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Regional Back Ground
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Project 199102900 began in 1991 to provide some of the first biological data on the contemporary population of fall Chinook salmon Oncorhynchus tshawytscha in the Snake River basin that was eventually listed in 1992 under the Endangered Species Act as the Snake River fall Chinook salmon evolutionary significant unit (ESU). Up until 2018, the project was implemented cooperatively by staff of the U.S. Fish and Wildlife Service and the U.S. Geological Survey. In 2018, the USGS assumed primary sponsorship of the project. As in past years, the project continue to complement and be coordinated with existing Snake River fall Chinook salmon ESU projects including staff of Idaho Power Company, the Nez Perce Tribe Department of Fisheries Resources Management, National Oceanographic and Atmospheric Administration, University of Idaho, Idaho Department of Fish and Game, Oregon Department of Fish and Wildlife, and Washington Department of Fish and Wildlife.

This project provides information that contributes to evaluating the effectiveness of recovery measures outlined in the 2020 Biological Opinion for the Columbia River System. Specifically, this project developed the only Snake River fall Chinook life-cycle model that was used to evaluate various operational scenarios for the 2020 BiOp. This model uses passage data collected on PIT tagged natural subyearlings and this project is the only project tagging natural-origin juveniles in the Snake River. It also uses abundance data on adult spawners that this helps collect. Collectively, the data and model are critical in monitoring the population's progress toward reaching recovery metrics specified in the Snake River Fall Chinook Recover Plan. Methods to estimate the annual abundance of juvenile fall Chinook passing Lower Granite Dam continues to be refined as well as life-cycle model development that includes covariates that effect the population of fall Chinook salmon.

We will also summarize historical data and collect new data to make progress towards answering two questions posed in the Snake River Fall Chinook Recovery Plan: (1) is the ESU abundant, diverse, productive, and spatially distributed; and (2) is the ESU responding to implemented actions as anticipated?  We recast these two questions as regional objectives: (1) increase the abundance, productivity, and spawning distribution of natural origin adults, and (2) increase the abundance and diversity of natural-origin subyearlings during early freshwater rearing and migration.  The success criteria for regional objective 1 will be: (1) an increased understanding of the anthropogenic, biological, and environmental factors that influenced historical and contemporary trends in adult abundance that will lead to measures implemented to meet delisting criteria of 3,000 natural-origin spawners (measured as a 10-year geometric mean), (2) an increased understanding of how varying influential anthropogenic, biological, and environmental factors might facilitate meeting the minimum viability threshold of 1% risk of quasi-extinction, and (3) documentation of the status of escapement of natural-origin adults to the spawning areas relative to the explicit population level spatial structure criteria, and (4) support for expanded life-cycle and passage modeling.  The success criteria for objective 2 will be: (1) estimates of passage abundance for natural-origin fall Chinook salmon subyearlings at Lower Granite Dam during the spring, summer, and fall, (2) an increased understanding of the anthropogenic, biological, and environmental factors that influence trends in passage abundance, (3) an increased understanding of how varying influential anthropogenic, biological, and environmental factors might increase passage abundance of natural-origin fall Chinook salmon subyearlings, (4) an increased understanding of the effect of predation in riverine habitat on passage abundance of natural-origin fall Chinook salmon subyearlings, and (5) support for expanded life-cycle and passage models.

We will accomplish the regional objectives by accomplishing several scientific objectives each of which will produce final deliverables including models to support the AMIP process.


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Regional Objective 1 Final Deliverables
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Final deliverable 1A will be a set of models that provide a historical retrospective of adult abundance and spawning distribution that will rely on adult counts made without distinction of adult origin, but with redd counts made throughout the Snake River basin from 1947 to 2023. These models will accomplish the following scientific objectives: (1) produce counts of adult spawners that will be used to determine if numerical trends in spawners is moving toward the recovery goal of 3000 natural-origin adults in the Snake River, (2) produce annual counts and locations of redds to determine if redds are spatially distributed throughout the contemporary spawning area; (3) produce correlations between adult and redd counts to determine if redd counts can accurately and precisely predict adult counts to gage meeting recovery criteria of 3000 natural-origin spawners in the Snake River, and (4) identify the anthropogenic, biological, and environmental factors that influence adult counts. In 2023, we will add to our existing adult data set to address these objectives. The models and continued analysis of adult productivity through empirical data collection and life-cycle modeling will help complete regional objective 1 success criterion 1.

