A protocol and calibration method for accurate multi-camera field videography

Protocol to record and analyze primate leaping in three-dimensional in the wild

Several studies comparing primate locomotion under lab versus field conditions have shown the importance of implementing both types of studies, as each has their advantages and disadvantages. However, three-dimensional (3D) motion capture of primates has been challenging under natural conditions. In this study, we provide a detailed protocol on how to collect 3D biomechanical data on primate leaping in their natural habitat that can be widely implemented. To record primate locomotion in the dense forest we use modified GoPro Hero Black cameras with zoom lenses that can easily be carried around and set up on tripods. We outline details on how to obtain camera calibrations at greater heights and how to process the collected data using the MATLAB camera calibration app and the motion tracking software DLTdv8a. We further developed a new MATLAB application "WildLeap3D" to generate biomechanical performance metrics from the derived x, y, z coordinates of the leaps. We provide details on how to collect data on support diameter, compliance, and orientation, and combine these with the jumps to study locomotor performance in an ecological context. We successfully reconstructed leaps of wild primates in the 3D space under natural conditions and provided data on four representative leaps. We provide exemplar data on primate velocity and acceleration during a leap and show how our protocol can be used to analyze segmental kinematics. This study will help to make motion capture of freely moving animals more accessible and help further our knowledge about animal locomotion and movement.

Wall-climbing performance of gecko-inspired robot with soft feet and digits enhanced by gravity compensation

Gravitational forces can induce deviations in body posture from desired configurations in multi-legged arboreal robot locomotion with low leg stiffness, affecting the contact angle between the swing leg's end-effector and the climbing surface during the gait cycle. The relationship between desired and actual foot positions is investigated here in a leg-stiffness-enhanced model under external forces, focusing on the challenge of unreliable end-effector attachment on climbing surfaces in such robots. Inspired by the difference in ceiling attachment postures of dead and living geckos, feedforward compensation of the stance phase legs is the key to solving this problem. A feedforward gravity compensation (FGC) strategy, complemented by leg coordination, is proposed to correct gravity-influenced body posture and improve adhesion stability by reducing body inclination. The efficacy of this strategy is validated using a quadrupedal climbing robot, EF-I, as the experimental platform. Experimental validation on an inverted surface (ceiling walking) highlights the benefits of the FGC strategy, demonstrating its role in enhancing stability and ensuring reliable end-effector attachment without external assistance. In the experiment, robots without FGC only completed 3 out of 10 trials, while robots with FGC achieved a 100% success rate in the same trials. The speed was substantially greater with FGC, achieving 9.2 mm s-1in the trot gait. This underscores the proposed potential of the FGC strategy in overcoming the challenges associated with inconsistent end-effector attachment in robots with low leg stiffness, thereby facilitating stable locomotion even at an inverted body attitude.

Flight behaviour diverges more between seasonal forms than between species in Pieris butterflies

In flying animals, wing morphology is typically assumed to influence flight behaviours. Whether seasonal polymorphism in butterfly morphology is linked to adaptive flight behaviour remains unresolved. Here, we compare the flight behaviours and wing morphologies of the spring and summer forms of two closely related butterfly species, Pieris napi and P. rapae. We first quantify three-dimensional flight behaviour by reconstructing individual flight trajectories using stereoscopic high-speed videography in an experimental outdoor cage. We then measure wing size and shape, which are characteristics assumed to influence flight behaviours in butterflies. We show that seasonal, but not interspecific, differences in flight behaviour might be associated with divergent forewing shapes. During spring, Pieris individuals are small and have elongated forewings, and generally fly at low speed and acceleration, while having a high flight curvature. On the contrary, summer individuals are larger and exhibit rounded forewings. They fly at high speed and acceleration, while having high turning acceleration and advance ratio. Our study provides one of the first quantitative pieces of evidence of different flight behaviours between seasonal forms of two Pieris butterfly species. We discuss the possibility that this co-divergence in flight behaviour and morphology is an adaptation to distinct seasonal environments. Properly identifying the mechanisms underpinning such divergence, nonetheless, requires further investigations to disentangle the interacting effects of microhabitats, predator community, parasitoid pressure and behavioural differences between sexes.

Application of a novel deep learning-based 3D videography workflow to bat flight

Studying the detailed biomechanics of flying animals requires accurate three-dimensional coordinates for key anatomical landmarks. Traditionally, this relies on manually digitizing animal videos, a labor-intensive task that scales poorly with increasing framerates and numbers of cameras. Here, we present a workflow that combines deep learning-powered automatic digitization with filtering and correction of mislabeled points using quality metrics from deep learning and 3D reconstruction. We tested our workflow using a particularly challenging scenario: bat flight. First, we documented four bats flying steadily in a 2 m3 wind tunnel test section. Wing kinematic parameters resulting from manually digitizing bats with markers applied to anatomical landmarks were not significantly different from those resulting from applying our workflow to the same bats without markers for five out of six parameters. Second, we compared coordinates from manual digitization against those yielded via our workflow for bats flying freely in a 344 m3 enclosure. Average distance between coordinates from our workflow and those from manual digitization was less than a millimeter larger than the average human-to-human coordinate distance. The improved efficiency of our workflow has the potential to increase the scalability of studies on animal flight biomechanics.

The role of vision and lateral line sensing for schooling in giant danios (Devario aequipinnatus)

Schooling is a collective behavior that relies on a fish's ability to sense and respond to the other fish around it. Previous work has identified 'rules' of schooling - attraction to neighbors that are far away, repulsion from neighbors that are too close and alignment with neighbors at the correct distance - but we do not understand well how these rules emerge from the sensory physiology and behavior of individual fish. In particular, fish use both vision and their lateral lines to sense each other, but it is unclear how much they rely on information from these sensory modalities to coordinate schooling behavior. To address this question, we studied how the schooling of giant danios (Devario aequipinnatus) changes when they are unable to see or use their lateral lines. We found that giant danios were able to school without their lateral lines but did not school in darkness. Surprisingly, giant danios in darkness had the same attraction properties as fish in light when they were in close proximity, indicating that they could sense nearby fish with their lateral lines. However, they were not attracted to more distant fish, suggesting that long-distance attraction through vision is important for maintaining a cohesive school. These results help us expand our understanding of the roles that vision and the lateral line play in the schooling of some fish species.

The spatiotemporal richness of hummingbird wing deformations

Animals exhibit an abundant diversity of forms, and this diversity is even more evident when considering animals that can change shape on demand. The evolution of flexibility contributes to aspects of performance from propulsive efficiency to environmental navigation. It is, however, challenging to quantify and compare body parts that, by their nature, dynamically vary in shape over many time scales. Commonly, body configurations are tracked by labelled markers and quantified parametrically through conventional measures of size and shape (descriptor approach) or non-parametrically through data-driven analyses that broadly capture spatiotemporal deformation patterns (shape variable approach). We developed a weightless marker tracking technique and combined these analytic approaches to study wing morphological flexibility in hoverfeeding Anna's hummingbirds (Calypte anna). Four shape variables explained >95% of typical stroke cycle wing shape variation and were broadly correlated with specific conventional descriptors such as wing twist and area. Moreover, shape variables decomposed wing deformations into pairs of in-plane and out-of-plane components at integer multiples of the stroke frequency. This property allowed us to identify spatiotemporal deformation profiles characteristic of hoverfeeding with experimentally imposed kinematic constraints, including through shape variables explaining <10% of typical shape variation. Hoverfeeding in front of a visual barrier restricted stroke amplitude and elicited increased stroke frequencies together with in-plane and out-of-plane deformations throughout the stroke cycle. Lifting submaximal loads increased stroke amplitudes at similar stroke frequencies together with prominent in-plane deformations during the upstroke and pronation. Our study highlights how spatially and temporally distinct changes in wing shape can contribute to agile fluidic locomotion.

