Harcourt
Robert
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Robert
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ArticleA standardisation framework for bio-logging data to advance ecological research and conservation(Wiley, 2021-03-15) Sequeira, Ana M. M. ; O'Toole, Malcolm ; Keates, Theresa R. ; McDonnell, Laura H. ; Braun, Camrin D. ; Hoenner, Xavier ; Jaine, Fabrice R. A. ; Jonsen, Ian ; Newman, Peggy ; Pye, Jonathan ; Bograd, Steven ; Hays, Graeme ; Hazen, Elliott L. ; Holland, Melinda ; Tsontos, Vardis ; Blight, Clint ; Cagnacci, Francesca ; Davidson, Sarah C. ; Dettki, Holger ; Duarte, Carlos M. ; Dunn, Daniel C. ; Eguíluz, Víctor M. ; Fedak, Michael ; Gleiss, Adrian C. ; Hammerschlag, Neil ; Hindell, Mark ; Holland, Kim ; Janekovic, Ivica ; McKinzie, Megan K. ; Muelbert, Monica M. C. ; Pattiaratchi, Charitha ; Rutz, Christian ; Sims, David W. ; Simmons, Samantha E. ; Townsend, Brendal ; Whoriskey, Frederick G. ; Woodward, Bill ; Costa, Daniel P. ; Heupel, Michelle R. ; McMahon, Clive R. ; Harcourt, Robert ; Weise, Michael1. Bio-logging data obtained by tagging animals are key to addressing global conservation challenges. However, the many thousands of existing bio-logging datasets are not easily discoverable, universally comparable, nor readily accessible through existing repositories and across platforms, slowing down ecological research and effective management. A set of universal standards is needed to ensure discoverability, interoperability and effective translation of bio-logging data into research and management recommendations. 2. We propose a standardisation framework adhering to existing data principles (FAIR: Findable, Accessible, Interoperable and Reusable; and TRUST: Transparency, Responsibility, User focus, Sustainability and Technology) and involving the use of simple templates to create a data flow from manufacturers and researchers to compliant repositories, where automated procedures should be in place to prepare data availability into four standardised levels: (a) decoded raw data, (b) curated data, (c) interpolated data and (d) gridded data. Our framework allows for integration of simple tabular arrays (e.g. csv files) and creation of sharable and interoperable network Common Data Form (netCDF) files containing all the needed information for accuracy-of-use, rightful attribution (ensuring data providers keep ownership through the entire process) and data preservation security. 3. We show the standardisation benefits for all stakeholders involved, and illustrate the application of our framework by focusing on marine animals and by providing examples of the workflow across all data levels, including filled templates and code to process data between levels, as well as templates to prepare netCDF files ready for sharing. 4. Adoption of our framework will facilitate collection of Essential Ocean Variables (EOVs) in support of the Global Ocean Observing System (GOOS) and inter-governmental assessments (e.g. the World Ocean Assessment), and will provide a starting point for broader efforts to establish interoperable bio-logging data formats across all fields in animal ecology.
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ArticleMulti-event modeling of true reproductive states of individual female right whales provides new insights into their decline(Frontiers Media, 2022-10-06) Reed, Joshua ; New, Leslie ; Corkeron, Peter ; Harcourt, RobertAbundance and population trends of Critically Endangered North Atlantic right whales (Eubalaena glacialis, NARW) have been estimated using mark-recapture analyses where an individual’s state is based upon set delineations of age, using historical estimates of age at first reproduction. Here we assigned individual females to states based upon their reproductive experience, rather than age. We developed a Bayesian mark-recapture-recovery model to investigate how survival, recapture, site-fidelity and dead-recovery probabilities vary for female NARW in different states, using data collected from 1977-2018. States were assigned as calves for individuals in their first year; pre-breeder for individuals greater than one year of age who had yet to produce a calf, or breeder if an individual had reproduced. A decline in abundance of female NARW was seen starting in 2014, with 185 females declining yearly to 142 by 2018. The largest decline was seen in breeding females, with 72 estimated to be alive at the beginning of 2018, while female pre-breeder abundance plateaued at around 70 between 2011- 2018. Females born from 2000 onwards had an average 4% (95% CI:0.03-0.06) chance of transitioning from pre-breeder to breeder, compared to 8% (95%CI:0.06-0.1) for females born prior. This reduction in transition rate from non-breeder to breeder for the current cohort resulted in breeding females declining to 51% of the female population by 2018. We show that a collapse in fecundity of breeding females, and the failure of pre-breeders to start breeding, is an important factor in understanding the current decline in abundance of the NARW.