Final deliverable 1B will be a second set of models that help to explain and predict increases in the abundance, productivity, and spawning distribution of natural origin adults by focusing on estimated counts of natural-origin adults at Lower Granite Dam from run construction and on redd counts made upstream of Lower Granite Reservoir after 1982 (or as early as possible depending on data availability).  It will accomplish the following scientific objectives: (1) increase the understanding of how the numerical trends in the estimated counts of natural-origin adults during 1983–2023 were influenced by anthropogenic, biological, and environmental change, (2) predict how varying influential anthropogenic, biological, and environmental factors might affect the status of natural-origin adults relative to the minimum viability threshold, and (3) predict the status of escapement of natural-origin adults to the spawning areas relative to the explicit population level spatial structure criteria.  

One of the recovery measures recently implemented for the Snake River fall Chinook salmon population was the creation of a natural production area in the upper reach of Hells Canyon above Pittsburg Landing. The intent of this action is to create a stronghold for natural-origin adults in this area. In 2018, hatchery supplementation releases were moved from Hells Canyon Dam to the Salmon River. With less hatchery influence, the area is expected to see an increase in natural-origin fish. Over time, population metrics (e.g., catch, timing of fry and parr presence, growth) of juvenile fall Chinook in Hells Canyon will be compared to these same metrics from the population of juvenile fall Chinook that are produced and rear in the Salmon River. The Hells Canyon population will serve as a control or baseline against which the growth of the Salmon River population can be compared. The proportions of hatchery and natural-origin spawners will be measured annually to determine the efficacy of ending hatchery supplementation releases in Hells Canyon. This is an important metric for NOAA Fisheries to gauge the effectiveness of this action.

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Regional Objective 2 Final Deliverables
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Final deliverable 2A will be set of models that help to explain and predict variation in passage abundance of natural-origin subyearlings at Lower Granite dam during 1992–2023. The scientific objectives will be to: (1) produce annual estimates of passage abundance of natural-origin fall Chinook salmon subyearlings estimated by reconstructing the run in order to examine annual trends in abundance; (2) compare annual passage timing distributions calculated using different methods, (3) Identify the anthropogenic, biological, and environmental changes that influence the numerical trends in juvenile passage abundance, (4) produce life-cycle modeling results using data from scientific objectives 1 and 2 to predict how varying influential anthropogenic, biological, and environmental factors might increase abundance of natural-origin fall Chinook salmon subyearlings. To date, a peer-reviewed journal article has been published detailing a state-space model to determine collection probability of juvenile fish at Lower Granite Dam (Hance et al. 2019). A draft manuscript on estimating juvenile fall Chinook abundance at Lower Granite Dam is currently in its final stage of editing before submission to a journal. Expected publication is late 2023.

To accomplish this objective, project staff will continue annual PIT tagging efforts in the Snake River. In addition, we began PIT tagging fall Chinook in the Salmon River starting in 2021 and this will continue in 2023 to evaluate the effectiveness of the relocated Hells Canyon supplementation releases to the Salmon River. Over time, population metrics (e.g., catch, timing of fry and parr presence, growth) of juvenile fall Chinook in the Salmon River will be compared to these same metrics from the population of juvenile fall Chinook that are produced and rear in Hells Canyon. The Hells Canyon population will serve as a control or baseline against which the growth of the Salmon River population can be compared. This will be an important monitoring activity because it is closely related to the effectiveness of the natural production area in Hells Canyon.

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Monitoring Total Dissolved Gas Effects
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The regional variable spill program implemented in 2020 increases the total dissolved gas (TDG) cap from 120 to 125%. Under the 2020 Biological Opinion for the Columbia River System, BPA is required to monitor the effects of increased TDG on native resident fishes. This will be a new task for project 199102900 that began in FY21 and will continue through FY2024. The tailrace areas of four projects (Bonneville, McNary, Ice Harbor, and Lower Granite) will be sampled for resident fish during the spring spill season (April through June). Fish will be examined for gas bubble trauma (GBT) using regional protocols and weekly reports will be provided. Sampling will continue in 2023 based on lessons learned in 2021 and 2022.