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USGS2025

Reconstructing relative abundance indices for Atlantic sturgeon using hierarchical ecological models

Objective The Atlantic Sturgeon Acipenser oxyrinchus is a wide-ranging, long-lived diadromous fish that is endangered in most of its range. Our objective was to develop and apply long-term, detection-corrected indices of relative abundance for juvenile and adult Atlantic Sturgeon in the Hudson River, New York, United States, to support population monitoring and stock assessment. Methods We used long-term gill-net catches to estimate relative abundances of juvenile and adult Atlantic Sturgeon while accounting for imperfect detection within an N- mixture modeling framework. We validated the model framework using a simulation–estimation framework based on mean parameter estimates from the adult Atlantic Sturgeon relative abundance index. Results Simulation testing indicated that absolute abundance estimates may be biased low due to poor characterization of detection probabilities. However, model estimates of relative abundance tracked simulated abundance trends well. Juvenile relative abundance estimates followed similar trends as raw gill-net catches but were less variable among years when corrected for detection probability. Relative abundance of juveniles increased from 2004 to 2015 prior to declining through 2022, with little evidence for change between the start and end of the survey. Detection-corrected indices for adult sturgeon indicated a consistent increase in relative abundance that was not readily apparent in raw catch indices. Conclusions Detection-corrected catch indices can provide improved characterization of Atlantic Sturgeon relative abundance dynamics over raw gill-net catches through use of N- mixture models. The approach has broad applicability to data types that are commonly collected for understanding population trends in stock assessment. Estimation of absolute abundance and other population demographics germane to management would benefit from alternative or auxiliary data collected through approaches such as side-scan sonar or acoustic telemetry, which are increasingly common for monitoring sturgeon populations.

New York↗

USGS2010

Global positioning system and associated technologies in animal behaviour and ecological research

Biologists can equip animals with global positioning system (GPS) technology to obtain accurate (less than or equal to 30 m) locations that can be combined with sensor data to study animal behaviour and ecology. We provide the background of GPS techniques that have been used to gather data for wildlife studies. We review how GPS has been integrated into functional systems with data storage, data transfer, power supplies, packaging and sensor technologies to collect temperature, activity, proximity and mortality data from terrestrial species and birds. GPS 'rapid fixing' technologies combined with sensors provide location, dive frequency and duration profiles, and underwater acoustic information for the study of marine species. We examine how these rapid fixing technologies may be applied to terrestrial and avian applications. We discuss positional data quality and the capability for high-frequency sampling associated with GPS locations. We present alternatives for storing and retrieving data by using dataloggers (biologging), radio-frequency download systems (e.g. very high frequency, spread spectrum), integration of GPS with other satellite systems (e.g. Argos, Globalstar) and potential new data recovery technologies (e.g. network nodes). GPS is one component among many rapidly evolving technologies. Therefore, we recommend that users and suppliers interact to ensure the availability of appropriate equipment to meet animal research objectives.

Philosophical Transactions of the Royal Society B:↗

USGS1996

Vertical spatial coherence model for a transient signal forward-scattered from the sea surface

The treatment of acoustic energy forward scattered from the sea surface, which is modeled as a random communications scatter channel, is the basis for developing an expression for the time-dependent coherence function across a vertical receiving array. The derivation of this model uses linear filter theory applied to the Fresnel-corrected Kirchhoff approximation in obtaining an equation for the covariance function for the forward-scattered problem. The resulting formulation is used to study the dependence of the covariance on experimental and environmental factors. The modeled coherence functions are then formed for various geometrical and environmental parameters and compared to experimental data.

