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 both microsatellite loci (variable-number simple-sequence repeats) and non-coding single nucleotide polymorphisms (SNPs, or base substitutions) 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.


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.

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.

Also, beginning in FY2011, Work Element K 157 was amended to implement a new fish-centric habitat protocol, described below, and  work elements L159 and M132 were added to support this implementation.  These work elements are  in support of a BiOp Fast track II project.  

In support of habitat restoration, rehabilitation and conservation action performance assessments and adaptive management requirements of the 2008 Federal Columbia River Power System Biological Opinion (FCRPS BiOp), the Bonneville Power Administration is working with NOAA and other regional fish management agencies to monitor status and trends of fish habitat for each major population group (MPG) in the Pacific Northwest identified through the Endangered Species Act (ESA).   Status monitoring provides information on the quantity and quality of current habitat and thus maximizes spatial coverage with a given number of sample sites.  Trend monitoring is used to detect changes in habitat through time and thus requires repeat samples at given sites.  Minimizing sampling and measurement error is crucial in order to differentiate this variability from natural variability though time and space.  In order to compare information across multiple MPGs, BPA is adopting a standardized fish habitat monitoring protocol, the Columbia Habitat Monitoring Program (CHaMP) for the Columbia River Basin monitoring programs.  

CHaMP is a Columbia River basin-wide habitat status and trends monitoring program built around a single habitat monitoring protocol with a program-wide approach to data collection and management which meets FCRPS Action Agency (2010) programmatic prescriptions for habitat monitoring.  CHaMP was developed by the Integrated Status and Effectiveness Monitoring Program (ISEMP) to capture habitat features that drive fish population biology and 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.  CHaMP is integrated with ongoing Pacific Northwest Aquatic Monitoring Program (PNAMP) and Recovery Planning efforts, as well as the collaborative process across Columbia Basin fish management agencies and tribes and other state and federal agencies that are monitoring anadromous salmonids and/or their habitat.  

The CHaMP is being proposed by the ISEMP and collaborating agencies  to help BPA meet the requirements of the 2008 FCRPS BiOp and RPA 56.3.  This program will provide information on the status/trends in habitat conditions, and will support habitat restoration, rehabilitation and conservation actions, performance assessments, and the adaptive management requirements of the 2008 FCRPS BiOp.  In addition, the CHaMP meets RPA 56.3, RPA 57, and RPA 3 by characterizing stream and fish responses to watershed restoration and/or management actions in at least one population within each steelhead and Chinook MPG which have, or will have, fish in-fish out monitoring (identified in RPA 50.6).  The watersheds originally identified for CHaMP include: Hood River, Wind River, Toppenish, Klickitat, Fifteen Mile, Lower Mainstem JD, North Fork JD, Upper Mainstem JD, Middle Fork JD, South Fork JD, Umatilla, Upper Grande Ronde, Catherine Ck, Imnaha, Lolo Ck, Tucannon, Asotin, SF Salmon, Big Ck, Lemhi, Pahsimeroi, Wenatchee, Entiat, Methow, and Okanogan.  These watersheds were chosen to maximize the contrast in current habitat conditions and also represent a temporal gradient of expected change in condition through planned habitat actions.  Following recommendations of the ISRP review, CHaMP will be implemented  in the first year of implementation FY11, in a subset of these subbasins, which are Lower Mainstem JD, North Fork JD, Upper Mainstem JD, Middle Fork JD, South Fork JD, Upper Grande Ronde, Catherine Ck, Tucannon, SF Salmon, Lemhi, Wenatchee, Entiat, and Methow,  CHaMP collaborators will be supported by cross-project data management, stewardship and analysis staff, annual pre- and post-season meetings, annual field protocol and data management tool implementation training sessions.  

Program Elements

(1) Sampling Design
A Generalized Random-Tessellation Sampling (GRTS) survey design was recommended by Crawford and Rumsey (2009) for monitoring habitat status and trend in the Columbia River Basin.  The GRTS design was initially developed under the EPA’s Environmental Monitoring and Assessment Program and is a probabilistic sampling design that has been shown to be advantageous for generating habitat condition parameters with known statistical characteristics.  The CHaMP monitoring design follows a  GRTS design with a 3 year rotating 1-to-1 split panel structure to distribute sampling effort in space and time, and has management tools for sampling design.  Implementing a GRTS survey design correctly is critical to producing a final dataset with known statistical characteristics requiring the implementation of strict procedures during the site evaluation and selection process.  A GRTS Site Selection Protocol and Tool will be provided to each collaborator to support field crews with efficiently completing the process while strictly enforcing design requirements.  

