Passive Acoustic Monitoring Research Articles

Harbour porpoise (Phocoena phocoena) in the Wadden Sea World Heritage Site and requirements for trilateral monitoring

The harbour porpoise (Phocoena phocoena) is considered part of the ‘Outstanding Universal Value’ characterising the Wadden Sea World Heritage Site (WS WHS). The Trilateral Wadden Sea Plan aims to preserve the conservation status of the Trilateral Wadden Sea Cooperation Area, encompassing the WS WHS. The plan has specified two conservation targets for the harbour porpoise: (1) viable stocks and a natural reproduction capacity and (2) conservation of habitat quality for its conservation. To assess the current occurrence of the harbour porpoise in the Wadden Sea area, we collated and analysed data from regional and national research projects using telemetry, aerial surveys, strandings and passive acoustic monitoring, obtained over the years 1990–2020. The results illustrate that porpoises occur in both offshore and intertidal waters, showing seasonal movements and changes in local occurrence over time. Some porpoises displayed limited home ranges throughout the year, suggesting a possible residency for some of the animals using the Wadden Sea area. We also showed that methods, frequency and spatial coverage of monitoring activities vary among the countries Denmark, Germany and the Netherlands. We discuss the suitability of the different methods both regarding the challenges of monitoring in the complex Wadden Sea habitat as well as their ability to target the conservation aims of the WHS. We give several recommendations to assess the status of the species to meet the identified conservation aims.

Passive acoustic data yields insights into bird vocalization behavior associated with invasive shrub removal

AbstractMonitoring biodiversity changes associated with ecological restoration is crucial in the current UN Decade on Restoration. Although several studies highlight the impacts of restoration on ecosystems, it is also important to understand how restoration alters species' behavior, including vocalization. Advances in conservation technology, such as passive acoustic monitoring, facilitate rapid and noninvasive monitoring. In this study, we quantified changes in the vocal behavior of a bird species in response to small‐scale restoration carried out by removing the invasive shrub, Lantana camara (lantana), in a Central Indian tropical dry forest. We examined associations between sites of varying lantana densities and the vocalization of one of its primary dispersers, red‐vented bulbul (RVBU). We found statistically significant differences in note‐length and bandwidth of RVBU vocalizations across sites. A random forest classification model showed that Lantana density was not an important predictor of RVBU vocalizations. Apart from the percentage of forest area and farms in our sites, total human population was the most important predictor for RVBU vocalizations suggesting RVBU's use of human habitations as possible resource hubs. Our findings suggest that lantana removal is not associated with significant changes in RVBU vocalization. This study provides empirical evidence that ecological restoration may not alter species' vocalization in the short term and highlights the importance of moving beyond species presence and understanding the impact of restoration on species behavior.

Underwater advertisement call of the threatened Telmatobius rubigo (Anura: Telmatobiidae)

Abstract Underwater Passive Acoustic Monitoring (UPAM) has been used infrequently to register subsurface vocal behaviour in anurans. This study describes the underwater advertisement call of Telmatobius rubigo based on recordings made with UPAM technique. Telmatobius rubigo call is a low-frequency trill composed of 6 to 22 pulses with amplitude modulation. The spectral and temporal characters showed differences from other Telmatobius species. The UPAM, combined with automated call identification software, showed effectiveness in monitoring the calling behaviour of this aquatic Andean frog in their natural environment. UPAM and soundscape/riverscape analysis should be incorporated as a non-invasive tool for monitoring threatened aquatic species.

Accurate species classification of Arctic toothed whale echolocation clicks using one-third octave ratios.

