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We tested the performance of two stationary interrogation systems designed for detecting the movement of fish with passive integrated transponder (PIT) tags. These systems allowed us to determine the direction of fish movement with high detection efficiency and high precision in a dynamic stream environment. We describe an indirect method for deriv...
Context in source publication
Context 1
... tested the efficiency of our instream PIT tag interrogation systems in two streams. Both streams are located within the Columbia River basin, with Rattlesnake Creek in south-central Washington's White Salmon River watershed and Beaver Creek in north-central Washington's Methow River watershed (Figure 1). ...
Citations
... Event probabilities at time t (Table 2) are stored in the matrix H t and this is used to generate η i,t , which is a vector of probabilities of the observed event of encounter history i at time t for each 2° state.Antenna detection event probabilities are a function of antenna detection probabilities (a) and the probability of lingering over the array (L) at time t. Antenna detection probabilities are both direction-(e.g.Connolly et al., 2008) and array-specific: array-1 detection probability for upstream swimmer (a U,1,t ), array-1 detection probability for downstream swimmer (a D,1,t ), array-2 detection probability for upstream swimmer (a U,2,t ) and array-2 detection probability for downstream swimmer (a D,2,t ). Similarly, lingering probabilities L are time-and direction-specific. ...
Many populations migrate between two different habitats (e.g. wintering/foraging to breeding area, mainstem–tributary, river–lake, river–ocean, river–side channel) as part of their life history. Detection technologies, such as passive integrated transponder (PIT) antennas or sonic receivers, can be placed at boundaries between habitats (e.g. near the confluence of rivers) to detect migratory movements of marked animals. Often, these detection systems have high detection probabilities and detect many individuals but are limited in their ability to make inferences about abundance because only marked individuals can be detected.
Here, we introduce a mark–recapture modelling approach that uses detections from a double‐array PIT antenna system to imply movement directionality from arrays and estimate migration timing. Additionally, when combined with physical captures, the model can be used to estimate abundances for both migratory and non‐migratory groups and help quantify partial migration. We first test our approach using simulation, and results indicate our approach displayed negligible bias for total abundance (less than ±1%) and slight biases for state‐specific abundance estimates (±1%–6%).
We fit our model to array detections and physical captures of three native fishes (humpback chub [Gila cypha], flannelmouth sucker [Catostomus latipinnis] and bluehead sucker [Catostomus discobolus]) in the Little Colorado River (LCR) in Grand Canyon, AZ, a system that exhibits partial migration (i.e. includes residents and migrants). Abundance estimates from our model confirm that, for all three species, migratory individuals are much more numerous than residents.
There was little difference in movement timing between 2021 (a year without preceding winter/spring floods) and 2022 (a year with a small flood occurring in early April). In both years, flannelmouth sucker arrived in mid‐March whereas humpback chub and bluehead sucker arrivals occurred early‐ to mid‐April. With humpback chub and flannelmouth sucker, movement timing was influenced by body size so that large individuals were more likely to arrive early compared to smaller individuals.
With more years of data, this model framework could be used to evaluate ecological questions pertaining to flow cues and movement timing or intensity, relative trends in migrants versus residents and ecological drivers of skipped spawning.
... Detection efficiency (i.e. the probability of detecting a migrating fish) in antenna systems is typically high (~96%-100%) (Connolly et al., 2008) but a proportion of downstream migrants are expected to be missed, especially in structurally complex habitats with features that enable migrating fish to evade detection (Weber et al., 2016). ...
In partially migratory species, individuals either migrate at some point(s) in life or reside within their natal habitat throughout life. For salmonid fish, migration creates opportunities for feeding and growth, but it is also associated with increased mortality risk. Such trade‐offs likely differ between the sexes, since reproductive output is more closely tied to body size in females than males. However, testing hypotheses on sex‐specific migratory behaviour in would‐be first‐time migratory salmonids is difficult, since sexes are generally morphologically indistinguishable prior to maturation. Previous studies have evaluated the influence of sex on migration based on dissection of migratory juveniles or the sex ratio of returning adults. However, both approaches are potentially biased by differential survival during migration. Here, we utilise advances in minimally invasive genetic sex‐determination methods for salmonids to investigate sex‐specific, spring out‐migration propensity in potamodromous brown trout ( Salmo trutta ) in a pre‐Alpine, central European lake. We show that there are marked differences in migratory behaviour between males and females, with small (~10 cm) females being approximately twice as likely to migrate out of their natal river in spring compared to similarly sized males, which generally migrate for the first time at larger sizes (in similar proportions to larger females). This study highlights how novel genetic sex‐determination techniques can provide insight into the sex‐ and size‐specific life‐history trade‐offs that shape migration propensity. Moving forward, these techniques should become useful tools for ecologists and fisheries managers.
