Patton, P.T., Cheeseman, T., Abe, K., Yamaguchi, T., Reade, W., Southerland, K., Howard, A., Oleson, E.M., Allen, J.B., Ashe, E., Athayde, A., Baird, R.W., Basran, C., Cabrera, E., Calabokidis, J., Cardoso, J., Carroll, E.L., Cesario, A., Cheney, B.J., Corsi, E., Currie, J., Durban, J.W., Falcone, E.A., Fearnbach, H., Flynn, K., Franklin, T., Franklin, W., Vernazzani, B.G., Genov, T., Hill, M., Johnston, D.R., Keene, E.L., Mahaffy, S.D., McGuire, T.L., McPherson, L., Meyer, C., Michaud, R., Miliou, A., Orbach, D.N., Pearson, H.C., Rasmussen, M.H., Rayment, W.J., Rinaldi, C., Rinaldi, R., Siciliano, S., Stack, S., Tintore, B., Torres, L.G., Towers, J.R., Trotter, C., Moore, R.T., Weir, C.R. Wellard, R., Wells, R., Yano, K.M., Zaeschmar, J.R. & Bejder, L. 2023. Methods Ecol. Evol. 2023,00-1-15
1. Researchers can investigate many aspects of animal ecology through noninvasive photo–identification. Photo–identification is becoming more efficient as matching
individuals between photos is increasingly automated. However, the convolutional
neural network models that have facilitated this change need many training images to generalize well. As a result, they have often been developed for individual species that meet this threshold. These single-species
methods might underperform, as they ignore potential similarities in identifying characteristics and the photo–identification process among species.
2. In this paper, we introduce a multi-species photo–identification model based on a state of-the-art method in human facial recognition, the ArcFace classification head. Our model uses two such heads to jointly classify species and identities, allowing species to share information and parameters within the network. As a demonstration, we trained this model with 50,796 images from 39 catalogues of 24 cetacean species, evaluating its predictive performance on 21,192 test images from the same catalogues. We further evaluated its predictive performance with two external catalogues entirely composed of identities that the model did not see during training.
3. The model achieved a mean average precision (MAP) of 0.869 on the test set. Of these, 10 catalogues representing seven species achieved a MAP score over 0.95. For some species, there was notable variation in performance among catalogues, largely explained by variation in photo quality. Finally, the model appeared to generalize well, with the two external catalogues scoring similarly to their species' counterparts in the larger test set.
4. From our cetacean application, we provide a list of recommendations for potential
users of this model, focusing on those with cetacean photo–identification catalogues.
For example, users with high quality images of animals identified by dorsal nicks and notches should expect near optimal performance. Users can expect
decreasing performance for catalogues with higher proportions of indistinct individuals
or poor quality photos. Finally, we note that this model is currently freely available as code in a GitHub repository and as a graphical user interface, with additional
functionality for collaborative data management, via Happywhale.com.
Foote, A.D., Alexander, A., Ballance, L.T., Constantine, R., Muñoz, B.G.V., Guinet, C., Robertson, K.M., Sinding, M.S., Sironi, M., Tixier, P., Totterdell, J., Towers, J.R., Wellard, R., Pitman, R.L. and Morin, P.A. 2023. "Type D" killer whale genomes reveal long-term small population size and low genetic diversity. Journal of Heredity 114-94-109:1-15
Genome sequences can reveal the extent of inbreeding in small populations. Here, we present the first genomic characterization of type D killer whales, a distinctive eco/morphotype with a circumpolar, subantarctic distribution. Effective population size is the lowest estimated from any killer whale genome and indicates a severe population bottleneck. Consequently, type D genomes show among the highest level of inbreeding reported for any mammalian species (FROH ≥ 0.65). Detected recombination cross-over events of different haplotypes are up to an order of magnitude rarer than in other killer whale genomes studied to date. Comparison of genomic data from a museum specimen of a type D killer whale that stranded in New Zealand in 1955, with 3 modern genomes from the Cape Horn area, reveals high covariance and identity-by-state of alleles, suggesting these genomic characteristics and demographic history are shared among geographically dispersed social groups within this morphotype. Limitations to the insights gained in this study stem from the nonindependence of the 3 closely related modern genomes, the recent coalescence time of most variation within the genomes, and the nonequilibrium population history which violates the assumptions of many model-based methods. Long-range linkage disequilibrium and extensive runs of homozygosity found in type D genomes provide the potential basis for both the distinctive morphology, and the coupling of genetic barriers to gene flow with other killer whale populations.
