pamlr: A toolbox for analysing animal behaviour using pressure, acceleration, temperature, magnetic or light data in R.

Light-level geolocators have revolutionised the study of animal behaviour. However, lacking spatial precision, their usage has been primary targeted towards the analysis of large-scale movements. Recent technological developments have allowed the integration of magnetometers and accelerometers into geolocator tags in addition to barometers and thermometers, offering new behavioural insights. Here, we introduce an R toolbox for identifying behavioural patterns from multisensor geolocator tags, with functions specifically designed for data visualisation, calibration, classification and error estimation. More specifically, the package allows for the flexible analysis of any combination of sensor data using k-means clustering, expectation maximisation binary clustering, hidden Markov models and changepoint analyses. Furthermore, the package integrates tailored algorithms for identifying periods of prolonged high activity (most commonly used for identifying migratory flapping flight), and pressure changes (most commonly used for identifying dive or flight events). Finally, we highlight some of the limitations, implications and opportunities of using these methods.

Les géolocalisateurs lumineux ont révolutionné l'étude du comportement animal. Toutefois, en raison de leur manque de précision spatiale, leur utilisation a été principalement dirigée vers l'analyse de mouvements à grandes échelles. Les développements technologiques récents ont permis l'intégration de magnétomètres et d'accéléromètres dans les balises de géolocalisation, en plus de baromètres et de thermomètres, permettant de nouvelles analyses du comportement animalier. Nous présentons ici notre R package pour l'identification de modèles comportementaux à partir de balises géolocalisatrices multisensoriels. Le package intègre des fonctions conçues spécifiquement pour la visualisation de données, la calibration des balises, la classification du comportement et l'estimation des erreurs d'analyses. Plus précisément, le package permet l'analyse flexible de n'importe quelle combinaison de capteurs de données en utilisant le k-means clustering, le expectation maximisation binary clustering, les hidden Markov models et les analyses changepoint. En outre, le package intègre des algorithmes adaptés pour identifier les périodes de haute activité prolongée (le plus souvent utilisé pour identifier le vol migratoire d'oiseaux), et les changements de pression (le plus souvent utilisé pour identifier des periodes où l'animal est en plongée ou au vol). Enfin, nous soulignons les limites, les implications et les opportunités d'utilisation de ces méthodes.

Ecological Influences and Morphological Correlates of Resting and Maximal Metabolic Rates across Teleost Fish Species.

Rates of aerobic metabolism vary considerably across evolutionary lineages, but little is known about the proximate and ultimate factors that generate and maintain this variability. Using data for 131 teleost fish species, we performed a large-scale phylogenetic comparative analysis of how interspecific variation in resting metabolic rates (RMRs) and maximum metabolic rates (MMRs) is related to several ecological and morphological variables. Mass- and temperature-adjusted RMR and MMR are highly correlated along a continuum spanning a 30- to 40-fold range. Phylogenetic generalized least squares models suggest that RMR and MMR are higher in pelagic species and that species with higher trophic levels exhibit elevated MMR. This variation is mirrored at various levels of structural organization: gill surface area, muscle protein content, and caudal fin aspect ratio (a proxy for activity) are positively related with aerobic capacity. Muscle protein content and caudal fin aspect ratio are also positively correlated with RMR. Hypoxia-tolerant lineages fall at the lower end of the metabolic continuum. Different ecological lifestyles are associated with contrasting levels of aerobic capacity, possibly reflecting the interplay between selection for increased locomotor performance on one hand and tolerance to low resource availability, particularly oxygen, on the other. These results support the aerobic capacity model of the evolution of endothermy, suggesting elevated body temperatures evolved as correlated responses to selection for high activity levels.

Fat King Penguins Are Less Steady on Their Feet.

Returning to the shore after a feeding sojourn at sea, king penguins often undertake a relatively long terrestrial journey to the breeding colony carrying a heavy, mostly frontal, accumulation of fat along with food in the stomach for chick-provisioning. There they must survive a fasting period of up to a month in duration, during which their complete reliance on endogenous energy stores results in a dramatic loss in body mass. Our aim was to determine if the king penguin's walking gait changes with variations in body mass. We investigated this by walking king penguins on a treadmill while instrumented with an acceleration data logger. The stride frequency, dynamic body acceleration (DBA) and posture of fat (pre-fasting; 13.2 kg) and slim (post fasting; 11 kg) king penguins were assessed while they walked at the same speed (1.4 km/h) on a treadmill. Paired statistical tests indicated no evidence for a difference in dynamic body acceleration or stride frequency between the two body masses however there was substantially less variability in both leaning angle and the leaning amplitude of the body when the birds were slimmer. Furthermore, there was some evidence that the slimmer birds exhibited a decrease in waddling amplitude. We suggest the increase in variability of both leaning angle and amplitude, as well as a possibly greater variability in the waddling amplitude, is likely to result from the frontal fat accumulation when the birds are heavier, which may move the centre of mass anteriorly, resulting in a less stable upright posture. This study is the first to use accelerometry to better understand the gait of a species within a specific ecological context: the considerable body mass change exhibited by king penguins.

