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Juvenile salmonids migrate hundreds of kilometers from their natal streams to mature in the ocean. Throughout this migration, they respond to environmental cues such as local water velocities and other stimuli to direct and modulate their movements, often through heavily modified riverine and estuarine habitats. Management strategies in an uncertain future of climate change and altered land use regimes depend heavily on being able to reliably predict their ocean entry timings, route use, and survival rates through rivers and estuaries. We developed a spatially-explicit agent-based model of fish movement in response to hydrodynamic flows that uses movement dynamics gleaned from multi-dimensional tracking datasets of acoustically tagged juveniles moving through an urbanized, branched tidal estuary. We demonstrate how such models can be calibrated, and we apply it to the Sacramento-San Joaquin Delta in Central California. The quality of the out-of-sample validation of the model to predict juvenile salmon survival and route selection indicates that the model is versatile and flexible enough to be used in novel hydroclimatological conditions

We developed a novel statistical model to relate the daily survival and migration dynamics of an endangered anadromous fish to river flow and water temperature during both extreme drought and severe flooding in an intensively managed river system. Our Bayesian temporally stratified multistate mark-recapture model integrates over unobserved travel times and route transitions to efficiently estimate covariate relationships and includes an adjustment for telemetry tag battery failure. We applied the model to acoustic-tagged juvenile Sacramento River winter-run Chinook salmon (Oncorhynchus tshawytscha) and found that survival decreased with decreasing river flows and increased water temperatures. We found that fish were likely to enter a large floodplain during flood conditions and that survival in the floodplain was comparable to the mainstem Sacramento River. Our study demonstrates the response of an endangered anadromous fish population to extreme spatial and temporal variability in habitat accessibility and quality. The general model framework we introduce here can be applied to telemetry of migratory fish through systems with multiple routes to efficiently estimate spatiotemporal variation in survival, travel time, and routing. Nous avons developpe un nouveau modele statistique pour relier la survie quotidienne et la dynamique de la migration d'un poisson anadrome en voie de disparition au debit de la riviere et a la temperature de l'eau durant des secheresses et des crues extremes dans un reseau hydrographique faisant l'objet d'une gestion intensive. Notre modele bayesien multi-etats de marquage-recapture stratifie dans le temps integre sur les durees de deplacement et les changements de routes non observes afin d'estimer efficacement des relations entre variables correlees et il comprend un ajustement pour tenir compte de la defaillance des piles d'etiquettes telemetriques. Nous appliquons le modele a des saumons chinooks (Oncorhynchus tshawytscha) juveniles de la migration hivernale dans le fleuve Sacramento dotes d'etiquettes acoustiques et constatons que la survie diminue quand les debits diminuent et que les temperatures de l'eau augmentent. Nous constatons aussi que les poissons sont susceptibles d'entrer dans une grande plaine inondable durant des conditions de crue et que la survie dans la plaine inondable est semblable a la survie dans le bras principal du fleuve Sacramento. L'etude illustre la reaction d'une population de poissons anadromes en voie de disparition a la variabilite spatiale et temporelle extreme de l'accessibilite et de la qualite des habitats. Le cadre general de modelisation que nous presentons peut etre applique a la telemetrie de poissons migrateurs dans des reseaux comptant des routes multiples, pour l'estimation efficace des variations spatiotemporelles de la survie, de la duree et des routes de deplacement. [Traduit par la Redaction], Introduction Populations of anadromous salmonids evolved in the context of significant spatial and temporal variation in riverine habitat. This variability includes daily, seasonal, and interannual fluctuations in discharge, temperature, and [...]

