2 Introduction
The Nez Perce Tribe’s (NPT; hereafter referred to as the Tribe) Department of Fisheries Resources Management (DFRM) has the responsibility of managing, restoring and recovering fish populations in the Snake River basin. The DFRM completes these tasks with work performed under six divisions: Administration, Conservation Enforcement, Harvest Monitoring, Production, Research, and Watershed Restoration. The Tribe’s fisheries activities encompass a vast geographic area, which includes, over 13 million acres within the present-day states of Idaho, Oregon, Washington, and Montana. Data collected under the six divisions is extensive, and quantifies fisheries resource condition and response to management actions supporting 1855 Treaty rights, the Federal Columbia River Power System Biological Opinion, U.S. vs. Oregon management agreement, Snake River Basin Adjudication, Northwest Power and Conservation Council Fish and Wildlife Program, and Lower Snake River Compensation Plan mitigation.
The DFRM Research Division is tasked with monitoring and evaluating natural- and hatchery-origin anadromous fish populations throughout the Tribe’s usual and accustomed areas within the Snake River basin. The Research Division’s mission statement is:
“to contribute to sound fisheries management through best available science. This involves collection of status and trends data, conduct management action effectiveness monitoring, and communication of knowledge (and uncertainties) that are unbiased, objective, collaborative, and available to the community at large.”
— NPT DFRM Management Plan
To accomplish our mission the division is made up of independent monitoring and evaluation projects that contribute to the status assessments of fall Chinook Salmon, spring/summer Chinook Salmon and steelhead populations identified by the Interior Columbia Technical Recovery Team (ICTRT 2003) through the collection, summarization, analysis and reporting of information. Salmonid population monitoring and evaluation is performed at multiple spatial scales (e.g., tributary, population, evolutionary significant units) and use a variety of data collection activities (e.g., spawning ground surveys, rotary screw traps). Implemented data collection activities vary across species and Research Division projects to answer specific population uncertainties identified through regional planning efforts and to meet data requirements for specific project objectives. Project objectives within the division include the assessment of hatchery program performance and effectiveness at individual tributary scales, hatchery program effects on natural origin populations, and the status and recovery monitoring of natural origin ICTRT populations and major population groups (MPG) (McElhany et al. 2000). Evaluation techniques at each spatial scale follow the mission statement and use the best available science to produce sound population metrics to guide fisheries management and salmon and steelhead recovery efforts.
Research Division projects evaluating hatchery program performance and the status of salmon and steelhead populations follow established monitoring and evaluation (M&E) plans (J. A. Hesse and Cramer 2000; J. Hesse et al. 2004; Vogel et al. 2005) using standardized fish population performance metrics. Established M&E plans identify each project’s objectives and describe testable hypotheses to assess hatchery program success. Plans often suggest monitoring and evaluating similar metrics to measure performance; however, plans do not clearly state metric definitions. To aid hatchery programs and population status evaluations, and to facilitate direct comparisons of fish metrics across all Columbia Basin Salmonid populations the Ad-Hoc Supplementation Workgroup (AHSWG) defined key performance measures (Beasley et al. 2008). Sixty-two performance measures were identified and grouped into abundance, life history, survival-productivity, distribution, genetic, habitat, and in-hatchery categories.
Similar to the AHSWG, in 2008 a regional workshop of Columbia River basin fish management, regulatory and funding agencies convened to integrate existing programs into a cohesive framework to improve monitoring strategies and to allow critical uncertainties to be addressed more effectively and efficiently (CBCAMW 2010). The Coordinated Assessments (CA) project was conceptualized at the workshop and initiated the development of Data Exchange Standards (DES; http://www.streamnet.org/coordinated-assessments-des/) to guide regional standardization of fisheries data for the purpose of efficient, reliable calculation, and transparent sharing of high level indicators (HLIs) of population abundance, productivity, habitat and hatchery metrics. The DES serves as metadata to the CA database which contains the regionally accepted population HLI and metric data stored on StreamNet (http://www.streamnet.org/data/coordinated-assessments/. CA indicators and metrics include performance measures defined by AHSWG, and others used for regional monitoring, Endangered Species Act (ESA) status reviews, and viability assessments.
The DFRM Research Division projects calculate and report fish summary metrics and HLIs following the AHSWG and CA standard definitions by using standardized estimation and analytical methods. In order to align similar methods and approaches, the Research Division standardized data collection protocols and repositories across all projects and geographic areas. Consistent and standard approaches ensure accurate hatchery program comparisons and scalability from individual tributaries to a population, and up to larger MPGs or geographic areas, NPT managers and other regional decision-makers.
