23 results on '"Clément Calenge"'
Search Results
2. Estimating the population size of a mountain galliform in the context of multi‐stakeholder adaptive management
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Clément Calenge, Emmanuel Ménoni, Blandine Milhau, Kévin Foulché, Jules Chiffard, and Stéphane Marchandeau
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Population Density ,Ecology ,Probability - Abstract
We designed a participatory monitoring program for the capercaillie population in the French Pyrenees based on lek censuses conducted during the breeding season. This program was implemented by a consortium of stakeholders interested in the conservation of French galliforms. The program, carried out since 2010, relied on a dual frame sampling approach: The first sampled frame was the list of all known leks in the study area. We distinguished two types of known leks: leks known to be active before the onset of the program (with at least one cock detected since 2000) and leks with an indeterminate activity status at the time of the onset of the program. The monitoring program also accounted for the existence of leks that were unknown due mainly to incomplete expert knowledge. We therefore built a complementary area frame by discretizing the study area into a set of 4-km
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- 2022
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3. Assessing spatiotemporal variation in abundance: A flexible framework accounting for sampling bias with an application to common pochard ( Aythya ferina )
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Benjamin Folliot, Alain Caizergues, Adrien Tableau, Guillaume Souchay, Matthieu Guillemain, Jocelyn Champagnon, and Clément Calenge
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Ecology ,common pochard ,ducks ,hierarchical modeling ,spatial autocorrelation ,sampling bias ,Ecology, Evolution, Behavior and Systematics ,population trends ,Nature and Landscape Conservation - Abstract
Assessing trends in the relative abundance of populations is a key yet complex issue for management and conservation. This is a major aim of many large-scale censusing schemes such as the International Waterbird Count (IWC). However, owing to the lack of sampling strategy and standardization, such schemes likely suffer from biases due to spatial heterogeneity in sampling effort. Despite huge improvements of the statistical tools that allow tackling these statistical issues (e.g., GLMM, Bayesian inference), many conservationists still prefer to rely on stand-alone turn-key statistical tools, often violating the prerequisites put forward by the developers of these tools. Here, we propose a straightforward and flexible approach to tackle the typical statistical issues one can encounter when analyzing count data of monitoring schemes such as the IWC. We rely on IWC counts of the declining common pochard populations of the Northwest European flyway as a case study (period 2002-2012). To standardize the size of sampling units and mitigate spatial autocorrelation, we grouped sampling sites using a 75 × 75 km grid cells overlaid over the flyway of interest. Then, we used a hierarchical modeling approach, assessing population trends with random effects at two spatial scales (grid cells, and sites within grid cells) in order to derive spatialized values and to compute the average population trend at the whole flyway scale. Our approach allowed to tackle many statistical issues inherent to this type of analysis but often neglected, including spatial autocorrelation. Concerning the case study, our main findings are that: (1) the northwestern population of common pochards experienced a steep decline (4.9% per year over the 2002-2012 period); (2) the decline was more pronounced at high than low latitude (11.6% and 0.5% per year at 60° and 46° of latitude, respectively); and, (3) the decline was independent of the initial number of individuals in a given site (random across sites). Beyond the case study of the common pochard, our study provides a conceptual statistical framework for estimating and assessing potential drivers of population trends at various spatial scales.
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- 2022
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4. Parasitized or non-parasitized, why? A study of factors influencing tick burden in roe deer neonates
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Léa Bariod, Sonia Saïd, Clément Calenge, Stéphane Chabot, Vincent Badeau, Gilles Bourgoin, Biodémographie évolutive, Département écologie évolutive [LBBE], 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 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)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), 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), Office français de la biodiversité (OFB), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
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[SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health ,Multidisciplinary ,Ixodes ,Deer ,parasitic diseases ,Infant, Newborn ,Animals ,Babesia ,Humans ,[SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology ,Bayes Theorem ,[SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis ,Tick Infestations - Abstract
Ixodes ricinus, the most common species of tick in Europe, is known to transmit major pathogens to animals and humans such as Babesia spp. or Borrelia spp.. Its abundance and distribution have been steadily increasing in Europe during recent decades, due to global environmental changes. Indeed, as ticks spend most of their life in the environment, their activity and life cycle are highly dependent on environmental conditions, and therefore on climate or habitat changes. Simultaneously, wild ungulates have expanded their range and increased dramatically in abundance worldwide, in particular roe deer (Capreolus capreolus), have allowed tick populations to grow and spread. Currently, tick infestation on newborn wild ungulates is poorly documented. However, newborn ungulates are considered more sensitive to tick bites and pathogen transmission because of their immature immune system. Thus, improving knowledge about the factors influencing tick infestation on newborns is essential to better understand their health risks. This study was conducted at Trois-Fontaines forest, Champagne-Ardenne, France (1992-2018). Based on a long-term monitoring of roe deer fawns, we used a novel Bayesian model of the infestation of fawns to identify which biotic or abiotic factors are likely to modify the level of infestation by ticks of 965 fawns over time. We show that tick burden increased faster during the first days of life of the fawns and became constant when fawns were 5 days old and more, which could be explained by the depletion of questing ticks or the turnover of ticks feeding on fawns. Moreover, the humidity, which favors tick activity, was weakly positively related to the tick burden. Our results demonstrate that tick infestation was highly variable among years, particularly between 2000 and 2009. We hypothesize that this results from a modification of habitat caused by hurricane Lothar.
