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This repository contains the code and data for the paperPerformance evaluation of the smartphone-based AI cough monitoring app - Hyfe Cough Tracker against solicited respiratory sounds

Photo-identification (photo-ID) databases can comprise versatile troves of information for well-studied animal populations and, when organized well and curated carefully, can be readily applied to a wide range of research questions, such as population abundance estimates, meta-population connectivity and social network structure. To bring the potential impact of photo-ID data within reach of a greater number of research groups, we introduce an R-based photo-ID project management system, named ‘catRlog’. As a computer directory with custom apps embedded throughout, catRlog serves as a workflow organizer that simplifies, streamlines, and improves the quality of photo-ID data processing. The system can be utilized by research teams in a number of ways, ranging from automated formatting and printing of a photo-ID catalog, to photo-ID matching, thereby creating and expanding a historical catalog, to processing of identification data to generate datasets necessary for site fidelity, mark–recapture, and social association analyses. As an R-based tool, the apps are open-source, cross-platform, readily customizable, and easily updated. catRlog has been tested using photo-ID databases of humpback whales (Megaptera novaeangliae) and fin whales (Balaenoptera physalus) within a mainland fjord system of Pacific Canada, but is a generalized system useful for almost any photo-ID project of any species in any habitat. A detailed user’s manual and example dataset are provided.

Fin whale 20 Hz calls were detected, localized, and tracked using a 10 km aperture network of three acoustic receivers deployed for 11 months in a Pacific Canadian fjord system. The area has been historically important for fin whales and is located along a route that tankers will begin using in 2024. A total of 6712 calls were localized, and trajectories were fitted for 55 acoustic tracks. Fin whale tracks occurred throughout the monitoring site. Call activity peaked in September and was low during winter months. Swimming characteristics varied significantly between day- and nighttime: at night, whales swam faster (7.1 vs 4.0 km/h median, +75.2%), which resulted in longer (+34.7%), less predictable (-70.6%) tracks as compared to daylight hours. Call frequencies varied between 16 and 32 Hz. Beside stereotypical song frequencies, fin whales also used irregular frequency components, which contributed the majority of calls in the summer but did not occur in the winter. The results suggest that the area is primarily used as a summer feeding ground, where fin whales follow a diel behavioral cycle. The observed activity patterns will aid in the assessment of strike risk and harassment mitigation and provide a baseline to document behavioral change.

Objective Respiratory illnesses have information-rich acoustic biomarkers, such as cough, that can potentially play an important role in screening populations for disease risk. To realize that potential, datasets of paired acoustic-clinical samples are needed for the development and validation of acoustic screening models, and protocols for collecting acoustic samples must be efficient and safe. We collected cough acoustic signatures at a high-throughput SARS-CoV-2 testing site on a college campus. Here, we share logistical details and the dataset of acoustic cough signatures paired with the gold standard in SARS-CoV-2 testing of SARS-CoV-2 genomic sequences using qRT-PCR. Methods Cough recordings were collected in winter-spring 2021 at a rural residential college (Sewanee, TN, USA), where approximately 2000 students were tested for SARS-CoV-2 on a weekly basis. Cough collection was managed by student volunteers using custom software. Results 4302 coughs were recorded from 960 participants over 11 weeks. All coughs were COVID-19 negative. Approximately 30 s were required to check-in a participant and collect their cough. Conclusion The value of acoustic screening tools depends upon our ability to develop and implement them reliably and quickly. For that to happen, high-quality datasets and logistical insights must be collected and shared on an ongoing basis.

