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Gimenez, O.

Publications and source records attributed to Gimenez, O..

At least 37 records · Page 2Linked to original sources

A dynamic and hierarchical spatial occupancy model for interacting species

Occupancy models have been extended to account for either multiple spatial scales or species interactions in a dynamic setting. However, as interacting species (e.g., predators and prey) often operate at different spatial scales, including nested spatial structure might be especially relevant to models of interacting species. Here we bridge these two model frameworks by developing a multi-scale, two-species occupancy model. The model is dynamic, i.e. it estimates initial occupancy, colonization and extinction probabilities--including probabilities conditional to the other species presence. With a simulation study, we demonstrate that the model is able to estimate most parameters without marked bias under low, medium and high average occupancy probabilities, as well as low, medium and high detection probabilities, with only a small bias for some parameters in low-detection scenarios. We further evaluate the models ability to deal with sparse field data by applying it to a multi-scale camera trapping dataset on a mustelid-rodent predator-prey system. Most parameters are estimated with low uncertainty (i.e. narrow posterior distributions). More broadly, our model framework creates opportunities to explicitly account for the spatial structure found in many spatially nested study designs, and to study interacting species that have contrasting movement ranges with camera traps.

ecology↗

Multispecies integrated population model reveals bottom-up dynamics in a seabird predator-prey system

Assessing the effects of climate and interspecific relationships on communities is challenging because of the complex interplay between species population dynamics, their interactions, and the need to integrate information across several biological levels (individuals - populations - communities). Usually used to quantify species interactions, integrated population models (IPMs) have recently been extended to communities. These models allow fitting multispecies matrix models to data from multiple sources while simultaneously accounting for various sources of uncertainty in each data source. We used multispecies IPMs accommodating climate conditions to quantify the relative contribution of climate vs. interspecific interactions on demographic parameters, such as survival and breeding success, in the dynamics of a predator-prey system. We considered a stage-structured predator-prey system combining 22 years of capture-recapture data and population counts of two seabirds, the Brown Skua (Catharacta lonnbergi) and its main prey the Blue Petrel (Halobaena caerulea) both breeding on the Kerguelen Islands in the Southern Ocean. Our results showed that climate and predator-prey interactions drive the demography of skuas and petrels in different ways. The breeding success of skuas appeared to be largely driven by the number of petrels and to a lesser extent by intraspecific density-dependence. In contrast, there was no evidence of predation effects on the demographic parameters of petrels, which were affected by oceanographic factors (chlorophyll a and sea surface temperature anomalies). We conclude that bottom-up mechanisms are the main drivers of this skua-petrel system. We discuss the mechanisms by which climate variability and predator-prey relationships may affect the demographic parameters of these seabirds. Taking into account both species interactions and environmental covariates in the same analysis improved our understanding of species dynamics.

ecology↗

Ecological and anthropogenic drivers of large carnivore depredation on sheep in Europe

O_LISharing space with large carnivores on a human-dominated continent like Europe results in multiple conflictful interactions with human interests, of which depredation on livestock is the most widespread. Wildlife management agencies maintain compensation programs for the damage caused by large carnivores, but the long-term effectiveness of such programs is often contested. Therefore, understanding the mechanisms driving large carnivore impact on human activities is necessary to identify key management actions to reduce it. C_LIO_LIWe conducted an analysis of the impact by all four European large carnivores on sheep husbandry in 10 European countries, during the period 2010-2015. We ran a hierarchical Simultaneous Autoregressive model, to assess the influence of ecological and anthropogenic factors on the spatial and temporal patterns in the reported depredation levels across the continent. C_LIO_LIOn average, about 35,000 sheep were compensated in the ten countries as killed by large carnivores annually, representing about 0.5% of the total sheep stock. Of them, 45% were recognized as killed by wolves, 24% by wolverines, 19% by lynx and 12% by bears. At the continental level, we found a positive relationship between wolf distribution and the number of compensated sheep, but not for the other three species. Impact levels were lower in the areas where large carnivore presence has been continuous compared to areas where they disappeared and recently returned. The model explained 62% of the variation in the number of compensated sheep per year in each administrative unit. Only 13% of the variation was related to the ecological components of the process. C_LIO_LISynthesis and Applications: Large carnivore distribution and local abundance alone are poor predictors of large carnivore impact on livestock at the continental level. A few individuals can produce high damage, when the contribution of environmental, social and economic systems predisposes for it, whereas large populations can produce a limited impact when the same components of the system reduce the probability that depredations occur. Time seems to play in favour of a progressive reduction in the costs associated with coexistence, provided that the responsible agencies focus their attention both on compensation and co-adaptation. C_LI