Aerodynamic response of a red-tailed hawk to discrete transverse gusts

A limiting factor in the design of smaller size uncrewed aerial vehicles is their inability to navigate through gust-laden environments. As a result, engineers have turned towards bio-inspired engineering approaches for gust mitigation techniques. In this study, the aerodynamics of a red-tailed hawk's response to variable-magnitude discrete transverse gusts was investigated. The hawk was flown in an indoor flight arena instrumented by multiple high-speed cameras to quantify the 3D motion of the bird as it navigated through the gust. The hawk maintained its flapping motion across the gust in all runs; however, it encountered the gust at different points in the flapping pattern depending on the run and gust magnitude. The hawk responded with a downwards pitching motion of the wing, decreasing the wing pitch angle to between -20∘and -5∘, and remained in this configuration until gust exit. The wing pitch data was then applied to a lower-order aerodynamic model that estimated lift coefficients across the wing. In gusts slower than the forward flight velocity (low gust ratio), the lift coefficient increases at a low-rate, to a maximum of around 2-2.5. In gusts faster than the forward flight velocity (high gust ratio), the lift coefficient initially increased rapidly, before increasing at a low-rate to a value around 4-5. In both regimes, the hawk's observed height change due to gust interaction was similar (and small), despite larger estimated lift coefficients over the high gust regime. This suggests another mitigation factor apart from the wing response is present. One potential factor is the tail pitching response observed here, which prior work has shown serves to mitigate pitch disturbances from gusts.

Three-dimensional kinematics of leaf-cutter ant mandibles: not all dicondylic joints are simple hinges

Insects use their mandibles for a variety of tasks, including food processing, material transport, nest building, brood care, and fighting. Despite this functional diversity, mandible motion is typically thought to be constrained to rotation about a single fixed axis. Here, we conduct a direct quantitative test of this 'hinge joint hypothesis' in a species that uses its mandibles for a wide range of tasks: Atta vollenweideri leaf-cutter ants. Mandible movements from live restrained ants were reconstructed in three dimensions using a multi-camera rig. Rigid body kinematic analyses revealed strong evidence that mandible movement occupies a kinematic space that requires more than one rotational degree of freedom: at large opening angles, mandible motion is dominated by yaw. But at small opening angles, mandibles both yaw and pitch. The combination of yaw and pitch allows mandibles to 'criss-cross': either mandible can be on top when mandibles are closed. We observed criss-crossing in freely cutting ants, suggesting that it is functionally important. Combined with recent reports on the diversity of joint articulations in other insects, our results show that insect mandible kinematics are more diverse than traditionally assumed, and thus worthy of further detailed investigation. This article is part of the theme issue 'Food processing and nutritional assimilation in animals'.

A hull reconstruction-reprojection method for pose estimation of free-flying fruit flies

Understanding the mechanisms of insect flight requires high-quality data of free-flight kinematics, e.g. for comparative studies or genetic screens. Although recent improvements in high-speed videography allow us to acquire large amounts of free-flight data, a significant bottleneck is automatically extracting accurate body and wing kinematics. Here, we present an experimental system and a hull reconstruction-reprojection algorithm for measuring the flight kinematics of fruit flies. The experimental system can automatically record hundreds of flight events per day. Our algorithm resolves a significant portion of the occlusions in this system by a reconstruction-reprojection scheme that integrates information from all cameras. Wing and body kinematics, including wing deformation, are then extracted from the hulls of the wing boundaries and body. This model-free method is fully automatic, accurate and open source, and can be readily adjusted for different camera configurations or insect species.

Putting a new spin on insect jumping performance using 3D modeling and computer simulations of spotted lanternfly nymphs

How animals jump and land on diverse surfaces is ecologically important and relevant to bioinspired robotics. Here, we describe the jumping biomechanics of the planthopper Lycorma delicatula (spotted lanternfly), an invasive insect in the USA that jumps frequently for dispersal, locomotion and predator evasion. High-speed video was used to analyze jumping by spotted lanternfly nymphs from take-off to impact on compliant surfaces. These insects used rapid hindleg extensions to achieve high take-off speeds (2.7-3.4 m s-1) and accelerations (800-1000 m s-2), with mid-air trajectories consistent with ballistic motion without drag forces or steering. Despite rotating rapidly (5-45 Hz) about time-varying axes of rotation, they landed successfully in 58.9% of trials. They also attained the most successful impact orientation significantly more often than predicted by chance, consistent with their using attitude control. Notably, these insects were able to land successfully when impacting surfaces at all angles, pointing to the importance of collisional recovery behaviors. To further understand their rotational dynamics, we created realistic 3D rendered models of spotted lanternflies and used them to compute their mechanical properties during jumping. Computer simulations based on these models and drag torques estimated from fits to tracked data successfully predicted several features of the measured rotational kinematics. This analysis showed that the rotational inertia of spotted lanternfly nymphs is predominantly due to their legs, enabling them to use posture changes as well as drag torque to control their angular velocity, and hence their orientation, thereby facilitating predominately successful landings when jumping.

Strategic predatory pursuit of the stealthy, highly manoeuvrable, slow flying bat Corynorhinus townsendii

A predator's capacity to catch prey depends on its ability to navigate its environment in response to prey movements or escape behaviour. In predator-prey interactions that involve an active chase, pursuit behaviour can be studied as the collection of rules that dictate how a predator should steer to capture prey. It remains unclear how variable this behaviour is within and across species since most studies have detailed the pursuit behaviour of high-speed, open-area foragers. In this study, we analyse the pursuit behaviour in 44 successful captures by Corynorhinus townsendii, Townsend's big-eared bat (n = 4). This species forages close to vegetation using slow and highly manoeuvrable flight, which contrasts with the locomotor capabilities and feeding ecologies of other taxa studied to date. Our results indicate that this species relies on an initial stealthy approach, which is generally sufficient to capture prey (32 out of 44 trials). In cases where the initial approach is not sufficient to perform a capture attempt (12 out of 44 trials), C. townsendii continues its pursuit by reacting to prey movements in a manner best modelled with a combination of pure pursuit, or following prey directly, and proportional navigation, or moving to an interception point.

Mean-field theory of chaotic insect swarms

The harmonically confined Vicsek model displays qualitative and quantitative features observed in natural insect swarms. It exhibits a scale-free transition between single and multicluster chaotic phases. Finite-size scaling indicates that this unusual phase transition occurs at zero confinement [Phys. Rev. E 107, 014209 (2023)2470-004510.1103/PhysRevE.107.014209]. While the evidence of the scale-free-chaos phase transition comes from numerical simulations, here we present its mean-field theory. Analytically determined critical exponents are those of the Landau theory of equilibrium phase transitions plus dynamical critical exponent z=1 and a new critical exponent φ=0.5 for the largest Lyapunov exponent. The phase transition occurs at zero confinement and noise in the mean-field theory. The noise line of zero largest Lyapunov exponents informs observed behavior: (i) the qualitative shape of the swarm (on average, the center of mass rotates slowly at the rate marked by the winding number and its trajectory fills compactly the space, similarly to the observed condensed nucleus surrounded by vapor) and (ii) the critical exponents resemble those observed in natural swarms. Our predictions include power laws for the frequency of the maximal spectral amplitude and the winding number.

