Collecting baleen whale blow samples by drone: A minimally intrusive tool for conservation genetics

In coastal British Columbia, Canada, marine megafauna such as humpback whales (Megaptera novaeangliae) and fin whales (Balaenoptera physalus velifera) have been subject to a history of exploitation and near extirpation. While their populations have been in recovery, significant threats are posed to these vulnerable species by proposed natural resource ventures in this region, in addition to the compounding effects of anthropogenic climate change. Genetic tools play a vital role in informing conservation efforts, but the associated collection of tissue biopsy samples can be challenging for the investigators and disruptive to the ongoing behaviour of the targeted whales. Here, we evaluate a minimally intrusive approach based on collecting exhaled breath condensate, or respiratory 'blow' samples, from baleen whales using an unoccupied aerial system (UAS), within Gitga'at First Nation territory for conservation genetics. Minimal behavioural responses to the sampling technique were observed, with no response detected 87% of the time (of 112 UAS deployments). DNA from whale blow (n = 88 samples) was extracted, and DNA profiles consisting of 10 nuclear microsatellite loci, sex identification and mitochondrial (mt) DNA haplotypes were constructed. An average of 7.5 microsatellite loci per individual were successfully genotyped. The success rates for mtDNA and sex assignment were 80% and 89% respectively. Thus, this minimally intrusive sampling method can be used to describe genetic diversity and generate genetic profiles for individual identification. The results of this research demonstrate the potential of UAS-collected whale blow for conservation genetics from a remote location.

High-throughput digital cough recording on a university campus: A SARS-CoV-2-negative curated open database and operational template for acoustic screening of respiratory diseases

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.

Fin whales of the Great Bear Rainforest: Balaenoptera physalus velifera in a Canadian Pacific fjord system

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 Caamaño 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.

Acoustic tracking of fin whales: Habitat use and movement patterns within a Canadian Pacific fjord system

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.

Determining marine mammal detection functions for a stationary land-based survey site

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.

Automated localization of whales in coastal fjords

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.

Distinct habitat use strategies of sympatric rorqual whales within a fjord system

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.