Columbia Basin Fish and Wildlife Program Columbia Basin Fish and Wildlife Program
SOW Report
Contract 74633: 2003-017-00 EXP ISEMP - SALMON R. QUANTITATIVE CONSULTANTS
Project Number:
Title:
Integrated Status and Effectiveness Monitoring Program (ISEMP)
BPA PM:
Stage:
Implementation
Area:
Province Subbasin %
Basinwide - 100.00%
Contract Number:
74633
Contract Title:
2003-017-00 EXP ISEMP - SALMON R. QUANTITATIVE CONSULTANTS
Continuation of Contract:
71131: 2003-017-00 EXP ISEMP - SALMON R. QUANTITATIVE CONSULTANTS
Contract Status:
Closed
Contract Description:
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.
Account Type(s):
Expense
Contract Start Date:
12/01/2016
Contract End Date:
11/30/2017
Current Contract Value:
$1,432,318
Expenditures:
$1,432,318

* Expenditures data includes accruals and are based on data through 31-Aug-2019.

Env. Compliance Lead:
Contract Contractor:
Work Order Number:
129074
Task Number:
1
Contract Type:
Contract
Pricing Method:
Time and Materials
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Viewing of Work Statement Elements

Deliverable Title WSE Sort Letter, Number, Title Start End Complete
Environmental Compliance Documentation A: 165. Environmental Compliance Documentation 11/30/2017 11/30/2017
All administrative tasks fulfilled with timely and quality products B: 119. Project Management 11/30/2017 11/30/2017
Juvenile survey data C: 157. Collect and sample juvenile salmonids in Lemhi River watershed (Priorities 4.3 - 4.4) 11/30/2017 11/30/2017
Juvenile Oncorhynchus mykiss PIT tag records D: 158. Tag juvenile Oncorhynchus mykiss captured in Lemhi River watershed (Priorities 4.3 - 4.4) 11/30/2017 11/30/2017
Juvenile Chinook salmon PIT tagging records E: 158. Tag juvenile Chinook salmon captured in Lemhi River watershed (Priorities 4.3 - 4.4) 11/30/2017 11/30/2017
Bull trout PIT tagging records F: 158. Tag bull trout captured in Lemhi River watershed (Priorities 4.3 - 4.4) 11/30/2017 11/30/2017
Westslope cutthroat trout PIT tagging records G: 158. Tag Westslope cutthroat trout captured in Lemhi River watershed (Priorities 4.3 - 4.4) 11/30/2017 11/30/2017
Brook trout PIT tagging records H: 158. Tag brook trout captured in Lemhi River watershed (Priorities 4.3 - 4.4) 11/30/2017 11/30/2017
Redband trout PIT tagging records I: 158. Tag redband trout captured in Lemhi River watershed (Priorities 4.3 - 4.4) 11/30/2017 11/30/2017
Report IPTDS detection and diagnostic data J: 157. Operate and maintain ISEMP IPTDS throughout the Columbia River basin (Priorities 4.3 - 4.4) 11/30/2017 11/30/2017
Secesh River, Lower Lemhi, and Hayden Creek Rotary Screw Trap Operations and Maintenance K: 157. Operate and maintain rotary screw traps in the Lemhi and lower Secesh rivers (Priorities 4.3 - 4.4) 11/30/2017 11/30/2017
IMW Habitat Data set and metadata secured and electronically available L: 157. Conduct habitat surveys in Lemhi River watershed (Priorities 4.1 - 4.2) 11/30/2017 11/30/2017
Sample and PIT tag 2,000 to 6,000 adult steelhead at LGR M: 158. Lower Granite Dam adult steelhead PIT tagging (Priorities 4.3 - 4.4) 11/30/2017 11/30/2017
Sample and PIT tag 2,000 to 6,000 adult Chinook salmon at LGR N: 158. Lower Granite Dam adult Chinook salmon PIT tagging (Priorities 4.3 - 4.4) 11/30/2017 11/30/2017
Scale age data and metadata for adults PIT Tagged at LGR O: 162. Lower Granite Dam adult steelhead and Chinook salmon scale ageing (Priorities 4.3 - 4.4) 11/30/2017 11/23/2017
Manage ISEMP database P: 160. Manage ISEMP database 11/30/2017 11/30/2017
Transfer data from IPTDS to QCI and cloud servers Q: 159. Upload IPTDS data to QCI server and cloud storage, parse, and upload to PTAGIS 11/30/2017 11/30/2017
Chinook salmon and O. mykiss Quantile Regression Forest capacity models. T: 162. Quantile Regression Forest development, improvement, and validation (Priority 3.5) 11/30/2017 11/30/2017
Project Coordination U: 189. Project coordination 11/30/2017 11/30/2017
Salmon Subbasin Coordination V: 191. Salmon subbasin coordination 11/30/2017 11/30/2017
IPTDS Operations and Maintenance Report W: 132. IPTDS Operations and Maintenance Report 04/12/2017 04/12/2017
Lemhi River Fish Survey Annual Report X: 132. Lemhi River Fish Survey Report 04/12/2017 04/12/2017
Secesh River and Hayden Creek Rotary Screw Trap Annual Report Y: 132. Secesh and Hayden Creek Rotary Screw Trap Annual Report 04/15/2017 04/15/2017
Lemhi River Restoration Site Habitat Survey Annual Report Z: 132. Lemhi River Restoration Site Habitat Survey Annual Report 04/12/2017 04/12/2017
Completed Annual Report AA: 132. Quantile Regression Forest development, improvement, and validation report. 11/30/2017 11/29/2017
Submit BiOp RPA Report in Taurus AB: 202. BiOp RPA report 03/15/2017 03/15/2017

