Description updated 05/12/2017. CCR-39031 reduces the fiscal year 2017 budget submitted for contract 74633. The budget reductions target two deliverables, Work Element (WE) R: 162 "Life Cycle Modeling" and WE S:162 "Quantitative framework to estimate effect size of alternative restoration actions." Work under WE R:162 will focus on the continued development of an Integrated Population Model (IPM); a statistically rigorous method of estimating intrinsic productivity, which allows for the direct incorporation of fish habitat relationships and the effects of habitat restoration to estimate population level abundance and productivity. Work under WE S:162 will focus on expanding the suite of habitat restoration actions that can be modeled using IPM.

This Contract Description is composed of four sections:
1. Mission Statement
2. SOW Structure and Supporting Materials
3. Proposed Tasks
4. Background and Accomplishments

Mission Statement: The Integrated Status and Effectiveness Monitoring Program (ISEMP, 2003-017-00) is an ongoing collaborative effort with two primary goals:
1. to design, test, implement and evaluate Status and Trends Monitoring for salmon and steelhead populations and their habitat and
2. implementation of habitat restoration effectiveness monitoring at the scale of Chinook salmon and steelhead populations as identified by the Interior Columbia Basin Technical Recovery Team.
ISEMP tools (i.e., fish/habitat relationships, models, monitoring approaches, designs, and effectiveness evaluations) are developed using fish data collected across all three ISEMP study basins - the John Day, upper-Columbia, and Snake and habitat data from implementation of the Columbia Habitat Monitoring Program (CHaMP) in the Asotin Creek, Entiat River, John Day River, Lemhi River, Lolo Creek, Methow River, Minam River, South Fork Salmon River, Tucannon River, Umatilla River, upper-Grande Ronde River, Walla Walla River, Wenatchee River, and the Yankee Fork Salmon River. The spatial distribution of fish and habitat data utilized by ISEMP has been demonstrated to represent nearly the entire interior Columbia River Basin, with the exception of the Clearwater River sub-basin. As such, the tools developed by ISEMP can be applied throughout the interior Columbia River domain.

SOW Structure and Supporting Materials: Work Element descriptions in this Statement of Work include numerical designations (e.g., 2.1.1), which reference a prioritized task list developed for ISEMP and CHaMP through negotiations between BPA and NOAA Fisheries. A description of those tasks, and their numerical designations is provided in the attachment labeled "ISEMP Task Descriptions." The ISEMP Mission Statement requires the development of novel fish/habitat relationships, tools, and models. We have adopted standardized language to describe the status of product development, quality assurance/quality (QA/QC) control and validation, and data generation. For example, virtually all products are initiated with manual data generation, exploratory analysis, and manual QA/QC. For models, relationships, or tools with extraordinary utility, the goal is the automation of data generation, full empirical validation, and external availability (i.e., the ability for practitioners to access and utilize the tool). Descriptions of product status are detailed in the attachment labeled "Status Concepts."

Proposed Tasks: The development of a prioritized list of products for 2017 (attached) has shifted emphasis from data collection to coordinated data analysis across ISEMP subbasins to facilitate product/tool development. Therefore, this SOW reflects the minimum fieldwork necessary to evaluate habitat restoration action effectiveness for the Lemhi River and increases efforts toward the development of exportable fish/habitat relationships and life-cycle models. Where applicable, Work Element descriptions contain a numerical designation (e.g., Priority 2.2.1) that can be cross-references to the attached list of ISEMP priorities. These priorities and tasks are supported by the ISEMP database (Work Element L) and transfer of data to regional databases (Work Element M). All ISEMP activities in the Snake River Basin are closely coordinated with the Idaho Department of Fish and Game and the Nez Perce Tribe, which is supported through Work Elements P and Q.

Background: ISEMP explicitly addresses work requirements of many 2008 FCRPS Biological Opinion RPAs (56.1, 56.2, 56.3, 57.1, 57.2, 57.3, 57.4, 57.5) and is directly related to additional 2008 FCRPS Biological Opinion implementation strategy requirements and recommendations. ISEMP takes a pilot-project approach to the research and development of monitoring by implementing experimental programs in several major subbasins of the Interior Columbia: the Wenatchee, Entiat, Methow, John Day, South Fork Salmon and Lemhi River basins. The overall goal of the project is to develop and implement sampling designs to evaluate the effectiveness of habitat restoration actions using the currency of freshwater productivity. This CR also addresses RPA 50.5; titled Provide Additional Status Monitoring of Snake River B-Run Steelhead Populations. Quantitative Consultants, Inc. was selected by its cooperators to develop the proposal for RPA 50.5, owing to their experience operating In-Stream PIT tag Detection Systems (IPTDS), data management and analysis of detection data. This effort supports age and sex-structured escapement estimates for 13 of 25 Snake River steelhead populations identified by the Interior Columbia Technical Recovery Team; including 5 of 7 populations believed to support the production of B-run steelhead.