Effect of walking speed on the gait of king penguins: An accelerometric approach.

Little is known about non-human bipedal gaits. This is probably due to the fact that most large animals are quadrupedal and that non-human bipedal animals are mostly birds, whose primary form of locomotion is flight. Very little research has been conducted on penguin pedestrian locomotion with the focus instead on their associated high energy expenditure. In animals, tri-axial accelerometers are frequently used to estimate physiological energy cost, as well as to define the behaviour pattern of a species, or the kinematics of swimming. In this study, we showed how an accelerometer-based technique could be used to determine the biomechanical characteristics of pedestrian locomotion. Eight king penguins, which represent the only family of birds to have an upright bipedal gait, were trained to walk on a treadmill. The trunk tri-axial accelerations were recorded while the bird was walking at four different speeds (1.0, 1.2, 1.4 and 1.6km/h), enabling the amplitude of dynamic body acceleration along the three axes (amplitude of DBAx, DBAy and DBAz), stride frequency, waddling and leaning amplitude, as well as the leaning angle to be defined. The magnitude of the measured variables showed a significant increase with increasing speed, apart from the backwards angle of lean, which decreased with increasing speed. The variability of the measured variables also showed a significant increase with speed apart from the DBAz amplitude, the waddling amplitude, and the leaning angle, where no significant effect of the walking speed was found. This paper is the first approach to describe 3D biomechanics with an accelerometer on wild animals, demonstrating the potential of this technique.

Reassessment of the cardio-respiratory stress response, using the king penguin as a model.

Research in to short-term cardio-respiratory changes in animals in reaction to a psychological stressor typically describes increases in rate of oxygen consumption (V̇(O2)) and heart rate. Consequently, the broad consensus is that they represent a fundamental stressor response generalizable across adult species. However, movement levels can also change in the presence of a stressor, yet studies have not accounted for this possible confound on heart rate. Thus the direct effects of psychological stressors on the cardio-respiratory system are not resolved. We used an innovative experimental design employing accelerometers attached to king penguins (Aptenodytes patagonicus) to measure and thus account for movement levels in a sedentary yet free-to-move animal model during a repeated measures stress experiment. As with previous studies on other species, incubating king penguins (N = 6) exhibited significant increases in both V̇(O2) and heart rate when exposed to the stressor. However, movement levels, while still low, also increased in response to the stressor. Once this was accounted for by comparing periods of time during the control and stress conditions when movement levels were similar as recorded by the accelerometers, only V̇(O2) significantly increased; there was no change in heart rate. These findings offer evidence that changing movement levels have an important effect on the measured stress response and that the cardio-respiratory response per se to a psychological stressor (i.e. the response as a result of physiological changes directly attributable to the stressor) is an increase in V̇(O2) without an increase in heart rate.

Pairs of cooperating cleaner fish provide better service quality than singletons.

Service providers may vary service quality depending on whether they work alone or provide the service simultaneously with a partner. The latter case resembles a prisoner's dilemma, in which one provider may try to reap the benefits of the interaction without providing the service. Here we present a game-theory model based on the marginal value theorem, which predicts that as long as the client determines the duration, and the providers cooperate towards mutual gain, service quality will increase in the pair situation. This prediction is consistent with field observations and with an experiment on cleaning mutualism, in which stable male-female pairs of the cleaner wrasse Labroides dimidiatus repeatedly inspect client fish jointly. Cleaners cooperate by eating ectoparasites off clients but actually prefer to cheat and eat client mucus. Because clients often leave in response to such cheating, the benefits of cheating can be gained by only one cleaner during a pair inspection. In both data sets, the increased service quality during pair inspection was mainly due to the smaller females behaving significantly more cooperatively than their larger male partners. In contrast, during solitary inspections, cleaning behaviour was very similar between the sexes. Our study highlights the importance of incorporating interactions between service providers to make more quantitative predictions about cooperation between species.