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Torkashvand E. Modeling three-dimensional T-cell motility using clustering and hidden Markov models. Stat Methods Med Res 2023; 32:1318-1337. [PMID: 37303122 DOI: 10.1177/09622802231172041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Recent advances in imaging technologies now allow for real-time tracking of fast-moving immune cells as they search for targets such as pathogens and tumor cells through complex three-dimensional tissues. Cytotoxic T cells are specialized immune cells that continually scan tissues for such targets to engage and kill, and have emerged as the principle mediators of breakthrough immunotherapies against cancers. Modeling the way these T cells move is of great value in furthering our understanding of their collective search efficiency. T-cell motility is characterized by heterogeneity at two levels: (a) Individual cells display different distributions of translational speeds and turning angles, and (b) each cell can during a given track, its motility, switch between local search and directional motion. Despite a likely considerable influence on a motile population's search performance, statistical models that accurately capture both such heterogeneities in a distinguishing manner are lacking. Here, we model three-dimensional T-cell trajectories through a spherical representation of their incremental steps and compare model outputs to real-world motility data from primary T cells navigating physiological environments. T cells in a population are clustered based on their directional persistence and characteristic "step lengths" therein capturing between-cell heterogeneity. The motility dynamics of cells within each cluster are individually modeled through hidden Markov model to capture within-cell transitions between local and more extensive search patterns. We explore the importance of explicitly capturing altered motility patterns when cells lie in close proximity to one another, through a non-homogenous hidden Markov model.
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Affiliation(s)
- Elaheh Torkashvand
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, US
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2
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Zhang D, Goodbar K, West N, Lesage V, Parks SE, Wiley DN, Barton K, Shorter KA. Pose-gait analysis for cetacean biologging tag data. PLoS One 2022; 17:e0261800. [PMID: 36149842 PMCID: PMC9506652 DOI: 10.1371/journal.pone.0261800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 09/09/2022] [Indexed: 12/04/2022] Open
Abstract
Biologging tags are a key enabling tool for investigating cetacean behavior and locomotion in their natural habitat. Identifying and then parameterizing gait from movement sensor data is critical for these investigations, but how best to characterize gait from tag data remains an open question. Further, the location and orientation of a tag on an animal in the field are variable and can change multiple times during a deployment. As a result, the relative orientation of the tag with respect to (wrt) the animal must be determined for analysis. Currently, custom scripts that involve species-specific heuristics tend to be used in the literature. These methods require a level of knowledge and experience that can affect the reliability and repeatability of the analysis. Swimming gait is composed of a sequence of body poses that have a specific spatial pattern, and tag-based measurements of this pattern can be utilized to determine the relative orientation of the tag. This work presents an automated data processing pipeline (and software) that takes advantage of these patterns to 1) Identify relative motion between the tag and animal; 2) Estimate the relative orientation of the tag wrt the animal using a data-driven approach; and 3) Calculate gait parameters that are stable and invariant to animal pose. Validation results from bottlenose dolphin tag data show that the average relative orientation error (tag wrt the body) after processing was within 11 degrees in roll, pitch, and yaw directions. The average precision and recall for detecting instances of relative motion in the dolphin data were 0.87 and 0.89, respectively. Tag data from humpback and beluga whales were then used to demonstrate how the gait analysis can be used to enhance tag-based investigations of movement and behavior. The MATLAB source code and data presented in the paper are publicly available (https://github.com/ding-z/cetacean-pose-gait-analysis.git), along with suggested best practices.
