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At least 181 records · Page 10Linked to original sources
USGS2020

Estimating population abundance with a mixture of physical capture and passive PIT tag antenna detection data

The inclusion of passive interrogation antenna (PIA) detection data has promise to increase precision of population abundance estimates ( ). However, encounter probabilities are often higher for PIAs than for physical capture. If the difference is not accounted for, may be biased. Using simulations, we estimated the magnitude of bias resulting from mixed capture and detection probabilities and evaluated potential solutions for removing the bias for closed capture models. Mixing physical capture and PIA detections ( p det ) resulted in negative biases in . However, using an individual covariate to model differences removed bias and improved precision. From a case study of fish making spawning migrations across a stream-wide PIA ( p det ≤ 0.9), the coefficient of variation (CV) of declined 39%–82% when PIA data were included, and there was a dramatic reduction in time to detect a significant change in . For a second case study, with modest p det (≤0.2) using smaller PIAs, CV ( ) declined 4%–18%. Our method is applicable for estimating abundance for any situation where data are collected with methods having different capture–detection probabilities.

Canadian Journal of Fisheries and Aquatic Sciences↗
USGS2020

Dietary versus nondietary fatty acid profiles of lake trout ecotypes from Lake Superior and Great Bear Lake: Are fish really what they eat?

Fatty acids are well-established biomarkers used to characterize trophic ecology, food-web linkages, and the ecological niche of many different taxa. Most often, fatty acids that are examined include only those previously identified as “dietary” or “extended dietary” biomarkers. Fatty acids considered as nondietary biomarkers, however, represent numerous fatty acids that can be extracted. Some studies may include nondietary fatty acids (i.e., combined with dietary fatty acids), but do not specifically assess them, whereas in other studies, these data are discarded. In this study, we explored whether nondietary biomarker fatty acids can provide worthwhile information by assessing their ability to discriminate intraspecific diversity within and between lakes. Nondietary fatty acids used as biomarkers delineated variation among regions, among locations within a lake, and among ecotypes within a species. Physiological differences that arise from differences in energy processing can be adaptive and linked to habitat use by a species’ ecotype and likely explains why nondietary fatty acid biomarkers can be a relevant tool to delineate intraspecific diversity. Little is known about the nondietary-mediated differences in fatty acid composition, but our results showed that nondietary fatty acid biomarkers can be useful tool in identifying variation.

Lake Superior↗
USGS2020

Modelling grass carp egg transport using a 3-D hydrodynamic river model: The role of egg retention in dead zones on spawning success

Invasive grass carp (Ctenopharyngodon idella) are known to spawn in the Sandusky River, Ohio, USA, within the Great Lakes Basin, and are threatening to expand throughout the Great Lakes. Successful spawning is thought to require that eggs remain in suspension until hatching, which depends on river hydrodynamics and temperature-dependent egg development. Previous modelling efforts used one-dimensional hydrodynamic models that simplify egg movement by not simulating low-velocity zones within the river. To examine the effect of low-velocity zones on egg transit times and hatching rates, we developed a novel coupling of a biophysical Lagrangian particle tracker and three-dimensional hydrodynamic model on the Sandusky River during a high-flow event. The model successfully predicted egg-capture data for a range of developmental stages and revealed a mechanism that resuspends eggs trapped in low-velocity zones. The resuspension mechanism increases the residence time of grass carp eggs in spawning tributaries and can lead to successful hatching occurring in shorter distances than previously estimated. Grass carp potentially spawning in shorter tributary lengths has widespread implications for efforts preventing establishment in the Great Lakes Basin.

Ohio↗
USGS2020

Integrating side-scan sonar and acoustic telemetry to estimate the annual spawning run size of Atlantic sturgeon in the Hudson River

There is considerable interest in evaluating the status and trends of sturgeon populations, yet many traditional approaches to estimating the abundance of fishes are intractable due to their biology and rarity. Side-scan sonar has recently emerged as an effective tool for censusing sturgeon in rivers, yet challenges remain for censusing open populations that may visit specific habitats over periods of time (e.g., spawning runs). We use a hierarchical model to integrate side-scan sonar with acoustic telemetry, to estimate the proportion of a spawning run fitted with acoustic tags (12%; 95% CRI = 8-16%) and extrapolate to the total run size in 2014. Our investigation represents a novel approach to generating run size estimates in a large river and provides the first estimate of Atlantic sturgeon spawning run size for the Hudson River (N ̂ = 466; 95% CRI = 310-745) since the fishery moratorium in the 1990’s. Our estimate suggests that the Hudson River holds one of the largest contemporary populations of Atlantic sturgeon, but also indicates that it remains sharply depleted relative to virgin conditions.

