Biology subjects

Garel, M.

Publications and source records attributed to Garel, M..

9 recordsLinked to original sources

bioRxiv2025

Evaluating camera trap methods for monitoring population trends in ungulates: insights from simulation

Camera traps have been widely used in the last decade to monitor abundance of unmarked animal populations. Most estimation methods rely either on the number of times animals pass through the detection zones, like random encounter models (REM) or on the number of capture occasions in a time-lapse program when animals were seen on the pictures, like the instantaneous sampling approach (IS). Yet, the ability of these two popular method classes to both reliably detect population trends and estimate population size has rarely been evaluated. We filled this gap by simulating a setup of either 100 or 25 camera traps randomly distributed on a 2600-ha area (respectively {approx} 4 and 1 trap/km2), along with the movements of a fictional population of 300 roe deer (Capreolus capreolus). Simulations were informed by field data on habitat, habitat selection and activity patterns of GPS-monitored roe deer. Under idealized conditions (e.g., perfect knowledge of day range and visibility), both IS and REM provided unbiased population estimates, though uncertainty remained substantial (CV from 15% to 30% with 4 and 1 trap/km2 respectively). However, our results show that neglecting imperfect detectability leads to severe biases in absolute density estimation. Moreover, despite idealized conditions and large sampling efforts, a simulated 20% population decline over 5 years went undetected by both approaches in 65-75% of simulations at high trap density and 80% at low trap density. Testing other sampling strategies to improve sensitivity either led to an unchanged population size estimation precision (stratified sampling) or to biased estimated trends (sampling only in high-quality habitats). Simulating animals with a 10 times larger home-range, led to miss the decline less frequently (5% - 40% at high trap density, 33% - 67% at low trap density). These results suggest that the key metric for camera trap use is the average number of different traps visited per animal, which in turn depends on trap density, home-range size and space use heterogeneity. We provide a R package allowing the reader to reproduce these simulations, and carry out their own.

ecology↗

bioRxiv2023

Cross-transmission of resistant gastrointestinal nematodes between wildlife and transhumant sheep

Wild and domestic ungulates can be infected with the same species of gastrointestinal parasitic nematodes. These parasites have free-living stages in the environment that contribute to the ease of transmission among different host species. In addition, gastrointestinal nematodes have developed resistance to anthelmintics which is now considered a major problem for the livestock sector. In a context where wild and domestic ungulates share the same pastures, the maintenance and circulation of resistant gastrointestinal nematodes between species have rarely been explored. In the European Alps, domestic sheep are driven to high-altitude summer pastures and live in sympatry with wild ungulates for several months each year. In this study, we investigated the nemabiome of domestic sheep and Alpine ibex, Capra ibex, in three different areas of the French Alps to evaluate parasite circulation between the two host species. The Alpine ibex is a protected mountain ungulate that is phylogenetically related to sheep and hosts nematode species common to sheep. Using internal transcribed spacer 2 (ITS-2) nemabiome metabarcoding, we found sheep and ibex share similar gastrointestinal nematodes, except for a few species such as Marshallagia marshalli and Trichostrongylus axei. This suggests that the long-term co-occurrence of sheep and ibex on mountain pastures has promoted the exchange of gastrointestinal nematodes between the two hosts. Based on the sequencing of the isotype 1 of the beta tubulin gene, associated with benzimidazole resistance, we found resistant nematodes in all sheep flocks and in all ibex populations. Our results demonstrated that ibex can host and shed resistant strains before transhumant sheep arrive on pastures, and thus could act as a refuge or even contribute to maintaining resistant gastrointestinal nematodes. The relative role of ibex in the maintenance and circulation of resistant strains in sheep remain to be determined.

ecology↗

bioRxiv2023

Identifying the environmental drivers of corridors and predicting connectivity between seasonal ranges in multiple populations of Alpine ibex (Capra ibex) as tools for conserving migration