IEEE Journal of Oceanic Engineering↗

USGS2018

A distributed pipeline for DIDSON data processing

Technological advances in the field of ecology allow data on ecological systems to be collected at high resolution, both temporally and spatially. Devices such as Dual-frequency Identification Sonar (DIDSON) can be deployed in aquatic environments for extended periods and easily generate several terabytes of underwater surveillance data which may need to be processed multiple times. Due to the large amount of data generated and need for flexibility in processing, a distributed pipeline was constructed for DIDSON data making use of the Hadoop ecosystem. The pipeline is capable of ingesting raw DIDSON data, transforming the acoustic data to images, filtering the images, detecting and extracting motion, and generating feature data for machine learning and classification. All of the tasks in the pipeline can be run in parallel and the framework allows for custom processing. Applications of the pipeline include monitoring migration times, determining the presence of a particular species, estimating population size and other fishery management tasks.

Conference Paper↗

USGS2008

Measuring gravity currents in the Chicago River, Chicago, Illinois

Recent studies of the Chicago River have determined that gravity currents are responsible for persistent bidirectional flows that have been observed in the river. A gravity current is the flow of one fluid within another caused by a density difference between the fluids. These studies demonstrated how acoustic Doppler current profilers (ADCP) can be used to detect and characterize gravity currents in the field. In order to better understand the formation and evolution of these gravity currents, the U.S. Geological Survey (USGS) has installed ADCPs and other instruments to continuously measure gravity currents in the Chicago River and the North Branch Chicago River. These instruments include stage sensors, thermistor strings, and both upward-looking and horizontal ADCPs. Data loggers and computers installed at gaging stations along the river are used to collect data from these instruments and transmit them to USGS offices. ?? 2008 IEEE.

Illinois↗

USGS2011

2-D inner-shelf current observations from a single VHF WEllen RAdar (WERA) station

The majority of High Frequency (HF) radars used worldwide operate at medium to high frequencies (8 to 30 MHz) providing spatial resolutions ranging from 3 to 1.5 km and ranges from 150 to 50 km. This paper presents results from the deployment of a single Very High Frequency (VHF, 48 MHz) WEllen RAdar (WERA) radar with spatial resolution of 150 m and range 10-15 km, used in the nearshore off Cape Hatteras, NC, USA. It consisted of a linear array of 12 antennas operating in beam forming mode. Radial velocities were estimated from radar backscatter for a variety of wind and nearshore wave conditions. A methodology similar to that used for converting acoustically derived beam velocities to an orthogonal system is presented for obtaining 2-D current fields from a single station. The accuracy of the VHF radar-derived radial velocities is examined using a new statistical technique that evaluates the system over the range of measured velocities. The VHF radar velocities showed a bias of 3 to 7 cm/s over the experimental period explainable by the differences in radar penetration and in-situ measurement height. The 2-D current field shows good agreement with the in-situ measurements. Deviations and inaccuracies are well explained by the geometric dilution analysis.

North Carolina↗

USGS2015

Velocity bias induced by flow patterns around ADCPs and associated deployment platforms

Velocity measurements near the Acoustic Doppler Current Profiler (ADCP) are important for mapping surface currents, measuring velocity and discharge in shallow streams, and providing accurate estimates of discharge in the top unmeasured portion of the water column. Improvements to ADCP performance permit measurement of velocities much closer (5 cm) to the transducer than has been possible in the past (25 cm). Velocity profiles collected by the U.S. Geological Survey (USGS) with a 1200 kHz Rio Grande Zedhead ADCP in 2002 showed a negative bias in measured velocities near the transducers. On the basis of these results, the USGS initiated a study combining field, laboratory, and numerical modeling data to assess the effect of flow patterns caused by flow around the ADCP and deployment platforms on velocities measured near the transducers. This ongoing study has shown that the negative bias observed in the field is due to the flow pattern around the ADCP. The flow pattern around an ADCP violates the basic assumption of flow homogeneity required for an accurate three-dimensional velocity solution. Results, to date (2014), have indicated velocity biases within the measurable profile, due to flow disturbance, for the TRDI 1200 kHz Rio Grande Zedhead and the SonTek RiverSurveyor M9 ADCPs. The flow speed past the ADCP, the mount and the deployment platform have also been shown to play an important role in the magnitude and extent of the velocity bias.