Passive acoustic monitoring has been an effective tool to study cetaceans in remote regions of the Arctic. Here, we advance methods to acoustically identify the only two Arctic toothed whales, the beluga (Delphinapterus leucas) and narwhal (Monodon monoceros), using echolocation clicks. Long-term acoustic recordings collected from moorings in Northwest Greenland were analyzed. Beluga and narwhal echolocation signals were distinguishable using spectrograms where beluga clicks had most energy >30 kHz and narwhal clicks had a sharp lower frequency limit near 20 kHz. Changes in one-third octave levels (TOL) between two pairs of one-third octave bands were compared from over one million click spectra. Narwhal clicks had a steep increase between the 16 and 25 kHz TOL bands that was absent in beluga click spectra. Conversely, beluga clicks had a steep increase between the 25 and 40 kHz TOL bands that was absent in narwhal click spectra. Random Forest classification models built using the 16 to 25 kHz and 25 to 40 kHz TOL ratios accurately predicted the species identity of 100% of acoustic events. Our findings support the use of echolocation TOL ratios in future automated click classifiers for acoustic monitoring of Arctic toothed whales and potentially for other odontocete species.

Effects of duty cycle on passive acoustic monitoring metrics: The case of blue whale songs.

Long-term fixed passive acoustic monitoring of cetacean populations is a logistical and technological challenge, often limited by the battery capacity of the autonomous recorders. Depending on the research scope and target species, temporal subsampling of the data may become necessary to extend the deployment period. This study explores the effects of different duty cycles on metrics that describe patterns of seasonal presence, call type richness richness, and daily call rate of three blue whale acoustics populations in the Southern Indian Ocean. Detections of blue whale calls from continuous acoustic data were subsampled with three different duty cycles of 50%, 33%, and 25% within listening periods ranging from 1 min to 6 h. Results show that reducing the percentage of recording time reduces the accuracy of the observed seasonal patterns as well as the estimation of daily call rate and call call type richness. For a specific duty cycle, short listening periods (5-30 min) are preferred to longer listening periods (1-6 h). The effects of subsampling are greater the lower the species' vocal activity or the shorter their periods of presence. These results emphasize the importance of selecting a subsampling scheme adapted to the target species.

Increased Yangtze finless porpoise presence in urban Wuhan waters of the Yangtze River during fishing closures.

Wuhan, a highly urbanized and rapidly growing region within China's Yangtze Economic Zone, has historically been identified as a gap area for the critically endangered Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) based on daytime visual surveys. However, there has been a noticeable increase in porpoise sightings since 2020. This study employed passive acoustic monitoring to investigate porpoise distribution in Wuhan between 2020 and 2022. Generalized linear models were used to explore the relationship between shipping, hydrological patterns, light intensity, and porpoise biosonar activity. Over 603 days of effective monitoring, the daily positive rate for porpoise biosonar detection reached 43%, with feeding-related buzz signals accounting for 55% of all porpoise biosonar signals. However, the proportion of minutes during which porpoise presence was detected was 0.18%, suggesting that while porpoises may frequent the area, their visits were brief and mainly focused on feeding. A significant temporal trend emerged, showing higher porpoise biosonar detection during winter (especially in February) and 2022. Additionally, periods without boat traffic correlated with increased porpoise activity. Hydrological conditions and light levels exhibited significant negative correlations with porpoise activity. Specifically, porpoise sonar detections were notably higher during the night, twilight, and new moon phases. It is highly conceivable that both fishing bans and COVID-19 pandemic-related lockdowns contributed to the heightened presence of porpoises in Wuhan. The rapid development of municipal transportation and shipping in Wuhan and resulting underwater noise pollution have emerged as a significant threat to the local porpoise population. Accordingly, it is imperative for regulatory bodies to effectively address this environmental stressor and formulate targeted protection measures to ensure the conservation of the finless porpoise.

Sampling Duration and Season Recommendations for Passive Acoustic Monitoring of Bats after White-Nose Syndrome

