Using Applied Technology in Fisheries Monitoring and Research (hosted by AFS)

Providing the best available science to stakeholders requires incorporating technological advances into study designs. Technological progress continues to expand our knowledge of fish behavior, fish assemblages, fish survival, and fish movement and distribution. Advances in equipment such as Passive Integrated Transponder (PIT) tags, acoustic tags, electrofishing, sonar cameras, drones, and eDNA allow scientists to acquire better data at a higher resolution than previously possible. Fisheries biologists have adopted these technologies in innovative ways to provide answers to challenging questions. This symposium will provide the most up-to-date information on advancements with each type of technology and/or present innovative ways scientists have used the technology to answer their research and monitoring questions.

8:00AM Overcoming Challenges in Salmon and Steelhead Monitoring Using Applied Technologies
  Andrea Pecharich, Aaron Johnson, Gregg Horton, Mariska Obedzinski
Monitoring populations of threatened and endangered salmonid species is crucial to evaluating progress toward recovery. However, traditional fisheries monitoring methods are often associated with negative impacts to fish through repeated handling and impeding movements and behavior. In the Russian River basin (California) Sonoma Water and California Sea Grant jointly conduct life cycle monitoring of Central California Coast Coho Salmon and steelhead and California Coastal Chinook Salmon. Monitoring these co-occurring species presents unique challenges and has led us to apply a variety of technologies to overcome these challenges. Examples include replacement of traditional methods for counting adult migrants in a live trap with underwater video recording, Dual-Frequency Identification Sonar (DIDSON) and stationary PIT antennas to estimate adult population abundance and depict run-timing. Quantifying the abundance of salmonid smolts using traditional downstream trapping methods works well for Coho and Chinook, but not for out-migrating steelhead due to winter/early spring migration timing and behavior. Instead, we use a combination of snorkel surveys, electrofishing, and stationary PIT antennas to replace downstream migrant trapping for estimating steelhead smolt abundance. Using applied technologies we are able to monitor these sensitive species over a wide geographic area and throughout most of their life cycle.
8:20AM Canceled Talk
8:40AM Estimating Atlantic Salmon (Salmo salar) Population Size in a Multispecies River Using Adaptive Resolution Imaging Sonars (ARIS) and Underwater Cameras.
  Jani Helminen, Tommi Linnansaari, Guillaume Dauphin
Adaptive Resolution Imaging Sonars (ARIS) are a common tool for fish population estimates. We have been testing the technology for monitoring Atlantic salmon (Salmo salar) population size in the Miramichi River, NB, Canada since 2016. The monitoring starts in May and lasts until November, thus large amounts of data are collected. We compare manual and automatic data analyzation methods and short-range (<15 m) and long-range (15–30 m) settings for improving the cost-efficiency and accuracy of the sonar counts in Bayesian framework. Throughout the monitoring season, many different species such as Striped Bass (Morone saxatilis), American Shad (Alosa sapidissima), American Eel (Anguilla rostrata), Alewife (Alosa pseudoharengus), and Blueback Herring (Alosa aestivalis) migrate through our study area. Since multiple species are present, we are developing methods for distinguishing between salmon and other similar-sized species. Our tests in controlled setup showed that calculating tail-beat frequency from short-range sonar image can be used for distinguishing between Striped Bass, Atlantic Salmon, and American Shad. We are currently testing the method in riverine environment where we have underwater (UW) cameras and lights in the sonar field. The UW cameras are also used for sampling the species diversity to improve the accuracy of ARIS population estimates.
9:00AM Use of Subsampling Techniques to Improve the Precision, Accuracy, and Efficiency of Imaging Sonar Results
  David Ayers, Matthew Young, Collin D. Smith, Fred Feyrer
In recent years imaging sonars have been commonly employed to passively monitor the movement, abundance, and behavior of fishes across various aquatic environments. This approach offers several advantages over traditional monitoring techniques including the ability to non-invasively observe untagged fish movement across dark, turbid, and other challenging aquatic conditions. Imaging sonars can also can operate continuously for long periods of time, allowing scientists to assess the effects of various environmental factors on fish habitat use. However, this approach generates large volumes of data and requires laborious and expensive post-processing procedures. Here we address this challenge by presenting an analytical framework to efficiently subsample data while generating estimates of result accuracy and precision. In doing so, we hope to contribute to the robust and responsible use of imaging sonar technology for various applications in fisheries and aquatic ecology.
