Shorter
K. Alex
Shorter
K. Alex
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ArticleDrag of suction cup tags on swimming animals : modeling and measurement(John Wiley & Sons, 2013-11-12) Shorter, K. Alex ; Murray, Mark M. ; Johnson, Mark P. ; Moore, Michael J. ; Howle, Laurens E.Bio-logging tags are widely used to study the behavior and movements of marine mammals with the tacit assumption of little impact to the animal. However, tags on fast-swimming animals generate substantial hydrodynamic forces potentially affecting behavior and energetics adversely, or promoting early removal of the tag. In this work, hydrodynamic loading of three novel tag housing designs are compared over a range of swimming speeds using computational fluid dynamics (CFD). Results from CFD simulation were verified using tag models in a water flume with close agreement. Drag forces were reduced by minimizing geometric disruptions to the flow around the housing, while lift forces were reduced by minimizing the frontal cross-sectional area of the housing and holding the tag close to the attachment surface. Hydrodynamic tag design resulted in an experimentally measured 60% drag force reduction in 5.6 m/s flow. For all housing designs, off-axis flow increased the magnitude of the force on the tag. Experimental work with a common dolphin (Delphinus delphis) cadaver indicates that the suction cups used to attach the types of tags described here provide sufficient attachment force to resist failure to predicted forces at swimming speeds of up to 10 m/s.
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ArticleAugmenting biologging with supervised machine learning to study in situ behavior of the medusa Chrysaora fuscescens(Company of Biologists, 2019-08-23) Fannjiang, Clara ; Mooney, T. Aran ; Cones, Seth ; Mann, David ; Shorter, K. Alex ; Katija, KakaniZooplankton play critical roles in marine ecosystems, yet their fine-scale behavior remains poorly understood because of the difficulty in studying individuals in situ. Here, we combine biologging with supervised machine learning (ML) to propose a pipeline for studying in situ behavior of larger zooplankton such as jellyfish. We deployed the ITAG, a biologging package with high-resolution motion sensors designed for soft-bodied invertebrates, on eight Chrysaora fuscescens in Monterey Bay, using the tether method for retrieval. By analyzing simultaneous video footage of the tagged jellyfish, we developed ML methods to: (1) identify periods of tag data corrupted by the tether method, which may have compromised prior research findings, and (2) classify jellyfish behaviors. Our tools yield characterizations of fine-scale jellyfish activity and orientation over long durations, and we conclude that it is essential to develop behavioral classifiers on in situ rather than laboratory data.
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PreprintBottlenose dolphins modify behavior to reduce metabolic effect of tag attachment( 2014-10) van der Hoop, Julie ; Fahlman, Andreas ; Hurst, Thomas P. ; Rocho-Levine, Julie ; Shorter, K. Alex ; Petrov, Victor ; Moore, Michael J.Attaching bio-telemetry or -logging devices (‘tags’) to marine animals for research and monitoring adds drag to streamlined bodies, thus affecting posture, swimming gaits and energy balance. These costs have never been measured in free-swimming cetaceans. To examine the effect of drag from a tag on metabolic rate, cost of transport and swimming behavior, four captive male dolphins (Tursiops truncatus) were trained to swim a set course, either non-tagged (n=7) or fitted with a tag (DTAG2; n=12), and surface exclusively in a flow-through respirometer in which oxygen consumption (Graphic) and carbon dioxide production (Graphic; ml kg−1 min−1) rates were measured and respiratory exchange ratio (Graphic/Graphic) was calculated. Tags did not significantly affect individual mass-specific oxygen consumption, physical activity ratios (exercise Graphic/resting Graphic), total or net cost of transport (COT; J m−1 kg−1) or locomotor costs during swimming or two-minute recovery phases. However, individuals swam significantly slower when tagged (by ~11%; mean ± s.d., 3.31±0.35 m s−1) than when non-tagged (3.73±0.41 m s−1). A combined theoretical and computational fluid dynamics model estimating drag forces and power exertion during swimming suggests that drag loading and energy consumption are reduced at lower swimming speeds. Bottlenose dolphins in the specific swimming task in this experiment slowed to the point where the tag yielded no increases in drag or power, while showing no difference in metabolic parameters when instrumented with a DTAG2. These results, and our observations, suggest that animals modify their behavior to maintain metabolic output and energy expenditure when faced with tag-induced drag.