ecology↗

From individual behavior and pack dynamics to population responses: An individual-based approach to model the wolf social life cycle

The occurrence of wolf populations in human-dominated landscapes is challenging worldwide because of conflicts with human activities. Modeling is an important tool to predict wolf dynamics and expansion, and help in decision making concerning management and conservation. However, some individual behaviors and pack dynamics of the wolf life cycle are still unclear to ecologists. Here we present an individual-based model (IBM) to project wolf populations while exploring the lesser-known processes of the wolf life cycle. IBMs are bottom-up models that simulate the fate of individuals interacting with each other, with population-level properties emerging from the individual-level simulations. IBMs are particularly adapted to represent social species such as the wolf that exhibits complex individual interactions. Our IBM predicts wolf demography including fine-scale individual behavior and pack dynamics based on up-to-date scientific literature. We explore four processes of the wolf life cycle whose consequences on population dynamics are still poorly understood: the pack dissolution following the loss of a breeder, the adoption of young dispersers by packs, the establishment of new packs through budding, and the different types of breeder replacement. While running different versions of the IBM to explore these processes, we also illustrate the modularity and flexibility of our model, an asset to model wolf populations experiencing different ecological and demographic conditions. The different parameterization of pack dissolution, territory establishment by budding, and breeder replacement processes influence the most the projections of wolf populations. As such, these processes require further field investigation to be better understood. The adoption process has a lesser impact on model predictions. Being coded in R to facilitate its understanding, we expect that our model will be used and further adapted by ecologists for their own specific applications.

ecology↗

Does seed mass drive interspecies variation in the effect of management practices on weed demography?

Optimizing the effect of management practices on weed population dynamics is challenging due to the difficulties in inferring demographic parameters in seed banks and their response to disturbance. Here, we used a long-term plant survey between 2006 and 2012 in 46 French vineyards and quantified the effects of management practices (tillage, mowing and herbicide) on colonization, germination and seed survival of 30 weed species in relation to their seed mass. To do so, we used a recent statistical approach to reliably estimate demographic parameters for plant populations with a seed bank using time series of presence-absence data, which we extended to account for interspecies variation in the effects of management practices on demographic parameters. Our main finding was that when the level of disturbance increased (i.e., in plots with a higher number of herbicide, tillage or mowing treatments), colonization and survival in large-seeded species increased faster than in small-seeded species. High disturbance through tillage increased survival in the seed bank of species with high seed mass. The application of herbicides, considered as an intermediate disturbance, increased germination, survival and colonization probabilities of species with high seed mass. Mowing, representing habitats more competitive for light, increased the survival of species with high seed mass. Overall, the strong relationships between the effects of management practices and seed mass provides an indicator for predicting the dynamics of weed communities under disturbance.

ecology↗

Combining single- and repeated-visit occupancy models to make the best of monitoring surveys

A major challenge in statistical ecology consists of integrating knowledge from different datasets to produce robust ecological indicators. To estimate species distribution, occupancy models are a flexible framework that can accommodate several datasets obtained from different sampling methods. However, repeating visits at sampling sites is a prerequisite for using standard occupancy models. Occupancy models were recently developed to analyze detection/non-detection data collected during a single visit. To date, single-visit occupancy models have never been used to integrate several different datasets. Here, we showcase an approach that combines two datasets into an integrated single-visit occupancy model. As a case study, we estimated the distribution of Bottlenose dolphins (Tursiops truncatus) over the North-western Mediterranean Sea by combining 24,624 km of aerial surveys and 21,464 km of at-sea monitoring. We compared the outputs of single- vs. repeated-visit occupancy models into integrated occupancy models. Integrated models allowed a better sampling coverage of species home-range, which provided a better precision for occupancy estimates than occupancy models using datasets in isolation. Overall, single- and repeated-visit integrated occupancy models produced similar inference about the distribution of bottlenose dolphins. We suggest that single-visit occupancy models open promising perspectives for the use of existing ecological datasets.