Hudson River↗
USGS2020

Keeping it classy: Classification of live fish and ghost PIT tags detected with a mobile PIT tag interrogation system using an innovative analytical approach

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.

Canadian Journal of Fisheries and Aquatic Sciences↗
USGS2021

Considerations of variability and power for long-term monitoring of stream fish assemblages

Little attention has been given to optimizing statistical power for monitoring stream fish assemblages. We explored the relationship between temporal variability and statistical power using 34 metrics from fish community data collected annually at six sites over 10 years via electrofishing. Metric variability differed by the life stage and group of species considered, use of abundance or mass data, and data standardization technique. Lower variability was associated with community data, abundance data, and time-based standardizations, while greater variability was associated with young-of-the-year data, mass data, and area-based standardizations. Simulation-based power analysis indicated metric choice, and to a lesser degree, monitoring design (annual, biennial, endpoints, or haphazard sampling) influenced power to detect change. Across a fixed number of surveys (N = 60), endpoints sampling performed best. The N needed to detect change was heavily dependent upon metric choice for all monitoring designs, with the most biologically specific metrics requiring greater N. Large savings in effort and resource expenditure can be obtained utilizing biologically relevant metrics that are robust to temporal noise within an appropriate sampling design.

Canadian Journal of Fisheries and Aquatic Sciences↗
USGS2020

Remarkable response of native fishes to invasive trout suppression varies with trout density, temperature, and annual hydrology

Recovery of imperiled fishes can be achieved through suppression of invasives, but outcomes may vary with environmental conditions. We studied the response of imperiled desert fishes to an invasive brown ( Salmo trutta ) and rainbow trout ( Oncorhynchus mykiss ) suppression program in a Colorado River tributary, with natural flow and longitudinal variation in thermal characteristics. We investigated trends in fish populations related to suppression and tested hypotheses about the impacts of salmonid densities, hydrologic variation, and spatial–thermal gradients on the distribution and abundance of native fish species using zero-inflated generalized linear mixed effects models. Between 2012 and 2018, salmonids declined 89%, and native fishes increased dramatically (∼480%) once trout suppression surpassed ∼60%. Temperature and trout density were consistently retained in the top models predicting the abundance and distribution of native fishes. The greatest increases occurred in warmer reaches and in years with spring flooding. Surprisingly, given the evolution of native fishes in disturbance-prone systems, intense, monsoon-driven flooding limited native fish recruitment. Applied concertedly, invasive species suppression and efforts to mimic natural flow and thermal regimes may allow rapid and widespread native fish recovery.

Arizona↗
USGS2021

The genetic composition of wild recruits in a recovering lake trout population in Lake Michigan

Strain performance evaluations are vital for developing successful fishery management and restoration strategies. Here, we utilized genotypes from 36 microsatellites to investigate hatchery strain contribution to collections of naturally produced lake trout ( Salvelinus namaycush ) sampled across Lake Michigan. Strain composition varied by area, with recoveries of Seneca Lake strain exceeding expectations based on stocking records in northern Lake Michigan but performing similarly to other strains in southern Lake Michigan. Interstrain hybrids were present at moderate frequencies similar to expectations based on simulations, suggesting that strains are interbreeding randomly. We hypothesize that the superior performance of the Seneca Lake strain in northern Lake Michigan is partially due to adaptive advantages that facilitate increased survival in areas with high mortality from sea lamprey ( Petromyzon marinus ) predation, such as northern Lake Michigan. However, when this selective pressure is lessened, the Seneca Lake strain performs similarly to other strains. Our study demonstrates that strain performance can vary across small spatial scales and illustrates the importance of conducting thorough strain evaluations to inform management and conservation.

Lake Michigan↗
USGS2021

Influence of water temperature and biotic interactions on the distribution of westslope cutthroat trout (Oncorhynchus clarkii lewisi) in a population stronghold under climate change

Climate warming is expected to have substantial impacts on native trout across the Rocky Mountains, but there is little understanding of how these changes affect future distributions of co-occurring native fishes within population strongholds. We used mixed-effects logistic regression to investigate the role of abiotic (e.g., temperature) and biotic factors (bull trout presence, Salvelinus confluentus ) on distributions of westslope cutthroat trout ( Oncorhynchus clarkii lewisi ; WCT) in the North Fork Flathead River, USA and Canada. The probability of WCT presence increased with stream temperature and decreased with channel gradient and bull trout presence, yet the effect of bull trout was reduced with increasing pool densities. Combining this model with spatially explicit stream temperature projections, we predict a 29% increase in suitable habitat under high emissions through 2075, with gains at mid-elevation sites predicted to exceed bull trout thermal tolerances and high-elevation sites expected to become more thermally suitable for WCT. Our study illustrates the importance of considering abiotic and biotic drivers to assess species response to climate change, helping to guide local-scale climate adaptation and management.