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- 2022
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5. Bayesian estimation of species relative abundances and habitat preferences using opportunistic data
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Clément Calenge, Christophe Giraud, Romain Julliard, and Camille Coron
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0106 biological sciences ,Statistics and Probability ,Bayes estimator ,Data collection ,Biometrics ,010604 marine biology & hydrobiology ,Bayesian probability ,Poisson distribution ,010603 evolutionary biology ,01 natural sciences ,symbols.namesake ,Geography ,Habitat ,Statistics ,symbols ,Statistics, Probability and Uncertainty ,Selection (genetic algorithm) ,General Environmental Science - Abstract
We develop a new statistical procedure to monitor relative species abundances and their respective preferences for different habitat types, using opportunistic data. Following Giraud et al. (Biometrics 72(2):649–658, 2015), we combine the opportunistic data with some standardized data in order to correct the bias inherent to the opportunistic data collection. Species observations are modeled by Poisson distributions whose parameters quantify species abundances and habitat preferences, and are estimated using Bayesian computations. Our main contributions are (i) to tackle the bias induced by habitat selection behaviors, (ii) to handle data where the habitat type associated to each observation is unknown, (iii) to estimate probabilities of selection of habitat for the species. As an illustration, we estimate common bird species habitat preferences and abundances in the region of Aquitaine (France).
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- 2018
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6. Determining the boundaries of migratory bird flyways: a Bayesian model for Eurasian teal Anas crecca in western Europe
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Clément Calenge, Matthieu Guillemain, Richard Hearn, and Jocelyn Champagnon
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0106 biological sciences ,education.field_of_study ,biology ,Ecology ,Population ,biology.organism_classification ,Bayesian inference ,010603 evolutionary biology ,01 natural sciences ,010605 ornithology ,Abundance (ecology) ,Western europe ,Flyway ,Anas crecca ,Conservation status ,Animal Science and Zoology ,Bayesian framework ,education ,Ecology, Evolution, Behavior and Systematics - Abstract
Accurate flyway delineation is a prerequisite for effective conservation and management of migratory bird populations, yet such limits have so far mostly been set subjectively. We present a statistical method to infer population boundaries from the analysis of ring recoveries, using a Bayesian framework. The approach was applied to Eurasian teal Anas crecca ringed in Camargue, southern France, and Abberton Reservoir, Essex, eastern England. The results presented show the boundaries of the two teal flyways in western Europe, with a zone of overlap, broadly matching those previously defined. The percentage of teal switching flyways (abmigration rate) was 2.4–2.6%, greater in birds ringed as juveniles than as adults. Abmigrants ended up at sites within the other flyway where the density of local birds was lower than expected by chance, suggesting abmigration resulted from exploratory or aberrant behaviour. The methodology presented here can be used to infer flyway boundaries of any bird with an adequate ring-re-encounter dataset, which has crucial consequences for the evaluation of their trends in abundance and hence conservation status, and the management of sustainable harvests.
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- 2017
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7. Altitude shapes the environmental drivers of large-scale variation in abundance of a widespread mammal species
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Ludovic Say, Sébastien Devillard, Mickaël Jacquier, Sandrine Ruette, Clément Calenge, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), and 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)
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0106 biological sciences ,Badger ,Mustelidae ,Meles ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Abundance (ecology) ,lcsh:QH540-549.5 ,biology.animal ,Relative species abundance ,climate ,large‐scale ,Ecology, Evolution, Behavior and Systematics ,ComputingMilieux_MISCELLANEOUS ,030304 developmental biology ,Nature and Landscape Conservation ,Original Research ,Abiotic component ,0303 health sciences ,Biotic component ,Ecology ,biology ,15. Life on land ,landscape ,biology.organism_classification ,soil features ,Geography ,Habitat ,lcsh:Ecology ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology ,food resources - Abstract
Aim Habitat quality and heterogeneity directly influence the distribution and abundance of organisms at different spatial scales. Determining the main environmental factors driving the variation in species abundance is crucial to understand the underlying ecological processes, and this is especially important for widely distributed species living in contrasting environments. However, the responses to environmental variation are usually described at relatively small spatial scales. Here, we studied the variation in abundance of a widely distributed mustelid, the European badger (Meles meles), across France. Location The whole metropolitan France. Methods We used (a) direct detections of 9,439 dead and living badgers, from 2006 to 2009, to estimate badger relative abundance in 703 small agricultural regions of metropolitan France and (b) a Bayesian modeling approach to identify the main environmental determinants influencing badger abundance. Results Despite a continuous distribution of badger in France, we found large variation in badger abundance between regions, explained by environmental factors. Among a set of 13 environmental variables, we demonstrated that badger abundance in lowlands (, We used direct detections of 9,439 badgers Meles meles, to estimate badger relative abundances in 703 small agricultural regions of metropolitan France and a Bayesian modeling approach to identify the main environmental determinants influencing badger abundances. Despite a continuous distribution of badger in this country, we demonstrated that badger abundances in lowlands were mostly driven by biotic factors such as potential food resources and forest fragmentation, while in mountainous areas, abiotic factors drove the variations in badger relative abundance. These results underline the importance of mapping the abundance of wildlife species based on environmental suitability and highlight the complexity of drivers influencing species abundance at large spatial scale.