ecology↗

Efficient use of harvest data: An integrated population model for exploited animal populations

O_LIMany populations are affected by hunting or fishing. Models designed to assess the sustainability of harvest management require accurate estimates of demographic parameters (e.g. survival, reproduction) hardly estimable with limited data collected on exploited populations. The joint analysis of different data sources with integrated population models (IPM) is an optimal framework to obtain reliable estimates for parameters usually difficult to estimate, while accounting for imperfect detection and observation error. The IPM built so far for exploited populations have integrated count-based surveys and catch-at-age data into ageclass structured population models. But the age of harvested individuals is difficult to assess and often not recorded, and population counts are often not performed on a regular basis, limiting their use for the monitoring of exploited populations.\nC_LIO_LIHere, we propose an IPM that makes efficient use of data commonly collected in exploited marine and terrestrial populations of vertebrates. As individual measures of body mass at both capture and death are often collected in fish and terrestrial game species, our model integrates capture-mark-recapture-recovery data and data collected at death into a body mass-structured population model. It allows the observed number of individuals harvested to be compared with the expected number and provides accurate estimates of demographic parameters.\nC_LIO_LIWe illustrate the usefulness of this IPM using an emblematic game species distributed worldwide, the wild boar Sus scrofa, as a case study. For this species that has increased in distribution and abundance over the last decades, the model provides accurate and precise annual estimates of key demographic parameters (survival, reproduction, growth) and of population size while accounting for imperfect detection and observation error.\nC_LIO_LITo avoid an overexploitation of declining populations or an under-exploitation of increasing populations, it is crucial to gain a good understanding of the dynamics of exploited populations. When managers or conservationists have limited demographic data, the IPM offers a powerful framework to assess population dynamics. Being highly flexible, the approach is broadly applicable to both terrestrial and marine exploited populations for which measures of body mass are commonly recorded and more generally, to all populations suffering from anthropogenic mortality causes.\nC_LI

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Distribution and abundance of bottlenose dolphin (Tursiops truncatus) over the French Mediterranean continental shelf

The Mediterranean bottlenose dolphin (Tursiops truncatus) sub-population is listed as vulnerable by the International Union for Conservation of Nature. This species is strictly protected in France and the designation of Special Areas of Conservation (SAC) is required under the European Habitat Directive. However, little information is available about the structure, dynamic and distribution of the population in the French Mediterranean waters. We collected photo-identification data over the whole French Mediterranean continental shelf all year round between 2013 and 2015. We sighted 151 groups of bottlenose dolphins allowing the individually photo-identification of 1,060 animals. The encounter rate distribution showed the presence of bottlenose dolphins over the whole continental shelf all year round. Using capture-recapture methods, we estimated for the first time the size of the bottlenose dolphin resident population at 557 individuals (95% confidence interval: 216-872) along the French Mediterranean continental coast. Our results were used in support of the designation of a new dedicated SAC in the Gulf of Lion and provide a reference state for the bottlenose dolphin monitoring in the French Mediterranean waters in the context of the Marine Strategy Framework Directive.

