Atlantic Undersea Test And Evaluation Center Research Articles

Quantification by droplet digital PCR and species identification by metabarcoding of environmental (e)DNA from Blainville's beaked whales, with assisted localization from an acoustic array.

Detection and identification of species, subspecies or stocks of whales, dolphins and porpoises at sea remain challenging, particularly for cryptic or elusive species like beaked whales (Family: Ziphiidae). Here we investigated the potential for using an acoustically assisted sampling design to collect environmental (e)DNA from beaked whales on the U.S. Navy's Atlantic Undersea Test and Evaluation Center (AUTEC) in The Bahamas. During 12 days of August 2019, we conducted 9 small-boat surveys and collected 56 samples of seawater (paired subsamples of 1L each, including controls) using both a spatial collection design in the absence of visual confirmation of whales, and a serial collection design in the proximity of whales at the surface. There were 7 sightings of whales, including 11 Blainville's beaked whales (Mesoplodon densirostris). All whales were located initially with the assistance of information from a bottom-mounted acoustic array available on the AUTEC range. Quantification by droplet digital (dd)PCR from the four spatial design collections showed no samples of eDNA above the threshold of detection and none of these 20 samples yielded amplicons for conventional or next-generation sequencing. Quantification of the 31 samples from four serial collections identified 11 likely positive detections. eDNA barcoding by conventional sequencing and eDNA metabarcoding by next-generation sequencing confirmed species identification for 9 samples from three of the four serial collections. We further resolved five intra-specific variants (i.e., haplotypes), two of which showed an exact match to previously published haplotypes and three that have not been reported previously to the international repository, GenBank. A minimum spanning network of the five eDNA haplotypes, with all other published haplotypes of Blainville's beaked whales, suggested the potential for further resolution of differences between oceanic populations.

Quantifying the response of Blainville's beaked whales to U.S. naval sonar exercises in Hawaii

AbstractBehavioral responses of beaked whales (family Ziphiidae) to naval use of mid‐frequency active sonar (MFAS) have been quantified for some species and regions. We describe the effects of MFAS on the probability of detecting diving groups of Blainville's beaked whales on the U.S. Navy Pacific Missile Range Facility (PMRF) in Hawaii and compare our results to previously published results for the same species at the Atlantic Undersea Test and Evaluation Center (AUTEC) in the Bahamas. We use passive acoustic data collected at bottom‐mounted hydrophones before and during six naval training exercises at PMRF along with modelled sonar received levels to describe the effect of training and MFAS on foraging groups of Blainville's beaked whales. We use a multistage generalized additive modeling approach to control for the underlying spatial distribution of vocalizations under baseline conditions. At an MFAS received level of 150 dB re 1 μPa rms the probability of detecting groups of Blainville's beaked whales decreases by 77%, 95% CI [67%, 84%] compared to periods when general training activity was ongoing and by 87%, 95% CI [81%, 91%] compared to baseline conditions. Our results indicate a more pronounced response to naval training and MFAS than has been previously reported.

Discrete-space continuous-time models of marine mammal exposure to Navy sonar.

Assessing the patterns of wildlife attendance to specific areas is relevant across many fundamental and applied ecological studies, particularly when animals are at risk of being exposed to stressors within or outside the boundaries of those areas. Marine mammals are increasingly being exposed to human activities that may cause behavioral and physiological changes, including military exercises using active sonars. Assessment of the population-level consequences of anthropogenic disturbance requires robust and efficient tools to quantify the levels of aggregate exposure for individuals in a population over biologically relevant time frames. We propose a discrete-space, continuous-time approach to estimate individual transition rates across the boundaries of an area of interest, informed by telemetry data collected with uncertainty. The approach allows inferring the effect of stressors on transition rates, the progressive return to baseline movement patterns, and any difference among individuals. We apply the modeling framework to telemetry data from Blainville's beaked whale (Mesoplodon densirostris) tagged in the Bahamas at the Atlantic Undersea Test and Evaluation Center (AUTEC), an area used by the U.S. Navy for fleet readiness training. We show that transition rates changed as a result of exposure to sonar exercises in the area, reflecting an avoidance response. Our approach supports the assessment of the aggregate exposure of individuals to sonar and the resulting population-level consequences. The approach has potential applications across many applied and fundamental problems where telemetry data are used to characterize animal occurrence within specific areas.