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Affiliation(s)
- Ding Zhang
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, United States of America
- * E-mail:
| | - Kari Goodbar
- Dolphin Quest Oahu, Honolulu, HI, United States of America
| | - Nicole West
- Dolphin Quest Oahu, Honolulu, HI, United States of America
| | | | - Susan E. Parks
- Department of Biology, Syracuse University, Syracuse, NY, United States of America
| | - David N. Wiley
- National Oceanic and Atmospheric Agency’s (NOAA) Stellwagen Bank National Marine Sanctuary, Scituate, MA, United States of America
| | - Kira Barton
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, United States of America
| | - K. Alex Shorter
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, United States of America
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3
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Gunner RM, Holton MD, Scantlebury DM, Hopkins P, Shepard ELC, Fell AJ, Garde B, Quintana F, Gómez-Laich A, Yoda K, Yamamoto T, English H, Ferreira S, Govender D, Viljoen P, Bruns A, van Schalkwyk OL, Cole NC, Tatayah V, Börger L, Redcliffe J, Bell SH, Marks NJ, Bennett NC, Tonini MH, Williams HJ, Duarte CM, van Rooyen MC, Bertelsen MF, Tambling CJ, Wilson RP. How often should dead-reckoned animal movement paths be corrected for drift? ANIMAL BIOTELEMETRY 2021; 9:43. [PMID: 34900262 PMCID: PMC7612089 DOI: 10.1186/s40317-021-00265-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/25/2021] [Indexed: 05/19/2023]
Abstract
BACKGROUND Understanding what animals do in time and space is important for a range of ecological questions, however accurate estimates of how animals use space is challenging. Within the use of animal-attached tags, radio telemetry (including the Global Positioning System, 'GPS') is typically used to verify an animal's location periodically. Straight lines are typically drawn between these 'Verified Positions' ('VPs') so the interpolation of space-use is limited by the temporal and spatial resolution of the system's measurement. As such, parameters such as route-taken and distance travelled can be poorly represented when using VP systems alone. Dead-reckoning has been suggested as a technique to improve the accuracy and resolution of reconstructed movement paths, whilst maximising battery life of VP systems. This typically involves deriving travel vectors from motion sensor systems and periodically correcting path dimensions for drift with simultaneously deployed VP systems. How often paths should be corrected for drift, however, has remained unclear. METHODS AND RESULTS Here, we review the utility of dead-reckoning across four contrasting model species using different forms of locomotion (the African lion Panthera leo, the red-tailed tropicbird Phaethon rubricauda, the Magellanic penguin Spheniscus magellanicus, and the imperial cormorant Leucocarbo atriceps). Simulations were performed to examine the extent of dead-reckoning error, relative to VPs, as a function of Verified Position correction (VP correction) rate and the effect of this on estimates of distance moved. Dead-reckoning error was greatest for animals travelling within air and water. We demonstrate how sources of measurement error can arise within VP-corrected dead-reckoned tracks and propose advancements to this procedure to maximise dead-reckoning accuracy. CONCLUSIONS We review the utility of VP-corrected dead-reckoning according to movement type and consider a range of ecological questions that would benefit from dead-reckoning, primarily concerning animal-barrier interactions and foraging strategies.
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Affiliation(s)
- Richard M. Gunner
- Swansea Lab for Animal Movement, Department of Biosciences, Swansea University, Singleton Park, Swansea SA2 8PP, Wales, UK
| | - Mark D. Holton
- Swansea Lab for Animal Movement, Department of Biosciences, Swansea University, Singleton Park, Swansea SA2 8PP, Wales, UK
| | - David M. Scantlebury
- School of Biological Sciences, Queen’s University Belfast, Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, Northern Ireland, UK
| | - Phil Hopkins
- Swansea Lab for Animal Movement, Department of Biosciences, Swansea University, Singleton Park, Swansea SA2 8PP, Wales, UK
| | - Emily L. C. Shepard
- Swansea Lab for Animal Movement, Department of Biosciences, Swansea University, Singleton Park, Swansea SA2 8PP, Wales, UK
| | - Adam J. Fell
- Biological and Environmental Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK
| | - Baptiste Garde
- Swansea Lab for Animal Movement, Department of Biosciences, Swansea University, Singleton Park, Swansea SA2 8PP, Wales, UK
| | - Flavio Quintana
- Instituto de Biología de Organismos Marinos (IBIOMAR), CONICET. Boulevard Brown, 2915, U9120ACD Puerto Madryn, Chubut, Argentina
| | - Agustina Gómez-Laich
- Departamento de Ecología, Genética y Evolución & Instituto de Ecología, Genética Y Evolución de Buenos Aires (IEGEBA), CONICET, Pabellón II Ciudad Universitaria, C1428EGA Buenos Aires, Argentina