Emerging biological insights enabled by high-resolution 3D motion data: promises, perspectives and pitfalls

Deconstructing motion to better understand it is a key prerequisite in the field of comparative biomechanics. Since Marey and Muybridge's work, technical constraints have been the largest limitation to motion capture and analysis, which, in turn, limited what kinds of questions biologists could ask or answer. Throughout the history of our field, conceptual leaps and significant technical advances have generally worked hand in hand. Recently, high-resolution, three-dimensional (3D) motion data have become easier to acquire, providing new opportunities for comparative biomechanics. We describe how adding a third dimension of information has fuelled major paradigm shifts, not only leading to a reinterpretation of long-standing scientific questions but also allowing new questions to be asked. In this paper, we highlight recent work published in Journal of Experimental Biology and influenced by these studies, demonstrating the biological breakthroughs made with 3D data. Although amazing opportunities emerge from these technical and conceptual advances, high-resolution data often come with a price. Here, we discuss challenges of 3D data, including low-throughput methodology, costly equipment, low sample sizes, and complex analyses and presentation. Therefore, we propose guidelines for how and when to pursue 3D high-resolution data. We also suggest research areas that are poised for major new biological advances through emerging 3D data collection.

Tracking the Body, Wing, and Leg Kinematics of Moving Mosquitoes

In this protocol, we discuss general techniques for tracking the three-dimensional (3D) locations of the mosquito body, wings, legs, or other features of interest using videos. Tracking data must be acquired to produce detailed kinematics of moving mosquitoes. The software of focus for this protocol, DLTdv, was chosen for its widespread use and excellent support and because it is open-source. In addition, DLTdv allows both manual and automatic tracking. The automatic tracking can be done using a classic machine vision or machine-learning algorithm. The software supports both single-camera analysis and multicamera systems and can take advantage of sophisticated calibration algorithms, both for intrinsic lens distortion correction and for 3D DLT-based reconstruction. For this protocol, we assume all kinematic data is acquired post hoc through video analysis.

The science and technology of kinematic measurements in a century of Journal of Experimental Biology

Kinematic measurements have been essential to the study of comparative biomechanics and offer insight into relationships between technological development and scientific progress. Here, we review the 100 year history of kinematic measurements in Journal of Experimental Biology (JEB) through eras that used film, analog video and digital video, and approaches that have circumvented the use of image capture. This history originated with the career of Sir James Gray and has since evolved over the generations of investigators that have followed. Although some JEB studies have featured technological developments that were ahead of their time, the vast majority of research adopted equipment that was broadly available through the consumer or industrial markets. We found that across eras, an emphasis on high-speed phenomena outpaced the growth of the number of articles published by JEB and the size of datasets increased significantly. Despite these advances, the number of species studied within individual reports has not differed significantly over time. Therefore, we find that advances in technology have helped to enable a growth in the number of JEB studies that have included kinematic measurements, contributed to an emphasis on high-speed phenomena, and yielded biomechanical studies that are more data rich, but are no more comparative now than in previous decades.

Animal Pose Tracking: 3D Multimodal Dataset and Token-based Pose Optimization

Accurate tracking of the 3D pose of animals from video recordings is critical for many behavioral studies, yet there is a dearth of publicly available datasets that the computer vision community could use for model development. We here introduce the Rodent3D dataset that records animals exploring their environment and/or interacting with each other with multiple cameras and modalities (RGB, depth, thermal infrared). Rodent3D consists of 200 min of multimodal video recordings from up to three thermal and three RGB-D synchronized cameras (approximately 4 million frames). For the task of optimizing estimates of pose sequences provided by existing pose estimation methods, we provide a baseline model called OptiPose. While deep-learned attention mechanisms have been used for pose estimation in the past, with OptiPose, we propose a different way by representing 3D poses as tokens for which deep-learned context models pay attention to both spatial and temporal keypoint patterns. Our experiments show how OptiPose is highly robust to noise and occlusion and can be used to optimize pose sequences provided by state-of-the-art models for animal pose estimation.

Model-Based Tracking of Fruit Flies in Free Flight

Insect flight is a complex interdisciplinary phenomenon. Understanding its multiple aspects, such as flight control, sensory integration, physiology and genetics, often requires the analysis of large amounts of free flight kinematic data. Yet, one of the main bottlenecks in this field is automatically and accurately extracting such data from multi-view videos. Here, we present a model-based method for the pose estimation of free-flying fruit flies from multi-view high-speed videos. To obtain a faithful representation of the fly with minimum free parameters, our method uses a 3D model that includes two new aspects of wing deformation: A non-fixed wing hinge and a twisting wing surface. The method is demonstrated for free and perturbed flight. Our method does not use prior assumptions on the kinematics apart from the continuity of the wing pitch angle. Hence, this method can be readily adjusted for other insect species.

The soundscape of swarming: Proof of concept for a noninvasive acoustic species identification of swarming Myotis bats

Bats emit echolocation calls to orientate in their predominantly dark environment. Recording of species-specific calls can facilitate species identification, especially when mist netting is not feasible. However, some taxa, such as Myotis bats can be hard to distinguish acoustically. In crowded situations where calls of many individuals overlap, the subtle differences between species are additionally attenuated. Here, we sought to noninvasively study the phenology of Myotis bats during autumn swarming at a prominent hibernaculum. To do so, we recorded sequences of overlapping echolocation calls (N = 564) during nights of high swarming activity and extracted spectral parameters (peak frequency, start frequency, spectral centroid) and linear frequency cepstral coefficients (LFCCs), which additionally encompass the timbre (vocal "color") of calls. We used this parameter combination in a stepwise discriminant function analysis (DFA) to classify the call sequences to species level. A set of previously identified call sequences of single flying Myotis daubentonii and Myotis nattereri, the most common species at our study site, functioned as a training set for the DFA. 90.2% of the call sequences could be assigned to either M. daubentonii or M. nattereri, indicating the predominantly swarming species at the time of recording. We verified our results by correctly classifying the second set of previously identified call sequences with an accuracy of 100%. In addition, our acoustic species classification corresponds well to the existing knowledge on swarming phenology at the hibernaculum. Moreover, we successfully classified call sequences from a different hibernaculum to species level and verified our classification results by capturing swarming bats while we recorded them. Our findings provide a proof of concept for a new noninvasive acoustic monitoring technique that analyses "swarming soundscapes" by combining classical acoustic parameters and LFCCs, instead of analyzing single calls. Our approach for species identification is especially beneficial in situations with multiple calling individuals, such as autumn swarming.