Estimating group size from acoustic footprint to improve Blainville’s beaked whale abundance estimation

The numbers of animals in groups and the density of Blainville’s beaked whale Mesoplodon densirostris (Md) were estimated using passive acoustic data collected on the Atlantic Undersea Test and Evaluation Center (AUTEC). Md typically associate in groups, producing ultrasonic echolocation signals when foraging, and are routinely detected year-round on the AUTEC range. AUTEC includes a large network of hydrophones cabled to shore that can be used to detect Md echolocation signals. Using a first data set, with known group sizes, we used generalized linear models (GLMs) to model group size as a function of the acoustic footprint of a detected deep dive as perceived on the AUTEC hydrophones. The most important variable to explain group size was the detected click rate (total number of clicks detected divided by total length of vocal period duration). Using a second data set, covering 3 separate time periods in 2011 with automated group dive detections, we estimated beaked whale density using a dive counting approach. False positives were removed through manual inspection, removing dives with biologically infeasible characteristics. This led to a total of 8271 detections of beaked whale deep dives, with the average number per day in the three time periods considered being 75, 80 and 76 respectively. Using the selected GLM, the mean estimated group size was 2.36 (95% CI 2.15–2.60), 2.30 (95% CI 2.08–2.56), and 2.33 (95% CI 2.19–2.58) whales/group for the 1st, 2nd and 3rd time period. Md density was estimated at 15.8 (95% CI 13.6–21.9), 16.5 (95% CI 13.8–22.4), and 15.8 (95% CI 13.2–21.2) whales/1000 km2, respectively. These results support findings from previous studies, and will allow a more precise estimation of group sizes and densities for Md in future research.

Behavioral responses of satellite tracked Blainville's beaked whales (Mesoplodon densirostris) to mid‐frequency active sonar

AbstractThe vulnerability of beaked whales (Family: Ziphiidae) to intense sound exposure has led to interest in their behavioral responses to mid‐frequency active sonar (MFAS, 3–8 kHz). Here we present satellite‐transmitting tag movement and dive behavior records from Blainville's beaked whales (Mesoplodon densirostris) tagged in advance of naval sonar exercises at the Atlantic Undersea Test and Evaluation Center (AUTEC) in the Bahamas. This represents one of the largest samples of beaked whales individually tracked during sonar operations (n = 7). The majority of individuals (five of seven) were displaced 28–68 km after the onset of sonar exposure and returned to the AUTEC range 2–4 days after exercises ended. Modeled sound pressure received levels were available during the tracking of four individuals and three of those individuals showed declines from initial maxima of 145–172 dB re 1 μPa to maxima of 70–150 dB re 1 μPa following displacements. Dive behavior data from tags showed a continuation of deep diving activity consistent with foraging during MFAS exposure periods, but also suggested reductions in time spent on deep dives during initial exposure periods. These data provide new insights into behavioral responses to MFAS and have important implications for modeling the population consequences of disturbance.

Marine mammal passive acoustics applied to the monitoring of long-term trends in beaked whale abundance and to the derivation of a behavioral risk function for exposure to mid-frequency active sonar

Knowledge of Cuvier’s (Ziphius cavirostris) and Blainville’s (Mesoplodon densirostris) beaked whales’ distinct dive and vocal behavior has allowed for the development of multiple methods of passive acoustic abundance and density estimation (Marques et al., 2009, Moretti et al., 2010). These methods are being applied to multiple years of data to estimate long-term trends in abundance for Blainville’s beaked whales at the Atlantic Undersea Test and Evaluation Center (AUTEC) in the Bahamas and at the Pacific Missile Range Facility (PMRF) in Hawaii, and for Cuvier’s beaked whales at the Southern California Offshore Range (SCORE). These passive acoustic beaked whale dive data were combined with sonar and Range ship-track data to derive a behavioral risk function for Blainville’s beaked whales at AUTEC, and are being extended to Cuvier’s beaked whales at SCORE and Blainville’s beaked whales at PMRF. The behavioral risk function maps the probability of beaked whale dive disruption as a function of the receive le...