| | - Ken Yoda
- Graduate School of Environmental Studies, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Takashi Yamamoto
- Organization for the Strategic Coordination of Research and Intellectual Properties, Meiji University, Nakano, Tokyo, Japan
| | - Holly English
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin, Ireland
| | - Sam Ferreira
- Savanna and Grassland Research Unit, Scientific Services Skukuza, South African National Parks, Kruger National Park, Skukuza 1350, South Africa
| | - Danny Govender
- Savanna and Grassland Research Unit, Scientific Services Skukuza, South African National Parks, Kruger National Park, Skukuza 1350, South Africa
| | - Pauli Viljoen
- Savanna and Grassland Research Unit, Scientific Services Skukuza, South African National Parks, Kruger National Park, Skukuza 1350, South Africa
| | - Angela Bruns
- Veterinary Wildlife Services, South African National Parks, 97 Memorial Road, Old Testing Grounds, Kimberley 8301, South Africa
| | - O. Louis van Schalkwyk
- Department of Agriculture, Government of South Africa, Land Reform and Rural Development, Pretoria 001, South Africa
- Department of Migration, Max Planck Institute of Animal Behavior, 78315 Radolfzell, Germany
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa
| | - Nik C. Cole
- Durrell Wildlife Conservation Trust, Les Augrès Manor, Channel Islands, Trinity JE3 5BP, Jersey, UK
- Mauritian Wildlife Foundation, Grannum Road, Indian Ocean, Vacoas, Mauritius
| | - Vikash Tatayah
- Mauritian Wildlife Foundation, Grannum Road, Indian Ocean, Vacoas, Mauritius
| | - Luca Börger
- Swansea Lab for Animal Movement, Department of Biosciences, Swansea University, Singleton Park, Swansea SA2 8PP, Wales, UK
- Centre for Biomathematics, Swansea University, Swansea SA2 8PP, UK
| | - James Redcliffe
- Swansea Lab for Animal Movement, Department of Biosciences, Swansea University, Singleton Park, Swansea SA2 8PP, Wales, UK
| | - Stephen H. Bell
- School of Biological Sciences, Queen’s University Belfast, Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, Northern Ireland, UK
| | - Nikki J. Marks
- School of Biological Sciences, Queen’s University Belfast, Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, Northern Ireland, UK
| | - Nigel C. Bennett
- Mammal Research Institute. Department of Zoology and Entomology, University of Pretoria, Pretoria 002., South Africa
| | - Mariano H. Tonini
- Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales, Grupo GEA, IPATEC-UNCO-CONICET, San Carlos de Bariloche, Río Negro, Argentina
| | - Hannah J. Williams
- Department of Migration, Max Planck Institute of Animal Behavior, 78315 Radolfzell, Germany
| | - Carlos M. Duarte
- Red Sea Research Centre, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Martin C. van Rooyen
- Mammal Research Institute. Department of Zoology and Entomology, University of Pretoria, Pretoria 002., South Africa
| | - Mads F. Bertelsen
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, Roskildevej 38, DK-2000 Frederiksberg, Denmark
| | - Craig J. Tambling
- Department of Zoology and Entomology, University of Fort Hare, Alice Campus, Ring Road, Alice 5700, South Africa
| | - Rory P. Wilson
- Swansea Lab for Animal Movement, Department of Biosciences, Swansea University, Singleton Park, Swansea SA2 8PP, Wales, UK
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Barlow J, Fregosi S, Thomas L, Harris D, Griffiths ET. Acoustic detection range and population density of Cuvier's beaked whales estimated from near-surface hydrophones. THE JOURNAL OF THE ACOUSTICAL SOCIETY OF AMERICA 2021; 149:111. [PMID: 33514185 DOI: 10.1121/10.0002881] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/17/2020] [Indexed: 06/12/2023]
Abstract
The population density of Cuvier's beaked whales is estimated acoustically with drifting near-surface hydrophone recorders in the Catalina Basin. Three empirical approaches (trial-based, distance-sampling, and spatially explicit capture-recapture) are used to estimate the probability of detecting the echolocation pulses as a function of range. These detection functions are used with two point-transect methods (snapshot and dive-cue) to estimate density. Measurement errors result in a small range of density estimates (3.9-5.4 whales per 1000 km2). Use of multiple approaches and methods allows comparison of the required information and assumptions of each. The distance-sampling approach with snapshot-based density estimates has the most stringent assumptions but would be the easiest to implement for large scale surveys of beaked whale density. Alternative approaches to estimating detection functions help validate this approach. The dive cue method of density estimation has promise, but additional work is needed to understand the potential bias caused by animal movement during a dive. Empirical methods are a viable alternative to the theoretical acoustic modeling approaches that have been used previously to estimate beaked whale density.
