Deep learning for automatic facial detection and recognition in Japanese macaques: illuminating social networks

Individual identification plays a pivotal role in ecology and ethology, notably as a tool for complex social structures understanding. However, traditional identification methods often involve invasive physical tags and can prove both disruptive for animals and time-intensive for researchers. In recent years, the integration of deep learning in research has offered new methodological perspectives through the automatisation of complex tasks. Harnessing object detection and recognition technologies is increasingly used by researchers to achieve identification on video footage. This study represents a preliminary exploration into the development of a non-invasive tool for face detection and individual identification of Japanese macaques (Macaca fuscata) through deep learning. The ultimate goal of this research is, using identification done on the dataset, to automatically generate a social network representation of the studied population. The current main results are promising: (i) the creation of a Japanese macaques' face detector (Faster-RCNN model), reaching an accuracy of 82.2% and (ii) the creation of an individual recogniser for the Kōjima Island macaque population (YOLOv8n model), reaching an accuracy of 83%. We also created a Kōjima population social network by traditional methods, based on co-occurrences on videos. Thus, we provide a benchmark against which the automatically generated network will be assessed for reliability. These preliminary results are a testament to the potential of this approach to provide the scientific community with a tool for tracking individuals and social network studies in Japanese macaques.

Using quantile regression and relative entropy to assess the period of anomalous behavior of marine mammals following tagging

Tagging of animals induces a variable stress response which following release will obscure natural behavior. It is of scientific relevance to establish methods that assess recovery from such behavioral perturbation and generalize well to a broad range of animals, while maintaining model transparency. We propose two methods that allow for subdivision of animals based on covariates, and illustrate their use onN = 20 narwhals (Monodon monoceros) andN = 4 bowhead whales (Balaena mysticetus), captured and instrumented with Acousonde™ behavioral tags, but with a framework that easily generalizes to other marine animals and sampling units. The narwhals were divided into two groups based on handling time, short (t < 58 min) and long (t ≥ 58 min), to measure the effect on recovery. Proxies for energy expenditure (VeDBA) and rapid movement (jerk) were derived from accelerometer data. Diving profiles were characterized using two metrics (target depth and dive duration) derived from depth data. For accelerometer data, recovery was estimated using quantile regression (QR) on the log-transformed response, whereas depth data were addressed using relative entropy (RE) between hourly distributions of dive duration (partitioned into three target depth ranges) and the long-term average distribution. Quantile regression was used to address location-based behavior to accommodate distributional shifts anticipated in aquatic locomotion. For all narwhals, we found fast recovery in the tail of the distribution (<3 h) compared with a variable recovery at the median (∼1-10 h) and with a significant difference between groups separated by handling time. Estimates of bowhead whale recovery times showed fast median recovery (<3 h) and slow recovery at the tail (>6 h), but were affected by substantial uncertainty. For the diving profiles, as characterized by the component pair (target depth, dive duration), the recovery was slower (narwhals-long:t < 16 h; narwhals-short:t < 10 h; bowhead whales: <9 h) and with a difference between narwhals with short vs long handling times. Using simple statistical concepts, we have presented two transparent and general methods for analyzing high-resolution time series data from marine animals, addressing energy expenditure, activity, and diving behavior, and which allows for comparison between groups of animals based on well-defined covariates.

Biologging of emperor penguins-Attachment techniques and associated deployment performance

An increasing number of marine animals are equipped with biologgers, to study their physiology, behaviour and ecology, often for conservation purposes. To minimise the impacts of biologgers on the animals’ welfare, the Refinement principle from the Three Rs framework (Replacement, Reduction, Refinement) urges to continuously test and evaluate new and updated biologging protocols. Here, we propose alternative and promising techniques for emperor penguin (Aptenodytes forsteri) capture and on-site logger deployment that aim to mitigate the potential negative impacts of logger deployment on these birds. We equipped adult emperor penguins for short-term (GPS, Time-Depth Recorder (TDR)) and long-term (i.e. planned for one year) deployments (ARGOS platforms, TDR), as well as juvenile emperor penguins for long-term deployments (ARGOS platforms) in the Weddell Sea area where they had not yet been studied. We describe and qualitatively evaluate our protocols for the attachment of biologgers on-site at the colony, the capture of the animals and the recovery of the devices after deployment. We report unprecedented recaptures of long-term equipped adult emperor penguins (50% of equipped individuals recaptured after 290 days). Our data demonstrate that the traditional technique of long-term attachment by gluing the biologgers directly to the back feathers causes excessive feather breakage and the loss of the devices after a few months. We therefore propose an alternative method of attachment for back-mounted devices. This technique led to successful year-round deployments on 37.5% of the equipped juveniles. Finally, we also disclose the first deployments of leg-bracelet mounted TDRs on emperor penguins. Our findings highlight the importance of monitoring potential impacts of biologger deployments on the animals and the need to continue to improve methods to minimize disturbance and enhance performance and results.

Categorising cheetah behaviour using tri-axial accelerometer data loggers: a comparison of model resolution and data logger performance

BACKGROUND

Extinction is one of the greatest threats to the living world, endangering organisms globally, advancing conservation to the forefront of species research. To maximise the efficacy of conservation efforts, understanding the ecological, physiological, and behavioural requirements of vulnerable species is vital. Technological advances, particularly in remote sensing, enable researchers to continuously monitor movement and behaviours of multiple individuals simultaneously with minimal human intervention. Cheetahs, Acinonyx jubatus, constitute a "vulnerable" species for which only coarse behaviours have been elucidated. The aims of this study were to use animal-attached accelerometers to (1) determine fine-scale behaviours in cheetahs, (2) compare the performances of different devices in behaviour categorisation, and (3) provide a behavioural categorisation framework.

METHODS

Two different accelerometer devices (CEFAS, frequency: 30 Hz, maximum capacity: ~ 2 g; GCDC, frequency: 50 Hz, maximum capacity: ~ 8 g) were mounted onto collars, fitted to five individual captive cheetahs. The cheetahs chased a lure around a track, during which time their behaviours were videoed. Accelerometer data were temporally aligned with corresponding video footage and labelled with one of 17 behaviours. Six separate random forest models were run (three per device type) to determine the categorisation accuracy for behaviours at a fine, medium, and coarse resolution.