Metabolic cost of flight and aerobic efficiency in the rose chafer, Protaetia cuprea (Cetoniinae)

Rose chafer beetles (Protetia cuprea) are pollinators as well as agricultural pests, flying between flowers and trees while foraging for pollen and fruits. Calculating the energy they expend on flying during foraging activity faces the challenge of measuring the metabolic rate (MR) of free-flying insects in an open space. We overcame this challenge by using the bolus injection of ¹³ C Na-bicarbonate technique to measure their metabolic energy expenditure while flying in a large flight arena. Concurrently, we tracked the insects with high-speed cameras to extract their flight trajectory, from which we calculated the mechanical power invested in flying for each flight bout. We found that the chemical (metabolic) energy input converted to mechanical flight energy output at a mean efficiency of 10.4% ± 5.2%, with a trend of increased efficiency in larger conspecifics (efficiency scaled with body mass to the power of 1.4). The transition in the summer from a diet of pollen to that of fruits may affect the energy budget available for foraging. Starved P. cuprea, feeding on apples ad libitum, increased their body mass by an average of 6% in 2 h. According to our calculations, such a meal can power a 630-m flight (assuming a carbohydrate assimilation efficiency of 90%). Pollen, with a low water and carbohydrate content but rich in proteins and lipids, has a higher caloric content and should assimilate differently when converting food to flight fuel. The high cost of aerial locomotion is inherent to the foraging behavior of rose chafers, explaining their short flight bouts followed by prolonged feeding activity.

Advances in non-invasive tracking of wave-type electric fish in natural and laboratory settings

Recent technological advances greatly improved the possibility to study freely behaving animals in natural conditions. However, many systems still rely on animal-mounted devices, which can already bias behavioral observations. Alternatively, animal behaviors can be detected and tracked in recordings of stationary sensors, e.g., video cameras. While these approaches circumvent the influence of animal-mounted devices, identification of individuals is much more challenging. We take advantage of the individual-specific electric fields electric fish generate by discharging their electric organ (EOD) to record and track their movement and communication behaviors without interfering with the animals themselves. EODs of complete groups of fish can be recorded with electrode arrays submerged in the water and then be tracked for individual fish. Here, we present an improved algorithm for tracking electric signals of wave-type electric fish. Our algorithm benefits from combining and refining previous approaches of tracking individual specific EOD frequencies and spatial electric field properties. In this process, the similarity of signal pairs in extended data windows determines their tracking order, making the algorithm more robust against detection losses and intersections. We quantify the performance of the algorithm and show its application for a data set recorded with an array of 64 electrodes distributed over a 12 m² section of a stream in the Llanos, Colombia, where we managed, for the first time, to track Apteronotus leptorhynchus over many days. These technological advances make electric fish a unique model system for a detailed analysis of social and communication behaviors, with strong implications for our research on sensory coding.

Divergence of climbing escape flight performance in Morpho butterflies living in different microhabitats

Habitat specialization can influence the evolution of animal movement in promoting divergent locomotor abilities adapted to contrasting environmental conditions, differences in vegetation clutter or predatory communities. While the effect of habitat on the evolution of locomotion and particularly escape performance has been well investigated in terrestrial animals, it remains understudied in flying animals. Here, we investigated whether specialization of Morpho butterfly species into different vertical strata of the Amazonian forest affects the performance of upward escape flight manoeuvres. Using stereoscopic high-speed videography, we compared the climbing flight kinematics of seven Morpho species living either in the forest canopy or in the understory. We show that butterflies from canopy species display strikingly higher climbing speed and steeper ascent angle compared with understory species. Although climbing speed increased with wing speed and angle of attack, the higher climb angle observed in canopy species was best explained by their higher body pitch angle, resulting in more upward-directed aerodynamic thrust forces. Climb angle also scales positively with weight-normalized wing area, and this weight-normalized wing area was higher in canopy species. This shows that a combined divergence in flight behaviour and morphology contributes to the evolution of increased climbing flight abilities in canopy species.

Summary: Quantification of climbing flight kinematics among closely related butterfly species living in different strata reveals contrasted climbing flight ability, probably resulting from divergent flight behaviour and morphology.

Resurrecting extinct cephalopods with biomimetic robots to explore hydrodynamic stability, maneuverability, and physical constraints on life habits

Externally shelled cephalopods with coiled, planispiral conchs were ecologically successful for hundreds of millions of years. These animals displayed remarkable morphological disparity, reflecting comparable differences in physical properties that would have constrained their life habits and ecological roles. To investigate these constraints, self-propelling, neutrally buoyant, biomimetic robots were 3D-printed for four disparate morphologies. These robots were engineered to assume orientations computed from virtual hydrostatic simulations while producing Nautilus-like thrusts. Compressed morphotypes had improved hydrodynamic stability (coasting efficiency) and experienced lower drag while jetting backwards. However, inflated morphotypes had improved maneuverability while rotating about the vertical axis. These differences highlight an inescapable physical tradeoff between hydrodynamic stability and yaw maneuverability, illuminating different functional advantages and life-habit constraints across the cephalopod morphospace. This tradeoff reveals there is no single optimum conch morphology, and elucidates the success and iterative evolution of disparate morphologies through deep time, including non-streamlined forms.

Evaluating acoustic signals to reduce avian collision risk

Collisions with human-made structures are responsible for billions of bird deaths each year, resulting in ecological damage as well as regulatory and financial burdens to many industries. Acoustic signals can alert birds to obstacles in their flight paths in order to mitigate collisions, but these signals should be tailored to the sensory ecology of birds in flight as the effectiveness of various acoustic signals potentially depends on the influence of background noise and the relative ability of various sound types to propagate within a landscape. We measured changes in flight behaviors from zebra finches released into a flight corridor containing a physical obstacle, either in no-additional-sound control conditions or when exposed to one of four acoustic signals. We selected signals to test two frequency ranges (4-6 kHz or 6-8 kHz) and two temporal modulation patterns (broadband or frequency-modulated oscillating) to determine whether any particular combination of sound attributes elicited the strongest collision avoidance behaviors. We found that, relative to control flights, all sound treatments caused birds to maintain a greater distance from hazards and to adjust their flight trajectories before coming close to obstacles. There were no statistical differences among different sound treatments, but consistent trends within the data suggest that the 4-6 kHz frequency-modulated oscillating signal elicited the strongest avoidance behaviors. We conclude that a variety of acoustic signals can be effective as avian collision deterrents, at least in the context in which we tested these birds. These results may be most directly applicable in scenarios when birds are at risk of collisions with solid structures, such as wind turbines and communication towers, as opposed to window collisions or collisions involving artificial lighting. We recommend the incorporation of acoustic signals into multimodal collision deterrents and demonstrate the value of using behavioral data to assess collision risk.

Sing or Jam? Density-Dependent Food Competition Strategies in Mexican Free-Tailed Bats (Tadarida brasiliensis)

Organisms compete for food in many ways, but it is often difficult to know why they use certain competition strategies over others. Bats compete for food either through aggression coupled with food-claiming signals or by actively interfering with a competitor’s sensory processing during prey pursuit (i.e., jamming). It is not known why these different behaviors are exhibited. I studied food competition between Mexican free-tailed bats (Tadarida brasiliensis) at foraging sites in Arizona and New Mexico using passive acoustic recording, insect sampling and 3-D infrared videography with or without supplemental lighting that concentrated prey. Bat activity was quantified by the number of recorded echolocation calls, while feeding behavior was indicated by feeding buzzes. Two competitive behaviors were observed—song, which was produced by bats chasing conspecifics, and sinFM calls, which jam echolocation of competitors pursuing prey. Song production was most common when few bats were present and feeding at low rates. In contrast, jamming signals were most common with many bats present and feeding at high rates. Supplemental lighting increased the numbers of bats, feeding buzzes and sinFM calls, but not song. These results indicate that bats employ different strategies—singing and chasing competitors at low bat densities but jamming competitors at high bat densities. Food claiming signals (song) may only be effective with few competitors present, whereas jamming can be effective with many bats at a foraging site. Multiple competition strategies appear to have evolved in bats that are used under different densities of competitors.