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Affiliation(s)
- Jay Barlow
- National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Southwest Fisheries Science Center, Marine Mammal and Turtle Division, 8901 La Jolla Shores Drive, La Jolla, California 92037, USA
| | - Selene Fregosi
- Cooperative Institute for Marine Resources Studies, Oregon State University and National Ocean and Atmospheric Administration Pacific Marine Environmental Laboratory, 2030 Marine Science Drive, Newport, Oregon 97365, USA
| | - Len Thomas
- Centre for Research into Ecological and Environmental Modelling, University of St Andrews, St Andrews, Fife, KY16 9LZ, United Kingdom
| | - Danielle Harris
- Centre for Research into Ecological and Environmental Modelling, University of St Andrews, St Andrews, Fife, KY16 9LZ, United Kingdom
| | - Emily T Griffiths
- Ocean Associates, Incorporated, 4007 North Abingdon Street, Arlington, Virginia 22207, USA
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5
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Nuijten RJM, Gerrits T, Shamoun-Baranes J, Nolet BA. Less is more: On-board lossy compression of accelerometer data increases biologging capacity. J Anim Ecol 2020; 89:237-247. [PMID: 31828775 PMCID: PMC7004173 DOI: 10.1111/1365-2656.13164] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 12/03/2019] [Indexed: 11/29/2022]
Abstract
GPS‐tracking devices have been used in combination with a wide range of additional sensors to study animal behaviour, physiology and interaction with their environment. Tri‐axial accelerometers allow researchers to remotely infer the behaviour of individuals, at all places and times. Collection of accelerometer data is relatively cheap in terms of energy usage, but the amount of raw data collected generally requires much storage space and is particularly demanding in terms of energy needed for data transmission. Here, we propose compressing the raw accelerometer (ACC) data into summary statistics within the tracking device (before transmission) to reduce data size, as a means to overcome limitations in storage and energy capacity. We explored this type of lossy data compression in the accelerometer data of tagged Bewick's swans Cygnus columbianus bewickii collected in spring 2017. Using software settings in which bouts of 2 s of both raw ACC data and summary statistics were collected in parallel but with different bout intervals to keep total data size comparable, we created the opportunity for a direct comparison of time budgets derived by the two data collection methods. We found that the data compression in our case yielded a six times reduction in data size per bout, and concurrent, similar decreases in storage and energy use of the device. We show that with the same accuracy of the behavioural classification, the freed memory and energy of the device can be used to increase the monitoring effort, resulting in a more detailed representation of the individuals’ time budget. Rare and/or short behaviours, such as daily roost flights, were picked up significantly more when collecting summary statistics instead of raw ACC data (but note differences in sampling rate). Such level of detail can be of essential importance, for instance to make a reliable estimate of the energy budgets of individuals. In conclusion, we argue that this type of lossy data compression can be a well‐considered choice in study situations where limitations in energy and storage space of the device pose a problem. Ultimately, these developments can allow for long‐term and nearly continuous remote monitoring of the behaviour of free‐ranging animals.