RESULTS

Fine- and medium-scale models had an overall categorisation accuracy of 83-86% and 84-88% respectively. Non-locomotory behaviours were best categorised on both loggers with GCDC outperforming CEFAS devices overall. On a coarse scale, both devices performed well when categorising activity (86.9% (CEFAS) vs. 89.3% (GCDC) accuracy) and inactivity (95.5% (CEFAS) vs. 95.0% (GCDC) accuracy). This study defined cheetah behaviour beyond three categories and accurately determined stalking behaviours by remote sensing. We also show that device specification and configuration may affect categorisation accuracy, so we recommend deploying several different loggers simultaneously on the same individual.

CONCLUSION

The results of this study will be useful in determining wild cheetah behaviour. The methods used here allowed broad-scale (active/inactive) as well as fine-scale (e.g. stalking) behaviours to be categorised remotely. These findings and methodological approaches will be useful in monitoring the behaviour of wild cheetahs and other species of conservation interest.

A simple tool for linking photo-identification with multimedia data to track mammal behaviour

Identifying individual animals is critical to describe demographic and behavioural patterns, and to investigate the ecological and evolutionary underpinnings of these patterns. The traditional non-invasive method of individual identification in mammals—comparison of photographed natural marks—has been improved by coupling other sampling methods, such as recording overhead video, audio and other multimedia data. However, aligning, linking and syncing these multimedia data streams are persistent challenges. Here, we provide computational tools to streamline the integration of multiple techniques to identify individual free-ranging mammals when tracking their behaviour in the wild. We developed an open-source R package for organizing multimedia data and for simplifying their processing a posteriori—“MAMMals: Managing Animal MultiMedia: Align, Link, Sync”. The package contains functions to (i) align and link the individual data from photographs to videos, audio recordings and other text data sources (e.g. GPS locations) from which metadata can be accessed; and (ii) synchronize and extract the useful multimedia (e.g. videos with audios) containing photo-identified individuals. To illustrate how these tools can facilitate linking photo-identification and video behavioural sampling in situ, we simultaneously collected photos and videos of bottlenose dolphins using off-the-shelf cameras and drones, then merged these data to track the foraging behaviour of individuals and groups. We hope our simple tools encourage future work that extend and generalize the links between multiple sampling platforms of free-ranging mammals, thereby improving the raw material needed for generating new insights in mammalian population and behavioural ecology.

Future trends in measuring physiology in free-living animals

Thus far, ecophysiology research has predominantly been conducted within controlled laboratory-based environments, owing to a mismatch between the recording technologies available for physiological monitoring in wild animals and the suite of behaviours and environments they need to withstand, without unduly affecting subjects. While it is possible to record some physiological variables for free-living animals using animal-attached logging devices, including inertial-measurement, heart-rate and temperature loggers, the field is still in its infancy. In this opinion piece, we review the most important future research directions for advancing the field of 'physiologging' in wild animals, including the technological development that we anticipate will be required, and the fiscal and ethical challenges that must be overcome. Non-invasive, multi-sensor miniature devices are ubiquitous in the world of human health and fitness monitoring, creating invaluable opportunities for animal and human physiologging to drive synergistic advances. We argue that by capitalizing on the research efforts and advancements made in the development of human wearables, it will be possible to design the non-invasive loggers needed by ecophysiologists to collect accurate physiological data from free-ranging animals ethically and with an absolute minimum of impact. In turn, findings have the capacity to foster transformative advances in human health monitoring. Thus, we invite biomedical engineers and researchers to collaborate with the animal-tagging community to drive forward the advancements necessary to realize the full potential of both fields. This article is part of the theme issue 'Measuring physiology in free-living animals (Part II)'.

Evaluation of spot patterns and carapace abnormalities of an Endangered freshwater turtle, Clemmys guttata, as a potential tool for population assignment

Many of the world’s contemporary species of turtle are extinct or threatened with extinction due to habitat loss, increases in anthropogenic sources of mortality, and poaching (illegal collection). The slow life-history strategy of most turtle species magnifies the effects of poaching because the loss of even a few mature individuals can impact population growth. Returning poached turtles to their population of origin, where possible, can mitigate these effects, but identifying the origin of these individuals can be challenging. We hypothesized that spot patterns might allow assignment of Endangered spotted turtles Clemmys guttata to their population of origin. We characterized and compared spot patterns from carapace photographs of 126 individuals from 10 sites. To explore other types of information these photographs might provide, we also documented carapacial scute abnormalities and quantified their association with genetic diversity and latitude. Spot pattern similarity was not higher within populations than among populations and did not accurately differentiate populations. Carapacial scute abnormalities occurred in 82% of turtles and were not correlated with estimates of neutral genetic diversity. Abnormalities were positively correlated with latitude, implicating thermal stress during the early stages of development in the generation of some scute deformities. However, this relationship became non-significant when line (scute seam) abnormalities were excluded from the data, suggesting a different primary cause for the more severe scute deformities. Further research should continue to investigate the drivers of these deformities, as monitoring shifts in the frequency of scute deformities may provide relevant information for conservation and recovery of endangered turtles.

Assessing the post-release effects of capture, handling and placement of satellite telemetry devices on narwhal (Monodon monoceros) movement behaviour

Animal-borne telemetry devices have become a popular and valuable means for studying the cryptic lives of cetaceans. Evaluating the effect of capture, handling and tagging procedures remains largely unassessed across species. Here, we examine the effect of capture, handling and tagging activities on an iconic Arctic cetacean, the narwhal (Monodon monoceros), which has previously been shown to exhibit an extreme response to extended capture and handling. Using accelerometry-derived metrics of behaviour, including activity level, energy expenditure and swimming activity, we quantify the post-release responses and time to recovery of 19 individuals following capture and tagging activities considering the intrinsic covariates of sex and individual size and the extrinsic covariates of handling time and presence of a 'bolt-on' satellite telemetry device. From accelerometer-derived behaviour, most narwhals appeared to return to mean baseline behaviour (recovery) within 24 hours after release, which was supported by longer-term measures of diving data. None of the covariates measured, however, had an effect on the time individuals took to recover following release. Using generalized additive models to describe changes in behaviour over time, we found handling time to be a significant predictor of activity levels, energy expenditure and swimming behaviour following release. Individuals held for the longest period (>40 min) were found to display the largest effect in behaviour immediately following release with respect to swimming behaviour and activity levels. We also found some support for relationships between activity levels, energy expenditure and swimming activity and two other covariates: sex and the attachment of a bolt-on configuration satellite tags. Our results indicate that narwhals recover relatively quickly following capture, handling and tagging procedures, but we suggest that researchers should minimize handling time and further investigation is needed on how to mitigate potential effects of bolt-on satellite tags in these sensitive species.