Effects of prey density and flow speed on plankton feeding by garden eels: A flume study

Feeding by zooplanktivorous fish depends on their foraging movements and the flux of prey to which they are exposed. While prey flux is a linear function of zooplankton density and flow speed, those two factors are expected to contribute differently to fish movements. Our objective was to determine the effects of these factors for garden eels, stationary fish that feed while anchored to the sandy bottom by keeping the posterior parts of their bodies inside a burrow. Using a custom-made flume with a sandy bottom, we quantified the effects of prey density and flow speed on feeding rates by spotted garden eels (Heteroconger hassi). Feeding rates increased linearly with prey density. However, feeding rates did not show a linear relationship with flow speed and decreased at 0.25 m s⁻¹. Using label-free tracking of body points and 3D movement analysis, we found that the reduction in feeding rates was related to modulation of the eel's movements, whereby the expected increase in energy expenditure was avoided by reducing exposure and drag. No effects of flow speed on strike speed, reactive distance or vectorial dynamic body acceleration (VeDBA) were found. A foraging model based on the body length extended from the burrow showed correspondence with observations. These findings suggest that as a result of their unique foraging mode, garden eels can occupy self-made burrows in exposed shelter-free sandy bottoms where they can effectively feed on drifting zooplankton.

Summary: Analysis of feeding by anchored garden eels in a flume shows their unique strategies, modulating dependence on burrows and foraging movements, to enable effective feeding at a wide range of flow speeds.

A physics perspective on collective animal behavior

The beautiful dynamic patterns and coordinated motion displayed by groups of social animals are a beautiful example of self-organization in natural farfrom-equilibrium systems. Recent advances in active-matter physics have enticed physicists to begin to consider how their results can be extended from microscale physical or biological systems to groups of real, macroscopic animals. At the same time, advances in measurement technology have led to the increasing availability of high-quality empirical data for the behavior of animal groups both in the laboratory and in the wild. In this review, I survey this available data and the ways that it has been analyzed. I then describe how physicists have approached synthesizing, modeling, and interpreting this information, both at the level of individual animals and at the group scale. In particular, I focus on the kinds of analogies that physicists have made between animal groups and more traditional areas of physics.

Convergent morphology and divergent phenology promote the coexistence of Morpho butterfly species

The coexistence of closely-related species in sympatry is puzzling because ecological niche proximity imposes strong competition and reproductive interference. A striking example is the widespread wing pattern convergence of several blue-banded Morpho butterfly species with overlapping ranges of distribution. Here we perform a series of field experiments using flying Morpho dummies placed in a natural habitat. We show that similarity in wing colour pattern indeed leads to interspecific territoriality and courtship among sympatric species. In spite of such behavioural interference, demographic inference from genomic data shows that sympatric closely-related Morpho species are genetically isolated. Mark-recapture experiments in the two most closely-related species unravel a strong temporal segregation in patrolling activity of males. Such divergence in phenology reduces the costs of reproductive interference while simultaneously preserving the benefits of convergence in non-reproductive traits in response to common ecological pressures. Henceforth, the evolution of multiple traits may favour species diversification in sympatry by partitioning niche in different dimensions.

The hunter and the hunted-A 3D analysis of predator-prey interactions between three-spined sticklebacks (Gasterosteus aculeatus) and larvae of different prey fishes

Predator-prey interactions play a key life history role, as animals cope with changing predation risk and opportunities to hunt prey. It has recently been shown that the hunting success of sticklebacks (Gasterosteus aculeatus) targeting fish larvae is dependent on both the size of the prey and the prior exposure of its species to stickleback predation. The purpose of the current study was to identify the behavioural predator-prey interactions explaining the success or failure of sticklebacks hunting larvae of three potential prey species [roach (Rutilus rutilus), perch (Perca fluviatilis) and whitefish (Coregonus wartmannii)] in a 3D environment. Trials were carried out for each prey species at four different size classes in a standardised laboratory setup and were recorded using a slow motion, stereo camera setup. 75 predator-prey interactions including both failed and successful hunts were subject to the analysis. 3D track analysis indicated that sticklebacks applied different strategies. Prey with less complex predator escape responses, i.e. whitefish larvae, were hunted using a direct but stealthy approach ending in a lunge, while the behaviourally more complex roach and perch larvae were hunted with a faster approach. A multivariate logistic regression identified that slow average speed and acceleration of the prey in the initial stages of the hunt increased the probability of stickleback success. Furthermore, predators adjusted their swimming direction more often when hunting larger whitefish compared to smaller whitefish. The results suggest that appropriate and adequately timed avoidance behaviours, which vary between prey species and ontogenetic stages, significantly increase the chances of outmanoeuvring and escaping stickleback predation. Small whitefish larvae can reach similar levels of swimming performance compared to older conspecifics, but display ineffective anti-predator behaviours, resulting in higher hunting success for sticklebacks. Thus, the development of appropriate anti-predator behaviours depending on size appears to be the crucial factor to escaping predation.

Vertical escape tactics and movement potential of orthoconic cephalopods

Measuring locomotion tactics available to ancient sea animals can link functional morphology with evolution and ecology over geologic timescales. Externally-shelled cephalopods are particularly important for their central roles in marine trophic exchanges, but most fossil taxa lack sufficient modern analogues for comparison. In particular, phylogenetically diverse cephalopods produced orthoconic conchs (straight shells) repeatedly through time. Persistent re-evolution of this morphotype suggests that it possesses adaptive value. Practical lateral propulsion is ruled out as an adaptive driver among orthoconic cephalopods due to the stable, vertical orientations of taxa lacking sufficient counterweights. However, this constraint grants the possibility of rapid (or at least efficient) vertical propulsion. We experiment with this form of movement using 3D-printed models of Baculites compressus, weighted to mimic hydrostatic properties inferred by virtual models. Furthermore, model buoyancy was manipulated to impart simulated thrust within four independent scenarios (Nautilus-like cruising thrust; a similar thrust scaled by the mantle cavity of Sepia; sustained peak Nautilus-like thrust; and passive, slightly negative buoyancy). Each model was monitored underwater with two submerged cameras as they rose/fell over ~2 m, and their kinematics were computed with 3D motion tracking. Our results demonstrate that orthocones require very low input thrust for high output in movement and velocity. With Nautilus-like peak thrust, the model reaches velocities of 1.2 m/s (2.1 body lengths per second) within one second starting from a static initial condition. While cephalopods with orthoconic conchs likely assumed a variety of life habits, these experiments illuminate some first-order constraints. Low hydrodynamic drag inferred by vertical displacement suggests that vertical migration would incur very low metabolic cost. While these cephalopods likely assumed low energy lifestyles day-to-day, they may have had a fighting chance to escape from larger, faster predators by performing quick, upward dodges. The current experiments suggest that orthocones sacrifice horizontal mobility and maneuverability in exchange for highly streamlined, vertically-stable, upwardly-motile conchs.

