Rotary Screw Trap Research Articles

Relationship Between Steelhead Parr Densities Observed During Snorkel Surveys and Emigration Estimates From Rotary Screw Traps

Abstract Snorkel surveys are widely used for monitoring fish populations because they are a versatile and cost-effective technique. However, snorkel surveys provide instantaneous measurements that might not describe continuous processes, such as the emigration of juvenile anadromous salmonids. A model capable of assessing the level of potential production of emigrating juvenile steelhead (anadromous Oncorhynchus mykiss) from watersheds in Idaho on the basis of snorkel surveys would be useful. Our objective was to determine the relationship between abundance of emigrants estimated from rotary screw traps (RSTs) and parr densities from snorkel surveys. We analyzed over 1,000 snorkel surveys and 70 year–watershed combinations of emigrant estimates. Density was positively related to emigrant abundance. The most reasonable model included a common slope among watersheds, a common year effect, and varying intercepts, supporting a hypothesis that some watersheds produce more emigrating juveniles at similar observed densities. This model explained 82.7% of the variation observed in emigrant abundance. Uncertainty was greater among watersheds than within a watershed. The model can be used to translate mean densities observed in snorkel surveys to abundance of steelhead emigrants and thus to infer the effects of a habitat restoration program or other management actions. This work is important as a step toward understanding juvenile emigrant abundance in watersheds without RSTs and to aid understanding of steelhead emigrant productivity in Idaho watersheds.

Applications of Age–Length Keys for Assigning Ages to Juvenile Steelhead

AbstractMany population metrics for wild steelhead Oncorhynchus mykiss are unquantified due to complex early life history strategies and a lack of juvenile age data. Juvenile steelhead can rear in freshwater systems for up to 7 years, with overlapping size distributions among age‐classes. As logistics for sampling and aging fish can be challenging, there are benefits to utilizing age–length keys (ALKs). We examined the potential benefits of applying ALKs to unaged juvenile steelhead from a rotary screw trap and to determine whether stratifying trapping data by season could improve accuracy in assigning ages to unaged fish. Additionally, we examined the effects of reducing samples of aged fish using a uniform sampling design in which there was a fixed number of aged fish across all length intervals of the size distributions. Using a leave‐one‐out cross validation method with aged fish, we found that ALKs assigned unbiased ages to unaged fish. When including fish with assigned ages from ALKs, results of mean length‐at‐age and brood year abundance estimates between using proportional‐sampled aged fish and uniform‐sampled aged fish were comparable. Typically, absolute differences in estimated brood year abundances were improved if age‐assigned fish were included, and mean absolute error did not exceed 0.4 years for any of the methods examined. Although seasons had a significant effect on mean length at age, overall brood year estimates of juvenile abundance derived from stratifying data by season did not notably differ from pooling summer and fall seasons together, likely because there was a higher portion of juveniles emigrating in the fall compared to the summer. Age–length keys can benefit trapping operations and aid in filling data gaps in age‐based movement and survival for steelhead by being able to accurately assign ages to unaged fish and include more data for population analyses.

Including environmental covariates clarifies the relationship between endangered Atlantic salmon (Salmo salar) abundance and environmental DNA

AbstractCollecting environmental DNA (eDNA) as a nonlethal sampling approach has been valuable in detecting the presence/absence of many imperiled taxa; however, its application to indicate species abundance poses many challenges. A deeper understanding of eDNA dynamics in aquatic systems is required to better interpret the substantial variability often associated with eDNA samples. Our sampling design took advantage of natural variation in juvenile Atlantic salmon (Salmo salar) distribution and abundance along 9 km of a single river in the Province of New Brunswick (Canada), covering different spatial and temporal scales to address the unknown seasonal impacts of environmental variables on the quantitative relationship between eDNA concentration and species abundance. First, we asked whether accounting for environmental variables strengthened the relationship between eDNA and salmon abundance by sampling eDNA during their spring seaward migration. Second, we asked how environmental variables affected eDNA dynamics during the summer as the parr abundance remained relatively constant. Spring eDNA samples were collected over a 6‐week period (12 times) near a rotary screw trap that captured approximately 18.6% of migrating smolts, whereas summer sampling occurred (i) at three distinct salmon habitats (9 times) and (ii) along the full 9 km (3 times). We modeled eDNA concentration as a product of fish abundance and environmental variables, demonstrating that (1) with inclusion of abundance and environmental covariates, eDNA was highly correlated with spring smolt abundance and (2) the relationships among environmental covariates and eDNA were affected by seasonal variation with relatively constant parr abundance in summer. Our findings underscore that with appropriate study design that accounts for seasonal environmental variation and life history phenology, eDNA salmon population assessments may have the potential to evaluate abundance fluctuations in spring and summer.