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PreprintConvergence of marine megafauna movement patterns in coastal and open oceans( 2017-09) Sequeira, Ana M. M. ; Rodríguez, Jorge P. ; Eguíluz, Víctor M. ; Harcourt, Robert ; Hindell, Mark ; Sims, David W. ; Duarte, Carlos M. ; Costa, Daniel P. ; Fernández-Gracia, Juan ; Ferreira, Luciana C. ; Hays, Graeme ; Heupel, Michelle R. ; Meekan, Mark G. ; Aven, Allen ; Bailleul, Frédéric ; Baylis, Alastair M. M. ; Berumen, Michael L. ; Braun, Camrin D. ; Burns, Jennifer ; Caley, M. Julian ; Campbell, R. ; Carmichael, Ruth H. ; Clua, Eric ; Einoder, Luke D. ; Friedlaender, Ari S. ; Goebel, Michael E. ; Goldsworthy, Simon D. ; Guinet, Christophe ; Gunn, John ; Hamer, D. ; Hammerschlag, Neil ; Hammill, Mike O. ; Hückstädt, Luis A. ; Humphries, Nicolas E. ; Lea, Mary-Anne ; Lowther, Andrew D. ; Mackay, Alice ; McHuron, Elizabeth ; McKenzie, J. ; McLeay, Lachlan ; McMahon, Cathy R. ; Mengersen, Kerrie ; Muelbert, Monica M. C. ; Pagano, Anthony M. ; Page, B. ; Queiroz, N. ; Robinson, Patrick W. ; Shaffer, Scott A. ; Shivji, Mahmood ; Skomal, Gregory B. ; Thorrold, Simon R. ; Villegas-Amtmann, Stella ; Weise, Michael ; Wells, Randall S. ; Wetherbee, Bradley M. ; Wiebkin, A. ; Wienecke, Barbara ; Thums, MicheleThe extent of increasing anthropogenic impacts on large marine vertebrates partly depends on the animals’ movement patterns. Effective conservation requires identification of the key drivers of movement including intrinsic properties and extrinsic constraints associated with the dynamic nature of the environments the animals inhabit. However, the relative importance of intrinsic versus extrinsic factors remains elusive. We analyse a global dataset of 2.8 million locations from > 2,600 tracked individuals across 50 marine vertebrates evolutionarily separated by millions of years and using different locomotion modes (fly, swim, walk/paddle). Strikingly, movement patterns show a remarkable convergence, being strongly conserved across species and independent of body length and mass, despite these traits ranging over 10 orders of magnitude among the species studied. This represents a fundamental difference between marine and terrestrial vertebrates not previously identified, likely linked to the reduced costs of locomotion in water. Movement patterns were primarily explained by the interaction between species-specific traits and the habitat(s) they move through, resulting in complex movement patterns when moving close to coasts compared to more predictable patterns when moving in open oceans. This distinct difference may be associated with greater complexity within coastal micro-habitats, highlighting a critical role of preferred habitat in shaping marine vertebrate global movements. Efforts to develop understanding of the characteristics of vertebrate movement should consider the habitat(s) through which they move to identify how movement patterns will alter with forecasted severe ocean changes, such as reduced Arctic sea ice cover, sea level rise and declining oxygen content.
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PreprintGiant Australian cuttlefish use mutual assessment to resolve male-male contests( 2015-05) Schnell, Alexandra K. ; Smith, Carolynn L. ; Hanlon, Roger T. ; Harcourt, RobertGame theory models provide a useful framework for investigating strategies of conflict resolution in animal contests. Model predictions are based on estimates of resource-holding potential (RHP) and vary in their assumptions about how opponents gather information about RHP. Models can be divided into self-assessment strategies (energetic war-of-attrition, E-WOA; cumulative assessment model, CAM) and mutual assessment strategies (sequential assessment model, SAM). We used laboratory-staged contests between male giant Australian cuttlefish, Sepia apama, to evaluate RHP traits and to test game theory models. Mantle length was a key indicator of RHP because it predicted contest outcome, whereby larger individuals were more likely to win a contest. Winners and losers did not match behaviours, ruling out the E-WOA. There was no relationship between contest outcome, duration and escalation rates, arguing against the CAM. Persistence to continue a contest was based on RHP asymmetry, rather than loser and/or winner RHP, providing support for the SAM. Motivation to fight was determined from a male’s latency to resume a contest following the introduction of a female during a contest. The latency to resume a contest was negatively related to the size of the focal male and positively related to the size of their opponent. These results show that competing males are able to gather information concerning RHP asymmetries, providing support for mutual assessment. Furthermore, males showed significant behavioural differences in their responses to relatively larger than to relatively smaller opponents. Using an integrative approach, our study provides a well-substantiated example of mutual assessment.