SpaRTA Tracking Across Occlusions via Partitioning of 3D Clouds of Points

Any 3D tracking algorithm has to deal with occlusions: multiple targets get so close to each other that the loss of their identities becomes likely; hence, potentially affecting the very quality of the data with interrupted trajectories and identity switches. Here, we present a novel tracking method that addresses the problem of occlusions within large groups of featureless objects by means of three steps: i) it represents each target as a cloud of points in 3D; ii) once a 3D cluster corresponding to an occlusion occurs, it defines a partitioning problem by introducing a cost function that uses both attractive and repulsive spatio-temporal proximity links; and iii) it minimizes the cost function through a semi-definite optimization technique specifically designed to cope with the presence of multi-minima landscapes. The algorithm is designed to work on 3D data regardless of the experimental method used: multicamera systems, lidars, radars, and RGB-D systems. By performing tests on public data-sets, we show that the new algorithm produces a significant improvement over the state-of-the-art tracking methods, both by reducing the number of identity switches and by increasing the accuracy of the estimated positions of the targets in real space.

Three-dimensional measurements of animal paths using handheld unconstrained GoPro cameras and VSLAM software

I present the system PATMOS (paths and tessellated meshes from ORB_SLAM2) for measuring three-dimensional paths of animalsin situusing two handheld GoPro cameras and a small spatial reference object. Animal paths were triangulated from mobile camera positions obtained from a modified version of ORB_SLAM2, an open-source visual simultaneous localization and mapping software package. In addition to path calculation, this process provided a virtual three-dimensional surface approximation to the environment from which path to environment distances can be quantified. PATMOS can also fit a tranquil water's surface to an analytic plane if there are a sufficient number of visible objects intersecting the water's surface and can track objects over the water's surfaces with a single camera by measuring the object with its reflection. This technology was highly portable, could follow moving animals, and gave comparable spatial and temporal resolutions to fixed camera systems that use commercial cameras. An investigation of falling objects yielded a gravitational constant measurement of 978 ± 40 cm s^-2. I demonstrated PATMOS's utility in terrestrial and aquatic environments by quantifying dragonfly flight characteristics and the inter-spatial distances between substrate and damselfish.

Angular variables of climbing geckos in two lateral undulation patterns

Geckos demonstrate flexible and agile locomotion on diverse terrains and surfaces. The lateral undulation pattern referring to the trunk-limbs coordination gives animals advantages in terms of motion speed, dynamical stability, and highly efficient movement. Quantitative analysis of the angular variables of the trunk and limbs was proposed to compare the kinematics of Gekko gecko on the vertical plane in the standing wave and traveling wave of lateral undulation patterns. Thirteen angular variables were measured to illustrate the kinematic characteristics of trunk flexion, girdles rotation, scapula rotation, trunk deflection, femoral/humeral protraction-retraction, abduction-adduction, and rotation around their axes, and knee/elbow flexion-extension. One-way analysis of variance (ANOVA) tested for mean differences between patterns for maximum value, minimum value, and range value of each angular variable. The geckos adapted to the changes in locomotion velocity by dynamically adjusting the joints angular variables. Twenty of the thirty-nine angular values showed a significant pattern effect that presented the variation of angular values or the timing of the peak of the angle curve in two different lateral undulation patterns. The climbing stability of a gecko is tightly associated with the coordination between the body and the limbs.

Elastic wing deformations mitigate flapping asymmetry during manoeuvres in rose chafers (Protaetia cuprea)

To manoeuvre in air, flying animals produce asymmetric flapping between contralateral wings. Unlike the adjustable vertebrate wings, insect wings lack intrinsic musculature, preventing active control over wing shape during flight. However, the wings elastically deform as a result of aerodynamic and inertial forces generated by the flapping motions. How these elastic deformations vary with flapping kinematics and flight performance in free-flying insects is poorly understood. Using high-speed videography, we measured how contralateral wings elastically deform during free-flight manoeuvring in rose chafer beetles (Protaetia cuprea). We found that asymmetric flapping during aerial turns was associated with contralateral differences in chord-wise wing deformations. The highest instantaneous difference in deformation occurred during stroke reversals, resulting from differences in wing rotation timing. Elastic deformation asymmetry was also evident during mid-strokes, where wing compliance increased the angle of attack of both wings, but reduced the asymmetry in the angle of attack between contralateral wings. A biomechanical model revealed that wing compliance can increase the torques generated by each wing, providing higher potential for manoeuvrability, while concomitantly contributing to flight stability by attenuating steering asymmetry. Such stability may be adaptive for insects such as flower chafers that need to perform delicate low-speed landing manoeuvres among vegetation.

Transfer Entropy Analysis of Interactions between Bats Using Position and Echolocation Data

Many animal species, including many species of bats, exhibit collective behavior where groups of individuals coordinate their motion. Bats are unique among these animals in that they use the active sensing mechanism of echolocation as their primary means of navigation. Due to their use of echolocation in large groups, bats run the risk of signal interference from sonar jamming. However, several species of bats have developed strategies to prevent interference, which may lead to different behavior when flying with conspecifics than when flying alone. This study seeks to explore the role of this acoustic sensing on the behavior of bat pairs flying together. Field data from a maternity colony of gray bats (Myotis grisescens) were collected using an array of cameras and microphones. These data were analyzed using the information theoretic measure of transfer entropy in order to quantify the interaction between pairs of bats and to determine the effect echolocation calls have on this interaction. This study expands on previous work that only computed information theoretic measures on the 3D position of bats without echolocation calls or that looked at the echolocation calls without using information theoretic analyses. Results show that there is evidence of information transfer between bats flying in pairs when time series for the speed of the bats and their turning behavior are used in the analysis. Unidirectional information transfer was found in some subsets of the data which could be evidence of a leader-follower interaction.

The Effects of Temperature on the Kinematics of Rattlesnake Predatory Strikes in Both Captive and Field Environments

The outcomes of predator-prey interactions between endotherms and ectotherms can be heavily influenced by environmental temperature, owing to the difference in how body temperature affects locomotor performance. However, as elastic energy storage mechanisms can allow ectotherms to maintain high levels of performance at cooler body temperatures, detailed analyses of kinematics are necessary to fully understand how changes in temperature might alter endotherm-ectotherm predator-prey interactions. Viperid snakes are widely distributed ectothermic mesopredators that interact with endotherms both as predator and prey. Although there are numerous studies on the kinematics of viper strikes, surprisingly few have analyzed how this rapid movement is affected by temperature. Here we studied the effects of temperature on the predatory strike performance of rattlesnakes (Crotalus spp.), abundant new world vipers, using both field and captive experimental contexts. We found that the effects of temperature on predatory strike performance are limited, with warmer snakes achieving slightly higher maximum strike acceleration, but similar maximum velocity. Our results suggest that, unlike defensive strikes to predators, rattlesnakes may not attempt to maximize strike speed when attacking prey, and thus the outcomes of predatory strikes may not be heavily influenced by changes in temperature.

