An understanding of population structure and connectivity at multiple spatial scales is required to assist wildlife conservation and management. This is particularly critical for widely distributed and highly mobile marine mammals subject to fisheries by-catch. Here, we present a population genomic assessment of a near-top predator, the common dolphin ( Delphinus delphis ), which is incidentally caught in multiple fisheries across the Australasian region. The study was carried out using 14,799 ddRAD sequenced genome-wide markers genotyped for 478 individuals sampled at multiple spatial scales across Australasia. A complex hierarchical metapopulation structure was identified, with three highly distinct and genetically diverse regional populations at large spatial scales (>1,500 km). The populations inhabit the southern coast of Australia, the eastern coast of Australia, New Zealand, and Tasmania, with the latter also showing a considerable level of admixture to Australia's east coast. Each of these regional populations contained two to four nested local populations (i.e., subpopulations) at finer spatial scales, with most of the gene flow occurring within distances of 50 to 400 km. Estimates of contemporary migration rates between adjacent subpopulations ranged from 6 to 25%. Overall, our findings identified complex common dolphin population structure and connectivity across state and international jurisdictions, including migration and gene flow across the Tasman Sea. The results indicate that inter-jurisdictional collaboration is required to implement conservation management strategies and mitigate fisheries interactions of common dolphins across multiple spatial scales in the Australasian region.

In contrast to previous reports that leopard seals (Hydrurga leptonyx) are rare vagrants to New Zealand, we show that this species is a regular member of the marine fauna of this region. We present a first analysis from the New Zealand Leopard Seal Database – an extensive collation of 2,711 records of leopard seals within New Zealand between 1200 and 2018. Of these records, 51.2% (n = 1,408) were photographic. Leopard seal sightings have increased over time and been reported in all seasons and regions of New Zealand. Sightings are predominantly of adult individuals of good or excellent body condition, which differs to previous hypotheses suggesting that leopard seals visiting New Zealand shores are primarily juvenile animals in poor health condition. A total of 176 unique individuals have been identified in the New Zealand Leopard Seal Catalogue between 2014 and 2018 and preliminary results indicate that numbers per annum have continued to increase over time. Three leopard seal births and a number of juvenile animals (34% of the NZ records) have been documented. Considering the information presented here and the current definitions in the New Zealand Threat Classification System, the threat status of leopard seals within New Zealand waters should be reclassified from Vagrant to Resident.

Population parameters of poorly marked gregarious species are difficult to estimate. This is the case for common dolphins (Delphinus sp.), a genus known for its lack of distinctive marks resulting in a low mark ratio. Furthermore, the widespread nature of common dolphins results in low recaptures. We developed reliable photo-identification protocols to ensure accurate identification of individuals in the Hauraki Gulf, New Zealand. These protocols combined the use of nicks and notches and pigmentation patterns for identification and included the development of a distinctiveness threshold. The data were further stratified by the level of distinctiveness of each individual (as distinctive or highly-distinctive). Photo-identification surveys were conducted from January 2010 to December 2013. Mark-recapture techniques were implemented through a POPAN super-population approach to estimate seasonal apparent survival, capture probability and abundance of dolphins. A total of 2,083 unique adult common dolphins were identified, 51.3% were classified as D1 (highly distinctive; n = 1,069) and 48.7% as D2 (distinctive; n = 1,014). Of all individuals identified, 34.3% (n = 704) were re-sighted over subsequent years. The proportion of marked dolphins (when compared to unmarked dolphins) was 26.3% for D1 and 46.4% for D1 & D2, respectively. Apparent survival was estimated at 0.767 (CI = 0.694-0.827) for D1 animals, and 0.796 (CI = 0.729-0.850) for D1 & D2 combined. For D1 only, seasonal abundance varied from 732 (CI = 460-1,177) in autumn 2010 to 5,304 (CI = 4,745-5,930) in spring 2013. While the inclusion of D2 individuals may offer a more precise estimate of total abundance, the inability to determine additional sources of bias (for example, arising from under or overestimated mark ratios) meant that estimates for D1 individuals were deemed the least biased for this population. The photo-identification protocol, stratification of the data and steps taken to eliminate potential model violations provided a useful and novel approach to estimate population parameters for common dolphins. These approaches could be implemented for other large gregarious populations (≥500 individuals) of animals with poor natural markings.

