades.  Many of the Columbia Basins' projects for "monitoring" fish and wildlife species (redds, spawners, juveniles, etc.) currently limit surveys to "index sites" selected by professional judgment in past years.  The objectives of these projects can only be met with Tier 2-level monitoring using probabilistic selection of survey sites with limited replication".  The sampling approach outlined in this study fulfills these requirements.

By implementing the program we will address many of the goals for Tier 1 monitoring, such as defining areas currently used by adult steelhead and spring chinook for holding and spawning habitats and summer rearing habitats for juvenile O. mykiss and spring chinook (adult/juvenile salmonid monitoring), determining range expansion or contraction of summer rearing and spawning populations of O. mykiss and spring chinook (adult/juvenile salmonid monitoring), and identifying associations between salmonid presence (adult/juvenile monitoring) and habitat attributes (habitat monitoring).  The BiOp describes Tier 2 goals as defining population growth rates (adult monitoring), detecting changes in those growth rates or relative abundance in a reasonable time (adult/juvenile monitoring), estimating juvenile abundance and survival rates (juvenile/smolt monitoring), and identifying stage-specific survival (adult-to-smolt, smolt-to-adult) and environmental attributes (habitat monitoring). This project provides much needed Tier-2 monitoring for the two anadromous focal species in the John Day basin.

Integration with on-going monitoring is accomplished in the following manner.  In annual reporting, we use data from on-going projects to develop a more complete picture of status and trends in resources and life stage-specific survival.  This project will be the vehicle to pull all related fish population and habitat monitoring data together into a synthetic analysis of resources at the provincial and subbasin scales.  For example, we use data from ongoing smolt and adult monitoring to calibrate surveys and to track trends in survival and productivity at life-stages not targeted under the EMAP program.  More detailed studies at finer scales will inform the EMAP program and vice-versa.  To accomplish these tasks, we work with co-managers and other interested publics to establish a monitoring oversight committee for the region that is tasked with coordinating and integrating on-going efforts into a comprehensive reporting system of regional resources.

This project provides information as directed under two measures of the Columbia Basin Fish and Wildlife Program.  Measure 4.3C specifies that key indicator naturally spawning populations should be monitored to provide detailed stock status information.  In addition, measure 7.1C identifies the need for collection of population status, life history, and other data on wild and naturally spawning populations.  This project was developed in direct response to the recommendations and needs of regional modeling efforts, the Independent Scientific Review Panel (ISRP), the Fish and Wildlife Program, and the Columbia Basin Fish and Wildlife Authority Multi-Year Implementation Plan.


APPROACH:  Implement the EMAP sampling framework, a statistically based and spatially explicit sampling design, to quantify the status and trends in the abundance of steelhead redds.  Based on the strong relationship between cumulative redd counts and adult steelhead abundance, cumulative redd counts is used to index the abundance and distribution of adult steelhead at the provincial and subbasin scales (Susac and Jacobs, 1999; Jacobs et al., 2000; Jacobs et al., 2001).  Fifty spatially balanced, randomly selected reaches are sampled and steelhead redds are quantified in the John Day subbasin from about March 1 through June 15 annually. Dam counts and index surveys tell only part of the story and include unknown biases.  Adding a statistically-based sample program gives unbiased estimates of abundance in addition to data on distribution and habitat use and life history patterns (timing of spawning, spatial distributions).  This information cannot be derived from dam counts or index surveys.

Sampling domains and site selection:  ODFW in cooperation with co-managers and other interested parties refine the sampling universe for steelhead redd surveys based on current ODFW distribution maps. The sampling domain is defined for the upper and lower ends of distributions based on available data and best professional judgment on the potential distribution of spawners.  The delineation of the sampling domain is currently liberal in its' extent at the outset to encompass all potential habitat.  To balance the needs of status (more random sites) and trend (more repeat sites), we implement a rotating panel design based on recommendations from the EPA EMAP Design Group.  The 50 sites drawn on an annual basis are assigned to the rotating panel design as follows:

3 panels with different repeat intervals
17 of the sites are sampled every year
16 sites are allocated to a 4 year rotating panel (sites visited once every 4 years on a staggered basis)
17 sites are new sites each year

With this sampling strategy, 50 sites were drawn the first year and 33 new sites are drawn in subsequent years because 17 of the originally drawn sites are repeated each year.  Once annual sample sites are drawn, the site is assigned to the river reach file based on site coordinates.  From these point coverage's, ODFW develops landowner contacts based on county plat maps.  Based on ownership maps, project personnel work with ODFW District Biologists and Co-Managers to obtain permission from landowners and set up sites.  A Geographic Information System (GIS) incorporating a 1:100,000 digital stream network is used to insure an unbiased and spatially balanced selection of sample sites across each subbasin.  The GIS site selection process provides the geographic coordinates (i.e. latitude and longitude) of each of the candidate sites.  We then produce topographic maps showing the location of each sample point.  Field crews use a handheld Geographic Positioning System to find the approximate location of the EMAP selected sample point, and then establish 2 km long survey reaches that encompass the sample point.  Site reconnaissance is conducted in the fall in preparation for spawning surveys the following spring.  Site reconnaissance involves obtaining landowner permission, verifying the presence of suitable habitat (e.g., presence of spawning gravel, barriers to upstream migration, gradient, etc.), marking the upper and lower boundaries of the survey with spawner survey signs, take Universal Transverse Mercator (UTM) coordinates of the upper and lower boundaries, and attempting to define upper and lower boundaries by distinctive landmarks.