ecology↗

Changes in social cohesion in a long-lived species under a perturbation regime

O_LIUnderstanding the behaviour of a population under perturbations is crucial and can help to mitigate the effects of global change. Sociality can influence the dynamics of behavioural processes and plays an important role on populations resilience. However little is known about the effects of perturbations on the social cohesion of group-living animals.\nC_LIO_LITo explore the strength of social cohesion and its dynamics under perturbations, we studied an ecological system involving a colonial, long-lived species living in a site experiencing a shift to a perturbed regime. This regime, caused by the invasion of predators, led this colony to hold from 70% to only 3% of the total world population in only one decade. Because birds breed aggregated in discrete and annually changing patches within large colonies, we could disentangle whether annual aggregation was random or resulted from social bonding among individuals. Our goals were 1) to uncover if there was any long-term social bonding between individuals and 2) to examine whether the perturbation regime affected social cohesion.\nC_LIO_LIWe explored social cohesion by means of contingency tables and, within the Social Network Analysis framework, by modeling interdependencies among observations using additive and multiplicative effects (AME) and accounted for missing data. We analysed 25 years of monitoring with an individual capture-recapture database of more than 3,500 individuals.\nC_LIO_LIWe showed that social bonding occurs over years in this species. We additionally show that social bonding strongly decreased after the perturbation regime. We propose that sociality and individual behavioural heterogeneity have been playing a major role driving dispersal and thus population dynamics over the study period.\nC_LIO_LIPerturbations may lead not only to changes in individuals behaviours and fitness but also to a change in populations social cohesion. The demographic consequences of the breaking down of social bonds are still not well understood, but they can be critical for population dynamics of social species. Further studies considering individual heterogeneity, sociality and different types of perturbations should be carried out to improve our understanding on the resilience of social species.\nC_LI

ecology↗

Estimating abundance with interruptions in data collection using open population spatial capture-recapture models

O_LIThe estimation of population size remains one of the primary goals and challenges in ecology and provides a basis for debate and policy in wildlife management. Despite the development of efficient non-invasive sampling methods and robust statistical tools to estimate abundance, maintenance of field sampling is still subject to economic and logistic constraints. These can result in intentional or unintentional interruptions in sampling and cause gaps in data time series, posing a challenge to abundance estimation, and ultimately conservation and management decisions.\nC_LIO_LIWe applied an open population spatial capture-recapture (OPSCR) model to simulations and a real case study to test the reliability of abundance inferences models to interruption in data collection. Using individual detections occurring over consecutive sampling occasions, OPSCR models allow the estimation of abundance from individual detection data while accounting for lack of demographic and geographic closure between occasions. First, we simulated sampling data with interruptions in field sampling of different lengths and timing. We checked the performance of an OPSCR model in deriving abundance for species with slow and intermediate life history strategies. Finally, we introduced artificial sampling interruptions of various magnitudes and timing to a five-year non-invasive monitoring data set of wolverines (Gulo gulo) in Norway and quantified the consequences for OPSCR model predictions.\nC_LIO_LIInferences from OPSCR models were reliable even with temporal interruptions in monitoring. Interruption did not cause any systematic bias, but increased uncertainty. Interruptions occurring at occasions towards the beginning and the end of the sampling caused higher uncertainty. The loss in precision was more severe for species with a faster life history strategy.\nC_LIO_LIWe provide a reliable framework to estimate abundance even in the presence of sampling interruptions. OPSCR allows monitoring studies to provide contiguous abundance estimates to managers, stakeholders, and policy makers even when data are non-contiguous. OPSCR models do not only help cope with unintentional interruptions during sampling but also offer opportunities for using intentional sampling interruptions during the design of cost-effective population surveys.\nC_LI

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Combining multiple data sources in species distribution models while accounting for spatial dependence and overfitting with combined penalised likelihood maximisation