... A single detection of fish resulted in fish presence only in a given hour of detection. Due to fish reproductive activity and circular movement between antennas in search of mating partners [54], this system detects individual fish on average multiple times per hour (average detections of males per hour in 2015 and 2016: 27 and 55; female detections: 15 and 25, respectively) [31]. ...
Background
Animal migrations are periodic and relatively predictable events, and their precise timing is essential to the reproductive success. Despite large scientific effort in monitoring animal reproductive phenology, identification of complex environmental cues that determine the timing of reproductive migrations and temporal changes in the size of reproductive aggregations in relation to environmental variables is relatively rare in the current scientific literature.
Methods
We tagged and tracked 1702 individuals of asp (Leuciscus aspius), a large minnow species, and monitored with a resolution of one hour the size of their reproductive aggregations (counts of sexes present at the breeding grounds standardized by the sum of individuals in the season) over seven breeding seasons using passive integrated transponder tag systems. We examined the size of reproductive aggregations in relation to environmental cues of day number within a reproductive season (intra-year seasonality), water temperature, discharge, hour in a day (intra-day pattern), temperature difference between water and air, precipitation, atmospheric pressure, wind speed and lunar phase. A generalized additive model integrating evidence from seven breeding seasons and providing typical dynamics of reproductive aggregations was constructed.
Results
We demonstrated that all environmental cues considered contributed to the changes in the size of reproductive aggregations during breeding season, and that some effects varied during breeding season. Our model explained approximately 50% of the variability in the data and the effects were sex-dependent (models of the same structure were fitted to each sex separately, so that we effectively stratified on sex). The size of reproductive aggregations increased unimodally in response to day in season, correlated positively with water temperature and wind speed, was highest before and after the full moon, and highest at night (interacting with day in a season). Males responded negatively and females positively to increase in atmospheric pressure.
Conclusion
The data demonstrate complex utilization of available environmental cues to time reproductive aggregations in freshwater fish and their interactions during the reproductive season. The study highlights the need to acquire diverse data sets consisting of many environmental cues to achieve high accuracy of interpretation of reproductive timing.
Graphical abstract
... Taken together, these factors illustrate the importance of using life-cycle analyses (e.g., Beckman et al. 1998Beckman et al. , 2017Harstad et al. 2018) to empirically evaluate and better understand the interrelationships between smolt size at release, smolt development, emigration timing, and ecosystem dynamics (e.g., freshwater, estuary, and marine conditions) and their effects on survival and adult demography. The widespread use of passive integrated transponder (PIT, Biomark, Boise, ID) tag technology (Prentice et al. 1990;Connolly et al. 2008;www. ptagis. ...
Many Pacific salmon populations are returning from sea at younger ages and smaller sizes. Hatchery culture, management practices, and environmental factors influence juvenile release size and emigration timing, which in turn affect important demographic characteristics in returning adults. We analyzed data from approximately 345,000 tagged spring Chinook Salmon juveniles exiting Cle Elum Supplementation and Research Facility (Yakima River, Washington, USA) acclimation sites over thirteen brood years (2002–2014), evaluating smolt size, emigration timing, river flow, juvenile survival, and age-at-return. We observed a relationship between size and volitional exit timing of smolts from acclimation sites, with larger fish tending to emigrate earlier than smaller fish. Early emigration was also coincident with lower river flows near acclimation sites. Later emigration timing was correlated with an increase in apparent survival of juveniles to Bonneville Dam (500–530 km downstream of acclimation sites), but also with a lower rate of survival to return from sea. In general, for juveniles successfully emigrating downstream of Bonneville Dam, age-at-return increased with decreasing juvenile fish size and later emigration timing. Our results support a growing body of evidence that hatchery practices may result in larger smolts that tend to return at younger ages. Given the biological and economic consequences of younger age-at-maturation, methods to reverse this trend should be further explored and implemented.
... Multiple factors can influence detection probability of PIT antennas, including environmental conditions, such as discharge or stage height, and characteristics or behaviors of the fish (Zydlewski et al. 2006). Placing multiple independent antennas or arrays in a stream can aid in the understanding of detection probability and enable direction of movement to be determined (Zydlewski et al. 2006;Connolly et al. 2008). We chose a semiconservative approach to classifying out-migration by considering fish as out-migrants if they were detected on at least one antenna downstream of the trap or captured in the trap. ...
