Simon Chamaillé-Jammes

French National Centre for Scientific Research | CNRS · Centre d'Ecologie Fonctionnelle et Evolutive

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...

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 p...

Ecological niche differences are necessary for stable species coexistence but are often dif- ficult to discern. Models of dietary niche differentiation in large mammalian herbivores invoke the quality, quantity, and spatiotemporal distribution of plant tissues and growth forms but are agnostic toward food plant species identity. Empirical support f...

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...

L’incertitude persiste au sujet de l’efficacité des prélèvements létaux de loup à réduire la prédation de cette espèce sur les troupeaux domestiques, que cela soit en France ou ailleurs où ces mesures sont appliquées. Dans cet article, nous résumons les résultats de la thèse d'Oksana Grente réalisée sous la direction de l’Office Français de la Biod...

Aim: Macroecological studies that require habitat suitability data for many species often derive this information from expert opinion. However, expert-based information is inherently subjective and thus prone to errors. The increasing availability of GPS tracking data offers opportunities to evaluate and supplement expert-based information with de...

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 predicta...

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 extraordina...

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 t...

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 t...

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...

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 cycl...

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 characteris...

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 male...

In semi-arid savannas, the availability of surface water constrains movements and space-use of wild animals. To accurately model their movements in relation to water selection at a landscape scale, innovative methods have to be developed to i) better discriminate water bodies in space while characterizing their seasonal occurrences and ii) integrat...

In social species, the transmission and maintenance of infectious diseases depend not only on the contact patterns among individuals within groups but also on the interactions between groups. In southern Africa, the Cape buffalo (Syncerus caffer caffer) is a vector for many pathogens that can infect sympatric livestock. Whilst intra-group contact p...

Proposed in 1849 by Charles Morren to depict periodical phenomena governed by seasons, the term ″phenology″ has spread in many fields, from evolutionary to molecular biology. The adoption of the concept of phenology in such diverse fields has been associated with the creation of a wide diversity of metrics, and we believe, some confusion about what...

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 aggregati...

Ecologists increasingly rely on camera-trap data to estimate biological parameters such as population abundance. Because of the huge amount of data camera trap can generate, the assistance of non-scientists is often sought after, but an assessment of the data quality is necessary. We tested whether volunteers data from one of the largest citizen sc...

Long-distance vocalization 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 pr...

An increasing number of ecological monitoring programmes 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 o...

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 sho...

Ecologists increasingly rely on camera-trap data to estimate biological parameters such as population abundance. Because of the huge amount of data, the assistance of non-scientists is often sought after, but an assessment of the data quality is necessary. We tested whether volunteers data from one of the largest citizen science projects - Snapshot...

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. Be...

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 was to investigate the role of the presence of predators in the functional adjustments of feeding parameters with patch qu...

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...

Previous research has shown that African lions (Panthera leo) have the ability to discriminate between conspecific vocalisations, but little is known about how individual identity is conveyed in the spectral structure of roars. Using acoustic – accelerometer biologgers that allow vocalisations to be reliably associated with individual identity, we...

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 l...

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 coexis...

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 elephan...

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...

• 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....

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...

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...

A comprehensive theory about when and how behaviourally responsive predators and prey should use the information they acquire about the environment and each other's presence while engaged in what is viewed as a space race is currently lacking. This limits our understanding of the role of behaviour in trophic relationships and our ability to predict...

Habitat selection models are used in ecology to link the spatial distribution of animals to environmental covariates, and identify preferred habitats. The most widely used models of this type, resource selection functions, aim to capture the steady‐state distribution of space use of the animal, but they assume independence between the observed loca...

Recent advances in bio‐logging 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‐serie...

This chapter examines the effects of structural defense traits on feeding rates of mammalian browsers. The set of structural defenses deployed by a woody plant strongly depends upon the herbivore species being targeted by those defenses. The chapter deals with structural defenses against medium‐to‐large savanna ungulates. First, the chapter discuss...

This chapter reviews the mechanisms underlying consumptive and non‐consumptive effects of predators on prey. It provides an overview of consumptive and non‐consumptive mechanisms, the current knowledge about their importance, and how they may interact. The chapter draws from the theoretical literature and from field studies conducted in biomes othe...

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 combine...

