Scientific Publications
Collecting baleen whale blow samples by drone: A minimally intrusive tool for conservation genetics
Éadin N. O'Mahony, Angela L. Sremba, Eric M. Keen, Nicole Robinson, Archie Dundas, Debbie Steel, Janie Wray, C. Scott Baker, Oscar E. Gaggiotti (2024)
Abstract: 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.
Ship-strike forecast and mitigation for whales in Gitga’at First Nation territory
Eric M. Keen, Éadin O’Mahony, Linda M. Nichol, Brianna M. Wright, Chenoah Shine, Benjamin Hendricks, Hermann Meuter, Hussein M. Alidina, Janie Wray (2023)
Abstract: As marine traffic increases globally, ship strikes have emerged as a primary threat to many baleen whale populations. Here we predict ship-strike rates for fin whales Balaenoptera physalus and humpback whales Megaptera novaeangliae in the central territorial waters of the Gitga’at First Nation (British Columbia, Canada), which face increases in existing marine traffic as well as new liquified natural gas (LNG) shipping in the next decade. To do so, we utilized Auto-matic Identification System (AIS) databases, line-transect surveys, shore-based monitoring, whale-borne tags, aerial drone-based focal follows, and iterative simulations. We predict that by 2030, whale encounters will triple for most vessel types, but the change is most extreme for large ships (length >180 m) in prime whale habitat, in which co-occurrences will increase 30-fold. Ship-strike mortalities are projected to increase in the next decade by 2.3× for fin whales and 3.9× for humpback whales, to 2 and 18 deaths yr−1, respectively. These unsustainable losses will likely deplete both species in the coastal region of BC. Models indicate that the largest single source of mortality risk in 2030 will be from the LNG Canada project. Of the mitigation options we evalu-ated, a 10 knot speed ceiling for all large ships is potentially effective, but the best measure for guaranteed mitigation would be seasonal restrictions on LNG traffic. While certain data gaps remain, particularly with respect to humpback whales, our predictions indicate that shipping trends within Gitga’at waters will impact whale populations at regional levels. We provide our analysis in the R package ‘shipstrike’.
A simulation-based tool for predicting whale-vessel encounter rates
Eric Keen, Benjamin Hendricks, Chenoah Shine, Janie Wray, Chris R. Picard, Hussein M. Alidina (2022)
Abstract: To understand the threat of ship strikes for marine predators such as whales, quantitative tools are needed that measure specific impacts without ignoring the many uncertain and stochastic elements of whale-vessel interactions. We developed a tool that focuses on one particularly complex aspect of the ship-strike problem: the encounter rate, the fraction of co-occurrences (i.e., times that whales and vessels occur within the same 1-km2) that result in an imminent collision. This tool uses iterative simulations, based in R, and basic inputs regarding marine traffic and whale biology to predict the rate at which the precise courses of the whale and the vessel intersect in space and time. The result of this simulator is a spatially explicit probability distribution of encounter rates, which can be summarized for reports as well as integrated into subsequent stages of a ship-strike impact analysis. We explain the design of this tool, provide its source code, and demonstrate its utility with four case applications. First, we estimate encounter rates for fin whales (Balaenoptera physalus) in Gitga'at First Nation waters (British Columbia, BC, Canada) and quantify the differences in encounter rate between vessel classes. Second, we predict encounter rates for the same area in 2030, by which time a new shipping lane is slated to be established in Gitga'at territory, highlighting the impact of shifting traffic composition vs. traffic volume. Third, we assess the sensitivity of these estimates to changes in vessel and whale characteristics, finding that vessel length is the most important determinant of the encounter rate, followed by whale speed. Fourth, we integrate the encounter rate estimator into a shipping impact assessment for Gitga'at fin whales. Our predictions indicate that this decade's traffic increase in Gitga'at waters alone could match Potential Biological Removal for coastal BC fin whales. However, the assumptions underlying our prediction require validation and further study. The encounter rate simulator is available in the R package, “shipstrike”.
catRlog: a photo-identification project management system based in R
eric keen, Éadin O’mahony, janie wray, julia wren (2021)
Abstract: 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.
Social survival: Humpback whales (Megaptera novaeangliae) use social structure to partition ecological niches within proposed critical habitat
Janie Wray, Eric Keen, Éadin N. O’Mahony (2021)
Abstract: 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.
