Author: "Simon Chamaillé-Jammes" - Searchworks@Jio Institute Digital Library Search Results

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133 results on '"Simon Chamaillé-Jammes"'

1. Hogs sleep like logs: Wild boars reduce the risk of anthropic disturbance by adjusting where they rest

Author: Gustave Fradin and Simon Chamaillé‐Jammes
Subjects: activity pattern, anthropization, habitat selection, human activities, sleep, Ecology, QH540-549.5
Abstract: Abstract Many animals living in anthropized landscapes try to avoid encountering people by being active at night. By doing so, however, they risk being disturbed while at rest during the day. To mitigate this risk, diurnally resting species may be highly selective about where they rest. Here, we used GPS and activity sensors to study how wild boars (Sus scrofa) might adjust their resting site selection and revisitation patterns to the risk of disturbance by people. We evaluated the probability of daytime relocation to assess the efficacy of wild boars' resting strategy in reducing the risk of human encounter while at rest. We attempted to identify the cause of some relocations using audio recordings. Generally, we found that wild boars did not specifically avoid resting near villages or roads, that is, where the risk of encountering people is higher, if they could find sites with suitable vegetation cover. The risk of disturbance by people was low, even near villages. Resting sites located close to villages were visited more repeatedly than those located further away, suggesting that focusing on a few familiar and quiet resting sites was a successful strategy for resting undisturbed in an anthropized landscape.
Published: 2023
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2. Energy-Efficient Audio Processing at the Edge for Biologging Applications

Author: Jonathan Miquel, Laurent Latorre, and Simon Chamaillé-Jammes
Subjects: low-power biologgers, audio recording, data reduction, edge classification, inline compression, Applications of electric power, TK4001-4102
Abstract: Biologging refers to the use of animal-borne recording devices to study wildlife behavior. In the case of audio recording, such devices generate large amounts of data over several months, and thus require some level of processing automation for the raw data collected. Academics have widely adopted offline deep-learning-classification algorithms to extract meaningful information from large datasets, mainly using time-frequency signal representations such as spectrograms. Because of the high deployment costs of animal-borne devices, the autonomy/weight ratio remains by far the fundamental concern. Basically, power consumption is addressed using onboard mass storage (no wireless transmission), yet the energy cost associated with data storage activity is far from negligible. In this paper, we evaluate various strategies to reduce the amount of stored data, making the fair assumption that audio will be categorized using a deep-learning classifier at some point of the process. This assumption opens up several scenarios, from straightforward raw audio storage paired with further offline classification on one side, to a fully embedded AI engine on the other side, with embedded audio compression or feature extraction in between. This paper investigates three approaches focusing on data-dimension reduction: (i) traditional inline audio compression, namely ADPCM and MP3, (ii) full deep-learning classification at the edge, and (iii) embedded pre-processing that only computes and stores spectrograms for later offline classification. We characterized each approach in terms of total (sensor + CPU + mass-storage) edge power consumption (i.e., recorder autonomy) and classification accuracy. Our results demonstrate that ADPCM encoding brings 17.6% energy savings compared to the baseline system (i.e., uncompressed raw audio samples). Using such compressed data, a state-of-the-art spectrogram-based classification model still achieves 91.25% accuracy on open speech datasets. Performing inline data-preparation can significantly reduce the amount of stored data allowing for a 19.8% energy saving compared to the baseline system, while still achieving 89% accuracy during classification. These results show that while massive data reduction can be achieved through the use of inline computation of spectrograms, it translates to little benefit on device autonomy when compared to ADPCM encoding, with the added downside of losing original audio information.
Published: 2023
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3. Are fission–fusion dynamics consistent among populations? A large‐scale study with Cape buffalo

Author: Elodie Wielgus, Daniel Cornélis, Michel deGarine‐Wichatitsky, Bradley Cain, Hervé Fritz, Eve Miguel, Hugo Valls‐Fox, Alexandre Caron, and Simon Chamaillé‐Jammes
Subjects: association patterns, dyadic interactions, home range overlap, multi‐population, seasonality, Ecology, QH540-549.5
Abstract: Abstract Fission–fusion dynamics allow animals to manage costs and benefits of group living by adjusting group size. The degree of intraspecific variation in fission–fusion dynamics across the geographical range is poorly known. During 2008–2016, 38 adult female Cape buffalo were equipped with GPS collars in three populations located in different protected areas (Gonarezhou National Park and Hwange National Park, Zimbabwe; Kruger National Park, South Africa) to investigate the patterns and environmental drivers of fission–fusion dynamics among populations. We estimated home range overlap and fission and fusion events between Cape buffalo dyads. We investigated the temporal dynamics of both events at daily and seasonal scales and examined the influence of habitat and distance to water on event location. Fission–fusion dynamics were generally consistent across populations: Fission and fusion periods lasted on average between less than one day and three days. However, we found seasonal differences in the underlying patterns of fission and fusion, which point out the likely influence of resource availability and distribution in time on group dynamics: During the wet season, Cape buffalo split and associated more frequently and were in the same or in a different subgroup for shorter periods. Cape buffalo subgroups were more likely to merge than to split in open areas located near water, but overall vegetation and distance to water were very poor predictors of where fission and fusion events occurred. This study is one of the first to quantify fission–fusion dynamics in a single species across several populations with a common methodology, thus robustly questioning the behavioral flexibility of fission–fusion dynamics among environments.
Published: 2020
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4. Multi-mode movement decisions across widely ranging behavioral processes.

Author: Marie-Caroline Prima, Thierry Duchesne, Jerod A Merkle, Simon Chamaillé-Jammes, and Daniel Fortin
Subjects: Medicine, Science
Abstract: Movement of organisms plays a fundamental role in the evolution and diversity of life. Animals typically move at an irregular pace over time and space, alternating among movement states. Understanding movement decisions and developing mechanistic models of animal distribution dynamics can thus be contingent to adequate discrimination of behavioral phases. Existing methods to disentangle movement states typically require a follow-up analysis to identify state-dependent drivers of animal movement, which overlooks statistical uncertainty that comes with the state delineation process. Here, we developed population-level, multi-state step selection functions (HMM-SSF) that can identify simultaneously the different behavioral bouts and the specific underlying behavior-habitat relationship. Using simulated data and relocation data from mule deer (Odocoileus hemionus), plains bison (Bison bison bison) and plains zebra (Equus quagga), we illustrated the HMM-SSF robustness, versatility, and predictive ability for animals involved in distinct behavioral processes: foraging, migrating and avoiding a nearby predator. Individuals displayed different habitat selection pattern during the encamped and the travelling phase. Some landscape attributes switched from being selected to avoided, depending on the movement phase. We further showed that HMM-SSF can detect multi-modes of movement triggered by predators, with prey switching to the travelling phase when predators are in close vicinity. HMM-SSFs thus can be used to gain a mechanistic understanding of how animals use their environment in relation to the complex interplay between their needs to move, their knowledge of the environment and navigation capacity, their motion capacity and the external factors related to landscape heterogeneity.
Published: 2022
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5. Addressing Power Issues in Biologging: An Audio/Inertial Recorder Case Study

Author: Jonathan Miquel, Laurent Latorre, and Simon Chamaillé-Jammes
Subjects: bio-logging, low power, audio, inertial data, MEMS sensors, Chemical technology, TP1-1185
Abstract: In the past decades, biologging, i.e., the development and deployment of animal-borne loggers, has revolutionized ecology. Despite recent advances, power consumption and battery size however remain central issues and limiting factors, constraining the quantity of data that can be collected and the size of the animals that can be studied. Here, we present strategies to achieve ultra-low power in biologging, using the design of a lightweight audio-inertial logger as an example. It is designed with low-power MEMS sensors, and a firmware based on a small embedded RTOS. Both methodologies for power reduction and experimental results are detailed. With an average power consumption reduced to 5.3 mW, combined with a battery of 1800 mAh, the logger provides 900 h of continuous 8 kHz audio, 50 Hz accelerometer and 10 Hz magnetometer data.
Published: 2022
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6. When water interacts with temperature: Ecological and evolutionary implications of thermo‐hydroregulation in terrestrial ectotherms

Author: David Rozen‐Rechels, Andréaz Dupoué, Olivier Lourdais, Simon Chamaillé‐Jammes, Sandrine Meylan, Jean Clobert, and Jean‐François Le Galliard
Subjects: behavioral decisions, body temperature, performance curves, physiological adjustments, water balance, Ecology, QH540-549.5
Abstract: Abstract The regulation of body temperature (thermoregulation) and of water balance (defined here as hydroregulation) are key processes underlying ecological and evolutionary responses to climate fluctuations in wild animal populations. In terrestrial (or semiterrestrial) ectotherms, thermoregulation and hydroregulation closely interact and combined temperature and water constraints should directly influence individual performances. Although comparative physiologists traditionally investigate jointly water and temperature regulation, the ecological and evolutionary implications of these coupled processes have so far mostly been studied independently. Here, we revisit the concept of thermo‐hydroregulation to address the functional integration of body temperature and water balance regulation in terrestrial ectotherms. We demonstrate how thermo‐hydroregulation provides a framework to investigate functional adaptations to joint environmental variation in temperature and water availability, and potential physiological and/or behavioral conflicts between thermoregulation and hydroregulation. We extend the classical cost–benefit model of thermoregulation in ectotherms to highlight the adaptive evolution of optimal thermo‐hydroregulation strategies. Critical gaps in the parameterization of this conceptual optimality model and guidelines for future empirical research are discussed. We show that studies of thermo‐hydroregulation refine our mechanistic understanding of physiological and behavioral plasticity, and of the fundamental niche of the species. This is illustrated with relevant and recent examples of space use and dispersal, resource‐based trade‐offs, and life‐history tactics in insects, amphibians, and nonavian reptiles.
Published: 2019
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7. Climate Effects on Prey Vulnerability Modify Expectations of Predator Responses to Short- and Long-Term Climate Fluctuations

Author: Aïssa Morin, Simon Chamaillé-Jammes, and Marion Valeix
Subjects: population dynamics, traits, vulnerability, climate changes, predator–prey interactions, Evolution, QH359-425, Ecology, QH540-549.5
Abstract: Climate changes affect the distribution and abundance of organisms, often via changes in species interactions. Most animals experience predation, and a number of models have investigated how climate fluctuations can influence predator–prey dynamics by affecting prey abundance through changes in resource availability. However, field studies have shown that prey vulnerability is a key feature determining the outcome of predator–prey interactions, which also varies with climatic conditions, via changes in prey body condition or in habitat characteristics (e.g. vegetation cover). In this theoretical work, we explore, with large mammals of African savannas in mind, how the interplay between climate-induced changes in prey abundance and climate-induced changes in prey vulnerability affects the immediate and long-term responses of predator populations. We account for prey body condition and habitat effects on prey vulnerability to predation. We show that predictions on how predator abundance responds to climate fluctuations differ depending on how climate influences prey vulnerability (habitat characteristics vs. prey body condition). We discuss how species traits influence the relative importance of the different sources of vulnerability. For example, our results suggest that populations of cursorial predators (such as spotted hyaenas) are expected to fare better than populations of ambush predators (such as African lions) in African ecosystems that will be characterised by an aridification. This study highlights the importance of understanding, and accounting for, the vulnerability factors associated to a given predator–prey pair, and improves our comprehension of predator–prey relationships in a changing climate.
Published: 2021
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8. Coping with change in predation risk across space and time through complementary behavioral responses

Author: Pierrick Blanchard, Christine Lauzeral, Simon Chamaillé-Jammes, Clément Brunet, Arnaud Lec’hvien, Guillaume Péron, and Dominique Pontier
Subjects: Vigilance, Habitat use, Prey, Predation risk, Predator, Behavior, Ecology, QH540-549.5
Abstract: Abstract Background Our picture of behavioral management of risk by prey remains fragmentary. This partly stems from a lack of studies jointly analyzing different behavioral responses developed by prey, such as habitat use and fine-scale behavior, although they are expected to complement each other. We took advantage of a simple system on the Kerguelen archipelago, made of a prey species, European rabbit Oryctolagus cuniculus, a predator, feral cat Felis catus, and a mosaic of closed and open foraging patches, allowing reliable assessment of spatio-temporal change in predation risk. We investigated the way such a change triggered individual prey decisions on where, when and how to perform routine activities. Results Rabbit presence and behavior were recorded both day and night in patches with similar foraging characteristics, but contrasted in terms of openness. Cats, individually recognizable, were more active at night and in closed patches, in line with their expected higher hunting success in those conditions. Accordingly, rabbits avoided using closed patches at night and increased their vigilance if they did. Both day and night, rabbits increased their use of closed patches as compared to open patches in windy conditions, thereby probably reducing the thermoregulatory costs expected under such harsh environmental conditions. Conclusions Overall, our data map the landscape of fear in this study system and indicate that prey habitat use and vigilance complement each other. Solely focusing on one or the other tactic may lead to erroneous conclusions regarding the way predation risk triggers prey decisions. Finally, future studies should investigate inter-individual variability in the relative use of these different types of complementary behavioral responses to perceived risk, along with the determinants and outcomes of such tactics.
Published: 2018
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9. Remote Sensing of Environmental Drivers Influencing the Movement Ecology of Sympatric Wild and Domestic Ungulates in Semi-Arid Savannas, a Review