A new model study species: high accuracy of discrimination between individual freckled hawkfish (Paracirrhites forsteri) using natural markings

Variations between distinct natural markings of freckled hawkfish (Paracirrhites forsteri) could allow in situ identification of individuals from underwater photography. Receiver operating characteristic analysis was used to assess the ability of the Interactive Individual Identification System (I³ S) software to assist in discriminating between images of P. forsteri individuals. This study's results show the high discriminant ability of I³ S to differentiate between unlike individuals and identify images of the same individual. The ability to use automatic computer-aided assistance in the study of this species will enable future research to explore behaviour and movements of individuals in the wild.

Identifying individual polar bears at safe distances: A test with captive animals

The need to recognise individuals in population and behavioural studies has stimulated the development of various identification methods. A commonly used method is to employ natural markers to distinguish individuals. In particular, the automated processing of photographs of study animals has gained interest due to the speed of processing and the ability to handle a high volume of records. However, automated processing requires high-quality photographs, which means that they need to be taken from a specific angle or at close distances. Polar bears Ursus maritimus, for example, may be identified by automated analysis of whisker spot patterns. However, to obtain photographs of adequate quality, the animals need to be closer than is usually possible without risk to animal or observer. In this study we tested the accuracy of an alternative method to identify polar bears at further distances. This method is based on distinguishing a set of physiognomic characteristics, which can be recognised from photographs taken in the field at distances of up to 400 m. During five trials, sets of photographs of 15 polar bears from six zoos, with each individual bear portrayed on different dates, were presented for identification to ten test observers. Among observers the repeatability of the assessments was 0.68 (SE 0.011). Observers with previous training in photogrammetric techniques performed better than observers without training. Experience with observing polar bears in the wild did not improve skills to identify individuals on photographs. Among the observers with photogrammetric experience, the rate of erroneous assessment was on average 0.13 (SE 0.020). For the inexperienced group this was 0.72 (SE 0.018). Error rates obtained with automated whisker spot analysis were intermediate (0.26–0.58). We suggest that wildlife studies will benefit from applying several identification techniques to collect data under different conditions.

A Ten-Stage Protocol for Assessing the Welfare of Individual Non-Captive Wild Animals: Free-Roaming Horses (Equus Ferus Caballus) as an Example

Knowledge of the welfare status of wild animals is vital for informing debates about the ways in which we interact with wild animals and their habitats. Currently, there is no published information about how to scientifically assess the welfare of free-roaming wild animals during their normal day-to-day lives. Using free-roaming horses as an example, we describe a ten-stage protocol for systematically and scientifically assessing the welfare of individual non-captive wild animals. The protocol starts by emphasising the importance of readers having an understanding of animal welfare in a conservation context and also of the Five Domains Model for assessing welfare. It goes on to detail what species-specific information is required to assess welfare, how to identify measurable and observable indicators of animals' physical states and how to identify which individuals are being assessed. Further, it addresses how to select appropriate methods for measuring/observing physical indicators of welfare, the scientific validation of these indicators and then the grading of animals' welfare states, along with assigning a confidence score. Finally, grading future welfare risks and how these can guide management decisions is discussed. Applying this ten-stage protocol will enable biologists to scientifically assess the welfare of wild animals and should lead to significant advances in the field of wild animal welfare.

Systematic review of equids and telemetry collars: implications for deployment and reporting

Abstract Data from animals equipped with global positioning system collars have advanced our understanding of vertebrates, but this technology has rarely been employed to study feral equids. Hesitation to equip feral equids with telemetry collars in the USA can often be attributed to safety concerns stemming from one study from the 1980s, where injuries were sustained by feral horses (Equus ferus caballus) equipped with radio-collars. Improvements in collar design over the ensuing quarter-century may have decreased risk of collar-related complications; however, telemetry-based studies on feral equids continue to be limited. In the present review, studies from wild and feral equids worldwide were systematically reviewed to better understand the mortality and injury risk in application of telemetry collars to equids. Our goals were to: (1) report the number of individual equids fitted with telemetry collars (1979–2017); and (2) document the number of individual equids that reportedly died or suffered injuries from collars or other sources. A comparative review of elk (Cervus canadensis), mule deer (Odocoileus hemionus) and pronghorn (Antilocapra americana) was also conducted to evaluate the relative risk of collar-related complications among equids and routinely collared North American ungulates. In total, 1089 wild and feral telemetered equids were identified across 48 studies. Of these, 87 (8.0%) were reported to have died, with only one (0.09%) mortality attributable to a collar. Comparatively, 23.0% (1095) of 4761 elk, mule deer and pronghorn fitted with telemetry collars were found to have died in the same number of studies, though no mortalities were reported to be related to the collar. Although wild and feral equids did not experience increased natural mortality compared with the other ungulates, studies have not provided sufficient information to assess relative risk of collar-related complications. Explicit reporting and discussion of telemetry collar impacts in future publications of all animal species are recommended, especially equids, to improve understanding of how telemetry collars can affect study individuals.

High detectability with low impact: Optimizing large PIT tracking systems for cave-dwelling bats

Passive integrated transponder (PIT) tag technology permits the "resighting" of animals tagged for ecological research without the need for physical re-trapping. Whilst this is effective if animals pass within centimeters of tag readers, short-distance detection capabilities have prevented the use of this technology with many species. To address this problem, we optimized a large (15 m long) flexible antenna system to provide a c. 8 m2 vertical detection plane for detecting animals in flight. We installed antennas at two roosting caves, including the primary maternity cave, of the critically endangered southern bent-winged bat (Miniopterus orianae bassanii) in south-eastern Australia. Testing of these systems indicated PIT-tags could be detected up to 105 cm either side of the antenna plane. Over the course of a three-year study, we subcutaneously PIT-tagged 2,966 bats and logged over 1.4 million unique detections, with 97% of tagged bats detected at least once. The probability of encountering a tagged bat decreased with increasing environmental "noise" (unwanted signal) perceived by the system. During the study, we mitigated initial high noise levels by earthing both systems, which contributed to an increase in daily detection probability (based on the proportion of individuals known to be alive that were detected each day) from <0.2 (noise level ≥30%) to 0.7-0.8 (noise level 5%-15%). Conditional on a low (5%) noise level, model-based estimates of daily encounter probability were highest (>0.8) during peak breeding season when both female and male southern bent-winged bats congregate at the maternity cave. In this paper, we detail the methods employed and make methodological recommendations for future wildlife research using large antennas, including earthing systems as standard protocol and quantifying noise metrics as a covariate influencing the probability of detection in subsequent analyses. Our results demonstrate that large PIT antennas can be used successfully to detect small volant species, extending the scope of PIT technology and enabling a much broader range of wildlife species to be studied using this approach.