"The Shepherd's beaked whale (Tasmacetus shepherdi) is among the least known cetacean species in the world (Mead, 2002)"
"The following details to the best of our knowledge, represent the first confirmed sighting record of T. shepherdi in the Indian Ocean that helps to substantiate its circumpolar distribution."
"The general location of this sighting was notable in that the sea surface temperature had risen from 9˚C to 16˚C over the previous 21 mmi (Figure 1) indicating that the ship was crossing through the western section of the Crozet Front."
"Based on previously published reports (Pitman et al., 2006; Gill et al., 2015; Donnelly et al., 2018; Thompson et al., 2019), this sighting represents the 24th record of live T. shepherdi for which species identity has been confirmed with photographs, video, or a descriptive report of diagnostic features, including pigmentation."
Gaston, A.J., Towers, J.R., Maftei, M., Pastran, S., Attia, Y. and Curry, G. 2022. An unusual influx of Short-tailed Shearwaters into nearshore waters of southern British Columbia in 2021. British Columbia Birds 33: 7-13.
An unusual influx of Shorttailed Shearwaters Ardenna tenuirostris occurred in British Columbia marine waters in 2021 with concentrations of thousands of birds in the Blackfish Sound region of eastern Queen Charlotte Strait and hundreds, possibly thousands, in the northern Salish Sea. Birds began to arrive in mid-August, built to a peak in mid-September and were mostly gone by early November. Most records were very close to shore and there is a strong likelihood that birds moved to the Salish Sea from Queen Charlotte Strait via Discovery Passage—an unusual route for an otherwise pelagic seabird. We make some tentative comments on possible causes of the influx.
Bowhead whales occur in the Arctic year-round. Their movements are largely correlated with seasonal expansions and reductions of sea ice, but a few recent extralimital sightings have occurred in the eastern and western North Atlantic and one was also documented in the western North Pacific over 50 years ago. Here we present details of a juvenile bowhead whale that was photographed and filmed from above and below the water while it was skim-feeding in Caamaño Sound, BC, Canada on May 31, 2016. This sighting occurred over 2000 km southeast from the nearest known range for this species in the Bering Sea at a time that most bowhead whales in that region would have been migrating northeast. This sighting represents the first and only documentation of a bowhead whale in the eastern North Pacific to date.
Bergler, C., Gebhard, A., Towers, J.R., Butyrev, L., Sutton, G.J., Shaw, T.J.H., Maier, A. and Nöth, E. 2021. FIN-PRINT a fully-automated multi-stage deep-learning-based framework for the individual recognition of killer whales. Scientific Reports 11:23480.
Biometric identification techniques such as photo-identification require an array of unique natural markings to identify individuals. From 1975 to present, Bigg’s killer whales have been photo-identified along the west coast of North America, resulting in one of the largest and longest-running cetacean photo-identification datasets. However, data maintenance and analysis are extremely time and resource consuming. This study transfers the procedure of killer whale image identification into a fully automated, multi-stage, deep learning framework, entitled FIN-PRINT. It is composed of multiple sequentially ordered sub-components. FIN-PRINT is trained and evaluated on a dataset collected over an 8-year period (2011–2018) in the coastal waters off western North America, including 121,000 human-annotated identification images of Bigg’s killer whales. At first, object detection is
performed to identify unique killer whale markings, resulting in 94.4% recall, 94.1% precision, and 93.4% mean-average-precision (mAP). Second, all previously identified natural killer whale markings are extracted. The third step introduces a data enhancement mechanism by filtering between valid and invalid markings from previous processing levels, achieving 92.8% recall, 97.5%, precision, and 95.2% accuracy. The fourth and final step involves multi-class individual recognition. When evaluated on the network test set, it achieved an accuracy of 92.5% with 97.2% top-3 unweighted accuracy (TUA) for the 100 most commonly photo-identified killer whales. Additionally, the method achieved an accuracy of 84.5% and a TUA of 92.9% when applied to the entire 2018 image collection of the 100
most common killer whales. The source code of FIN-PRINT can be adapted to other species and will be publicly available.
Climatic changes have had significant impacts on marine ecosystems, including apex predators such as cetaceans. A more complete understanding of the potential impacts of climate change on cetaceans is necessary to ensure their conservation. Here we present a review of the literature on the impacts of climate change on cetacean dis- tribution, habitat and migrations and highlight research gaps. Our results indicate that due to rising sea surface temperatures (SSTs) and/or reducing sea ice extent, a variety of impacts on the distribution, habitat and migra- tion of cetaceans have been observed to date and several more are predicted to occur over the next century. Many species have demonstrated a poleward shift, following their preferred SSTs to higher latitudes, and some have altered the timing of their migrations, while others appear not to be affected. These changes may benefit certain species, while others will be placed under extreme pressure and may face increased risk of extinction. Broader implications may include increased inter-specific competition, genetic alterations, ecosystem-level changes and conservation challenges. Existing research on the topic is both extremely limited and unevenly distributed (geo- graphically and phylogenetically). Further research is necessary to determine which species and populations are most vulnerable and require the earliest conservation action.
