DOI: 10.5061/dryad.jm63xsjj0
title: Beneath the Antarctic sea-ice: Fine-scale analysis of Weddell seal (Leptonychotes weddellii) behaviour and predator-prey interactions, using micro-sonar data in Terre Adélie

description: In this study, we tried to assess:i) whether and how female Weddell seals
 feed (frequency, depth, duration) during lactation,ii) what is their
 utilization of a limited foraging area (benthic or pelagic dives) as they
 are spatially constrained by the presence of their pup, andiii) how can we
 characterize their foraging dives and the approach/catching phases using
 new tools providing a more detailed description of their behaviour.Sonar
 tags were deployed on three breeding female Weddell seals in Terre Adélie
 (East Antarctica) in November 2019, to study animals’ movements and dives
 at high resolution (3D acceleration, magnetometry, time and depth and GPS
 location), as well as information on prey and predator-prey interactions
 using acoustic data.
description: Sonar tags were deployed for a
 week on three breeding female Weddell seals in Terre Adélie (East
 Antarctica) in November 2019, to study animals’ movements and dives at
 high resolution (3D acceleration, magnetometry, time and depth and GPS
 location), as well as information on prey and predator-prey interactions
 using acoustic data (Goulet et al. 2019). The individuals are identified
 respectively as #314a, #314b and #315a. The sonars tags also included 3D
 acceleration and magnetometry sensors providing unprecedented data to
 document the approach and pursuit of prey by predators.
 Deployment started on
 November 11th (2 individuals) and November 12<sup>th</sup> (1
 individual) and ended on November 17<sup>th</sup> and
 18<sup>th</sup> (7 days deployment) respectively. Females were
 temporarily captured with a canvas head-bag and anesthetized with a 1:1
 combination of Tiletamine and Zolazepam (Zoletil), at a dosage of 0.5
 mg.kg<sup>-1</sup> (Wheatley et al. 2006). Seals were
 monitored until fully recovered from anaesthesia and were allowed to go
 back to sea when no longer sedated. The tags were glued to the fur using
 quick-setting two-part epoxy (Araldite AW 2101 and Hardener HW 2951). Two
 types of equipment were deployed: i) an Argos-transmitting GPS tag was
 glued on the back of the animal, and recorded GPS position at the surface
 (Wildlife Computers Inc., Splash10-BF, 86 x 55 x 27 mm, 132 g in air); ii)
 a sonar tag designed by M. Johnson and P. Goulet, containing several types
 of sensors (SMRU tags, 85x44x32 mm, 120 g in air) was attached on the head
 of the animal. The sonar tag recorded pressure and magnetometry at 50Hz.
 It also recorded acceleration in the three axes at 250Hz (individuals
 #314a and #314b) or 200Hz (individual #315a). The tag was configured to
 emit 10µs pings at a rate of 25Hz (i.e., 25 sound signals per second),
 with a -3dB beamwidth of approximately 3.4 degrees and detection range of
 7m. The tag was programmed to record continuously throughout the
 deployment. For one individual, #314a, the depth sensor stopped working
 properly after approximately 142.3 hours (the 370<sup>th</sup>
 dive, at the end of the fifth day) until the end of the deployment. Data
 analysis was conducted in Matlab version R2021b (The MathWorks, Natick,
 MA, USA), using functions from www.animaltags.org, and in R Studio software, version 1.3.1093 (R Core Team, 2020). Movement data (depth, magnetometry, tri-axial acceleration) were calibrated using custom-made script and function do.cal (www.animaltags.org). Magnetometry was calibrated based on location of true magnetic south and date. Magnetometry and depth were downsampled to a sampling frequency of 5Hz for the rest of the analysis. Acceleration data were kept at their full bandwidth. All experiments were conducted under the ethical regulation approval of the French sub-Antarctic and Antarctic territories (TAAF) ethic committee. All animals in this study were treated in accordance with the “Comité de l’Environnement Polaire” Ethic Committee guidelines and the work was conducted under permit #2019-107 of Terre Australes et Antarctiques Française. We warmly thank all the fieldworkers of the 69<sup>th</sup> (2019) and 70<sup>th</sup> (2020) expeditions to Dumont D’Urville, and the IPEV program 109 who assisted in the field. Animal Tag Tools Wiki. 2017. URL https:// animaltags.Org/ Goulet P, Guinet C, Swift R, Madsen PT, Johnson M. 2019. A miniature biomimetic sonar and movement tag to study the biotic environment and predator-prey interactions in aquatic animals. Deep Sea Res Part Oceanogr Res Pap. 148:1–11. Doi:10.1016/j.Dsr.2019.04.007. MATLAB, 2014. Version r2014b. Natick, Massachusetts: The mathworks Inc. URL https://fr.Mathworks.Com/ R core team, 2020. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.Org/ Ramsay J.O., Graves S., Hooker G. 2021. ‘fda: Functional Data Analysis’. R package version 5.5.1.  Wheatley KE, Bradshaw CJ, Harcourt RG, Davis LS, Hindell MA. 2006. Chemical immobilization of adult female Weddell seals with tiletamine and zolazepam: effects of age, condition and stage of lactation. BMC Vet Res. 2(1):8. Doi:10.1186/1746-6148-2-8.
