Detection, classification, and density estimation of marine mammals: final report

Detection, classification, and localization (DCL) research on marine mammal vocalizations has been in development for decades, and methods for marine mammal population density estimation using acoustic data have been in development since at least 2007. These efforts have been supported by MobySound, an archive of cetacean sounds used for studying call detection and localization that are annotated to facilitate research in DCL. This project was aimed to begin development of high‐performing automatic detection methods for the sounds of beaked whales and other odontocetes. Specifically, this report [1] details the newly collected odontocete recordings that have been added to the MobySound archive; [2] documents continuing development of methods for detection and classification, including improvements to the Energy Ratio Mapping Algorithm (ERMA) method for use on gliders and its extension to new species and populations; [3] reports on application of a newly developed method for population density estimation to field recordings; and [4] also reports on the successful production of datasets focused on odontocete whistles and clicks and baleen whale calls for the Fifth Workshop on Detection, Classification, Localization, and Density Estimation of Marine Mammals using Passive Acoustics.Chief of Naval Operations, Energy and Environmental Readiness Division, Washington DC. The report was prepared by Oregon State University and supported under NPS Grant N00244-10-1-0047.Approved for public release; distribution is unlimited

A comparison of methods for detecting right whale calls,”

ABSTRACT North Atlantic, North Pacific, and southern right whales all produce the up call, a frequency-modulated upsweep in the 50-200 Hz range. This call is one of the most common sounds, and frequently the most common sound, received from right whales, and as such is a useful indicator of the presence of right whales for acoustic surveys. A data set was prepared of 1857 calls and 6359 non-call sounds recorded from North Atlantic right whales (Eubalaena glacialis) near Georgia and Massachusetts. Two methods for the detection of the calls were compared: spectrogram correlation and a neural network. Spectrogram correlation parameters were chosen two ways, by manual choice using a sample of 20 calls, and by an optimization procedure that used all available calls. Neural network weights were trained via backpropagation on 9/10 of the test data set. Performance was measured separately for calls of different signal-to-noise ratio, as SNR heavily influences the performance of any detector. Results showed that the neural network performed best at this task, achieving an error rate of less than 6%, and is thus the preferred detection method here. Spectrogram correlation may be useful in situations in which a large set of training data is not available, as manual training on a small set of examples achieved an error rate (26%) that may be acceptable for many applications. SOMMAIRE Les baleines franches de l'Atlantique Nord, du Pacific Nord et Sud produisent toutes une vocalisation montante, soit un balayage ascendant modulé en fréquence dans la région de 50 à 200 Hz. Cette vocalisation est un des sons les plus communs produit par les baleines franches et, par le fait même, est un indicateur très utile de la présence des baleines lors de sondages acoustiques. Un ensemble de données a été préparé avec 1857 vocalisations et 6359 sons non vocalisés enregistrés auprès de baleines franches de l'Atlantique Nord (Eubalaena glacialis) près de la Georgie et du Massachusetts. Deux méthodes de détection des vocalisations ont été comparées: la corrélation de spectrogramme et le réseau neuronal. Les paramètres de la corrélation de spectrogramme ont été choisis de deux façons: par choix manuel, en utilisant seulement 20 vocalisations, et par une optimisation de la procédure utilisant toutes les vocalisations. Les coefficients de pondération du réseau neuronal ont été établi par rétropropagation sur 9/10 des données de test. Les performances ont été mesurées séparément pour des vocalisations ayant des rapports signal sur bruit différents, le rapport signal sur bruit ayant une grande influence sur tout détecteur. Les résultats démontrent que le réseau neuronal performe mieux dans ce genre de tâche, atteignant un taux d'erreur de moins de 6% et, par conséquent, est défini ici comme la meilleure méthode de détection. La corrélation de spectrogramme peut être utile dans les situations où un grand nombre de données de formation ne sont pas disponibles. Le choix manuel sur de petite tranche d'échantillons a atteint un taux d'erreur (26%) qui pourrait être acceptable dans plusieurs applications

The energy ratio mapping algorithm: A tool to improve the energy-based detection of odontocete echolocation clicks

The energy ratio mapping algorithm (ERMA) was developed to improve the performance of energy-based detection of odontocete echolocation clicks, especially for application in environments with limited computational power and energy such as acoustic gliders. ERMA systematically evaluates many frequency bands for energy ratio-based detection of echolocation clicks produced by a target species in the presence of the species mix in a given geographic area. To evaluate the performance of ERMA, a Teager-Kaiser energy operator was applied to the series of energy ratios as derived by ERMA. A noise-adaptive threshold was then applied to the Teager-Kaiser function to identify clicks in data sets. The method was tested for detecting clicks of Blainville’s beaked whales while rejecting echolocation clicks of Risso’s dolphins and pilot whales. Results showed that the ERMA-based detector correctly identified 81.6% of the beaked whale clicks in an extended evaluation data set. Average false-positive detection rate was 6.3% (3.4% for Risso’s dolphins and 2.9% for pilot whales). VC 2011 Acoustical Society of America. [DOI: 10.1121/1.3531924