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- 2019
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8. Estimating disease prevalence and temporal dynamics using biased capture serological data in a wildlife reservoir: The example of brucellosis in Alpine ibex (Capra ibex)
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Sébastien Lambert, Carole Toïgo, Elodie Petit, Emmanuelle Gilot-Fromont, Clément Calenge, Sophie Rossi, Anne Thébault, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), and 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)
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Male ,Capra ibex ,040301 veterinary sciences ,030231 tropical medicine ,Population ,Prevalence ,Wildlife ,Animals, Wild ,Force of infection ,Brucellosis ,Serology ,0403 veterinary science ,03 medical and health sciences ,0302 clinical medicine ,Food Animals ,Seroepidemiologic Studies ,medicine ,Animals ,Seroprevalence ,education ,ComputingMilieux_MISCELLANEOUS ,education.field_of_study ,Goat Diseases ,biology ,Goats ,Bayes Theorem ,04 agricultural and veterinary sciences ,biology.organism_classification ,medicine.disease ,Female ,[SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie ,Animal Science and Zoology ,France ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology ,Demography - Abstract
The monitoring of the disease prevalence in a population is an essential component of its adaptive management. However, field data often lead to biased estimates. This is the case for brucellosis infection of ibex in the Bargy massif (France). A test-and-cull program is being carried out in this area to manage the infection: captured animals are euthanized when seropositive, and marked and released when seronegative. Because this mountainous species is difficult to capture, field workers tend to focus the capture effort on unmarked animals. Indeed, marked animals are less likely to be infected, as they were controlled and negative during previous years. As the proportion of marked animals in the population becomes large, captured animals can no longer be considered as an unbiased sample of the population. We designed an integrated Bayesian model to correct this bias, by estimating the seroprevalence in the population as the combination of the separate estimates of the seroprevalence among unmarked animals (estimated from the data) and marked animals (estimated with a catalytic infection model, to circumvent the scarcity of the data). As seroprevalence may not be the most responsive parameter to management actions, we also estimated the proportion of animals in the population with an active bacterial infection. The actual infection status of captured animals was thus inferred as a function of their age and their level of antibodies, using a model based on bacterial cultures carried out for a sample of animals. Focusing on the population of adult females in the core area of the massif, i.e. with the highest seroprevalence, this observational study shows that seroprevalence has been divided by two between 2013 (51%) and 2018 (21%). Moreover, the likely estimated proportion of actively infected females in the same population, though very imprecise, has decreased from a likely estimate of 34% to less than 15%, suggesting that the management actions have been effective in reducing infection prevalence.
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- 2021
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9. Should I stay or should I go? Determinants of immediate and delayed movement responses of female red deer (Cervus elaphus) to drive hunts
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Eric Baubet, Clément Calenge, Pascal Marchand, Sonia Saïd, Emmanuelle Richard, Agathe Chassagneux, Etienne Guillaumat, and Office français de la biodiversité (OFB)
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Male ,0106 biological sciences ,Predation ,Social Sciences ,Wildlife ,01 natural sciences ,Geographical locations ,Psychology ,ComputingMilieux_MISCELLANEOUS ,Mammals ,Sex Characteristics ,Multidisciplinary ,Behavior, Animal ,Ecology ,Animal Behavior ,05 social sciences ,Eukaryota ,Ruminants ,Trophic Interactions ,Habitats ,Europe ,Geography ,Community Ecology ,Vertebrates ,[SDE]Environmental Sciences ,Medicine ,Cervus elaphus ,Female ,France ,Research Article ,Science ,Movement ,Animal Types ,010603 evolutionary biology ,Dogs ,Animals ,Hunting Behavior ,0501 psychology and cognitive sciences ,Animal behavior ,Wildlife management ,European Union ,050102 behavioral science & comparative psychology ,Behavior ,Deer ,Ecology and Environmental Sciences ,Organisms ,Biology and Life Sciences ,15. Life on land ,Fishery ,Remote Sensing Technology ,Amniotes ,People and places ,Zoology - Abstract
Hunting can be used as a tool for wildlife management, through limitation of population densities and dissuading game from using sensitive areas. The success of these approaches requires in depth knowledge of prey movement. Indeed, movement decisions of game during hunting may affect the killing success of hunters as well as the subsequent location of surviving animals. We thus investigated red deer movement responses to drive hunts and their causal factors. We studied 34 hunting events in the National Estate of Chambord (France) and thereby provided a fine-scale characterization of the immediate and delayed movement responses of red deer to drive hunts. Red deer responded to drive hunts either by immediately fleeing the hunted area, or by initially remaining before ultimately fleeing after the hunters had departed. A few hours after the hunt, all individuals were located in distant areas (> 2 kilometres) from the hunted area. Immediate flight responses were less common when drive hunts occurred in areas with dense understorey. However, neither beater/dog densities nor site familiarity influenced the immediate flight decision. Following a drive hunt, red deer remained outside the hunted areas for periods twice as long compared to periods when no hunting occurred (34 hours vs. 17 hours). Such knowledge of game movement rates in response to drive hunts may help the development of informed management policy for hunted red deer populations.