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ArticleFrom the track to the ocean : using flow control to improve marine bio-logging tags for cetaceans(Public Library of Science, 2017-02-14) Fiore, Giovani ; Anderson, Erik J. ; Garborg, C. Spencer ; Murray, Mark M. ; Johnson, Mark P. ; Moore, Michael J. ; Howle, Laurens ; Shorter, K. AlexBio-logging tags are an important tool for the study of cetaceans, but superficial tags inevitably increase hydrodynamic loading. Substantial forces can be generated by tags on fast-swimming animals, potentially affecting behavior and energetics or promoting early tag removal. Streamlined forms have been used to reduce loading, but these designs can accelerate flow over the top of the tag. This non-axisymmetric flow results in large lift forces (normal to the animal) that become the dominant force component at high speeds. In order to reduce lift and minimize total hydrodynamic loading this work presents a new tag design (Model A) that incorporates a hydrodynamic body, a channel to reduce fluid speed differences above and below the housing and wing to redirect flow to counter lift. Additionally, three derivatives of the Model A design were used to examine the contribution of individual flow control features to overall performance. Hydrodynamic loadings of four models were compared using computational fluid dynamics (CFD). The Model A design eliminated all lift force and generated up to ~30 N of downward force in simulated 6 m/s aligned flow. The simulations were validated using particle image velocimetry (PIV) to experimentally characterize the flow around the tag design. The results of these experiments confirm the trends predicted by the simulations and demonstrate the potential benefit of flow control elements for the reduction of tag induced forces on the animal.
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ArticleITAG : an eco-sensor for fine-scale behavioral measurements of soft-bodied marine invertebrates(BioMed Central, 2015-09-28) Mooney, T. Aran ; Katija, Kakani ; Shorter, K. Alex ; Hurst, Thomas P. ; Fontes, Jorge ; Afonso, PedroSoft-bodied marine invertebrates comprise a keystone component of ocean ecosystems; however, we know little of their behaviors and physiological responses within their natural habitat. Quantifying ocean conditions and measuring organismal responses to the physical environment is vital to understanding the species or ecosystem-level influences of a changing ocean. Here we describe a novel, soft-bodied invertebrate eco-sensor tag (the ITAG), its trial attachments to squid and jellyfish, and the fine-scale behavioral measurements recorded on captive animals. Tags were deployed on five jellyfish (Aurelia aurita) and eight squid (Loligo forbesi) in laboratory conditions for up to 24 h. Using concurrent video and tag data, movement signatures for specific behaviors were identified. These behaviors included straight swimming (for jellyfish), and finning, jetting, direction reversal and turning (for squid). Overall activity levels were quantified using the root-mean-squared magnitude of acceleration, and finning was found to be the dominant squid swimming gait during captive squid experiments. External light sensors on the ITAG were used to compare squid swimming activity relative to ambient light across a ca. 20-h trial. The deployments revealed that while swimming was continuous for captive squid, energetically costly swimming behaviors (i.e., jetting and rapid direction reversals) occurred infrequently. These data reflect the usefulness of the ITAG to study trade-offs between behavior and energy expenditure in captive and wild animals. These data demonstrate that eco-sensors with sufficiently high sampling rates can be applied to quantify behavior of soft-bodied taxa and changes in behavior due to interactions with the surrounding environment. The methods and tool described here open the door for substantial lab and field-based measurements of fine-scale behavior, physiology, and concurrent environmental parameters that will inform fisheries management, and elucidate the ecology of these important keystone taxa.
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ArticleSwimming energy economy in bottlenose dolphins under variable drag loading(Frontiers Media, 2018-12-11) van der Hoop, Julie ; Fahlman, Andreas ; Shorter, K. Alex ; Gabaldon, Joaquin ; Rocho-Levine, Julie ; Petrov, Victor ; Moore, Michael J.Instrumenting animals with tags contributes additional resistive forces (weight, buoyancy, lift, and drag) that may result in increased energetic costs; however, additional metabolic expense can be moderated by adjusting behavior to maintain power output. We sought to increase hydrodynamic drag for near-surface swimming bottlenose dolphins, to investigate the metabolic effect of instrumentation. In this experiment, we investigate whether (1) metabolic rate increases systematically with hydrodynamic drag loading from tags of different sizes or (2) whether tagged individuals modulate speed, swimming distance, and/or fluking motions under increased drag loading. We detected no significant difference in oxygen consumption rates when four male dolphins performed a repeated swimming task, but measured swimming speeds that were 34% (>1 m s-1) slower in the highest drag condition. To further investigate this observed response, we incrementally decreased and then increased drag in six loading conditions. When drag was reduced, dolphins increased swimming speed (+1.4 m s-1; +45%) and fluking frequency (+0.28 Hz; +16%). As drag was increased, swimming speed (-0.96 m s-1; -23%) and fluking frequency (-14 Hz; 7%) decreased again. Results from computational fluid dynamics simulations indicate that the experimentally observed changes in swimming speed would have maintained the level of external drag forces experienced by the animals. Together, these results indicate that dolphins may adjust swimming speed to modulate the drag force opposing their motion during swimming, adapting their behavior to maintain a level of energy economy during locomotion.