Detections of whale vocalizations by simultaneously deployed bottom-moored and deep-water mobile autonomous hydrophones

Funding for this work was provided by the Living Marine Resources Program (N39430-14-C-1435 and N39430-14-C-1434), the Office of Naval Research (N00014-15-1-2142, N00014-10-1-0534, and N00014-13-1-0682), and NOAA’s Southwest Fisheries Science Center. SF was supported by the National Science and Engineering Graduate Fellowship.Advances in mobile autonomous platforms for oceanographic sensing, including gliders and deep-water profiling floats, have provided new opportunities for passive acoustic monitoring (PAM) of cetaceans. However, there are few direct comparisons of these mobile autonomous systems to more traditional methods, such as stationary bottom moored recorders. Cross-platform comparisons are necessary to enable interpretation of results across historical and contemporary surveys that use different recorder types, and to identify potential biases introduced by the platform. Understanding tradeoffs across recording platforms informs best practices for future cetacean monitoring efforts. This study directly compares the PAM capabilities of a glider (Seaglider) and a deep-water profiling float (QUEphone) to a stationary seafloor system (High-frequency Acoustic Recording Package, or HARP) deployed simultaneously over a 2 week period in the Catalina Basin, California, United States. Two HARPs were deployed 4 km apart while a glider and deep-water float surveyed within 20 km of the HARPs. Acoustic recordings were analyzed for the presence of multiple cetacean species, including beaked whales, delphinids, and minke whales. Variation in acoustic occurrence at 1-min (beaked whales only), hourly, and daily scales were examined. The number of minutes, hours, and days with beaked whale echolocation clicks were variable across recorders, likely due to differences in the noise floor of each recording system, the spatial distribution of the recorders, and the short detection radius of such a high-frequency, directional signal type. Delphinid whistles and clicks were prevalent across all recorders, and at levels that may have masked beaked whale vocalizations. The number and timing of hours and days with minke whale boing sounds were nearly identical across recorder types, as was expected given the relatively long propagation distance of boings. This comparison provides evidence that gliders and deep-water floats record cetaceans at similar detection rates to traditional stationary recorders at a single point. The spatiotemporal scale over which these single hydrophone systems record sounds is highly dependent on acoustic features of the sound source. Additionally, these mobile platforms provide improved spatial coverage which may be critical for species that produce calls that propagate only over short distances such as beaked whales.Publisher PDFPeer reviewe

Repertoire and classification of non-song calls in Southeast Alaskan humpback whales (Megaptera novaeangliae)

On low-latitude breeding grounds, humpback whales produce complex and highly stereotyped songs as well as a range of non-song sounds associated with breeding behaviors. While on their Southeast Alaskan foraging grounds, humpback whales produce a range of previously unclassified non-song vocalizations. This study investigates the vocal repertoire of Southeast Alaskan humpback whales from a sample of 299 non-song vocalizations collected over a 3-month period on foraging grounds in Frederick Sound, Southeast Alaska. Three classification systems were used, including aural spectrogram analysis, statistical cluster analysis, and discriminant function analysis, to describe and classify vocalizations. A hierarchical acoustic structure was identified; vocalizations were classified into 16 individual call types nested within four vocal classes. The combined classification method shows promise for identifying variability in call stereotypy between vocal groupings and is recommended for future classification of broad vocal repertoires

Assessing the cross platform performance of marine mammal indicators between two collocated acoustic recorders

Equipment and deployment strategies for remote passive acoustic sensing of marine environments must balance memory capacity, power requirements, sampling rate, duty-cycle, deployment duration, instrument size, and environmental concerns. The impact of different parameters on the data and applicability of the data to the specific questions being asked should be considered before deployment. Here we explore the effect of recording and detection parameters on marine mammal acoustic data across two platforms. Daily classifications of marine mammal vocalizations from two passive acoustic monitors with different subsampling parameters, an AURAL and a Passive Aquatic Listener (PAL), collocated in the Bering Sea were compared. The AURAL subsampled on a preset schedule, whereas the PAL sampled via an adaptive protocol. Detected signals of interest were manually classified in each dataset independently. The daily classification rates of vocalizations were similar. Detections from the higher duty-cycle but lower sample rate AURAL were limited to species and vocalizations with energy below 4 kHz precluding detection of echolocation signals. Temporal coverage from the PAL audio files was limited by the adaptive sub-sampling protocol. A method for classifying ribbon (Histriophoca fasciata) and bearded seal (Erignathus barbatus) vocalizations from the sparse spectral time histories of the PAL was developed. Although application of the acoustic entropy as a rapid assessment of biodiversity was not reflective of the number of species detected, acoustic entropy was robust to changes in sample rate and window length.Keywords: Acoustic diversity, Marine mammal classification, Spectral detection, Acoustic entropy, Ocean acousticsKeywords: Acoustic diversity, Marine mammal classification, Spectral detection, Acoustic entropy, Ocean acousticsKeywords: Acoustic diversity, Marine mammal classification, Spectral detection, Acoustic entropy, Ocean acoustic