Studies on invertebrates and small vertebrates demonstrated the underappreciated importance of the non-consumptive effects (NCE) of predators on their prey. Recently, there has been a growing interest for such effects in large vertebrates. Here, we review the empirical literature on large carnivore-ungulate systems to map our knowledge of predation...

Alarm calls and predator vocalizations convey information on predator presence and potential risk. Generally, prey employ anti-predator behaviours more in response to alarm calls. However, occasionally prey respond more to the vocalizations of specific predators. A key question is do prey still respond to alarm calls and predator vocalizations when...

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 t...

1.Diel migrations (DM; back and forth diel movements along an ecological gradient) undertaken by prey to avoid predators during the day have been demonstrated in many taxa in aquatic ecosystems. In terrestrial ecosystems, prey often shift between various vegetation types whose cover determine their vulnerability (i.e. likelihood of being killed whe...

The functional response describes how food abundance affects the intake rate of foraging individuals, and as such, it can influence a wide range of ecological processes. In social species, dominance status can affect the functional response of competing individuals, but studies conducted in an interference-free context have provided contrasting res...

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 arch...

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 a...

Habitat selection models are used in ecology to link the distribution of animals to environmental covariates, and identify habitats that are important for conservation. The most widely used models of this type, resource selection functions, assume independence between the observed locations of an animal. This is unrealistic when location data displ...

Recent advances in bio-logging open promising perspectives in the study 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 a...

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 conse...

Dilution of predation risk within groups allows individuals to be less vigilant and forage more while still facing lower risk than if they were alone. How group size influences vigilance when individuals can also adjust their space use, and whether this relationship differs among individuals contributing differently to space use decisions, remain u...

Much research on large herbivore movement has focused on the annual scale to distinguish between resident and migratory tactics, commonly assuming that individuals are sedentary at the within-season scale. However, apparently sedentary animals may occupy a number of sub-seasonal functional home ranges (sfHR), particularly when the environment is sp...

Restrictions on roaming Until the past century or so, the movement of wild animals was relatively unrestricted, and their travels contributed substantially to ecological processes. As humans have increasingly altered natural habitats, natural animal movements have been restricted. Tucker et al. examined GPS locations for more than 50 species. In ge...

Context The spatial distribution of non-substitutable resources implies diverging predictions for animal movement patterns. At broad scales, animals should respond to landscape complementation by selecting areas where resource patches are close-by to minimize movement costs. Yet at fine scales, central place effects lead to the depletion of patches...

Top-order carnivores are naturally returning, or are being reintroduced, in a number of places where they have previously been extirpated. To explore how prey species adjust their antipredator behavior in response to these predators, we measured giving-up densities (GUDs) in experimental feeding patches and time spent vigilant for greater kudu (Tra...

Most population dynamics studies assume that individuals use space uniformly, and thus mix well spatially. In numerous species, however, individuals do not move randomly, but use spatial memory to visit renewable resource patches repeatedly. To understand the extent to which memory-based foraging movement may affect density-dependent population dyn...

Successful conservation of large mammals requires vast areas to maintain viable populations. This often requires to embrace large-scale approaches that extend beyond the borders of formally protected areas. However, the quality of the scientific knowledge about animal movement across large conservation areas vary, and could limit the effectiveness...

Diel migrations (DMs) undertaken by prey to avoid visual predators during the day have been demonstrated in many taxa in aquatic ecosystems. We reveal that zebras in Hwange National Park (Zimbabwe) employ a similar anti-predator strategy. Zebras forage near waterholes during the day but move away from them at sunset. We demonstrate that this DM, oc...

These files contains model code for a manuscript in preparation "Space Use and Leadership Modify Dilution Effects on Optimal Vigilance under Food-Safety Trade-Offs" published in American Naturalist

Prey species may adjust their use of antipredator behaviours to counter the hunting strategies (e.g. ambush versus cursorial) and the level of risk imposed by different predators. Studies of suites of behaviours across well-defined contrasts of predation risk and type are rare, however. Here we explored the degree to which six herbivore species adj...

1.Where large browsers are abundant, the survival of trees depends upon their ability to deploy defences, either chemical or structural. Structural defences include the arrangement of dense and intricate architecture, termed ‘cage’ architecture. Previous studies showed that trees developing in herbivore-rich environments tend to have more cage arch...