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Elucidating the habitat-related processes driving variation in juvenile recruitment and population fluctuation is crucial for the conservation of freshwater fishes, particularly for species at risk, where recruitment variation increases at small population size. We used a combination of instream enclosure experiments and habitat use observations to investigate between-stream variation in recruitment of juvenile Nooksack Dace (Rhinichthys cataractae sp. cataractae), a federally endangered stream-dwelling minnow endemic to the lower Fraser Valley of British Columbia, Canada. There was no evidence for a recruitment bottleneck associated with high water temperature or low dissolved oxygen in spawning riffles at the egg incubation stage, or during a two week juvenile growth experiment in enclosures, although larval dace growth was positively related to temperature. However, immediately post-hatch dace showed a very strong preference for shallow (<5 cm deep), fine substrate marginal shoal habitat with no overhanging or instream vegetation cover, which was associated with well-developed pool-riffle channel structure. Shallow marginal rearing habitat was absent in the stream experiencing recruitment failure, where encroachment by invasive reed canarygrass (Phalaris arundinacea) created homogenous steep-bank habitat with heavy instream vegetation cover, implicating loss of critical marginal rearing habitat as the recruitment bottleneck. [ABSTRACT FROM AUTHOR]

Conservation planning requires understanding population sizes and trajectories. As with many imperiled species, green sturgeon (Acipenser medirostris) census data are limited, making it difficult to contextualize current threats and promote quantitative conservation goals. We combined spawning census, growth, and demographic data for the southern population of green sturgeon to build a population size and trajectory estimate. We generated a distribution of population size estimates and trajectories reflecting uncertainty from multiple sources. We then propagate these estimates through a demographic model to assess the potential impact of fishing bycatch. Our model suggests the population is below the recovery goal of 3000 adults. The most probable current total population estimate (including juveniles) is approximately 10 000 fish (5300–18 400 95% high density interval (HDI)), with 2400 adults (2197–2624 95% HDI). Simulated fishing bycatch pressure on the adults and subadults reduced abundance by a median value of 0.4% per year, which could be an impediment to recovery. Fisheries bycatch is one of many threats this population faces; this integrated framework may be used to assess how other threats may affect this population. [ABSTRACT FROM AUTHOR]

Sturgeons are among the most endangered fishes in the world. Identifying habitat use characteristics to inform restoration projects is crucial for recovery. However, small sample sizes, inadequate replication of studies, and limited spatial extents complicate our ability to effectively apply the findings of single studies to endangered species conservation across the larger riverscape. We synthesized information from amphidromous and anadromous sturgeons in North America to identify species-specific knowledge gaps and conduct a quantitative comparison of species–habitat relationships. We provided a qualitative summary of substrate use and synthesized estimates of depth and velocity during spawning and non-spawning activity. Generalized patterns among species were identified, such as spawning in fast water on hard substrate and then using slow water with soft substrate areas when not spawning. We noted species-specific variability during spawning that may be attributed to historical maximum length, egg characteristics, and watershed features. This study provides some of the first estimates of habitat use that can be adapted for many populations. Results can contribute to empirically grounded decision-support tools used to prioritize information needs for recovery. [ABSTRACT FROM AUTHOR]

Effective evaluation of technological and operational approaches to reduce entrainment of marine organisms at cooling water intake structures (CWIS) requires accurate organism-sensing systems. Current detection methods lead to large temporal data gaps, require tedious manual analysis, and are fatal to organisms. Here, we describe integrating deep learning with a non-lethal, non-intrusive imaging method—digital holography—to rapidly detect fish larvae. Laboratory experiments demonstrated that the instrument could successfully image fish larvae at flow rates exceeding ranges seen in CWIS. Holograms of two fish larvae species, in the presence of bubbles and detritus, were collected to build a large database for training a lightweight convolutional neural network. The model achieves 97% extraction accuracy in quantifying larvae, and distinguishing them from other particles, including detritus and bubbles, when applied to a dataset of manually classified images, exceeding previous metrics for non-lethal, accurate, and real-time detection. These results demonstrate the potential of in situ holographic imaging for monitoring endangered larval fish species at power plant intake structures, and for high-fidelity, real-time applications in monitoring aquatic ichthyoplankton. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

