Long-term Passive Acoustic Monitoring Research Articles

Long-Term Passive Acoustic Monitoring to Support Adaptive Management in a Sciaenid Fishery (Tagus Estuary, Portugal)

AbstractPassive acoustic monitoring (PAM) is useful for monitoring vocal fish but has had so far limited application in fisheries management. Here, four years (2016–2019) of concurrent daily catch and effort fishery data in Portugal and species-specific vocal activity in the Tagus estuary are compared to describe biological and small-scale fishery dynamics for a large sciaenid fish, the meagre (Argyrosomus regius), that aggregates to spawn. Consistent patterns in seasonality of acoustic and fisheries variables indicate that most fishing takes place within the Tagus estuary in spring and summer months, when higher vocal activity related to spawning aggregations is detected in the PAM station. Good fit of statistical models shows that PAM (sound pressure level in the third-octave band with centre frequency at 500 kHz during dusk) and PAM-supported variables (mean weekly catch per first sale transaction) can provide useful surveillance indicators to improve local management. Signs of overexploitation and hyperstability are detected and communicated to the estuarine fishing communities with the aim to initiate an adaptive local management cycle. The approach can be relevant for fisheries targeting other vocal fish that seasonally aggregate and face similar threats of overexploitation. Graphical Abstract

Odontocete detections are linked to oceanographic conditions in the Hawaiian Archipelago

Understanding environmental drivers of species’ behavior is key for successful conservation. Within cetacean research, studies focused on understanding such drivers often consider local conditions (e.g., sea surface temperature), but rarely include large-scale, long-term parameters such as climate indices. Here we make use of long-term passive acoustic monitoring data to examine relationships between eight classes of toothed whales and climate indices, specifically El Niño Southern Oscillation, Pacific Decadal Oscillation, and North Pacific Gyre Oscillation, as well as local surface conditions (temperature, salinity, sea surface height) at two sites in the Hawaiian Archipelago. We find that El Niño Southern Oscillation most influenced cetacean detections at monitored sites. In many cases, detection patterns matched well with combinations of one or more climate indices and surface conditions. Our results highlight the importance of considering climate indices in efforts to understand relationships between marine top predators and environmental conditions.

Transient sounds of hydrothermal vents

Transient acoustic signals were recently detected at the Main Endeavour Hydrothermal Vent Field which are believed to be generated by both geological and biological sources, including vent chimney collapse, impulsive geological signals, fish grunts, and snapping. These signals provide an opportunity for long-term passive acoustic monitoring of hydrothermal vent activity and ecology. This method offers advantages of longevity and robustness compared with other monitoring techniques, as the sensor can remain a safe distance away from the high-temperature, caustic vent fluid. Utilizing recordings from a bottom-mounted hydrophone on Ocean Networks Canada’s NEPTUNE observatory, a detector was implemented to identify and classify these signals in more than one year of acoustic data after 2016. While only a single hydrophone is available at this site, an array of three seismic accelerometers also on the NEPTUNE observatory was used to localize transient events when sufficient signal-to-noise ratio was available to provide confidence in the location estimate. Correlation of the transient sounds with seismic activity at the vent field was also evaluated, suggesting that passive acoustic monitoring can augment seismic records to provide additional information regarding geological activity at hydrothermal vent sites.

Using a deep neural network to classify echolocation clicks and identify biogeographic patterns of Pacific white-sided dolphins

Pacific white-sided dolphins are endemic to the Pacific Ocean; and two genetically distinct populations overlap along the west coast of North America. However, they are visually indistinguishable and the degree of spatial overlap remains unknown. Here, we use a deep neural network to show that the populations are acoustically distinguishable. Previous studies described two distinct echolocation click types associated with pacific white-sided dolphins and hypothesized that they were population-specific. Our neural network was trained to classify the click types based on spectral and temporal properties described previously. The neural network enabled us to analyze passive acoustic recordings from sites between the Gulf of California and the Gulf of Alaska over multiple years to investigate possible population-specific trends. The latitudinal occurrence pattern of the two click types supports the population-specific hypothesis: type A clicks continue to associate with the northern population distribution, and type B clicks with the southern population distribution. At long-term monitoring sites in Southern California, type B clicks were dominant during periods of warm water anomalies. This pattern may be an early indicator of future biogeographic shifts in the distribution of pacific white-sided dolphins and demonstrates the utility of long-term passive acoustic monitoring.