Conference Paper↗

USGS2015

Workgroup for Hydraulic laboratory Testing and Verification of Hydroacoustic Instrumentation

An international workgroup was recently formed for hydraulic laboratory testing and verification of hydroacoustic instrumentation used for water velocity measurements. The activities of the workgroup have included one face to face meeting, conference calls and an inter-laboratory exchange of two acoustic meters among participating laboratories. Good agreement was found among four laboratories at higher tow speeds and poorer agreement at the lowest tow speed.

Conference Paper↗

USGS2002

Porometric properties of siliciclastic marine sand: A comparison of traditional laboratory measurements with image analysis and effective medium modeling

During the 1999 sediment acoustics experiment (SAX99), porometric properties were measured and predicted for a well sorted, medium sand using standard laboratory geotechnical methods and image analysis of resin-impregnated sediments. Sediment porosity measured by laboratory water-weight-loss methods (0.372 ?? 0.0073 for mean ??1 standard deviation) is 0.026 lower than determined by microscopic image analysis of resin-impregnated sediments (0.398 ?? 0.029). Values of intrinsic permeability (m2) determined from constant-head permeameter measurements (3.29 ?? 10-11 ?? 0.60 ?? 10-11) and by microscopic image analysis coupled with effective medium theory modeling (2.78 ?? 10-11 ?? 1.01 ?? 10-11) are nearly identical within measurement error. The mean value of tortuosity factor measured from images is 1.49 ?? 0.09, which is in agreement with tortuosity factor determined from electrical resistivity measurements. Slight heterogeneity and anisotropy are apparent in the top three centimeters of sediment as determined by image-based porometric property measurements. However, the overall similarity for both measured and predicted values of porosity and permeability among and within SAX99 sites indicates sediments are primarily homogeneous and isotropic and pore size distributions are fairly uniform. The results indicate that an effective medium theory technique and two-dimensional image analysis accurately predicts bulk permeability in resin-impregnated sands.

IEEE Journal of Oceanic Engineering↗

USGS2007

In situ time-series measurements of subseafloor sediment properties

The capabilities and diversity of subsurface sediment sensors lags significantly from what is available for the water column, thereby limiting progress in understanding time-dependent seabed exchange and high-frequency acoustics. To help redress this imbalance, a new instrument, the autonomous sediment profiler (ASP), is described herein. ASP consists of a four-electrode, Wenner-type resistivity probe and a thermistor that log data at 0.1-cm vertical intervals over a 58-cm vertical profile. To avoid resampling the same spot on the seafloor, the probes are moved horizontally within a 20 times 100-cm -2 area in one of three preselected patterns. Memory and power capacities permit sampling at hourly intervals for up to 3-mo duration. The system was tested in a laboratory tank and shown to be able to resolve high-frequency sediment consolidation, as well as changes in sediment roughness. In a field test off the southern coast of France, the system collected resistivity and temperature data at hourly intervals for 16 d. Coupled with environmental data collected on waves, currents, and suspended sediment, the ASP is shown to be useful for understanding temporal evolution of subsurface sediment porosity, although no large depositional or erosional events occurred during the deployment. Following a rapid decrease in bottom-water temperature, the evolution of the subsurface temperature field was consistent with the 1-D thermal diffusion equation coupled with advection in the upper 3-4 cm. Collectively, the laboratory and field tests yielded promising results on time-dependent seabed change.

IEEE Journal of Oceanic Engineering↗

USGS2020

In situ measurements of compressional wave speed during gravity coring operations in the New England mud patch

This paper presents measurements of sediment sound-speed profiles measured in situ using the acoustic coring system (ACS). The reported measurements were obtained from seven gravity cores collected in the New England Mud Patch. The ACS uses two sets of transducers mounted below the penetrating tip of a sediment corer to make in situ measurements of geoacoustic properties as the corer penetrates the seabed. The in situ sound-speed profiles are interpreted in the context of stratigraphic layering measured by a seismic survey, and the measured sound-speed profiles are consistent with the geophysical description. The in situ sound-speed profiles measured by the ACS were compared to conventional measurements of sound speed on the recovered cores using the multisensor core logger (MSCL). The MSCL data displayed both random and systematic errors that were attributed to disturbance from the coring process and/or the handling of the sediments after collection. Finally, using porosity and grain size distributions measured from discrete samples of the cored sediments, the in situ sound-speed measurements were compared to empirical regressions based on independent data sets.