Evaluating Alternative Hierarchical Modeling Approaches for the Estimation of Salmonid Smolt Abundance

AbstractCalibrated estimates of fisheries population abundance are vital in the development and appraisal of management actions. Capture–recapture (CR) experiments are invaluable monitoring tools for estimating abundance of biological populations in general. Many researchers, including those studying out‐migrating juvenile Chinook Salmon Oncorhynchus tshawytscha in the Klamath Basin of Oregon and California, have attempted to employ Bayesian B‐splines to smooth temporal variation in abundance estimates. However, concerns about overfitting and reduced precision are common with this approach. We conducted a simulation study assessing the relative fit of the standard Bayesian B‐spline implementation—a B‐spline model of abundance with a random effects (RE) binomial model of recapture probabilities—in comparison with that of three alternative model options: a B‐spline model of abundance with an autoregressive (AR) model of recapture; an AR model of abundance with an RE model of recapture, and an AR model of abundance with an AR model of recapture. We analyzed 1–3 years of CR data from three rotary screw trap sites and simulated data sets of variable completeness to assess each model’s strengths and weaknesses in estimating the underlying data. Results demonstrated that in general, an AR model of abundance coupled with an RE binomial model of recapture was the least biased model, consistently exhibiting no greater than 5% bias in abundance estimates across data sets. The B‐spline abundance models were able to produce narrower 95% credible intervals (CRIs), ranging from 15% to 30% of the parameterized annual abundance value, compared to CRI widths between 23% and 54% from the AR models. However, these narrower CRI widths were commonly errant, with coverage probability rates as low as 50–70% in half of the simulated data set collections compared to over 90% coverage for the AR models. These analyses provide valuable insight and caution for researchers employing modern methods of modeling abundance in natural populations.

Evaluation of Long-Term Mark-Recapture Data for Estimating Abundance of Juvenile Fall-Run Chinook Salmon on the Stanislaus River from 1996 to 2017

Conservation and management of culturally and economically important species rely on monitoring programs to provide accurate and robust estimates of population size. Rotary screw traps (RSTs) are often used to monitor populations of anadromous fish, including fall-run Chinook Salmon (Oncorhynchus tshawytscha) in California’s Central Valley. Abundance estimates from RST data depend on estimating a trap's efficiency via mark-recapture releases. Because efficiency estimates are highly variable and influenced by many factors, abundance estimates can be highly uncertain. An additional complication is the multiple accepted methods for how to apply a limited number of trap efficiency estimates, each from discrete time-periods, to a population’s downstream migration, which can span months. Yet, few studies have evaluated these different methods, particularly with long-term monitoring programs. We used 21 years of mark-recapture data and RST catch of juvenile fall-run Chinook Salmon on the Stanislaus River, California, to investigate factors associated with trap efficiency variability across years and mark-recapture releases. We compared annual abundance estimates across five methods that differed in treatment of trap efficiency (stratified versus modeled) and statistical approach (frequentist versus Bayesian) to assess the variability of estimates across methods, and to evaluate whether method affected trends in estimated abundance. Consistent with short-term studies, we observed negative associations between estimated trap efficiency and river discharge as well as fish size. Abundance estimates were robust across all methods, frequently having overlapping confidence intervals. Abundance trends, for the number of increases and decreases from year to year, did not differ across methods. Estimated juvenile abundances were significantly related to adult escapement counts, and the relationship did not depend on estimation method. Understanding the sources of uncertainty related to abundance estimates is necessary to ensure that high-quality estimates are used in life cycle and stock-recruitment modeling.