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Affiliation(s)
- Rascha J M Nuijten
- Department of Animal Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | | | - Judy Shamoun-Baranes
- Department of Theoretical and Computational Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Bart A Nolet
- Department of Animal Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands.,Department of Theoretical and Computational Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
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6
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Gunner RM, Wilson RP, Holton MD, Scott R, Hopkins P, Duarte CM. A new direction for differentiating animal activity based on measuring angular velocity about the yaw axis. Ecol Evol 2020; 10:7872-7886. [PMID: 32760571 PMCID: PMC7391348 DOI: 10.1002/ece3.6515] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 12/11/2022] Open
Abstract
The use of animal-attached data loggers to quantify animal movement has increased in popularity and application in recent years. High-resolution tri-axial acceleration and magnetometry measurements have been fundamental in elucidating fine-scale animal movements, providing information on posture, traveling speed, energy expenditure, and associated behavioral patterns. Heading is a key variable obtained from the tandem use of magnetometers and accelerometers, although few field investigations have explored fine-scale changes in heading to elucidate differences in animal activity (beyond the notable exceptions of dead-reckoning).This paper provides an overview of the value and use of animal heading and a prime derivative, angular velocity about the yaw axis, as an important element for assessing activity extent with potential to allude to behaviors, using "free-ranging" Loggerhead turtles (Caretta caretta) as a model species.We also demonstrate the value of yaw rotation for assessing activity extent, which varies over the time scales considered and show that various scales of body rotation, particularly rate of change of yaw, can help resolve differences between fine-scale behavior-specific movements. For example, oscillating yaw movements about a central point of the body's arc implies bouts of foraging, while unusual circling behavior, indicative of conspecific interactions, could be identified from complete revolutions of the longitudinal axis.We believe this approach should help identification of behaviors and "space-state" approaches to enhance our interpretation of behavior-based movements, particularly in scenarios where acceleration metrics have limited value, such as for slow-moving animals.
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Affiliation(s)
- Richard M. Gunner
- Swansea Lab for Animal Movement, BiosciencesCollege of ScienceSwansea UniversitySwanseaUK
| | - Rory P. Wilson
- Swansea Lab for Animal Movement, BiosciencesCollege of ScienceSwansea UniversitySwanseaUK
| | - Mark D. Holton
- Swansea Lab for Animal Movement, BiosciencesCollege of ScienceSwansea UniversitySwanseaUK
| | - Rebecca Scott
- Future Ocean Cluster of ExcellenceGEOMAR Helmholtz Centre for Ocean ResearchKielGermany
- Natural Environmental Research Council, Polaris HouseSwindonUK
| | - Phil Hopkins
- Swansea Lab for Animal Movement, BiosciencesCollege of ScienceSwansea UniversitySwanseaUK
| | - Carlos M. Duarte
- Red Sea Research CentreKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
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7
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Grouping Behaviors of Dolphins and Other Toothed Whales. ETHOLOGY AND BEHAVIORAL ECOLOGY OF ODONTOCETES 2019. [DOI: 10.1007/978-3-030-16663-2_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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8
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Barlow J, Griffiths ET, Klinck H, Harris DV. Diving behavior of Cuvier's beaked whales inferred from three-dimensional acoustic localization and tracking using a nested array of drifting hydrophone recorders. THE JOURNAL OF THE ACOUSTICAL SOCIETY OF AMERICA 2018; 144:2030. [PMID: 30404483 DOI: 10.1121/1.5055216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 08/31/2018] [Indexed: 06/08/2023]
Abstract
Echolocation pulses from Cuvier's beaked whales are used to track the whales' three-dimensional diving behavior in the Catalina Basin, California. In 2016, five 2-element vertical hydrophone arrays were suspended from the surface and drifted at ∼100-m depth. Cuvier's beaked whale pulses were identified, and vertical detection angles were estimated from time-differences-of-arrival of either direct-path signals received on two hydrophones or direct-path and surface-reflected signals received on the same hydrophone. A Bayesian state-space model is developed to track the diving behavior. The model is fit to these detection angle estimates from at least four of the drifting vertical arrays. Results show that the beaked whales were producing echolocation pulses and are presumed to be foraging at a mean depth of 967 m (standard deviation = 112 m), approximately 300 m above the bottom in this basin. Some whales spent at least some time at or near the bottom. Average swim speed was 1.2 m s-1, but swim direction varied during a dive. The average net horizontal speed was 0.6 m s-1. Results are similar to those obtained from previous tagging studies of this species. These methods may allow expansion of dive studies to other whale species that are difficult to tag.