Trap‐and‐haul programs can maintain connection among habitats for migratory salmonids in fragmented systems. To conserve diversity within and among life history strategies, downstream trap and transport of juvenile salmonids could ideally mimic the natural, underlying out‐migration dynamics of the population. A two‐way trap‐and‐haul program is implemented in the lower Clark Fork River, Montana, to conserve adfluvial Bull Trout Salvelinus confluentus. We used PIT technology to assess whether downstream trapping efforts are effectively capturing variation in the out‐migration dynamics of juvenile Bull Trout in Graves Creek, a key spawning and rearing tributary in the system. We tagged 821 juvenile Bull Trout in Graves Creek and used these tagged Bull Trout in conjunction with stationary PIT antennas to monitor out‐migration and evaluate efficiency of the downstream trapping program. Capture efficiency in Graves Creek varied substantially from autumn to spring, with 89–96% of autumn out‐migrating Bull Trout captured and 5–10% of spring out‐migrating Bull Trout captured. Overall, we found that Bull Trout transported during the autumn out‐migration periods generally reflect the natural out‐migration dynamics of the population; however, Bull Trout that out‐migrate in the spring are currently underrepresented in the downstream transport program. By understanding the underlying out‐migration dynamics of the Bull Trout population in Graves Creek, management of the downstream trapping efforts can focus on minimizing potential selection for or against out‐migrants based on timing and age at out‐migration. Minimizing selection will conserve variation within the adfluvial life history strategy and therefore maximize resilience of the adfluvial Bull Trout populations.
... First, it is possible that some migrants were not recorded at the stationary antenna (efficiency typically between 96% and 100%; Connolly et al., 2008). Second, it is possible that predation by terrestrial predators is stronger on smaller trout, partially supported by heron colony tracking (data not shown) and past studies that showed the strong effect of salmonid size on avian predation susceptibility (Hostetter et al., 2012;Osterback et al., 2014). ...
While PIT‐tag tracking using mobile antennas is being increasingly used to study fish movement and survival in streams, little is known about the limitations of the method, especially over longer periods of time and under different environmental settings. We used 6 years of data combining tagging, mobile antenna tracking and recaptures of Salmo trutta in multiple small streams in the Lake Lucerne drainage area in Switzerland to evaluate the relative importance of different environmental and intrinsic factors affecting the efficiency of the method. Our study system and experimental design allowed us to accurately verify the continuous presence and survival of recaptured fish in the stream after tracking, which meant that we could estimate detection probability with high confidence. The mean detection probability of tagged trout was 43%, but we found that fish length had a strong negative effect on detection probability, especially in males. Multivariate axes of stream environmental features did not predict efficiency but stream width alone was significantly positively correlated with efficiency. Additionally, stream temperature when tracking had a positive effect on fish detectability. Tag loss at recapture was globally rare (<8%) but common in large postspawn females (>30%). Based on the escape response of fish after detection, we could estimate the proportion of ghost tags, which reached a plateau of around 80% 2 years after tagging. We finally showed that our models of tag loss, fish detection and escape response are needed to interpret detection events. Our results highlight that individual variation in detection probability and tag loss is high and has to be considered for analysis.
... Overwintering and prespawn tributary entry behaviors have been also difficult to monitor due to radio transmitter battery life. In comparison, PIT tags are unconstrained by batteries, but PIT monitoring antennas have very short read ranges (mostly <1 m; Connolly et al. 2008;Burnett et al. 2013) and have been deployed primarily in constricted sites like fishways. As a result, the final detection locations for many Pacific Lampreys in previous radio and PIT telemetry studies have been in and near dam fishways, including at top-of-ladder antennas (Keefer et al. 2009a(Keefer et al. , 2013b. ...