Author: Florent Rumiano, Elodie Wielgus, Eve Miguel, Simon Chamaillé-Jammes, Hugo Valls-Fox, Daniel Cornélis, Michel De Garine-Wichatitsky, Hervé Fritz, Alexandre Caron, and Annelise Tran
Subjects: African savanna, animal movements, earth observation imagery, remote sensing, sympatric wild and domestic ungulates, wildlife-livestock interface, Science
Abstract: Interfaces between protected areas and their peripheries in southern Africa are subject to interactions between wildlife and livestock that vary in frequency and intensity. In these areas, the juxtaposition between production and conservation land uses in a context of increasing anthropisation can create issues associated with human-wildlife coexistence and raises concerns for biodiversity conservation, local development and livelihoods. This literature review aimed at addressing the need to consolidate and gather in one article current knowledge on potential uses of satellite remote sensing (SRS) products by movement ecologists to investigate the sympatry of wildlife/domestic ungulates in savanna interface environments. A keyword querying process of peer reviewed scientific paper, thesis and books has been implemented to identify references that (1) characterize the main environmental drivers impacting buffalo (Syncerus caffer caffer) and cattle (Bos taurus & Bos indicus) movements in southern Africa environments, (2) describe the SRS contribution to discriminate and characterize these drivers. In total, 327 references have been selected and analyzed. Surface water, precipitation, landcover and fire emerged as key drivers impacting the buffalo and cattle movements. These environmental drivers can be efficiently characterized by SRS, mainly through open-access SRS products and standard image processing methods. Applying SRS to better understand buffalo and cattle movements in semi-arid environments provides an operational framework that could be replicated in other type of interface where different wild and domestic species interact. There is, however, a need for animal movement ecologists to reinforce their knowledge of remote sensing and/or to increase pluridisciplinary collaborations.
Published: 2020
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10. Listening to Lions: Animal-Borne Acoustic Sensors Improve Bio-logger Calibration and Behaviour Classification Performance

Author: Matthew Wijers, Paul Trethowan, Andrew Markham, Byron du Preez, Simon Chamaillé-Jammes, Andrew Loveridge, and David Macdonald
Subjects: African lion, acoustic monitoring, behaviour classification, bio-logger calibration, machine learning, random forest, Evolution, QH359-425, Ecology, QH540-549.5
Abstract: Efforts to better understand patterns of animal behaviour have often been restricted by several environmental, human and experimental limitations associated with the collection of animal behavioural data. The introduction of new bio-logging technology has offered an alternative means of recording animal behaviour continuously and is being used in an increasing number of studies. Accurately calibrating these bio-loggers, however, still remains a challenge in many cases. Using lions as an example species, we test how audio recordings from animal-borne acoustic sensors can improve calibration and behaviour classification. Through a collaborative effort between computer scientists, engineers, and zoologists, custom designed acoustic bio-loggers were fitted to eight lions and recorded audio simultaneously with accelerometer and magnetometer data. Audio recordings were then used as the source of ground truth to train random forest classification models as well as to provide additional predictor variables for behaviour classification. We demonstrated near-perfect classification performance for five lion behaviour classes when all component variables were combined, with an average per-class precision of 98.5%. Using accelerometer features only, the audio-trained classifier predicted behaviours with an average per-class precision of 94.3%. On-animal audio recordings are therefore able to provide a valuable source of ground-truth for calibrating bio-loggers while also offering additional predictive features for increasing the accuracy of behaviour classification. This technological innovation has wide ranging application and provides a useful tool for behavioural ecologists wishing to collect fine scale behavioural data for animal research and conservation.
Published: 2018
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11. The 2013–2014 vegetation structure map of Hwange National Park, Zimbabwe, produced using free satellite images and software

Author: Eduardo M. Arraut, Andrew J. Loveridge, Simon Chamaillé-Jammes, Hugo Valls-Fox, and David W. Macdonald
Subjects: Remote sensing, Protected Areas, Management, General. Including nature conservation, geographical distribution, QH1-199.5
Abstract: Vegetation mapping of protected areas is a cornerstone of conservation worldwide. Established in 1928 and covering over 1.4 million hectares, Hwange National Park (HNP) is the largest natural reserve in Zimbabwe. In 1993, the sole comprehensive map of its vegetation to date was produced and since then it has been used in numerous research and conservation endeavours. Over the last two decades, however, the park’s vegetation changed, safari areas and forest reserves were created at its edge and high-positional accuracy data on a suite of species were collected. To tend to contemporary mapping needs, in this article, we present the 2013–2014 vegetation structure map of HNP and its surroundings. It was produced by supervised classification of Landsat-8 Operational Land Imager (OLI) images, indices derived from these and the Landsat Tree Cover Continuous Field product. Its accuracy was assessed statistically using samples collected from high-resolution satellite imagery and basic ancillary field data. Of its total pixels, 83.2% were correctly classified. Mean omission and commission error were, respectively, 0.82 (0.74–0.90) and 0.82 (0.72–0.89), and this similarity held on a per class basis, indicating reliable area estimates. It was produced using only freely available imagery and software. Conservation implications: In addition to providing researchers and conservationists working within and around HNP with an updated vegetation map, aiming at an even broader audience, we provide a step-by-step approach for using modern freely available imagery and software for cost-effectively mapping HNP in future or other protected savannas across Africa.
Published: 2018
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12. Analyzing the proximity to cover in a landscape of fear: a new approach applied to fine-scale habitat use by rabbits facing feral cat predation on Kerguelen archipelago

Author: Pierrick Blanchard, Christine Lauzeral, Simon Chamaillé-Jammes, Nigel G. Yoccoz, and Dominique Pontier
Subjects: Behavioral ecology, Landscape of fear, Predator-prey system, Habitat use, Field method, Protective cover, Medicine, Biology (General), QH301-705.5
Abstract: Although proximity to cover has been routinely considered as an explanatory variable in studies investigating prey behavioral adjustments to predation pressure, the way it shapes risk perception still remains equivocal. This paradox arises from both the ambivalent nature of cover as potentially both obstructive and protective, making its impact on risk perception complex and context-dependent, and from the choice of the proxy used to measure proximity to cover in the field, which leads to an incomplete picture of the landscape of fear experienced by the prey. Here, we study a simple predator-prey-habitat system, i.e., rabbits Oryctolagus cuniculus facing feral cat Felis catus predation on Kerguelen archipelago. We assess how cover shapes risk perception in prey and develop an easily implementable field method to improve the estimation of proximity to cover. In contrast to protocols considering the “distance to nearest cover”, we focus on the overall “area to cover”. We show that fine-scale habitat use by rabbits is clearly related to our measure, in accordance with our hypothesis of higher risk in patches with smaller area to cover in this predator-prey-habitat system. In contrast, classical measures of proximity to cover are not retained in the best predictive models of habitat use. The use of this new approach, together with a more in-depth consideration of contrasting properties of cover, could help to better understand the role of this complex yet decisive parameter for predator-prey ecology.
Published: 2016
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13. Spatial Distribution of a Large Herbivore Community at Waterholes: An Assessment of Its Stability over Years in Hwange National Park, Zimbabwe.

Author: Simon Chamaillé-Jammes, Anaïs Charbonnel, Stéphane Dray, Hillary Madzikanda, and Hervé Fritz
Subjects: Medicine, Science
Abstract: The spatial structuring of populations or communities is an important driver of their functioning and their influence on ecosystems. Identifying the (in)stability of the spatial structure of populations is a first step towards understanding the underlying causes of these structures. Here we studied the relative importance of spatial vs. interannual variability in explaining the patterns of abundance of a large herbivore community (8 species) at waterholes in Hwange National Park (Zimbabwe). We analyzed census data collected over 13 years using multivariate methods. Our results showed that variability in the census data was mostly explained by the spatial structure of the community, as some waterholes had consistently greater herbivore abundance than others. Some temporal variability probably linked to Park-scale migration dependent on annual rainfall was noticeable, however. Once this was accounted for, little temporal variability remained to be explained, suggesting that other factors affecting herbivore abundance over time had a negligible effect at the scale of the study. The extent of spatial and temporal variability in census data was also measured for each species. This study could help in projecting the consequences of surface water management, and more generally presents a methodological framework to simultaneously address the relative importance of spatial vs. temporal effects in driving the distribution of organisms across landscapes.
Published: 2016
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14. African elephants adjust speed in response to surface-water constraint on foraging during the dry-season.

Author: Simon Chamaillé-Jammes, Godfrey Mtare, Edwin Makuwe, and Hervé Fritz
Subjects: Medicine, Science
Abstract: Most organisms need to acquire various resources to survive and reproduce. Individuals should adjust their behavior to make optimal use of the landscape and limit the costs of trade-offs emerging from the use of these resources. Here we study how African elephants Loxodonta africana travel to foraging places between regular visits to waterholes. Elephant herds were tracked using GPS collars during two consecutive dry seasons in Hwange National Park, Zimbabwe. We segmented each individual movement track at each visit to water to define foraging trips, and then used trip-level statistics to build an understanding of movement strategies. Travel speed within these individually-consistent movement bouts was also analyzed to understand if speed was better linked to distance to water or progression in the trip over time. We found that elephants went further from water when drinking less often, which could result from a trade-off between drinking and foraging in less depleted, far from water, places. Speed increased towards the beginning and the end of the trips, and was also greater than observed during the wet season, suggesting that elephants were trying to save time. Numerous short trips traveled at greater speed, particularly when commuting to a different waterhole, was tentatively explained by the inability to drink at specific waterholes due to intra-specific interference. Unexpectedly elephants did not always minimize travel time by drinking at the closest waterhole, but the extra distance traveled remained never more than a few kilometers. Our results show how individuals may adjust movement behavior to deal with resource trade-offs at the landscape scale. We also highlight how behavioral context, here progression in the trip, may be more important than spatial context, here distance to water, in explaining animal movement patterns.
Published: 2013
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15. Evaluating expert-based habitat suitability information of terrestrial mammals with GPS-tracking data