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ArticleRegional variation in winter foraging strategies by Weddell Seals in Eastern Antarctica and the Ross Sea(Frontiers Media, 2021-09-22) Harcourt, Robert ; Hindell, Mark ; McMahon, Clive R. ; Goetz, Kimberly T. ; Charrassin, Jean-Benoit ; Heerah, Karine ; Holser, Rachel R. ; Jonsen, Ian ; Shero, Michelle R. ; Hoenner, Xavier ; Foster, Rose ; Lenting, Baukje ; Tarszisz, Esther ; Pinkerton, Matthew H.The relative importance of intrinsic and extrinsic determinants of animal foraging is often difficult to quantify. The most southerly breeding mammal, the Weddell seal, remains in the Antarctic pack-ice year-round. We compared Weddell seals tagged at three geographically and hydrographically distinct locations in East Antarctica (Prydz Bay, Terre Adélie, and the Ross Sea) to quantify the role of individual variability and habitat structure in winter foraging behaviour. Most Weddell seals remained in relatively small areas close to the coast throughout the winter, but some dispersed widely. Individual utilisation distributions (UDi, a measure of the total area used by an individual seal) ranged from 125 to 20,825 km2. This variability was not due to size or sex but may be due to other intrinsic states for example reproductive condition or personality. The type of foraging (benthic vs. pelagic) varied from 56.6 ± 14.9% benthic dives in Prydz Bay through 42.1 ± 9.4% Terre Adélie to only 25.1 ± 8.7% in the Ross Sea reflecting regional hydrographic structure. The probability of benthic diving was less likely the deeper the ocean. Ocean topography was also influential at the population level; seals from Terre Adélie, with its relatively narrow continental shelf, had a core (50%) UD of only 200 km2, considerably smaller than the Ross Sea (1650 km2) and Prydz Bay (1700 km2). Sea ice concentration had little influence on the time the seals spent in shallow coastal waters, but in deeper offshore water they used areas of higher ice concentration. Marine Protected Areas (MPAs) in the Ross Sea encompass all the observed Weddell seal habitat, and future MPAs that include the Antarctic continental shelf are likely to effectively protect key Weddell seal habitat.
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ArticleFirst description of in situ chlorophyll fluorescence signal within East Antarctic coastal polynyas during fall and winter(Frontiers Media, 2023-07-27) Bourreau, Lucie ; Pauthenet, Etienne ; Le Ster, Loic ; Picard, Baptiste ; Portela, Esther ; Salle, Jean-Baptiste ; McMahon, Clive R. ; Harcourt, Robert ; Hindell, Mark ; Guinet, Christophe ; Bestley, Sophie ; Charrassin, Jean-Benoit ; DuVivier, Alice ; Sylvester, Zephyr ; Krumhardt, Kristen ; Jenouvrier, Stephanie ; Labrousse, SaraAntarctic coastal polynyas are persistent and recurrent regions of open water located between the coast and the drifting pack-ice. In spring, they are the first polar areas to be exposed to light, leading to the development of phytoplankton blooms, making polynyas potential ecological hotspots in sea-ice regions. Knowledge on polynya oceanography and ecology during winter is limited due to their inaccessibility. This study describes i) the first in situ chlorophyll fluorescence signal (a proxy for chlorophyll-a concentration and thus presence of phytoplankton) in polynyas between the end of summer and winter, ii) assesses whether the signal persists through time and iii) identifies its main oceanographic drivers. The dataset comprises 698 profiles of fluorescence, temperature and salinity recorded by southern elephant seals in 2011, 2019-2021 in the Cape-Darnley (CDP;67˚S-69˚E) and Shackleton (SP;66˚S-95˚E) polynyas between February and September. A significant fluorescence signal was observed until April in both polynyas. An additional signal occurring at 130m depth in August within CDP may result from in situ growth of phytoplankton due to potential adaptation to low irradiance or remnant chlorophyll-a that was advected into the polynya. The decrease and deepening of the fluorescence signal from February to August was accompanied by the deepening of the mixed layer depth and a cooling and salinification of the water column in both polynyas. Using Principal Component Analysis as an exploratory tool, we highlighted previously unsuspected drivers of the fluorescence signal within polynyas. CDP shows clear differences in biological and environmental conditions depending on topographic features with higher fluorescence in warmer and saltier waters on the shelf compared with the continental slope. In SP, near the ice-shelf, a significant fluorescence signal in April below the mixed layer (around 130m depth), was associated with fresher and warmer waters. We hypothesize that this signal could result from potential ice-shelf melting from warm water intrusions onto the shelf leading to iron supply necessary to fuel phytoplankton growth. This study supports that Antarctic coastal polynyas may have a key role for polar ecosystems as biologically active areas throughout the season within the sea-ice region despite inter and intra-polynya differences in environmental conditions.