Tixier, P., Gasco, N., Towers, J.R. and Guinet, C. 2021. Killer whales of the Crozet Archipelago and adjacent waters: photo-identification catalogue, population status and distribution in 2020. Centre d'Etudes Biologiques de Chizé, Centre National de la Recherche Scientifique, France, 167 p..
Three forms of killer whales (Orcinus orca) occur around the subantarctic islands of the southern Indian Ocean (42-53°S; 34-74°E). The form encountered in both inshore and offshore waters, described as generalist in its feeding preferences (seals, whales, penguins and fish as prey) and known to depredate toothfish from longliners has been opportunistically photo-identified around the Crozet archipelago since the 1960s. Together with photo-identification data collected in the Prince Edward/Marion EEZ, Kerguelen
EEZ and international waters, this report provides up to date information on the abundance and distribution of the Crozet killer whales. In total, 124,313 photographs taken during 2,109 encounters since 1964 were analysed, allowing for 299 individuals to be identified. Most encounters with available data were from the Crozet EEZ (1,432 from longliners, 602 from Île de la Possession) and occurred after 2003 when photoidentification was implemented in the fishery observer program. Among the 188 individuals recorded in the Crozet EEZ since 2003, 22 (12%) were also photographed in the Kerguelen EEZ, 13 (7%) in the Prince Edward/Marion EEZ and 13 (7%) in adjacent international waters. The frequently encountered subset of the Crozet killer whale population was composed of 23 social units (maternal groups), 19 of which included individuals alive in 2020. These social units ranged in size from 1 to 11 individuals with a mean (± SD) of 4 ± 3 per unit. As of June 2020 when the latest photographs included in the study were taken, abundance of this subset was 89-94 individuals. However, detailed analysis of data collected between 2005 and 2020 shows that the number of confirmed deaths (n = 51) exceeds the number of recorded births (n = 46), resulting in a 5% decrease of the population size over this period. These deaths were distributed across the population with the majority occurring in the most common sex and age classes - adult females and juveniles. Factors contributing to mortalities are unclear, but may include lethal interactions with illegal fisheries. When paired with the fact that the Crozet killer whales already underwent a severe mortality episode in the 1990s, these findings raise strong concerns about the future of the population and stress the necessity of conservation actions while maintaining an intensive monitoring effort.
Killer whales are known to live strand in many regions around the world. Some populations regularly and repeatedly do so in pursuit of prey, but this behaviour is otherwise relatively rare. Off the west coast of North America, historical records of live stranded killer whales indicate that most individuals perished, were euthanized, or captured for aquariums where they subsequently died. Few details are available on which of the three culturally distinct killer whale ecotypes in this region have been involved in live stranding events (LSEs) and on the survival of any individuals that were able to unstrand. In this article, we report details on four LSEs since 2002 and, together with previous records, show that all live-stranded killer whales documented in this region during the last four decades have been of the Bigg’s ecotype. There was no predominant sex or age class involved in these events, but among the five individuals reported herein, all three adults stranded on sandy shores, whereas both juveniles stranded on rocky outcroppings while hunting harbour seals. Stranded individuals were kept cool and wet by human responders during three of the four LSEs, and efforts were twice made to move the animals off the shore. All individuals survived the LSEs, although one adult male was never seen again. The other four individuals rejoined their respective families soon after becoming unstranded and have been photo-identified with them on numerous occasions since. One adult female that was pregnant when stranded gave birth to a healthy calf several months later. These results indicate that (1) human responses to live-stranded killer whales are not always necessary, but when they are, they can help preserve their lives, family bonds, and culture and (2) LSEs are a natural risk associated with the foraging ecology of the Bigg’s killer whale ecotype.