Abstract Since 2006, white-nose syndrome has caused drastic declines in populations of several hibernating bat species throughout eastern North America. Thus, there is a growing need to establish long-term monitoring programs to assess changes in bat populations over time. Information on the seasonal timing of species occurrence and the sampling effort required to acoustically detect individual bat species and obtain complete inventories will enable researchers to design and implement more effective monitoring programs. From April to October 2018 to 2021, we passively sampled for bats using full-spectrum detectors at eight permanent sites at Fort Indiantown Gap National Guard Training Center, Pennsylvania. We examined seasonal activity patterns and estimated bat species richness among sites and seasons using species accumulation curves. We also estimated probability of detection (p) and site occupancy (Ψ) using single-season occupancy models in PRESENCE software and then determined the minimum number of sampling nights needed to reliably infer the absence of each species. We identified 286,131 bat passes of eight species in 4,107 detector-nights. Seasonal patterns of activity varied among species. We needed approximately 20 sampling nights to detect 90% of the total bat species richness among sites, and we needed 4 to 10 nights to detect 90% of species richness among seasons. We needed relatively few nights (≤12 nights) to detect most species during summer; however, we needed many more nights to detect acoustically rare species. Our results indicate that the acoustic sampling effort currently required to determine the presence or probable absence of Indiana myotis Myotis sodalis, northern long-eared myotis M. septentrionalis, and tricolored bats Perimyotis subflavus during summer may not be adequate for these species in some areas and that a considerable level of effort (>40 nights) is needed to detect little brown myotis M. lucifugus. Monitoring programs that incorporate efficient sampling methodologies will be critical for future conservation efforts as populations of several bat species continue to decline.

Rerouting of a major shipping lane through important harbour porpoise habitat caused no detectable change in annual occurrence or foraging patterns

Shipping is one of the largest industries globally, with well-known negative impacts on the marine environment. Despite the known negative short-term (minutes to hours) impact of shipping on individual animal behavioural responses, very little is understood about the long-term (months to years) impact on marine species presence and area use. This study took advantage of a planned rerouting of a major shipping lane leading into the Baltic Sea, to investigate the impact on the presence and foraging behaviour of a marine species known to be sensitive to underwater noise, the harbour porpoise (Phocoena phocoena). Passive acoustic monitoring data were collected from 15 stations over two years. Against predictions, no clear change occurred in monthly presence or foraging behaviour of the porpoises, despite the observed changes in noise and vessel traffic. However, long-term heightened noise levels may still impact communication, echolocation, or stress levels of individuals, and needs further investigation.

North Atlantic right whale density surface model for the US Atlantic evaluated with passive acoustic monitoring

The Critically Endangered North Atlantic right whale Eubalaena glacialis entered a population decline around 2011. To save this species without closing the ocean to human activities requires detailed information about its intra-annual density patterns that can be used to assess and mitigate human-caused risks. Using 2.9 million km of visual line-transect survey effort from the US Atlantic and Canadian Maritimes conducted in 2003-2020 by 11 institutions, we modeled the absolute density (ind. km-2) of the species using spatial, temporal, and environmental covariates at a monthly time step. We accounted for detectability differences between survey platforms, teams, and conditions, and corrected all data for perception and availability biases, accounting for platform differences, whale dive behavior, group composition, and group size. We produced maps of predicted density and evaluated our results using independently collected passive acoustic monitoring (PAM) data. Densities correlated positively (r = 0.46, ρ = 0.58, τ = 0.46) with acoustic detection rates obtained at 492 stationary PAM recorders deployed across the study area (mean recorder duration = 138 d). This is the first study to quantify the concurrence of visual and acoustic observations of the species in US waters. We summarized predictions into mean monthly density and uncertainty maps for the 2003-2009 and 2010-2020 eras, based on the significant changes in the species’ spatial distribution that began around 2010. The results quantify the striking distribution shifts and provide effort- and bias-corrected density surfaces to inform risk assessments, estimations of take, and marine spatial planning.

The harbour porpoise Phocoena phocoena in the Belgian part of the North Sea: trends in abundance and distribution