State-space population models are becoming a common tool to guide natural resource management, because they address the statistical challenges arising from high observation error and process variation while improving inference by integrating multiple, disparate datasets. A hierarchical state-space life cycle model was developed, motivated by delta smelt (Hypomesus transpacificus), an estuarine fish experiencing simultaneous risks of entrainment mortality from out-of-basin water export and natural mortality. Notable model features included a covariate-dependent instantaneous rates formulation of survival, allowing estimation of multiple sources of mortality, and inclusion of relative observation bias parameters, allowing integration of differently scaled abundance indices and entrainment estimates. Simulation testing confirmed that two sources of mortality, process variation, and data integration parameters could be estimated. Delta smelt entrainment mortality was associated with environmental conditions used to manage entrainment, and recruitment and natural mortality were related to temperature, freshwater flow, food, and predators. Although entrainment mortality was reduced in recent years, ecosystem conditions did not appear to support robust spawning or over-summer survival of new recruits, manifesting as a 98% reduction of adults during 1995–2015. [ABSTRACT FROM AUTHOR]

Choosing whether or not to migrate is an important life history decision for many fishes. Here we combine data from physical captures and detections on autonomous passive integrated transponder (PIT) tag antennas to study migration in an endangered fish, the humpback chub (Gila cypha). We develop hidden Markov mark–recapture models with and without antenna detections and find that the model fit without antenna detections misses a large proportion of fish and underestimates migration and survival probabilities. We then assess survival and growth differences associated with life history strategy and migration for different demographic groups (small male, small female, large male, large female). We find large differences in survival according to life history strategy, where residents had much lower overwinter survival than migrants. However, within the migratory life history strategy, survival and growth were similar for active migrants and skipped migrants for all demographic groups. We discuss some common challenges to incorporating detections from autonomous antennas into population models and demonstrate how these data can provide insight about fish movement and life history strategies. [ABSTRACT FROM AUTHOR]

The ability of passive integrated transponder (PIT) tag data to improve demographic parameter estimates has led to the rapid advancement of PIT tag systems. However, ghost tags create uncertainty about detected tag status (i.e., live fish or ghost tag) when using mobile interrogation systems. We developed a method to differentiate between live fish and ghost tags using a random forest classification model with a novel data input structure based on known fate PIT tag detections in the San Juan River (New Mexico, Colorado, and Utah, USA). We used our model to classify detected tags with an overall error rate of 6.8% (1.6% ghost tags error rate and 21.8% live fish error rate). The important variables for classification were related to distance moved and response to monsoonal flood flows; however, habitat variables did not appear to influence model accuracy. Our results and approach allow the use of mobile detection data with confidence and allow for greater accuracy in movement, distribution, and habitat use studies, potentially helping identify influential management actions that would improve our ability to conserve and recover endangered fish. [ABSTRACT FROM AUTHOR]

Fishways are a common tool for mitigating the effects of habitat fragmentation on fish, but their utility in low-gradient, sand-bed rivers of the Great Plains is not well studied. The Lincoln Street Fishway on the Arkansas River became operational in 2015 and was built specifically to pass small-bodied threatened fishes. We compared current and historical surveys up- and downstream of the barrier to test the effect of the fishway on community structure and conducted tagging experiments to test the ability of fishes to move into and through the fishway. Differences in community structure and species richness between communities up- and downstream of the dam were reduced following construction of the fishway. Surveys within the fishway revealed that 74% of species from the sampled community were using the fishway. Fishes marked with visible implant elastomer downstream of the dam were recaptured in the fishway, qualitatively showing that small-bodied fishes could move into and upstream within the fishway. We further quantified upstream movement for three species of small-bodied minnow tagged with passive integrated transponder tags during manipulations of flows through the fishway. Our results illustrate the potential for fishways to mitigate the effects of habitat fragmentation on fishes in sand-bed rivers. [ABSTRACT FROM AUTHOR]