Funding: This research was supported by a Mitacs Accelerate Internship (IT21479); the Save Our Seas Foundation; Willow Grove Foundation; Donner Canadian Foundation; Tides Canada; LUSH Charity Pot; private donations to North Coast Cetacean Society; Fisheries and Oceans Canada; and the Canada Nature Fund for Aquatic Species at Risk (CANAFSAR 2019-2021). Fin whales (Balaenoptera physalus) are widely considered an offshore and oceanic species, but certain populations also use coastal areas and semi-enclosed seas. Based upon fifteen years of study, we report that Canadian Pacific fin whales (B. p. velifera) have returned to the Kitimat Fjord System (KFS) in the Great Bear Rainforest, and have established a seasonally resident population in its intracoastal waters. This is the only fjord system along this coast or elsewhere in which fin whales are known to occur regularly with strong site fidelity. The KFS was also the only Canadian Pacific fjord system in which fin whales were commonly found and killed during commercial whaling, pointing to its long-term importance. Traditional knowledge, whaling records, and citizen science databases suggest that fin whales were extirpated from this area prior to their return in 2005-2006. Visual surveys and mark-recapture analysis documented their repopulation of the area, with 100-120 whales using the fjord system in recent years, as well as the establishment of a seasonally resident population with annual return rates higher than 70%. Line transect surveys identified the central and outer channels of the KFS as the primary fin whale habitat, with the greatest densities occurring in Squally Channel and Caamano Sound. Fin whales were observed in the KFS in most months of the year. Vessel- and shore-based surveys (27,311 km and 6,572 hours of effort, respectively) indicated regular fin whale presence (2,542 detections), including mother-calf pairs, from June to October and peak abundance in late August-early September. Seasonal patterns were variable year-to-year, and several lines of evidence indicated that fin whales arrived and departed from the KFS repeatedly throughout the summer and fall. Additionally, we report on the population's social network and morphometrics. These findings offer insights into the dynamics of population recovery in an area where several marine shipping projects are proposed. The fin whales of the Great Bear Rainforest represent a rare exception to general patterns in this species' natural history, and we highlight the importance of their conservation. Publisher PDF

Funding: JW received a grant from the following: Save Our Seas Foundation Grant No. 217-2010- 2020 https://saveourseas.com, Willow Grove Foundation Grant No. 001-2010-2020, Fisheries and Oceans Canada Grant CA No.: 2016-2019- HSP-PAC-8287-A, https://www.dfo-mpo.gc.ca/species-especes/sara-lep/hsp-pih/index-eng.html, Donner Canadian Foundation Grant No. E-50-20,E50-19, E-50-18 https://www.donnerfoundation.org, Tides Canada Grant No. GF04712. https://makeway.org. Animal culture and social bonds are relevant to wildlife conservation because they influence patterns of geography, behavior, and strategies of survival. Numerous examples of socially-driven habitat partitioning and ecological-niche specialization can be found among vertebrates, including toothed whales. But such social-ecological dynamics, described here as ‘social niche partitioning’, are not known among baleen whales, whose societies—particularly on foraging grounds—are largely perceived as unstructured and incidental to matters of habitat use and conservation. However, through 16 years of behavioral observations and photo-identifications of humpback whales (Megaptera novaeangliae) feeding within a fjord system in the Canadian Pacific (primarily within Gitga’at First Nation waters), we have documented long-term pair bonds (up to 12 years) as well as a complex societal structure, which corresponds closely to persistent patterns in feeding strategy, long-term site fidelity (extended occupancy and annual rate of return up to 75%), specific geographic preferences within the fjord system, and other forms of habitat use. Randomization tests of network congruency and clustering algorithms were used to test for overlap in patterns of social structure and habitat use, which confirmed the occurrence of social niche partitioning on the feeding grounds of this baleen whale species. In addition, we document the extensive practice of group bubble net feeding in Pacific Canada. This coordinated feeding behavior was found to strongly mediate the social structure and habitat use within this humpback whale society. Additionally, during our 2004–2019 study, we observed a shift in social network structure in 2010–2012, which corresponded with environmental and demographic shifts including a sudden decline in the population’s calving rate. Our findings indicate that the social lives of humpback whales, and perhaps baleen whales generally, are more complex than previously supposed and should be a primary consideration in the assessment of potential impacts to important habitat. Publisher PDF