9:20AM Use of Low-Cost, Autonomous, Underwater Camera Systems to Advance Understanding of Fish Habitat Usage and Behavior
  Matthew Peterson, Dana Lee, Mathew Simenc, Garth Jaehnig, Andrea Fuller, Doug Demko
Recent technological advancements have led to a proliferation in alternative sampling methods that can provide refined fisheries and habitat data. Recent advances in camera technology, motion detection software, high-capacity cloud storage, solar systems, and machine learning systems, have provided scientists with a variety of tools to examine fish populations and habitats. Although camera systems can have imperfect detection, they can be deployed continuously and offer a non-invasive alternative to compare with other monitoring approaches. Further, they can be more effective than traditional sampling methods in complex habitats and can be cost-effective. We use three versions of underwater, automated camera systems to passively monitor for fishes in a variety of situations where handling fish is not possible or desirable. These camera systems, which incorporate motion detection software, have high storage capacity and can be deployed in remote locations using solar power. In addition, the systems can be paired with more traditional sampling techniques to maximize results and supplement long-term monitoring data. We highlight our current applications and explore future applications to improve our understanding of key species of interest. Additionally, processing of the videos collected can incorporate machine-learning software to reduce review time and aid in species identification.
09:40AM Break
1:10PM Using Environmental DNA to Detect the Invasive New Zealand Mud Snail (Potamopyrgus antipodarum) in Freshwaters
  Jake Ponce, Ivan Arismendi, Austen Thomas
Recent developments in environmental DNA (eDNA) technologies have advanced the detection and monitoring of rare, indicator, and invasive species. However, standard lab analysis can take days or weeks before results are available and is prohibitive when rapid management decisions are needed. We investigated the efficacy of a real-time quantitative PCR (qPCR) system for on-site species detections (Biomeme) while comparing to traditional sampling methods in search of New Zealand mud snails. We hypothesized that we would observe no significant difference in site identifications (i.e. positive or negative for mud snails) between on-site eDNA detection sampling and traditional sampling techniques. Here we will present presence and absence data obtained from six locations in western Washington. Sampling sites were selected based on previously positive identified locations of mud snails. Understanding which method is more efficient for positive identification of an invasive species would help initiate management protocols more rapidly to help control invasions.
1:30PM Adaptation of Technology: A Glimpse into the Future of Aquatic Environmental DNA Monitoring in the Sacramento-San Joaquin Delta.
  Katie Karpenko, Gregg Schumer
Environmental DNA (eDNA) is an innovative sampling method that has been successfully implemented as a non-invasive molecular monitoring tool to determine species presence or absence in aquatic ecosystems. With increasing demand for eDNA applications in fisheries management, there is a clear need to enhance sampling capabilities and expand sampling capacity through automation. Currently, no autonomous sampling methods exist that can reliably satisfy the growing demand for eDNA monitoring required by resource managers and stakeholders in the Sacramento-San Joaquin Delta. However, technologies do exist that may be modified to accomplish these goals. We conducted a series of experiments in the Sacramento-San Joaquin Delta to evaluate the McLane phytoplankton sampler (PPS) in terms of its ability to (1) capture DNA; (2) produce results comparable to current sampling methods, and (3) collect samples over an extended period of time during simulated monitoring events. Manual eDNA sampling methods were used alongside the PPS to determine automated sampling adaptability and functionality. Samples were analyzed using quantitative PCR (qPCR) and multi-species metabarcoding which allowed us to assess the efficacy of the McLane PPS as a semi-autonomous eDNA monitoring tool.