Aquatic and terrestrial takeoffs require different hindlimb kinematics and muscle function in mallard ducks

Mallard ducks are capable of performing a wide range of behaviors including nearly vertical takeoffs from both terrestrial and aquatic habitats. The hindlimb plays a key role during takeoffs from both media. However, because force generation differs in water versus on land, hindlimb kinematics and muscle function are likely modulated between these environments. Specifically, we hypothesize that hindlimb joint motion and muscle shortening are faster during aquatic takeoffs, but greater hindlimb muscle forces are generated during terrestrial takeoffs. In this study, we examined the hindlimb kinematics and in vivo contractile function of the lateral gastrocnemius (LG), a major ankle extensor and knee flexor, during takeoffs from water versus land in mallard ducks. In contrast to our hypothesis, we observed no change in ankle angular velocity between media. However, the hip and metatarsophalangeal joints underwent large excursions during terrestrial takeoffs but exhibited almost no motion during aquatic takeoffs. The knee extended during terrestrial takeoffs but flexed during aquatic takeoffs. Correspondingly, LG fascicle shortening strain, shortening velocity and pennation angle change were greater during aquatic takeoffs than during terrestrial takeoffs because of the differences in knee motion. Nevertheless, we observed no significant differences in LG stress or work, but did see an increase in muscle power output during aquatic takeoffs. Because differences in the physical properties of aquatic and terrestrial media require differing hindlimb kinematics and muscle function, animals such as mallards may be challenged to tune their muscle properties for movement across differing environments.

The development of flight behaviours in birds

Flight is a unique adaptation at the core of many behaviours in most bird species, whether it be foraging, migration or breeding. Birds have developed a wide diversity of flight modes (e.g. flapping, gliding, soaring, hovering) which involves very specialized behaviours. A key issue when studying flight behaviours is to understand how they develop through all the ontogenetic stages of birds, from the embryo to the flying adult. This question typically involves classical debates on animal behaviour about the importance of maturation and experience. Here, we review the literature available on the development of flight behaviours in birds. First, we focus on the early period when young birds are not yet capable of flight. We discuss examples and show how endogenous processes (e.g. wing flapping in the nest, flight development timing) and environmental factors (e.g. maternal stress, nutritional stress) can influence the development of flight behaviours. Then, we review several examples showing the different processes involved in the development of flight in flight-capable juveniles (e.g. practice, trial and error learning, social learning). Despite the lack of experimental studies investigating this specific question at different developmental stages, we show that several patterns can be identified, and we anticipate that the development of new tracking techniques will allow us to study this question more thoroughly in more bird species.

Wing morphing allows gulls to modulate static pitch stability during gliding

A gliding bird's ability to stabilize its flight path is as critical as its ability to produce sufficient lift. In flight, birds often morph the shape of their wings, but the consequences of avian wing morphing on flight stability are not well understood. Here, we investigate how morphing the gull elbow joint in gliding flight affects their static pitch stability. First, we combined observations of freely gliding gulls and measurements from gull wing cadavers to identify the wing configurations used during gliding flight. These measurements revealed that, as wind speed and gusts increased, gulls flexed their elbows to adopt wing shapes characterized by increased spanwise camber. To determine the static pitch stability characteristics of these wing shapes, we prepared gull wings over the anatomical elbow range and measured the developed pitching moments in a wind tunnel. Wings prepared with extended elbow angles had low spanwise camber and high passive stability, meaning that mild perturbations could be negated without active control. Wings with flexed elbow angles had increased spanwise camber and reduced static pitch stability. Collectively, these results demonstrate that gliding gulls can transition across a broad range of static pitch stability characteristics using the motion of a single joint angle.

Behavioural plasticity and the transition to order in jackdaw flocks

Collective behaviour is typically thought to arise from individuals following fixed interaction rules. The possibility that interaction rules may change under different circumstances has thus only rarely been investigated. Here we show that local interactions in flocks of wild jackdaws (Corvus monedula) vary drastically in different contexts, leading to distinct group-level properties. Jackdaws interact with a fixed number of neighbours (topological interactions) when traveling to roosts, but coordinate with neighbours based on spatial distance (metric interactions) during collective anti-predator mobbing events. Consequently, mobbing flocks exhibit a dramatic transition from disordered aggregations to ordered motion as group density increases, unlike transit flocks where order is independent of density. The relationship between group density and group order during this transition agrees well with a generic self-propelled particle model. Our results demonstrate plasticity in local interaction rules and have implications for both natural and artificial collective systems.

Modelling collective behaviour in different circumstances remains a challenge because of uncertainty related to interaction rule changes. Here, the authors report plasticity in local interaction rules in flocks of wild jackdaws with implications for both natural and artificial collective systems.

Competition and cooperation among chimney swifts at roost entry

Chimney swifts (Chaetura pelagica) are highly aerial, small, insectivorous birds well known for roosting en masse in chimneys during their autumn migration. These roosting events require hundreds to thousands of birds to enter a small opening (here 0.64 m²) within a short amount of time (15-30 min). Thus, these entry events pose a complex navigational and behavioral challenge as birds identify their entry route, cooperate with other birds present to form an entry flock, and compete with other birds at the time of chimney entry. We used six synchronized cameras to capture and reconstruct the 3D flight trajectories of swifts before and during chimney entry. Navigation into the chimney is consistent with use of a relative retinal expansion velocity cue, which results in an entry/non-entry decision point about 1.5 m above the chimney, or 0.4 s at typical entry speeds. Entries were highly clustered with 91 of 136 entries occurring within 1 s of another entry. We observed both synchronous (entry within 0.2 s) and sequential entry behavior (entry separated by ~0.4 s). Birds entering the chimney flew in close proximity to other birds (median minimum distance 0.51 m; 1.7 wingspans). In cases where two birds appeared to attempt a near-simultaneous entry, the bird either slightly to the rear or with a velocity vector bringing it closer to the current position of the other bird tended to make an avoidance maneuver and abandon its entry attempt. Overall, these results show how groups of animals execute complex landing and collision avoidance maneuvers in a natural setting without central control authority.

Aerodynamically Interacting Vertical-Axis Wind Turbines: Performance Enhancement and Three-Dimensional Flow

This study examined three-dimensional, volumetric mean velocity fields and corresponding performance measurements for an isolated vertical-axis wind turbine (VAWT) and for co- and counter-rotating pairs of VAWTs with varying incident wind direction and turbine spacings. The purpose was to identify turbine configurations and flow mechanisms that can improve the power densities of VAWT arrays in wind farms. All experiments were conducted at a Reynolds number of R e D = 7.3 × 10 4 . In the paired arrays, performance enhancement was observed for both the upstream and downstream turbines. Increases in downstream turbine performance correlate with bluff–body accelerations around the upstream turbine, which increase the incident freestream velocity on the downstream turbine in certain positions. Decreases in downstream turbine performance are determined by its position in the upstream turbine’s wake. Changes in upstream turbine performance are related to variations in the surrounding flow field due to the presence of the downstream rotor. For the most robust array configuration studied, an average 14% increase in array performance over approximately a 50° range of wind direction was observed. Additionally, three-dimensional vortex interactions behind pairs of VAWT were observed that can replenish momentum in the wake by advection rather than turbulent diffusion. These effects and their implications for wind-farm design are discussed.