Juvenile Life History Diversity and Freshwater Productivity of Chinook Salmon in the Green River, Washington

AbstractLife history diversity and productivity are key metrics used to evaluate the status of salmon populations. In this paper, we use long‐term monitoring data from spawning escapement and a rotary screw trap to describe juvenile migration strategies and identify factors affecting freshwater productivity of Chinook Salmon Oncorhynchus tshawytscha inhabiting the Green River, Washington. Similar to other populations in Puget Sound, Green River Chinook Salmon exhibit two distinct pulses of downstream, subyearling, juvenile migration. Small‐bodied fry move downstream in late winter shortly after emergence (peaking in March), whereas larger‐bodied parr migrate downstream after spending some time rearing and growing in freshwater (peaking in late May or early June). A series of stock–recruit models demonstrated that the production of parr was density dependent, as the Green River reaches rearing capacity at most observed spawner abundances and river conditions. By contrast, the production of fry was density independent. Furthermore, several river discharge metrics were significantly related to Chinook Salmon productivity. Total juvenile production was lower in years when incubating embryos experienced high‐magnitude peak flows, most likely due to redd scour. Parr productivity was greater in years with higher discharge during the spring (April–June), which we hypothesize is related to increased accessibility of side channels for rearing and/or increased survival during migration. Combined, these results suggest that restoration of juvenile rearing habitats offers substantial potential benefits to parr productivity. Setting escapement goals for fishery planning that consider freshwater habitat capacity and life history diversity will largely depend on the relative marine survival of the fry and parr migration strategies. Our analysis also provides insight to managing water at an upstream dam to benefit Chinook Salmon productivity, though any such strategy faces trade‐offs with other fish conservation goals and will be constrained by the dam's primary purpose of reducing flood risk.

Diel migration pattern of Atlantic salmon (Salmo salar) and sea trout (Salmo trutta) smolts: an assessment of environmental cues

AbstractThe timing of smolt migration is a key phenological trait with profound implications for individual survival during both river descent and the subsequent sea sojourn of anadromous fish. We studied relationships between the time of smolt migration, water temperature and light intensity for Atlantic salmon (Salmo salar) and sea trout (Salmo trutta). During 2006–2012, migrating smolts descending the southern Norway River Storelva were caught in a rotary screw trap located at the river mouth. The date of 50% cumulative smolt descent correlated significantly with the date when the river temperature exceeded 8°C for both Atlantic salmon and sea trout smolts. In 2010, smolts of both species were passive integrated transponder (PIT)‐tagged, and the diel timing of their migration was precisely documented. The degree of night migration decreased in both species as the river temperature rose, and at temperatures above 12–13°C, more smolts migrated during day than during night. A multinomial model was fitted for estimating temperature and species effects on probabilities of migration during night, daytime, dusk and dawn. Atlantic salmon smolts preferred migrating under lower light intensities than sea trout smolts during early, but not late spring when both species migrated during bright daylight. In accordance with the early‐season tendency to migrate at night, Atlantic salmon smolts migrated more during darker hours of the day than sea trout. In both species, smaller smolts migrated under dark conditions than during light conditions. Most of the findings on thermal, light and temporal effects on the observed smolt migration pattern can be explained as adaptations to predation avoidance.

The relationship between migration speed and release date for chum salmon Oncorhynchus keta fry exiting a 110-km northern Japanese river

The relationship between release date and migration speed was examined for hatchery chum salmon Oncorhynchus keta fry exiting the Nishibetsu River in eastern Hokkaido, northern Japan so that future releases might be scheduled so that fry arrive at the ocean during periods favoring high survival. Separate marked groups of chum salmon released in early April, mid-April, and early May in 2008, late March and mid-April in 2009, and mid-April in 2010 were recaptured with a rotary screw trap 12 km above the river mouth. Chum salmon in later release groups tended to migrate downstream faster than fish in earlier release groups. Those released after mid-April arrived in the lower river on average 9 days after release, while those released before mid-April arrived on average 26–28 days after release. Most marked fish arrived in the lower river during late April to mid-May. These results suggest that chum salmon are adapted to adjust their migratory speed so as to arrive at the ocean during a relatively discrete period, presumably during a time of high productivity favoring good survival.