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- 2020
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10. Studying spatial interactions between sympatric populations of large herbivores: a null model approach
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Clément Calenge, Sonia Saïd, Jean-Luc Hamann, Jean-Michel Gaillard, Emmanuelle Richard, Biodémographie évolutive, Département écologie évolutive [LBBE], 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 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)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), and 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)
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0106 biological sciences ,Community ,biology ,Null model ,Ecology ,[SDV]Life Sciences [q-bio] ,media_common.quotation_subject ,Null (mathematics) ,Interspecific competition ,15. Life on land ,Population ecology ,010603 evolutionary biology ,01 natural sciences ,Competition (biology) ,010601 ecology ,Roe deer ,Sympatric speciation ,biology.animal ,Ecology, Evolution, Behavior and Systematics ,media_common - Abstract
Sympatric populations of species with similar ecology are limited by competition for available resources. While quantifying niche overlap between species in interaction offers a useful description of coexistence patterns, the lack of correspondence between niche overlap and competition prevents any functional interpretation. Using an innovative approach for analysing spatial distributions of individuals from two sympatric species, we aim to fill the gap. We applied our models to data collected on sympatric females of roe deer and red deer. Using the null model approach commonly applied in community ecology, we tested in a first model for deviation from a random distribution of female roe deer in relation to female red deer. We took into account constraints generated by both the marked sedentary habits and habitat use (avoidance of mature forest) of roe deer in this null model. In a second null model, we removed the habitat constraints to avoid any lack of power of our tests. We then compared the overlap index calculated from roe deer and red deer locations with the distribution expected under each of these null models. As we failed to reject the null model in both cases, we tested a third null model simulating an identical distribution of roe deer and red deer home ranges and we rejected it. Our results show that the distribution of female roe deer does not depend on the distribution of female red deer, indicating an absence of competitive interactions between the deer species. This conclusion relies on the application of the null model approach, which provides a suitable way of performing a formal test of interspecific competition rooted in explicitly defined hypotheses, and could not have been reached using simple overlap indices as generally performed when assessing competitive interactions. We thus encourage scientists to apply this null model analysis to population ecology.
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- 2012
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11. Spatial distribution and habitat selection in coexisting species of mountain ungulates
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Clément Calenge, Jean-François Lopez, Daniel Maillard, Gaëlle Darmon, Jean-Michel Jullien, and Anne Loison
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Ecological niche ,Community ,Ecology ,Ecological release ,media_common.quotation_subject ,Niche segregation ,Rupicapra ,Biology ,biology.organism_classification ,Competition (biology) ,Spatial ecology ,Species richness ,Ecology, Evolution, Behavior and Systematics ,media_common - Abstract
One of the main objectives of community ecology is to understand the conditions allowing species to coexist, which requires identifying how co-occurring species use and share space and resources. Species of the same trophic level, such as large herbivores, are of fundamental interest in that context because competition for resources is likely. Segregation in space or on some axes of the ecological niche are processes allowing coexistence, yet, both are seldom studied jointly. Based on annual spring censuses collected for 11 yr, we analysed the degree of overlap in spatial distribution among chamois Rupicapra rupicapra and mouflon Ovis gmelini musimon, 2 species of similar size that coexist on the same alpine pastures. We further investigated whether they differed in terms of habitat selection processes, and identified which environmental factors led to species being aggregated or segregated. The areas of intensive use for 2 species were more spatially aggregated than expected by chance. Habitat selection was studied using multivariate methods based on the niche concept, considering the presence of 1 species as an environmental variable for the other. Despite a large overlap in niches (88%), segregation was significant as chamois preferred meadows dominated by Sesleria and Carex sempervirens while mouflon selected meadows dominated by Carex ferruginea and avoided being close to areas affected by human activities. Importantly, habitat selection within each species was not affected by the presence of the other species. Coexistence between these 2 species and spatial overlap may be permitted because resource partitioning occurs at a fine temporal and/or spatial scale. We underscore that joint approaches of spatial and ecological processes are necessary to disclose the type of interaction (neutral, facilitation or competition) at play within a community.