O_LIThe increase in availability of species data sets means that approaches to species distribution modelling that incorporate multiple data sets are in greater demand. Recent methodological developments in this area have led to combined likelihood approaches, in which a log-likelihood comprised of the sum of the log-likelihood components of each data source is maximised. Often, these approaches make use of at least one presence-only data set and use the log-likelihood of an inhomogeneous Poisson point process model in the combined likelihood construction. While these advancements have been shown to improve predictive performance, they do not currently address challenges in presence-only modelling such as checking and correcting for violations of the independence assumption of a Poisson point process model or more general challenges in species distribution modelling such as overfitting.\nC_LIO_LIIn this paper, we present an extension of the combined likelihood frame-work which accommodates alternative presence-only likelihoods in the presence of spatial dependence as well as lasso-type penalties to account for potential overfitting. We compare the proposed combined penalised likelihood approach to the standard combined likelihood approach via simulation and apply the method to modelling the distribution of the Eurasian lynx in the Jura Mountains in eastern France.\nC_LIO_LIThe simulations show that the proposed combined penalised likelihood approach has better predictive performance than the standard approach when spatial dependence is present in the data. The lynx analysis shows that the predicted maps vary significantly between the model fitted with the proposed combined penalised approach accounting for spatial dependence and the model fitted with the standard combined likelihood.\nC_LIO_LIThis work highlights the benefits of careful consideration of the presence-only components of the combined likelihood formulation, and allows greater flexibility and ability to accommodate real datasets.\nC_LI

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Spatial density estimates of Eurasian lynx (Lynx lynx) in the French Jura and Vosges Mountains

Obtaining estimates of animal population density is a key step in providing sound conservation and management strategies for wildlife. For many large carnivores however, estimating density is difficult because these species are elusive and wide-ranging. Here, we focus on providing the first density estimates of the Eurasian lynx (Lynx lynx) in the French Jura and Vosges mountains. We sampled a total of 413 camera trapping sites (with 2 cameras per site) between January 2011 and April 2016 in seven study areas across seven counties of the French Jura and Vosges mountains. We obtained 592 lynx detections over 19,035 trap days in the Jura mountain and 0 detection over 6,804 trap days in the Vosges mountain. Based on coat patterns, we identified a total number of 92 unique individuals from photographs, including 16 females, 13 males and 63 individuals of unknown sex. Using spatial capture-recapture (SCR) models, we estimated abundance in the study areas between 5 (SE = 0.1) and 29 (0.2) lynx and density between 0.24 (SE = 0.02) and 0.91 (SE = 0.03) lynx per 100 km2. We also provide a comparison with non-spatial density estimates and discuss the expected discrepancies. Our study is yet another example of the advantage of combining SCR methods and non-invasive sampling techniques to estimate density for elusive and wide-ranging species, like large carnivores. While the estimated densities in the French Jura mountain are comparable to other lynx populations in Europe, the fact that we detected no lynx in the Vosges mountain is alarming. Connectivity should be encouraged between the French Jura mountain, the Vosges mountain and the Palatinate Forest in Germany where a reintroduction program is currently ongoing. Our density estimates will help in setting a baseline conservation status for the lynx population in France.

ecology↗

Modeling the demography of species providing extended parental care: A capture-recapture approach with a case study on Polar Bears (Ursus maritimus)

O_LIIn species providing extended parental care, one or both parents care for altricial young over a period including more than one breeding season. We expect large parental investment and long-term dependency within family units to cause high variability in life trajectories among individuals with complex consequences at the population level. So far, models for estimating demographic parameters in free-ranging animal populations mostly ignore extended parental care, thereby limiting our understanding of its consequences on parents and offspring life histories. C_LIO_LIWe designed a capture-recapture multi-event model for studying the demography of species providing extended parental care. It handles statistical multiple-year dependency among individual demographic parameters grouped within family units, variable litter size, and uncertainty on the timing at offspring independence. It allows to evaluate trade-offs among demographic parameters, the influence of past reproductive history on the caring parent survival status, breeding probability and litter size probability, while accounting for imperfect detection of family units. We assess the model performances using simulated data, and illustrate its use with a long-term dataset collected on the Svalbard polar bears (Ursus maritimus). C_LIO_LIOur model performed well in terms of bias and mean square error and in estimating demographic parameters in all simulated scenarios, both when offspring departure probability from the family unit occurred at a constant rate or varied during the field season depending on the date of capture. For the polar bear case study, we provide estimates of adult and dependent offspring survival rates, breeding probability and litter size probability. Results showed that the outcome of the previous reproduction influenced breeding probability. C_LIO_LIOverall, our results show the importance of accounting for i) the multiple-year statistical dependency within family units, ii) uncertainty on the timing at offspring independence, and iii) past reproductive history of the caring parent. If ignored, estimates obtained for breeding probability, litter size, and survival can be biased. This is of interest in terms of conservation because species providing extended parental care are often long-living mammals vulnerable or threatened with extinction. C_LI

ecology↗

Integrating multiple data sources to fit matrix population models for interacting species