In the California Current off the United States West Coast, there are three offshore cetacean species that produce narrow-band high frequency (NBHF) echolocation pulses: Dall's porpoise (Phocoenoides dalli) and two species of Kogia. NBHF pulses exist in a highly specialized acoustic niche thought to be outside the hearing range of killer whales and other potential mammal-eating odontocetes. Very little is known about the dwarf and pygmy sperm whales (K. sima and K. breviceps), including their NBHF pulse characteristics. This paper presents a multivariate clustering method using data from unmanned drifting acoustic recorders and visually verified porpoise recordings to discriminate between probable porpoise and Kogia clicks. Using density clustering, this study finds three distinct clusters whose geographic distributions are consistent with the known habitat range for Kogia and Dall's porpoise. A Random Forest classification model correctly assigned 97% of the clicks to their cluster. Visually verified Dall's porpoise clicks from towed hydrophones were strongly associated with one of the clusters, while a second cluster tended to be outside the geographic range of Dall's porpoise and unlike the Dall's porpoise cluster. These clicks, presumed to be made by Kogia, exhibited greater spectral variance than previous Kogia echolocation studies. It is possible that the structure of Kogia NBHF pulses may not be as stereotypical as previously described.

Localization and tracking of vocalizing marine mammals are powerful tools for understanding and mitigating the impacts of anthropogenic stressors such as vessel noise on habitat use of cetaceans. A large-aperture hydrophone network has been installed in the Kitimat Fjord System, an ecologically, culturally, and economically valued marine environment in northern British Columbia, Canada. This network consists of four synchronized bottom-mounted hydrophones that permanently record and radio-transmit data to a land-based laboratory. An automated system has been developed which includes routines to localize transient bio-acoustic signals from three or more streaming hydrophones in near real-time. These routines comprise the correlation of hydrophone signals, the construction of a time lag model, and signal localization and error estimation from a spatial likelihood surface. The localization method was tested experimentally and subsequently applied to vocalizations from humpback whales, fin whales, and killer whales. Refractive and reflective sound propagation effects in the confined fjords are assessed using ray tracing propagation models. Automated localization results are compared to ground-truth data and shown to provide good accuracy.

Collisions with ships (ship strikes) are a pressing conservation concern for fin whales (Balaenoptera physalus) along western North America. Fin whales exhibit strong diel patterns in dive behavior, remaining near the surface for most of the night, but how this behavior affects ship-strike risk is unknown. We combined diel patterns of surface use, habitat suitability predictions, and ship traffic data to evaluate spatial and temporal trends in ship-strike risk to fin whales of the California Current System (CCS). We tested a range of surface-use scenarios and found that both increased use of the upper water column and increased ship traffic contribute to elevated ship-strike risk at night. Lengthening nights elevate risk during winter throughout the CCS, though the Southern California Bight experienced consistently high risk both day and night year-round. Within designated shipping lanes, total annual nighttime strike risk was twice daytime risk. Avoidance probability models based on ship speed were used to compare the potential efficacy of speed restrictions at various scales. Speed reductions within lanes may be an efficient remediation, but they would address only a small fraction (13%) of overall ship-strike risk. Additional speed restrictions in the approaches to lanes would more effectively reduce overall risk.

