The Retrospective Analysis of Antarctic Tracking (Standardised) Data from the Scientific Committee on Antarctic Research

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Comment citer

Les chercheurs doivent citer cette ressource comme suit:

Ropert-Coudert Y, Van de Putte A P, Bornemann H, Charrassin J, Costa D P, Danis B, Hückstädt L A, Jonsen I D, Lea M, Reisinger R R, Thompson D, Torres L G, Trathan P N, Wotherspoon S, Ainley D G, Alderman R, Andrews-Goff V, Arthur B, Ballard G, Bengtson J, Bester M N, Boehme L, Bost C, Boveng P, Cleeland J, Constantine R, Crawford R J M, Dalla Rosa L, de Bruyn P N, Delord K, Descamps S, Double M, Emmerson L, Fedak M, Friedlander A, Gales N, Goebel M, Goetz K T, Guinet C, Goldsworthy S D, Harcourt R, Hinke J, Jerosch K, Kato A, Kerry K R, Kirkwood R, Kooyma G L, Kovacs K M, Lawton K, Lowther A D, Lydersen C, Lyver P O, Makhado A B, Márquez M E I, McDonald B, McMahon C, Muelbert M, Nachtsheim D, Nicholls K W, Nordøy E S, Olmastroni S, Phillips R A, Pistorius P, Plötz J, Pütz K, Ratcliffe N, Ryan P G, Santos M, Schytte Blix A, Southwell C, Staniland I, Takahashi A, Tarroux A, Trivelpiece W, Wakefield E, Weimerskirch H, Wienecke B, Xavier J C, Raymond B, Hindell M A (2020): The Retrospective Analysis of Antarctic Tracking (Standardised) Data from the Scientific Committee on Antarctic Research. v1.3. SCAR - AntOBIS. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=raatd_scar_trackingdata&v=1.3

Droits

Les chercheurs doivent respecter la déclaration de droits suivante:

L’éditeur et détenteur des droits de cette ressource est SCAR - AntOBIS. Ce travail est sous licence Creative Commons Attribution (CC-BY) 4.0.

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Cette ressource a été enregistrée sur le portail GBIF, et possède l'UUID GBIF suivante : b86fe411-8e62-4cd0-aab2-914d75401598.  SCAR - AntOBIS publie cette ressource, et est enregistré dans le GBIF comme éditeur de données avec l'approbation du Ocean Biodiversity Information System.

Mots-clé

Occurrence; ANIMAL ECOLOGY AND BEHAVIOR BIRDS ALBATROSSES/PETRELS AND ALLIES PENGUINS MAMMALS SEALS/SEA LIONS/WALRUSES BALEEN WHALES

Données externes

Les données de la ressource sont disponibles dans d'autres formats

Contacts

Yan Ropert-Coudert

• Auteur ●
• Créateur ●
• Personne De Contact

Centre d’Etudes Biologiques de Chizé, Station d’Écologie de Chizé-Université de La Rochelle

CNRS UMR7372

79360 Villiers-en-Bois

FR

yan.ropert-coudert@cebc.cnrs.fr

http://www.biodiversity.aq

Anton P. Van de Putte

• Créateur ●
• Personne De Contact

BEDIC, OD Nature, Royal Belgian Institute for Natural Sciences

Rue Vautierstraat 29

B-1000 Brussels

BE

bruno.danis@gmail.com

http://orcid.org/0000-0003-1336-5554

Horst Bornemann

• Auteur ●
• Créateur

Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung

Am Handelshafen 12

27570 Bremerhaven

bruno.danis@gmail.com

Jean-Benoît Charrassin

• Auteur ●
• Créateur

Sorbonne Universités, UPMC University, Paris 06

FR

Daniel P. Costa

• Auteur ●
• Créateur

Department of Ecology and Evolutionary Biology, University of California Santa Cruz

US

Bruno Danis

• Auteur ●
• Créateur

Université Libre de Bruxelles, Marine Biology Lab

Luis A. Hückstädt

• Créateur

Department of Ecology and Evolutionary Biology, University of California Santa Cruz

US

Ian D. Jonsen

• Créateur

Department of Biological Sciences, Macquarie University

Mary-Anne Lea

• Auteur ●
• Créateur

Institute for Marine and Antarctic Studies, University of Tasmania

Ryan R. Reisinger

• Auteur ●
• Créateur

Centre d’Etudes Biologiques de Chizé, Station d’Écologie de Chizé-Université de La Rochelle