The Influence of Release Strategy and Migration History on Capture Rate of Oncorhynchus mykiss in a Rotary Screw Trap

AbstractRotary screw traps are used in rivers throughout the west coast of North America to capture emigrating juvenile salmonids. Calibrating the capture efficiency of each trap is essential for valid estimates of fish passage. We released PIT‐tagged Oncorhynchus mykiss upstream of a rotary screw trap in the South Fork John Day River, Oregon, to estimate capture efficiency. We used three strategies for release of fish recently captured in the trap. We recaptured 28% of medium‐sized fish (86–145 mm FL) and 14% of large‐sized fish (146–230 mm FL) released during daylight 1.6 km upstream from the trap. We recaptured 33% of medium‐sized fish and 17% of large‐sized fish released during daylight 4.8 km upstream from the trap. We recaptured 42% of medium‐sized fish and 23% of large‐sized fish released at twilight 1.8 km upstream from the trap. A PIT tag antenna detected summer‐tagged parr (which were PIT‐tagged upstream 1–5 months before migration) as they approached the trap to evaluate potential bias from reduced recapture of recently trapped fish. We captured 53% of the medium‐sized first‐time migrants and 40% of the large‐sized first‐time migrants. Although average capture efficiencies of first‐time migrants were greater than those from any of the recently trapped fish from the three release strategies, twilight releases of recently trapped fish were the least negatively biased, especially for medium‐sized fish.Received May 7, 2012; accepted December 6, 2012

Comparison of Recapture Rates of Wild and Hatchery-Reared Masu Salmon Smolts by a Rotary-Screw Trap

Comparison of Recapture Rates of Wild and Hatchery-Reared Masu Salmon Smolts by a Rotary-Screw Trap

Magnitude and Causes of Smolt Mortality in Rotary Screw Traps: An Atlantic Salmon Case Study

AbstractRotary screw traps (RSTs) are commonly used for collecting and holding fish swimming downstream. We used these traps to collect Atlantic salmon Salmo salar smolts from multiple rivers draining to the Gulf of Maine from 1996 to 2008. Limited prior evaluations suggest that RSTs cause only minimal mortality, but detailed evaluation of the potential for negative impacts specific to Atlantic salmon and other smolts has not occurred. There are concerns that RSTs contribute to smolt mortality via physical injury during collection or via exposure to stressful holding conditions within RST live‐cars. We evaluated the magnitude and causes of mortality associated with our use of RSTs and recorded the water temperatures and velocities present within the live‐cars at the times smolts were moving downstream. Of the 24,675 Atlantic salmon smolts collected, 48 (0.2%) were classified as trap‐caused mortalities. The most frequent causes of death were physical injuries associated with the clogging of traps with debris and overcrowding of the live‐cars. Water velocities within the live‐cars ranged from 0.09 to 0.57 m/s, and mean velocities never exceeded the published tolerance limits for Atlantic salmon smolts. The seasonal water temperatures within the live‐cars (range, 4.2–20.8°C) were not significantly different from those of the water columns (4.3–21.0°C) adjacent to the traps. Our analysis suggests that, under typical operations, RSTs represent a minimal threat to Atlantic salmon smolts, and we present methods to further reduce the risk.

A portable, cost effective, pass-through system to detect downstream migrating salmonids marked with 12 mm passive integrated transponder tags

We developed and tested an efficient, portable, cost effective, pass-through system to detect downstream migrating salmonids marked with 12 mm passive integrated transponder (PIT) tags. The design combines two established technologies, one for the capture of downstream migrating salmonid (the rotary screw trap), and one for fish detection (12 mm PIT tag technology). Detection rates were 100% for PIT-tagged fish passed through separately, and 95% for PIT-tagged fish passed through in pairs.

