Articles

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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

Abstract

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

Abstract

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.

Towers, J.R. and Tixier, P. 2022. Indian Ocean sighting of Shepherd's beaked whale (Tasmacetus shepherdi) helps confirm circumpolar distribution in Southern Hemisphere. Aquatic Mammals 48:462-467.

Excerpts

"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.

Abstract

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.

Towers, J.R., Pilkington, J.F., Mason, E.A. and Mason E.V. 2022. A bowhead whale in the eastern North Pacific. Ecology and Evolution 12:e8664.

Abstract

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.

Abstract

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.

van Weelden, C., Towers, J.R. and Bosker, T. 2021. Impacts of climate change on cetacean distribution, habitat and migration. Climate Change Ecology 1:100009

Abstract

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..

Abstract

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.

Towers, J. R., Keen, E. M., Balcomb-Bartok, K. Vonick, J. and Davis, D. 2020. Live stranding of Bigg's killer whales (Orcinus orca) along the west coast of North America. Aquatic Mammals 46: 466-477.

Abstract

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.