Atlantic Ocean, New England Mud Patch↗

USGS2012

Observations of ocean circulation and sediment transport experiment offshore of Fire Island, NY

Researchers from the U.S. Geological Survey (USGS) Woods Hole Coastal and Marine Science Center (WHCMSC), in collaboration with Coastal Carolina University (CCU) and University of South Carolina (USC), conducted a scientific field study to investigate the ocean circulation and sediment transport processes offshore of Fire Island, NY. Although the physical processes along the entire linear extent of Fire Island (~50 km) are of interest to the project, one particular region of focus is at the western end of the island where offshore sand ridges out to depths of 20 m extend across the inner shelf and connect to the near-shore bar system. The primary objective was to measure the physical processes around the sand ridges, including circulation patterns, wave parameters, bottom stress, and suspended sediment. Transects of instrumentation were positioned along and across the crests and troughs of the ridge field. A site at the top of a ridge and a site at the bottom of an adjacent trough were each populated with two tripods designed to provide high-resolution measurements near the sea-bed to record sediment re-suspension events. Measurements at these two sites include near bottom velocity profiles, acoustic Doppler velocimeters, pressure, optical transmission and backscatter at high sampling rates. Other measurements include upward looking velocity profiles, temperature, salinity, sonar images and profiles, and sediment size classes. Five smaller tripods were deployed to complete lines alongshore and across shore over a 5 km area to provide a regional picture. These tripods recorded upward looking velocity profiles and near bottom temperature, pressure and salinity. Surface buoys marked the position of the tripods and collected surface measurements at six of the sites. One buoy gathered meteorological measurements. The sites were occupied from January to April, 2012. This deployment was similar to previous efforts off Cape Hatteras, NC, in 2009, and is part of an ongoing effort to understand regional patterns in circulation and sediment transport and the interaction of inner shelf and near shore processes. New instrumentation for the USGS was introduced, including a variety of current and wave measurement equipment, acquisition and telemetry in near-realtime of the weather data, time series sonar imaging equipment, and anti-fouling wipers. Preliminary results suggest a complex and subtle relationship between wind and across shore current velocity in this region, and a more straightforward relationship between winds and alongshore currents. This paper also includes a preliminary report on the effectiveness of new measurement techniques used during this experiment.

New York↗

USGS2026

Development and field testing of a UAS-based software-defined radar for measuring freshwater bathymetry

We provide an overview of an uncrewed aircraft system (UAS)-based software-defined radar (SDRadar) system for high-resolution geophysical observations. The radar transceiver is implemented on a Radio Frequency System-on-Chip (RFSoC) platform, along with an ultra-wideband Vivaldi antenna that has a starting operating frequency of 150 MHz, enabling the system to be used across different applications, including measurements of freshwater bathymetry. In addition to system design and subsystem performance assessments, this paper presents the results of field testing conducted along the Sacramento River near Glenn, California, USA. The radar-derived river depth measurements are compared with ground truth data collected from a crewed boat using an acoustic Doppler current profiler (ADCP). The results show good agreement, with a root mean square error (RMSE) of 0.079 m.