Where are the whales? Continued acoustic monitoring efforts of California’s Central Coast

Understanding and conserving ocean ecosystems is a difficult, but important task made easier with bioacoustic technology. Although marine mammal monitoring efforts can be done with visual surveys, they often lack temporal information on a finer scale. Long-term passive acoustic monitoring efforts of critical migratory species can provide detailed information about the region’s marine soundscape that is key to conservation efforts. The aim of our project is to establish a long-term bioacoustic monitoring station off the coast of central California and help close the gap in our understanding of marine mammal presence along the Pacific coastline. The goals put forth by the bioacoustic lab for this academic year include (1) determining probable species presence, (2) ascertaining temporal (day/night) variations of vocalizations, and (3) examining key differences in species and call type between two deployments from Fall 2022 and Winter 2023. These comparisons will be crucial to help develop a baseline understanding of seasonal and temporal variations of the soundscape in our region. We aim to implement various long-term deployments in order to gather more complete and consistent bioacoustic data in our local waters. These deployments and the subsequent analysis will contribute to large scale marine mammal monitoring and conservation efforts. [This project was made possible by a grant from the Santa Rosa Creek Foundation and the COAST undergraduate research fund.]

Application of long-term passive acoustic monitoring to evaluate spatial and temporal patterns of multi-species acoustic assemblages of marine mammals in the western North Atlantic Ocean

Passive acoustic monitoring (PAM) is an efficient method for large-scale marine mammal monitoring. PAM technologies concurrently sample multiple soniferous marine mammal species, and when coupled with verified detectors, provide information that can be used to evaluate community composition. This analysis used data collected by an array of high-frequency PAM recorders at eight sites between 30°0’N and 42°0’N along the shelf-break in the western North Atlantic Ocean. Daily acoustic presence of 13 known marine mammal species and grouped unknown odontocetes was determined for all months between June 2016 and May 2019. Classification trees were generated from monthly summaries of daily detections to identify community composition dissimilarities. Detections of Gervais’s beaked whale (Mesoplodon europaeus) represented the root node and split sites by latitude, grouping the three sites south of 34°0’N and the five sites north of 38°0’N. Tree nodes were further divided by other odontocetes. The presence of mysticetes also varied by site and season. Distinctive communities were identified for each site, with odontocetes being resident and mysticetes more migratory. The root and secondary splits were all driven by beaked whale species, demonstrating the importance of identifying these whales to species instead of aggregating them as is common for visual survey data.

Effects of duty cycles on passive acoustic monitoring of southern resident killer whale (Orcinus orca) occurrence and behavior

Long-term passive acoustic monitoring of cetaceans is frequently limited by the data storage capacity and battery life of the recording system. Duty cycles are a mechanism for subsampling during the recording process that facilitates long-term passive acoustic studies. While duty cycles are often used, there has been little investigation on the impact that this approach has on the ability to answer questions about a species' behavior and occurrence. In this study, the effects of duty cycling on the acoustic detection of southern resident killer whales (SRKW) (Orcinus orca) were investigated. Continuous acoustic data were subsampled to create 288 subsampled datasets with cycle lengths from 5 to 180 min and listening proportions from 1% to 67%. Duty cycles had little effect on the detection of the daily presence of SRKW, especially when using cycle lengths of less than an hour. However, cycle lengths of 15–30 min and listening proportions of at least 33% were required to accurately calculate durations of acoustic bouts and identify those bouts to ecotype. These results show that the optimal duty cycle depends on the scale of the research question and provide a framework for quantitative analysis of duty cycles for other marine species.

Performance metrics for marine mammal signal detection and classification.