Abstract ContextThe shore-based survey is a common, non-invasive, and low-cost method in marine mammal science, but its scientific applications are currently limited. Such studies typically target populations whose distributions are not random with respect to nearshore sites and involve repeated scans of the same area from single, stationary platforms. These circumstances prohibit the use of classic distance sampling techniques for estimating animal densities or distributions, particularly the derivation of a detection function that describes the probability of detecting targets at various distances from the observer. AimsHere, we present a technique for estimating land-based detection functions, as well as quantifying uncertainty in their parameterisation, on the basis of the range-specific variability of observations from one scan to the next. MethodsThis Bayesian technique uses Monte Carlo simulation to determine the likelihood of thousands of candidate detection functions, then conducts weighted sampling to generate a posterior distribution estimate of the detection function parameterisation. We tested the approach with both archival and artificial datasets built from known detection functions that reflect whale and porpoise detectability. Key resultsWhen the base distribution of targets was random, the whale detection function was estimated without error (i.e. the difference of the median of the posterior and the true value was 0.00), and the porpoise detection function was estimated with an error equal to 4.23% of the true value. When the target base distribution was non-random, estimation error remained low (2.57% for targets concentrated offshore, 1.14% when associated with nearshore habitats). When applied to field observations of humpback whales and Dall’s porpoises from a land-based study in northern British Columbia, Canada, this technique yielded credible results for humpback whales, but appeared to underestimate the detectability of Dall’s porpoises. ConclusionThe findings presented here indicate that this approach to detection function estimation is appropriate for long-running surveys in which scan regularity is high and the focus is on large, slow-moving, low herd-size, and easily detectable species. ImplicationsThe derivation of a detection function is a critical step in density estimation. The methodology presented here empowers land-based studies to contribute to quantitative monitoring and assessment of marine mammal populations in coastal habitats.

In the north-eastern Pacific, fin whales (Balaenoptara physalus) are typically found and studied in open waters near or seaward of the continental shelf. The Kitimat fjord system is a network of sounds and channels along the coast of British Columbia, Canada, and is one of only a few known fin whale habitats within confined coastal waters. In 2018, we deployed a network of hydrophones in Squally Channel, a proposed shipping lane located at the center of the fjord system, to monitor and track fin whales for a period of 2 years. The work is part of an effort to mitigate anthropogenic stressors on whales in the traditional territory of the Gitga'at First Nation. Here, we present spatial-temporal habitat use by fin whales in this confined inshore ecosystem based on more than 30 000 call detections and 7000 source localizations. Two distinct call types were recorded, a 20 Hz and a 40 Hz pulse, with distinctly different seasonal and diel trends. About 100 individual tracks were reconstructed from 20 Hz call sequences and analyzed for calling characteristics and movement patterns. A better understanding of fin whale habitat in the north-east Pacific is of special importance in light of an active discussion about the conservation status of this large baleen whale in Canadian waters.

A partnership of the Gitga'at First Nation, WWF-Canada and the North Coast Cetacean Society has installed a long baseline hydrophone array in Squally Channel; a culturally, ecologically, and economically important marine environment in northern British Columbia (BC), Canada. The array consists of four synchronized bottom-mounted hydrophones that permanently record and radio-transmit data to a land-based laboratory in real-time. The array covers an area of approximately 200 km2 to realize long-term and wide-range monitoring of marine mammals. To allow for efficient data analysis, automated detectors for cetacean vocalizations have been developed in collaboration with the University of Victoria. The detection performance has been tested using manually annotated data. We present an overview of the detectors for orca and humpback whales, and their computational and analytic performance as a function of signal-to-noise ratio. The ability to adapt to different ocean environments and target species is demonstrated by applying the detectors to 100 days of archival acoustic data recorded at two different places along the BC coast. Data recorded during pilot studies in 2017 from Squally Channel (approximately 30 days) is used to provide an overview of cetacean vocalization detections. Finally, we show acoustic activity variations and trends based on environmental factors.