Adaptive Energy-Based Acoustic Sperm Whale Echolocation Click Detection

Sperm whales (Physeter macrocephalus) generate a series of broadband impulsive echolocation signals called clicks when diving in search of prey. These acoustic signals can be divided into usual clicks and creak clicks. They have a frequency spectrum that lies primarily between 2 and 18 kHz. In this paper, an adaptive energy-based click detector called the adaptive Teager energy operator (ATEO) is developed. A windowing technique is used to account for the time-varying characteristics of these signals, and the window length is adapted by estimating the interclick interval (ICI). The usual clicks and creak clicks are classified via ICI differences. The proposed method is compared with several well-known techniques using real data provided by the Atlantic Undersea Test and Evaluation Center (AUTEC). Performance results are presented which show that the proposed technique is a robust and efficient detector that can improve the click detection true positive rate (TPR) as well as reduce the false positive rate (FPR).

Tracking beaked whales with a passive acoustic profiler float

Acoustic methods are frequently used to monitor endangered marine mammal species. Advantages of acoustic methods over visual ones include the ability to detect submerged animals, to work at night, and to work in any weather conditions. A relatively inexpensive and easy-to-use acoustic float, the QUEphone, was developed by converting a commercially available profiler float to a mobile platform, adding acoustic capability, and installing the ERMA cetacean click detection algorithm of Klinck and Mellinger [(2011). J. Acoust. Soc. Am. 129(4), 1807-1812] running on a high-power DSP. The QUEphone was tested at detecting Blainville's beaked whales at the Atlantic Undersea Test and Evaluation Center (AUTEC), a Navy acoustic test range in the Bahamas, in June 2010. Beaked whale were present at AUTEC, and the performance of the QUEphone was compared with the Navy's Marine Mammal Monitoring on Navy Ranges (M3R) system. The field tests provided data useful to evaluate the QUEphone's operational capability as a tool to detect beaked whales and report their presence in near-real time. The range tests demonstrated that the QUEphone's beaked whale detections were comparable to that of M3R's, and that the float is effective at detecting beaked whales.

Population density of sperm whales in the Bahamas estimated using non-linked sensors

Estimates are presented of sperm whale click detection probability and sperm whale population density at the U.S. Navy’s Atlantic Undersea Test and Evaluation Center (AUTEC) in the Bahamas. The estimation of the probability of detecting whale echolocation clicks at multiple non-linked sensors uses estimates of sperm whale source level distribution, beam pattern of click emission, distribution of whale locations and orientations with respect to the sensors while clicking, acoustic transmission loss from source (whale) to receiver (bottom hydrophone), and noise levels at the receiver. These data are combined in a Monte Carlo model that propagates simulated clicks from whales at various random positions to each receiving hydrophone to estimate the signal-to-noise ratio at the receiver and the detection function, the probability of detecting clicks as a function of distance. The estimated detection function for each receiving hydrophone is then combined with information on the detector’s rate of missed calls and false detections as a function of signal-to-noise ratio, average sperm whale click rates, and the actual number of clicks detected in a given period of time in order to estimate population density. Results are compared to multi-sensor cases where detection functions were estimated analytically.

