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Survival of juvenile salmonids in the Sacramento–San Joaquin Delta (Delta) varies by migration route, and thus the proportion of fish that use each route affects overall survival through the Delta. Understanding factors that drive routing at channel junctions along the Sacramento River is therefore critical to devising management strategies that maximize survival. Here, we examine entrainment of acoustically tagged juvenile Chinook Salmon into Sutter and Steamboat sloughs from the Sacramento River. Because these sloughs divert fish away from the downstream entrances of the Delta Cross Channel and Georgiana Slough (where fish access the low-survival region of the interior Delta), management actions to increase fish entrainment into Sutter and Steamboat sloughs are being investigated to increase through-Delta survival. Previous studies suggest that fish generally “go with the flow”—as net flow into a divergence increases, the proportion of fish that enter that divergence correspondingly increases. However, complex tidal hydrodynamics at sub-daily time-scales may be decoupled from net flow. Therefore, we modeled routing of acoustic tagged juvenile salmon as a function of tidally varying hydrodynamic data, which was collected using temporary gaging stations deployed between March and May of 2014. Our results indicate that discharge, the proportion of flow that entered the slough, and the rate of change of flow were good predictors of an individual’s probability of being entrained. In addition, interactions between discharge and the proportion of flow revealed a non-linear relationship between flow and entrainment probability. We found that the highest proportions of fish are likely to be entrained into Steamboat Slough and Sutter Slough on the ascending and descending limbs of the tidal cycle, when flow changes from positive to negative. Our findings characterize how patterns of entrainment vary with tidal flow fluctuations, providing information critical for understanding the potential effect of management actions (e.g., fish guidance structures) to modify routing probabilities at this location.

Because fish that enter the interior Delta have poorer survival than those emigrating via the Sacramento River, understanding the mechanisms that drive entrainment rates at side channel junctions is critically important for the management of imperiled juvenile salmon. Here, we implement a previously proposed process-based conceptual model to study entrainment rates based on three linked elements: the entrainment zone, critical streakline, and cross-sectional distribution of fish. The critical streakline is the location along a channel cross-section immediately upstream of a junction that forms the spatial divide between parcels of water that enter a side channel or remain in the main channel. The critical streakline therefore divides the main channel into entrainment zones within which fish would likely enter each channel. Combined with information about the cross-sectional distribution of fish upstream of a junction, this conceptual model provides a means to predict fish entrainment into each channel. To apply this conceptual model, we combined statistical models of the critical streakline, the cross-sectional distribution of acoustic tagged juvenile Chinook salmon, and their probability of entrainment into Georgiana Slough. We fit joint beta regression and logistic regression models to acoustic telemetry data gathered in 2011 and 2012 to estimate the cross-sectional distribution of fish upstream of the junction, and to estimate the probability of entrainment for fish on either side of the critical streakline. We show that entrainment rates can be predicted by understanding how the combination of critical streakline position and cross-sectional distribution of fish co-vary as a function of environmental covariates. By integrating over individual positions and entrainment fates to arrive at population-level entrain probability in relation to environmental covariates, our model offers managers a simple but powerful tool to evaluate how alternative actions affect migrating fish.

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 [...]

A robust monitoring network that provides quantitative information about the status of imperiled species at key life stages and geographic locations over time is fundamental for sustainable management of fisheries resources. For anadromous species, management actions in one geographic domain can substantially affect abundance of subsequent life stages that span broad geographic regions. Quantitative metrics (e.g., abundance, movement, survival, life history diversity, and condition) at multiple life stages are needed to inform how management actions (e.g., hatcheries, harvest, hydrology, and habitat restoration) influence salmon population dynamics. The existing monitoring network for endangered Sacramento River winter-run Chinook Salmon (SRWRC, Oncorhynchus tshawytscha) in California’s Central Valley was compared to conceptual models developed for each life stage and geographic region of the life cycle to identify relevant SRWRC metrics. We concluded that the current monitoring network was insufficient to diagnose when (life stage) and where (geographic domain) chronic or episodic reductions in SRWRC cohorts occur, precluding within- and among-year comparisons. The strongest quantitative data exist in the Upper Sacramento River, where abundance estimates are generated for adult spawners and emigrating juveniles. However, once SRWRC leave the upper river, our knowledge of their identity, abundance, and condition diminishes, despite the juvenile monitoring enterprise. We identified six system-wide recommended actions to strengthen the value of data generated from the existing monitoring network to assess resource management actions: (1) incorporate genetic run identification; (2) develop juvenile abundance estimates; (3) collect data for life history diversity metrics at multiple life stages; (4) expand and enhance real-time fish survival and movement monitoring; (5) collect fish condition data; and (6) provide timely public access to monitoring data in open data formats. To illustrate how updated technologies can enhance the existing monitoring to provide quantitative data on SRWRC, we provide examples of how each recommendation can address specific management issues