Author: Maarten J. E. Broekman, Jelle P. Hilbers, Mark A. J. Huijbregts, Thomas Mueller, Abdullahi H. Ali, Henrik Andrén, Jeanne Altmann, Malin Aronsson, Nina Attias, Hattie L. A. Bartlam‐Brooks, Floris M. van Beest, Jerrold L. Belant, Dean E. Beyer, Laura Bidner, Niels Blaum, Randall B. Boone, Mark S. Boyce, Michael B. Brown, Francesca Cagnacci, Rok Černe, Simon Chamaillé‐Jammes, Nandintsetseg Dejid, Jasja Dekker, Arnaud L. J. Desbiez, Samuel L. Díaz‐Muñoz, Julian Fennessy, Claudia Fichtel, Christina Fischer, Jason T. Fisher, Ilya Fischhoff, Adam T. Ford, John M. Fryxell, Benedikt Gehr, Jacob R. Goheen, Morgan Hauptfleisch, A. J. Mark Hewison, Robert Hering, Marco Heurich, Lynne A. Isbell, René Janssen, Florian Jeltsch, Petra Kaczensky, Peter M. Kappeler, Miha Krofel, Scott LaPoint, A. David M. Latham, John D. C. Linnell, A. Catherine Markham, Jenny Mattisson, Emilia Patricia Medici, Guilherme de Miranda Mourão, Bram Van Moorter, Ronaldo G. Morato, Nicolas Morellet, Atle Mysterud, Stephen Mwiu, John Odden, Kirk A. Olson, Aivars Ornicāns, Nives Pagon, Manuela Panzacchi, Jens Persson, Tyler Petroelje, Christer Moe Rolandsen, David Roshier, Daniel I. Rubenstein, Sonia Saïd, Albert R. Salemgareyev, Hall Sawyer, Niels Martin Schmidt, Nuria Selva, Agnieszka Sergiel, Jared Stabach, Jenna Stacy‐Dawes, Frances E. C. Stewart, Jonas Stiegler, Olav Strand, Siva Sundaresan, Nathan J. Svoboda, Wiebke Ullmann, Ulrich Voigt, Jake Wall, Martin Wikelski, Christopher C. Wilmers, Filip Zięba, Tomasz Zwijacz‐Kozica, Aafke M. Schipper, Marlee A. Tucker, MAARTEN J. E. BROEKMAN, Radboud University, JELLE P. HILBERS, Radboud University, MARK A. J. HUIJBREGTS, Radboud University, THOMAS MUELLER, Radboud University, ABDULLAHI H. ALI, Hirola Conservation Programme, Garissa, HENRIK ANDRÉN, Swedish University of Agricultural Sciences, JEANNE ALTMANN, Princeton University, MALIN ARONSSON, Swedish University of Agricultural Sciences, NINA ATTIAS, Federal University of Mato Grosso do Sul, HATTIE L. A. BARTLAM-BROOKS, Royal Veterinary College, London, FLORIS M. VAN BEEST, Aarhus University, Roskilde, JERROLD L. BELANT, State University of New York College of Environmental Science and Forestry, DEAN E. BEYER, Michigan State University, LAURA BIDNER, University of California, NIELS BLAUM, University of Potsdam, RANDALL B. BOONE, Colorado State University, MARK S. BOYCE, University of Alberta, MICHAEL B. BROWN, Giraffe Conservation Foundation, Eros, FRANCESCA CAGNACCI, Research and Innovation Centre, ROK CERNE, Slovenia Forest Service, Ljubljana, SIMON CHAMAILLÉ-JAMMES, Univ Paul Valéry Montpellier, NANDINTSETSEG DEJID, Senckenberg Gesellschaft für Naturforschung, JASJA DEKKER, Bionet Natuuronderzoek, ARNAUD L. J. DESBIEZ, Instituto de Conservação de Animais Silvestres (ICAS), SAMUEL L. DÍAZ-MUÑOZ, University of California, JULIAN FENNESSY, Giraffe Conservation Foundation, CLAUDIA FICHTEL, Behavioral Ecology and Sociobiology Unit, Göttingen, CHRISTINA FISCHER, Anhalt University of Applied Sciences, JASON T. FISHER, University of Victoria, ILYA FISCHHOFF, Cary Institute of Ecosystem Studies, Millbrook, ADAM T. FORD, University of British Columbia, JOHN M. FRYXELL, University of Guelph, Guelph, BENEDIKT GEHR, University of Zurich, JACOB R. GOHEEN, University of Wyoming, MORGAN HAUPTFLEISCH, Namibia University of Science and Technology, A. J. MARK HEWISON, Université de Toulouse, ROBERT HERING, University of Potsdam, MARCO HEURICH, Bavarian Forest National Park, LYNNE A. ISBELL, University of California, RENÉ JANSSEN, Bionet Natuuronderzoek, FLORIAN JELTSCH, University of Potsdam, PETRA KACZENSKY, Inland Norway University of Applied Sciences, PETER M. KAPPELER, Behavioral Ecology and Sociobiology Unit, MIHA KROFEL, Biotechnical Faculty, University of Ljubljana, SCOTT LAPOINT, Black Rock Forest, Cornwall, A. DAVID M. LATHAM, University of Alberta, JOHN D. C. LINNELL, Inland Norway University of Applied Sciences, A. CATHERINE MARKHAM, Stony Brook University, JENNY MATTISSON, Norwegian Institute for Nature Research, EMILIA PATRICIA MEDICI, Instituto de Pesquisas Ecológicas, GUILHERME DE MIRANDA MOURAO, CPAP, BRAM VAN MOORTER, Norwegian Institute for Nature Research, RONALDO G. MORATO, Chico Mendes Institute for the Conservation of Biodiversity, NICOLAS MORELLET, Université de Toulouse, ATLE MYSTERUD, Chico Mendes Institute for the Conservation of Biodiversity, STEPHEN MWIU, Wildlife Research and Training Institute, JOHN ODDEN, Norwegian Institute for Nature Research, KIRK A. OLSON, Wildlife Conservation Society, AIVARS ORNICANS, Latvian State Forest Research Institute, NIVES PAGON, Slovenia Forest Service, MANUELA PANZACCHI, Norwegian Institute for Nature Research, TYLER PETROELJE, State University of New York College of Environmental Science and Forestry, CHRISTER MOE ROLANDSEN, Norwegian Institute for Nature Research, DAVID ROSHIER, Australian Wildlife Conservancy, DANIEL I. RUBENSTEIN, Princeton University, SONIA SAÏD, Office Français de la Biodiversité, ALBERT R. SALEMGAREYEV, Association for the Conservation of Biodiversity of Kazakhstan (ACBK), HALL SAWYER, Western Ecosystems Technology Inc., NIELS MARTIN SCHMIDT, Aarhus University, NURIA SELVA, Institute of Nature Conservation Polish Academy of Sciences, AGNIESZKA SERGIEL, Institute of Nature Conservation Polish Academy of Sciences, JARED STABACH, Smithsonian National Zoo and Conservation Biology Institute, JENNA STACY-DAWES, Conservation Science and Wildlife Health, FRANCES E. C. STEWART, University of Victoria, JONAS STIEGLER, University of Potsdam, OLAV STRAND, Norwegian Institute for Nature Research, SIVA SUNDARESAN, Greater Yellowstone Coalition, NATHAN J. SVOBODA, Mississippi State University, WIEBKE ULLMANN, University of Potsdam, ULRICH VOIGT, University of Veterinary Medicine Hannover Foundation, JAKE WALL, Mara Elephant Project, MARTIN WIKELSKI, Max Planck Institute of Animal Behavior, CHRISTOPHER C. WILMERS, University of California, FILIP ZIEBA, Tatra National Park, Zakopane, TOMASZ ZWIJACZ-KOZICA, Tatra National Park, Zakopane, AAFKE M. SCHIPPER, Radboud University, MARLEE A. TUCKER, Radboud University., Radboud University [Nijmegen], Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Goethe-Universität Frankfurt am Main-Senckenberg – Leibniz Institution for Biodiversity and Earth System Research - Senckenberg Gesellschaft für Naturforschung, Leibniz Association-Leibniz Association, Hirola Conservation Programme, Swedish University of Agricultural Sciences (SLU), Princeton University, Instituto de Conservação de Animais Silvestres, Royal Veterinary College [London], University of London [London], Aarhus University [Aarhus], State University of New York (SUNY), Michigan State University [East Lansing], Michigan State University System, University of California [Davis] (UC Davis), University of California (UC), University of Potsdam = Universität Potsdam, Colorado State University [Fort Collins] (CSU), University of Alberta, Giraffe Conservation Foundation, Fondazione Edmund Mach - Edmund Mach Foundation [Italie] (FEM), SLOVENIA FOREST SERVICE SVN, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Senckenberg – Leibniz Institution for Biodiversity and Earth System Research - Senckenberg Gesellschaft für Naturforschung, Leibniz Association, German Primate Center - Deutsches Primatenzentrum -- Leibniz Insitute for Primate Research -- [Göttingen, Allemagne] (GPC - DPZ), Anhalt University of Applied Sciences, University of Victoria [Canada] (UVIC), Cary Institute of Ecosystem Studies, University of British Columbia (UBC), University of Guelph, Universität Zürich [Zürich] = University of Zurich (UZH), University of Wyoming (UW), Namibia University of Science and Technology (NUST), Unité de recherche Comportement et Ecologie de la Faune Sauvage (CEFS), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Freiburg [Freiburg], Inland Norway University of Applied Sciences - Høgskolen i Innlandet, Bionet Natuuronderzoek, Norwegian Institute for Nature Research (NINA), University of Veterinary Medicine [Vienna] (Vetmeduni), University of Ljubljana, Columbia University [New York], Stony Brook University [SUNY] (SBU), Instituto de Pesquisas Ecológicas (IPÊ), Instituto de Pesquisas Ecológicas, National Research Center for Carnivores Conservation, University of Oslo (UiO), Wildlife Research and Training Institute, Wildlife Conservation Society [Mongolia], Latvian State Forest Research Institute 'Silava', Australian Wildlife Conservancy, Office français de la biodiversité (OFB), Association for the Conservation of Biodiversity of Kazakhstan, Western Ecosystems Technology Inc., Polish Academy of Sciences (PAN), Smithsonian National Zoo and Conservation Biology Institute, San Diego Zoo Wildlife Alliance, Wilfrid Laurier University (WLU), Greater Yellowstone Coalition, Mississippi State University [Mississippi], University of Veterinary Medicine [Hannover], Mara Elephant Project, Max Planck Institute of Animal Behavior, University of California [Santa Cruz] (UC Santa Cruz), Tatra National Park, Partenaires INRAE, ANR-16-CE02-0001,LANDTHIRST,Les paysages de la soif: changement climatique et ajustements comportementaux face au manque d'eau(2016), and ANR-16-CE02-0010,Mov-It,Le mouvement des ongulés au sein de paysages hétérogènes: identification des processus comportementaux reliant les changements globaux aux performances démographiques et à la gestion spatialement explicite(2016)
Subjects: SELECTION, [SDV]Life Sciences [q-bio], GPS, VDP::Zoologiske og botaniske fag: 480, RANGING BEHAVIOR, telemetrija, Physical Geography and Environmental Geoscience, sesalci, IUCN, Telemetry, habitatni tip, Mammals, Global and Planetary Change, Ecology, telemetry, THREAT, telemetry expert opinion, EXTINCTION RISK, expert opinion, CAPTURE, Comportamento Animal, Habitat use, Expert opinion, Habitat suitability, [SDE]Environmental Sciences, selitev, movement, Animal behavior, LAND, habitat suitability, Movement, selection ratio, raba prostora, ROE DEER, ddc:570, Settore BIO/07 - ECOLOGIA, habitat type, udc:630*15, mammals, Ecology, Evolution, Behavior and Systematics, AVAILABILITY, Expert opinion, GPS, habitat suitability, habitat type, habitat use, IUCN, mammals, movement, selection ratio, telemetry, habitat use, primernost habitata, Climate Action, Ecological Applications, strokovno mnenje, PATTERNS, VDP::Zoology and botany: 480, Environmental Sciences, FUNCTIONAL-RESPONSES
Abstract: Aim: Macroecological studies that require habitat suitability data for many species often derive this information from expert opinion. However, expert- based informa-tion is inherently subjective and thus prone to errors. The increasing availability of GPS tracking data offers opportunities to evaluate and supplement expert- based in-formation with detailed empirical evidence. Here, we compared expert- based habitat suitability information from the International Union for Conservation of Nature (IUCN) with habitat suitability information derived from GPS-tracking data of 1,498 individu-als from 49 mammal species.Location: Worldwide.Time period: 1998–2021.Major taxa studied: Forty- nine terrestrial mammal species.Methods: Using GPS data, we estimated two measures of habitat suitability for each individual animal: proportional habitat use (proportion of GPS locations within a habi-tat type), and selection ratio (habitat use relative to its availability). For each individual we then evaluated whether the GPS- based habitat suitability measures were in agree-ment with the IUCN data. To that end, we calculated the probability that the ranking of empirical habitat suitability measures was in agreement with IUCN's classification into suitable, marginal and unsuitable habitat types.Results: IUCN habitat suitability data were in accordance with the GPS data (> 95% probability of agreement) for 33 out of 49 species based on proportional habitat use estimates and for 25 out of 49 species based on selection ratios. In addition, 37 and 34 species had a > 50% probability of agreement based on proportional habitat use and selection ratios, respectively.Main conclusions: We show how GPS-tracking data can be used to evaluate IUCN habitat suitability data. Our findings indicate that for the majority of species in-cluded in this study, it is appropriate to use IUCN habitat suitability data in macro-ecological studies. Furthermore, we show that GPS-tracking data can be used to identify and prioritize species and habitat types for re-evaluation of IUCN habitat suitability data. expert opinion, GPS, habitat suitability, habitat type, habitat use, IUCN, mammals, movement, selection ratio, telemetry
Published: 2022
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16. MoveFormer: a Transformer-based model for step-selection animal movement modelling

Author: Ondřej Cífka, Simon Chamaillé-Jammes, Antoine Liutkus, Scientific Data Management (ZENITH), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Université de Montpellier (UM), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Computations were performed using HPC/AI resources from GENCI-IDRIS (Grant AD011012019R1)., ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), and ANR-16-IDEX-0006,MUSE,MUSE(2016)
Subjects: [SDV.EE]Life Sciences [q-bio]/Ecology, environment
Abstract: The movement of animals is a central component of their behavioural strategies. Statistical tools for movement data analysis, however, have long been limited, and in particular, unable to account for past movement information except in a very simplified way. In this work, we propose MoveFormer, a new step-based model of movement capable of learning directly from full animal trajectories. While inspired by the classical step-selection framework and previous work on the quantification of uncertainty in movement predictions, MoveFormer also builds upon recent developments in deep learning, such as the Transformer architecture, allowing it to incorporate long temporal contexts. The model predicts an animal’s next movement step given its past movement history, including not only purely positional and temporal information, but also any available environmental covariates such as land cover or temperature. We apply our model to a diverse dataset made up of over 1550 trajectories from over 100 studies, and show how it can be used to gain insights about the importance of the provided context features, including the extent of past movement history. Our software, along with the trained model weights, is released as open source.
Published: 2023

17. Hogs sleep like logs: wild boars reduce the risk of anthropic disturbance by adjusting where they rest

Author: Simon Chamaillé-Jammes and Gustave Fradin
Abstract: Many animals living in anthropized landscapes try to avoid encountering people by being active at night. By doing so, however, they risk being disturbed while at rest during the day. To mitigate this risk, diurnally resting species may be highly selective about where they rest. Here, we used GPS and activity sensors to study how wild boars (Sus scrofa) adjust their resting site selection and visitation patterns to the risk of disturbance by people. The data was complemented with audio recordings from animal-borne loggers to evaluate the efficacy of wild boars’ resting strategy in reducing the probability of encountering people while at rest. Generally, we found that wild boars did not specifically avoid resting near villages or roads, i.e. where the risk of encountering people is higher, if they could find sites with suitable vegetation cover. Wild boars could actually rest close to villages with very little risk of being disturbed. Resting sites located close to villages were visited more repeatedly that those located further away, suggesting that focusing on a few familiar and quiet resting sites was a successful strategy for resting undisturbed in an anthropized landscape.
Published: 2023
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18. Time-varying habitat selection analysis: a model and applications for studying diel, seasonal and post-release changes