Seasonal migrations are central ecological processes connecting populations, species and ecosystems in time and space. Land migrations, such as those of ungulates, are particularly threatened by habitat transformations and fragmentation, climate change and other environmental changes caused by anthropogenic activities. Mountain ungulate migrations are neglected because they are relatively short, although traversing highly heterogeneous altitudinal gradients particularly exposed to anthropogenic threats. Detecting migration routes of these species and understanding their drivers is therefore of primary importance to predict connectivity and preserve ecosystem functions and services. The populations of Alpine ibex Capra ibex, an iconic species endemic to the Alps, have all been reintroduced from the last remnant source population. Because of their biology and conservation history, Alpine ibex populations are mostly disconnected. Hence, despite a general increase in abundance and overall distribution range, their conservation is strictly linked to the interplay between external threats and related behavioral responses, including space use and migration. By using 337 migratory tracks from 425 GPS-collared individuals from 15 Alpine ibex populations distributed across their entire range, we (i) identified the environmental drivers of movement corridors in both spring and autumn and (ii) compared the abilities of three modeling approaches to predict migratory movements between seasonal ranges of the 15 populations. Trade-offs between energy expenditure, food, and cover seemed to be the major driver of migration routes: steep south-facing snow-free slopes were selected while high elevation changes were avoided. This revealed the importance of favorable resources and an attempt to limit energy expenditures and perceived predation risk. Based on these findings, we provided efficient connectivity models to inform conservation of Alpine ibex and its habitats, and a framework for future research investigating connectivity in migratory species.

ecology↗

bioRxiv2023

Too disturbed or too hot: summer temperatures more than hikers disturbance affect circadian activity of females in northern chamois

Recreational activities often result in a spatial and/or temporal activity shift in wildlife. With the concurrent development of outdoor activities and increase in temperatures due to climate change, mountain species face increasing pressures in terms of managing their activity pattern to limit both risk exposure and thermal discomfort. Using more than 15 years of long-term GPS and activity sensor data, we investigated how female northern chamois, Rupicapra rupicapra rupicapra, adjust their summer circadian activity to spatiotemporal variation in both temperatures and hikers presence. Chamois behaviour was more affected by high temperatures than by hikers presence. During the hottest days, they shifted their activity peak earlier in the morning, were more active at night, less active during daytime and had longer morning and evening peaks compared to the coldest days. Global activity was only slightly different during the hottest than the coldest days. Conversely, hikers disturbance had weak effects on activity levels and on the timing of activity peaks. This is especially true for temporal disturbance (weekdays versus weekends and public holidays), possibly because most weekdays in summer fell during school holidays. During the hottest conditions, the morning activity peak was shorter and the evening peak longer in females living in the most exposed areas compared to females living in the least exposed areas. One possible explanation for the overall low effect of hikers disturbance may be that behavioural changes buffering animals from high temperatures and hikers presence (e.g. moving away from trails) allow them to just marginally modify their activity pattern. In the context of ongoing socioenvironmental changes, it is critical to conserve habitats providing thermal refuges against summer heat and protection from disturbance to mitigate potential detrimental consequences.

animal behavior and cognition↗

bioRxiv2022

A ready-to-use logistic Verhulst model implemented in R shiny to estimate growth parameters of microorganisms

In microbiology, the estimation of the growth rate of microorganisms is a critical parameter to describe a new strain or characterize optimal growth conditions. Traditionally, this parameter is estimated by selecting subjectively the exponential phase of the growth, and then determining the slope of this curve section, by linear regression. However, for some experiments, the number of points to describe the growth can be very limited, and consequently such linear model will not fit, or the parameters estimation can much lower and strongly variable. In this paper, we propose a tools to estimate growth parameters using a logistic Verhulst model that take into account the entire growth curve for the estimation of the growth rate. The efficiency of such model is compared to the linear model. Finally, the novelty of our work is to propose a "Shiny-web application", online, without any programming or modelling skills, to allow estimating growth parameters including growth rate, maximum population, and beginning of the exponential phase, as well as an estimation of their variability. The final results can be displayed in the form of a scatter plot representing the model, its efficiency and the estimated parameters are downloadable.

microbiology↗

bioRxiv2022

The DeepFaune initiative: a collaborative effort towards the automatic identification of the French fauna in camera-trap images