We estimated the abundance, survival, movement, and recruitment of non-native rainbow trout ( Oncorhynchus mykiss) in the Colorado River in Grand Canyon to determine what controls their abundance near the Little Colorado River (LCR) confluence where endangered humpback chub ( Gila cypha) rear. Over a 3-year period, we tagged more than 70 000 trout and recovered over 8200 tagged fish. Trout density was highest (10 000-25 000 fish·km-1) in the reach closest to Glen Canyon Dam, where the majority of trout recruitment occurs, and was 30- to 50-fold lower (200-800 fish·km-1) in reaches near the LCR confluence ∼100 km downstream. The extent of rainbow trout movement was limited with less than 1% of recaptures making movements greater than 20 km. However, because of high trout densities in upstream source areas, this small dispersal rate was sufficient to explain the threefold increase in the relatively small population near the LCR. Reducing dispersal rates of trout from upstream sources is the most feasible solution to maintain low densities near the LCR to minimize negative effects of competition and predation on humpback chub. [ABSTRACT FROM AUTHOR]

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Marine conservation is often perceived as being in conflict with fisheries management. In Canada, at-risk marine fishes denied listing under the Species at Risk Act (SARA) are meant to receive comparable measures under the Fisheries Act. We assess the effectiveness of these Acts by examining ( i) how long it takes a marine fish assessed as being at risk to move through the process and receive conservation measures, ( ii) whether there are biases against marine fishes in the SARA process additional to the known listing bias, and ( iii) when denied listing, to what extent these species are protected by the Fisheries Act. Overall, at-risk marine fishes typically spend 3.25 years under consideration for SARA, during which time they receive no additional protection. Endangered and Threatened marine fishes (i.e., those most at risk) face the greatest bias and receive the least protection; their SARA decisions are typically delayed, with almost 5 years usually passing between their COSEWIC (Committee on the Status of Endangered Wildlife in Canada) assessment and listing decision; most (70.6%) are then denied listing, after which the Fisheries Act provides few of the SARA-required measures. For SARA-listed marine fishes, recovery strategies are usually late and to date no action plans have been produced. Marine fish conservation is hindered by SARA's slow pace, incomplete recovery measures, and inadequate implementation of the Fisheries Act. We provide recommendations for improving conservation of at-risk marine fishes in Canada. [ABSTRACT FROM AUTHOR]

Rapid increases in native riverine fish populations associated with trophic upsurge immediately following reservoir construction are well documented. Repeated upsurge periods and extended benefits to populations are, however, less understood. We used sclerochronology to investigate fish growth and netting surveys to estimate recruitment and abundance of a lacustrine population of an Australian riverine fish, the Macquarie perch ( Macquaria australasica) in Lake Dartmouth. Record low inflows from 1997 to 2008 caused the reservoir to shrink to its lowest volume since construction. Refilling began in 2008, reaching 99% capacity in 2013. We hypothesized that fish growth, recruitment, and abundance would increase in response to the refilling of the lake, reproducing a similar response to the initial filling period. Our findings supported this hypothesis. Macquarie perch growth, recruitment, and abundance were enhanced during the refilling of Lake Dartmouth. Growth, best explained by the effects of dam height, change in dam height, temperature (and their interactions), and recruitment, were highest during the first years of refilling when lake levels and temperatures were low. We propose one or a combination of varying levels of intraspecific competition (low during initial filling and high following population expansion) and improved riverine conditions for reproductive success as the most plausible explanation. Our results suggest extended periods of low lake levels followed by rapid inundation events are likely to enhance recruitment and population growth opportunities for this species. While reservoir construction in general impacts negatively on native fish populations, the potential to offset these impacts for conservation management purposes should be considered. [ABSTRACT FROM AUTHOR]