Automatic algorithms for the detection and classification of sound are essential to the analysis of acoustic datasets with long duration. Metrics are needed to assess the performance characteristics of these algorithms. Four metrics for performance evaluation are discussed here: receiver-operating-characteristic (ROC) curves, detection-error-trade-off (DET) curves, precision-recall (PR) curves, and cost curves. These metrics were applied to the generalized power law detector for blue whale D calls [Helble, Ierley, D'Spain, Roch, and Hildebrand (2012). J. Acoust. Soc. Am. 131(4), 2682-2699] and the click-clustering neural-net algorithm for Cuvier's beaked whale echolocation click detection [Frasier, Roch, Soldevilla, Wiggins, Garrison, and Hildebrand (2017). PLoS Comp. Biol. 13(12), e1005823] using data prepared for the 2015 Detection, Classification, Localization and Density Estimation Workshop. Detection class imbalance, particularly the situation of rare occurrence, is common for long-term passive acoustic monitoring datasets and is a factor in the performance of ROC and DET curves with regard to the impact of false positive detections. PR curves overcome this shortcoming when calculated for individual detections and do not rely on the reporting of true negatives. Cost curves provide additional insight on the effective operating range for the detector based on the a priori probability of occurrence. Use of more than a single metric is helpful in understanding the performance of a detection algorithm.

Beluga whale (Delphinapterus leucas) acoustic foraging behavior and applications for long term monitoring.

Cook Inlet, Alaska, is home to an endangered and declining population of 279 belugas (Delphinapterus leucas). Recovery efforts highlight a paucity of basic ecological knowledge, impeding the correct assessment of threats and the development of recovery actions. In particular, information on diet and foraging habitat is very limited for this population. Passive acoustic monitoring has proven to be an efficient approach to monitor beluga distribution and seasonal occurrence. Identifying acoustic foraging behavior could help address the current gap in information on diet and foraging habitat. To address this conservation challenge, eight belugas from a comparative, healthy population in Bristol Bay, Alaska, were instrumented with a multi-sensor tag (DTAG), a satellite tag, and a stomach temperature transmitter in August 2014 and May 2016. DTAG deployments provided 129.6 hours of data including foraging and social behavioral states. A total of 68 echolocation click trains ending in terminal buzzes were identified during successful prey chasing and capture, as well as during social interactions. Of these, 37 click trains were successfully processed to measure inter-click intervals (ICI) and ICI trend in their buzzing section. Terminal buzzes with short ICI (minimum ICI <8.98 ms) and consistently decreasing ICI trend (ICI increment range <1.49 ms) were exclusively associated with feeding behavior. This dual metric was applied to acoustic data from one acoustic mooring within the Cook Inlet beluga critical habitat as an example of the application of detecting feeding in long-term passive acoustic monitoring data. This approach allowed description of the relationship between beluga presence, feeding occurrence, and the timing of spawning runs by different species of anadromous fish. Results reflected a clear preference for the Susitna River delta during eulachon (Thaleichthys pacificus), Chinook (Oncorhynchus tshawytscha), pink (Oncorhynchus gorbuscha), and coho (Oncorhynchus kisutch) salmon spawning run periods, with increased feeding occurrence at the peak of the Chinook and pink salmon runs.

Understanding marine life through long-term passive acoustic time series

Sound allows us to study the ocean on a much finer time scales than other methods of study as it is feasible to collect continuous underwater recordings over months or years at a time. My work has been focused on using such long recordings to improve our understanding of the ecology of large whales and marine fishes. However, ecological insights can only be gained from data that are truly comparable across time and space. The initial steps to achieving comparable time series from long-term recordings collected at vastly different locations include: effective detection of signals of interest, full knowledge of the characteristics of those signals and interfering noise, and normalization of those detections by appropriate recording effort across time and space. I will highlight a few things we have learned about baleen whale and fish species through long-term passive acoustic monitoring effort, such as an improved understanding of call function for some baleen whales or a better sense of animal occurrence. This, in turn, will allow us to start coupling the occurrence of these animals into the larger patterns of ecosystem dynamics, ultimately leading to a fuller understanding of their roles in the ocean.