Camera traps have revolutionized how ecologists monitor wildlife, but their full potential is realized only when the hundreds of thousands of collected images can be readily classified with minimal human intervention. Deep-learning classification models have allowed extraordinary progress towards this end, but trained models remain rare and are only now emerging for European fauna. We report on the first milestone of the DeepFaune initiative (https://www.deepfaune.cnrs.fr), a large-scale collaboration between more than 50 partners involved in wildlife research, conservation and management in France. We developed a classification model trained to recognize 26 species or higher-level taxa. The classification model achieved 0.97 validation accuracy and often >0.95 precision and recall for many classes. These performances were generally higher than 0.90 when tested on independent out-of-sample datasets for which we used image redundancy contained in sequence of images. We implemented our model in a software to classify images stored locally on a personal computer, so as to provide a free, user-friendly and high-performance tool for wildlife practitioners to automatically classify camera-trap images.

ecology↗

bioRxiv2020

Path tortuosity changes the transport cost paradigm in terrestrial animals

Animal movement paths are variously tortuous, with high turn rates predicted to be energetically costly, especially at high speeds. Animals travel most efficiently at the speed that gives the lowest cost of transport (COT), a well-defined point for movement in fluid media. However, theoretically, land animals should travel at their maximum speed to minimize COT, which they do not, instead travelling at walking pace. We measured oxygen consumption in humans to demonstrate that the energetic costs of turning increase disproportionately with both speed and angular velocity. This resulted in the minimum COT speed occurring at very low speeds, which reduced with increased path tortuosity. Data on turn rates from six free-ranging terrestrial species underpinned this because all individuals turned faster at the slowest speeds across the full speed range. The optimum movement speed for minimum COT in land animals thus depends on the environment and behavior since both affect track tortuosity.

ecology↗

bioRxiv2020

Why did the animal turn? Time-varying step selection analysis for inference between observed turning points in high frequency data

O_LIStep selection analysis (SSA) is a fundamental technique for uncovering the drivers of animal movement decisions. Its typical use has been to view an animal as "selecting" each measured location, given its current (and possibly previous) locations. Although an animal is unlikely to make decisions precisely at the times its locations are measured, if data are gathered at a relatively low frequency (every few minutes or hours) this is often the best that can be done. Nowadays, though, tracking data is increasingly gathered at very high frequencies, often [≥]1Hz, so it may be possible to exploit these data to perform more behaviourally-meaningful step selection analysis. C_LIO_LIHere, we present a technique to do this. We first use an existing algorithm to determine the turning-points in an animals movement path. We define a "step" to be a straight-line movement between successive turning-points. We then construct a generalised version of integrated SSA (iSSA), called time-varying iSSA (tiSSA), which deals with the fact that turning-points are usually irregularly spaced in time. We demonstrate the efficacy of tiSSA by application to data on both simulated animals and free-ranging goats (Capra aegagrus hircus), comparing our results to those of regular iSSA with locations that are separated by a constant time-interval. C_LIO_LIUsing (regular) iSSA with constant time-steps can give results that are misleading compared to using tiSSA with the actual turns made by the animals. Furthermore, tiSSA can be used to infer covariates that are dependent on the time between turns, which is not possible with regular iSSA. As an example, we show that our study animals tend to spend less time between successive turns when the ground is rockier and/or the temperature is hotter. C_LIO_LIBy constructing a step selection technique that works between observed turning-points of animals, we enable step selection to be used on high-frequency movement data, which are becoming increasingly prevalent in modern biologging studies. Furthermore, since turning-points can be viewed as decisions, our method places step selection analysis on a more behaviourally-meaningful footing compared to previous techniques. C_LI

ecology↗

bioRxiv2018

ANALYSING PATTERNS IN POPULATION DYNAMICS USING REPEATED POPULATION SURVEYS WITH THREE TYPES OF DETECTION DATA

O_LIWe generalize the distance sampling protocol to accommodate three types of detection data in population surveys (population counts): distance to the observer, multiple observers, and time-to-detection. We also account for the effect of a partially-observed individual covariate, with the aim to account for the non-independence of individuals in groups and the effect of group size on detection probability. Finally, we separate the probability of availability to detection and the probability of detection when available.\nC_LIO_LIWe compute the statistical power of our new model using simulations and illustrate some of the biases in the simpler alternative analytical procedures that oue new formulation allows to avoid. We discuss issues of weak identifiability (an issue shared with other state-space models) and the bias-precision tradeoff in population survey analyses.\nC_LIO_LIWe recommend maintaining both simple analyses of population survey data and more complex analyses of the detection process, maybe in a dashboard of indicators. Discrepancies between results from simple and complex analyses can help identify sources of biases and loss of precision.\nC_LI

ecology↗