description: # Beneath the Antarctic sea-ice: Fine-scale analysis of Weddell seal
 (Leptonychotes weddellii) behaviour and predator-prey interactions, using
 micro-sonar data in Terre Adélie. ## Abstract In this study, we tried to
 assess i) whether and how female Weddell seals feed (frequency, depth,
 duration) during lactation, ii) what is their utilization of a limited
 foraging area (benthic or pelagic dives) as they are spatially constrained
 by the presence of their pup, iii) how can we characterize their foraging
 dives and the approach/catching phases using new tools providing a more
 detailed description of their behaviour. Sonar tags were deployed on three
 breeding female Weddell seals in Terre Adélie (East Antarctica) in
 November 2019, to study animals’ movements and dives at high resolution
 (3D acceleration, magnetometry, time and depth and GPS location), as well
 as information on prey and predator-prey interactions using acoustic data.
 ## Description of the data and file structure ### Usage note Raw data were
 calibrated and pre-processed following a routine that has been developed
 by Mark P. Johnson, with the help of Pauline Goulet. Please refer to Mark
 Johnson () for code distribution. Codes for
 acceleration data processing, isolation of prey capture attempts from
 acceleration data, and visual analysis of the echograms for fine scale
 predator-prey interaction description have been written by Pauline Goulet.
 Please refer to Pauline Goulet () for
 code distribution. The tags were deployed for seven days in Terre Adélie
 (East Antarctica). The three tags are hereafter referred to as 314a, 314b
 and 315a respectively. ### Datasets included "NameOfTag" is
 either “314a”, “314b” or “315a”. ***1) lw19_NameOfTag_sensor.nc***: NetCDF
 file containing calibrated data recorded by the tag (acceleration in each
 of the three axis, depth, magnetometry) and general information on tag
 deployment, with: * in the “A” structure: acceleration data in each of the
 three axis, with metadata, * in the “info” structure:
 metadata on the tag deployment date, location, type, and other
 information, * in the “J” structure: RMS norm-jerk data
 (magnitude of the quick acceleration of the head), obtained from tri-axial
 acceleration data, with metadata, * in the “P” structure:
 calibrated depth data in meters, with metadata, * in the “T”
 structure: temperature data in degrees Celsius, with metadata. ***2)
 lw19_NameOfTag_dives.mat***: MATLAB structure containing information on
 dives, dives shallower than 5m were removed during pre-processing of the
 data, with: * dive start and end time, expressed as the number of seconds
 elapsed since the tag was turned on, * other time
 information such as the duration of the dive, or the start time in datenum
 format, * maximum depth (dives.max), *
 coordinates, latitude and longitude in degrees. ***3)
 lw19_NameOfTag_summary_dives.csv***: CSV file summarising available dive
 data, with the depth (meters), time (datenum format) and dive index of
 each recorded point of the dive. ***4) lw19_NameOfTag_cluster.csv***: CSV
 file containing the cluster analysis result, with the cluster number and
 the index of the corresponding dive (obtained after running code
 “lw1_functional_pca_on_dive_shapes”). ***5)
 lw19_NameOfTag_jerks_fullbandwidth.mat***: jerk data, i.e., rapid head
 movement detected from tri-axial acceleration data, at full bandwidth
 (initial frequency of recording, 200 to 250Hz), and metadata on tag
 deployment, with: \- In the “info” structure: metadata on tag deployment
 \- In the “jerks” structure: * jerk start and end time, expressed as the
 number of seconds elapsed since the tag was turned on, *
 other time information such as the duration of the jerk, or the start time
 in datenum format, * depth of the jerk, in meters,