The ISEMP project relies heavily on instream PIT tag detection systems (IPTDS) to generate estimates of adult and juvenile abundance, survival, and distribution. Unlike many data collection approaches, IPTDS technology is commonly deployed in remote locations with limited seasonal access with the expectation that IPTDS infrastructure will operate autonomously in a reliable and continuous fashion. Thus the ability to remotely monitor site diagnostics and data in real-time is critical to the effective use of IPTDS technology. Beginning in 2009, ISEMP has tested and developed IPTDS components to identify a reliable and cost-effective suite of standardized infrastructure that supports real-time site diagnostics and data access. Additionally, ISEMP has developed an automated process for data upload, reduction, parsing, and distribution to regional databases (e.g., PTAGIS).  In 2011, the scope of ISEMP was expanded to coordinate the installation and long-term administration of instream PIT Tag arrays in the South Fork Clearwater River, Lolo Creek, the Grande Ronde River, Joseph Creek, the Imnaha River, and the mainstem upper Salmon River. Additionally, ISEMP was tasked to undertake the operation and administration of existing PIT tag arrays in Valley Creek (upper Salmon River) and Big Creek (Middle Fork Salmon River). ISEMP was identified as the project lead for this work owing to efforts beginning in 2005 to implement instream PIT tag arrays in the South Fork Salmon River and Lemhi Rivers as part of the ISEMP project. In concert with the installation and operation of these arrays, ISEMP, in cooperation with the Nez Perce Tribe, Idaho Department of Fish and Game, PTAGIS, NOAA, and Biomark has undertaken the development of standardized data storage/retrieval and analysis approaches specifically for adult and juvenile interrogation data generated by instream PIT tag array systems.

Quantitative Consultants, Inc. was first contracted to participate in the ISEMP project in 2005 via a subcontract through NOAA Fisheries. That contract funded  the completion of a study design (http://www.nwfsc.noaa.gov/research/divisions/cbd/mathbio/isemp/docs_salmon.cfm#2005), which received a positive review by the Independent Scientific Review Panel in 2006 (ISRP 2006-1; attached and available at http://www.nwfsc.noaa.gov/research/divisions/cbd/mathbio/isemp/docs_salmon.cfm#2005).The Salmon Subbasin ISEMP project was funded in December 2008, and began on-the-ground implementation of the ISRP reviewed study design in 2009. As implemented in 2009, the Salmon Subbasin ISEMP project included the following components:
1. Sampling and PIT tagging up to 4,000 unmarked steelhead and spring/summer Chinook salmon at Lower Granite Dam (LGR). Development of a model to decompose the natural-origin runs-at-large at LGR into population-specific sex and age-structured estimates of escapement.
2. Remote-site juvenile salmonid sampling at PIT tagging in the South Fork Salmon River (SFSR) and Lemhi River. Site surveys were originally conducted within a generalized random tesellation stratified (GRTS) design in order to support abundance and survival estimates at spatial scales ranging from individual sites, to key tributaries, to populations.
3. Habitat surveys in the SFSR and Lemhi River within a GRTS-based design.
4. Operation of rotary screw traps on the lower Secesh River (SFSR), mainstem SFSR, and at three locations in the Lemhi River (lower Lemhi River, upper-mainstem Lemhi River, and Hayden Creek.
5. Installation and operation of IPTDS at three locations in the SFSR and three locations in the Lemhi River (paired with rotary screw traps).
6. Development of green Light Detection an Ranging (LiDAR) methods and equipment as a means to survey in-stream features over greater spatial extents and in deep water areas that cannot be surveyed using traditional methods.
7. Empirical population of the watershed model, which was the backbone of the Salmon Subbasin ISEMP design.

In 2010, this contract funded significant participation in the development of the CHaMP habitat protocol.

In 2011, the Salmon Subbasin IPTDS infrastructure was substantially increased as a result of a successful proposal to address RPA 50.5.

In 2011, GRTS-based habitat sampling in the Lemhi and SFSR were replaced by CHaMP.

In 2012, remote-site juvenile surveys in the SFSR and operation of the mainstem SFSR were abandoned to compensate for a reduction in the ISEMP project budget.