81592: Focal Species Summary

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Focal Species Summary

Contract 81592: 2019-006-00 EXP SNAKE RIVER FISH AND HABITAT BIOMARK

Viewing 12 of 12 Focal Species


	Sort Order	WE ID	Work Element Name	Title	Description	Primary Focal Species	Secondary Focal Species


	A	119	Manage and Administer Projects	Project Management	Biomark will manage and administer projects tasks and contracts in accordance with guidance from BPA's assigned COTR. This includes administrative work, providing oversight of the project, responding to BPA as requested, and providing financial and administrative documents. Manage the project, including administrative work in support of sampling efforts and BPA's programmatic requirements such as metric reporting, financial reporting (e.g., accruals), and development of an SOW package (includes draft SOW, budget, spending plan, and property inventory).
	B	185	Produce CBFish Status Report	Periodic Status Reports for BPA	The Contractor shall report on the status of milestones and deliverables in Pisces. Reports shall be completed either monthly or quarterly as determined by the BPA COTR. Additionally, when indicating a deliverable milestone as COMPLETE, the contractor shall provide metrics and the final location (latitude and longitude) prior to submitting the report to the BPA COTR.
	C	165	Produce Environmental Compliance Documentation	Environmental Compliance Documentation	Provide copies of permit documents such as Section 10, 404-D, and cultural resources survey documents to lead EC Officer.
	D	157	Collect/Generate/Validate Field and Lab Data	Operate and maintain the lower Lemhi River (LLRTP) Rotary Screw trap	This work element funds Biomark to operate a rotary screw trap located on the lower mainstem Lemhi River (LLRTP). This rotary screw traps provides an estimate of the total abundance of emigrating anadromous salmonids and provides the opportunity to PIT tag fish to estimate survival to the Federal Columbia River Power System. This work element is documented under Protocol: ISEMP Cooperator Rotary Screw Trap Operation (ID: 2267).	Chinook (O. tshawytscha) - Snake River Spring/Summer ESU (Threatened), Steelhead (O. mykiss) - Snake River DPS (Threatened)	Cutthroat Trout, Westslope (O. c. lewisi), Trout, Brook (Salvelinus fontinalis), Trout, Bull (S. confluentus) (Threatened), Trout, Interior Redband (O. mykiss gairdnerii), Trout, Rainbow (Oncorhynchus mykiss)
	E	189	Coordination-Columbia Basinwide	Coordination	This Work Element funds travel and labor to support the coordination of Work Elements F115, G115, H115, and I115. Each of those Work Elements will require considerable collaboration with (at a minimum), BPA, NOAA Fisheries, ODFW, WDFW, IDFG, and the Nez Perce Tribe. Collaboration will include data sharing, sharing of draft products, and development of protocols. Coordination will typically occur via teleconference, although some in-person meetings will be required.
	F	115	Produce Inventory or Assessment	Incorporation of GSI data into IPTDS escapement estimators above LGR.	Natural-origin adult spring/summer Chinook salmon and steelhead escapement into tributaries and populations upstream of Lower Granite Dam (LGR) is estimated by PIT tagging a subsample of adults as they pass LGR and detecting tagged adults at In-stream PIT tag detection systems (IPTDS) in tributaries upstream of LGR using the Dam Adult Branch Occupancy Model (DABOM). We propose to integrate estimates of escapement to genetic stocks or Major Population Groups (MPGs) from Genetic Stock Identification (GSI) into DABOM to improve model fit and convergence times. GSI data is already collected on every adult that is PIT tagged at LGR, thus this will merge the genetic data with PIT tag interrogation data into a single analysis. This should have the added benefit of helping to account for some portion of the fish that are never observed after Lower Granite Dam, often because they return to watersheds without PIT tag detection infrastructure. However, watersheds not covered with PIT detection infrastructure are covered by GSI, allowing DABOM to place fish never observed again into the appropriate reporting group. Additionally, re-coding DABOM to initially account for GSI groups will allow for estimates of escapement at larger spatial scales than currently possible.	Chinook (O. tshawytscha) - Snake River Spring/Summer ESU (Threatened), Steelhead (O. mykiss) - Snake River DPS (Threatened)	Chinook (O. tshawytscha) - Snake River Spring/Summer (not listed)
	G	115	Produce Inventory or Assessment	Simulations of hatchery-origin adult PIT tagging at Lower Granite Dam.	DABOM is currently used to estimate adult escapement of natural-origin Chinook salmon and steelhead into watersheds and populations. However, DABOM could easily be used to generate estimates of hatchery escapement to various watersheds as well, which can be useful for estimating hatchery abundance in natural areas and the proportion of hatchery fish on the spawning grounds (pHOS). Doing so requires a random sample of hatchery fish be PIT tagged at Lower Granite Dam. We propose to determine the tagging rate or number of tags required to achieve unbiased estimates of hatchery escapement (and pHOS) with appropriate levels of precision. To determine the appropriate level of tagging, we propose to conduct a power analysis using the existing version of DABOM. Some of the assumptions to be made include: • Appropriate transition probabilities for hatchery fish along each branch. o Do they mimic wild fish movement? o Do some branches contain no hatchery fish? o Should branches further upstream of Lower Granite automatically include lower transition probabilities due to fishing on the mainstem? o Do we include time-varying movement probabilities? • Appropriate detection probabilities for each detection node in the