The harbour porpoise Phocoena phocoena is currently common in the Belgian part of the North Sea (BPNS), after decades of virtual absence. This article describes the results of aerial surveys to assess its distribution and density in Belgian waters, in concert with the first results of tests with passive acoustic monitoring devices (Porpoise Detectors - PoDs), and a basic analysis of strandings. The strandings data over four decades clearly demonstrate an increase of harbour porpoises in the BPNS, with only few stranded animals between 1970 and 1997 (0 to 6 per year), increasing numbers between 1998 and 2004 (8 to 40 per year), and even higher numbers between 2005 and 2009 (62 to 94 per year). The combined results of aerial surveys, strandings monitoring and tests with passive acoustic monitoring reveal a seasonal pattern, with harbour porpoises being abundant from February to April, and more scarce from May to January. Average densities in 2008 and 2009, as estimated by aerial monitoring covering most of the BPNS (with the exclusion of the nearshore 5 km strip), ranged from 0.05 animals per km², or in total less than 200 animals in an area equivalent to the BPNS in August 2009, to 1.01 animals per km², or in total almost 3,700 animals in an area equivalent to the BPNS during April 2008. In the first quarter of the year porpoises occur throughout the BPNS, including territorial waters (12 mile zone), whereas they are restricted to more offshore and northerly waters later in the year. Erratic invasions in the BPNS however blur general seasonal spatio-temporal patterns, which complicates our understanding of spatial distribution and migration.

Efficient quality assurance and quality control for passive acoustic monitoring data: reducing and documenting false-positive and false-negative errors

ABSTRACT Autonomous Recording Units (ARUs) are widely used to survey for a variety of taxa. This survey method allows for high spatial and temporal coverage but will typically include identification errors that can bias estimates of occupancy. In some instances, verifying all individual detections is prohibitive. To direct verification effort, we developed a model to estimate the probability that transcribers would agree on an identification. Agreement probability was positively influenced by transcriber skill, identification confidence, species commonness and some song types. In contrast, agreement probability was lower when an acoustic signal was classified as a trill. We evaluated our model on independent data where all species detections were verified, and verification effort (time) was quantified. Our model performed well at predicting transcriber agreement on independent data (AUC = 0.71). We applied the model to randomised subsets of the independent data to compare the cost benefit of three approaches to verification under varying effort. We show how modelling probability of transcriber agreement can be used to more efficiently direct verification of species acoustic tags. Our approach could be adapted elsewhere to quantify and reduce species misidentifications in unverified passive acoustic monitoring data for either manual processing or detections from automated classifiers.

In the Spotlight: Bat Activity Shifts in Response to Intense Lighting of a Large Railway Construction Site

Artificial light at night (ALAN) is a major form of anthropogenic pollution, disrupting nocturnal wildlife behaviour and ecosystem function. Large construction sites are typically located at the intersection of urban and natural areas, introducing intense lighting into previously dark natural habitats. This study examines the responses of bats to intense nighttime lighting at a major construction site associated with a linear transport infrastructure (LTI) project. We used passive acoustic monitoring to record bat activity and species richness at the construction site and in adjacent urban and natural areas with different lighting levels. Generalist species, such as Pipistrellus kuhlii and Nyctalus leisleri, were attracted to illuminated areas, likely due to increased prey availability. Conversely, sensitive species, such as those from the Myotis and Plecotus genera, along with Barbastella barbastellus, avoided illuminated areas, particularly the construction site. Species richness was significantly lower at the construction site compared to other environments, reflecting ALAN’s barrier effect on movements and habitat accessibility for more sensitive species. The findings highlight the ecological impacts of introducing ALAN to previously unlit natural environments, underscoring the urgent need for implementing ALAN mitigation strategies in urban planning and construction practices to protect biodiversity in urbanising areas.

High Arctic “hotspots” for sperm whales (Physeter macrocephalus) off western and northern Svalbard, Norway, revealed by multi-year Passive Acoustic Monitoring (PAM)

Despite the well-documented, broad global distribution of sperm whales (Physeter macrocephalus), their distributional patterns remain poorly known in Arctic regions, where year-round monitoring is challenging. Adult male sperm whales are known to migrate seasonally between nutrient-rich high latitude waters and low latitude breeding grounds. However, knowledge is limited regarding fine-scale distribution and seasonal presence at high latitudes. To investigate the acoustic occurrence of this vocally active species in the High Arctic of the Northeast Atlantic, this study combined automated and manual click detection methods to analyze passive acoustic data collected at eight locations around the Svalbard Archipelago, Norway, between 2012 and 2021. The results revealed the presence of sperm whales at six recording sites and demonstrated sperm whale “hotspots” in ice-free areas in eastern Fram Strait along the shelf break and close to the west coast of Spitsbergen from May–January, with some variation between years and locations. Although acoustic presence decreased with increasing latitude, even the northern-most location (81° N) recorded sperm whale vocal activity between August and January. This study provides a baseline for sperm whale acoustic presence in the High Arctic, which will be essential in the context of detecting future changes and also for predicting future distribution patterns in the rapidly changing Arctic marine environment.