David Thompson

• Auteur ●
• Créateur

National Institute of Water and Atmospheric Research Ltd

Leigh G. Torres

• Auteur ●
• Créateur

Hatfield Marine Science Center

Philip N. Trathan

• Auteur ●
• Créateur

British Antarctic Survey, Natural Environment Research Council

Simon Wotherspoon

• Auteur ●
• Créateur

Institute for Marine and Antarctic Studies, University of Tasmania

David G Ainley

• Créateur

Rachael Alderman

• Créateur

Virginia Andrews-Goff

• Créateur

Ben Arthur

• Créateur

Grant Ballard

• Créateur

John Bengtson

• Créateur

Marthán N. Bester

• Créateur

Lars Boehme

• Créateur

Charles-André Bost

• Créateur

Peter Boveng

• Créateur

Jaimie Cleeland

• Créateur

Rochelle Constantine

• Créateur

Robert J. M. Crawford

• Créateur

Luciano Dalla Rosa

• Créateur

P.J. Nico de Bruyn

• Créateur

Karine Delord

• Créateur

Sébastien Descamps

• Créateur

Mike Double

• Créateur

Louise Emmerson

• Créateur

Mike Fedak

• Créateur

Ari Friedlander

• Créateur

Nick Gales

• Créateur

Mike Goebel

• Créateur

Kimberly T. Goetz

• Créateur

Christophe Guinet

• Créateur

Simon D. Goldsworthy

• Créateur

Rob Harcourt

• Créateur

Jefferson Hinke

• Créateur

Kerstin Jerosch

• Créateur

Akiko Kato

• Créateur

Knowles R. Kerry

• Créateur

Roger Kirkwood

• Créateur

Gerald L. Kooyma

• Créateur

Kit M. Kovacs

• Créateur

Kieran Lawton

• Créateur

Andrew D. Lowther

• Créateur

Christian Lydersen

• Créateur

Phil O'B. Lyver

• Créateur

Azwianewi B. Makhado

• Créateur

Maria E. I. Márquez

• Créateur

Birgitte McDonald

• Créateur

Clive McMahon

• Créateur

Monica Muelbert

• Créateur

Dominik Nachtsheim

• Créateur

Keith W. Nicholls

• Créateur

Erling S. Nordøy

• Créateur

Silvia Olmastroni

• Créateur

Richard A. Phillips

• Créateur

Pierre Pistorius

• Créateur

Joachim Plötz

• Créateur

Klemens Pütz

• Créateur

Norman Ratcliffe

• Créateur

Peter G. Ryan

• Créateur

Mercedes Santos

• Créateur

Arnoldus Schytte Blix

• Créateur

Colin Southwell

• Créateur

Iain Staniland

• Créateur

Akinori Takahashi

• Créateur

Arnaud Tarroux

• Créateur

Wayne Trivelpiece

• Créateur

Ewan Wakefield

• Créateur

Henri Weimerskirch

• Créateur

Barbara Wienecke

• Créateur

José C. Xavier

• Créateur

Ben Raymond

• Auteur ●
• Créateur

Mark A. Hindell

• Créateur

Anton Van de Putte

• Fournisseur Des Métadonnées ●
• Auteur

BEDIC, OD Nature, Royal Belgian Institute for Natural Sciences

Rue Vautierstraat 29

B-1000 Brussels

BE

antonarctica@gmail.com

Mark Hindell

• Auteur

Professor

Antarctic Climate and Ecosystems Cooperative Research Centre, University of Tasmania,

Hobart

AU

http://orcid.org/0000-0002-7823-7185

Luis Huckstadt

• Auteur

Researcher

Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Long Marine Lab

115 McAllister Way

CA 95060 Santa Cruz

California

US

http://orcid.org/0000-0002-2453-7350

Ian D Jonsen

• Auteur

Professor

Department of Biological Sciences, Macquarie University

Sydney, NSW 2109 Sydney

AU

David G. Ainley

• Fournisseur De Contenu

H.T. Harvey & Associates

983 University Avenue

CA 95032 Los Gatos

California

US

Couverture géographique

The dataset is restricted to the Southern Ocean, in a broad sense. All species considered in this dataset have circumpolar distributions with a longitudinal range spanning 180°W to 180°E. The species breed either on the coast of the Antarctic continent or on the sub-Antarctic islands to the north

Couverture taxonomique

Seventeen species of meso- and top predators were included in the dataset, five marine mammals (one baleen whale, one otariid and three phocid seals) and twelve seabirds (five penguin, five albatross, and two petrels). The species cover a diverse range of ecological niches and life history traits and include dietary specialists (e.g. crabeater seals), deep divers (e.g. elephant seal Mirounga leonina and emperor penguin Aptenodytes forsteri), wide ranging, highly migratory species (e.g. wandering albatross Diomedea exulans), nearshore foragers (e.g. Adélie penguin Pygoscelis adeliae) and capital (e.g. Weddell seal) versus income (e.g. Antarctic fur seal Arctocephalus gazella) breeders.