Author: Romain DEJEANTE, Simon Chamaillé-Jammes, and Marion VALEIX
Abstract: Resource selection functions are commonly employed to evaluate animals’ habitat selection, e.g. the disproportionate use of habitats relative to their availability. While environmental conditions or animal motivations may vary over time, sometimes in an unknown manner, studying changes in habitat selection usually requiresa prioritime discretization. This limits our ability to precisely answer the question ‘when is an animal’s habitat selection changing?’. Here, we present a straightforward and flexible alternative approach based on fitting dynamic logistic models to used/available data. First, using simulated dataset, we demonstrate that dynamic logistic models performed well to recover temporal variations in habitat selection. We then show real-world applications for studying diel, seasonal, and post-release changes in habitat selection of blue wildebeest (Connochaetes taurinus). Finally, we provide the relevant R scripts to facilitate the adoption of the method by ecologists. Dynamic logistic models allow to study temporal changes in habitat selection in a framework consistent with resource selection functions, but without the need to discretize time, which can be a difficult task when little is known about the process studied, or may obscure inter-individual variability in timing of change. These models should undoubtedly find their place in the movement ecology toolbox.
Published: 2023
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19. Factors driving the discovery and utilization of a newly available area by African elephants

Author: Simon Chamaillé-Jammes, Craig Sholto-Douglas, Anne Pandraud, Adrian M. Shrader, Mammal Research Institute, Department of Zoology & Entomology, University of Pretoria, South Africa, and Chamaillé-Jammes, Simon
Subjects: 0106 biological sciences, Fence (finance), Extinction, Range (biology), 010604 marine biology & hydrobiology, 15. Life on land, 010603 evolutionary biology, 01 natural sciences, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, Fishery, Geography, Habitat, Gps data, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics
Abstract: For large mammals, area expansion is a key conservation measure to prevent species’ decline and extinction. Yet, its success depends on whether animals discover and later use these areas. Here, using GPS data, we investigated how herds of elephants detected and used an area made available to them after the removal of a fence. We studied the elephants’ behaviour before and after the fence removal, accounting for seasonal changes in movement patterns. In contrast to previous studies, herds visited the newly available area within a month of the fence removal, and the maximum distance they moved into the new area was reached between 5 and 9 months after the fence removal. Yet, elephants did not preferentially visit the new area at night. By the second year, all herds had shifted their seasonal home ranges and incorporated the new area, in contrast to a previous range expansion event. Our analyses show that the regular proximity of elephants to the original fence, and the fact that the new area was generally composed of preferred habitats of the elephants, probably explained the rapid discovery and use of the area. Our study improves our understanding of animal exploration and the role of habitat quality, and thus may improve range expansion and corridor programmes.
Published: 2020
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20. The DeepFaune initiative: a collaborative effort towards the automatic identification of French fauna in camera-trap images

Author: Noa Rigoudy, Abdelbaki Benyoub, Aurélien Besnard, Carole Birck, Yoann Bollet, Yoann Bunz, Jules Chiffard Carriburu, Gérard Caussimont, Elias Chetouane, Pierre Cornette, Anne Delestrade, Nina De Backer, Lucie Dispan, Maden Le Barh, Jeanne Duhayer, Jean-François Elder, Jean-Baptiste Fanjul, Jocelyn Fonderflick, Nicolas Froustey, Mathieu Garel, William Gaudry, Agathe Gérard, Olivier Gimenez, Arzhela Hemery, Audrey Hemon, Jean-Michel Jullien, Isabelle Malafosse, Mircea Marginean, Vincent Prunet, Julien Rabault, Malory Randon, Antoine Régnier, Romain Ribière, Jean-Claude Ricci, Sandrine Ruette, Jérôme Sentilles, Nathalie Siefert, Bethany Smith, Guillaume Terpereau, Wilfried Thuiller, Antonio Uzal, Valentin Vautrain, Gaspard Dussert, Bruno Spataro, Vincent Miele, Simon Chamaillé-Jammes, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Parc national des Ecrins, Fédération Départementale des Chasseurs de l'Ain, Parc naturel régional du Perche, Centre de Recherches sur les Ecosystèmes d'Altitude (CREA Mont-Blanc), Centre de Recherche et de Formation en Eco-éthologie (2C2A-CERFE), Université de Reims Champagne-Ardenne (URCA), Fédération Départementale des Chasseurs du Jura (FDCJ), Parc national des Cévennes (PnC), Ministère de l'Écologie, de l'Energie, du Développement durable et de l'Aménagement du territoire, Office français de la biodiversité (OFB), Parc naturel régional des Ballons des Vosges, Etablissement public du Mont-Saint-Michel, Fédération Départementale des Chasseurs de la Drôme, Parc naturel régional de l’Aubrac, Laboratoire d'Ecologie Alpine (LECA ), and Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)
Subjects: [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences
Abstract: Camera-traps have revolutionized the way ecologists monitor biodiversity and population abundances. Their full potential is however only realized when the hundreds of thousands of images collected can be rapidly classified with minimal human intervention. Machine learning approaches, and in particular deep learning methods, have allowed extraordinary progress towards this end. Trained classification models remain rare however, and for instance are only emerging for the European fauna. This can be explained by the technical expertise they require but also by the limited availability of large datasets of annotated pictures, which are key to obtaining successful recognition models. In this context, we set-up the DeepFaune initiative ( https://deepfaune.cnrs.fr ), a large-scale collaboration between dozens of partners involved in research, conservation and management of wildlife in France. The aim of DeepFaune is to aggregate individual datasets of annotated pictures to train species classification models based on convolutional neural networks, an established deeplearning approach. Here we report on our first milestone, a two-step pipeline built upon the MegaDetector algorithm for detection (discarding empty pictures and cropping the animal) and a classification model for 18 species or higher-level taxa as well as people and vehicles. The classification model achieved 92% validation accuracy and showed > 90% sensitivity and specificity for many classes. Most importantly, these performances were generally conserved when tested on an independent out-of-sample dataset. In addition, we developed a cross-platform graphical-user-interface that allows running the pipeline on images stored locally on a personal computer. In conclusion, the DeepFaune initiative provides a freely available (for non-commercial purposes) toolbox with high performance to classify the French fauna in camera-trap images.
Published: 2022
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21. Beyond spatial overlap: harnessing new technologies to resolve the complexities of predator–prey interactions

Author: Justin P. Suraci, Justine A. Smith, Simon Chamaillé‐Jammes, Kaitlyn M. Gaynor, Menna Jones, Barney Luttbeg, Euan G. Ritchie, Michael J. Sheriff, Andrew Sih, Conservation Science Partners, University of California [Davis] (UC Davis), University of California (UC), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), University of Pretoria [South Africa], University of California [Santa Barbara] (UC Santa Barbara), University of Tasmania [Launceston] (UTAS), Oklahoma State University [Stillwater] (OSU), Deakin University [Burwood], University of Massachusetts [Dartmouth], University of Massachusetts System (UMASS), and ANR-16-CE02-0001,LANDTHIRST,Les paysages de la soif: changement climatique et ajustements comportementaux face au manque d'eau(2016)
Subjects: predation risk effects, home range overlap, predator-prey interactions, [SDV]Life Sciences [q-bio], predation sequence, spatial ecology, [SDE]Environmental Sciences, encounter rates, Ecology, Evolution, Behavior and Systematics
Abstract: International audience; Predation risk, the probability that a prey animal will be killed by a predator, is fundamental to theoretical and applied ecology. Predation risk varies with animal behavior and environmental conditions, yet attempts to understand predation risk in natural systems often ignore important ecological and environmental complexities, relying instead on proxies for actual risk such as predator-prey spatial overlap. Here we detail the ecological and environmental complexities driving disconnects between three stages of the predation sequence that are often assumed to be tightly linked: spatial overlap, encounters, and prey capture. Our review highlights several major sources of variability in natural predator-prey systems that lead to the decoupling of spatial overlap estimates from actual encounter rates (e.g., temporal activity patterns, predator and prey movement capacity, resource limitations) and that affect the probability of prey capture given encounter (e.g., predator hunger levels, temporal, topographic, and other environmental influences on capture success). Emerging technologies and statistical methods are facilitating a transition to a more spatiotemporally detailed, mechanistic understanding of predator-prey interactions, allowing for the concurrent examination of multiple stages of the predation sequence in mobile, free-ranging animals. We describe crucial applications of this new understanding to fundamental and applied ecology, highlighting opportunities to better integrate ecological contingencies into dynamic predator-prey models and to harness a mechanistic understanding of predator-prey interactions to improve targeting and effectiveness of conservation interventions.
Published: 2022
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22. How to describe and measure phenology? An investigation on the diversity of metrics using phenology of births in large herbivores

Author: Lucie Thel, Christophe Bonenfant, Simon Chamaillé-Jammes, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), and This work was supported by a grant from the ‘Ministère Français de l’Enseignement Supérieur, de la Recherche et de l’Innovation’ through the ‘Ecole Doctorale E2M2’ of the ‘Université Claude Bernard Lyon 1’
Subjects: regularity, seasonality, rhythmicity, synchrony, timing, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ecology, Evolution, Behavior and Systematics
Abstract: International audience; Proposed in 1849 by Charles Morren to depict periodical phenomena governed by seasons, the term ‘phenology' has spread in many fields of biology. With the wide adoption of the concept of phenology flourished a large number of metrics with different meaning and interpretation. Here, we first a priori classified 52 previously published metrics used to characterise the phenology of births in large herbivores according to four biological characteristics of interest: timing, synchrony, rhythmicity and regularity of births. We then applied each metric retrieved on simulation data, considering normal and non-normal distributions of births, and varying distributions of births in time. We then evaluated the ability of each metric to capture the variation of the four phenology characteristics via a sensitivity analysis. Finally, we scored each metric according to eight criteria we considered important to describe phenology correctly. The high correlation we found among the many metrics we retrieved suggests that such diversity of metrics is unnecessary. We further show that the best metrics are not the most commonly used, and that simpler is often better. Circular statistics with the mean vector orientation and mean vector length seems, respectively, particularly suitable to describe the timing and synchrony of births in a wide range of phenology patterns. Tests designed to compare statistical distributions, like Mood and Kolmogorov–Smirnov tests, allow a first and easy quantification of rhythmicity and regularity of birth phenology respectively. By identifying the most relevant metrics our study should facilitate comparative studies of phenology of births or of any other life-history event. For instance, comparative studies of the phenology of mating or migration dates are particularly important in the context of climate change.
Published: 2022
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23. Does timing of birth affect juvenile and mare survival in wild plains zebra?

Author: Simon Chamaillé-Jammes, Christophe Bonenfant, Lucie Thel, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon, and Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 2. Zero hunger, Wet season, 0303 health sciences, Herbivore, education.field_of_study, biology, National park, Population, 15. Life on land, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, 13. Climate action, Dry season, Plains zebra, Juvenile, Ecosystem, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, education, 030304 developmental biology, Demography
Abstract: In large herbivores, the timing of births is mainly driven by the seasonal availability of their food resource. Population dynamics is strongly influenced by juvenile survival and recruitment, which highly depend on whether individuals are born during a favourable period or not. If births often occur during the most suitable season in northern cyclical environments for many large herbivore species, zebra give birth year-round at Hwange National Park, Zimbabwe, a tropical bushland characterized by the succession of a favourable wet season and a less favourable dry season. We used capture-recapture models for analysing long term observation data collected between 2008 and 2019 in this zebra population. We investigated the effect of the season (as a categorical variable) and the time spent in dry season on three categories of juveniles (younger foals of less than six months old, older foals between six and twelve months old, and yearlings between one and two years old) and mares survival, according to their reproductive state. The season had no effect on any survival. Younger foals annual survival was not affected by the time spent in dry season, whereas older foals and yearlings annual survival decreased with an increasing exposure to the dry season. Mares annual survival also decreased with an increasing time spent in dry season, whatever the reproductive status, but to a large extend when non-reproducing. The timing of birth, by determining the external conditions experienced by the offspring and their mothers during critical phases of their life cycle, plays a determinant role in their survival. As climate change is expected to lead to more frequent droughts, longer and harsher dry seasons in tropical ecosystems, we hypothesize a detrimental effect on zebra population dynamics in the future.
Published: 2021

24. Cueing on distant conditions before migrating does not prevent false starts: a case study with African elephants

Author: Anne Pandraud, Adrian M. Shrader, Arnold Tshipa, Nobesuthu Ngwenya, Simon Chamaillé-Jammes, University of Pretoria [South Africa], National University of Science and Technology [Bulawayo], Zimbabwe Parks and Wildlife Management Authority, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), CNRS Zone Atelier Hwange, and ANR-16-CE02-0001,LANDTHIRST,Les paysages de la soif: changement climatique et ajustements comportementaux face au manque d'eau(2016)
Subjects: [SDV]Life Sciences [q-bio], Rain, Elephants, Reproducibility of Results, migration, time-to-event model, [SDE]Environmental Sciences, sensory ecology, Animals, movement, Cues, climate, Ecology, Evolution, Behavior and Systematics, Ecosystem
Abstract: International audience; Migratory animals often use environmental cues to time their seasonal migrations. Local conditions may, however, differ from distant ones, and current conditions may poorly predict future conditions. This may be particularly true for early wet season conditions in tropical systems, as storms and associated rainfall events are generally not predictable at the scale of weeks or days and are heterogeneously distributed even at the scale of a few kilometres. How migratory animals cope with such challenges, and the consequences they may have, remain poorly known. We used time-to-event models based on GPS data from 19 African elephant herds from Hwange National Park (Zimbabwe) to study the effect of local and distant rainfall events on the elephants' decision to initiate their wet season migration. Elephants relied more on distant rainfall events occurring along the future migration route than on local events when initiating their migration. Such ability to use distant cues does not, however, ensure an immediate migration success. In over 30% of the cases the elephants came back to their dry season range, sometimes after having travelled >80% of the expected migration distance. This happened particularly when there was little additional rain falling during the migration. All elephants successfully migrated later in the season. Our study improves the understanding of the migratory ecology of elephants. More broadly, it raises questions about the reliability of rainfall as a migratory cue in tropical systems, and shed light on one of its potential consequences, the poorly quantified phenomenon of migration false starts.
Published: 2021
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25. MEMS based Low-Power Multi-Sensors device for Bio-Logging Applications