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Affiliation(s)
- Jay Barlow
- National Oceanic and Atmospheric Administration National Marine Fisheries Service, Southwest Fisheries Science Center, Marine Mammal and Turtle Division, 8901 La Jolla Shores Drive, La Jolla, California 92037, USA
| | - Emily T Griffiths
- Ocean Associates, Inc., 4007 North Arlington Street, Arlington, Virginia 22207, USA
| | - Holger Klinck
- Bioacoustics Research Program, Cornell Laboratory of Ornithology, Cornell University, 159 Sapsucker Woods Road, Ithaca, New York 14850, USA
| | - Danielle V Harris
- Centre for Research into Ecological and Environmental Modelling, The Observatory, Buchanan Gardens, University of St. Andrews, St. Andrews, Fife, KY16 9LZ, United Kingdom
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9
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Goldbogen JA, Cade DE, Boersma AT, Calambokidis J, Kahane-Rapport SR, Segre PS, Stimpert AK, Friedlaender AS. Using Digital Tags With Integrated Video and Inertial Sensors to Study Moving Morphology and Associated Function in Large Aquatic Vertebrates. Anat Rec (Hoboken) 2018; 300:1935-1941. [PMID: 28971623 DOI: 10.1002/ar.23650] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 06/20/2017] [Accepted: 06/21/2017] [Indexed: 12/20/2022]
Abstract
The anatomy of large cetaceans has been well documented, mostly through dissection of dead specimens. However, the difficulty of studying the world's largest animals in their natural environment means the functions of anatomical structures must be inferred. Recently, non-invasive tracking devices have been developed that measure body position and orientation, thereby enabling the detailed reconstruction of underwater trajectories. The addition of cameras to the whale-borne tags allows the sensor data to be matched with real-time observations of how whales use their morphological structures, such as flukes, flippers, feeding apparatuses, and blowholes for the physiological functions of locomotion, feeding, and breathing. Here, we describe a new tag design with integrated video and inertial sensors and how it can be used to provide insights to the function of whale anatomy. This technology has the potential to facilitate a wide range of discoveries and comparative studies, but many challenges remain to increase the resolution and applicability of the data. Anat Rec, 300:1935-1941, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- J A Goldbogen
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California
| | - D E Cade
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California
| | - A T Boersma
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California
| | | | - S R Kahane-Rapport
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California
| | - P S Segre
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California
| | - A K Stimpert
- Vertebrate Ecology Laboratory, Moss Landing Marine Laboratories, Moss Landing, California
| | - A S Friedlaender
- Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, Newport, Oregon
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10
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Bras YL, Jouma’a J, Guinet C. Three-dimensional space use during the bottom phase of southern elephant seal dives. MOVEMENT ECOLOGY 2017; 5:18. [PMID: 28861272 PMCID: PMC5577837 DOI: 10.1186/s40462-017-0108-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 08/18/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND In marine pelagic ecosystems, the spatial distribution of biomass is heterogeneous and dynamic. At large scales, physical processes are the main driving forces of biomass distribution. At fine scales, both biotic and abiotic parameters are likely to be key determinants in the horizontal and vertical distribution of biomass, with direct consequences on the foraging behaviour of diving predators. However, fine scale three-dimensional (3D) spatial interactions between diving predators and their prey are still poorly known. RESULTS We reconstructed and examined the patterns of southern elephant seals 3D path during the bottom phase of their dives, and related them to estimated prey encounter density. We found that southern elephant seal tracks at bottom are strongly dominated by a single horizontal direction. In high prey density areas, seals travelled shorter distances but their track remained strongly orientated according to a main linear direction. Horizontal, and more importantly, vertical deviations from this main direction, were related negatively to the estimated prey density. We found that prey encounter density decreased with diving depth but tended to be more predictable. CONCLUSION Southern elephant seal behaviour during the bottom phase of their dives suggest that the prey are dispersed and distributed into layers in which their density relates to the vertical spread of the layer. The linear trajectories performed by the elephant seals would allow to explore the largest volume of water, maximizing the opportunities of prey encounter, while travelling great horizontal distances.