The next wave of passive acoustic data management: How centralized access can enhance science

Passive acoustic data collection has grown exponentially over the past decade resulting in petabytes of data that document our ocean soundscapes. This effort has resulted in two big data challenges: the curation, management, and global dissemination of passive acoustic datasets and efficiently extracting critical information and comparing it to other datasets in the context of ecosystem-based research and management. To address the former, the NOAA National Centers for Environmental Information established a passive acoustic data archive, which contains over 100 TB of audio files mainly collected from stationary recorders throughout waters in the U.S. These datasets are documented with standards-based metadata and are freely available to the public. To begin to address the latter, through standardized processing and centralized stewardship and access, we will present a previously unattainable comparison of first order sound level-patterns from archived data collected across three distinctly separate long-term passive acoustic monitoring efforts conducted at regional and national scales: NOAA/National Park Service Ocean Noise Reference Station Network, the NOPP-funded Atlantic Deepwater Ecosystem Observatory Network, and the NOAA-Navy Sanctuary Soundscape Monitoring Project. Further, we will propose the next frontier for scalable data stewardship, access, and processing flow to help the community collaboratively move forward.

Cetacean occurrence offshore of Washington from long-term passive acoustic monitoring

A variety of cetacean species inhabit the productive waters offshore of Washington State, USA. Although the general presence of many of these species has been documented in this region, our understanding of fine-scale habitat use is limited. Here, passive acoustic monitoring was used to investigate the spatial and temporal distributions of ten cetacean species at three locations offshore of Washington. Between 2004 and 2013, a total of 2845 days of recordings were collected from sites on the continental shelf and slope, and in a submarine canyon. Acoustic presence was higher for all species at sites farther offshore. Detections were highest during the fall and winter for blue (Balaenoptera musculus), fin (B. physalus), and humpback whales (Megaptera novaeangliae), likely related to reproductive behavior, while minke whales (B. acutorostrata) were only detected on two days. Odontocetes showed temporal separation, with sperm whale (Physeter macrocephalus) detections highest in spring, Risso’s (Grampus griseus) and Pacific white-sided dolphins (Lagenorhynchus obliquidens) highest in summer, and Stejneger’s beaked whales (Mesoplodon stejnegeri), Cuvier’s beaked whales (Ziphius cavirostris), and the BW37V signal type highest in winter or spring. There was interannual variation in detections for most mysticete species, which may be linked to oceanographic conditions: blue and fin whale detections increased during 2007 and 2008, and fin and humpback whale detections increased in 2011. These results inform our understanding of cetacean behavior and habitat use in this region and may aid in the development of conservation strategies suited to the dynamic conditions that drive cetacean distribution.

The Next Wave of Passive Acoustic Data Management: How Centralized Access Can Enhance Science

Passive acoustic data collection has grown exponentially over the past decade resulting in petabytes of data that document our ocean soundscapes. This effort has resulted in two big data challenges: (1) the curation, management, and global dissemination of passive acoustic datasets and (2) efficiently extracting critical information and comparing it to other datasets in the context of ecosystem-based research and management. To address the former, the NOAA National Centers for Environmental Information recently established an archive for passive acoustic data. This fast-growing archive currently contains over 100 TB of passive acoustic audio files mainly collected from stationary recorders throughout waters in the United States. These datasets are documented with standards-based metadata and are freely available to the public. To begin to address the latter, through standardized processing and centralized stewardship and access, we provide a previously unattainable comparison of first order sound level-patterns from archived data collected across three distinctly separate long-term passive acoustic monitoring (PAM) efforts conducted at regional and national scales: NOAA/National Park Service Ocean Noise Reference Station Network, the Atlantic Deepwater Ecosystem Observatory Network, and the Sanctuary Soundscape Monitoring Project. Nine sites were selected from these projects covering the Alaskan Arctic, Northeast and Central Pacific, Gulf of Mexico, Caribbean Sea, and Mid and Northwest Atlantic. Sites could generally be categorized into those strongly influenced by anthropogenic noise (e.g., vessel traffic) and those that were not. Higher sound levels, specifically for lower frequencies (&amp;lt;125 Hz), and proximity to densely populated coastal zones were common characteristics of sites influenced by anthropogenic noise. Conversely, sites with lower overall sound levels and away from dense populations resulted in soundscape patterns influenced by biological sources. Seasonal variability in sound levels across selected decidecade bands was apparent for most sites and often represented changes in the presence or behavior of sound-producing species. This first order examination of levels across projects highlights the utility of these initial metrics to identify patterns that can then be examined in more detail. Finally, to help the PAM community collectively and collaboratively move forward, we propose the next frontier for scalable data stewardship, access, and processing flow.