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- 2012
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12. On the effects of grid size and shape when mapping the distribution range of a recolonising wolf (Canis lupus) population
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Marie Pruszek, Clément Calenge, Christophe Duchamp, and Eric Marboutin
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education.field_of_study ,biology ,Grid size ,Ecology ,Population ,Lupus (constellation) ,Area of interest ,Management, Monitoring, Policy and Law ,biology.organism_classification ,Canis ,Distribution (mathematics) ,Statistics ,Principal component analysis ,Range (statistics) ,education ,Ecology, Evolution, Behavior and Systematics ,Nature and Landscape Conservation ,Mathematics - Abstract
An estimate of changes in a species' distribution range is a key variable in assessing its conservation status. It may be based on the direct detection of individuals, or on the use of indirect presence sign surveys. In both cases, the process requires one to switch from a point-based approach, where individuals/presence signs are located using a coordinate system, to an area-based one, each original point being replaced by a cell area unit (CAU), with a given shape and size. The estimated distribution range (EDR) is the spatial union of the CAUs over the area of interest. Based on wolf presence signs collected in France (1996- 2006), we analysed the influence of the shape and size of types of CAUs (circular area versus square grid mesh; 6, 25, 50 and 100 km 2 ) on the changes in EDR. EDR increased with time and a saturating phase was noticed by the end of the period. We assessed the effects of the year and the type of CAU on EDR using exploratory data analysis. Larger CAUs resulted logically in larger EDR values, whatever the CAU shape. For a given CAU size, contiguous square grids yielded larger EDR values than overlapping circular buffers. The effect of the interactions between the year and the type of CAU on EDR changes was evidenced using an auto-modelling method based on principal component analysis. Compared to smaller units, larger CAUs resulted in larger growth rates during the range increase phase, and in smaller rates during the saturating phase. A basic and descriptive conceptual model helped interpreting this pattern as a consequence of the character- istics of the colonisation process in the wolf population. We discuss the present results within the framework of conservation status assessment and management of the wolf population.
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- 2010
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13. A new exploratory approach to the study of the spatio-temporal distribution of ring recoveries: the example of Teal (Anas crecca) ringed in Camargue, Southern France
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Matthieu Guillemain, Clément Calenge, Michel Gauthier-Clerc, and Géraldine Simon
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Time effect ,education.field_of_study ,geography.geographical_feature_category ,biology ,Ecology ,business.industry ,Population ,Distribution (economics) ,Spatial distribution ,biology.organism_classification ,Geography ,Product kernel ,Spring (hydrology) ,Anas crecca ,education ,business - Abstract
We use a new method called “product kernel estimator” to explore the spatial and temporal distribution of 9,114 recoveries of Teal (Anas crecca) ringed in Camargue, southern France, and recovered over the whole of Europe. This method allows exploration of the changes in time of the probability density to recover a ringed bird over a grid covering the study area. We thus identified two migration corridors for this species to the north and south of the Alps, whereas earlier analyses mostly suggested a southern route from Camargue, especially in spring. The northern route seems to be used to a greater extent in autumn than in spring, indicating a frequent abmigration (animals switching from one corridor to the other). Moreover, migration of the population seems faster in spring than in autumn. The simultaneous presence of Teal recoveries in many distinct geographical areas in spring is consistent with the idea that these ducks are not limited by their migratory speed in spring, nor do they wait until favorable environmental conditions before colonizing their breeding areas.
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- 2010
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14. Influence of fish-farming management on duck breeding in French fish pond systems
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Joël Broyer and Clément Calenge
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education.field_of_study ,biology ,business.industry ,Fish farming ,Population ,Aquatic Science ,biology.organism_classification ,Brood ,Predation ,Macrophyte ,Fishery ,Diving duck ,Aquaculture ,Waterfowl ,education ,business - Abstract
Fish ponds host a relatively important share of the breeding population of waterfowl in Europe. The objective of this study was to investigate the influence of fish-farming management on the distribution of dabbling and diving duck breeding, in 103 fishponds from four regions important for duck breeding in France. Duck breeding in fish ponds was apparently influenced by food resource and nesting site availability. Dabbling duck pair density was generally higher when invertebrates were abundant in macrophytes beds and when competition for food with carps Cyprinus carpio was potentially decreased by lower fish stock biomass. Diving duck pair abundance seemed to be negatively influenced by low invertebrates biomasses in pond sediment and by the absence of large reed beds at the edge of waterbodies. The difference between dabbling and diving ducks was also confirmed by a study of the variation in brood numbers standardized by pair numbers. This brood:pair ratio corresponded to a measure of nesting success and the possible attraction of fish ponds for some broods hatched in neighbouring waterbodies. Dabbling duck brood:pair ratio was lower in one of the study regions where most of meadow areas surrounding fish ponds have been transformed into cereal crops in the past few decades. Diving duck brood:pair ratio was positively linked to pond fertilization due to fish farming. Fish farming, therefore, influenced duck breeding by an interaction between carp density and fertilization. We hypothesize that fertilization increases zooplankton density, thereby decreasing the competition between carps and waterfowl for benthic prey.
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- 2009
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15. Social and spatial patterns determine the population structure and colonization processes in mouflon
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Gaëlle Darmon, J.-M. Jullien, Anne Loison, Daniel Maillard, and Clément Calenge
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education.field_of_study ,Ecology ,Population ,Introduced species ,Biology ,biology.organism_classification ,Mouflon ,Colonisation ,Spatial ecology ,Animal Science and Zoology ,Colonization ,Social organization ,education ,Ecology, Evolution, Behavior and Systematics ,Wildlife conservation - Abstract
Although it is widely accepted that populations vary in space and time, defining the spatial scale of population structure relevant for understanding temporal variation or for management and conservation purposes remains a challenge. We studied jointly temporal patterns of social and spatial structures in an introduced population of mouflon ( Ovis gmelini musimon (Schreber, 1782)) to define the temporal stability of these structures and to uncover the history of the colonization process. We expected social organization to remain stable between years, mouflon to stay sedentary, and colonization to have occurred through a diffusion process. We used yearly censuses performed between 1994 and 2004, and collected information in managers’ archives and newspapers reporting the presence of mouflon in different areas since its introduction in 1954 in the Bauges mountains, France. Mouflons were divided into male and nursery groups, whose number (1.88 ± 0.31 for males and 7.54 ± 0.58 for nurseries) and composition (7.05 ± 1.25 individuals in male groups; 13.6 ± 1.41 females, 8.11 ± 0.72 lambs, and 6.51 ± 0.65 males in the nurseries) remained stable over years. The spatial distribution of nursery groups was clustered in five areas, highly correlated between years (p < 0.001), suggesting that the same groups were observed in given areas every year and confirming the sedentary lifestyle of the species. The presence–absence data of the species since its introduction suggested a colonization by diffusion. We discuss the social and spatial structures of the population and the type of colonization process that could have led to this kind of structure.