Using DeepLabCut for 3D markerless pose estimation across species and behaviors

Noninvasive behavioral tracking of animals during experiments is critical to many scientific pursuits. Extracting the poses of animals without using markers is often essential to measuring behavioral effects in biomechanics, genetics, ethology, and neuroscience. However, extracting detailed poses without markers in dynamically changing backgrounds has been challenging. We recently introduced an open-source toolbox called DeepLabCut that builds on a state-of-the-art human pose-estimation algorithm to allow a user to train a deep neural network with limited training data to precisely track user-defined features that match human labeling accuracy. Here, we provide an updated toolbox, developed as a Python package, that includes new features such as graphical user interfaces (GUIs), performance improvements, and active-learning-based network refinement. We provide a step-by-step procedure for using DeepLabCut that guides the user in creating a tailored, reusable analysis pipeline with a graphical processing unit (GPU) in 1-12 h (depending on frame size). Additionally, we provide Docker environments and Jupyter Notebooks that can be run on cloud resources such as Google Colaboratory.

Dragonflies use underdamped pursuit to chase conspecifics

Pursuit is a common behavior exhibited by animals chasing prey, competitors and potential mates. Because of their speed and maneuverability, dragonflies are frequently studied as a model system for biological pursuit. Most quantitative studies have focused on prey pursuits in captive environments. To determine whether a different pursuit strategy is used when chasing conspecifics of nearly equal speed and agility, we recorded 3D flight trajectories from nine territorial chases between male Erythemis simplicicollis dragonflies in natural field conditions. During chases, dragonflies used an interception strategy with an unusually high-magnitude gain (k=-10.03 s^-1 horizontal; -8.86 s^-1 vertical) and short time delay (τ=50 ms). The product kτ determines how aggressively a pursuer corrects course to achieve interception. Previous studies of prey pursuit have found kτ values close to -1/e (-0.37), the time-optimal value for achieving pursuit without overshooting. However, we found that dragonflies chasing conspecifics use more negative kτ (-0.50 horizontal; -0.44 vertical), resulting in pursuits with a high degree of overshooting (i.e. moving past the target and alternating position from side to side). We confirmed via simulation that the observed gain and delay produce overshooting. We propose that overshooting is an adaptive feature of conspecific chases that can be achieved with only slight modification of the strategy used for intercepting prey. Overshooting might help avoid potentially damaging collisions while exhibiting the pursuing animal's flight performance and competitive ability. Repeated close approaches might also evoke evasive responses from the other dragonfly, effectively herding the competitor out of the territory.

Compound-V formations in shorebird flocks

Animal groups have emergent properties that result from simple interactions among individuals. However, we know little about why animals adopt different interaction rules because of sparse sampling among species. Here, we identify an interaction rule that holds across single and mixed-species flocks of four migratory shorebird species spanning a seven-fold range of body masses. The rule, aligning with a one-wingspan lateral distance to nearest neighbors in the same horizontal plane, scales linearly with wingspan but is independent of nearest neighbor distance and neighbor species. This rule propagates outward to create a global flock structure that we term the compound-V formation. We propose that this formation represents an intermediary between the cluster flocks of starlings and the simple-V formations of geese and other large migratory birds. We explore multiple hypotheses regarding the benefit of this flock structure and how it differs from structures observed in other flocking species.

Birds often fly in flocks ranging from very structured V-formations to unstructured clusters. Many studies have tried to prove what causes birds to flock and how it benefits them. Flocks, for example, may help birds to avoid predators and to navigate. Flying in a V-shaped formation likely also gives aerodynamic benefits that can make it easier to fly long distances.

Few studies, however, have measured how the positions of birds in a flock relate to things like flying speed or the frequency of wing flaps. This is because it was difficult to take such measurements in large flocks of moving birds. Advances in cameras and computers are now making it easier to track individual birds flying in large flocks. The technology allows scientists to measure how birds position themselves in relation to other birds, or how flock-positioning varies by bird size, species, ecology, and behaviors. Such measurements may help scientists better understand why and how birds flock.

Corcoran and Hedrick now show that four different types of shorebirds position themselves in the same way when flying in a flock. In the experiments, digital cameras recorded video of 18 cluster-like flocks of four different species of birds flying over a bird sanctuary or agricultural fields. The flocks ranged in size from a hundred to a thousand birds. Some flocks had two types of bird. The four types of birds – dunlin, short-billed dowitcher, American avocet, and marbled godwit – live in similar environments but greatly vary in size and fly at different speeds. Corcoran and Hedrick measured individual bird positions using three-dimensional computer reconstructions of the flocks.

Each bird – regardless of size or species – most commonly flew about one wingspan to the side and between a half to one-and-a-half wingspans back from the bird in front of it. Birds flying in simple V-shaped formations follow similar rules. This suggests that birds flying in clusters may also gain aerodynamic benefits.

Avian surface reconstruction in free flight with application to flight stability analysis of a barn owl and peregrine falcon

Birds primarily create and control the forces necessary for flight through changing the shape and orientation of their wings and tail. Their wing geometry is characterised by complex variation in parameters such as camber, twist, sweep and dihedral. To characterise this complexity, a multi-view stereo-photogrammetry setup was developed for accurately measuring surface geometry in high resolution during free flight. The natural patterning of the birds was used as the basis for phase correlation-based image matching, allowing indoor or outdoor use while being non-intrusive for the birds. The accuracy of the method was quantified and shown to be sufficient for characterising the geometric parameters of interest, but with a reduction in accuracy close to the wing edge and in some localised regions. To demonstrate the method's utility, surface reconstructions are presented for a barn owl (Tyto alba) and peregrine falcon (Falco peregrinus) during three instants of gliding flight per bird. The barn owl flew with a consistent geometry, with positive wing camber and longitudinal anhedral. Based on flight dynamics theory, this suggests it was longitudinally statically unstable during these flights. The peregrine falcon flew with a consistent glide angle, but at a range of air speeds with varying geometry. Unlike the barn owl, its glide configuration did not provide a clear indication of longitudinal static stability/instability. Aspects of the geometries adopted by both birds appeared to be related to control corrections and this method would be well suited for future investigations in this area, as well as for other quantitative studies into avian flight dynamics.

Adaptive evolution of butterfly wing shape: from morphology to behaviour

Butterflies display extreme variation in wing shape associated with tremendous ecological diversity. Disentangling the role of neutral versus adaptive processes in wing shape diversification remains a challenge for evolutionary biologists. Ascertaining how natural selection influences wing shape evolution requires both functional studies linking morphology to flight performance, and ecological investigations linking performance in the wild with fitness. However, direct links between morphological variation and fitness have rarely been established. The functional morphology of butterfly flight has been investigated but selective forces acting on flight behaviour and associated wing shape have received less attention. Here, we attempt to estimate the ecological relevance of morpho-functional links established through biomechanical studies in order to understand the evolution of butterfly wing morphology. We survey the evidence for natural and sexual selection driving wing shape evolution in butterflies, and discuss how our functional knowledge may allow identification of the selective forces involved, at both the macro- and micro-evolutionary scales. Our review shows that although correlations between wing shape variation and ecological factors have been established at the macro-evolutionary level, the underlying selective pressures often remain unclear. We identify the need to investigate flight behaviour in relevant ecological contexts to detect variation in fitness-related traits. Identifying the selective regime then should guide experimental studies towards the relevant estimates of flight performance. Habitat, predators and sex-specific behaviours are likely to be major selective forces acting on wing shape evolution in butterflies. Some striking cases of morphological divergence driven by contrasting ecology involve both wing and body morphology, indicating that their interactions should be included in future studies investigating co-evolution between morphology and flight behaviour.