model. • We must assume a fraction of hatchery fish will be harvested prior to reaching tributary habitats. • How many total hatchery fish escape past Lower Granite? We can run STADEM to determine range of values over the last several years. Alternatively, to determine the appropriate level of tagging, we may examine the last several years of DABOM results and focus on the number of tags observed within a number of different tributaries and the level of precision of the accompanying escapement estimates, accounting for detection probability. We could then build a relationship to predict the precision based on the number of tags detected and the detection probability. After making some assumption about the transition probability of hatchery fish to a particular tributary, we can use the estimate of detection probability to predict the precision of the escapement estimate under a variety of tagging rates.	Chinook (Oncorhynchus tshawytscha) - All Populations, Steelhead (Oncorhynchus mykiss) - All Populations
	H	115	Produce Inventory or Assessment	Salmonid Habitat Assessment Protocol (SHAP)	The Columbia Habitat Monitoring Protocol (CHaMP; BPA Project 2011-006-00) implemented a generalized random tessellation stratified design (GRTS) to representatively subsample anadromous fish habitat across 14 waterheds in the Columbia River Basin. Irrespective of subsequent criticism, CHaMP remains the single largest standardized and representative habitat sampling program ever prosecuted in the Columbia River Basin. Factually, CHaMP, in concert with the Integrated Status and Effectiveness Monitoring Project (ISEMP; BPA Project 2003-017-00), enabled the development of "global" and predictive fish/habitat relationships. SHAP capitalizes on global fish/habitat relationships and seeks to extend those relationships in a cost-effective manner utilizing imagery. Factually, many of the habitat metrics found to be useful in ISEMP/CHaMP fish/habitat relationships can be collected from imagery. Problematically, little effort has been expended towards the automation of imagery post-processing. This work-element funds this automation, in the form of neural-network models (and others) to reduce post-processing effort. Ultimately, if successful, this will enable the development of "cross-walks" between CHaMP metrics and aerially-derived metrics - thus allowing a far most cost-effective and comprehensive habitat sampling program that can capitalize on the investment in CHaMP.	Chinook (Oncorhynchus tshawytscha) - All Populations, Steelhead (Oncorhynchus mykiss) - All Populations
	I	115	Produce Inventory or Assessment	Protocol for statistically robust juvenile interrogation data.	The use of Passive Integrated Transponder (PIT) tags to estimate adult escapement (see Work Element F:115) is well-established. From the inception of In-stream PIT Tag Detection systems (IPTDS) proponents desired to extend interrogation data to juvenile salmonids. Factually, this was a cornerstone of the Inter=grated status and Effectiveness Monitoring Project (BPA Project 2003-017-00). Tests with paired IPTDS and Rotary Screw Traps (RST) initiated in 2009 in the South Fork Salmon River illustrated significant bias in juvenile interrogation data. Despite demonstrated bias (and underlying mechanisms), juvenile interrogation data are still routinely utilized. While recent advancements in detection infrastructure reduce these biases, they still exist. This Work Element funds an analysis to determine the circumstances under which juvenile interrogation will/not support unbiased analyses of juvenile abundance and/or survival.	Chinook (Oncorhynchus tshawytscha) - All Populations, Steelhead (Oncorhynchus mykiss) - All Populations
	J	132	Produce Progress (Annual) Report	Annual Project Report: Lemhi Outmigrant, PIT Assessments and Habitat monitoring findings	This annual report summarizes work completed in 2019, and will include the following chapters: 1. Operation report and juvenile abundance estimates generated by the lower-Lemhi River rotary screw trap. 2. Summary of approach and outcome of including Genetic Stock Identification data into statistical routines used to estimate spring/summer Chinook salmon and steelhead upstream of Lower Granite Dam. 3. Results of simulations to test the reliability and precision of escapement estimates for hatchery-origin fish upstream of Lower Granite Dam. 4. Summary of progress towards automating post-processing tasks associated with Salmonid Habitat Protocol. 5. Summary of findings with respect to the reliability of juvenile interrogation data at In-stream PIT Tag Detection Systems.
	K	156	Develop RM&E Methods and Designs	Yakima adult steelhead run reconstruction.	Develop a statistical model to estimate adult steelhead escapement to the Yakima River using detection data generated by In-stream PIT Tag Detection Systems (IPTDS).
	L	159	Transfer/Consolidate Regionally Standardized Data	Format and transfer ISEMP database to StreamNet DataStore	This Work Element funds the formatting and transfer of the entirety of ISEMP database to BPA in a format specified by BPA to the StreamNet DataStore. This is payment for completion of work conducted under project 2003-017-00, contract 77480.	Chinook (O. tshawytscha) - Mid-Columbia River Spring ESU, Chinook (O. tshawytscha) - Snake River Spring/Summer ESU (Threatened), Chinook (O. tshawytscha) - Upper Columbia River Spring ESU (Endangered), Chinook (O. tshawytscha) - Upper Columbia River Summer/Fall ESU, Cutthroat Trout, Coastal (O. c. clarkii) - Southwest Washington/Columbia River ESU, Steelhead (O. mykiss) - Middle Columbia River DPS (Threatened), Steelhead (O. mykiss) - Snake River DPS (Threatened)	Cutthroat Trout, Coastal (O. clarkii clarkii)- Resident Populations, Trout, Brook (Salvelinus fontinalis), Trout, Bull (S. confluentus) (Threatened), Trout, Rainbow (Oncorhynchus mykiss)