1:50PM Using Wagon-Wheel Antennas to Pioneer the West: How New PIT Detection Technology Has Expanded Our Knowledge on Imperiled Fish Conservation and Management
  Peter Mackinnon, Mark McKinstry, Casey Pennock, C. Nate Cathcart, Richard Wilkison, Travis Francis
Radio Frequency Identification was first introduced into Pacific Northwest fisheries science in the mid-1980’s with the introduction of the Passive Integrated Transponder (PIT) tag. PIT-tags were first used to evaluate survival of anadromous fish through hydroelectric projects. Innovations such as multiplexing antenna readers, smaller high-performance tags, and larger more robust antennas broadened fisheries applications of PIT-tag technology. Traditionally, PIT-tag antennas were fixed arrays that detected PIT-tagged fish moving through a specific point in a river or facility. However, the need for alternative detection techniques and methods has become apparent. Various river basins and fish species present unique challenges to fish detection; such as fish longevity, unpredictable movement tendencies, and diverse use of complex and remote habitats. New fish detection antennas – tailored to the needs of field biologists – have been developed, tested, and adopted in long-term studies where biologists can “actively” detect fish instead of “passively” waiting for them. These innovative methods expand the use of PIT-tag data from traditional mark-recapture studies to habitat use and movement studies. We present data from several successful projects where smaller, temporary, submersible, and floating PIT-Tag antennas have been successfully used to detect PIT-tagged fish where traditional sampling methods have been less effective.
2:10PM Wells Dam Juvenile Bypass Baffle PIT Detection System
  Steve Anglea, Tom Kahler
Douglas County Public Utility District (DCPUD) installed a juvenile PIT-tag detection system at Wells Dam in 2016 and 2017 to determine compliance with FERC-license obligations. Detections at Wells Dam are used to determine travel time between Wells Dam and Rocky Reach Dam, the next dam downstream, and those data are used to calculate passage date at Wells Dam for the thousands of fish detected at Rocky Reach Dam but not at Wells Dam. DCPUD worked with Biomark to design and install a PIT-tag array in a subset of the Spill Bay 2 bypass baffle openings. Biomark used thin-wall shielded antennas to minimize the amount of flow constriction and allow placement within the steel structure. Each antenna is connected to a Biomark IS1001 reader housed in a submersible enclosure and mounted to the downstream side of the bypass baffle. The 16-IS1001s are connected to a pair of Biomark IS1001-Master Controllers. Power to the IS1001-MCs is provided using an isolation transformer. All diagnostic and tag-detection data is transmitted to a data-collection computer through a fiber optic cable and then to Biomark’s BioLogic web portal.
2:30PM The Aquatic Habitat Sampling Platform: A Non-Traditional Look at Traditional Estuary Questions
  Whitney Thorpe, Jesse Anderson, Erwin Van Nieuwenhuyse, Joseph Merz
Estuaries are naturally complex, diverse and productive habitats. The inherent variability and anthropogenically altered conditions of estuaries, combined with limitations in habitat-specific sampling methodologies make system level research difficult, and comparisons of results from different methods incongruous. Additionally, sensitive life stages of many estuarine, catadromous, and anadromous fishes require vegetated littoral habitats that are often under-sampled due to traditional method limitations. Therefore, new technology is needed for system-wide research that can inform management regarding habitat utilization of estuarine environments. The Aquatic Habitat Sampling Platform (Platform) was developed as an integrated sampling system that can passively sample fish and elucidate habitat associations with minimal impact to sensitive species. Versatility of the Platform expands data collection from deeper open-water habits to shallow, off-channel habitats, providing reliable estimates of gear efficiency and catch (CPUE), and allowing direct comparisons of data from variable estuarine habitats. Field tests of the Platform in California’s Sacramento-San Joaquin Delta indicate that it effectively samples across habitat types in a standardized manner, detects differences in fish communities associated with habitat variables, and is more efficient than traditional gear types. Future goals include improving automated fish species identification and testing the platform in additional habitat types.