California↗

USGS2019

Nest structure affects auditory and visual detectability, but not predation risk, in a tropical songbird community

Offspring mortality varies dramatically among species with critical demographic and evolutionary ramifications, yet the causes of this variation remain unclear. Nests are widely used for breeding across taxa and thought to influence offspring mortality risk. Traditionally, more complex, enclosed nest structures are thought to reduce offspring predation by reducing the visibility of nest contents and muffling offspring sounds compared to open nests. Direct tests of the functional bases for nest structure influence on predation risk are lacking. We used experiments and 10 years of observational data to examine how nest structure influences nest predation risk in a diverse community of tropical songbirds. First, we examined how nest size was related to nest structure and nest predation rates across species. Second, we assessed how nest structure influences the detectability of nestling begging calls both in field and in laboratory settings. Finally, we examined how the acoustic properties of different nest structures influence nest predation risk. Specifically, we experimentally broadcast begging calls from open and enclosed nests to determine how auditory cues and nest structure interact to affect predation on plasticine and quail eggs. We also tested whether nest structure was associated with differences in nest predation rates between the incubation (no begging cues) and nestling (begging cues) stages. We found that enclosed nests are larger than open nests after accounting for adult size, and larger nests had increased predation rates. Moreover, enclosed nests did not consistently alter nestling begging calls in ways that reduce the likelihood of predation compared to open nests. Indeed, begging cues increased predation rates for enclosed but not open‐cup nests in our playback experiment, and nest predation rates showed greater increases after hatching in enclosed than open‐cup nests. Ultimately, enclosed nests do not necessarily provide greater predation benefits than open nests in contrast to long‐standing theory.

Functional Ecology↗

USGS2022

NABat ML: Utilizing deep learning to enable crowdsourced development of automated, scalable solutions for documenting North American bat populations

Bats play crucial ecological roles and provide valuable ecosystem services, yet many populations face serious threats from various ecological disturbances. The North American Bat Monitoring Program (NABat) aims to use its technology infrastructure to assess status and trends of bat populations, while developing innovative and community-driven conservation solutions. Here, we present NABat ML , an automated machine-learning algorithm that improves the scalability and scientific transparency of NABat acoustic monitoring. This model combines signal processing techniques and convolutional neural networks (CNNs) to detect and classify recorded bat echolocation calls. We developed our CNN model with internet-based computing resources (‘cloud environment’), and trained it on >600,000 spectrogram images. We also incorporated species range maps to improve the robustness and accuracy of the model for future ‘unseen’ data. We evaluated model performance using a comprehensive, independent, holdout dataset. NABat ML successfully distinguished 31 classes (30 species and a noise class) with overall weighted-average accuracy and precision rates of 92%, and ≥90% classification accuracy for 19 of the bat species. Using a single cloud-environment computing instance, the entire model training process took <16 h. Synthesis and applications . Our convolutional neural network (CNN)-based model, NABat ML , classifies 30 North American bat species using their recorded echolocation calls with an overall accuracy of 92%. In addition to providing highly accurate species-level classification, NABat ML and its outputs are compatible with Bayesian and other statistical techniques for measuring uncertainty in classification. Our model is open-source and reproducible, enabling future implementations as software on end-user devices and cloud-based web applications. These qualities make NABat ML highly suitable for applications ranging from grassroots community science initiatives to big-data methods developed and implemented by researchers and professional practitioners. We believe the transparency and accessibility of NABat ML will encourage broad-scale participation in bat monitoring, and enable development of innovative solutions needed to conserve North American bat species.

Journal of Applied Ecology↗

USGS2016

Discharge and nutrient transport between lakes in a hydrologically complex area of Voyageurs National Park, Minnesota, 2010-2012

An acoustic Doppler velocity meter (ADVM) was deployed in the narrows between Namakan and Kabetogama Lakes in Voyageurs National Park, Minnesota, from November 3, 2010, through October 3, 2012. The ADVM can account for wind, seiche, and changing flow direction in hydrologically complex areas. The objectives were to (1) estimate discharge and document the direction of water flow, (2) assess whether specific conductance can be used to determine flow direction, and (3) document nutrient and chlorophyll a concentrations at the narrows. The discharge direction through the narrows was seasonal. Water generally flowed out of Kabetogama Lake and into Namakan Lake throughout the ice-covered season. During spring, water flow was generally from Namakan Lake to Kabetogama Lake. During the summer and fall, the water flowed in both directions, affected in part by wind. Water flowed into Namakan Lake 70% of water year 2011 and 56% of water year 2012. Nutrient and chlorophyll a concentrations were highest during the summer months when water-flow direction was unpredictable. The use of an ADVM was effective for assessing flow direction and provided flow direction under ice. The results indicated the eutrophic Kabetogama Lake may have a negative effect on the more pristine Namakan Lake. The results also provide data on the effects of the current water-level management plan and may help determine if adjustments are necessary to help protect the aquatic ecosystem of Voyageurs National Park.