AbstractRelationships between seabirds and cetaceans can vary from symbiotic to predatory. At high latitude seas in the Southern Hemisphere, giant petrels (Macronectes spp.) and male sperm whales (Physeter macrocephalus) are often solitary, but commercial longlining for Patagonian toothfish (Dissostichus eleginoides) provides consistent feeding opportunities that result in persistent aggregations of both. From ~ 1997 to 2019, we opportunistically photographed 23 events where individual giant petrels preyed on the flesh of live sperm whales that were depredating from Patagonian toothfish longliners near South Georgia, Crozet, and Kerguelen Islands. Both immature and adult southern (M. giganteus) and northern (M. halli) giant petrels were implicated in these predation events. Sperm whales reacted to attacks from one or more giant petrels by sinking or flinching, and then arching, rolling, diving, and snorkelling at the surface during subsequent predation attempts. Depredating sperm whales will dive deep, fast, and for long periods which can result in limited dive ability while replenishing oxygen stores at the surface. This behaviour, and the relatively high density of both species around longlining vessels may facilitate unique opportunities for giant petrels to exploit live sperm whales that are not likely as common under circumstances not sustained by longlining operations.
Towers, J. R. and Wellard, R. 2020. Killer Whales of the Southern Hemisphere. In Spirits Of The Coast: Orcas in Science, Art, and History. Edited by Black, M., Hammond, L., Hanke, G. and Sanchez, N. Published by Royal BC Museum, Victoria, BC, Canada.
The killer whale is the apex marine predator. It preys on a wide range of species throughout the world’s oceans, making it one of the most ecologically diverse and widespread species on the planet. Several types of killer whale exist, and culturally distinct high-latitude populations that typically exploit different prey resources are referred to as ecotypes. In the Southern Hemisphere at least five ecotypes can be readily distinguished by their dramatically different appearances and behavioural characteristics. Although these physically and ecologically unique typesof killer whale often occur in the same area at the same time, they rarely, if ever, socialize, and genetic evidence indicates that some populations haven’t interbred for hundreds of generations. This multi-component divergence is indicative of a species complex that may warrant recognition of several distinct species or sub-species within the genus Orcinus.
Globally, killer whales display a surprising amount of phenotypic diversity, with numerous described “ecotypes”: forms that are morphologically, ecologically, and phylogenetically distinct but ostensibly all the same species. For example, in the Southern Ocean (i.e., south of 60°S), five different killer whale ecotypes are currently recognized: types A, B1, B2, C and D (Fig. 2; Pitman and Ensor 2003, Pitman et al. 2011, Durban et al. 2016). Even to laypeople, most of these are readily distinguishable in the field, in addition to having different habitat and prey preferences. Moreover, although their ranges are often sympatric, they do not mix socially, and genetic studies confirm that they rarely interbreed. Of these, type D is the most distinctive and, by far, the least well-known killer whale ecotype.
Towers, J. R., McMillan, C. J., and Piercey, R. S. 2019. Sighting rates and prey of Minke Whales (Balaenoptera acutorostrata) and other cetaceans off Cormorant Island, British Columbia. Canadian Field-Naturalist 133: 144-150.
From June to August 2012, we conducted over 500 h of visual surveys from Cormorant Island, British Columbia, to determine behaviour and habitat use patterns of nearby cetaceans. Seven species were documented, but Minke Whales (Balaenoptera acutorostrata) were by far the most common and were observed lunge feeding at the surface on 15 occasions. In addition, this species was documented surface lunge feeding on Pacific Herring (Clupea pallasi) and Pacific Sand Lance (Ammodytes personatus) on 32 occasions during vessel-based cetacean surveys around Cormorant Island between 2010 and 2014. Although Minke Whales are relatively uncommon in British Columbia, these results indicate that they can regularly be found in specific feeding areas during the summer.
Towers, J. R., Sutton, G. J., Shaw, T. J. H., Malleson, M., Matkin, D., Gisborne, B., Forde, J., Ellifrit, D., Ellis, G. M., Ford, J. K. B., and Doniol-Valcroze, T. 2019. Photo-identification Catalogue, Population Status, and Distribution of Bigg’s Killer Whales known from Coastal Waters of British Columbia, Canada. Canadian Technical Report Fisheries and Aquatic Sciences 3311: vi + 299 p.
In British Columbia, Bigg’s (transient) killer whales have been opportunistically photo-identified for several decades. This report uses a 61-year archive of photo-identification data from 1958-2018 to provide information on the abundance and distribution of Bigg’s killer whales known from BC. In total, 766 unique individuals were identified in a total of 6277 encounters during this time period. To identify the subset of this population that is most likely to be impacted by human activity due to showing the most fidelity to coastal waters over time, we developed criteria based on rates of occurrence, both overall and during recent years. A total of 206 mature individuals that were alive in 2018 were encountered at least once since 2014 and were documented during at least seven years or 11 or more encounters during the study period. Their offspring and other inferred maternally related kin include an additional 143 individuals. This population subset of 349 individuals has grown at an observed average annual rate of 4.1% since 2012 due to relatively low mortality and the birth of over 100 calves during this time period. Identification images of the dorsal fins, saddle patches, and eyepatches of all of these individuals as well as calves born to date in 2019 are provided. Details on the birth years, sex, maternal ancestry, social cohesion, and distribution of these individuals are also provided, when known.