We evaluated the interacting influences of river flows and tides on travel time, routing, and survival of juvenile late-fall Chinook salmon (Oncorhynchus tshawytscha) migrating through the Sacramento-San Joaquin River Delta. To quantify these effects, we jointly modeled the travel time, survival, and migration routing in relation to individual time-varying covariates of acoustic-tagged salmon within a Bayesian framework. We used observed arrival times for detected individuals and imputed arrival times for undetected individuals to assign covariate values in each reach. We found travel time was inversely related to river inflow in all reaches, yet survival was positively related to inflow only in reaches that transitioned from bidirectional tidal flows to unidirectional flow with increasing inflows. We also found that the probability of fish entering the interior Delta, a low-survival reach, declined as inflow increased. Our study illustrates how river inflows interact with tides to influence fish survival during the critical transition between freshwater and ocean environments. Furthermore, our analytical framework introduces new techniques to integrate formally over missing covariate values to quantify effects of time-varying covariates. Nous avons evalue l'interaction des influences des debits de riviere et des marees sur le temps de deplacement, l'itineraire et la survie de saumons quinnats (Oncorhynchus tshawytscha) juveniles de fin d'automne migrant dans le delta des fleuves Sacramento et San Joaquin. Pour quantifier ces effets, nous avons modelise conjointement le temps de deplacement, la survie et l'itineraire de migration par rapport a differentes covariables variant dans le temps de saumons dotes d'etiquettes acoustiques dans un cadre bayesien. Nous avons utilise les temps d'arrivee observes pour les individus detectes et impute des temps d'arrivee pour les individus non detectes afin d'affecter des valeurs aux covariables dans chaque tronqon. Nous constatons que le temps de deplacement est inversement relie au debit entrant dans tous les tronqons, alors que la survie n'est positivement reliee au debit entrant que dans les tronqons ou des debits tidaux bidirectionnels passent a un ecoulement unidirectionnel quand les debits entrants augmentent. Nous constatons aussi que la probabilite que les poissons entrent dans le delta interieur, un tronqon caracterise par une faible survie, diminue quand le debit entrant augmente. L'etude illustre comment les debits entrants de rivieres interagissent avec les marees pour influencer la survie des poissons durant le passage critique du milieu d'eau douce au milieu oceanique. En outre, notre cadre d'analyse presente de nouvelles methodes permettant l'integration formelle sur des valeurs de covariables manquantes pour quantifier les effets de covariables variant dans le temps. [Traduit par la Redaction], Introduction Anadromous salmonids have evolved diverse life history strategies that capitalize on spatial and temporal variation in their habitat to maximize productivity. Understanding how salmonids use habitat over space and [...]

The Yakama Nation manages a program for reintroducing Sockeye Salmon Oncorhynchus nerka upstream of Cle Elum Dam in the Yakima River basin. The program involves transplanting of a mix of adult Sockeye Salmon from two middle Columbia River donor stocks, Lake Wenatchee (WEN) and Osoyoos Lake (OSO), with the goal of establishing a self‐sustaining population in the basin. In 2017, a subset of the transplanted population was radio‐tagged and monitored to assess stock‐specific responses to transplanting, including downstream entrainment at Cle Elum Dam ("fallback") and prespawn mortality. Tagged fish were active during the first 2 weeks after release. Some fish moved upstream into the Cle Elum River and then returned to the reservoir; other fish moved downstream and passed Cle Elum Dam. Movement within the study area diminished during August but increased in September when fish began migrating up the Cle Elum River for spawning. A greater proportion of WEN fish (76.3%) was detected entering the river compared to OSO fish (53.9%). The hazard ratio from a multistate analysis of fish behavior indicated that WEN fish were nine times more likely to enter the river than OSO fish. The WEN fish also initiated upstream movement 3 weeks earlier than OSO fish. We found that 27.0% of all tagged fish were lost to the spawning population through fallback (20.7%) and prespawn mortality (6.3%). Fallback and prespawn mortality occurred for a greater percentage of OSO fish (26.9% and 7.7%) than WEN fish (15.3% and 5.1%), but these differences were not statistically different. These results provide foundational information from the early phase of a reintroduction effort. Continued monitoring will be required as Sockeye Salmon evolve to conditions upstream of Cle Elum Dam, and results from these efforts will provide valuable insights for this reintroduction effort and others in river systems with similar characteristics. [ABSTRACT FROM AUTHOR]

Understanding drivers of temporal variation in demographic parameters is a central goal of mark‐recapture analysis. To estimate the survival of migrating animal populations in migration corridors, space‐for‐time mark–recapture models employ discrete sampling locations in space to monitor marked populations as they move past monitoring sites, rather than the standard practice of using fixed sampling points in time. Because these models focus on estimating survival over discrete spatial segments, model parameters are implicitly integrated over the temporal dimension. Furthermore, modeling the effect of time‐varying covariates on model parameters is complicated by unknown passage times for individuals that are not detected at monitoring sites. To overcome these limitations, we extended the Cormack–Jolly–Seber (CJS) framework to estimate temporally stratified survival and capture probabilities by including a discretized arrival time process in a Bayesian framework. We allow for flexibility in the model form by including temporally stratified covariates and hierarchical structures. In addition, we provide tools for assessing model fit and comparing among alternative structural models for the parameters. We demonstrate our framework by fitting three competing models to estimate daily survival, capture, and arrival probabilities at four hydroelectric dams for over 200 000 individually tagged migratory juvenile salmon released into the Snake River, USA. [ABSTRACT FROM AUTHOR]