Importance of Flood Dynamics versus Intrinsic Physical Habitat in Structuring Fish Communities: Evidence from Two Adjacent Engineered Floodplains on the Sacramento River, California

AbstractWe examined the factors structuring fish communities at two adjacent engineered floodplain systems on the Sacramento River, California: Yolo and Sutter bypasses. We intensively sampled fishes at each location during January–June 2002 and 2004 by rotary screw trap, collecting a total of 126,635 fish comprised of 29 species. Nonmetric multidimensional scaling indicated that distinct fish communities persisted between the locations during our study, despite nearly identical hydrographs and water temperature regimes. Regression models evaluated with an information‐theoretic approach also indicated that location was an important factor explaining the abundances of selected species. Overall, Yolo Bypass had more species and a greater proportion of native species than did Sutter Bypass. Sutter Bypass had a greater proportion of species classified as freshwater, while Yolo Bypass had a greater proportion of species classified as either estuarine or anadromous. We believe these results are related to substantial differences in the underlying physical habitat within the floodplains, which are primarily associated with connectivity to the adjacent river. Although the dynamic flooding that occurs at both locations appeared unable to override the underlying physical habitat differences in structuring the overall fish communities, it was important in controlling the abundances of two prominent native species, Chinook salmon Oncorhynchus tshawytscha and splittail Pogonichthys macrolepidotus, which represented 79% of all individuals collected; splittails spawn on the inundated floodplains, and age‐0 individuals of both species use these areas as rearing habitat. Our results have important restoration implications in that they illustrate the importance of both flood pulse dynamics and underlying physical habitat associated with connectivity in structuring river–floodplain fish communities.

Residence Time and Seasonal Movements of Juvenile Coho Salmon in the Ecotone and Lower Estuary of Winchester Creek, South Slough, Oregon

Abstract The juvenile life history of coho salmon Oncorhynchus kisutch in the stream−estuary ecotone of Winchester Creek, South Slough, Oregon, was investigated in 1999–2001. Seines and a rotary screw trap were used to capture fish for dye-marking, and residence time within the ecotone was determined for recaptured marked fish. In the lower estuary, ultrasonic transmitters were used to document residence time and patterns of movement for smolts migrating to the ocean. Nearly half of each brood year moved to the estuary as subyearlings. A portion of age-0 juveniles that moved downstream during spring lived in the ecotone through summer for up to 8 months, then most moved back upstream to overwinter. Fish that moved to the ecotone during fall and winter had mean minimum residence times of 48 d in 1999 and 64 d in 2000. Some of the fish that moved to the ecotone during fall and winter moved into an off-channel beaver pond and resided there for a mean of 49 d. Spring age-1 smolts had a mean minimum residence ...

Determination of Salmonid Smolt Yield with Rotary-Screw Traps in the Situk River, Alaska, to Predict Effects of Glacial Flooding

Abstract Hubbard Glacier is expected to dam Russell Fiord and cause glacial flooding of the lower 20 km of the Situk River near Yakutat, Alaska. To determine probable effects of the flooding on juvenile salmonids Oncorhynchus spp., two rotary-screw traps were used to estimate smolt yield inside and outside the predicted flood zone. Traps were fished from April to mid-August 1990: one at the predicted upstream limit of flooding and the other 3 km upstream from the river mouth. Every week, a sample of each salmonid species was tattoo-marked and released 1 km above each trap; recaptures were used to expand catches to estimate smolt yield. Trap efficiency ranged widely among species, from 3% for steelhead O. mykiss to 24% for chinook salmon O. tshawytscha. Estimated total smolt yields were 900,000 sockeye salmon O. nerka, 213,000 coho salmon O. kisutch, 67,000 chinook salmon, and 26,000 steelhead; only sockeye salmon (34% of this species' smolts) originated in the flood zone. Estimated mortality between traps...