Author: L. Latorre, Simon Chamaillé-Jammes, and J. Miquel
Subjects: Microelectromechanical systems, Battery (electricity), Asynchronous communication, Computer science, business.industry, Logging, Accelerometer, USable, business, Computer hardware, Multi sensor, Power (physics)
Abstract: This paper presents a low-power recorder for bio- logging applications. Based on 3 MEMS sensors, it provides up to 750h of 8kHz audio, 50Hz accelerometer and 10Hz magnetometer time-aligned data using a compact 1950mAH Li- Ion battery. This work comes as a follow-up of a previous study concerning an audio-only device. Having 3 asynchronous sensors raises new issues regarding buffering and CPU sharing that are addressed by using a real-time OS. Results demonstrate that logger autonomy is slightly impaired but still very usable in several applications.
Published: 2021
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26. Do infanticides occur in harem-forming equids? A test with long-term sociodemographic data in wild plains zebras

Author: Simon Chamaillé-Jammes, Andre Ganswindt, Patrick Duncan, Camille Vitet, Cheryl Mabika, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and ANR-16-CE02-0001,LANDTHIRST,Les paysages de la soif: changement climatique et ajustements comportementaux face au manque d'eau(2016)
Subjects: 0106 biological sciences, biology, National park, media_common.quotation_subject, 05 social sciences, Zoology, Population ecology, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Equus, Breed, Harem, Foal, biology.animal, [SDE]Environmental Sciences, Plains zebra, 0501 psychology and cognitive sciences, Animal Science and Zoology, 050102 behavioral science & comparative psychology, Reproduction, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, media_common
Abstract: Social dynamics can play a major role in shaping the population ecology and evolutionary trajectory of a species. This is, for instance, the case in species known to experience infanticide when a dominant male is replaced by another. Infanticide by males has been observed in many taxa, mostly in species that breed year-round and in which a few males monopolize reproduction. In such species, infanticide often occurs after take-overs of breeding groups, and the frequency of take-overs often increases with increasing female group size, therefore raising the risk of infanticide in larger groups. Among ungulates, male infanticide has been reported mostly in harem-forming equids in captive populations, usually following harem-male turnover. In this study, we empirically tested in the wild whether the rate of stallion (i.e. harem-male) turnover increases with the number of reproductive females in harems, and whether these events reduce foal survival. We used a long-term study of wild plains zebra, Equus quagga, in Hwange National Park, Zimbabwe, where, for more than 15 years, stallion turnovers have been recorded and accurate data on pregnancy obtained by hormone assays. We show that stallion turnovers were frequent and, as expected, particularly in harems with many reproductive females. We found that foal survival did not differ significantly between situations when a stallion turnover occurred shortly before or after their birth and when it did not. This result was consistent with the fact that no attacks by stallions on foals of their group or forced matings were observed during the study. Our study offers rare data showing that if male infanticide occurs in wild plains zebra, this should be rare, and has no important consequences for foal survival at the population level.
Published: 2021
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27. When water interacts with temperature: Ecological and evolutionary implications of thermo‐hydroregulation in terrestrial ectotherms

Author: Simon Chamaillé-Jammes, Jean Clobert, Olivier Lourdais, Sandrine Meylan, Jean-François Le Galliard, Andréaz Dupoué, David Rozen-Rechels, Institut d'écologie et des sciences de l'environnement de Paris (IEES (UMR_7618 / UMR_D_242 / UMR_A_1392 / UM_113) ), Institut National de la Recherche Agronomique (INRA)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Station d'écologie théorique et expérimentale (SETE), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), Institut National de la Recherche Agronomique (INRA)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Arizona State University [Tempe] (ASU), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), CEREEP-Ecotron Ile de France (UMS 3194), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Centre National de la Recherche Scientifique (CNRS), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), ESPE de Paris, Université Paris Sorbonne , Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université Paris-Sorbonne - Paris 4 - École supérieure du professorat et de l'éducation - Académie de Paris (ESPE Paris), Université Paris-Sorbonne (UP4), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), ANR-16-CE02-0001,LANDTHIRST,Les paysages de la soif: changement climatique et ajustements comportementaux face au manque d'eau(2016), and ANR-17-CE02-0013,AQUATHERM,Rôles de la régulation hydrique et thermique dans les réponses écologiques au changement climatique(2017)
Subjects: 0106 biological sciences, Resource (biology), Niche, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Water balance, water balance, behavioral decisions, lcsh:QH540-549.5, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Nature and Landscape Conservation, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, Ecology, performance curves, Hypotheses, physiological adjustments, Thermoregulation, Optimality model, 13. Climate action, Ectotherm, [SDE]Environmental Sciences, Biological dispersal, lcsh:Ecology, body temperature, Adaptive evolution
Abstract: International audience; The regulation of body temperature (thermoregulation) and of water balance (defined here as hydroregulation) are key processes underlying ecological and evolutionary responses to climate fluctuations in wild animal populations. In terrestrial (or semiterrestrial) ectotherms, thermoregulation and hydroregulation closely interact and combined temperature and water constraints should directly influence individual performances. Although comparative physiologists traditionally investigate jointly water and temperature regulation, the ecological and evolutionary implications of these coupled processes have so far mostly been studied independently. Here, we revisit the concept of thermo‐hydroregulation to address the functional integration of body temperature and water balance regulation in terrestrial ectotherms. We demonstrate how thermo‐hydroregulation provides a framework to investigate functional adaptations to joint environmental variation in temperature and water availability, and potential physiological and/or behavioral conflicts between thermoregulation and hydroregulation. We extend the classical cost–benefit model of thermoregulation in ectotherms to highlight the adaptive evolution of optimal thermo‐hydroregulation strategies. Critical gaps in the parameterization of this conceptual optimality model and guidelines for future empirical research are discussed. We show that studies of thermo‐hydroregulation refine our mechanistic understanding of physiological and behavioral plasticity, and of the fundamental niche of the species. This is illustrated with relevant and recent examples of space use and dispersal, resource‐based trade‐offs, and life‐history tactics in insects, amphibians, and nonavian reptiles.
Published: 2019
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28. Predator Effects on Herbivore Dynamics and Behavior

Author: Simon Chamaillé-Jammes, Joris P. G. M. Cromsigt, and Marion Valeix
Subjects: Herbivore, Lead (geology), Ecology, Biology, Trophic cascade, Predator, Predation
Published: 2019
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29. How to describe and measure phenology? An investigation on the diversity of metrics using phenology of births in large herbivores

Author: Christophe Bonenfant, Simon Chamaillé-Jammes, and Lucie Thel
Subjects: Quantitative analysis (finance), Computer science, Phenology, Metric (mathematics), Statistics, Context (language use), Variation (game tree), Set (psychology), Measure (mathematics), Term (time)
Abstract: Proposed in 1849 by Charles Morren to depict periodical phenomena governed by seasons, the term “phenology” has spread in many fields of biology. With the wide adoption of the concept of phenology flourished a large number of metrics with different meaning and interpretation. Here, we first a priori classified 52 previously published metrics used to characterise the phenology of births in large herbivores according to four biological characteristics of interest: timing, synchrony, rhythmicity and regularity of births. We then applied each metric retrieved on simulation data, considering normal and non-normal distributions of births, and varying distributions of births in time. We then evaluated the ability of each metric to capture the variation of the four phenology characteristics via a sensitivity analysis. Finally, we scored each metric according to eight criteria we considered important to describe phenology correctly. The high correlation we found among the many metrics we retrieved suggests that such diversity of metrics is unnecessary. We further show that the best metrics are not the most commonly used, and that simpler is often better. Circular statistics with the mean vector orientation and mean vector length seems, respectively, particularly suitable to describe the timing and synchrony of births in a wide range of phenology patterns. Tests designed to compare statistical distributions, like Mood and Kolmogorov-Smirnov tests, allow a first and easy quantification of rhythmicity and regularity of birth phenology respectively. By identifying the most relevant metrics our study should facilitate comparative studies of phenology of births or of any other life-history event. For instance, comparative studies of the phenology of mating or migration dates are particularly important in the context of climate change.
Published: 2021
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30. Mapping out a future for ungulate migrations

Author: Yasuyuki Tachiki, Norman Owen-Smith, Claude S. Fischer, Atle Mysterud, Elie Gurarie, Stefano Focardi, Rafał Kowalczyk, Matthew J. Kauffman, Moses Selebatso, Kirk A. Olson, William F. Fagan, Chris Geremia, Leonid Kolpaschikov, Andrew J. Plumptre, Michael J. Suitor, Carly Vynne, Anne Loison, Andrés J. Novaro, Pavel Kochkarev, Aleksandr Savchenko, Jerod A. Merkle, Wenjing Xu, Albert Salemgareyev, Binbin V. Li, Hattie L. A. Bartlam-Brooks, Matthew Skroch, Robin Naidoo, Nandintsetseg Dejid, Jodi A. Hilty, Mark Hebblewhite, Steffen Mumme, Piotr Savchenko, Sonia Saïd, Simon Chamaillé-Jammes, Marco Heurich, Arthur D. Middleton, Alfred Oteng-Yeboah, Jared A. Stabach, Kyle Joly, Christer Moe Rolandsen, Kasahun Abera, Antti Paasivaara, Benito A. González, Ramiro Ovejero, Wibke Peters, David Mallon, Malik Morjan, Erling Johan Solberg, Erling L. Meisingset, Emily Bennitt, James E. Meacham, Kevin L. Monteith, Stephanie Ward, Petra Kaczensky, Christiane Roettger, Alethea Steingisser, Alex Lobora, Evelyn H. Merrill, Luthando Dziba, John M. Fryxell, Olav Strand, Thomas Mueller, Thomas A. Morrison, Lucie Debeffe, Arnold Tshipa, Francesca Cagnacci, Mark A. Hurley, Charlotte Boyd, J. Grant C. Hopcraft, Corinne J. Kendall, George Wittemyer, Rodrigo A. Medellín, Joel Berger, Richard W.S. Fynn, Steffen Zuther, Tinaapi H. Madiri, Aran Johnson, Hall Sawyer, Steeve D. Côté, Joseph O. Ogutu, Jan Adamczewski, Pascal Marchand, Frank van Langevelde, Ellen O. Aikens, Luca Pedrotti, Craig Packer, Andrea S. Dekrout, Danila Panchenko, Anne Gunn, Emiliano Donadio, Anne M. Trainor, Munir Z. Virani, WYOMING COOPERATIVE FISH AND WILDLIFE RESEARCH UNIT DEPARTMENT OF ZOOLOGY AND PHYSIOLOGY UNIVERSITY OF WYOMING USA, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Unité de recherche Comportement et Ecologie de la Faune Sauvage (CEFS), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-16-CE02-0001,LANDTHIRST,Les paysages de la soif: changement climatique et ajustements comportementaux face au manque d'eau(2016), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, Conservation of Natural Resources, Ungulate, Ecology (disciplines), Wildlife, Biodiversity, 010603 evolutionary biology, 01 natural sciences, Indigenous, Predation, 03 medical and health sciences, Life Science, Animals, Carnivore, Traditional knowledge, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Mammals, 0303 health sciences, Multidisciplinary, biology, Ecology, 15. Life on land, PE&RC, biology.organism_classification, Environmental Policy, Geography, 13. Climate action, Wildlife Ecology and Conservation, [SDE]Environmental Sciences, WIAS, Animal Migration, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Migration of ungulates (hooved mammals) is a fundamental ecological process that promotes abundant herds, whose effects cascade up and down terrestrial food webs. Migratory ungulates provide the prey base that maintains large carnivore and scavenger populations and underpins terrestrial biodiversity (fig. S1). When ungulates move in large aggregations, their hooves, feces, and urine create conditions that facilitate distinct biotic communities. The migrations of ungulates have sustained humans for thousands of years, forming tight cultural links among Indigenous people and local communities. Yet ungulate migrations are disappearing at an alarming rate (1). Efforts by wildlife managers and conservationists are thwarted by a singular challenge: Most ungulate migrations have never been mapped in sufficient detail to guide effective conservation. Without a strategic and collaborative effort, many of the world's great migrations will continue to be truncated, severed, or lost in the coming decades. Fortunately, a combination of animal tracking datasets, historical records, and local and Indigenous knowledge can form the basis for a global atlas of migrations, designed to support conservation action and policy at local, national, and international levels.
Published: 2021
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31. Can citizen science analysis of camera trap data be used to study reproduction? Lessons from Snapshot Serengeti program