Fin whales of the Great Bear Rainforest: Balaenoptera physalus velifera in a Canadian Pacific fjord system
Eric M. Keen, James Pilkington, Éadin O’Mahony, Kim-Ly Thompson, Benjamin Hendricks, Nicole Robinson, Archie Dundas, Linda Nichol, Hussein M. Alidina, Hermann Meuter, Chris R. Picard, Janie Wray (2021)
Abstract: 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
Benjamin Hendricks, Eric M. Keen, Chenoah Shine, Janie L. Wray, Hussein M. Alidina, Chris R. Picard (2021)
Abstract: 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.
Calving rate decline in humpback whales(Megaptera novaeangliae) of northern British Columbia, Canada
Janie wray, eric keen (2020)
Determining marine mammal detection functions for a stationary land-based survey site
Eric M. Keen, Janie Wray, Benjamin Hendricks, Éadin O’Mahony, Chris R. Picard, Hussein Alidina (2020)
Abstract: The 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. Here, 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. This 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. When 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. The 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. The 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
Benjamin Hendricks, Janie L. Wray, Eric M. Keen, Hussein M. Alidina, T. Aaron Gulliver, Chris R. Picard (2019)
Abstract: 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.
‘whale wave’: Shifting strategies structure the complex use of critical fjord habitat by Humpbacks
Eric M. Keen, Janie Wray, Hermann Meuter, Kim-Ly Thompson, Jay P. Barlow, Chris R. Picard (2017)
Abstract: A decade of visual surveys (2005-2014) revealed that humpbacks Megaptera novaeangliae occupy a temperate fjord system in British Columbia, Canada, in a wave pattern that propagates from outer channels in the summer to deep inland channels in late fall. Monte Carlo randomization confirmed this apparent pattern statistically. ‘Before’ and ‘after’ shift phases were most evident in July and October, respectively. We hypothesized that the ‘whale wave’ was being driven by (1) prey following, (2) the tracking of environmental proxies, (3) fine-scale philopatry, or some combination of these three factors. To evaluate these hypotheses, we collected new data in 2015, including visual and hydroacoustic surveys and oceanographic sampling. To both full-season and monthly datasets, we fit generalized additive models (GAMs) in a stepwise procedure, using variable sets that represent our hypotheses. Prey models were generally the worst predictors of humpback distribution, while the most complex habitat models were the best. The Prey model performed best in June but increasingly poorly in remaining months. The performance of all models declined throughout the season, suggesting not only that this whale wave is being driven by needs other than food, but also that untested variable(s) inform late-season distribution. Alternative explanations of the wave include physiological maintenance and social habitat partitioning. Our findings demonstrate that marine predators can use complex spatial strategies not only to navigate vast areas of ocean but also to exploit specific habitats thoroughly. Though annually persistent and specific in structure, the whale wave would go (and has gone) unnoticed in typical marine mammal surveys.
Abundance and Survival of Pacific Humpback Whales in a Proposed Critical Habitat Area
Erin Ashe, Janie Wray, Christopher R. Picard, Rob Williams (2013)
Abstract: Humpback whales (Megaptera novaeangliae) were hunted commercially in Canada’s Pacific region until 1966. Depleted to an estimated 1,400 individuals throughout the North Pacific, humpback whales are listed as Threatened under Canada’s Species at Risk Act (SARA) and Endangered under the US Endangered Species Act. We conducted an 8-year photo-identification study to monitor humpback whale usage of a coastal fjord system in British Columbia (BC), Canada that was recently proposed as candidate critical habitat for the species under SARA. This participatory research program built collaborations among First Nations, environmental non-governmental organizations and academics. The study site, including the territorial waters of the Gitga’at First Nation, is an important summertime feeding destination for migratory humpback whales, but is small relative to the population’s range. We estimated abundance and survivorship using mark-recapture methods using photographs of naturally marked individuals. Abundance of humpback whales in the region was large, relative to the site’s size, and generally increased throughout the study period. The resulting estimate of adult survivorship (0.979, 95% CI: 0.914, 0.995) is at the high end of previously reported estimates. A high rate of resights provide new evidence for inter-annual site fidelity to these local waters. Habitat characteristics of our study area are considered ecologically significant and unique, and this should be considered as regulatory agencies consider proposals for high-volume crude oil and liquefied natural gas tanker traffic through the area. Monitoring population recovery of a highly mobile, migratory species is daunting for low-cost, community-led science. Focusing on a small, important subset of the animals’ range can make this challenge more tractable. Given low statistical power and high variability, our community is considering simpler ecological indicators of population health, such as the number of individuals harmed or killed each year by human activities, including ship strikes and entanglement in fishing gear.