The Relationship among Oceanography, Prey Fields, and Beaked Whale Foraging Habitat in the Tongue of the Ocean

Beaked whales, specifically Blainville's (Mesoplodon densirostris) and Cuvier's (Ziphius cavirostris), are known to feed in the Tongue of the Ocean, Bahamas. These whales can be reliably detected and often localized within the Atlantic Undersea Test and Evaluation Center (AUTEC) acoustic sensor system. The AUTEC range is a regularly spaced bottom mounted hydrophone array covering >350 nm2 providing a valuable network to record anthropogenic noise and marine mammal vocalizations. Assessments of the potential risks of noise exposure to beaked whales have historically occurred in the absence of information about the physical and biological environments in which these animals are distributed. In the fall of 2008, we used a downward looking 38 kHz SIMRAD EK60 echosounder to measure prey scattering layers concurrent with fine scale turbulence measurements from an autonomous turbulence profiler. Using an 8 km, 4-leaf clover sampling pattern, we completed a total of 7.5 repeat surveys with concurrently measured physical and biological oceanographic parameters, so as to examine the spatiotemporal scales and relationships among turbulence levels, biological scattering layers, and beaked whale foraging activity. We found a strong correlation among increased prey density and ocean vertical structure relative to increased click densities. Understanding the habitats of these whales and their utilization patterns will improve future models of beaked whale habitat as well as allowing more comprehensive assessments of exposure risk to anthropogenic sound.

Changes in spatial and temporal distribution and vocal behavior of Blainville's beaked whales (Mesoplodon densirostris) during multiship exercises with mid‐frequency sonar

AbstractThe number and distribution of vocalizing groups of Blainville's beaked whales (Mesoplodon densirostris) were analyzed before, during, and after multiship mid‐frequency active sonar operations at the US Navy's Atlantic Undersea Test and Evaluation Center (AUTEC) in the Bahamas. Groups of foraging animals were isolated by detecting their echolocation clicks using an array of bottom‐mounted hydrophones. Two data sets were evaluated consisting of 115 and 240 h of acoustic data in May 2007 and 2008, respectively. Vocal activity was observed to decline during active sonar exercises and increase upon cessation of sonar transmissions in both data sets. Vocal activity did not recover to preexposure levels in the postexposure time period in 2007 nor in the initial postexposure period in the 2008 data set. Clicks detected during sonar operations were generally found to be on the periphery of the hydrophone field and vocal durations declined for those groups that remained on the range in that time period. Receive levels were calculated for several vocal groups of whales and indicated that animals continued to forage when exposed to sonar at levels as high as 157 dB re: μPa.

A dive counting density estimation method for Blainville’s beaked whale ( Mesoplodon densirostris) using a bottom-mounted hydrophone field as applied to a Mid-Frequency Active (MFA) sonar operation

We present a passive acoustic method for estimating the density of echolocating cetaceans that dive synchronously, based on isolation of dive starts using a field of distributed bottom-mounted hydrophones. The method assumes that all dive starts of the target species within a defined area are detected, and that independent estimates of dive rate and group size are available. We apply the method to estimate the density of Blainville’s beaked whales ( Mesoplodon densirostris) at the Atlantic Undersea Test and Evaluation Center (AUTEC) in the Bahamas during the time of a multi-ship active sonar exercise. Estimated densities for the 65 h before the exercise, 68 h during, 65 h after, and the final 43 h monitored were 16.99 (95% CI 13.47–21.43), 4.76 (3.78–6.00), 8.67 (6.87–10.94), and 24.75 (19.62–31.23) respectively, illustrating a possible avoidance reaction. Results for the 65 h before were compared with those from the click count density estimation algorithm developed by Marques et al. [Marques T, Thomas L, Ward J, DiMarzio N, Tyack P. Estimating cetacean population density using fixed passive acoustic sensors. An example with Blainville’s beaked whales. J Acoust Soc Am 2009;125(4):1982–1994]. The click count-based estimate was 19.23 animals/1000 km 2 (95% CI 12.69–29.13)—similar (13% higher), but with higher variance (CV 21% for click count method versus 12% for the dive count method). We discuss potential reasons for the differences, and compare the utility of the two methods. For both, obtaining reliable estimates of the factors that scale the measured quantity (dive starts or detected clicks) to density is the key hurdle. Defining the area monitored in the dive count method can also be problematic, particularly if the array is small.