Couverture temporelle

Données sur le projet

The Retrospective Analysis of Antarctic Tracking Data (RAATD) was initiated in 2010 by the Expert Group on Birds and Marine Mammals (EG-BAMM) and the Expert Group on Antarctic Biodiversity Informatics (EGABI) of the Scientific Committee on Antarctic Research (SCAR). RAATD aims to advance our understanding of both fundamental and applied questions in a data-driven way, matching research priorities already identified by the SCAR Horizon Scanand key questions in animal movement ecology. For these reasons, we worked on the collation, validation and preparation of tracking data collected south of 45° S. Data from over 70 contributors were collated. This database includes information from 17 predator species, including 4,060 individuals and over 2.9 million at-sea locations. To exploit this unique dataset, RAATD undertook a multi-species assessment of habitat use for higher predators in the Southern Ocean (Hindell et al. in prep.).

Les personnes impliquées dans le projet:

Méthodes d'échantillonnage

Original deployment of tracking devices The RAATD core group (Fig. 1) aggregated data from three types of tracking device used by individual research teams. In increasing order of precision these are light recording Global Location Sensors (GLS loggers or geolocators), satellite-relayed Platform Terminal Transmitters (PTTs), and Global Positioning System devices (GPS). Typically, GLS and GPS devices record data in internal memory, and so must be physically recovered in order to download the data. PTTs transmit a carrier signal to satellites, and so can deliver data remotely and in near-real time. Some modern devices now combine the capabilities of PTT and GPS (or other) devices, relaying data to satellites. A GLS device, which is the smallest thus allowing deployment on the smaller predators, typically records ambient light levels through the day from which relatively coarse estimates of latitude and longitude can be calculated (~100–200 km) using day length and timing of local noon. Some GLS units can also record sea surface temperature, and this can help refine position estimates. GLS locations were estimated by the data contributors using five methods (Phillips et al. 2004, Sumner et al. 2009, Lisovski & Hahn 2012, Bindoff 2017, Wotherspoon 2017) (Supplementary File S2). With very small batteries, the data are usually archived and thus animals must be recaptured to download the data. GPS tags make use of global navigation satellite systems and provide very high resolution (~10 m) location fixes and time information. PTT tags transmit signals to ARGOS satellites which transfer the received signals and their frequencies to a receiving station at the Collecte de Localisation Satellites (CLS) in Toulouse, France, to estimate locations based on Doppler shifts in the received signals to a medium level of accuracy(~1,000 m). Processing by CLS involved a least-squares filtering method up to 2008, thereafter using Kalman filters (Lopez et al. 2014). Different models of GLS, PTT, and GPS devices from different manufactures have been used throughout the years, each of these having specific characteristics (size, operating modes, etc.) that may influence accuracy of the locations, but as device type was not always provided by the data providers, we applied standard corrections (see below). Device attachment to animals was also species-specific. When loggers are small enough, like GLS, they are mounted on leg or flipper bands, while larger data-loggers and transmitters are often attached to the plumage or fur on the back or head of the animal, a position that optimizes data communication with satellites. Modes of attachment on the back varied from using harnesses, glue or marine tape. For whales, transmitters with cutaneous anchors were attached to the back, using poles, cross bows or air guns. Scientists limited handling time and stress as much as possible during attachment and retrieval of devices (e.g. Field et al. 2012), following established animal handling guidelines, and institutional ethical review. However, it should be noted that our dataset contains tracking data that span almost three decades during which time substantial progress has been made in terms of miniaturization and advances in electronic components. Any adverse effects of devices on animals are therefore likely to be less acute in recent years than in the earlier years of tracking. Consideration of adverse reaction on study animals has been reviewed in the past (e.g. Phillips et al. 2003, Vandenabeele et al. 2012, Bannasch et al. 1994).