Author: Craig Packer, Christophe Bonenfant, Lucie Thel, Lea Keurinck, Simon Chamaillé-Jammes, Maxime Catala, Sarah Huebner, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), University of Minnesota [Twin Cities] (UMN), University of Minnesota System, Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, Ungulate, Occupancy, media_common.quotation_subject, Damaliscus jimela, Alcelaphus cokii, Management, Monitoring, Policy and Law, African ungulates, Positive correlation, 010603 evolutionary biology, 01 natural sciences, 010605 ornithology, Snapshot (photography), Citizen science, Alcelaphus, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation, media_common, biology, 010604 marine biology & hydrobiology, age determination, Nanger granti, biology.organism_classification, Population abundance, Geography, Data quality, Trait, Camera trap, Reproduction, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Topi, Demography
Abstract: Ecologists increasingly rely on camera trap data to estimate a wide range of biological parameters such as occupancy, population abundance or activity patterns. Because of the huge amount of data collected, the assistance of non-scientists is often sought after, but an assessment of the data quality is a prerequisite to their use. We tested whether citizen science data from one of the largest citizen science projects - Snapshot Serengeti - could be used to study breeding phenology, an important life-history trait. In particular, we tested whether the presence of juveniles (less than one or 12 months old) of three ungulate species in the Serengeti: topi Damaliscus jimela, kongoni Alcelaphus buselaphus and Grant9s gazelle Nanger granti could be reliably detected by the "naive" volunteers vs. trained observers. We expected a positive correlation between the proportion of volunteers identifying juveniles and their effective presence within photographs, assessed by the trained observers. We first checked the agreement between the trained observers for age classes and species and found a good agreement between them (Fleiss9 κ > 0.61 for juveniles of less than one and 12 month(s) old), suggesting that morphological criteria can be used successfully to determine age. The relationship between the proportion of volunteers detecting juveniles less than a month old and their actual presence plateaued at 0.45 for Grant9s gazelle and reached 0.70 for topi and 0.56 for kongoni. The same relationships were however much stronger for juveniles younger than 12 months, to the point that their presence was perfectly detected by volunteers for topi and kongoni. Volunteers9 classification allows a rough, moderately accurate, but quick, sorting of photograph sequences with/without juveniles. Obtaining accurate data however appears more difficult. We discuss the limitations of using citizen science camera traps data to study breeding phenology, and the options to improve the detection of juveniles, such as the addition of aging criteria on the online citizen science platforms, or the use of machine learning.
Published: 2021
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32. Revisiting animal photo-identification using deep metric learning and network analysis

Author: Dominique Allainé, Gaspard Dussert, Christophe Bonenfant, Bruno Spataro, Vincent Miele, Simon Chamaillé-Jammes, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0106 biological sciences, Statement (computer science), File Transfer Protocol, Information retrieval, Computer science, 010604 marine biology & hydrobiology, Ecological Modeling, 010603 evolutionary biology, 01 natural sciences, Data availability, Test case, Metric (mathematics), Photo identification, [SDE]Environmental Sciences, Code (cryptography), Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Network analysis
Abstract: DATA AVAILABILITY STATEMENT: The curated dataset of re-identified giraffe individuals is freely available at ftp://pbil.univ-lyon1.fr/pub/datasets/miele2021. The code to reproduce the analysis is available at https://plmlab.math.cnrs.fr/vmiele/animal-reid/ with explanations and test cases.
Published: 2021
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33. African elephants can detect water from natural and artificial sources via olfactory cues

Author: Matthew, Wood, Simon, Chamaillé-Jammes, Almuth, Hammerbacher, and Adrian M, Shrader
Subjects: Smell, Elephants, Odorants, Animals, Water, Cues
Abstract: Water is vital for mammals. Yet, as ephemeral sources can be difficult to find, it raises the question, how do mammals locate water? Elephants (Loxodonta africana) are water-dependent herbivores that possess exceptional olfactory capabilities, and it has been suggested that they may locate water via smell. However, there is no evidence to support this claim. To explore this, we performed two olfactory choice experiments with semi-tame elephants. In the first, we tested whether elephants could locate water using olfactory cues alone. For this, we used water from two natural dams and a drinking trough utilised by the elephants. Distilled water acted as a control. In the second, we explored whether elephants could detect three key volatile organic compounds (VOCs) commonly associated with water (geosmin, 2-methylisoborneol, and dimethyl sulphide). We found that the elephants could locate water olfactorily, but not the distilled water. Moreover, they were also able to detect the three VOCs associated with water. However, these VOCs were not in the odour profiles of the water sources in our experiments. This suggests that the elephants were either able to detect the unique odour profiles of the different water sources or used other VOCs that they associate with water. Ultimately, our findings indicate that elephants can locate water olfactorily at small spatial scales, but the extent to which they, and other mammals, can detect water over larger scales (e.g. km) remains unclear.
Published: 2021

34. Body size and digestive system shape resource selection by ungulates: A cross-taxa test of the forage maturation hypothesis

Author: Briana Abrahms, Luca Pedrotti, Jeff R. Muntifering, Dorj Usukhjargal, Sarah R. B. King, Melissa Songer, John Derek Scasta, Nandintsetseg Dejid, Johannes Signer, Ellen O. Aikens, Brett R. Jesmer, John F. McEvoy, Jacob D. Hennig, Jagdag Enkhbyar, Hall Sawyer, Kirk A. Olson, Geir Rune Rauset, Francesca Cagnacci, Jacob R. Goheen, John M. Fryxell, Adam T. Ford, Ilya R. Fischhoff, Manuela Panzacchi, Simon Chamaillé-Jammes, Jerod A. Merkle, Jeffrey L. Beck, Joerg Melzheimer, Bayarbaatar Buuveibaatar, John C. Payne, Randall B. Boone, Takehiko Y. Ito, Matthew J. Kauffman, John D. C. Linnell, Mahmoud-Reza Hemami, Thomas Mueller, Buyanaa Chimeddorj, Siva R. Sundaresan, Saeideh Esmaeili, Olav Strand, Petra Kaczensky, Badamjav Lkhagvasuren, Daniel I. Rubenstein, Atle Mysterud, Jared A. Stabach, Kathryn A. Schoenecker, Shannon E. Albeke, Kate Jenks, Seth Stapleton, Paul C. Cross, Ganbold Uuganbayar, Department of Zoology and Physiology and Program in Ecology, University of Wyoming, Laramie, WY, USA, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and ANR-16-CE02-0001,LANDTHIRST,Les paysages de la soif: changement climatique et ajustements comportementaux face au manque d'eau(2016)
Subjects: 0106 biological sciences, Forage biomass, Ungulate, Ruminant, VDP::Zoologiske og botaniske fag: 480, Biome, Forage, 010603 evolutionary biology, 01 natural sciences, Water requirements, 03 medical and health sciences, Settore BIO/07 - ECOLOGIA, Animals, Body Size, Macroecology, Ecology, Evolution, Behavior and Systematics, Selection (genetic algorithm), ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Hindgut fermentation, 0303 health sciences, biology, Ecology, Equidae, Ruminants, biology.organism_classification, Step-selection function, [SDE]Environmental Sciences, VDP::Zoology and botany: 480, Allometry, Digestive System
Abstract: The forage maturation hypothesis (FMH) states that energy intake for ungulates is maximised when forage biomass is at intermediate levels. Nevertheless, metabolic allometry and different digestive systems suggest that resource selection should vary across ungulate species. By combining GPS relocations with remotely sensed data on forage characteristics and surface water, we quantified the effect of body size and digestive system in determining movements of 30 populations of hindgut fermenters (equids) and ruminants across biomes. Selection for intermediate forage biomass was negatively related to body size, regardless of digestive system. Selection for proximity to surface water was stronger for equids relative to ruminants, regardless of body size. To be more generalisable, we suggest that the FMH explicitly incorporate contingencies in body size and digestive system, with small-bodied ruminants selecting more strongly for potential energy intake, and hindgut fermenters selecting more strongly for surface water.
Published: 2021
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35. The influence of spatial features and atmospheric conditions on African lion vocal behaviour

Author: Matthew Wijers, Andrew J. Loveridge, David W. Macdonald, Simon Chamaillé-Jammes, Andrew Markham, Paul Trethowan, Byron du Preez, Wildlife Conservation Research Unit, Recanati-Kaplan Centre, Department of Zoology, University of Oxford, United Kingdom, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, biology, Home range, Biologging, 05 social sciences, Vocalisation, Panthera leo, 010603 evolutionary biology, 01 natural sciences, Roar, Geography, Short lifetime, biology.animal, Vocal behaviour, [SDE]Environmental Sciences, 0501 psychology and cognitive sciences, Animal Science and Zoology, 050102 behavioral science & comparative psychology, Panthera, Cartography, Ecology, Evolution, Behavior and Systematics, Acoustic attenuation, Animal Vocalizations
Abstract: International audience; Long-distance vocalisation is a characteristic of African lion (Panthera leo) behaviour and is important for maintaining territorial boundaries as well as locating distant group members. Vocal signalling is, however, a flexible behaviour that involves varying costs and benefits depending on environmental, social and spatial factors. Motivated by previous data collection limitations, we developed a novel approach to investigate the influence of atmospheric conditions and animal home range geography on lion vocal behaviour using acoustic and accelerometer biologgers. To compensate for the short lifetime of the acoustic biologger, we trained a machine learning model to detect lion roars from long term acceleration signals which yielded over 500 nights of data from 7 individual lions. Analysis of detected roar events revealed that vocalisations occurred mainly at night with a peak just before dawn. The relative likelihood of vocalisation was negatively related to wind speed and temperature and positively related to absolute humidity suggesting that lions preferred to roar under conditions that reduce sound attenuation and thereby maximise calling area. Roar occurrence was found to be dependent on an animal's location relative to its home range with lions demonstrating an apparent avoidance for vocalising beyond the home range boundary. Lions were also more likely to roar repetitively while closer to rivers and water points within their home range. This study is the first of its kind and not only improves the understanding of lion vocal behaviour but can inform new approaches for recording animal vocalisations remotely.
Published: 2021
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36. Passer les limites, rythmer le territoire. Paysage et mobilités du sanglier en Valbonnais (Isère, France)

Author: Roméo Bondon, Raphaël Mathevet, Coralie Mounet, and Simon Chamaillé-Jammes
Subjects: 0106 biological sciences, hunting, géographie animale, wildlife, Geography, Planning and Development, 0507 social and economic geography, 010603 evolutionary biology, 01 natural sciences, Landscape dynamics, Wild boar, biology.animal, Situated, Local population, chasse, sanglier, Global and Planetary Change, relation humains et animaux sauvages, human wildlife relationships, biology, 05 social sciences, animal geography, 15. Life on land, faune sauvage, Urban Studies, Participatory approach, protected area, Ethnology, 050703 geography, wild boar, aire protégée
Abstract: Par la confrontation d'entretiens semi-directifs dans la vallée alpine du Valbonnais (Isère, France) avec l'observation de données de déplacements de sangliers, nous questionnons la contribution de la mobilité animale au devenir du paysage. Le sanglier se joue des limites administratives, révèle et anime les controverses spatiales et économiques des territoires humains, il pousse aussi, par sa biologie et ses spatialités à questionner les catégories d’analyse habituelles. Nous proposons de le qualifier d’« animal-frontière » et nous mettons en œuvre une approche à la fois interdisciplinaire et participative pour faciliter l’élaboration d’une connaissance située de l’espèce et des enjeux liés à ses déplacements. Nous explorons ainsi comment le sanglier participe d’un paysage vivant. Our study takes place into the Valbonnais alpine valley (Isère, France) and is based on semi-structured interviews which are confronted with the analysis of the movements of a local population of wild boars. We aim to question the contribution of animal mobility to the landscape dynamics. The wild boar interacts with administrative limits, reveals and stimulates the spatial and economic controversies of human territories, it also leads, by its biology and spatiality, to question the usual analytic categories. We suggest to understand wild boar as a « boundary-animal » and to implement an interdisciplinary and participatory approach to elaborate a situated knowledge of the species and the issues related to its movements, and thus to explore how wild boars shape a living landscape.
Published: 2021
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37. Author response for 'Revisiting animal photo‐identification using deep metric learning and network analysis'

Author: Vincent Miele, Dominique Allainé, Simon Chamaillé-Jammes, Gaspard Dussert, Bruno Spataro, and Christophe Bonenfant
Subjects: Computer science, Metric (mathematics), Photo identification, Data mining, computer.software_genre, computer, Network analysis
Published: 2021
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38. A reformulation of the selection ratio shed light on resource selection functions and leads to a unified framework for habitat selection studies