Detection of Blainville’s beaked whales with towed arrays

The detection performance of a towed hydrophone array for deep-diving species is quantified by comparing detections of echolocation clicks from foraging groups of Blainville’s beaked whales ( Mesoplodon densirostris) from the TNO Delphinus array to detections from bottom-mounted hydrophones at the Atlantic Undersea Test and Evaluation Center (AUTEC) in the Bahamas. A beaked whale group detection probability of 40% is obtained at close ranges ( R < 2000 m) with the Delphinus towed array, and a maximum detection range of 5000 m is measured. The detection function can be explained by models, when taking into account the range in rms source levels (200–220 dB re 1 μPa 2 m 2), and the high system noise levels during the experiment. The model results suggest that detection ranges up to about 7 km are possible under favourable conditions, and demonstrate the effectiveness of using towed arrays to monitor deep-diving species, such as beaked whales.

Population density of sperm whales in the Bahamas estimated using propagation modeling.

The population density of sperm whales is estimated using an acoustic model to calculate the probability of receiving their clicks. The model uses estimates of (1) the source level of clicks, (2) the beampattern of the whales’ emitted clicks, (3) the distribution of whale orientations, (4) the loss between source and receiver (derived from acoustic propagation modeling), (5) noise levels at the receiver, (6) the detector’s rates of missed calls and false detections, and (7) sperm whales’ average click rate. These data are combined in a model that propagates simulated clicks from whales at various simulated positions to the receiving hydrophone to estimate the detection function—the probability of receiving a click as a function of distance. This function is then combined with information on whale click rates (performed at a chosen time of day when sperm whales appear to click at a measurably predictable rate) to estimate the population density corresponding to the number of received clicks in a given period of time. Data from the U.S. Navy’s Atlantic Undersea Test and Evaluation Center (AUTEC) in the Bahamas are used to estimate sperm whale population density there. [Thanks to ONR, NOAA, and the Navy’s Environmental Readiness Division for funding.]

Beaked whale density estimation from single hydrophones by means of propagation modeling.

Passive acoustic sonar systems offer many advantages to the study of marine mammals. For density estimation studies, it is important to evaluate the probability of detecting an animal as a function of its distance from the receiving sensor. In this work, acoustic propagation modeling is used to estimate the transmission loss as a function of depth and range between a source whale and a single‐hydrophone receiver. The computed transmission loss is compared to ambient noise levels and source level distributions to estimate the detection probability as a function of range. Results will be compared to beaked whale data recorded on bottom‐mounted sensors in the Atlantic Undersea Test and Evaluation Center (AUTEC) in the Bahamas, where the location of clicks is relative to one hydrophone. Source level and beam pattern extracted from digital acoustic tags (DTags) applied to a sample of animals at the same location will also be used in the detection model, and beaked whale spatial density will be estimated. The d...

Effects of sound on the behavior of toothed whales

We report initial results from a study on behavioral responses of beaked and other whales to sonar and other sounds. This research is designed to provide new science-based approaches for mitigating the risk of sonar to beaked and other whales. The study was conducted at the Atlantic Undersea Test and Evaluation Center (AUTEC) range near Andros Island in the Bahamas, where Blainville's beaked whales (Mesoplodon densirostris) can regularly be detected using passive acoustic monitoring of their echolocation clicks. Tags recorded sound at the whale and behavior of the whale. Data were collected from 10 tag deployments, 6 on Blainville's beaked whales and 4 on pilot whales. 109 hours of data were collected from tags, 74 hours from beaked whales and 34 hours from pilot whales. Playbacks of mid-frequency sonar and killer whale calls were performed on 3 of the tagged whales, 1 beaked whale and 2 pilot whales. The tagged beaked whale responded to both sonar and killer whale sounds by premature cessation of clicking during foraging dives (RL = ∼117 dB re 1 μPa for the killer whale sound, ∼145 dB for the sonar), and an unusually slow and long ascent.