Source levels of foraging humpback whale calls

Humpback whales produce a wide range of low-to mid-frequency vocalizations throughout their migratory range. Non-song "calls" dominate this species' vocal repertoire while on high-latitude foraging grounds. The source levels of 426 humpback whale calls in four vocal classes were estimated using a four-element planar array deployed in Glacier Bay National Park and Preserve, Southeast Alaska. There was no significant difference in source levels between humpback whale vocal classes. The mean call source level was 137 dB(RMS) re 1 mu Pa @ 1m in the bandwidth of the call (range 113-157 dBRMS re 1 mu Pa @ 1m), where bandwidth is defined as the frequency range from the lowest to the highest frequency component of the call. These values represent a robust estimate of humpback whale source levels on foraging grounds and should append earlier estimates. (C) 2018 Acoustical Society of Americ

Extracellular Vesicles from Pseudomonas aeruginosa Suppress MHC-Related Molecules in Human Lung Macrophages

Pseudomonas aeruginosa, a Gram-negative bacterium, is one of the most common pathogens colonizing the lungs of cystic fibrosis patients. P. aeruginosa secrete extracellular vesicles (EVs) that contain LPS and other virulence factors that modulate the host\u27s innate immune response, leading to an increased local proinflammatory response and reduced pathogen clearance, resulting in chronic infection and ultimately poor patient outcomes. Lung macrophages are the first line of defense in the airway innate immune response to pathogens. Proper host response to bacterial infection requires communication between APC and T cells, ultimately leading to pathogen clearance. In this study, we investigate whether EVs secreted from P. aeruginosa alter MHC Ag expression in lung macrophages, thereby potentially contributing to decreased pathogen clearance. Primary lung macrophages from human subjects were collected via bronchoalveolar lavage and exposed to EVs isolated from P. aeruginosa in vitro. Gene expression was measured with the NanoString nCounter gene expression assay. DNA methylation was measured with the EPIC array platform to assess changes in methylation. P. aeruginosa EVs suppress the expression of 11 different MHC-associated molecules in lung macrophages. Additionally, we show reduced DNA methylation in a regulatory region of gene complement factor B (CFB) as the possible driving mechanism of widespread MHC gene suppression. Our results demonstrate MHC molecule downregulation by P. aeruginosa-derived EVs in lung macrophages, which is consistent with an immune evasion strategy employed by a prokaryote in a host-pathogen interaction, potentially leading to decreased pulmonary bacterial clearance

Sounds from airguns and fin whales recorded in the mid-Atlantic Ocean, 1999-2009

Between 1999 and 2009, autonomous hydrophones were deployed to monitor seismic activity from 16° N to 50° N along the Mid-Atlantic Ridge. These data were examined for airgun sounds produced during offshore surveys for oil and gas deposits, as well as the 20 Hz pulse sounds from fin whales, which may be masked by airgun noise. An automatic detection algorithm was used to identify airgun sound patterns, and fin whale calling levels were summarized via long-term spectral analysis. Both airgun and fin whale sounds were recorded at all sites. Fin whale calling rates were higher at sites north of 32° N, increased during the late summer and fall months at all sites, and peaked during the winter months, a time when airgun noise was often prevalent. Seismic survey vessels were acoustically located off the coasts of three major areas: Newfoundland, northeast Brazil, and Senegal and Mauritania in West Africa. In some cases, airgun sounds were recorded almost 4000 km from the survey vessel in areas that are likely occupied by fin whales, and at some locations airgun sounds were recorded more than 80% days/month for more than 12 consecutive months

Confirmation of right whales near a historic whaling ground east of southern Greenland

North Atlantic right whales (Eubalaena glacialis) were found in an important nineteenth century whaling area east of southern Greenland, from which they were once thought to have been extirpated. In 2007–2008, a 1-year passive acoustic survey was conducted at five sites in and near the ‘Cape Farewell Ground’, the former whaling ground. Over 2000 right whale calls were recorded at these sites, primarily during July–November. Most calls were northwest of the historic ground, suggesting a broader range in this region than previously known. Geographical and temporal separation of calls confirms use of this area by multiple animals.This is the author's final peer-reviewed manuscript as accepted by the publisher, Royal Society. The publisher's pdf can be found at Biology Letters: http://rsbl.royalsocietypublishing.org