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ArticleQuantifying the swimming gaits of veined squid (Loligo forbesi) using bio-logging tags(Company of Biologists, 2019-10-21) Flaspohler, Genevieve Elaine ; Caruso, Francesco ; Mooney, T. Aran ; Katija, Kakani ; Fontes, Jorge ; Afonso, Pedro ; Shorter, K. AlexSquid are mobile, diverse, ecologically important marine organisms whose behavior and habitat use can have substantial impacts on ecosystems and fisheries. However, as a consequence in part of the inherent challenges of monitoring squid in their natural marine environment, fine-scale behavioral observations of these free-swimming, soft-bodied animals are rare. Bio-logging tags provide an emerging way to remotely study squid behavior in their natural environments. Here, we applied a novel, high-resolution bio-logging tag (ITAG) to seven veined squid, Loligo forbesii, in a controlled experimental environment to quantify their short-term (24 h) behavioral patterns. Tag accelerometer, magnetometer and pressure data were used to develop automated gait classification algorithms based on overall dynamic body acceleration, and a subset of the events were assessed and confirmed using concurrently collected video data. Finning, flapping and jetting gaits were observed, with the low-acceleration finning gaits detected most often. The animals routinely used a finning gait to ascend (climb) and then glide during descent with fins extended in the tank's water column, a possible strategy to improve swimming efficiency for these negatively buoyant animals. Arms- and mantle-first directional swimming were observed in approximately equal proportions, and the squid were slightly but significantly more active at night. These tag-based observations are novel for squid and indicate a more efficient mode of movement than suggested by some previous observations. The combination of sensing, classification and estimation developed and applied here will enable the quantification of squid activity patterns in the wild to provide new biological information, such as in situ identification of behavioral states, temporal patterns, habitat requirements, energy expenditure and interactions of squid through space–time in the wild.
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ArticleTag-based estimates of bottlenose dolphin swimming behavior and energetics(The Company of Biologists, 2022-11-30) Gabaldon, Joaquin T ; Zhang, Ding ; Rocho-Levine, Julie ; Moore, Michael J ; van der Hoop, Julie ; Barton, Kira ; Shorter, K AlexCurrent estimates of marine mammal hydrodynamic forces tend to be made using camera-based kinematic data for a limited number of fluke strokes during a prescribed swimming task. In contrast, biologging tag data yield kinematic measurements from thousands of strokes, enabling new insights into swimming behavior and mechanics. However, there have been limited tag-based estimates of mechanical work and power. In this work, we investigated bottlenose dolphin (Tursiops truncatus) swimming behavior using tag-measured kinematics and a hydrodynamic model to estimate propulsive power, work and cost of transport. Movement data were collected from six animals during prescribed straight-line swimming trials to investigate swimming mechanics over a range of sustained speeds (1.9-6.1 m s-1). Propulsive power ranged from 66 W to 3.8 kW over 282 total trials. During the lap trials, the dolphins swam at depths that mitigated wave drag, reducing overall drag throughout these mid- to high-speed tasks. Data were also collected from four individuals during undirected daytime (08:30-18:00 h) swimming to examine how self-selected movement strategies are used to modulate energetic efficiency and effort. Overall, self-selected swimming speeds (individual means ranging from 1.0 to 1.96 m s-1) tended to minimize cost of transport, and were on the lower range of animal-preferred speeds reported in literature. The results indicate that these dolphins moderate propulsive effort and efficiency through a combination of speed and depth regulation. This work provides new insights into dolphin swimming behavior in both prescribed tasks and self-selected swimming, and presents a path forward for continuous estimates of mechanical work and power from wild animals.