Comparing the underwater soundscape of the Hawaiian Islands Humpback Whale National Marine Sanctuary and potential influences of the COVID-19 pandemic

Passive acoustic monitoring is an effective technique for long-term monitoring of the soundscape in marine protected areas. Ocean noise is a key concern for the U.S. Office of National Marine Sanctuaries and has been identified as a research priority. The Sanctuary Soundscape Monitoring Project (“SanctSound”) was implemented to support efforts to address ocean noise across seven U.S. sanctuaries using a comprehensive and standardized approach. In this study, acoustic recordings were collected in the Hawaiian Islands Humpback Whale National Marine Sanctuary during the humpback whale seasons (November-May) from 2018-2022. Data encompassed 14 deployments across four sites in the main Hawaiian Islands: Hawaiʻi, Maui, O’ahu, and Kauaʻi. The soundscape was dominated by biological sources, most prominently the seasonal detection of humpback whale song. Third octave level monthly medians ranged from 70.4-105 dB re 1 µPa across sites with distinct peaks from January to April particularly at both Hawaiʻi and Maui sites. Overall, we reported relatively low vessel detection rates, with Maui having the highest daily average of vessel detections (x = 19.16). No COVID-19 impact could be observed acoustically using soundscape metrics which was likely due to the dominance of humpback whale chorusing. However, vessel detections and AIS data revealed a reduction in vessel activity after the onset of the pandemic at the Maui and Hawaiʻi sites. This study demonstrates that standardized metrics are a useful tool for obtaining long-term, baseline soundscape levels to understand the various contributions to the underwater soundscape and potential changes within marine protected areas in Hawaiʻi.

Acoustic indices are responsive to local-scale but not landscape-scale agricultural land use

Agricultural land use shapes biodiversity patterns. In the literature, land use and land cover at both local and landscape scales has been shown to be important to understanding variation in biodiversity in agricultural systems including measures of occupancy, abundance, and diversity, with landscape scale processes moderating local patterns. The relative role of these processes in explaining variation in acoustic indices, an increasingly frequent measure of biological and environmental change, remains unknown. To address this gap, we recorded acoustic data by passive sampling for two months across 39 farms in central Kansas, USA with automated recording units. We used these data to calculate eight different acoustic indices. We found that acoustic indices were associated with local land use composition (within 100 m) but not landscape composition (within 1000 m). These data suggest that passive acoustic monitoring may be used explain how local land use shapes the soundscape and perhaps biodiversity, but future research should seek to understand the lack of response to landscape variation.

Bottom water hypoxia suppresses fish chorusing in estuariesa).

Hypoxia in coastal ecosystems is increasing as a result of water quality declines from nutrient pollution. Hypoxia negatively affects fish populations and marine life, limiting their spawning habitats, population size, and growth. In this study, two approaches were used to understand the effect of hypoxia on the chorusing and reproductive behavior of fishes in estuaries. One approach used a water quality meter integrated with a prototype passive acoustic recorder, developed to monitor dissolved oxygen and fish chorusing simultaneously and continuously at sites with normoxic and hypoxic conditions. In a second approach, passive acoustic recorders were deployed near ambient water quality monitoring stations, monitored by the North Carolina agencies in estuaries where hypoxia occurs periodically. In both approaches, when hypoxia (dissolved oxygen < 4.0 mg/L) occurred, fish chorusing was diminished or ceased. A strong correlation was observed between bottom water dissolved oxygen and the power spectral density in a 100-200 Hz frequency band associated with red drum (Sciaenops ocellatus, Sciaenidae) calling. Passive acoustic monitoring stations and integrated passive acoustic and water quality meters should be used in estuarine hypoxia monitoring efforts to examine the expanding areas of hypoxia and its impact on fish critical spawning habitats.