As juvenile salmon enter the Sacramento–SanJoaquin River Delta (“the Delta”) they disperse among its complex channel network where they are subject to channel-specific processes that affect their rate of migration, vulnerability to predation, feeding success, growth rates, and ultimately, survival. In the decades before 2006, tools available to quantify growth, dispersal, and survival of juvenile salmon in this complex channel network were limited.Fortunately, thanks to technological advances such as acoustic telemetry and chemical and structural otolith analysis, much has been learned over the past decade about the role of the Delta in the life cycle of juvenile salmon. Here, we review new science between 2006and 2016 that sheds light on how different life stages and runs of juvenile salmon grow, move, and survive in the complex channel network of the Delta. One of the most important advances during the past decade has been the widespread adoption of acoustic telemetry techniques. Use of telemetry has shed light on how survival varies among alternative migration routes and the proportion of fish that use each migration route. Chemical and structural analysis of otoliths has provided insights about when juveniles left their natal river and provided evidence of extended rearing in the brackish or saltwater regions of the Delta. New advancements in genetics now allow individuals captured by trawls to be assigned to specific runs. Detailed information about movement and survival in the Delta has spurred development of agent-based models of juvenile salmon that are coupled to hydrodynamic models. Although much has been learned, knowledge gaps remain about how very small juvenile salmon (fry and parr) use theDelta. Understanding how all life stages of juvenile salmon grow, rear, and survive in the Delta is critical for devising management strategies that support a diversity of life history strategies.

Objective: Managers can modify river flow regimes using fish monitoring data to minimize impacts from water management infrastructure. For example, operation of the gate-controlled Delta Cross Channel (DCC) in California can negatively affect the endangered Sacramento River winter-run Chinook Salmon Oncorhynchus tshawytscha. Although guidelines have been developed for DCC operations by using real-time juvenile fish sampling count data, there is uncertainty about how environmental conditions influence fish occupancy and the extent to which those relationships are affected by sampling and identification error. Methods: We evaluated the effect of environmental conditions, imperfect detection, and misidentification error on salmon occupancy by analyzing data using hierarchical multistate occupancy models. A total of 14,147 trawl tows and beach seine hauls were conducted on 1058 sampling days between October and December from 1996 to 2019. During these surveys, 2803 juvenile winter-run Chinook Salmon were identified, and approximately 29% of the sampling days had at least one winter-run juvenile detected. Result: The probability of misidentifying an individual juvenile winter-run Chinook Salmon in the field was estimated to be 0.056 based on fish identification examinations and genetic sampling. Occupancy varied considerably and was related to flow characteristics, water clarity, weather, time of year, and whether occupancy was detected during the previous sampling day. However, these relationships and their significance changed considerably when accounting for imperfect detection and the probability of misidentifying individual juvenile salmon. Detection was <0.3 under average sampling conditions during a single sample and was influenced by flow, water clarity, site, and volume sampled. Conclusion: Our modeling results indicate that DCC gate closure decisions could occur on fewer days when imperfect detection and misidentification error are not accounted for. These findings demonstrate the need to account for identification and detection error while using monitoring data to assess factors influencing fish occupancy and inform future management decisions. [ABSTRACT FROM AUTHOR]

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 [...]

Models that formulate mathematical linkages between fish use and habitat characteristics are applied for many purposes. For riverine fish, these linkages are often cast as resource selection functions with variables including depth and velocity of water and distance to nearest cover. Ecologists are now recognizing the role that detection plays in observing organisms, and failure to account for imperfect detection can lead to spurious inference. Herein, we present a flexible N-mixture model to associate habitat characteristics with the abundance of riverine salmonids that simultaneously estimates detection probability. Our formulation has the added benefits of accounting for demographics variation and can generate probabilistic statements regarding intensity of habitat use. In addition to the conceptual benefits, model application to data from the Trinity River, California, yields interesting results. Detection was estimated to vary among surveyors, but there was little spatial or temporal variation. Additionally, a weaker effect of water depth on resource selection is estimated than that reported by previous studies not accounting for detection probability. N-mixture models show great promise for applications to riverine resource selection. Les modeles qui formulent des liens mathematiques entre l'utilisation d'habitats par les poissons et les caracteristiques des habitats sont utilises a differentes fins. Pour les poissons de riviere, ces liens sont souvent presentes sous forme de fonctions de selection de ressources avec des variables comme la profondeur et la vitesse de l'eau et la distance du couvert le plus proche. Les ecologistes reconnaissent maintenant le role que joue la detection dans l'observation d'organismes, et le defaut de tenir compte d'une detection imparfaite peut mener a des inferences erronees. Nous presentons un modele de melange de N souple pour associer des caracteristiques de l'habitat a l'abondance de salmonides de riviere qui estime simultanement la probabilite de detection. Notre formulation a aussi l'avantage de tenir compte des variations demographiques et peut generer des enonces probabilistes concernant l'intensite de l'utilisation de l'habitat. En plus des avantages conceptuels, l'application du modele a des donnees de la riviere Trinity (Californie, Etats-Unis) donne des resultats interessants. S'il est estime que la detection varie selon la personne qui realise le releve, il y a peu de variation spatiale ou temporelle. En outre, l'effet estime de la profondeur de l'eau sur la selection de ressources est plus faible que ce dont font etat des etudes anterieures qui ne tiennent pas compte de la probabilite de detection. Les modeles de melange de N sont tres prometteurs pour des applications touchant a la selection de ressources dans les cours d'eau. [Traduit par la Redaction], Introduction Coupled physical and biological models often focus on interactions of target species with their environment for the purposes of exploring emergent properties (Harvey and Railsback 2009), evaluating management scenarios [...]