Author: Simon Chamaillé-Jammes, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0106 biological sciences, 010604 marine biology & hydrobiology, Context (language use), Density estimation, 15. Life on land, 010603 evolutionary biology, 01 natural sciences, Regression, Resource (project management), Habitat, Statistics, Metric (mathematics), [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Categorical variable, Selection (genetic algorithm), Mathematics
Abstract: The selection ratio (SR), i.e. the ratio of proportional use of a habitat over proportional availability of this habitat, has for long been the standard metric of habitat selection analyses. It is easy to compute and directly estimates disproportionate use. Its apparent restriction to habitat selection analyses using categorical predictors led to the development of the resource selection functions (RSF) approach, which has now become the norm.The RSF approach has however led to debates and confusion. For instance, what functional form can be used remains debated, and the concept of relative probability of selection is often misunderstood.I propose a reformulation of the SR demonstrating that it can be estimated in a regression context, and thus even with continuous predictors. This reformulation suggests that RSF can be seen as an intermediate step in the calculation of SR. This reformulation also clarifies some longstanding debates about RSF and data-selection/fitting practices.I further suggest that SR estimates the strength of habitat selection, but that the contribution of selection in determining use, which should be more directly linked to fitness than selection per se, should be estimated by another metric, the selection effect on use (SE). SE could be estimated simply as thedifferencebetween proportional use and proportional availability, and can be computed from SR and a density estimation of availability.I conduct a habitat selection analysis of plains zebras to demonstrate the added-value of going beyond RSF scores and using SR estimated in a regression context, and of combining SR and SE.Overall, I highlight the inter-relation between various metrics used to study habitat selection (i.e., SR, other selection indices, RSF scores, marginality). I conclude by proposing that SR and SE can be the unifying metrics of habitat selection, as together they offer a comprehensive view on the strength of habitat selection and its effect on habitat use.
Published: 2020

39. Temperature as a constraint on the timing and duration of African elephant foraging trips

Author: Cheryl Mabika, David Rozen-Rechels, Simon Chamaillé-Jammes, Hugo Valls-Fox, Université Paris 1 Panthéon-Sorbonne - Formation continue Panthéon Sorbonne (UP1 FCPS), Université Paris 1 Panthéon-Sorbonne (UP1), Max Planck Institute of Animal Behavior, Systèmes d'élevage méditerranéens et tropicaux (UMR SELMET), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), CNRS, LTSER France, Zone Atelier Hwange, Hwange Natl Pk,Bag 62, Dete, Zimbabwe, Partenaires INRAE, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, University of Pretoria [South Africa], Research Platform 'Production and Conservation in Partnership', ANR-16-CE02-0001,LANDTHIRST,Les paysages de la soif: changement climatique et ajustements comportementaux face au manque d'eau(2016), ANR-11-CEPL-0003,SAVARID,Effet de l'augmentation de l'aridité et de la fréquence des sécheresses sur les systèmes socio-écologiques de savane dépendant de la biodiversité : scénarios exploratoires pour une aire protégée contrainte par l'eau de surface(2011), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: 0106 biological sciences, Resource (biology), nycthemeral, Foraging, 010603 evolutionary biology, 01 natural sciences, activity rhythm, African elephant, 03 medical and health sciences, large herbivore, biology.animal, Perennial water, Dry season, Genetics, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Nature and Landscape Conservation, 2. Zero hunger, 0303 health sciences, Herbivore, Ecology, biology, National park, surface water, 15. Life on land, Arid, savanna, Geography, movement ecology, Animal Science and Zoology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: In arid and semiarid environments, water is a key resource that is limited in availability. During the dry season, perennial water sources such as water pans often are far apart and shape the daily movement routines of large herbivores. In hot environments, endotherms face a lethal risk of overheating that can be buffered by evaporative cooling. Behavioral adjustments are an alternative way to reduce thermal constraints on the organism. The trade-off between foraging and reaching water pans has been studied widely in arid environments; however, few studies have looked into how ambient temperature shapes individual trips between two visits to water. In this study, we tracked during the dry season the movement of eight GPS-collared African elephants (Loxodonta africana) cows from different herds in Hwange National Park, Zimbabwe. This species, the largest extant terrestrial animal, is particularly sensitive to heat due to its body size and the absence of sweat glands. We show that most foraging trips depart from water at nightfall, lowering the average temperature experienced during walking. This pattern is conserved across isolated elephant populations in African savannas. We also observed that higher temperatures at the beginning of the trip lead to shorter trips. We conclude that elephants adjust the timing of foraging trips to reduce the thermal constraints, arguing that further considerations of the thermal landscape of endotherms are important to understand their ecology.
Published: 2020
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40. Disentangling the roles of bottom-up and top-down drivers in the trade-off between food acquisition and safety in prey with multiple predators

Author: Godfrey Mtare, Olivier Pays, Esther van der Meer, Andrew J. Loveridge, Patrick Duncan, Marion Valeix, David W. Macdonald, Hervé Fritz, Simon Chamaillé-Jammes, Stéphanie Périquet, Pierrick Blanchard, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université Paul-Valéry - Montpellier 3 (UPVM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, 2. Zero hunger, Herbivore, Foraging, Zoology, 15. Life on land, Biology, Trade-off, Crocuta crocuta, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Predation, Vigilance (behavioural ecology), biology.animal, [SDE]Environmental Sciences, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Panthera, Predator, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, 010606 plant biology & botany
Abstract: 1. Prey face a trade-off between acquiring food and avoiding predation, but food availability, and therefore its effect, is rarely measured in field studies investigating non-lethal effects of predation. The main aim of this study is to investigate the role of the presence of predators in the functional adjustments of feeding parameters with patch quality in a medium-size herbivore. 2. In Hwange National Park (Zimbabwe), we set up an experiment by manipulating, over two years, patch quality for impala (Aepyceros melampus), a medium-sized herbivore. We assess predation risk by monitoring the presence of three GPS-equipped predators: African lions (Panthera leo), spotted hyaenas (Crocuta crocuta) and African wild dogs (Lycaon pictus). 3. In enriched, fertilised plots the impalas reduced step rates (i.e. the rates of change in feeding stations), and increased their number of bites per feeding station while bite rates were not affected. Thus, the main adjustment of their feeding was the step rate. The total time the impalas spent vigilant appeared to be a good predictor of the variation of their bite rate. Although vigilance caused a reduction in bite rate when at a feeding station, the impalas reduced the relative costs of vigilance by continuing chewing and processing their food when scanning for predators. 4. When predators were in the vicinity, the impalas increased their exclusive vigilance (high-cost vigilance) but not their vigilance while chewing (low-cost vigilance) and decreased their bite rate while their step rate and the number of bites per feeding station did not change significantly. The impalas were thus visually disconnected from their patch, and reduced their bite rate when actually foraging. Exclusive vigilance increased when both lions and hyaenas were in the vicinity, and when wild dogs were nearby. 5. Patterns of vigilance that altered bite rate were linked to the presence of predators during the previous 24h. Over the long term patch quality was the main determinant of the feeding parameters (step rate and bite rate). This study shows how predators, by affecting the time prey devote to predator detection, shape the functional adjustments of food acquisition by prey to local patch quality.
Published: 2020
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41. Tirs dérogatoires de loups en France : état des connaissances et des enjeux pour la gestion des attaques aux troupeaux

Author: Oksana Grente, Christophe Duchamp, Sarah Bauduin, Thomas Opitz, Simon Chamaillé-Jammes, Nolwenn Drouet-Hoguet, Olivier Gimenez, Office français de la biodiversité (OFB), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Gimenez, Olivier, Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: [SDE.BE] Environmental Sciences/Biodiversity and Ecology, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [MATH.MATH-ST] Mathematics [math]/Statistics [math.ST]
Abstract: International audience; En France, la protection des troupeaux contre les attaques de loup prévoit l'utilisation de tirs dérogatoires dans des contextes précis, notamment lorsque la pression des attaques est forte. Néanmoins, les effets de ces tirs sur les attaques restent mal connus. Nous dressons ici un état des connaissances scientifiques sur le sujet puis présentons les enjeux et le cadre méthodologique de l'étude en cours, qui s'attache à évaluer les effets des tirs dérogatoires sur les attaques et la population de loups en France.
Published: 2020

42. Low-Power Embedded Audio Recording using MEMS Microphones

Author: Simon Chamaillé-Jammes, L. Latorre, Smart Integrated Electronic Systems (SmartIES), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, Audio recording, Focus (computing), Bio-logging, business.industry, Computer science, 010401 analytical chemistry, MEMS microphone, 010603 evolutionary biology, 01 natural sciences, 0104 chemical sciences, Power (physics), Sound recording and reproduction, Set (abstract data type), Microcontroller, Computer data storage, Low-power, [INFO.INFO-ES]Computer Science [cs]/Embedded Systems, Sound quality, [SPI.NANO]Engineering Sciences [physics]/Micro and nanotechnologies/Microelectronics, business, Embodied energy, Computer hardware
Abstract: International audience; This paper introduces the design of a low-power and low-cost audio recorder. Although the initial purpose is the study of wildlife behavior, the result can be applied to many other fields including urban noise cartography or industrial monitoring. The system is based on a minimal set of low-cost, off-the-shelf components (MEMS microphone, microcontroller, and SD card). Focus is given to autonomy both in terms of embedded energy and data storage. The paper demonstrates that both are improved by applying an online embedded compression to the audio data. Together with an ingenious use of available hardware resources, we were able to lower the overall power consumption compared to existing solutions by an order of magnitude, at equivalent audio quality.
Published: 2020
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43. Revisiting animal photo-identification using deep metric learning and network analysis

Author: Vincent Miele, Gaspard Dussert, Bruno Spataro, Dominique Allainé, Simon Chamaillé-Jammes, and Christophe Bonenfant
Subjects: 0106 biological sciences, 0303 health sciences, Similarity (geometry), Computer science, business.industry, Context (language use), Machine learning, computer.software_genre, 010603 evolutionary biology, 01 natural sciences, Pipeline (software), Convolutional neural network, Object detection, Set (abstract data type), 03 medical and health sciences, Metric (mathematics), Pattern matching, Artificial intelligence, business, computer, 030304 developmental biology
Abstract: An increasing number of ecological monitoring programs rely on photographic capture-recapture of individuals to study distribution, demography and abundance of species. Photo-identification of individuals can sometimes be done using idiosyncratic coat or skin patterns, instead of using tags or loggers. However, when performed manually, the task of going through photographs is tedious and rapidly becomes too time consuming as the number of pictures grows.Computer vision techniques are an appealing and unavoidable help to tackle this apparently simple task in the big-data era. In this context, we propose to revisit animal re-identification using image similarity networks and metric learning with convolutional neural networks (CNNs), taking the giraffe as a working example.We first developed an end-to-end pipeline to retrieve a comprehensive set of re-identified giraffes from about 4, 000 raw photographs. To do so, we combined CNN-based object detection, SIFT pattern matching, and image similarity networks. We then quantified the performance of deep metric learning to retrieve the identity of known individuals and detect unknown individuals never seen in the previous years of monitoring.After a data augmentation procedure, the re-identification performance of the CNN reached a Top-1 accuracy of about 90%, despite the very small number of images per individual in the training data set. While the complete pipeline succeeded in re-identifying known individuals, it slightly under-performed with unknown individuals.Fully based on open-source software packages, our work paves the way for further attempts to build automatic pipelines for re-identification of individual animals, not only in giraffes but also in other species.
Published: 2020
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44. A theory of the use of information by enemies in the predator-prey space race

Author: Rémi Patin, Simon Chamaillé-Jammes, Daniel Fortin, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0106 biological sciences, species interaction, Forage (honey bee), Ecology, space use, 010604 marine biology & hydrobiology, trophic interaction, vulnerability, Space (commercial competition), Biology, 010603 evolutionary biology, 01 natural sciences, Predation, memory, Race (biology), predation risk, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Trophic level
Abstract: We currently lack a comprehensive theory about how behaviourally responsive predators and prey use the information they acquire about the environment and each other’s presence while engaged in the ‘space race’. This limits our understanding of the role of behaviour in trophic relationships and our ability to predict predators and prey distributions. Here we combined a simulation model with a genetic algorithm to discover how predators and prey behaving optimally should use information in environments with different levels of heterogeneity in prey forage distribution and prey vulnerability. Our results demonstrate the key role of movement unpredictability in successful strategies for both predators and prey, supporting the ‘shell-game’ hypothesis. We however reveal striking differences between predators and prey in the magnitude of this unpredictability, and in how it varies with the environment. Our work offers a robust theoretical framework to better understand predator-prey space use and interpret empirical studies.
Published: 2020
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45. Plains zebras bring evidence that dilution and detection effects may not always matter behaviorally and demographically

Author: Simon Chamaillé-Jammes, Camille Vitet, Olivier Gimenez, Patrick Duncan, Cheryl Mabika, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Pretoria [South Africa], ANR-16-CE02-0001,LANDTHIRST,Les paysages de la soif: changement climatique et ajustements comportementaux face au manque d'eau(2016), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, demography, Ungulate, Ecology, 05 social sciences, Biology, sociality, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Dilution, predation risk, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, ungulate, 0501 psychology and cognitive sciences, 050102 behavioral science & comparative psychology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, grouping behavior, Ecology, Evolution, Behavior and Systematics, Sociality, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; Group living is assumed to benefit prey by reducing predation risk due to dilution and detection effects. This increased safety could be exchanged against a reduced individual vigilance leading to increased foraging and fitness until costs of intra‐group competition offset this benefit. However, very few studies have been able to directly test the relationship between individual fitness and group size in non‐cooperative breeding species. Therefore, evidence that dilution and detection effects do indeed translate into increased fitness under predation risk remains mostly theoretical. Here, we aimed at empirically testing whether group size influences beneficial and costly behaviors, and ultimately the survival of individuals, in a prey species facing heavy predation pressure. We focused on plains zebra Equus quagga of Hwange National Park in Zimbabwe, a high lion density area. We collected behavioral data (i.e., individual vigilance and foraging, collective vigilance, and agonistic interactions) that we used as proxies to investigate the costs and benefits of grouping in this species. We then fitted multistate capture‐mark‐recapture and Cox proportional‐hazards models to estimate apparent survival of adults and young zebras, respectively, and assess whether a demographic signal of group size could be found. Our results show that collective vigilance increases with group size, a prerequisite of the detection effect, but individual vigilance does not consistently decrease with group size, which suggests that there is no group size effect on individual vigilance. Agonistic interactions were rare. These results suggest that there are no foraging costs of grouping here, and even some benefits such as a better collective vigilance. However, any benefits of being in larger groups did not translate into increased survival, as we found no effect of group size on the apparent survival of individuals. Since dilution and detection effects do not matter behaviorally and demographically in these plains zebras living under high predation risk, these results challenge our understanding of how predation shapes animal sociality: fitness benefits of dilution or detection should not be assumed.
Published: 2020
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46. Are fission–fusion dynamics consistent among populations? A large‐scale study with Cape buffalo