Dams and reservoirs present diverse hazards for riverine fishes, including slowed migration, reduced or blocked access to essential habitats, and direct and delayed mortality risks. Many of these hazards are evident for Pacific Lamprey Entosphenus tridentatus in the highly‐dammed Columbia River basin, where the species’ distribution and abundance has sharply declined. In a three‐year study, we used acoustic telemetry to investigate behavior and apparent survival of 784 adult lamprey in Columbia River reservoirs and turbulent dam tailraces, two environments where previous monitoring efforts have been somewhat ineffectual. We released lamprey upstream and downstream from Bonneville Dam to test whether lamprey passage at one dam negatively affected upstream dam and reservoir passage metrics (i.e., delayed effects on migration rate or reach passage success), and whether upstream release groups migrated further than their downstream‐released counterparts. Overall, results showed that lamprey migrated very rapidly (median rates = 50–62 km/d) in reservoir reaches and slowly (1–3 km/d) in reaches with tailraces or fishways. Lamprey also had much higher passage success in reservoir reaches (reach×year estimates = 0.93–0.99) than in reaches with tailraces or fishways (most estimates = 0.58–0.82). We found little statistical evidence for negative delayed effects of dam passage. Lamprey released in the Bonneville forebay were far more likely to pass upstream dams (~26–57%) than were lamprey released in the Bonneville tailrace (~20–36%). We conclude that tailraces and fishways constrained the upstream distribution of adult Pacific Lamprey, that reservoirs were not associated with high mortality during active upstream migration, and that translocation past individual dams can increase the upstream migration distance of individuals and population distribution. Areas of continuing uncertainty include behavior and survival during overwintering (i.e., prespawn holding) and the potential delayed effects of tailrace and fishway passage on Pacific Lamprey fitness.
... The San Juan River measures up to 150 m in width; at most, all of our boats combined could only sample 18 m at a time. Second, the detection distance of the antennas or the depth of the river could also account for undetected tags (Connolly et al. 2008;O'Donnell et al. 2010;Fischer et al. 2012). This effect was evident in the canyon reach, where we only resighted 12 PIT tags, most likely due to the depth of the river. ...
The use of passive integrated transponder (PIT) tags has rapidly proliferated since their introduction, and new mobile detection methods have been developed. However, the presence of ghost tags (i.e., PIT‐tags left in the system after a fish dies) creates uncertainty about the status (live or dead) of tags detected. Herein, we describe our raft‐based mobile PIT‐tag antenna system and use it to describe the movements of “seeded tags” (i.e., PIT‐tags we placed in the river as ghost tag analogs) and their interactions with habitat features. We deployed 5,000 seeded tags into the San Juan River, a large sand bed river in the southwest U.S. Total distances moved by PIT‐tags ranged from 0.8 to 4,124 m, but 75% of movements were less than 100 m. Flow conditions causing the smallest to largest movements were (1) base flows, (2) spring runoff flows, (3) flash flood flows, and (4) the combination of runoff and flood flows. Based on Ivlev’s electivity index, tags were more likely to be detected in riffles than runs. These findings will help classify mobile PIT‐tag detections as ghost tags or live fish, a critical data gap limiting accurate estimation of demographic rates, population status metrics, and descriptions of habitat use of fishes.
... Innovative ways to enhance fish population inferences ( et al., 2010), evaluate study methods (Sloat et al., 2011), actively search for tagged fish (Ledgerwood et al., 2004), evaluate antenna efficiencies (Horton et al., 2007), and monitor fish during migrations (Connolly et al., 2008) using mobile or stationary antennas are becoming more common. We frame our definition of capture probability similar to Guy et al. (2009), where the probability of capturing an individual fish is conditional on the individual occupying the site; therefore, known presence was a critical component of the study. ...
... False negative means the scanner did not detect a tag, but the shelter was occupied by a tagged individual. To align with the terminology of other studies employing similar PIT tag scanning technology (Zydlewski et al. 2006;Connolly et al. 2008), we use the term detection efficiency to refer to the proportion of true positives obtained for shelters occupied by a previously tagged individual. ...
Secretive species are difficult to study and often of conservation concern, as exemplified by the Eastern Hellbender (Cryptobranchus alleganiensis). Traditional methods for sampling Hellbenders involves moving rocks, which damages essential habitat. Use and installation of artificial shelters has made studying Hellbenders less dangerous for the animal and less disruptive to stream habitat; however, researchers using shelters generally capture occupying animals to identify them. We tested the ability of a submersible portable Passive Integrated Transponder (PIT) antenna to accurately detect PIT-tagged Hellbenders in shelters. We tested the effects of the presence and depth of cover rocks on top of shelters, PIT tag location within the shelter, and tag orientation on detection efficiency of Hellbenders. For the 32 shelters occupied by a tagged individual with cover rocks in place, the scanner accurately detected 31% of the animals versus 88% when cover rocks were removed. The detection efficiency of the scanner dropped below 50% once cover rock depth exceeded 11 cm. Tags placed near the interface of the entrance tunnel and chamber, or along the chamber walls, had higher detection efficiencies than those in other locations within the shelter. Vertically oriented tags were 18% more likely to be detected than horizontally oriented tags. Our study demonstrates that while this technology has certain limitations, it shows potential as a research tool for studying Hellbenders and other taxa without the need to frequently handle individuals.