Verified passive acoustic detection of beaked whales (Mesoplodon densirostris) using distributed bottom-mounted hydrophones in the tongue of the ocean, Bahamas

Passive detection of beaked whales has become increasingly important as at least two species, Blainville’s beaked whales (Mesoplodon densirostris) and Cuvier’s beaked whales (Ziphius cavorostris) have stranded in events associated with sonar. Passive acoustic detection and localization algorithms develop as part of the Office of Naval Research (ONR) Marine Mammal Monitoring on Navy Range (M3R) program will be presented along with results from a series of tests that demonstrate the efficacy of passive acoustic detection of vocalizing M. densirostris. Ninety-two bottom-mounted sensors at the Atlantic Undersea Test and Evaluation Center (AUTEC) were monitored for vocalizations. M3R systems were used to detect and localize vocalizing animals. Based on these real-time data, trained observers were vectored to the animals and verified the species. Focal follows coordinated with passive acoustics were completed. Observer photos along with raw sensor, detection and localization data were collected.

Aerial and Acoustic Marine Mammal Detection and Localization on Navy Ranges

Acoustic monitoring and aerial visual surveys of marine mammal activity were conducted simultaneously at the Navy's Pacific Missile Range Facility near Kauai, HI, during times of both high- and low-whale density from February 2002 to March 2003. Specifically, recordings from the range's 24 broadband hydrophones were made during 11 of 16 "in-season" and during six of ten "off-season" aerial surveys. Basic acoustic detections consisted primarily of humpback whale calls and sperm-whale clicks, and those two species were also reported in the visual surveys. The relative number of acoustic detections roughly corresponded with the visual survey results throughout the year. The same acoustic data were also provided to a passive-acoustic-localization algorithm based on acoustic propagation models which generated estimates of sperm-whale movement through the range. The acoustic localizations are in close proximity in space and time to the visual observations of sperm whales. Verification of the model-based localization algorithm's accuracy was demonstrated in a controlled-source experiment at the Navy's Atlantic Undersea Test and Evaluation Center (AUTEC) range in the Bahamas where the recordings of sperm-whale clicks were broadcast and successfully tracked. The localization accuracy of the model-based technique and traditional hyperbolic techniques is compared. These results raise the possibility of using existing Navy assets to detect and track marine mammals, particularly during times when visual sighting conditions are not favorable, in efforts to minimize their exposure to underwater sound.

Passive detection, data association, and localization of marine mammal calls using traditional 3D hyperbolic tracking algorithms

The Office of Naval Research Marine Mammal Monitoring on Navy Ranges (M3R) project has developed a toolset for passive detection and localization of marine mammals using the existing infrastructure of Navy undersea ranges. The tools are designed to work across a broad class of calls including clicks, sweeps, and whistles. Using vocalizations received by widely spaced omni-directional hydrophones, the M3R tools can detect and localize marine mammals in real-time. Signal detection algorithms, data association algorithm, and tracking algorithm have been developed, and demonstrated. The tools have also been successfully fielded to conduct extended monitoring of a 500 square nautical mile area located in the Tongue of the Ocean. This presentation will present the passive acoustic monitoring and localization tools developed under M3R. It will also present results of the application of these tools to the real-time detection and tracking as well as extended monitoring of various toothed whale species at the Atlantic Undersea Test and Evaluation Center (AUTEC), Andros Island, Bahamas.

Passive monitoring and localization of marine mammals in open ocean environments using widely spaced bottom mounted hydrophones

The Marine Mammal Monitoring on Navy Ranges (M3R) project has developed a toolset for passive detection and localization of marine mammals using the existing infrastructure of Navy’s undersea ranges. The Office of Naval Research funded the M3R project as part of the Navy’s effort to determine the effects of acoustic and other emissions on marine mammals and threatened/endangered species. A necessary first step in this effort is the creation of a baseline of behavior, which requires long-term monitoring of marine mammals. Such monitoring, in turn, requires the ability to detect and localize the animals. This paper will present the passive acoustic monitoring and localization tools developed under M3R. It will also present results of the deployment of the M3R tools at the Atlantic Undersea Test and Evaluation Center (AUTEC), Andros Island, Bahamas from June through November 2003. Finally, it will discuss current work to improve automated species classification.