Alberta, British Columbia, Montana↗
USGS2021

As the prey thickens: Rainbow trout select prey based upon width not length

Drift-feeding fish are typically considered size-selective predators. Yet, few studies have explicitly tested which aspect of prey “size” best explains size selection by drift-foraging fish. Here, we develop a Bayesian discrete choice model to evaluate how attributes of both prey and predator simultaneously influence size-selective foraging. We apply the model to a large dataset of paired invertebrate drift ( n = 784) and rainbow trout ( Oncorhynchus mykiss ) diets ( n = 1028). We characterized prey “size” using six metrics (length, width, area, hemispherical area, volume, mass) and used pseudo- R 2 to determine which metric best explained observed prey selection across seven taxa. We found that rainbow trout are positively size-selective, they are selecting prey based upon differences in prey width, and size-selectivity increases with fish length. Rainbow trout demonstrated strong selection for the adult and pupae stages of aquatic insects relative to their larval stages. Our study provides strong empirical evidence for size-selective foraging in rainbow trout and demonstrates prey selection is based primarily upon width, not length or area as has been widely reported.

Arizona↗
USGS2021

Effects of a diatom ecosystem engineer (Didymosphenia geminata) on stream food webs: Implications for native fishes

Stream habitat changes affecting primary consumers often indirectly impact secondary consumers such as fishes. Blooms of the benthic algae Didymosphenia geminata (Didymo) are known to affect stream macroinvertebrates, but the potential indirect trophic impacts on fish consumers are poorly understood. In streams of the Kootenai River basin, we quantified the diet, condition, and growth rate of species of trout, char, and sculpin. In 2018, macroinvertebrate taxa composition was different between a stream with Didymo and a stream without, but trout diets, energy demand, and growth rates were similar. Trout abundance was higher in the stream with Didymo, but the amount of drifting invertebrates was higher in the stream without. In 2019, we surveyed 28 streams with a gradient of coverage. Didymo abundance was correlated only with the percentage of aquatic invertebrates in trout diets and was not related to diets of char or sculpin or condition of any species. Thus, we found no evidence for a trophic link between Didymo blooms and the condition or growth of trout, char, or sculpin in mountainous headwater streams.

Alberta, British Columbia, Idaho, Montana↗
USGS2021

Reduced recruitment of Chinook salmon in a leveed bar-built estuary

Estuaries are commonly touted as nurseries for salmonids, providing numerous advantages for smolts prior to ocean entry. In bar-built estuaries, sandbars form at the mouth of rivers during periods of low stream flow, closing access to the ocean and preventing outmigration. We evaluated how summer residency in a leveed bar-built estuary affects the growth, survival, and recruitment of a Chinook salmon ( Oncorhynchus tshawytscha ) population. We performed a mark–recapture study on outmigrants to determine juvenile estuary abundance, growth, and survival. We used returning adult scales and otoliths to determine the relative proportion of summer estuary residents in spawning adults. Juveniles in the estuary grew less after mouth closure, and ultimately summer estuary residents had lower smolt-to-adult survival and contributed disproportionately less to the spawning population than juveniles that reared in the ocean their first summer. Mouth closure may lower food availability and deteriorate estuary conditions by reducing marine prey influx and estuary circulation. This research demonstrates the complexity of estuary dynamics and function as salmonid nurseries, particularly when considering the extensive modification of estuaries.

California↗
USGS2021

It’s complicated…environmental DNA as a predictor of trout and char abundance in streams

The potential to provide inferences about fish abundance from environmental (e)DNA samples has generated great interest. However, the accuracy of these abundance estimates is often low and variable across species and space. A plausible refinement is the use of common aquatic habitat monitoring data to account for attributes that influence eDNA dynamics. We therefore evaluated the relationships between eDNA concentration and abundance of bull trout ( Salvelinus confluentus ), westslope cutthroat trout ( Oncorhynchus clarkii lewisi ) and rainbow trout ( Oncorhynchus mykiss ) at 42 stream sites in the Intermountain West (USA and Canada) and tested whether accounting for site-specific habitat attributes improved the accuracy of fish abundance estimates. eDNA concentrations were positively associated with fish abundance, but these relationships varied by species and site, and there was still considerable variation unaccounted for. Random site-level differences explained much of this variation, but specific habitat attributes of those sites explained relatively small amounts of this variation. Our results underscore that either eDNA sampling or environmental characterization will require further refinement before eDNA can be used reliably to estimate fish abundance in streams.