Background: Common bottlenose dolphins (Tursiops truncatus) are distributed globally in tropical and warmtemperate waters with coastal and offshore ecotypes known. In the eastern North Pacific Ocean, common bottlenose dolphins are typically found in offshore waters as far as 41° N and in coastal waters as far as 38° N. Despite considerable survey effort, the species has not been previously recorded in Canadian Pacific waters. Results: On 29 July 2017, a group of approximately 200 common bottlenose dolphins were observed together with approximately 70 false killer whales (Pseudorca crassidens) in waters of 16.5° C at 50° N during a pelagic seabird and marine mammal survey off the west coast of northern Vancouver Island, British Columbia, Canada.
Conclusions: This sighting represents the only occurrence of common bottlenose dolphins recorded in Canadian Pacific waters and, to our knowledge, is the most northerly record for this species in the eastern North Pacific. It is also the first sighting record of false killer whales in non-coastal waters in British Columbia, Canada. The occurrence of both species may be associated with a prolonged period of warming in offshore regions of the
eastern North Pacific.
Towers, J. R., Tixier, P., Ross, K. A., Bennett, J., Arnould, J. P. Y., Pitman, R. L., and Durban, J. W. 2018. Movements and dive behaviour of a tooth fish-depredating killer and sperm whale. ICES Journal of Marine Science 76: 298-311.
Depredation of demersal longlines by killer and sperm whales is a widespread behaviour that impacts fisheries and whale populations. To better understand how depredating whales behave in response to fishing activity, we deployed satellite-linked location and dive profile tags on a sperm and killer whale that were depredating Patagonian toothfish from commercial longlines off South Georgia. The sperm and killer whale followed one fishing vessel for >180 km and >300 km and repeatedly depredated when longlines were being retrieved over periods of 6 and
7 d, respectively. Their behaviours were also sometimes correlated with the depths and locations of deployed gear. They both dove significantly deeper and faster when depredating compared with when foraging naturally. The killer whale dove >750m on five occasions while depredating (maximum: 1087 m), but these deep dives were always followed by long periods (3.9–4.6 h) of shallow (<100 m) diving. We hypothesize that energetically and physiologically costly dive behaviour while depredating is driven by intra- and inter-specific competition due to the limited availability of this abundant resource.
Towers, J. R., Hallé, M. J., Symonds, H. K., Sutton, G. J., Morton, A. B., Spong, P., Borrowman, J. P., and Ford, J. K. B. 2018. Infanticide in a mammal-eating killer whale population. Scientific Reports 8: 4366.
Infanticide can be an extreme result of sexual conflict that drives selection in species in which it occurs. It is a rarely observed behaviour but some evidence for its occurrence in cetaceans exists in three species of dolphin. Here we describe observations of an adult male killer whale (Orcinus orca) and his postreproductive mother killing a neonate belonging to an unrelated female from the same population in the North Pacific. This is the first account of infanticide reported in killer whales and the only case committed jointly by an adult male and his mother outside of humans. Consistent with findings in other social mammals, we suggest that infanticide is a sexually selected behaviour in killer whales that could provide subsequent mating opportunities for the infanticidal male and thereby provide inclusive fitness benefits for his mother.
The minke whale (Balaenoptera acutorostrata) is a small species of baleen whale with a cosmopolitan distribution. Despite extensive study on the vocalizations of other balaenopterids, the acoustic repertoire of minke whales is not well known. Individuals of the North Pacific subspecies (B. acutorostrata scammoni) produce unique vocalizations (‘boings’) during their putative breeding season from fall to spring. However, no vocalizations have been previously reported for this subspecies in any eastern North Pacific feeding ground. We present two call types recorded in the presence of six minke whales, two of which were confirmed as female, in Cormorant Channel, British Columbia, Canada, during the summer of 2012. The calls consist of downsweeps and pulse chains. These call types share some characteristics with calls described elsewhere, although they are not identical to similar call types observed for other populations. Calling rates for minke whales in this study region are very low compared to those reported for this subspecies on its putative breeding grounds, as well as for other subspecies on their feeding grounds. We propose predation risk, sexual segregation and acoustic masking as potential causes of the low calling rates observed for minke whales in Cormorant Channel.
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