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- 2007
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16. Geographic variation in body mass of rock ptarmigan Lagopus mutus in the Alps and the Pyrenees
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Claude Novoa, Clément Calenge, Jean-François Brenot, Emmanuel Ménoni, Patrick Léonard, Luca Rotelli, and Laurence N. Ellison
- Subjects
Geography ,biology ,Ecology ,Lagopus ,Geographic variation ,Tetrao urogallus ,Management, Monitoring, Policy and Law ,biology.organism_classification ,Perdix ,Grey partridge ,Ecology, Evolution, Behavior and Systematics ,Nature and Landscape Conservation - Abstract
We compared the body mass of adult rock ptarmigan Lagopus mutus shot in autumn in the French Pyrenees (Ariege), the French Alps (Hautes-Alpes) and the Italian Alps (Province of Verbania). Mean body mass of adults was greater in the Ariege than in the Hautes-Alpes both for cocks (466 vs 433 g) and hens (429 vs 406 g), with the body mass of Italian birds being intermediate (cocks 448 g, hens 418 g). The relatively large mass of rock ptarmigan in the Pyrenees contrasts with the geographic trends found in capercaillie Tetrao urogallus and grey partridge Perdix perdix in France. For the last two species, birds in the Pyrenees are smaller than those further north. The site differences that we observed in body mass of rock ptarmigan may be related to differences in availability of high quality foods, particularly ericaceous shrubs. However, at the continental scale within Europe, the body mass of rock ptarmigan appears to be greatest in northern latitudes.
- Published
- 2005
- Full Text
- View/download PDF
17. Climate predictability and breeding phenology in red deer: timing and synchrony of rutting and calving in Norway and France
- Author
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Atle Mysterud, Torbjørn Ergon, Nathalie Pettorelli, François Klein, Clément Calenge, Nils Chr. Stenseth, Christophe Bonenfant, Leif Egil Loe, Rolf Langvatn, and Jean-Michel Gaillard
- Subjects
Herbivore ,education.field_of_study ,Natural selection ,Ecology ,Phenology ,media_common.quotation_subject ,Population ,Ice calving ,Biology ,Seasonality ,medicine.disease ,medicine ,Animal Science and Zoology ,Reproduction ,education ,Norwegian Red ,Ecology, Evolution, Behavior and Systematics ,media_common - Abstract
Summary 1. Timing and synchrony of reproduction are regarded as crucially important factors for fitness in seasonal environments. Natural selection has probably favoured temperate and arctic female herbivores that match reproduction with onset of plant growth in spring. However, breeding synchrony may also be affected by variation in phenotypic quality of females in a population, because females in poor body condition have been found to delay ovulation and subsequent calving. 2. We compared breeding phenology, i.e. the timing and synchrony of rutting (roaring, sexual aggregation) and calving of red deer ( Cervus elaphus L.) in France (latitude: 49 ° N) and Norway (latitude: 63 ° N). We hypothesized (H 1 ) that calving and rutting were later at the site with latest onset of plant growth. 3. We further quantified overall environmental predictability as the sum of annual constancy and seasonality and tested three different (not mutually exclusive) hypotheses about breeding synchrony: (H 2a ) the population experiencing most seasonal plant phenology should show the highest breeding synchrony; (H 2b ) overall predictability of plant phenology should determine breeding synchrony; and (H 2c ) breeding should be more synchronized in the population with lowest female body weight variation within age classes because they ovulate more synchronously. 4. Calving and rutting, as well as onset of plant phenology, were later in Norway than in France, complying with the first hypothesis. Plant growth in spring was overall more predictable and also more seasonal in Norway than France. Hence we expected higher breeding synchrony in Norway than in France according to H 2a and H 2b . Variance in female body weight was slightly higher in France than in Norway, which should also cause more synchronized breeding in Norway than in France (H 2c ). Contrary to all predictions, variance in rutting and calving dates was around two times higher in Norway than in France. 5. We suggest two alternative explanations of breeding synchrony. A more variable topography in Norway can make optimal birth date more variable on a local scale than in France, thereby maintaining a higher genetic variance for calving date in Norwegian red deer. Further, population age structure may play a role, as ovulation varies according to female age. Clearly, processes of breeding synchrony are far more complex than previously realized.