Effects of handling and short-term captivity: a multi-behaviour approach using red sea urchins, Mesocentrotus franciscanus

Understanding the effects of captivity-induced stress on wild-caught animals after their release back into the wild is critical for the long-term success of relocation and reintroduction programs. To date, most of the research on captivity stress has focused on vertebrates, with far less attention paid to invertebrates. Here, we examine the effect of short-term captivity (i.e., up to four days) on self-righting, aggregation, and predator-escape behaviours in wild-caught red sea urchins, Mesocentrotus franciscanus, after their release back into the wild. Aggregation behaviour, which has been linked to feeding in sea urchins, was not affected by handling or captivity. In contrast, the sea urchins that had been handled and released immediately, as well as those that were handled and held captive, took longer to right themselves and were poorer at fleeing from predators than wild, unhandled sea urchins. These results indicate that handling rather than captivity impaired these behaviours in the short term. The duration of captivity did not influence the sea urchin behaviours examined. Longer-term monitoring is needed to establish what the fitness consequences of these short-term behavioural changes might be. Our study nevertheless highlights the importance of considering a suite of responses when examining the effects of capture and captivity. Our findings, which are based on a locally abundant species, can inform translocation efforts aimed at bolstering populations of ecologically similar but depleted invertebrate species to retain or restore important ecosystem functions.

Noninvasive Featherlight Wearable Compliant "Marine Skin": Standalone Multisensory System for Deep-Sea Environmental Monitoring

Advances in marine research to understand environmental change and its effect on marine ecosystems rely on gathering data on species physiology, their habitat, and their mobility patterns using heavy and invasive biologgers and sensory telemetric networks. In the past, a lightweight (6 g) compliant environmental monitoring system: Marine Skin was demonstrated. In this paper, an enhanced version of that skin with improved functionalities (500-1500% enhanced sensitivity), packaging, and most importantly its endurance at a depth of 2 km in the highly saline Red Sea water for four consecutive weeks is reported. A unique noninvasive approach for attachment of the sensor by designing a wearable, stretchable jacket (bracelet) that can adhere to any species irrespective of their skin type is also illustrated. The wearable featherlight (<0.5 g in air, 3 g with jacket) gadget is deployed on Barramundi, Seabream, and common goldfish to demonstrate the noninvasive and effective attachment strategy on different species of variable sizes which does not hinder the animals' natural movement or behavior.

Why implantation of bio-loggers may improve our understanding of how animals cope within their natural environment

Bio-loggers are miniaturized autonomous devices that record quantitative data on the state of free-ranging animals (e.g. behavior, position and physiology) and their natural environment. This is especially relevant for species where direct visual observation is difficult or impossible. Today, ongoing technical development allows the monitoring of numerous parameters in an increasing range of species over extended periods. However, the external attachment of devices might affect various aspects of animal performance (energetics, thermoregulation, foraging as well as social and reproductive behavior), which ultimately affect fitness. External attachment might also increase entanglement risk and the conspicuousness of animals, leaving them more vulnerable to predation. By contrast, implantation of devices can mitigate many of these undesirable effects and might be preferable, especially for long-term studies, provided that the many challenges associated with surgical procedures can be mastered. Implantation may then allow us to gather data that would be impossible to obtain otherwise and thereby may provide new and ecologically relevant insights into the life of wild animals. Here, we: (i) discuss the pros and cons of attachment methods; (ii) highlight recent field studies that used implanted bio-loggers to address eco-physiological questions in a wide range of species; and (iii) discuss logger implantation in light of ethical considerations.

J, Mate BR. Fin whale movements in the Gulf of California, Mexico, from satellite telemetry

Fin whales (Balaenoptera physalus) have a global distribution, but the population inhabiting the Gulf of California (GoC) is thought to be geographically and genetically isolated. However, their distribution and movements are poorly known. The goal of this study was to describe fin whale movements for the first time from 11 Argos satellite tags deployed in the southwest GoC in March 2001. A Bayesian Switching State-Space Model was applied to obtain improved locations and to characterize movement behavior as either "area-restricted searching" (indicative of patch residence, ARS) or "transiting" (indicative of moving between patches). Model performance was assessed with convergence diagnostics and by examining the distribution of the deviance and the behavioral parameters from Markov Chain Monte Carlo models. ARS was the predominant mode behavior 83% of the time during both the cool (December-May) and warm seasons (June-November), with slower travel speeds (mean = 0.84 km/h) than during transiting mode (mean = 3.38 km/h). We suggest ARS mode indicates either foraging activities (year around) or reproductive activities during the winter (cool season). We tagged during the cool season, when the whales were located in the Loreto-La Paz Corridor in the southwestern GoC, close to the shoreline. As the season progressed, individuals moved northward to the Midriff Islands and the upper gulf for the warm season, much farther from shore. One tag lasted long enough to document a whale's return to Loreto the following cool season. One whale that was originally of undetermined sex, was tagged in the Bay of La Paz and was photographed 10 years later with a calf in the nearby San Jose Channel, suggesting seasonal site fidelity. The tagged whales moved along the western GoC to the upper gulf seasonally and did not transit to the eastern GoC south of the Midriff Islands. No tagged whales left the GoC, providing supporting evidence that these fin whales are a resident population.

Evaluating the efficacy of two insect detection methods with Riptortus pedestris (Hemiptera: Alydidae): portable harmonic radar system and fluorescent marking system

BACKGROUND

Although portable harmonic radar system and fluorescent marking system are two widely used detection methods, their comparative effectiveness has not been studied. Therefore, we first tested the applicability of fluorescent marking system on Riptortus pedestris (Hemiptera: Alydidae). Then, we evaluated the efficacy of the two methods used either alone or combined in a grass field and bean field, varying with complexity, during day and night.

