Rebecca A. Buchanan

Review of marking methods and release-recapture designs for estimating the survival of very small fish: examples from the assessment of salmonid fry survival.

The survival of very small fish can have a major impact on the dynamics of fisheries stocks. Numerous marking techniques have been developed or adapted to small fish in order to investigate either early life histories or small-sized species. Some techniques provide batch marks, while others provide individually unique identification with or without the need for destructive sampling. We review 20 marking techniques in the context of conducting survival studies for small fish, with examples focused on salmonid fry survival. Sixteen alternative release-recapture designs for conducting survival investigations are also examined. Eleven approaches are found capable of estimating survival parameters, while five are not. Of those methods capable of estimating fish survival, five require unique marks, and six permit batch-specific marks. No approach based on a single release of batch-marked fish is capable of statistically estimating survival. Investigators are encouraged to carefully coordinate their choice of marking technique with the design and analysis of the release-recapture model used.

A Multiple-Release Model to Estimate Route-Specific and Dam Passage Survival at a Hydroelectric Project

Abstract Previous methods of estimating route-specific passage and survival probabilities for anadromous salmonids past hydroelectric dams have often failed because of faulty assumptions. We present a robust, multiple-release model that combines release–recapture methods that are known to solve parts of the overall problem. Release 1 allows estimation of route-specific passage proportions and relative route-specific survival probabilities. Releases 2 and 3 provide an estimate of absolute survival through a particular route, which gives estimates of absolute route-specific survival probabilities and dam survival when combined with release 1. Releases 1 and 4 together provide an estimate of project (dam and pool) survival. Combining information from all four releases gives estimates of pool survival. The method is demonstrated through a 2006 study of sockeye salmon Oncorhynchus nerka passing Rocky Reach Dam on the Columbia River in Washington State. We estimate that the majority of tagged smolts passed via ...

Route Use and Survival of Juvenile Chinook Salmon through the San Joaquin River Delta

Abstract The survival of juvenile Chinook Salmon through the lower San Joaquin River and Sacramento–San Joaquin River Delta in California was estimated using acoustic tags in the spring of 2009 and 2010. The focus was on route use and survival within two major routes through the Delta: the San Joaquin River, which skirts most of the interior Delta to the east, and the Old River, a distributary of the San Joaquin River leading to federal and state water export facilities that pump water out of the Delta. The estimated probability of using the Old River route was 0.47 in both 2009 and 2010. Survival through the southern (i.e., upstream) portion of the Delta was very low in 2009, estimated at 0.06, and there was no significant difference between the Old River and San Joaquin River routes. Estimated survival through the Southern Delta was considerably higher in 2010 (0.56), being higher in the Old River route than in the San Joaquin route. Total estimated survival through the entire Delta (estimated only in 2...

Estimating the Effects of Smolt Transportation from Different Vantage Points and Management Perspectives

Abstract Smolt transportation is a major mitigation strategy in the Columbia River hydrosystem, yet measures of its effects on adult return rates are often unclear. Managers use a variety of transportation effect measures that need to be clearly defined and easy to understand. We develop eight alternative transportation effect measures based on a release–recapture model of juvenile and adult passive integrated transponder tag data and relate the measures to different management perspectives. The performance measures include site-specific transport−in-river ratios (T/Is) that view the effect of transportation operations at a site either separate from (“isolated”) or in the context of (“contextual”) the rest of the transportation system. Both relative and absolute systemwide measures of transportation effects are developed, as well as measures for fish in the release group had they been untagged. All performance measures are calculated by the program ROSTER. Transportation effect measures for summer Chinook...

Calculating the variance of the finite rate of population change from a matrix model in Mathematica

Abstract The finite annual rate of population increase ( λ ) is a fundamental demographic parameter that characterizes the relative annual change in animal numbers. Uncertainty in the estimation of λ from demographic population viability analyses (PVAs) has been largely limited to sensitivity analysis, calculating a pseudo-distribution for λ ˆ using Monte Carlo methods, or by use of bootstrap methods. The delta method has been used and suggested by several researchers, but no one has provided the computational means to implement it. In this paper, we present Mathematica code to calculate λ and its variance based on eigenvalue calculations of a Leslie transition matrix. We demonstrate the procedure using data from a Hawaiian hawk ( Buteo solitarius ) study.

Evaluating Surrogacy of Hatchery Releases for the Performance of Wild Yearling Chinook Salmon from the Snake River Basin

Abstract The combined juvenile and adult detections of Snake River yearling Chinook salmon Oncorhynchus tshawytscha implanted with passive integrated transponder tags migrating through the hydroelectric facilities in the Federal Columbia River Power System were analyzed using the ROSTER statistical release–recapture model. This model was used to estimate the downriver survival of smolts, ocean survival, adult passage success, and smolt-to-adult ratios (SARs) for wild and hatchery-reared Chinook salmon released as yearlings in the Snake River basin from 1996 through 2004. Estimates from wild and hatchery release groups were compared to assess the extent to which hatchery stocks may be used as surrogates for endangered wild stocks. Wild release groups included both spring and summer Chinook salmon runs, while hatchery release groups were separated by run (spring versus summer). Overall, there was a significant difference between estimates from wild release groups and hatchery spring-run release groups for a...

The effects of high detection probabilities on model selection in paired release-recapture studies in the era of electronic tagging studies

BackgroundAcoustic-tag studies with their high to very high detection rates defy traditional statistical wisdom regarding analysis of tagging studies. Conventional wisdom has been to use a parsimonious model with the fewest parameters that adequately describes the data to estimate survival parameters in release-recapture studies in order to find a reasonable trade-off between precision and accuracy. This quest has generated considerable debate in the statistical community on how to best accomplish this task. Among the debated options are likelihood ratio tests, Bayesian information criterion, Akaike information criterion, and model averaging.ResultsOur Monte Carlo simulation studies of paired release-recapture, acoustic-tag investigations indicate precision is the same if a fully parameterized or a reduced parameter model is used for data analysis if detection probabilities are very high. In addition, the fully parameterized model is robust to heterogeneous survival and detection processes, while a reduced parameter model may be sensitive to misspecification.ConclusionsUse fully parameterized, paired release-recapture models when detection probabilities are very high (≥0.90) to analyze acoustic-tagging data in order to retain both robustness and precision, and without the subjectivity and ambiguity introduced by the choice and application of model selection techniques.

A migratory life-cycle release-recapture model for salmonid PIT-tag investigations

AbstractSince 1987, millions of juvenile salmonids (smolts; Oncorhynchus species) in the Snake and upper Columbia rivers have been tagged with Passive Integrated Transponder (PIT) tags, and detected at hydroelectric projects as theymigrate downriver to the Pacific Ocean. Since the late 1990s, detection of PIT-tagged adults has been possible at some dams. Existing release-recapture models are designed for either juvenile data or adult data, but not both.We present amigratory life-cycle release-recapture model that follows tagged individuals from their release as juveniles through their return migration as adults, accounting for downstream barge transportation of juveniles, right-censoring due to known removals at dams, and adult age at maturity. This branching model estimates river survival, age-specific probabilities of adult return, and relative effects of smolt transportation on survival. Performance measures are defined using model parameters. We analyze a dataset of 58,447 PIT-tagged summer Chinook salmon released in 2000 in the Snake River. For nontransported fish, juvenile survival from passage at Lower Granite Dam to Bonneville Dam was estimated at 60.3% (

Generation of multistate release–recapture models using a graphic user interface (GUI)

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