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Affiliation(s)
- Yves Le Bras
- Centre d’Études Biologiques de Chizé, UMR 7372, CNRS-ULR, Villiers-en-bois, 79360 France
| | - Joffrey Jouma’a
- Centre d’Études Biologiques de Chizé, UMR 7372, CNRS-ULR, Villiers-en-bois, 79360 France
| | - Christophe Guinet
- Centre d’Études Biologiques de Chizé, UMR 7372, CNRS-ULR, Villiers-en-bois, 79360 France
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11
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Statistical modelling of individual animal movement: an overview of key methods and a discussion of practical challenges. ASTA-ADVANCES IN STATISTICAL ANALYSIS 2017. [DOI: 10.1007/s10182-017-0302-7] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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12
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Cade DE, Barr KR, Calambokidis J, Friedlaender AS, Goldbogen JA. Determining forward speed from accelerometer jiggle in aquatic environments. J Exp Biol 2017; 221:jeb.170449. [DOI: 10.1242/jeb.170449] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/26/2017] [Indexed: 11/20/2022]
Abstract
How fast animals move is critical to understanding their energetic requirements, locomotor capacity, and foraging performance, yet current methods for measuring speed via animal-attached devices are not universally applicable. Here we present and evaluate a new method that relates forward speed to the stochastic motion of biologging devices since tag jiggle, the amplitude of the tag vibrations as measured by high sample rate accelerometers, increases exponentially with increasing speed. We successfully tested this method in a flow tank using two types of biologging devices and tested the method in situ on wild cetaceans spanning ∼3 to >20 m in length using two types of suction cup-attached and two types of dart-attached tag. This technique provides some advantages over other approaches for determining speed as it is device-orientation independent and relies only on a pressure sensor and a high sample rate accelerometer, sensors that are nearly universal across biologging device types.
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Affiliation(s)
- David E. Cade
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950, USA
| | - Kelly R. Barr
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950, USA
- Present address: Center for Tropical Research, Institute for the Environment and Sustainability, Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - John Calambokidis
- Cascadia Research Collective, 218 1/2 W. 4th Avenue, Olympia, WA 98501, USA
| | - Ari S. Friedlaender
- Marine Mammal Institute, Hatfield Marine Science Center, Department of Fish and Wildlife, Oregon State University, Newport, OR 97365, USA
- Present address: Institute of Marine Sciences, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Jeremy A. Goldbogen
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950, USA
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Börger L. EDITORIAL: Stuck in motion? Reconnecting questions and tools in movement ecology. J Anim Ecol 2016; 85:5-10. [PMID: 26768334 DOI: 10.1111/1365-2656.12464] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Luca Börger
- Department of Biosciences, College of Science, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
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Segre PS, Cade DE, Fish FE, Potvin J, Allen AN, Calambokidis J, Friedlaender AS, Goldbogen JA. Hydrodynamic properties of fin whale flippers predict maximum rolling performance. J Exp Biol 2016; 219:3315-3320. [DOI: 10.1242/jeb.137091] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 08/24/2016] [Indexed: 11/20/2022]
Abstract
Maneuverability is one of the most important and least understood aspects of animal locomotion. The hydrofoil-like flippers of cetaceans are thought to function as control surfaces that effect maneuvers, but quantitative tests of this hypothesis have been lacking. Here we construct a simple hydrodynamic model to predict the longitudinal-axis roll performance of fin whales, and we test its predictions against kinematic data recorded by on-board movement sensors from 27 free-swimming fin whales. We found that for a given swimming speed and roll excursion, the roll velocity of fin whales calculated from our field data agrees well with that predicted by our hydrodynamic model. Although fluke and body torsion may further influence performance, our results indicate that lift generated by the flippers is sufficient to drive most of the longitudinal-axis rolls used by fin whales for feeding and maneuvering.