RESULTS

Fluorescent marking did not affect the behavior or fitness of Riptortus pedestris except for vertical walking, while allowing the detection from >25 m when paired with a handheld laser. Generally, the portable harmonic radar system and both methods combined were more successful in sample detection, although the fluorescent marking system in the bean field at night was as competitive as the two. Combining both methods made sample retrieval easier at night than the portable harmonic radar system. Nevertheless, the total detection time showed a large variance across the methods.

CONCLUSION

The portable harmonic radar system can be an effective detection method in either landscape during both day and night. Furthermore, the fluorescent marking system can be a reliable tool at night as well. Lastly, combining both methods can improve the night detection. © 2018 Society of Chemical Industry.

"Feelings and Fitness" Not "Feelings or Fitness"-The Raison d'être of Conservation Welfare, Which Aligns Conservation and Animal Welfare Objectives

Increasingly, human activities, including those aimed at conserving species and ecosystems (conservation activities) influence not only the survival and fitness but also the welfare of wild animals. Animal welfare relates to how an animal is experiencing its life and encompasses both its physical and mental states. While conservation biology and animal welfare science are both multi-disciplinary fields that use scientific methods to address concerns about animals, their focus and objectives sometimes appear to conflict. However, activities impacting detrimentally on the welfare of individual animals also hamper achievement of some conservation goals, and societal acceptance is imperative to the continuation of conservation activities. Thus, the best outcomes for both disciplines will be achieved through collaboration and knowledge-sharing. Despite this recognition, cross-disciplinary information-sharing and collaborative research and practice in conservation are still rare, with the exception of the zoo context. This paper summarizes key points developed by a group of conservation and animal welfare scientists discussing scientific assessment of wild animal welfare and barriers to progress. The dominant theme emerging was the need for a common language to facilitate cross-disciplinary progress in understanding and safeguarding the welfare of animals of wild species. Current conceptions of welfare implicit in conservation science, based mainly on "fitness" (physical states), need to be aligned with contemporary animal welfare science concepts which emphasize the dynamic integration of "fitness" and "feelings" (mental experiences) to holistically understand animals' welfare states. The way in which animal welfare is characterized influences the way it is evaluated and the emphasis put on different features of welfare, as well as, the importance placed on the outcomes of such evaluations and how that information is used, for example in policy development and decision-making. Salient examples from the New Zealand and Australian context are presented to illustrate. To genuinely progress our understanding and evaluation of wild animal welfare and optimize the aims of both scientific disciplines, conservation and animal welfare scientists should work together to evolve and apply a common understanding of welfare. To facilitate this, we propose the formal development of a new discipline, Conservation Welfare, integrating the expertise of scientists from both fields.

Long-Term Safety of Intraperitoneal Radio Transmitter Implants in Brown Bears (Ursus arctos)

Intraperitoneal radio transmitters have been widely used in free-ranging wild mammals, but there are no long-term studies on their biocompatibility or technical stability within the abdominal cavity of animals. Possible negative health effects may bias results from ecological studies on instrumented animals and raise concerns over animal welfare issues. The aim of this study was to evaluate the long-term technical stability and pathological effects of Telonics intraperitoneal very high frequency (VHF) radio transmitters in brown bears (Ursus arctos). We instrumented 305 individual bears with intraperitoneal VHF radio transmitters during a 19-year period. We surgically removed devices that had been in bears for 1-9 years and collected transmitters from animals that died 1-13 years after implantation. We took biopsies for histopathology from tissue encapsulating implants in live bears. Retrieved transmitters underwent a technical inspection. Of the 125 transmitters removed from live bears, 66 were free-floating in the peritoneal cavity [a mean (SD) of 3.8 (1.5) years after implantation], whereas 59 were encapsulated in the greater omentum [4.0 (1.8) years after implantation]. Histopathology of biopsies of the 1-15 mm thick capsules in 33 individuals showed that it consisted of organized layers of connective tissue. In one third of the bears, the inner part of the capsule was characterized by a foreign body reaction. We inspected 68 implants that had been in bears for 3.9 (2.4) years. The batteries had short-circuited four (5.9%) of these devices. This resulted in the death of two animals 10 and 13 years after implantation. In two other bears that underwent surgery, we found the short-circuited devices to be fully encapsulated within the peritoneal cavity 5 and 6 years after implantation. A significant proportion of the other 64 inspected implants showed serious technical problems, such as corrosion of metal parts or the batteries (50%), detachment of the end cap (11.8%), and erosion (7.4%) or melting (5.9%) of the wax coating. We conclude that the wax coating of the transmitters was not biocompatible, that the technical quality of the devices was poor, and that these implants should not be used in brown bears.

Fine-scale movement responses of free-ranging harbour porpoises to capture, tagging and short-term noise pulses from a single airgun

Knowledge about the impact of anthropogenic disturbances on the behavioural responses of cetaceans is constrained by lack of data on fine-scale movements of individuals. We equipped five free-ranging harbour porpoises (Phocoena phocoena) with high-resolution location and dive loggers and exposed them to a single 10 inch3 underwater airgun producing high-intensity noise pulses (2-3 s intervals) for 1 min. All five porpoises responded to capture and tagging with longer, faster and more directed movements as well as with shorter, shallower, less wiggly dives immediately after release, with natural behaviour resumed in less than or equal to 24 h. When we exposed porpoises to airgun pulses at ranges of 420-690 m with noise level estimates of 135-147 dB re 1 µPa2s (sound exposure level), one individual displayed rapid and directed movements away from the exposure site and two individuals used shorter and shallower dives compared to natural behaviour immediately after exposure. Noise-induced movement typically lasted for less than or equal to 8 h with an additional 24 h recovery period until natural behaviour was resumed. The remaining individuals did not show any quantifiable responses to the noise exposure. Changes in natural behaviour following anthropogenic disturbances may reduce feeding opportunities, and evaluating potential population-level consequences should be a priority research area.