Cetacean occurrence in the Gulf of Alaska from long-term passive acoustic monitoring

The Gulf of Alaska is an important habitat for a diverse array of marine mammals, many of which were severely depleted by historical whaling. To study current cetacean distributions in this region, passive acoustic monitoring was used to detect species-specific call types between 2011 and 2015 at five locations spanning the continental shelf, slope, and offshore seamounts. Spatial and temporal detection patterns were examined for nine species to compare differences in behavior and habitat use. Mysticetes showed seasonal increases in calling that indicated possible behavioral shifts between feeding and breeding in blue (Balaenoptera musculus), fin (B. physalus), and humpback (Megaptera novaeangliae) whales, and matched known migration timing of gray whales (Eschrichtius robustus). Interannual changes in blue and fin whale calling may relate to the marine heat wave that began in 2013 and lasted through the end of the monitoring period. Odontocete detections revealed unique spatial distributions, with killer whales (Orcinus orca) most common on the continental shelf and sperm whales (Physeter macrocephalus) most common on the continental slope, where detections occurred year-round. Beaked whales showed both spatial and temporal separation: Baird’s beaked whale (Berardius bairdii) detections were highest at Quinn Seamount in the spring, Cuvier’s (Ziphius cavirostris) at Pratt Seamount in winter, and Stejneger’s (Mesoplodon stejnegeri) on the continental slope in the fall. The year-round presence of many species highlights the ecological importance of the Gulf of Alaska and the spatiotemporal information reported here should inform future conservation efforts.

Automatic detection and classification of fish calls in the Northern Gulf of Mexico using energy detectors and a convolutional neural network

Long-term passive acoustic monitoring datasets can require substantial effort for manual analysis; therefore, automatic methods are a more effective way to conduct these analyses and extract calls of interest. In this study, acoustic recordings from the northern Gulf of Mexico, about 60 km north of the 2010 Deepwater Horizon oil spill location, collected between July 2010 and May 2017 were analyzed to determine if fish call abundance has changed after the oil spill. An energy detector was created to extract six likely fish calls found in these data and a neural network was subsequently applied to classify the detections into different call categories. Data augmentation and iterative training were used to optimize classification and compensate for the low number of training images for a couple call types. Daily, monthly, and yearly patterns in calls were investigated and a hypothesis was tested that there was an increase in call abundance over time, indicating recovery of fish populations since the oil spill. Such long-term studies demonstrate that PAM can be used as a population assessment tool for fisheries management.

Passive acoustic monitoring of the bottlenose dolphin &lt;i&gt;Tursiops truncatus&lt;/i&gt; to determine continuous presence in Ensenada de La Paz, Mexico

Bottlenose dolphins (Tursiops truncatus) are ecosystem sentinels. In the Gulf of California, Mexico, they are found in areas that overlap with human activities, as in the case of the Ensenada de La Paz lagoon. A custom-made recorder -moored at medium depth (2.0 m) in the entrance to the lagoon- recorded acoustic data from June to November 2017 (8 deployments; 293 h). Whistles -an indicative of bottlenose dolphin presences- were pooled over time to acquire acoustic encounters, which were analysed to infer continuity of animal presence and test for statistically significant differences between deployments, day and night, and hours. Whistles were recorded during all deployments and evidenced night-time presence of bottlenose dolphins in the lagoon. Significant differences of acoustic encounters were observed between ‘Jun-Jul’ and ‘Sep-Nov’. Acoustic encounters were higher at night but were not different at an hourly level. Acoustical data proved the continuous presence of bottlenose dolphins, highlighting the importance of the Ensenada de La Paz for their population. This initial study highlights the usefulness of long-term passive acoustic monitoring to inform stake holders involved in management and conservation plans.