HLIs and metrics are shared throughout the region annually via progress reports, management briefings, and the CA database updates for all Chinook Salmon and steelhead populations monitored by the Research Division. Each individual division project is considered the main contact and reference for all data collection, summarization, analysis and reporting. Standardized data collection methods and minimum quality assurance and control procedures for data integrity can be found on http://www.monitoringresources.org for each field activity and method. Summarized data, HLIs and metrics, and annual project reports are available for public access on the Kus web appliation (https://nptfisheries.shinyapps.io/kus-data/). Raw fisheries data are stored within the DFRM’s Centralized Data Management System (CDMS) and secured on Research Division servers. Permission to access raw data is restricted only to DFRM staff through CDMS (https://npt-cdms.nezperce.org) and Kus web applications. Raw data can be made available with a special request through the division’s Data Coordinator, Ryan N. Kinzer, or Data Steward, Clark Watry.
This document provides detailed documentation of standardized Research Division methods for calculating AHSWG performance measures and CA HLIs and metrics. Our objectives are to: (1) standardize analytical methods across all division projects and monitoring locations, (2) identify common alternative methods when project or annual conditions necessitate, (3) identify uncertainty estimators, and (4) create a transparent and citable reference for interested parties when using or referencing NPT DFRM Research Division methods and data. The document is organized into a single introduction chapter, and three chapters grouping HLI and metric calculations into life stages: Adult Abundance and Life History, Juvenile Abundance and Life History, and Population Productivity. The document is not inclusive of all AHSWG and CA metrics (e.g., Distribution, Genetic and Habitat), but instead focuses on the main building blocks of population and hatchery effectiveness monitoring. The document is considered living and is subject to regular updates as missing metrics are added, and new data or methods are made available.
2.1 Data Collection and Management
Processing, summarizing, and disseminating data and project results are as critical to the scientific process as the original collection of data itself. However, the data management process is often an afterthought with less attention to detail as a result. As a proactive step towards thoughtful data stewardship and maintaining data integrity, the Research Division follows predetermined work flows and protocols for all data activities. Standardized work flows and protocols utilize established cyber-infrastructure that efficiently support fisheries data acquisition, storage, integration, mining, and visualization required to meet Research Division objectives. The division acquires data from two sources: original collection by DFRM staff, or through external data sharing agreements with fisheries co-managers and the original data collector. After acquisition, data collected by DFRM staff is entered and maintained in CDMS. Stored data is examined for accuracy and corrected within the CDMS online web application. External data is pulled onto servers from their source repository (e.g., Lower Snake River Compensation Plan’s FINS [Fish INventory System] database) at a frequency necessary to meet management requirements. Both data sources are then merged with automated computer processing scripts to facilitate more efficient and reproducible summaries, analyses and standardized reports.
Research Division staff collect field data associated with adult picket (fixed and floating) and passive weirs, in-stream PIT tag detection systems (IPTDS), radio telemetry tracking, spawning ground surveys, juvenile rotary screw traps, beach and boat seining and in-hatchery evaluations. Depending on the field activity newly collected raw data is captured electronically (e.g.,FINS, PSMFC P4, Survey123) and later uploaded to CDMS or onto hard copy datasheets for manual entry into CDMS. Each field activity uses standardized protocols developed to ensure staff collect high-quality, consistent, and transparent data. Field activity protocols include the objectives and location of each activity, step-by-step guides for proper data collection, minimum quality assurance and control (QA/QC) standards and descriptions of how to record raw data. Field protocols are available for download on the Kus web application or from MonitoringResources.
External data originally collected by entities other than NPT is acquired through data use and sharing agreements. The Research Division currently consumes raw field and summarized data collected and/or maintained by: Idaho Department of Fish and Game (IDFG), Oregon Department of Fish and Wildlife (ODFW), Washington Department of Fish and Wildlife (WDFW), Columbia River Inter-Tribal Fisheries Commission (CRITFC), Pacific State Marine Fisheries Commission (PSMFC), and the Data Access in Real-Time (DART, http://www.cbr.washington.edu/dart) website. External data consumed from other entities allows Research Division projects to report HLIs and metrics that would be unobtainable with only NPT collected data. Data citations are provided when external sources assist in calculations.