Understanding mortality rates and movement patterns across a species' distribution can provide key insight necessary for developing effective conservation, recovery, and management plans. We directly estimated site fidelity and natural mortality rates for the threatened Gulf sturgeon ( Acipenser oxyrinchus desotoi) across a large portion of their range in the northern Gulf of Mexico using acoustic telemetry methods and a simulation-tested, multistate mark-recapture model. Our results suggest that fidelity rates to riverine habitats used during spring and summer are high, but natural mortality rates vary widely. Our results are highly relevant for managing this species. The high fidelity rates, coupled with supporting genetic analyses, suggest that management of individual riverine populations of Gulf sturgeon should be considered. The need for individual river-based management is exacerbated by the variation in natural mortality rates among rivers. The reasons for these differences in mortality are unclear, but are an important area of future research because higher mortality rates may impede recovery of some Gulf sturgeon populations to stated management targets. [ABSTRACT FROM AUTHOR]

How sea lampreys ( Petromyzon marinus) search for and select reproductive habitat is poorly understood. Manual tracking of acoustically tagged migrants confirms the hypothesis that sea lampreys transition from extensive search to intensive search upon encounter with river water and return to extensive search upon leaving the plume. In addition, we document a previously unknown search tactic used to localize river mouths termed coastal rebounding. Increased intensive search in the river plume and subsequent approach to the river mouth is hypothesized to occur as a consequence of detection of a pheromone released by river resident larvae that indicate the presence of high-quality reproductive habitat. Application of two synthesized pheromone components caused migrants to increase time spent searching a plume by 57%; applications did not increase the likelihood of river entry. These findings suggest that partial pheromones constitute information that facilitates the search for river entrances, but prove insufficient to affect the decision to select a habitat. Proposed management tactics that rely on luring migrants into rivers with larval odor may prove ineffective without a complete blend of pheromone components. [ABSTRACT FROM AUTHOR]

We investigated the fish community approaching the Veazie Dam on the Penobscot River, Maine, prior to implementation of a major dam removal and river restoration project. Multibeam sonar (dual-frequency identification sonar, DIDSON) surveys were conducted continuously at the fishway entrance from May to July in 2011. A 5% subsample of DIDSON data contained 43 793 fish targets, the majority of which were of Excellent (15.7%) or Good (73.01%) observation quality. Excellent quality DIDSON targets ( n = 6876) were apportioned by species using a Bayesian mixture model based on four known fork length distributions (river herring (alewife, Alosa psuedoharengus, and blueback herring, Alosa aestivalis), American shad, Alosa sapidissima) and two size classes (one sea-winter and multi-sea-winter) of Atlantic salmon ( Salmo salar). 76.2% of targets were assigned to the American shad distribution; Atlantic salmon accounted for 15.64%, and river herring 8.16% of observed targets. Shad-sized (99.0%) and salmon-sized (99.3%) targets approached the fishway almost exclusively during the day, whereas river herring-sized targets were observed both during the day (51.1%) and at night (48.9%). This approach demonstrates how multibeam sonar imaging can be used to evaluate community composition and species-specific movement patterns in systems where there is little overlap in the length distributions of target species. [ABSTRACT FROM AUTHOR]

