Contract Description: The Integrated Status and Effectiveness Monitoring Program (ISEMP, 2003-017-00) is an ongoing collaborative effort to design, test, implement and evaluate Status and Trends Monitoring for salmon and steelhead populations and their habitat, and watershed-scale Effectiveness Monitoring for management actions impacting salmon and steelhead populations and habitat in the Interior Columbia River Basin.

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.

Specifically, ISEMP generates quantitative guidance on and examples of: the robustness and limitations of population and habitat monitoring protocols, indicators and metrics; sampling design approaches for the distribution of monitoring effort in time and space; analytical approaches to the evaluation of monitoring data, information and programs; effective data management and communication designs that support the use, standardization and compilation of implementation, compliance, status, trends and effectiveness monitoring data by regional data generators and decision makers; and finally the design and implementation of watershed-scale restoration actions to maximize both the biological impact and associated learning opportunities resulting from the design and implementation strategy.

Through its work to date, ISEMP has developed expertise in the coordination and implementation of large-scale monitoring data collection programs. Applying this experience, ISEMP coordinates the installation, maintenance and calibration of in-stream PIT tag arrays across the Snake River basin and has developed and is coordinating the implementation of a Columbia River basin-wide stream habitat status and trends monitoring. These programmatic implementation facets of ISEMP leverage previous experience with logistics and social factors to effectively implement comprehensive, standardized monitoring research and development at an unprecedented scale.  

This contract is one of several contracts that will implement this project.

The final report for this contract will contain data that will 1) be submitted to NOAA Fisheries (also a contractor under this project) for use in a project level integrated Annual Report and 2) be submitted to BPA as a contract final report according to the terms of this contract.  Quantitative Consultants, Inc. role has been, and continues to be, to enable the Bonneville Power Administration to implement Project #2003-017-00 in the Salmon River subbasin and other pilot subbasins.

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.

The Salmon portion of the ISEMP project began in 2005 with the completion of a study design (attached and available at 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). Implementation of the ISEMP project in the Salmon subbasin was funded in FY2008, with on-the-ground actions commencing in FY2009.

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.

The primary task funded through this CR is the continuation of sampling in the Lemhi River to support evaluations of the effectiveness of tributary habitat restoration. Additional tasks include the operation of IPTDS for status and trend and action effectiveness monitoring across the Snake River Basin. In addition to these tasks, the following products will be completed in 2016:
1. A finalized statistical method to support age and sex-structured escapement estimates for spring/summer Chinook salmon and steelhead in the Snake Basin using IPTDS interrogation data.
2. Finalized statistical methods to develop continuous capture probabilities for remote-site, spatially-continuous juvenile survey efforts.
3. Analysis of alternative methods to generate survival estimates for spatially-continuous juvenile survey efforts.