This project will be conducted by the US Geological Survey (USGS), US Fish and Wildlife Service (USFWS),  NOAA Fisheries, and the University of Idaho.  This goal of this project is to understand the mechanisms underlying Snake River juvenile fall Chinook salmon life history diversity and its consequences to management activities such as transportation and flow augmentation. It also seeks to quantify mortality risks that ultimately affect population productivity.

This project will explore two main avenues of research. First, we will explore the potential mortality risks faced by subyearlings that delay seaward migration and adopt a reservoir-type life history. This will include predation by smallmouth bass and channel catfish. We will also continue our sampling of food resources for both subyearling and reservoir-type fall Chinook salmon and the role they play in life history diversity.  Second, we will develop otolith microchemistry as a tool to determine juvenile life history and origin from the otoliths of returning adults.

Many of the subyearling fall Chinook salmon produced (both hatchery and natural) in the Clearwater River delay their seaward migration and ultimately adopt a reservoir-type life history. Much of this delay occurs in the last 4 miles of the Clearwater River and in the area just downstream of its confluence with the Snake River. This is important because mortality of delaying fish due to predation is likely one of the costs of fish adopting a reservoir-type life history. We propose to examine predation as a potential cost (in terms of survival) to fish that delay seaward migration. With the implementation of hatchery supplementation and increase in natural production, the abundance of subyearlings is far greater today than it was 15 years ago when the last subyearling predation studies were done. Therefore, predation may pose a significant risk to subyearlings and may reduce the productivity of the Snake River population. We will estimate the loss of subyearlings to predation, which will indicate whether predation is a significant problem. Managers could then use that information to decide whether predator control is warranted through changing sport harvest regulations for smallmouth bass and channel catfish.

The life-history complexity of Snake River fall Chinook salmon has hindered efforts to manage this ESU. For example, the existence of an overwintering behavior in a portion of the population has complicated our ability to estimate survival through the hydropower system. In addition, because many of the yearling migrants move downstream after PIT-tag detection systems are disabled in the fall/winter, we have limited information on migratory patterns of these fish, which comprise a substantial proportion of returning adults. Because of this uncertainty, major modeling efforts, such as COMPASS modeling and life-cycle modeling of the Interior Columbia Technical Recovery Team, were not able to model the population dynamics of Snake River fall Chinook, and there is a strong desire with the region to rectify this problem. In addition, it is still unclear whether Snake River fall Chinook benefit from transportation. Until we have a better understanding of this life-history complexity, particularly the habitat usage of overwintering juveniles, it will be difficult to efficiently manage the entire ESU. Effective management of reservoir-type fish will require an understanding of the details of their life-history, including the proportion of juveniles that exhibit the strategy, where they over-winter, when they initiate downstream migration in the spring, and estuarine residence time.

Our proposed otolith work is important because it will useful for identifying fish origin and juvenile life history patterns from returning adults. Currently, many of the adults that pass Lower Granite Dam, where a portion is collected for broodstock, are unmarked. These unmarked adults comprise fish of hatchery and natural origin, fish produced in different spawning areas and hatcheries, and fish with both ocean-type and reservoir-type juvenile life histories. Because this information is currently lacking, it complicates run reconstruction and introduces uncertainty in resulting estimates of different population segments. Run reconstruction is critically important to determining whether progress toward recovery is being made and if goals are likely to be met. Our work will contribute to life cycle modeling for fall Chinook salmon by removing some of the uncertainty in run reconstruction. This approach will be more reliable for determining whether fish are of hatchery or natural origin than scale pattern analysis, the accuracy of which has recently been questioned. Furthermore, it will allow us to determine the hatchery or river of origin for each fish, how long fish spent in different rearing environments, and where they overwintered. This approach has a large advantage of being less expensive and labor-intensive, and with fewer restrictions than methods like telemetry, which have been used in the past. In addition, it is also more useful for collecting data and making inferences at the population level. Telemetry as a tool to study juvenile life history is often limited by small sample sizes (not being able to capture enough fish), tags that are too large for smaller fish, tags that do not last long enough, tag effects on behavior and survival, and not adequately representing the population of interest. Our approach will enhance ongoing run reconstruction by providing information on the proportion of different juvenile life history types that contribute to the adult population and will support inferences made at this level. It will provide insight into which rivers and rearing areas (including the estuary) are most productive, which should be useful for focusing research, management, and recovery actions.

We will use established peer-reviewed methods to collect and analyze predation data so our results can be compared with those of past studies. We will collect smallmouth bass and channel catfish by electrofishing and hoop nets, respectively, throughout the subyearling outmigration. Predators will be tagged and released to subsequently estimate their abundance using a mark-recapture analysis. Stomach contents will be examined to describe predator diets and to estimate the number of subyearlings consumed. Predator abundance and consumption estimates of subyearlings will be used to estimate the annual loss of subyearlings. We will continue with monthly food resources sampling to determine if prey items such as Neomysis and Siberian prawns are also important to predators of juvenile fall Chinook.  Microchemistry to determine juvenile life history will be performed on otoliths collected from adults at Lower Granite Dam and taken to Lyons Ferry and the Nez Perce Tribal hatcheries. Otoliths from known-origin fish and water samples from different rearing environments will be collected to validate methods and chemical signatures of water sources. This study will take place in the Snake and Clearwater rivers and the lower Snake River reservoirs. Predation work will be conducted in the Snake and Clearwater River arms and the confluence area in the upper portion of Lower Granite Reservoir.  Life history information obtained from otoliths will span the entire Snake and Columbia rivers to the estuary. Our proposed study will take place from FY12-14. The USGS and USFWS will conduct all predation food resources work and will participate in the otolith work. The NOAA Fisheries and the UI will be responsible for conducting the otolith work.