- Published
- 2005
- Full Text
- View/download PDF
18. Capitalizing on opportunistic data for monitoring relative abundances of species
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Camille Coron, Clément Calenge, Romain Julliard, and Christophe Giraud
- Subjects
0106 biological sciences ,Statistics and Probability ,Generalized linear model ,Biometry ,Computer science ,Rare species ,Population Dynamics ,computer.software_genre ,010603 evolutionary biology ,01 natural sciences ,General Biochemistry, Genetics and Molecular Biology ,Birds ,Statistics ,Citizen science ,Statistical inference ,Animals ,Relative species abundance ,Population Density ,Models, Statistical ,General Immunology and Microbiology ,Applied Mathematics ,Sampling (statistics) ,General Medicine ,010601 ecology ,Data Interpretation, Statistical ,Data mining ,France ,General Agricultural and Biological Sciences ,computer - Abstract
With the internet, a massive amount of information on species abundance can be collected by citizen science programs. However, these data are often difficult to use directly in statistical inference, as their collection is generally opportunistic, and the distribution of the sampling effort is often not known. In this article, we develop a general statistical framework to combine such "opportunistic data" with data collected using schemes characterized by a known sampling effort. Under some structural assumptions regarding the sampling effort and detectability, our approach makes it possible to estimate the relative abundance of several species in different sites. It can be implemented through a simple generalized linear model. We illustrate the framework with typical bird datasets from the Aquitaine region in south-western France. We show that, under some assumptions, our approach provides estimates that are more precise than the ones obtained from the dataset with a known sampling effort alone. When the opportunistic data are abundant, the gain in precision may be considerable, especially for rare species. We also show that estimates can be obtained even for species recorded only in the opportunistic scheme. Opportunistic data combined with a relatively small amount of data collected with a known effort may thus provide access to accurate and precise estimates of quantitative changes in relative abundance over space and/or time.
- Published
- 2014
19. Bayesian modelling of hunting data may improve the understanding of host-parasite systems: wild boar diseases and vaccination as an example
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Sophie Rossi and Clément Calenge
- Subjects
Statistics and Probability ,Time Factors ,Swine ,Population ,Sus scrofa ,Prevalence ,Wildlife ,Models, Biological ,General Biochemistry, Genetics and Molecular Biology ,Host-Parasite Interactions ,Classical Swine Fever ,Wild boar ,biology.animal ,Parasite hosting ,Animals ,education ,Probability ,Swine Diseases ,education.field_of_study ,General Immunology and Microbiology ,biology ,Geography ,Host (biology) ,Applied Mathematics ,Vaccination ,Bayes Theorem ,General Medicine ,biology.organism_classification ,Markov Chains ,3. Good health ,Classical swine fever ,Modeling and Simulation ,Immunology ,France ,General Agricultural and Biological Sciences ,Monte Carlo Method ,Demography - Abstract
Wildlife diseases are often studied using hunting data. In such studies, inferences about diseases are often made by comparing raw disease prevalence levels, ignoring complications like stochasticity in recruitment. We carried out a field trial to study the effectiveness of oral vaccination of wild boar (Sus scrofa) against classical swine fever (CSF) in the Vosges mountains (Northeastern France) for 3 years (2008–2010). Since August 2004, hunters had carried out three vaccination sessions per year in spring, summer and autumn. During our study period, we determined whether each wild boar hunted in our study area was immunized or not against CSF. We used a Bayesian approach to model the changes in the proportion of vaccinated animals in the population of young animals (i.e., 12 months old). This approach allowed to disentangle the effects of the birth peaks (leading to a decrease) and of both the vaccination sessions and natural infection (leading to an increase) on this proportion. We thus inferred, at the individual level, the probability that a non-immunized animal became vaccinated after a particular session. There was a high between-year variability in the effectiveness of the vaccination: the observed patterns were similar in 2008 and 2010, but 2009 was characterized by an overall greater effectiveness of the vaccination. Within a particular year, the spring vaccination session was more effective than the autumn session, probably because of the higher food availability in autumn that render the vaccination places less attractive to the animals. The vaccination effectiveness was rather low in summer, except in 2009, probably because of higher age identification error this year. This model also highlighted an immunisation of animals occurring outside vaccination periods, which suggests either the presence of the CSF virus in our study area, or the consumption of the vaccine outside the vaccination sessions. Finally, we observed a high spatial variability of the probability of vaccination. The effectiveness of the vaccination was indeed strongly related to both the distribution of the forests and the distribution of the vaccination places in our study area. This study highlights an optimal vaccination effort of 1.25 places per km2 to maximize the proportion of immune wild boar in that area.