Laterally bent dorsal fins are rarely observed in free-ranging populations of cetaceans, contrary to captivity, where most killer whale Orcinus orca adult males have laterally collapsed fins. This topic has been poorly explored, and data/information on its occurrence and possible causes are limited. The present study: (i) undertakes a review of the available information on bent dorsal fins in free-ranging cetaceans, and updates it with new records, (ii) reports on the proportion of bent fins in different study populations, and (iii) discusses possible causes. An empirical approach based on bibliographic research and compilation of 52 new records collected worldwide resulted in a total of 17 species of cetaceans displaying bent dorsal fins. The species with the highest number of records (64%) and from most locations was O. orca. On average, individuals with bent dorsal fins represent < 1 % of their populations, with the exception of false killer whales Pseudorca crassidens and O. orca. While line injuries associated with fisheries interactions may be the main cause for P. crassidens, and the vulnerability to health issues caused by the evolutionary enlargement of the fin may be the cause for O. orca adult males, factors contributing to this abnormality for other species are still unclear. The occurrence of bent dorsals could be influenced by a set of variables rather than by a single factor but, irrespective of the cause, it is suggested that it does not directly affect the animals' survivorship. While still rare in nature, this incident is more common (at least 101 known cases) and widespread (geographically and in species diversity) than hypothesized, and is not confined only to animals in captive environments. Investigation into the occurrence of bent fins may be an interesting avenue of research.

Discussing the process from death to display for two significant Rāpoka, leopard seals, (Hydrurga leptonyx) undertaken as preservation projects by the Otago Museum. The first of these is a large female which died within the takiwa (district) of Kāti Huirapa Rūnaka ki Puketeraki in 2008. This seal was significant in the sense that it was the first marine mammal preservation project undertaken by the museum in collaboration with local iwi in the following the Ngāi Tahu Treaty of Waitangi settlement, where iwi regained the management rights of kā kararehe o takaroa (marine mammals) remains within the Marine Mammal Protection Act framework. This preservation project became a successful model for collaboration between iwi, government wildlife organisations, researchers and the museums when a marine mammal dies in the Otago Region. In 2017 the death of a neonate leopard seal pup, significant given its birth on St Kilda Beach, Dunedin within the takiwa of Te Rūnanga o Ōtākou sees the Otago Museum working to preserve this important leopard seal. This talk discusses the parallels and differences between the two projects, the importance of collaboration, recent applications of Magnetic Resonance Imaging (MRI) and Computed Tomography (CT) scanning preservation methods as well as using more traditional methods of taxidermy and skeltonisation. The guiding principles have been to preserve voucher information for the future, educate visitors about this Antarctic species, to expose our local community to the ongoing links between Māori and the natural world, and to demonstrate how wildlife management, science, museums and practitioners in indigenous knowledge can successfully collaborate in the practical and interpretive context of curation.

Photo-identification (photo-id) of dolphin individuals is a commonly used technique in ecological sciences to monitor state and health of individuals, as well as to study the social structure and distribution of a population. Traditional photo-id involves a laborious manual process of matching each dolphin fin photograph captured in the field to a catalogue of known individuals. We examine this problem in the context of open-set recognition and utilise a triplet loss function to learn a compact representation of fin images in a Euclidean embedding, where the Euclidean distance metric represents fin similarity. We show that this compact representation can be successfully learnt from a fairly small (in deep learning context) training set and still generalise well to out-of-sample identities (completely new dolphin individuals), with top-1 and top-5 test set (37 individuals) accuracy of 90.5 ± 2 and 93.6 ± 1 percent. In the presence of 1200 distractors, top-1 accuracy dropped by 12%; however, top-5 accuracy saw only a 2.8% drop.

[This corrects the article DOI: 10.1371/journal.pone.0198167.].

We address the problem of identifying individual cetaceans from images showing the trailing edge of their fins. Given the trailing edge from an unknown individual, we produce a ranking of known individuals from a database. The nicks and notches along the trailing edge define an individual's unique signature. We define a representation based on integral curvature that is robust to changes in viewpoint and pose, and captures the pattern of nicks and notches in a local neighborhood at multiple scales. We explore two ranking methods that use this representation. The first uses a dynamic programming time-warping algorithm to align two representations, and interprets the alignment cost as a measure of similarity. This algorithm also exploits learned spatial weights to downweight matches from regions of unstable curvature. The second interprets the representation as a feature descriptor. Feature keypoints are defined at the local extrema of the representation. Descriptors for the set of known individuals are stored in a tree structure, which allows us to perform queries given the descriptors from an unknown trailing edge. We evaluate the top-k accuracy on two real-world datasets to demonstrate the effectiveness of the curvature representation, achieving top-1 accuracy scores of approximately 95% and 80% for bottlenose dolphins and humpback whales, respectively.