We used ecosystem sampling during systematic surveys and opportunistic focal follows, comparison tests, and random forest models to evaluate fin whale (Balaenoptera physalus) and humpback whale (Megaptera novaeangliae) habitat associations within an inland feeding ground (Kitimat Fjord System, British Columbia, Canada). Though these species are sympatric and share a common prey source, they were attuned to different aspects of the local habitat. The fin whales were associated with habitat properties reminiscent of the open ocean. Humpback whales, in contrast, were associated with features more commonly associated with the inland waters of fjords. Fixed habitat features, such as seafloor depth and distance from the fjord mouth, were the most important predictors of fin whale presence, but fixed and dynamic variables, such as surface properties, predicted humpback whale presence with equal (moderate) success. With the exception of strong salinity gradients for humpback whales, habitat conditions were poor predictors of feeding state. Fin whales practiced a spatially confined, seasonally stable, and thus more predictable use of certain channels within the fjord system. These findings are compatible with site loyal behavior, which is interesting in light of the species' historical, unique use of this fjord system. The relatively lackluster performance of humpback-habitat models, coupled with the importance of oceanographic properties, makes the humpback's habitat use strategy more uncertain. The fact that two sympatric species sharing a common prey source exhibited different habitat use strategies suggests that at least one species was informed by something in addition to prey. Given that the two species are attuned to different aspects of the fjord habitat, their responses to habitat changes, including anthropogenic impacts, would likely be different in both nature and degree. Our findings highlight the value of comparative studies and the complexity of rorqual habitat use, which must be understood in order for critical habitat to be identified and protected.

Dual-platform studies in confined marine habitats can contribute to the calibration of passive acoustic data for purposes of density estimation. We established a long baseline hydrophone array in northern coastal British Columbia, Canada, that consists of four synchronized, bottom-mounted, continuously recording hydrophones. Automated detectors have been developed for vocalizations of humpback whales, orcas, and fin whales. Visual surveys are conducted from an observation platform overseeing the same area of approximately 200 sq. km. Here we compare humpback whale detections between the visual and acoustic platforms for 78 days of surveys in 2018. Two call types were analyzed: bubble net feeding calls and miscellaneous other. Acoustic surveys yielded higher detection rates (15x) of bubble net feeding groups than visual surveys, but visual detection rates of humpback whales engaged in other behaviors were twice that of acoustic surveys. When summarizing data into 24-hour periods, we found strong correlations between visual and acoustic detection rates for both call types. These correlations were strongest when all visual detections were included, and weakest when we excluded distant sightings from our dataset. These preliminary results are an encouraging first step in the derivation of call rates and the estimation of local species densities using passive acoustics.

Maritime forest communities on barrier islands along the Atlantic and Gulf coasts have been severely fragmented by a continuous history of human land use and natural disturbance. Isolated populations of certain tree species in maritime forest fragments may now be too small to be viable and their inability to regenerate may result in their eventual elimination from barrier islands. Using an 11-year study of a population of pignut hickory (Carya glabra), a common species of remnant maritime forest stands on St. Catherine's Island, Georgia, we present a case study of tree regeneration failure on a barrier island. We found that there has been no recruitment of new hickory individuals into the canopy of this population over the last 65 years. Field evidence of browse and a strong correlation between seedling density distributions and microsite protection from herbivory suggest that this trend in recruitment failure is related to an increased abundance of deer (Odocoileus) and pigs (Sus) on the island. Using a size class population projection model, we estimated that, if such recruitment failure and mortality rates continue, the hickory population will be extirpated from the maritime forest within 200 years. Tree species that are failing to regenerate within maritime forests represent a special challenge that is not currently being addressed in the long-term management of barrier island biodiversity.

The 9.0 magnitude Tohoku earthquake that struck off the coast of Japan on March 11, 2011, was the fourth largest earthquake in recorded history and the largest ever to hit a densely populated region (Bertero, 2011; Lekkas et al., 2011). The ensuing tsunami inundated an area of about 561 km2 (Geospatial Information Authority, 2011), washing away an estimated 24.9 million tonnes of debris, including wood, sediments, plastics, industrial chemicals, and structural components (Oh, 2011). Two weeks following the tsunami, the meltdown of the Fukushima Daiichi nuclear reactors released radioactive elements into the atmosphere and coastal waters. Atmospheric deposition was found to be an important source of radioactivity in surface waters and may have contaminated the debris field, although the extent of this contamination remains unknown (Buesseler et al., 2012; Honda et al., 2012).Here, we follow the debris field along its predicted path from its source in Japanese coastal waters through the Kuroshio-Oyashio Extension, the North Pacific Current, and the California Current. From there, it will loop back toward the Hawaiian Islands, ultimately accumulating in the North Pacific Gyre (International Pacific Research Center, 2011b; Figure 1). Relying on precedents from previous natural disasters and ongoing observations, we attempt to predict the impact of this debris field on marine and coastal ecosystems in each of these regions. We predict that the Tohoku debris field will create a rare perturbation for ecosystems interconnected across the North Pacific, exacerbating the accumulating human impacts on the world ocean.