Difficulties identifying Australian sea lions (Neophoca cinerea) in the wild using whisker spot patterns

Individual identification is a beneficial tool in behavioural and ecological research. In mark–recapture studies, for example, it can improve abundance, residency and site fidelity estimates. Two non-invasive, photo-identification approaches, using whisker spot patterns, were tested to identify wild individual Australian sea lions (Neophoca cinerea). The Chamfer distance transform algorithm has shown promising results when applied to captive individuals. An alternative matching method using row/column locations of whisker spots, previously applied to lions (Panthera leo) was also tested. Resighting wild N. cinerea in this study proved unfeasible with both methods. Excessive variation between photographs of the same individual was found when applying the Chamfer distance transform, and similarity between photograph-pairs appeared to decrease with increasing time between photographs. Insufficient variation among N. cinerea row/column pattern was detected to successfully discriminate among individuals, averaging 39 mystacial spots (range 30–46, n = 20) in seven rows and 9–10 columns. Additionally, different observers marking the same photographs introduced considerable variation. Colour difference (red, green and blue colour levels) between the whisker spots and surrounding fur affected marking spot locations significantly, increasing uncertainty when contrast decreased. While other pattern-matching algorithms may improve performance, accurate identification of spot locations was the current limitation.

wisepair: a computer program for individual matching in genetic tracking studies

Individual-based data sets tracking organisms over space and time are fundamental to answering broad questions in ecology and evolution. A 'permanent' genetic tag circumvents a need to invasively mark or tag animals, especially if there are little phenotypic differences among individuals. However, genetic tracking of individuals does not come without its limits; correctly matching genotypes and error rates associated with laboratory work can make it difficult to parse out matched individuals. In addition, defining a sampling design that effectively matches individuals in the wild can be a challenge for researchers. Here, we combine the two objectives of defining sampling design and reducing genotyping error through an efficient Python-based computer-modelling program, wisepair. We describe the methods used to develop the computer program and assess its effectiveness through three empirical data sets, with and without reference genotypes. Our results show that wisepair outperformed similar genotype matching programs using previously published from reference genotype data of diurnal poison frogs (Allobates femoralis) and without-reference (faecal) genotype sample data sets of harbour seals (Phoca vitulina) and Eurasian otters (Lutra lutra). In addition, due to limited sampling effort in the harbour seal data, we present optimal sampling designs for future projects. wisepair allows for minimal sacrifice in the available methods as it incorporates sample rerun error data, allelic pairwise comparisons and probabilistic simulations to determine matching thresholds. Our program is the lone tool available to researchers to define parameters a priori for genetic tracking studies.

Diving physiology of seabirds and marine mammals: Relevance, challenges and some solutions for field studies

To fully understand how diving seabirds and marine mammals balance the potentially conflicting demands of holding their breath while living their lives underwater (and maintaining physiological homeostasis during exercise, feeding, growth, and reproduction), physiological studies must be conducted with animals in their natural environments. The purpose of this article is to review the importance of making physiological measurements on diving animals in field settings, while acknowledging the challenges and highlighting some solutions. The most extreme divers are great candidates for study, especially in a comparative and mechanistic context. However, physiological data are also required of a wide range of species for problems relating to other disciplines, in particular ecology and conservation biology. Physiological data help with understanding and predicting the outcomes of environmental change, and the direct impacts of anthropogenic activities. Methodological approaches that have facilitated the development of field-based diving physiology include the isolated diving hole protocol and the translocation paradigm, and while there are many techniques for remote observation, animal-borne biotelemetry, or "biologging", has been critical. We discuss issues related to the attachment of instruments, the retrieval of data and sensing of physiological variables, while also considering negative impacts of tagging. This is illustrated with examples from a variety of species, and an in-depth look at one of the best studied and most extreme divers, the emperor penguin (Aptenodytes forsteri). With a variety of approaches and high demand for data on the physiology of diving seabirds and marine mammals, the future of field studies is bright.

Integrating animal welfare into wild herbivore management: lessons from the Australian Feral Camel Management Project

The Australian Feral Camel Management Project (AFCMP) was initiated in 2009 to manage the growing impacts of feral camels (Camelus dromedarius) in Australia. One of the most important considerations for the project was achieving high standards of animal welfare and demonstrating this to stakeholders and the public. The novelty of feral camels as an invasive species meant that relatively little was known about the animal welfare aspects of the available management techniques. To address this knowledge gap, quantitative animal-based assessment tools were developed to allow independent observers to perform repeatable in situ field auditing of the two main control methods used: aerial (helicopter) shooting and live capture (mustering and transport for slaughter). Although observation protocols allowed most stages of aerial shooting (in situ killing) to be assessed, not all stages of live capture operations could be assessed (namely transport and slaughter at ex situ abattoirs) due to the limitations of the jurisdiction of the Australian Feral Camel Management Project. For assessments that were performed, audit results were made available to project partners to allow procedures to be reviewed and published through peer-reviewed literature to improve transparency. Empirical evidence produced through the audit system was also used to refine humaneness ranking assessments comparing management methods. We present the lessons learnt through the animal welfare approach of the AFCMP to assist future wild herbivore management programs.

An animal welfare assessment framework for helicopter darting: a case study with a newly developed method for feral horses

Context Helicopter darting (chemical immobilisation) is a very useful technique for large wild herbivores, such as feral horses (Equus caballus). There is currently no reliable framework to report on the animal welfare impacts of helicopter darting methods. Aim The aim of this study was to develop an animal welfare assessment framework for helicopter darting methods, using quantifiable parameters, and to test it with a case study using a newly developed feral horse capture technique. Methods Quantifiable animal welfare parameters were recorded for 11 feral horses captured using a traditional helicopter darting method in north-western Australia in October 2014. Welfare parameters chosen focused on quantifying the duration of procedures and the frequency of adverse events. They included chase time (CT; min) before darting, induction time (IT; min) between darting and recumbency, recumbency time (RT; min), total time (TT; CT+IT+RT; min), repeat-darting rate (animals requiring >1 dart; %), target zone accuracy rate (darts striking the intended anatomical area; %) and mortality rate (at time of capture and 14 days post-capture; %). Results Median CT was 2 min, median IT was 19 min, median RT was 16 min and median TT was 38 min. Repeat-darting rate was 45%, target zone accuracy rate was 53% and mortality rates (time of capture and 14 days post-capture) were zero. Conclusions Animal welfare parameters can be quantified for helicopter darting through estimation of the duration of procedures and the frequency of adverse events. Use of this framework will allow the identification of parameters requiring refinement for newly developed helicopter darting techniques. Implications Animal welfare parameters are particularly important for helicopter-based darting methods. Pilot studies, using quantified parameters, should be performed for newly developed capture techniques before they are approved for large-scale programs.