Bryde's whales Balaenoptera edeni in New Zealand are classified as 'nationally critical' according to the New Zealand Threat Classification System. In the Hauraki Gulf, Bryde's whales occur year-round and are subject to ship-strike mortality events. Photo-identification surveys were conducted to estimate local abundance, apparent survival and site fidelity during 2 periods from 2004 to 2006 (261 daily surveys) and from 2011 to 2013 (382 daily surveys). The photo-identification database contained a total of 364 sighting records of 72 Bryde's whales. Overall, 20 whales were sighted across the 2 survey periods, indicating long-term site fidelity. Local abundance was estimated using the robust design (RD) and POPAN mark-recapture approaches for each period, including upward adjustment for the proportion of unmarked whales. RD seasonal abundance estimates varied from 17 to 43 whales between 2004 and 2006, and from 13 to 31 whales between 2011 and 2013. Temporary emigration followed a random pattern (gamma' = gamma'') and was estimated at 0.557 between 2004 and 2006, and 0.610 between 2011 and 2013. POPAN seasonal abundance ranged from 38 to 74 whales for the 2004 to 2006 period and from 42 to 68 whales for 2011 to 2013. Apparent survival was estimated across periods at 0.878 (95% CI = 0.811-0.923). From the 'super population' estimate of the 2011 to 2013 survey period ((N) over cap (super) = 135 whales, CI = 100-183), we calculated a potential biological removal (PBR) of 1 whale yr(-1). Given the impact of ship strikes on this local unit, it is important to continue long-term photo-identification of Bryde's whales. This technique provides valuable demographic information for a poorly known species.

Lesions on cetacea can be useful to assess the natural and anthropogenic pressures faced by a population. The aim of this study was to assess the viability of photo-identification (photo-IL)) as a tool to examine potential pressures affecting gregarious, free-ranging common dolphins (Delphinus sp.). Photo-ID was collected between 2010 and 2013 in the Hauraki Gulf (HG), New Zealand. From 1,411 independent encounters, 2,083 individuals were identified from permanent nicks and notches on their dorsal fins. Of these individuals, the number of lesions on 12 body sectors was assessed. Prevalence was determined by weighting the number of lesions by the cumulative number of images for each body sector. Of the 2,083 individuals identified, 77.9% (n = 1,622) exhibited lesions. Of all body segments examined, the anterior peduncle exhibited the highest percentage of lesions (91.1%). Most lesions observed were represented by indentations and impressions (84.2%, n = 1,368), followed by cut-like indentations (54.1%, n = 878), hyper-pigmented lesions (43.1%, n = 700), and hypo-pigmented lesions (37.4%, n = 607). A significant difference in the prevalence of lesions between the leading and trailing edges of dorsal fins was evident. Possible causes of lesions are discussed, including intra-or interspecific interactions, environmental conditions, infectious origins, fisheries and vessel interactions, and/or human-induced environmental stressors. Findings suggest that despite limitations, photo-ID can he used as an opportunistic, non-invasive research tool to examine lesions on free-ranging delphinids.

Ecologists commonly use photo-identification of individual animals to monitor the behaviour, state and health of a population, since it is a cost-effective technique that eliminates the need to physically capture and tag animals. With dolphins, the nicks and notches of the dorsal fin are typically used as the unique identifying features for each individual; however New Zealand common dolphins are relatively unmarked, so most of the population cannot be identified. Here, we investigate how computer vision can be used to extract information from the pigmentation patterns that are typically seen on adult common dolphin dorsal fins. We develop features that are relatively robust to changes in the fin orientation and compare the classification rates of 779 photos of 169 different adult common dolphins. Using pigmentation-based features, we correctly classified individuals 75% of the time, with our top-5 estimates containing the correct dolphin in 86% of the cases.

We present the first fine-scale data relating to the occurrence and group characteristics for killer whales (Orcinus orca) in the Hauraki Gulf, New Zealand, as observed from a platform of opportunity (PoP). Group size and composition were examined in relation to water depth and sea surface temperature (SST). From 2000 to 2010, 119 orca encounters were recorded, involving 1 to 18 animals. The encounter rate varied seasonally, being highest in austral spring and lowest in summer. Water depth in which whales were observed was significantly affected by group composition. Sixty-seven percent of groups contained immature animals. Group size was highly skewed towards smaller groups comprising two animals. While this study illustrates that PoPs can be used to indicate the occurrence and group characteristics of highly mobile social species, biases clearly exist. Through identifying such inaccuracies, we present recommendations on how future data should be collected to minimise error and improve datasets for scientific use.

Photo-identification of dolphin individuals is a commonly used technique in ecological sciences to monitor state and health of individuals, as well as to study the social structure and distribution of a population. Uniqueness of some forms of damage sustained by the trailing edge of the dorsal fin throughout an individual's life allows it to be used to identify the individual. Traditional photo-identification involves a laborious manual process of matching each dolphin fin photograph captured in the field to a catalogue of known individuals. A number of efforts have been made in the past to automate this process through the use of digital image processing; however, none of them correct for the different fin orientations (3D pose) prior to performing matching in a robust way. This paper provides an overview of these existing methods and offers a novel approach of utilising the iterative closest point (ICP) algorithm for performing the projective registration of two fin shapes and shows that this proposed method is robust to segmentation noise, partial occlusions and new nicks and notches appearing since last encounter.