Description des étapes de la méthode:

1. Data Collection Starting from 2010, the core group of RAATD compiled a catalogue of existing (both published and unpublished) tracking data by contacting international experts and asking them to contribute data. The data collection phase ended in 2016. Besides directly contacting researchers, the team also harvested data from existing repositories, including the Australian Antarctic Data Center (https://data.aad.gov.au/), the Integrated Marine Observing System (http://imos.org.au/), PANGAEA (https://www.pangaea.de/), BirdLife International (http://www.seabirdtracking.org/), the Antarctic Biodiversity Portal (http://www.biodiversity.aq/), Ocean Biogeographic Information System (http://www.iobis.org/), and the Global Biodiversity Information Facility (http://www.gbif.org/).
2. Associated metadata Where available, information on the deployment site and relevant characteristics of the animal at the time of deployment was standardized by the data editors. Where age class and sex were known, these were included in the metadata
3. Data standardization Location dates and times were converted to UTC (Coordinated Universal Time). Records with missing latitude or longitude values were removed, and all longitudes were transformed to lie between 180° W and 180° E. Data files were row-ordered by individual, with rows within an individual in their correct temporal sequence. Near-duplicate positions were removed, those positions defined as having occurred 3 seconds or less after an existing position fix from the same animal, and which had identical longitude and latitude values (for GPS devices) or longitude and latitude values that differed by less than 1e-05 and which had the same location quality value (for PTT devices). Entries in the age class, breeding stage, device type, location quality, scientific, common, and abbreviated name, sex, and deployment site columns were validated against controlled vocabularies. Mandatory entries (e.g. deployment date, device type, individual animal identifier) were checked for missing values. Deployment locations were recorded by the original field team either at the individual animal level (using e.g. a hand-held GPS device) or at the deployment-site level (i.e. one deployment location per group of animals). The latter was common for deployments at colonies, whereas the former was most common for non-colony deployments (e.g. on seals and whales). Where deployment locations were not recorded by the field team, the first location estimate(s) in the tracking data were used. Deployment site names were standardized to colony granularity wherever possible (e.g. to the beach-on-island level). Periods at the start or end of deployments were identified and discarded if there was evidence that location data during these periods did not represent the animals’ at-sea movement. For example, tags may have been turned on early (thereby recording locations prior to their deployment on animals) or animals may have remained at the deployment site, e.g. the breeding colony, for an extended period at the start or end of the tag deployment. Some tracks also showed a marked deterioration in the frequency and quality (for PTTs) of location estimates near the end of a track. Such locations were visually identified based on maps of each track in conjunction with plots of location distance from deployment site against time. This information is captured in the location_to_keep column appended to each species’ raw data file (1 = keep, 0 = discard).
4. Data filtering The trimmed data were subjected to a number of automated quality control checks to remove individual deployments that: 1) were flagged for removal by the Data Editor Group (using the keepornot column in the metadata file); 2) had fewer than 20 location records; and 3) had deployments lasting less than 1 day. Additionally, individual deployments were checked to ensure that: 1) duplicate records in PTTs (locations occurring within 2 min of each other) were removed; 2) PTT Argos Z-class locations were reclassified as B-class locations (the least precise Argos location quality class that has an associated error variance; Jonsen et al. 2005); and 3) locations implying unrealistic travel rates (> 10 m s-1 for penguins and marine mammals and > 30 m s-1 for flying seabirds) were removed. Note that the definition of “duplicate locations” in this filtering context is more aggressive than that used during data standardization: for standardization purposes, the intention was to keep the data as close to original as possible, whereas for filtering the presence of multiple positions in a short period of time (< 2 min) has a negative effect on the filter performance. A state-space model (SSM) was used to estimate locations at regular time intervals (1 h for GPS data; 2 h for Argos data; 12 h for GLS data) and account for measurement error in the original observations (Jonsen et al. 2005, Block et al. 2011). The data were SSM-filtered and subject to a final quality control where tracks that failed to converge, as judged by nlminb convergence criteria (Nash 2014), were re-fit using different initial values. If re-fit tracks continually failed to converge they were removed from the final filtered dataset. For converged tracks, longitude and latitude residuals were examined for systematic trends indicative of lack of fit. Tracks that failed this inspection were removed from the final filtered dataset.
5. Data publication The core working team of RAATD established a data sharing and publication agreement with all data providers in 2017. The standardized (trimmed) data are held here. The filtered data are published in international repositories (see details below, in the ‘Filtered Data’ section).

Métadonnées additionnelles