Viewing of Implementation Metrics
Viewing of Environmental Metrics

Primary Focal Species Work Statement Elements
Chinook (O. tshawytscha) - Snake River Spring/Summer ESU (Threatened)
  • 4 instances of WE 157 Collect/Generate/Validate Field and Lab Data
  • 2 instances of WE 158 Mark/Tag Animals
  • 1 instance of WE 159 Transfer/Consolidate Regionally Standardized Data
  • 4 instances of WE 162 Analyze/Interpret Data
Chinook (O. tshawytscha) - Snake River Spring/Summer (not listed)
  • 1 instance of WE 159 Transfer/Consolidate Regionally Standardized Data
Chinook (O. tshawytscha) - Upper Columbia River Spring ESU (Endangered)
  • 1 instance of WE 159 Transfer/Consolidate Regionally Standardized Data
Chinook (O. tshawytscha) - Upper Columbia River Summer/Fall ESU
  • 1 instance of WE 159 Transfer/Consolidate Regionally Standardized Data
Steelhead (O. mykiss) - Middle Columbia River DPS (Threatened)
  • 1 instance of WE 159 Transfer/Consolidate Regionally Standardized Data
Steelhead (O. mykiss) - Snake River DPS (Threatened)
  • 4 instances of WE 157 Collect/Generate/Validate Field and Lab Data
  • 2 instances of WE 158 Mark/Tag Animals
  • 1 instance of WE 159 Transfer/Consolidate Regionally Standardized Data
  • 4 instances of WE 162 Analyze/Interpret Data
Steelhead (O. mykiss) - Upper Columbia River DPS (Threatened)
  • 1 instance of WE 159 Transfer/Consolidate Regionally Standardized Data
Cutthroat Trout, Westslope (O. c. lewisi)
  • 1 instance of WE 158 Mark/Tag Animals
Trout, Brook (Salvelinus fontinalis)
  • 1 instance of WE 158 Mark/Tag Animals
Trout, Bull (S. confluentus) (Threatened)
  • 1 instance of WE 158 Mark/Tag Animals
Trout, Interior Redband (O. mykiss gairdnerii)
  • 1 instance of WE 158 Mark/Tag Animals

Sort WE ID WE Title NEPA Public Involvement NOAA USFWS NHPA Has Provisions Inadvertent Discovery Completed
A 165 Environmental Compliance Documentation 12/01/2016
B 119 Project Management 12/01/2016
C 157 Collect and sample juvenile salmonids in Lemhi River watershed (Priorities 4.3 - 4.4) 08/04/2017
D 158 Tag juvenile Oncorhynchus mykiss captured in Lemhi River watershed (Priorities 4.3 - 4.4) 08/04/2017
E 158 Tag juvenile Chinook salmon captured in Lemhi River watershed (Priorities 4.3 - 4.4) 08/04/2017
F 158 Tag bull trout captured in Lemhi River watershed (Priorities 4.3 - 4.4) 08/04/2017
G 158 Tag Westslope cutthroat trout captured in Lemhi River watershed (Priorities 4.3 - 4.4) 08/04/2017
H 158 Tag brook trout captured in Lemhi River watershed (Priorities 4.3 - 4.4) 08/04/2017
I 158 Tag redband trout captured in Lemhi River watershed (Priorities 4.3 - 4.4) 08/04/2017
J 157 Operate and maintain ISEMP IPTDS throughout the Columbia River basin (Priorities 4.3 - 4.4) 08/04/2017
K 157 Operate and maintain rotary screw traps in the Lemhi and lower Secesh rivers (Priorities 4.3 - 4.4) 08/04/2017
L 157 Conduct habitat surveys in Lemhi River watershed (Priorities 4.1 - 4.2) 08/04/2017
M 158 Lower Granite Dam adult steelhead PIT tagging (Priorities 4.3 - 4.4) 08/04/2017
N 158 Lower Granite Dam adult Chinook salmon PIT tagging (Priorities 4.3 - 4.4) 08/04/2017
O 162 Lower Granite Dam adult steelhead and Chinook salmon scale ageing (Priorities 4.3 - 4.4) 12/01/2016
P 160 Manage ISEMP database 12/01/2016
Q 159 Upload IPTDS data to QCI server and cloud storage, parse, and upload to PTAGIS 12/01/2016
R 162 Life Cycle Modeling (Priorities 2.1.1-2.2.1, 2.3.1-2.3.3, and 5.3) 12/01/2016
S 162 Quantitative framework to estimate effect size of restoration actions (priorities 3.1-3.3) 12/01/2016
T 162 Quantile Regression Forest development, improvement, and validation (Priority 3.5) 12/01/2016
U 189 Project coordination 12/01/2016
V 191 Salmon subbasin coordination 12/01/2016
W 132 IPTDS Operations and Maintenance Report 12/01/2016
X 132 Lemhi River Fish Survey Report 12/01/2016
Y 132 Secesh and Hayden Creek Rotary Screw Trap Annual Report 12/01/2016
Z 132 Lemhi River Restoration Site Habitat Survey Annual Report 12/01/2016
AA 132 Quantile Regression Forest development, improvement, and validation report. 12/01/2016
AB 202 BiOp RPA report
AC 132 Contribute to joint ISEMP/CHaMP annual report 12/01/2016
AD 185 Periodic Status Reports for BPA 12/01/2016