Idaho, Montana, Oregon, Washington↗
USGS2021

Behavioral responses of sea lamprey (Petromyzon marinus) and white sucker (Catostomus commersonii) to turbulent flow during fishway passage attempts

An understanding of how undesirable and desirable fish species respond behaviorally to turbulent flow in fishways would guide development of selective fish passage techniques. We applied high-resolution computational fluid dynamics modeling and competing risks analysis towards the development of predictive selective passage models. Sea lamprey ( Petromyzon marinus ; an invasive fish in the Great Lakes Basin, North America) upstream passage probability declined from 0.73 to 0.03 as flow conditions became increasingly turbulent, while declines in white sucker ( Catostomus commersonii , a native fish in the region) upstream passage probability were less substantial (0.53 to 0.44). Deploying a sea lamprey trap in the fishway did not effectively reduce sea lamprey upstream passage probability, though capture rate increased during trials with cooler water temperature and low total kinetic energy. Bifurcated fishways that maintain low turbulent flow in the entrapment route and high turbulent flow in the upstream passage route could increase the effectiveness of trapping sea lamprey in fishways as a means to advance selective passage goals.

Wisconsin↗
USGS2021

Recruitment dynamics of non-native largemouth bass within the Sacramento-San Joaquin delta

Largemouth bass (LMB; Micropterus salmoides ) recruitment is limited by a critical developmental period during early life stages, but this mechanism may be less important within non-native habitats. We conducted boat electrofishing surveys in four tidal lakes of California’s Sacramento–San Joaquin Delta (SSJD) from 2010 to 2011 to describe introduced LMB recruitment dynamics. We evaluated growth, proximate composition, and health indices of young-of-the-year (YOY) LMB among tidal lakes and developed an integrated count model to determine how factors known to affect LMB recruitment shape SSJD population structure. Our results show a mismatch among growth, nutrition, and YOY abundance, where the tidal lake with the most abundant and fastest-growing LMB had the poorest nutritional status. The warm winter water temperatures and lack of a hatching-cohort growth advantage suggests overwinter starvation plays a less important role in SSJD LMB recruitment than in many native LMB habitats. Collectively, our results suggest that habitat characteristics (submerged aquatic vegetation) and not overwinter mortality shapes SSJD LMB population structure, a mechanism consistent with contemporary hypotheses about the altered fish community structure of the SSJD.

California↗
USGS2021

Partial migration and spawning movements of humpback chub in the Little Colorado River are better understood using data from autonomous PIT tag antennas

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 over-winter 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.

Arizona↗
USGS2021

Surface water with more natural temperatures promotes physiological and endocrine changes in landlocked Atlantic salmon smolts

Hatchery salmonid smolts are often reared using groundwater with elevated temperatures to maximize growth. Previous work has shown that rearing hatchery smolts in surface water with a more natural thermal regime resulted in increased return rates of adult landlocked Atlantic salmon ( Salmo salar ). We evaluated whether landlocked Atlantic salmon reared in surface water with a natural temperature regime have altered physiological smolt characteristics compared with fish reared in groundwater with elevated winter temperatures. Hatchery fish were sampled three consecutive years from January to May. Additional fish were released as smolts, recaptured, and compared with fry-stocked smolts. Surface water smolts had earlier peaks of plasma T 4 , lower T 3 levels, later peak cortisol, and lower gill Na + /K + -ATPase activity as compared with groundwater smolts. After release and recapture, surface water fish had elevated plasma T 4 and gill Na + /K + -ATPase activity compared with groundwater fish, but less than stream-reared fish. Elevated plasma T 4 in surface water fish in the hatchery and after release may have promoted imprinting and other aspects of smolt development, contributing to the higher adult return rates of a cohort reared in surface water.

Vermont↗
USGS2021

Behavioural response of sea lamprey (Petromyzon marinus) to acoustic stimuli in a small stream

Sea lamprey ( Petromyzon marinus ) are invasive in the Laurentian Great Lakes and parasitically feed on valued fishes. Migration barriers and selective pesticides are used to control sea lamprey, but there is a desire to develop additional control tools such as traps with nonphysical deterrents. Sound has been used as a deterrent for other invasive species, but its potential for manipulating sea lamprey behavior in natural stream conditions remains untested. Here, behavioral responses of upstream-migrating adult sea lamprey in response to low frequency sounds of 70 or 90 Hz was tracked in a small stream (8 m wide) using passive integrated transponder (PIT) telemetry. The low frequency sounds shifted sea lamprey distribution, with up to 30% more sea lamprey detected on PIT antennas without sound compared with PIT antennas with sound playing. Future studies could continue testing low frequency sounds in larger rivers with larger speakers for use as a natural deterrent at sea lamprey barriers to push sea lamprey toward traps.

Canadian Journal of Fisheries and Aquatic Sciences↗