Navigating uncertain waters: a critical review of inferring foraging behaviour from location and dive data in pinnipeds

In the last thirty years, the emergence and progression of biologging technology has led to great advances in marine predator ecology. Large databases of location and dive observations from biologging devices have been compiled for an increasing number of diving predator species (such as pinnipeds, sea turtles, seabirds and cetaceans), enabling complex questions about animal activity budgets and habitat use to be addressed. Central to answering these questions is our ability to correctly identify and quantify the frequency of essential behaviours, such as foraging. Despite technological advances that have increased the quality and resolution of location and dive data, accurately interpreting behaviour from such data remains a challenge, and analytical methods are only beginning to unlock the full potential of existing datasets. This review evaluates both traditional and emerging methods and presents a starting platform of options for future studies of marine predator foraging ecology, particularly from location and two-dimensional (time-depth) dive data. We outline the different devices and data types available, discuss the limitations and advantages of commonly-used analytical techniques, and highlight key areas for future research. We focus our review on pinnipeds - one of the most studied taxa of marine predators - but offer insights that will be applicable to other air-breathing marine predator tracking studies. We highlight that traditionally-used methods for inferring foraging from location and dive data, such as first-passage time and dive shape analysis, have important caveats and limitations depending on the nature of the data and the research question. We suggest that more holistic statistical techniques, such as state-space models, which can synthesise multiple track, dive and environmental metrics whilst simultaneously accounting for measurement error, offer more robust alternatives. Finally, we identify a need for more research to elucidate the role of physical oceanography, device effects, study animal selection, and developmental stages in predator behaviour and data interpretation.

Effect of a cooling gel on pain sensitivity and healing of hot-iron cattle brands

Hot-iron branding is painful for cattle, but little is known about how long this pain lasts or effective alleviation methods. Previous work with pigs indicated that cooling burns with a gel (active ingredient: tea tree oil) improved healing compared to untreated wounds. Steers (210±21 kg) were hot-iron branded and allocated to 1 of 3 treatments: control (n=24), 1 gel application immediately after branding (1X; n=12), or 2 gel applications, 1 immediately after branding and one 1 d later (2X; n=12). Pain sensitivity was assessed by applying a known and increasing force with a von Frey anesthesiometer in 5 locations (in the center, at the top of, and 5 and 10 cm above the brand and on the equivalent location on the nonbranded side of the body) until animals showed a behavioral response. Healing was measured with a 6-point scale (1=fresh brand and 6=no scabbing and fully repigmented). Both measures, along with weight gain and surface temperature of the wound, were recorded before and 1, 2, 3, 7, 14, 21, 28, 35, 56, and 70 d after branding. The gel cooled the brand, with the most obvious differences on the day it was applied (3.7 to 4.2°C cooler than control; day×gel interaction, P=0.004). All wounds were at least partially repigmented by 70 d, but only 46% of brands were fully healed at this time. The healing process was slowed when a gel was applied twice (e.g., at 21 d, healing score of 2.5±0.1 and 2.7±0.1 vs. 2.0±0.2 for control and 1X vs. 2X, respectively; P=0.001). Brands tended to remain painful throughout the 70 d (in the center of the brand; before vs. d 1-35, P≤0.001; d 56, P=0.058; and d 70, P=0.092). Overall, gel had little effect on pain sensitivity. Weight gain was reduced on d 1 after branding compared to all other time points (P<0.001) but was not affected by gel application (P=0.277). In conclusion, applying gel did not improve outcomes after branding. In addition, by 70 d after the procedure, hot-iron brands still tended to be more painful than nonbranded tissue and 54% were not fully healed. These results raise additional animal welfare concerns about hot-iron branding.

Is Wildlife Fertility Control Always Humane?

Investigation of fertility control techniques to reduce reproductive rates in wildlife populations has been the source of much research. Techniques targeting wildlife fertility have been diverse. Most research into fertility control methods has focused upon efficacy, with few studies rigorously assessing animal welfare beyond opportunistic anecdote. However, fertility control techniques represent several very different mechanisms of action (modalities), each with their own different animal welfare risks. We provide a review of the mechanisms of action for fertility control methods, and consider the role of manipulation of reproductive hormones ("endocrine suppression") for the long-term ability of animals to behave normally. We consider the potential welfare costs of animal manipulation techniques that are required to administer fertility treatments, including capture, restraint, surgery and drug delivery, and the requirement for repeated administration within the lifetime of an animal. We challenge the assumption that fertility control modalities generate similar and desirable animal welfare outcomes, and we argue that knowledge of reproductive physiology and behaviour should be more adeptly applied to wild animal management decisions. We encourage wildlife managers to carefully assess long-term behavioural risks, associated animal handling techniques, and the importance of positive welfare states when selecting fertility control methods as a means of population control.

Whisker spot patterns: a noninvasive method of individual identification of Australian sea lions (Neophoca cinerea)

Reliable methods for identification of individual animals are advantageous for ecological studies of population demographics and movement patterns. Photographic identification, based on distinguishable patterns, unique shapes, or scars, is an effective technique already used for many species. We tested whether photographs of whisker spot patterns could be used to discriminate among individual Australian sea lion (Neophoca cinerea). Based on images of 53 sea lions, we simulated 5,000 patterns before calculating the probability of duplication in a study population. A total of 99% (± 1.5 SD) of patterns were considered reliable for a population of 50, 98% (± 1.7 SD) for 100, 92% (± 4.7 SD) for 500, and 88% (± 5.7 SD) for 1,000. We tested a semiautomatic approach by matching 16 known individuals at 3 different angles (70°, 90°, and 110°), 2 distances (1 and 2 m), and 6 separate times over a 1-year period. A point-pattern matching algorithm for pairwise comparisons produced 90% correct matches of photographs taken on the same day at 90°. Images of individuals at 1 and 2 m resulted in 89% correct matches, those photographed at different angles and different times (at 90°) resulted in 48% and 73% correct matches, respectively. Our results show that the Chamfer distance transform can effectively be used for individual identification, but only if there is very little variation in photograph angle. This point-pattern recognition application may also work for other otariid species.