Fluctuations in Hawaii’s humpback whale Megaptera novaeangliae population inferred from male song chorusing off Maui

Approximately half of the North Pacific humpback whaleMegaptera novaeangliaestock visits the shallow waters of the main Hawaiian Islands seasonally. Within this breeding area, mature males produce an elaborate acoustic display known as song, which becomes the dominant source of ambient underwater sound between December and April. Following reports of unusually low whale numbers that began in 2015/16, we examined song chorusing recorded through long-term passive acoustic monitoring at 6 sites off Maui as a proxy for relative whale abundance between 2014 and 2019. Daily root-mean-square sound pressure levels (RMS SPLs) were calculated to compare variations in low-frequency acoustic energy (0-1.5 kHz). After 2014/15, the overall RMS SPLs decreased between 5.6 and 9.7 dB re 1 µPa2during the peak of whale season (February and March), reducing ambient acoustic energy from chorusing by over 50%. This change in song levels co-occurred with a broad-scale oceanic heat wave in the northeast Pacific termed the ‘Blob,’ a major El Niño event in the North Pacific, and a warming period in the Pacific Decadal Oscillation cycle. Although it remains unclear whether our observations reflect a decrease in population size, a change in migration patterns, a shift in distribution to other areas, a change in the behavior of males, or some combination of these, our results indicate that continued monitoring and further studies of humpback whales throughout the North Pacific are warranted to better understand the fluctuations occurring in this recently recovered population and other populations that continue to be endangered or threatened.

The advertisement call of Gastrotheca chrysosticta Laurent, 1976 (Anura: Hemiphractidae).

The genus Gastrotheca Fitzinger, 1843 currently harbors 75 species (Frost 2020). These marsupial frogs have a broad latitudinal distribution range in Central and South America, from Costa Rica southward to Argentina (Duellman 2015). The advertisement call features as the pulse structure, call duration, and repetition pulse rate are used by researchers to recognize the species of Gastrotheca (Duellman 2015). The availability of call descriptions is also crucial for recognizing these species with secretive life habits and implementing long-term passive acoustic monitoring programs (Vaira et al. 2011; Akmentins et al. 2014).

Cetacean occurrence near the South Shetland Islands based on long-term passive acoustic monitoring

Passive acoustic monitoring is an effective tool to investigate cetacean ecology, particularly in remote locations and over long time periods. Several cetacean species occur in Antarctic waters, but knowledge of their year-round relative abundance, distribution, and seasonality is relatively sparse. Long-term, broadband recordings were collected near the South Shetland Islands between 2014 and 2016, and spatio-temporal patterns in cetacean acoustic occurrence were investigated at three different locations within this area. Baleen whales detected included blue (Balaenoptera musculus), fin (B. physalus), and humpback whales (Megaptera novaeangliae), and several toothed whales, including sperm (Physeter macrocephalus) and killer whales (Orcinus orca) were also present in the datasets. Overall detection rates of these species varied across the recording sites and also showed strong seasonal trends. Sea ice dynamics will be explored as a possible driver for the shifts in seasonal relative abundance of cetaceans in this region of the Southern Ocean, and proximity to the Southern Antarctic Circumpolar Current Front (SACCF) will be examined to evaluate differences in habitat use across the sites.

Marine mammal distribution in the Gulf of Alaska from long-term passive acoustic monitoring

The Gulf of Alaska is an important habitat for a diverse array of marine mammals. Conservation of these populations requires understanding how they utilize different habitats. Passive acoustic monitoring can be used to study marine mammal distributions because the unique call types produced by many species are well documented. Between 2011 and 2015, a total of 3793 days of recordings were collected from autonomous acoustic recorders at five locations broadly distributed around the continental shelf, slope, and offshore seamounts in the Gulf of Alaska. The spatial and temporal patterns of seven cetacean species were examined and differences in habitat use and behavior were compared. Inshore habitats featured higher detections of humpback (Megaptera novaeangliae) and gray (Eschrichtius robustus) whales, while blue (Balaenoptera musculus) and sperm (Physeter macrocephalus) whales were more commonly detected offshore. The presence of most species was seasonal, with peak calling in spring and summer for gray and sperm whales, and fall and winter for fin (B. physalus) and humpback whales. Call type distributions within a species differed spatially for fin and killer (Orcinus orca) whales, and seasonally for blue whales. Spatial differences may indicate prey preferences, while seasonal changes are likely related to behavioral shifts from feeding to mating.