Real-time localization and tracking of vocalizing marine mammals is a powerful tool to a) mitigate the risk of ship strikes and disturbance of the animals as well as b) to understand the impact of anthropogenic noise on habitat use of cetaceans. A long baseline hydrophone array has been installed in Squally Channel, a culturally, ecologically, and economically important marine environment in northern British Columbia, Canada. The array consists of four synchronized bottom-mounted hydrophones that permanently record and radio-transmit data to a land-based laboratory. Automated analysis tools have been developed to detect and localize transient bioacoustic signals from three or more hydrophones in real-time. They comprise the correlation of hydrophone signals, the construction of a replica surface using acoustic propagation models, and signal localization from a spatial likelihood surface. An overview of the localization method is presented. We assess spatial localization precision and discuss random and systematic sources of error stemming from the signal type and quality, bathymetry, sound speed profile, as well as the spatial distribution of hydrophones and acoustic sources. Simulation results are compared to field measurements. Based on our findings, challenges and opportunities associated with localization using long baseline arrays in coastal environments are discussed.

Monitoring the aquatic soundscape provides critical information about marine mammal habitat use. It is essential for developing mitigation strategies for areas with expanding marine shipping and industrial activity. A long baseline hydrophone array has been installed in Squally Channel, a culturally, ecologically, and economically important marine environment in northern British Columbia, Canada. The array consists of four synchronized bottom-mounted hydrophones that permanently record and radio-transmit data to a land-based laboratory in real-time. The acoustic monitoring is supplemented with a land-based visual observatory that oversees the same area of approximately 200 km2. Automated detectors have been developed for vocalizations of humpback whales, orcas, and fin whales. Acoustic data and visual surveys were analyzed for a period of more than 100 days between 2017 and 2018. We present an overview of the acoustic detection functions and their performance by call type and summarize visual survey procedures. Cetacean activity derived from automated acoustic detections and visual observations is analyzed. Finally, acoustic and visual survey methods are compared to assess a) the fraction to which different species are acoustically active while in the area, and b) the effectiveness of both acoustic and visual monitoring efforts for the purpose of cetacean monitoring.

Rorqual whales (f. Balaenopteridae) supposedly respond to increases in prey supply according to both aggregative and feeding thresholds. With the former, they gather in areas above a minimum prey density set by their basal metabolic needs. With the latter, feeding occurs only above a prey density set by the energetic cost of lunge feeding. To compare prey preferences and the two threshold types in sympatric rorquals, I conducted systematic transect surveys and behavioral observations of humpback whales (Megaptera novaeangliae) and fin whales (Balaenoptera physalus) in a British Columbia fjord system. While multiple prey features were found to influence whale aggregation and feeding, both threshold types were observed in each species' response to krill volume. Humpback response to prey features was less predictable and influenced by more factors than that of fin whales, which appeared to be exclusively euphausivorous and interested in the deepest high-volume krill patches within the deepest channels. Compared with fin whales, humpbacks found higher-volume krill patches and had higher aggregative thresholds, but had lower feeding thresholds. Findings aligned overall with the expectations that aggregative behavior is responsive to local prey supply, while feeding thresholds are governed by less mutable energetic constraints imposed by body size and feeding mode. Both aggregative and feeding threshold responses appeared to be a function of local conditions: As total krill-like backscatter increased, feeding thresholds stabilized (became more nonlinear and more nonrandom), while aggregative thresholds destabilized. All results emphasized the importance of incorporating observations of feeding effort in studies of prey preference and habitat use.