Development of a machine learning detector for North Atlantic humpback whale song.

The study of humpback whale song using passive acoustic monitoring devices requires bioacousticians to manually review hours of audio recordings to annotate the signals. To vastly reduce the time of manual annotation through automation, a machine learning model was developed. Convolutional neural networks have made major advances in the previous decade, leading to a wide range of applications, including the detection of frequency modulated vocalizations by cetaceans. A large dataset of over 60 000 audio segments of 4 s length is collected from the North Atlantic and used to fine-tune an existing model for humpback whale song detection in the North Pacific (see Allen, Harvey, Harrell, Jansen, Merkens, Wall, Cattiau, and Oleson (2021). Front. Mar. Sci. 8, 607321). Furthermore, different data augmentation techniques (time-shift, noise augmentation, and masking) are used to artificially increase the variability within the training set. Retraining and augmentation yield F-score values of 0.88 on context window basis and 0.89 on hourly basis with false positive rates of 0.05 on context window basis and 0.01 on hourly basis. If necessary, usage and retraining of the existing model is made convenient by a framework (AcoDet, acoustic detector) built during this project. Combining the tools provided by this framework could save researchers hours of manual annotation time and, thus, accelerate their research.

Meet the authors: Georgios Rizos, Jenna L. Lawson, and Björn W. Schuller

In their recent publication in Patterns, the authors proposed a methodology based on sample-free Bayesian neural networks and label smoothing to improve both predictive and calibration performance on animal call detection. Such approaches have the potential to foster trust in algorithmic decision making and enhance policy making in applications about conservation using recordings made by on-site passive acoustic monitoring equipment. This interview is a companion to these authors' recent paper, "Propagating Variational Model Uncertainty for Bioacoustic Call Label Smoothing".

Dolphin and porpoise detections by the F-POD are not independent: Implications for sympatric species monitoring.

The F-POD is designed for passive acoustic monitoring of odontocetes. The offline classifiers can identify and separate porpoise-like sounds from dolphin-like sounds. We show that these two classifiers are not working independently. Run together, virtually no detections of both species were reported within the same minute, whereas 10% of the detection positive minutes were reported positive for both species when the two classifiers were run sequentially. This has important implications for interpretation of data in areas containing both species groups, and we call for reporting all analysis details in such studies and for further description and analysis of the classifiers.

Intertidal Soundscapes of Hardened and Living Shorelines: A Case Study of Habitat Enhancement

Abstract Organisms, such as fishes and invertebrates and including their larval stages, listen to underwater soundscapes to detect information about nearby habitats. Such soundscapes may be influenced by habitat degradation or enhancement, which can lead to acoustically mediated feedback loops affecting the overall ecosystem. Despite the importance of underwater sounds on ecological functioning, there have been limited studies documenting soundscapes of intertidal ecosystems and few, if any, of living shoreline soundscapes. Living shorelines would especially benefit from acoustically mediated effects for objectives like encouraging fish and invertebrate settlement. This case study used a Before‐After‐Control‐Impact design to sample soundscapes and nekton (i.e., fishes and mobile macroinvertebrates) at a living shoreline construction and a nearby hardened shoreline in Cedar Key, FL (USA). Diel soundscape patterns and acoustic attenuation at the two sites were also described a year following the living shoreline construction. In the acoustic sampling, the high frequency bands of both shorelines were dominated by invertebrate sounds that were influenced by season, site and time of day, while the low frequency band of the living shoreline was often dominated by a loud anthropogenic sound. About a year after the living shoreline installation—despite similar measured acoustic attenuation at both sites—the living shoreline featured louder sound pressure levels compared to the hardened shoreline, which may be particularly beneficial for promoting foundational species and other organism settlement. These results demonstrate that Gulf of Mexico intertidal habitats may have soundscape differences even within close proximity and that living shorelines may enhance acoustic characteristics in ways beneficial to continued shoreline development. This represents an important step in better understanding the relationships between habitat structures, nekton communities, and their associated soundscapes as well as the application of passive acoustic monitoring to improve coastal management and conservation.