We conducted a meta-analysis of laboratory- and hatchery-based growth data to estimate broadly applicable parameters of mass- and temperature-dependent growth of juvenile coho salmon (Oncorhynchus kisutch). Following studies of other salmonid species, we incorporated the Ratkowsky growth model into an allometric model and fit this model to growth observations from eight studies spanning ten different populations. To account for changes in growth patterns with food availability, we reparameterized the Ratkowsky model to scale several of its parameters relative to ration. The resulting model was robust across a wide range of ration allocations and experimental conditions, accounting for 99% of the variation in final body mass. We fit this model to growth data from coho salmon inhabiting tributaries and constructed ponds in the Klamath Basin by estimating habitat-specific indices of food availability. The model produced evidence that constructed ponds provided higher food availability than natural tributaries. Because of their simplicity (only mass and temperature are required as inputs) and robustness, ration-varying Ratkowsky models have utility as an ecological tool for capturing growth in freshwater fish populations. Nous avons realise une meta-analyse de donnees sur la croissance obtenues en laboratoire et en ecloserie afin d'estimer des parametres largement applicables de la croissance dependant de la masse et de la temperature pour les saumons cohos (Oncorhynchus kisutch) juveniles. A l'instar d'etudes sur d'autres especes de salmonides, nous avons incorpore le modele de croissance de Ratkowsky dans un modele allometrique et cale ce modele sur des observations sur la croissance provenant de huit etudes portant sur dix populations differentes. Pour expliquer des variations des motifs de croissance en fonction de la disponibilite de nourriture, nous avons reparametre le modele de Ratkowsky pour ajuster a la ration l'echelle de plusieurs de ses parametres. Le modele en decoulant est robuste pour une grande fourchette d'allocations de rations et de conditions experimentales, expliquant 99 % de la variation de la masse corporelle finale. Nous avons cale ce modele sur des donnees de croissance pour des saumons cohos habitant des affluents et des etangs amenages dans le bassin du fleuve Klamath en estimant des indices de disponibilite de nourriture propres a l'habitat. Les resultats du modele indiquent que les etangs amenages presentent une plus grande disponibilite de nourriture que les affluents naturels. En raison de leur simplicite (les seules entrees requises sont la masse et la temperature) et leur robustesse, les modeles de Ratkowsky a rations variables constituent un outil ecologique utile pour decrire la croissance dans les populations de poissons d'eau douce. [Traduit par la Redaction], Introduction In Pacific salmon (Oncorhynchus spp.), growth rates of juvenile fish are an important factor underlying productivity (Koenings et al. 1993; Beamish and Mahnken 2001; Ebersole et al. 2006; Connor [...]

Worldwide, many productive rivers are dam‐regulated and rely on flow management strategies that must balance support of ecological processes with human water use. One component of evaluating this balance is to understand ecological consequences of alternative flow management strategies, which has often been accomplished by coupling population dynamics models with models that relate streamflow to habitat availability and quality. Numerous methods assign habitat availability to locations within a river basin: These include fine‐scale field‐measured values that are extrapolated to other locations within the basin having similar physical characteristics or equation‐driven values created by functions of model‐predicted values of physical characteristics. The array of options for creating habitat models is evolving rapidly as high‐resolution remote‐sensing data becomes more accessible and computational capacity improves. Our objective was to identify trade‐offs among approaches that assign habitat relationships to large rivers and to create a decision support tool to supplement choices of extent and granularity. Using a selection of case studies that represent a breadth of scales and diverse trade‐offs, we demonstrate the need for a transparent process of data evaluation and assessment to determine the appropriate fit for model scope or context that best supports management needs and recognize sources of uncertainty. The structured approach proposed here aims at improving future model development and refine population dynamics models that inform the management of rivers. [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]