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Affiliation(s)
- P. S. Segre
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950, USA
| | - D. E. Cade
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950, USA
| | - F. E. Fish
- Department of Biology, West Chester University, West Chester, PA 19383, USA
| | - J. Potvin
- Department of Physics, Saint Louis University, St. Louis, MO 63103, USA
| | - A. N. Allen
- Cascadia Research Collective, 218 ½ W. 4th Avenue, Olympia, WA 98501, USA
| | - J. Calambokidis
- Cascadia Research Collective, 218 ½ W. 4th Avenue, Olympia, WA 98501, USA
| | - A. S. Friedlaender
- Department of Fisheries and Wildlife, Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, Newport, OR 97365, USA
| | - J. A. Goldbogen
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950, USA
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15
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Wensveen PJ, Thomas L, Miller PJO. A path reconstruction method integrating dead-reckoning and position fixes applied to humpback whales. MOVEMENT ECOLOGY 2015; 3:31. [PMID: 26392865 PMCID: PMC4576411 DOI: 10.1186/s40462-015-0061-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 09/06/2015] [Indexed: 05/07/2023]
Abstract
BACKGROUND Detailed information about animal location and movement is often crucial in studies of natural behaviour and how animals respond to anthropogenic activities. Dead-reckoning can be used to infer such detailed information, but without additional positional data this method results in uncertainty that grows with time. Combining dead-reckoning with new Fastloc-GPS technology should provide good opportunities for reconstructing georeferenced fine-scale tracks, and should be particularly useful for marine animals that spend most of their time under water. We developed a computationally efficient, Bayesian state-space modelling technique to estimate humpback whale locations through time, integrating dead-reckoning using on-animal sensors with measurements of whale locations using on-animal Fastloc-GPS and visual observations. Positional observation models were based upon error measurements made during calibrations. RESULTS High-resolution 3-dimensional movement tracks were produced for 13 whales using a simple process model in which errors caused by water current movements, non-location sensor errors, and other dead-reckoning errors were accumulated into a combined error term. Positional uncertainty quantified by the track reconstruction model was much greater for tracks with visual positions and few or no GPS positions, indicating a strong benefit to using Fastloc-GPS for track reconstruction. Compared to tracks derived only from position fixes, the inclusion of dead-reckoning data greatly improved the level of detail in the reconstructed tracks of humpback whales. Using cross-validation, a clear improvement in the predictability of out-of-set Fastloc-GPS data was observed compared to more conventional track reconstruction methods. Fastloc-GPS observation errors during calibrations were found to vary by number of GPS satellites received and by orthogonal dimension analysed; visual observation errors varied most by distance to the whale. CONCLUSIONS By systematically accounting for the observation errors in the position fixes, our model provides a quantitative estimate of location uncertainty that can be appropriately incorporated into analyses of animal movement. This generic method has potential application for a wide range of marine animal species and data recording systems.
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Affiliation(s)
- Paul J. Wensveen
- />Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, St Andrews, Fife, KY16 8LB UK
| | - Len Thomas
- />Centre for Research into Ecological and Environmental Modelling, University of St Andrews, St Andrews, Fife, KY16 9LZ UK
| | - Patrick J. O. Miller
- />Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, St Andrews, Fife, KY16 8LB UK
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