Minnesota↗

USGS2022

Evaluation of select velocity measurement techniques for estimating discharge in small streams across the United States

Multiple instruments and methods exist for collecting discrete streamflow measurements in small streams with low flows, defined here as less than 5.7 m 3 /s (200 ft3/s). Included in the available methods are low-cost approaches that are infrequently used, in part, because their uncertainty is not well known. In this work, we evaluated the accuracy and suitability of three low-cost velocity measurement methods (surface float [SF], velocity head rod [VR], and rising body [RB]) and three conventional current meters (acoustic Doppler velocimeter, and mechanical Price type AA and Price Pygmy meters) relative to discharge calculated from stable artificial hydraulic controls. A total of 231 measurements were made by 20 individuals during 88 site visits to 24 sites in eight states. Accuracies were assessed for all methods and precision was evaluated for the low-cost methods. The median percent error was below 5% for conventional methods, and below 20% for the low-cost methods. The SF was the most accurate (median absolute percent error 14%) and precise (mean percent precision of 11%) low-cost method. The RB and VR, respectively, had 15% and 20% median absolute percent error and 29% and 12% mean percent precision. Results suggest that low-cost methods, when used appropriately, can be used to estimate discharge data under low flow conditions when measurements with conventional methods are not feasible and the associated accuracies meet end-user measurement objectives.

continental United States↗

USGS2022

Estimating occupancy from autonomous recording unit data in the presence of misclassifications and detection heterogeneity

1. Autonomous Recording Units (ARUs) are now widely used to survey communities of species. These surveys generate spatially and temporally replicated counts of unmarked animals, but such data typically include false negatives and misclassified detections, both of which may vary across sites in proportion to abundance. These data challenges can bias estimates of occupancy, and the typical approach of verifying individual detections is expensive. 2. We developed a Bayesian implementation of a two-species, false-positive N-mixture model for estimating occupancy from ARU data or other counts of unmarked animals that does not require manual verification. The model accounts for species misclassification and abundance-induced detection heterogeneity, as well as false negatives. To evaluate this model, we simulated 200 data sets for each of 29 scenarios, including scenarios in which misclassifications outnumbered correct classifications for rare species. We also applied the model to acoustic surveys of bats conducted on Fort Carson Army Post and Piñon Canyon Maneuver Site, Colorado, USA. 3. In the simulation study, bias, coverage, and root mean square error for occupancy estimates obtained from the two-species false-positive N-mixture model were superior to metrics obtained from two competing two-species false-positive occupancy models. Across 29 scenarios, absolute bias was consistently low (range: -0.03–0.07), while coverage averaged 93% (range: 74%–98%). For alternative occupancy models, absolute bias was often high (range: -0.36–0.39), and coverage averaged from 47%–65%. Although our model included an abundance parameter, abundance estimates were not reliable. For two species of Myotis bats, we estimated that 1%–5% of field-recorded detections were misclassified. Estimated occupancy (0.91 and 0.76) was lower than naïve estimates (1.00 and 0.94). Competing occupancy models implausibly estimated local occupancy of 0.00 at sites with numerous detections. 4. Our two-species, false-positive N-mixture model is significant because it accounts for detection heterogeneity and improves occupancy estimates without expensive manual verification of detections. Our field application indicated that misclassifications were not common, yet affected occupancy inferences. Given that ARUs are increasingly used to survey a broad range of taxa, such an occupancy model could be widely useful.

Methods in Ecology and Evolution↗