- Published
- 2013
20. Wildlife tracking data management: a new vision
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Clément Calenge, Ferdinando Urbano, Holger Dettki, Alison Cameron, Markus Neteler, and Francesca Cagnacci
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Geographic information system ,Group method of data handling ,Data management ,Interoperability ,Information Storage and Retrieval ,Animals, Wild ,General Biochemistry, Genetics and Molecular Biology ,Data modeling ,Settore BIO/07 - ECOLOGIA ,Animals ,Biotelemetry ,Behavior, Animal ,Ecology ,business.industry ,Spatial database ,Articles ,Models, Theoretical ,GIS ,Data science ,GPS tracking ,Data model ,Animal ecology ,Wildlife ecology ,Geographic Information Systems ,Database Management Systems ,Data modelling ,General Agricultural and Biological Sciences ,business - Abstract
To date, the processing of wildlife location data has relied on a diversity of software and file formats. Data management and the following spatial and statistical analyses were undertaken in multiple steps, involving many time-consuming importing/exporting phases. Recent technological advancements in tracking systems have made large, continuous, high-frequency datasets of wildlife behavioural data available, such as those derived from the global positioning system (GPS) and other animal-attached sensor devices. These data can be further complemented by a wide range of other information about the animals' environment. Management of these large and diverse datasets for modelling animal behaviour and ecology can prove challenging, slowing down analysis and increasing the probability of mistakes in data handling. We address these issues by critically evaluating the requirements for good management of GPS data for wildlife biology. We highlight that dedicated data management tools and expertise are needed. We explore current research in wildlife data management. We suggest a general direction of development, based on a modular software architecture with a spatial database at its core, where interoperability, data model design and integration with remote-sensing data sources play an important role in successful GPS data handling.
- Published
- 2010
21. A general framework for the statistical exploration of the ecological niche
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Mathieu Basille and Clément Calenge
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Statistics and Probability ,Ecological niche ,Mahalanobis distance ,General Immunology and Microbiology ,Applied Mathematics ,Niche ,Population Dynamics ,General Medicine ,Rupicapra ,Models, Biological ,General Biochemistry, Genetics and Molecular Biology ,Environmental niche modelling ,Set (abstract data type) ,Modeling and Simulation ,Statistics ,Vector map ,Geographic Information Systems ,Animals ,Point (geometry) ,General Agricultural and Biological Sciences ,Focus (optics) ,Factor Analysis, Statistical ,Algorithms ,Ecosystem ,Mathematics - Abstract
We propose a new statistical framework for the exploratory analysis of the ecological niche, the "General niche-environment system factor analysis" (GNESFA). The data required for this analysis are (i) a table giving the values of the environmental variables in each environment unit (EU, e.g., the patches of habitat on a vector map), (ii) a set of weights measuring the availability of the EUs to the species (e.g., the proportion of the study area covered by a given patch), and (iii) a set of utilization weights describing the use of the EUs by the focal species (e.g., the proportion of detections of the species in each patch). Each row of the table corresponds to a point in the multidimensional space defined by the environmental variables, and each point is associated with two weights. The GNESFA searches the directions in this space where the two weight distributions differ the most, choosing one distribution as the reference, and the other one as the focus. The choice of the utilization as the reference corresponds to the MADIFA (Mahalanobis distances factor analysis), which identifies the directions on which the available EUs are in average the furthest from the optimum of the niche, allowing habitat suitability modelling. The choice of the availability as the reference corresponds to the FANTER (Factor analysis of the niche, taking the environment as the reference), which identifies the directions on which the niche is the furthest from the average environment (marginality) and those on which the niche is the narrowest compared with the environment (specialization). The commonly used ENFA (Ecological niche factor analysis) is at the middle point between the MADIFA and the FANTER, considering both distributions as the reference and the focus simultaneously. When used concurrently, these three analyses allow an extensive exploration of the system.
- Published
- 2007
22. Biogeography of the Forests of the Paraguay-Paraná Basin
- Author
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Clément Calenge, Cyrille Chatelain, Rodolphe Spichiger, and Bastian Bise
- Subjects
Geography ,Insular biogeography ,Ecology ,Biogeography ,Structural basin - Published
- 2006
- Full Text
- View/download PDF
23. Efficiency of spreading maize in the garrigues to reduce wild boar (Sus scrofa) damage to Mediterranean vineyards
- Author
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P. Fournier, C. Fouque, Clément Calenge, and Daniel Maillard
- Subjects
Mediterranean climate ,Agronomy ,Wild boar ,biology ,biology.animal ,Botany ,Mediterranean area ,Patchy distribution ,Management, Monitoring, Policy and Law ,Vineyard ,Ecology, Evolution, Behavior and Systematics ,Nature and Landscape Conservation - Abstract
The aim of this work was to assess the efficiency of dissuasive spreading of maize to reduce the level of wild boar damage to vines in a Mediterranean area (Puechabon, southern France). The 50 wine growers of Puechabon were all questioned about the annual losses caused by the wild boar in each vineyard of the study area between 1990 and 1992. We also studied the distribution of the damage on a smaller scale, by mapping the damaged vines within two vineyards. In summer 1993, we distributed 4.7 tons of maize in the woods , and then questioned the wine growers about the losses in each vineyard for 1993. During 1990–1992, on both large and small scales, the damage had a patchy distribution, with more patches of damage occurring close to the woods. Moreover, the later the vines ripened, the less frequent the damage. The severity of the damage was only affected by the distance of the vineyard from woods. In total, the wild boar consumed 20,049 kg of grapes each year between 1990–1992 (193 kg/ha), and 63% of the vineyards were damaged. In 1993, both the density and the compensation paid in the departement increased threefold. However, in our study area, both the proportion of damaged vineyards (36%) and the level of damage in the vineyards (151 kg/ha) were reduced, saving more than 60% in compensation. The dissuasive spreading of maize is therefore an efficient tool to reduce the level of damage to vineyards.
- Published
- 2004
- Full Text
- View/download PDF
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