 * coordinates, latitude and longitude in degrees. ***6)
 lw19_NameOfTag_argos_track.mat***: 3D reconstruction of the animal’s
 trajectory, in local coordinates (dead-reckoned track), from Argos
 transmitted localisation data, with: * serial date numbers (datenum MATLAB
 format) elapsed from the reference date 1-Jan-0000, *
 coordinates, latitude and longitude in degrees. ***7)
 lw19_NameOfTag_sunangle.mat***: sun elevation during dives, with: * the
 sun angle at the moment of the dive, expressed in degrees, *
 dive start and end time, expressed as the number of seconds elapsed since
 the tag was turned on, * other time information such as the
 duration of the dive, or the start time in datenum format, *
 maximum depth (dives.max), * coordinates, latitude and
 longitude in degrees. ***8) lw19_sonar_visual_analysis_results.mat***:
 MATLAB structure containing results from the visual analysis of the
 echograms (sonar data) corresponding to the moment when jerks (rapid
 acceleration of the head) where identified, in random order, with: *
 information on the corresponding jerk: individual (“prefix”), jerk number
 for the given individual (“index_relative_indiv”), start and end time of
 the jerk, depth in meters, and date (in datetime and datenum format),
 * results of the visual analysis: whether the bottom or a
 prey were visible (“presence_bottom” and “presence_prey”, 1:yes, 0: no),
 whether there was a single prey or a school of prey (“indiv_prey”, 1:
 single, 0: school), whether the prey reacted or not (“prey_reaction”, 1:
 yes, 0: not), the type of reaction (“prey_reaction_type”, 1: the prey
 leaves the bottom, 2: the prey escapes from the predator), the time and
 distance of the reaction (“prey_reaction_time” expressed as the number of
 seconds after the start of the corresponding jerk, and
 “prey_reaction_distance” in meters), and the prey acoustic size estimated
 from the number of pixels (“prey_size”). Missing values are denoted by
 NaN. ## Code/Software To run the analysis, we used Matlab version R2021b
 (The MathWorks, Natick, 242 MA, USA) and R Studio software, version
 1.3.1093 (R Core Team, 2020). The code for the functional principal
 component analysis (“lw1_functional_pca_on_dive_shapes”) has been written
 with the help of David Nerini (Mediterranean Institute of Oceanography,
 Pytheas Institute, UMR 7294, 13288 Marseille, France). The code is shared
 here in Markdown script and HTML knitted formats. Codes are numbered in
 the order that they should be run. ## Acknowledgements We are greatly
 indebted to Mark P. Johnson who designed the sonar tags, supervised this
 work, and developed the algorithm necessary to analyse the sonar tag data.
 This work was supported by the French Polar Institute (IPEV) program 1182
 ASSET, the “Sentinel of the Sea-Ice Environment” SENSEI BNP-Paribas
 Fondation project, and the CNES-TOSCA program “Weddell seals
 bio-oceanographers of the Antarctic sea-ice” (P.I.: J.B. Charrassin and S.
 Labrousse). We also thank Prof. P. T. Madsen and the MSCA EU grant
 ‘’FEAST’’. Karine Heerah received fundings from a Marie Sklodowska Curie
 fellowship for this project (project 792042 - FEAST - H2020-MSCA-IF-2017).
 Adelie Antoine received a PhD fellowship for the GDR OMER (CNRS). All
 experiments were conducted under the ethical regulation approval of the
 French sub-Antarctic and Antarctic territories (TAAF) ethic committee. All
 animals in this study were treated in accordance with the “Comité de
 l’Environnement Polaire” Ethic Committee guidelines and the work was
 conducted under permit #2019-107 of Terre Australes et Antarctiques
 Française. We warmly thank all the fieldworkers of the 69th (2019) and
 70th (2020) expeditions to Dumont D’Urville, and the IPEV program 109 who
 assisted in the field.