Identification of critical habitat is a key step in conservation and recovery of endangered and threatened freshwater fish. Critical habitat under Canadian and US legislation may include habitat that is not directly used by listed fish, provided it is necessary for species conservation or recovery. Riparian habitat meets biological criteria for critical habitat because riparian zones are integral to aquatic ecosystem functions of importance to many fish species and other organisms. These functions include provision of shade for temperature-sensitive species, control of channel complexity and sediment inputs through bank stabilization, input of large wood and allochthonous energy sources, and filtering of nutrients and toxins from adjacent land. In response to decades of stream-riparian research, widespread implementation of regulations to protect riparian zones in most developed countries represent a de facto consensus that riparian buffers are essential for aquatic ecosystem health and the maintenance of populations of fish and other species. Consistent with widespread riparian regulations deemed necessary to protect not-at-risk species, riparian habitat adjacent to a body of water containing a listed freshwater species should be considered biologically critical unless the habitat requirements of individual taxa are demonstrated to be insensitive to the ecological functions associated with riparian habitat. L’identification de l’habitat critique est une étape essentielle dans la conservation et la récupération des poissons d’eau douce menacés et en voie de disparation. Dans les législations canadienne et américaine, l’habitat critique peut inclure des milieux qui ne sont pas directement utilisés par les poissons concernés, à la condition qu’ils soient nécessaires pour la conservation ou la récupération de ces espèces. Les habitats riverains possèdent les critères biologiques d’habitats critiques parce que les zones riveraines sont nécessaires pour assurer des fonctions de l’écosystème aquatique d’importance pour plusieurs espèces de poissons et pour d’autres organismes. Ces fonctions incluent la production d’ombre pour les espèces sensibles à la température, le contrôle de la complexité du chenal et des apports de sédiments par la stabilisation des rives, l’apport de sources d’énergie allochtones et de débris ligneux de grande taille et la filtration des nutriments et des toxines provenant des terres adjacentes. À la suite de décennies de recherche sur la relation entre les cours d’eau et la zone riveraine, la mise en application très commune dans la plupart des pays développés de règlements pour protéger les zones riveraines représente un consensus de facto reconnaissant que les zones tampons riveraines sont essentielles à la santé des écosystèmes aquatiques et le maintien des populations de poissons et d’autres espèces. En accord avec les règlements largement répandus sur les zones riveraines jugées nécessaires pour la protection des espèces non vulnérables, tout habitat riverain adjacent à un milieu aquatique contenant une espèce d’eau douce figurant sur la liste des espèces en péril devrait être considéré comme biologiquement critique, à moins qu’on démontre que les besoins d’habitat de ce taxon particulier sont insensibles aux fonctions écologiques associées à l’habitat riverain. [ABSTRACT FROM AUTHOR]

Stable isotope analysis of diet switching by fishes often is hampered by slow turnover rates of the tissues analyzed (usually muscle or fins). We examined epidermal mucus as a potentially faster turnover “tissue” that might provide a more rapid assessment of diet switching. In a controlled hatchery experiment, we switched the diet of juvenile steelhead (sea-run rainbow trout, Oncorhynchus mykiss) from a plant-based feed with low δ13C and δ15N to a fish-meal-based diet with higher delta values. We found mucus to provide a significantly more rapid response to diet switching (half-life = 36 days for δ15N, 30 days for δ13C) than muscle tissue (half-life = 94 days for δ15N, 136 days for δ13C), even for growing juvenile fish. Mucus may provide a rapid turnover “tissue” for analysis of diet (or habitat) switching by fish. It has the additional advantage that it may be sampled nonlethally in some fishes, thereby avoiding problems in studying threatened or endangered species. This is the first report of the use of fish mucus in stable isotope analyses of fish tissues. [ABSTRACT FROM AUTHOR]

Recovery plans for many endangered fishes include production of large numbers of individuals in hatcheries to augment wild populations. However, effects of hatchery culture on phenotypic development are poorly documented for most species. June sucker (Chasmistes liorus) is an endangered lake sucker endemic to Utah Lake (Utah, USA), and recovery plans include raising thousands of juveniles to stock in the lake. To determine effects of hatchery culture on morphology of young June sucker, we raised individuals from four different families in both lake and hatchery environments and compared shape variation among families and between environments. We compared shape from three perspectives: lateral body, ventral mouth, and lateral head views. Mean shape varied between hatchery-reared and lake-reared individuals in each of the three views. In addition, hatchery-reared individuals exhibited higher variance in shape both within and among families compared with shape variance in lake-reared individuals. Hatchery-reared individuals exhibited divergent phenotypes compared with lake-reared individuals. These results suggest that exposure to the native environment during early life stages may be important for phenotypic development suitable to native habitats. Hatcheries should incorporate designs and practices to minimize divergent phenotypic development of individuals. [ABSTRACT FROM AUTHOR]