Spatial and temporal occurrence of blue whales off the U.S. West Coast, with implications for management

Mortality and injuries caused by ship strikes in U.S. waters are a cause of concern for the endangered population of blue whales (Balaenoptera musculus) occupying the eastern North Pacific. We sought to determine which areas along the U.S. West Coast are most important to blue whales and whether those areas change inter-annually. Argos-monitored satellite tags were attached to 171 blue whales off California during summer/early fall from 1993 to 2008. We analyzed portions of the tracks that occurred within U.S. Exclusive Economic Zone waters and defined the 'home range' (HR) and 'core areas' (CAU) as the 90% and 50% fixed kernel density distributions, respectively, for each whale. We used the number of overlapping individual HRs and CAUs to identify areas of highest use. Individual HR and CAU sizes varied dramatically, but without significant inter-annual variation despite covering years with El Niño and La Niña conditions. Observed within-year differences in HR size may represent different foraging strategies for individuals. The main areas of HR and CAU overlap among whales were near highly productive, strong upwelling centers that were crossed by commercial shipping lanes. Tagged whales generally departed U.S. Exclusive Economic Zone waters from mid-October to mid-November, with high variability among individuals. One 504-d track allowed HR and CAU comparisons for the same individual across two years, showing similar seasonal timing, and strong site fidelity. Our analysis showed how satellite-tagged blue whales seasonally used waters off the U.S. West Coast, including high-risk areas. We suggest possible modifications to existing shipping lanes to reduce the likelihood of collisions with vessels.

Effects of capturing and collaring on polar bears: findings from long-term research on the southern Beaufort Sea population

Context The potential for research methods to affect wildlife is an increasing concern among both scientists and the public. This topic has a particular urgency for polar bears because additional research is needed to monitor and understand population responses to rapid loss of sea ice habitat. Aims This study used data collected from polar bears sampled in the Alaska portion of the southern Beaufort Sea to investigate the potential for capture to adversely affect behaviour and vital rates. We evaluated the extent to which capture, collaring and handling may influence activity and movement days to weeks post-capture, and body mass, body condition, reproduction and survival over 6 months or more. Methods We compared post-capture activity and movement rates, and relationships between prior capture history and body mass, body condition and reproductive success. We also summarised data on capture-related mortality. Key results Individual-based estimates of activity and movement rates reached near-normal levels within 2–3 days and fully normal levels within 5 days post-capture. Models of activity and movement rates among all bears had poor fit, but suggested potential for prolonged, lower-level rate reductions. Repeated captures was not related to negative effects on body condition, reproduction or cub growth or survival. Capture-related mortality was substantially reduced after 1986, when immobilisation drugs were changed, with only 3 mortalities in 2517 captures from 1987–2013. Conclusions Polar bears in the southern Beaufort Sea exhibited the greatest reductions in activity and movement rates 3.5 days post-capture. These shorter-term, post-capture effects do not appear to have translated into any long-term effects on body condition, reproduction, or cub survival. Additionally, collaring had no effect on polar bear recovery rates, body condition, reproduction or cub survival. Implications This study provides empirical evidence that current capture-based research methods do not have long-term implications, and are not contributing to observed changes in body condition, reproduction or survival in the southern Beaufort Sea. Continued refinement of capture protocols, such as the use of low-impact dart rifles and reversible drug combinations, might improve polar bear response to capture and abate short-term reductions in activity and movement post-capture.

Weighed down by science: do collar-mounted devices affect domestic cat behaviour and movement?

Context Animals carrying tracking and logging devices are subject to a range of instrument effects that negatively affect survival, reproduction and behaviour. The common recommendation is that device weight should not exceed 5% body mass (BM) for terrestrial species; however, this rule-of-thumb has little empirical basis. Modelling indicates that devices weighing less than 3% BM may still have impacts. Several studies have used telemetry and data loggers on domestic cats (Felis catus) with instruments ranging in weight from 30 g to 125 g, but there has been no quantitative evaluation of instrument effects. In addition, inexpensive GPS tags such as iGotU are increasingly being used to track domestic cats, but often with little acknowledgement of habitat-related location error. Aims We evaluated the impact of wearing devices of different weights on domestic cat movements, and quantified location error across typical suburban habitats. Methods We recorded movements of cats wearing three different GPS collar weights for a week at a time: light, 30 g (<1% BM); medium, 80 g (~2% BM); and heavy, 130 g (~3% BM). Location error (LE) and fix success rates (FSR) were compared between backyard habitats and up- or downward orientation of the GPS tags on collars. Key results Home-range size and distance travelled from home were smaller when cats wore the heaviest collar. LE was lower and FSR higher for GPS tags with direct-line-of-sight to satellites (e.g. on lawns), but there was no difference between tags placed in dense vegetation (hedges) or more open vegetation (trees), or tags oriented up or down. Conclusions Collars carrying instruments on cats should be no more than 2% BM (medium-weight collar). LE was large relative to typical urban habitat size, indicating that misclassification of locations into habitats could easily occur in habitat-selection studies. Implications Some published accounts of cat home-range sizes may be underestimates, resulting in underestimates of the extent of impacts on prey species. Habitat-use studies should acknowledge the error associated with GPS tags and incorporate it into analyses using techniques such as Brownian Bridges.

Effect of monitoring technique on quality of conservation science

Monitoring free-ranging animals in their natural habitat is a keystone of ecosystem conservation and increasingly important in the context of current rates of loss of biological diversity. Data collected from individuals of endangered species inform conservation policies. Conservation professionals assume that these data are reliable-that the animals from whom data are collected are representative of the species in their physiology, ecology, and behavior and of the populations from which they are drawn. In the last few decades, there has been an enthusiastic adoption of invasive techniques for gathering ecological and conservation data. Although these can provide impressive quantities of data, and apparent insights into animal ranges and distributions, there is increasing evidence that these techniques can result in animal welfare problems, through the wide-ranging physiological effects of acute and chronic stress and through direct or indirect injuries or compromised movement. Much less commonly, however, do conservation scientists consider the issue of how these effects may alter the behavior of individuals to the extent that the data they collect could be unreliable. The emerging literature on the immediate and longer-term effects of capture and handling indicate it can no longer be assumed that a wild animal's survival of the process implies the safety of the procedure, that the procedure is ethical, or the scientific validity of the resulting data. I argue that conservation professionals should routinely assess study populations for negative effects of their monitoring techniques and adopt noninvasive approaches for best outcomes not only for the animals, but also for conservation science.