(2) Field Sampling
Habitat field sampling will follow the Bouwes et al. (2011) protocol that was developed after a review of fish habitat requirements, interactions of processes that influence fish habitat, the spatial scales for the context of these interactions, and current monitoring programs.  The protocol has the greatest probability of being comparable to other protocols and most relevant to salmonids and has been designed to be applied across varying spatial contexts depending on the logistical constrains of the sites.  In areas where GPS signals can be obtained, along with aerial photos, habitat units within reaches can be superimposed onto aerial photos with a map grade GPS.  In situations, where a GPS signal is not obtainable, units can be referenced to aerial photos and supplemented with on the ground measurements.  Finally, in situations where a GPS signal and aerial photos cannot be obtained a stick-and-tape method can be employed to delineate the reach into habitat units.  All approaches use a GPS map-grade data logger and thus do not require new gear for differing spatial contexts across related approaches.  

(i) Standardized Crew Training: Sampling and Data Capture Tool
Standardized field crew training in the recommended methods will be provided/required of all CHaMP field crews.  This standardized approach will promote crew efficiency and improved standardization across the region.  In addition to agency-specific safety and other training, ISEMP will provide training to support cooperating agencies that implement the recommended habitat protocol.

(ii) QA/QC crews to do repeat sampling across all participating watersheds
Repeated sampling of habitat monitoring sites within the same sampling season has proven to be an important component of GRTS-based, watershed-scale habitat monitoring.  Repeat sampling assists with 1) quality assurance/quality control, 2) the assessment of crew variability as a component of variation, and 3) providing improvements to temporal variability recognition (i.e., trend detection).  Furthermore, repeat sampling will be important to ISEMP’s research goals of testing the performance of the recommended protocols across the Columbia Basin.  To achieve these objectives, ISEMP will conduct repeat sampling visits for all watersheds in this program at 10 percent of all sampling sites during the low-flow index period.

(3) Data Management
For a monitoring program at the scale of the Columbia River Basin to be successful a robust data management system must be in place before initiating data collection.  Monitoring habitat in the CHaMP watersheds will generate a massive volume of data.  A system of data processing, storage, analysis, reporting, and distribution is available to meet the needs of a large-scale monitoring program, such as (a) documenting monitoring objectives, study design and intended analysis; (b) summarizing how, when, and where the monitoring data were collected, (c) supporting a range of analytical methods, such as hypothesis testing, time series analysis, structural equation modeling, and GIS support; and (d) adapting to changing requirements in the future.  The data system includes a centralized data warehouse and web-based data discovery tool (CHaMP Website); data exchange and loading procedures; a database schema that defines data storage format (Aquatic Resources Schema, ARS); metadata tools; data capture, validation, and summary tools; quality control and assurance procedures; and data stewards who support the system.

(i) Field Data Capture Tools: Hand Held Loggers
Field crews will need applications to support data capture, review, summarization, and reporting and a suite of handheld and desktop tools to support both habitat and fish monitoring is available.  These tools have XML-based mechanisms to synchronize data.  This workflow includes documenting metadata about project and statistical design, entering survey event information and observations, performing quality assurance procedures, deriving metrics, and submitting data for archiving.

(ii) GIS Data Management and Geoprocessing
The large spatial scales that the CHaMP will cover means that assimilating and managing spatial datasets in GIS, accounting for the geomorphic context of sampling, and performing watershed or subbasin-scale analyses are important data features within these programs.  GIS data management support, coordination, and basic processing for monitoring programs that require data management guidance or processing assistance is available and development of geospatial models, the use of remote sensing technologies to collect continuous GIS datasets, such as LIDAR and aerial photos, and integrating field-based tabular data within a geospatial context is ongoing.  

(iii) Data Storage and Retrieval
The CHaMP will have multiple groups collecting data and it will be critical to have data accessible and available for use by all groups within the program.  The CHaMP data management system serves as a long-term storage facility for monitoring datasets including metadata and features online interfaces for searching, viewing, and downloading datasets and documents associated with the coordinated monitoring program.

(4) Reporting
In such a large and geographically dispersed program such as CHaMP it is important to have an annual review of the data collection events so that any issues experienced or lessons learned over the field season can be addressed in a timely manner and with each collaborators' input.  To that end,  collaborators will submit a summary of their field season to the CHaMP Lead Coordinator who will collate and summarize the data collected, logistics of implementation and lessons learned from each field season into an Annual Synthesis Report.  This report will be used to inform full implementation in 2012, including any adjustments that may be appropriate on the design or scope of the project.