Adult Steelhead Redd Surveys:  Adult steelhead redd surveys are conducted from March 1 - June 15 annually based on standard ODFW methods for conducting steelhead redd surveys (Susac and Jacobs, 1999; Jacobs et al., 2000; Jacobs et al., 2001).  Fifty sites arebe selected and visited every 2-3 weeks throughout the season to quantify the cumulative redd count at each site. Surveyors sample upstream from the downstream end of each survey reach.  Each surveyor counts live fish and determines the fin-mark status of all live fish through observations.  All redds are counted and flagged.  Data are recorded on the spawning survey form, redd longevity form, and spawning location description form.  Survey crews review survey forms daily and deliver hard copies bi-weekly to the crew chief.  Crew chiefs conduct weekly site visits with each crew.  Data entry is conducted as time allows throughout the survey season and is completed within one month of the end of fieldwork.  The population status is indexed through cumulative redd counts.  Expected precision is ±40% at the subbasin scale.  Hatchery: wild ratios are estimated by observing the occurrence of adipose fin-clipped and unmarked live fish on spawning grounds.

To quantify observer error we implement the following procedures.  Each site is visited every two weeks with the surveyors swapping sample reaches every survey.  The surveyor records the number of flagged redds, new redds, and redds missed during the previous survey.  Missed redds are distinguished from new redds by the amount of periphytic growth in the redd pocket.  New redds are devoid of periphyton whereas older redds become obscured by periphytic growth.  The independent estimate of marked versus unmarked redds from survey to survey provides an estimate of the error associated with identifying steelhead redds.  To validate whether cumulative redd counts are a reliable indicator of populations status, we will begin exploring where we can develop the data to allow the conversion of redd counts to population estimates.  The necessary data would include the sex ratio of returning adults and redd:female ratios. This validation effort will need to be conducted outside of the John Day subbasin so it can be calibrated with permanent weir counts.

Where we have on-going index surveys, these surveys will continue through a transition period from index surveys to probabilistic sampling.  We are developing a dataset that covers the range of abundance seen under the historic index surveys to examine the relationship between the two.  From this analysis we should be able to develop a strong relationship that will allow us to index the historic surveys to the probabilistic surveys.  This will take an unknown length of time but will probably be on the order of 5-10 years.



LITERATURE CITED
Bisson. P.A., J.A. Nielsen, R.A. Palmason, and E.L. Grove.  1982.  A system of naming
habitat types in small streams, with examples of habitat utilization by salmonids during low stream flow.  Pages 62-73 in: N.B. Armantrout, ed. Acquisition and utilization of Aquatic Habitat Inventory Information.  Western Division, American Fisheries Society, Portland OR.

Chilcote, M.W. 2001. Conservation assessment of steelhead populations in Oregon. Oregon Department of Fish and Wildlife, Portland, OR.

Cupp, C.E.  1989.  Stream corridor classification for forested lands of Washington.  Hosey and Assoc.  Bellevue, WA  46 p.

Dambacher, J.M. and K.K. Jones.  1997.  Stream habitat of juvenile bull trout populations in Oregon and benchmarks for habitat quality.  Pages 353-360 in Mackay, W. C., Brewin, M. K., and M. Monita, editors.  Friends of the bull trout conference proceedings.  Bull Trout Task Force (Alberta), c/o Trout Unlimited Canada, Calgary.

Dempson, J.B., and D.E. Stansbury. 1991. Using partial counting fences and a two-sample stratified design for mark-recapture estimation of an Atlantic salmon population. North American Journal of Fisheries Management. 11:27-37.

Everest, F.H., R.L. Beschta, J.C. Scrivener, K.V. Koski, J.R. Sedell, and C.J. Cederholm. 1987. Fine sediment and salmonid production: A paradox. Pages 98-142 In: E.O. Salo and T.E. Cundy eds., Streamside Management: Forestry and Fishery Interactions. Contribution No. 57. Institute of Forest Resources, University of Washington, Seattle, Washington.

Firman, J.C., and S.E. Jacobs.  2001.  A survey design for integrated monitoring of salmonids.  First Int. Symp. On GIS in Fishery Science.

Frissell, C.A., W.J. Liss, C.E. Warren, and M.D. Hurley.  1986.  A hierarchical framework for stream habitat classification: viewing streams in a watershed context.  Environ. Manage. 10: 199-214.

Grant, G.E. 1988. Morphology of high gradient streams at different spatial scales, Western Cascades, Oregon. Pages 1-12 in: Shizouka Symposium on Geomorphic Change and the Control of Sedimentary Load in Devastated Streams, Oct. 13-14, 1988. Shizouka University, Shizouka, Japan.