2:50PM Refreshment Break
3:20PM The Use of Carbon Dioxide to Remove Resident Piscivorous Striped Bass (Morone saxatilis) from the Tracy Fish Collection Facility in the Sacramento-San Joaquin River Delta, California
  Brandon Wu
The U.S. Department of the Interior, Bureau of Reclamation (Reclamation), Tracy Fish Collection Facility (TFCF; Byron, California) functions to salvage fish from Sacramento-San Joaquin River Delta water exported south by the C.W. “Bill” Jones Pumping Plant. Predation by resident piscivorous fish is a contributing factor to fish loss at the TFCF and Striped Bass (Morone saxatilis) are generally considered the most prevalent piscivorous fish species within the facility. To improve fish salvage and meet regulatory requirements, Reclamation is investigating the use of carbon dioxide (CO2) as an anesthetic to remove predatory fish from the TFCF system. The treatment of various water conveyance channels and components of the TFCF with CO2 has demonstrated that elevated CO2 concentrations (50–350 mg/L) increase the number and size of Striped Bass in collection tanks, suggesting that this application is feasible and effective. In addition, replicates performed with acoustically tagged Striped Bass suggest that fish appear to exhibit an avoidance response to elevated CO2 concentrations. Future efforts will focus on increasing removal efficiency in TFCF collection tanks as well as developing a method to direct piscivorous fish out of the facility to a location where there is no impact on salvageable fish.
3:40PM Assessing the Use of Predation-Detection Acoustic Transmitters to Examine Predation Loss of Juvenile Chinook Salmon
  Clarence Fullard
Emerging advancements in acoustic telemetry technology, such as predation detection acoustic transmitters, may provide clarity to our understanding of predator-prey relationships in wild systems. Standard acoustic transmitters are common in longitudinal survival studies, but they may not clearly identify differences between predator and prey behavior since acoustically tagged fish continue to transmit once consumed by a predator. This study intended to measure near-field predation around a fish salvage release site, where predators are known to key in on fish releases. We used VEMCO acoustic transmitters capable of detecting predation events in laboratory and field trials to develop a methodology to measure predation loss of Chinook Salmon in the Sacramento-San Joaquin River Delta. Laboratory trials revealed positive predation detection for all tags, but variable predation detection time (5 to 60 hours). Field trials revealed similarly high predation detection times, which was likely a result of predator size and gut content. These results show that VEMCO’s predation tags are a useful tool in detection predation events during acoustic telemetry studies, however future studies should carefully consider the temporal and spatial patterns in predator-prey interactions before undertaking such research to ensure that predation trigger times can provide the necessary resolution for research goals.
4:00PM Paired Satellite and Acoustic Tagging to Monitor the Movements of Bigheaded Carp in the Upper Illinois River
  Chelsea Center, Jehnsen Lebsock, James Lamer, Brent Knights, Kevin S. Irons
Monitoring bigheaded carp has been a priority since their introduction and particularly important in the last decade as efforts to prevent them from entering Lake Michigan gained momentum. The advent of satellite telemetry has the potential to complement traditional acoustic passive and active telemetry efforts with the advantage that satellite telemetry provides the capability to track multiple individuals at once without the time and space limitations of traditional technologies to attain similar information. Twenty-two Bighead Carp and Silver Carp were dual-tagged with real-time GPS transmitters and acoustic tags in the Dresden Island reach of the Upper Illinois River waterway to directly compare the performance of each tag to inform management efforts. While limitations were evident during testing, satellite telemetry paired with acoustic telemetry could be useful for identifying real-time aggregations to inform contracted removal and characterizing spawning and feeding habitat to inform other management efforts.
4:20PM Evaluation of the Juvenile Salmonid Acoustic Telemetry System (JSATS) Detection Range and Efficiency in Saltwater Estuarine Environments
  Audrey Thompson
The Juvenile Salmonid Acoustic Telemetry System (JSATS) is used to evaluate freshwater behavior and survival of salmon, trout, and other fish. Particularly in riverine survival evaluations, the downstream extent of detection arrays is often placed upstream of any marine influence assuming that poor signal propagation in salt water renders JSATS ineffective in estuarine environments. To evaluate this assumption, we tested the performance of the JSATS in an estuarine environment by estimating the detection range and detection efficiency of Lotek model L-AMT 5.2 transmitters on a Teknologic Model SLER Autonomous Acoustic Receiver operating at 416 +/- 4.5KHz (with 6kt doppler tolerance) near Bellingham, Washington State. The observed maximum detection range of ~230m, and detection efficiency of 100% observed within 180m of the receiver, we suggest that the JSAT system could be an effective tool for monitoring movement and transit of tagged fish in estuarine environments.

Organizers: Kevin W. Clark, Javier Miranda
Supported by: California Department of Water Resources

Location: Reno-Sparks CC Date: September 30, 2019 Time: 8:00 am - 4:40 pm