Author: Simon Chamaillé-Jammes, Elodie Wielgus, Hugo Valls-Fox, Michel De Garine-Wichatitsky, Hervé Fritz, Bradley Cain, Alexandre Caron, Daniel Cornélis, Eve Miguel, Manchester Metropolitan University (MMU), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Forêts et Sociétés (UPR Forêts et Sociétés), Département Environnements et Sociétés (Cirad-ES), Kasetsart University - KU (THAILAND), Kasetsart University (KU), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), CNRS, LTSER France, Zone Atelier Hwange, Hwange Natl Pk,Bag 62, Dete, Zimbabwe, Partenaires INRAE, Systèmes d'élevage méditerranéens et tropicaux (UMR SELMET), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Eduardo Mondlane University, Department of Zoology and Entomology [Pretoria], University of Pretoria [South Africa], ANR-08-BLAN-0022,FEAR,Paysage de la peur et utilisation de l'hétérogénéité spatiale des ressources par des herbivores de taille corporelle différente: nouvelles hypothèses de coexistence interspécique(2008), ANR-11-CEPL-0003,SAVARID,Effet de l'augmentation de l'aridité et de la fréquence des sécheresses sur les systèmes socio-écologiques de savane dépendant de la biodiversité : scénarios exploratoires pour une aire protégée contrainte par l'eau de surface(2011), ANR-16-CE02-0001,LANDTHIRST,Les paysages de la soif: changement climatique et ajustements comportementaux face au manque d'eau(2016), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro
Subjects: 0106 biological sciences, multi‐population, [SDV]Life Sciences [q-bio], dyadic interactions, 01 natural sciences, Dynamique des populations, Original Research, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, Ecology, biology, Fission fusion, National park, seasonality, Facteur du milieu, Geography, Habitat, home range overlap, association patterns, multi-population, L20 - Écologie animale, Wet season, Buffle africain, Facteur écologique, Home range, 010603 evolutionary biology, Intraspecific competition, 03 medical and health sciences, Variation génétique, Syncerus, lcsh:QH540-549.5, medicine, Ecology, Evolution, Behavior and Systematics, Cape buffalo, 030304 developmental biology, Nature and Landscape Conservation, 15. Life on land, Seasonality, biology.organism_classification, medicine.disease, 13. Climate action, lcsh:Ecology
Abstract: Fission–fusion dynamics allow animals to manage costs and benefits of group living by adjusting group size. The degree of intraspecific variation in fission–fusion dynamics across the geographical range is poorly known. During 2008–2016, 38 adult female Cape buffalo were equipped with GPS collars in three populations located in different protected areas (Gonarezhou National Park and Hwange National Park, Zimbabwe; Kruger National Park, South Africa) to investigate the patterns and environmental drivers of fission–fusion dynamics among populations. We estimated home range overlap and fission and fusion events between Cape buffalo dyads. We investigated the temporal dynamics of both events at daily and seasonal scales and examined the influence of habitat and distance to water on event location. Fission–fusion dynamics were generally consistent across populations: Fission and fusion periods lasted on average between less than one day and three days. However, we found seasonal differences in the underlying patterns of fission and fusion, which point out the likely influence of resource availability and distribution in time on group dynamics: During the wet season, Cape buffalo split and associated more frequently and were in the same or in a different subgroup for shorter periods. Cape buffalo subgroups were more likely to merge than to split in open areas located near water, but overall vegetation and distance to water were very poor predictors of where fission and fusion events occurred. This study is one of the first to quantify fission–fusion dynamics in a single species across several populations with a common methodology, thus robustly questioning the behavioral flexibility of fission–fusion dynamics among environments., The frequency at which Cape buffalos split and join allows them to adjust to environmental conditions. In 3 distinct populations, the associations between individuals last on average between 1 and 3 days, but seasonal differences exist: In the dry season, buffalos split and join less frequently but stay in the same subgroup for longer periods than in wet season. Vegetation openness and distance to water are poor predictors of where fission and fusion events occur.
Published: 2020
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47. Predator Effects on Herbivore Dynamics and Behavior - What Mechanisms Lead to Trophic Cascades in Savannas?

Author: Simon Chamaillé-Jammes, Marion VALEIX, Cromsigt, Joris P. G. M., Centre National de la Recherche Scientifique (CNRS), Scogings PF & Sankaran M, and VALEIX, Marion
Subjects: [SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2020

48. Movement ecology of large herbivores in African savannas: current knowledge and gaps

Author: Robyn S. Hetem, Simon Chamaillé-Jammes, Grant C. Hopcraft, Thomas A. Morrison, Frank van Langevelde, Emily Bennitt, Norman Owen-Smith, University of the Witwatersrand [Johannesburg] (WITS), Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Botswana, Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0106 biological sciences, Range (biology), Ecology (disciplines), Home range, media_common.quotation_subject, home range, Context (language use), migration, 010603 evolutionary biology, 01 natural sciences, Predation, Daily activity, Ecosystem, ungulates, Ecology, Evolution, Behavior and Systematics, media_common, 2. Zero hunger, Herbivore, Ecology, 010604 marine biology & hydrobiology, 15. Life on land, PE&RC, Agricultural and Biological Sciences (miscellaneous), Geography, 13. Climate action, population dispersion, Wildlife Ecology and Conservation, Africa, WIAS, Animal Science and Zoology, predation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, daily activity, Diversity (politics)
Abstract: International audience; Nearly 90% of the world's large herbivore diversity occurs in Africa, yet there is a striking dearth of information on the movement ecology of these organisms compared to herbivores living in higher latitude ecosystems.The environmental context for movements of large herbivores in African savanna ecosystems has several distinguishing features. African large herbivores move in landscapes with high spatiotemporal variability, low predictability, seasonal restrictions in surface water as well as food resources, and exposure to a diverse assemblage of competitors, predators, and pathogens. These features influence mobility, diel activity routines, home‐range fidelity, and exposure to predation.We review the knowledge that has been gained about the movements of African herbivores from Global Positioning System (GPS) telemetry and identify important gaps in knowledge that exist. Topics addressed include seasonal movement patterns, daily activity schedules, space utilisation, water dependency, responses to risks of predation, pathogen transmission, social affiliations, and local population density determination.While the growing number of GPS telemetry studies has addressed a wide range of topics in Africa, they remain fragmentary in terms of places and species represented. Most research has been focussed on three species, and practices for data sharing and analysis should be improved. African landscapes are changing perhaps faster than any other region on Earth, with rapidly expanding human populations, massive infrastructure development projects, and changes in climatic regimes. There is a crucial need to establish relationships between herbivore movements and their changing environments, especially in Africa where most of the world's large herbivore diversity resides.
Published: 2020
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49. Identifying stationary phases in multivariate time series for highlighting behavioural modes and home range settlements

Author: Simon Chamaillé-Jammes, Emilie Lebarbier, Marie-Pierre Etienne, Simon Benhamou, Rémi Patin, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UPVM), Département de mathématiques - Université de Rennes 1, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Recherche Mathématique de Rennes (IRMAR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-INSTITUT AGRO Agrocampus Ouest, Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Modélisation aléatoire de Paris X (MODAL'X), Université Paris Nanterre (UPN), ANR-16-CE02-0001,LANDTHIRST,Les paysages de la soif: changement climatique et ajustements comportementaux face au manque d'eau(2016), ANR-11-LABX-0020,LEBESGUE,Centre de Mathématiques Henri Lebesgue : fondements, interactions, applications et Formation(2011), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université Paul-Valéry - Montpellier 3 (UPVM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paul-Valéry - Montpellier 3 (UPVM)-École pratique des hautes études (EPHE), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-INSTITUT AGRO Agrocampus Ouest, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)
Subjects: 0106 biological sciences, Computer science, Movement, home range, Bivariate analysis, migration, area- concentrated searching, 010603 evolutionary biology, 01 natural sciences, foraging, Homing Behavior, transit, Animals, Computer Simulation, Segmentation, K E Y W O R D S area-concentrated searching, Hidden Markov model, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Series (mathematics), 010604 marine biology & hydrobiology, segmentation, Variance (accounting), Temporal resolution, Piecewise, movement ecology, Animal Science and Zoology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Scale (map), Algorithm, [STAT.ME]Statistics [stat]/Methodology [stat.ME], clustering
Abstract: International audience; Recent advances in biologging open promising perspectives in the study of animal movements at numerous scales. It is now possible to record time series of animal locations and ancillary data (e.g. activity level derived from on‐board accelerometers) over extended areas and long durations with a high spatial and temporal resolution. Such time series are often piecewise stationary, as the animal may alternate between different stationary phases (i.e. characterized by a specific mean and variance of some key parameter for limited periods). Identifying when these phases start and end is a critical first step to understand the dynamics of the underlying movement processes. We introduce a new segmentation‐clustering method we called segclust2d (available as a r package at cran.r-project.org/package=segclust2d). It can segment bivariate (or more generally multivariate) time series and possibly cluster the various segments obtained, corresponding to different phases assumed to be stationary. This method is easy to use, as it only requires specifying a minimum segment length (to prevent over‐segmentation), based on biological rather than statistical considerations. This method can be applied to bivariate piecewise time series of any nature. We focus here on two types of time series related to animal movement, corresponding to (a) at large scale, series of bivariate coordinates of relocations, to highlight temporary home ranges, and (b) at smaller scale, bivariate series derived from relocations data, such as speed and turning angle, to highlight different behavioural modes such as transit, feeding and resting. Using computer simulations, we show that segclust2d can rival and even outperform previous, more complex methods, which were specifically developed to highlight changes of movement modes or home range shifts (based on hidden Markov and Ornstein–Uhlenbeck modelling), which, contrary to our method, usually require the user to provide relevant initial guesses to be efficient. Furthermore, we demonstrate it on actual examples involving a zebra's small‐scale movements and an elephant's large‐scale movements, to illustrate how various movement modes and home range shifts, respectively, can be identified.
Published: 2020
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50. Deer, wolves, and people: costs, benefits and challenges of living together

Author: Simon Chamaillé-Jammes, Jean-Louis Martin, Donald M. Waller, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), University of Wisconsin-Madison, Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, Value (ethics), carnivores, Cost-Benefit Analysis, Context (language use), human health, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Cultural learning, 03 medical and health sciences, Human health, Human-Animal Interaction, Animals, Humans, 030304 developmental biology, 0303 health sciences, Herbivore, Wolves, human–wildlife conflict, Human–wildlife conflict, Deer, Intrinsic value (animal ethics), Agriculture, Forestry, Environmental ethics, 15. Life on land, herbivores, Europe, livestock, Geography, Tick-Borne Diseases, 13. Climate action, Predatory Behavior, North America, Wasting Disease, Chronic, Safety, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, General Agricultural and Biological Sciences, ecological cascades, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; Human‐driven species annihilations loom as a major crisis. However the recovery of deer and wolf populations in many parts of the northern hemisphere has resulted in conflicts and controversies rather than in relief. Both species interact in complex ways with their environment, each other, and humans. We review these interactions in the context of the ecological and human costs and benefits associated with these species. We integrate scattered information to widen our perspective on the nature and perception of these costs and benefits and how they link to each other and ongoing controversies regarding how we manage deer and wolf populations. After revisiting the ecological roles deer and wolves play in contemporary ecosystems, we explore how they interact, directly and indirectly, with human groups including farmers, foresters, shepherds, and hunters. Interactions with deer and wolves generate various axes of tension, posing both ecological and sociological challenges. Resolving these tensions and conflicts requires that we address key questions using integrative approaches: what are the ecological consequences of deer and wolf recovery? How do they influence each other? What are the social and socio‐ecological consequences of large deer populations and wolf presence? Finally, what key obstacles must be overcome to allow deer, wolves and people to coexist? Reviewing contemporary ecological and sociological results suggests insights and ways to improve our understanding and resolve long‐standing challenges to coexistence. We should begin by agreeing to enhance aggregate benefits while minimizing the collective costs we incur by interacting with deer and wolves. We should also view these species, and ourselves, as parts of integrated ecosystems subject to long‐term dynamics. If co‐existence is our goal, we need deer and wolves to persevere in ways that are compatible with human interests. Our human interests, however, should be inclusive and fairly value all the costs and benefits deer and wolves entail including their intrinsic value. Shifts in human attitudes and cultural learning that are already occurring will reshape our ecological interactions with deer and wolves.
Published: 2020
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