Inferring interactions between populations of different species is a challenging statistical endeavour, which requires a large amount of data. There is therefore some incentive to combine all available sources of data into a single analysis to do so. In demography and single-population studies, Integrated Population Models combine population counts, capture-recapture and reproduction data to fit matrix population models. Here, we extend this approach to the community level in a stage-structured predator-prey context. We develop Integrated Community Models (ICMs), implemented in a Bayesian framework, to fit multispecies nonlinear matrix models to multiple data sources. We assessed the value of the different sources of data using simulations of ICMs under different scenarios contrasting data availability. We found that combining all data types (capture-recapture, counts, and reproduction) allows the estimation of both demographic and interaction parameters, unlike count-only data which typically generate high bias and low precision in interaction parameter estimates for short time series. Moreover, reproduction surveys informed the estimation of interactions particularly well when compared to capture-recapture programs, and have the advantage of being less costly. Overall, ICMs offer an accurate representation of stage structure in community dynamics, and foster the development of efficient observational study designs to monitor communities in the field.

ecology↗

How many cubs can a mum raise? Maternal age and size influence litter size in polar bears

Life history theory predicts that females age and size affect the level of maternal investment in current reproduction, balanced against future reproductive effort, maintenance and survival. Using long-term (30 years) individual data on 231 female polar bears (Ursus maritimus), we assessed age- and size-specific variation on litter size. Litter size varied with maternal age, younger females had higher chances of losing a cub during their first months of life. Results suggest an improvement of breeding abilities early in life due to experience with subsequent reproductive senescence. Litter size increased with maternal size, indicating that size may reflect individual quality. Heterogeneity was observed among the largest females, suggesting that large size comes at a cost. Maternal traits and environmental conditions may act together to influence reproductive success.

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Inferring wildlife poaching in Southeast Asia with multispecies dynamic site-occupancy models

Determining the space race between sympatric species is crucial to understand the effects of interspecific interactions on the extinction risk of species threatened by poachers, predators, pathogens, and invasive competitors. Dynamic two-species occupancy models provide a flexible framework to decompose complex species interaction patterns while accounting for imperfect detection. In particular, these models can describe poachers-wildlife interactions by considering the occupancy, the extinction and colonisation probabilities of wildlife conditional on the presence or absence of poachers and vice versa. We apply our model to a case study on wildlife poaching in the Eastern plains of Cambodia. We used co-occurrence data extracted from the database of the SMART partnership to study the distribution dynamics between poachers and six ungulate species regarded as main prey of tigers. We used 4 years of survey data reporting the locations of ranger patrols on the detection of snares with visual detections or presence signs of the ungulates. Our results showed that a substantial proportion of the sites occupied by ungulate species went extinct over the years of the study while the proportion of sites colonised by poachers increased. We also showed, for the first time, that spatio-temporal heterogeneity in the patrolling effort explains a great deal of the variation in the detection of poachers and ungulates. Our approach provides practitioners with a flexible and robust tool to assess conservation status of species and extinction risk of wildlife populations. It can assist managers in better evaluating, learning and adapting the patrolling strategies of rangers.

ecology↗

Identifying priority conservation areas for recovering large carnivores using citizen science data

Understanding the processes related to wildlife recoveries is not only essential in solving human - wildlife conflicts, but also for identifying priority conservation areas and in turn, for effective conservation planning. We used data from a large citizen science program to study the spatial processes related to the demographic and genetic recovery of brown bears in Greece and to identify new areas for their conservation. This was achieved by visually comparing our data with an estimation of the past distribution of brown bears in Greece and by using a Point Process Model to model habitat suitability, and then comparing our results with the current distribution of brown bear records and with that of protected areas. Our results indicate that in the last 15 years bears may have increased their range by as much as 100%, by occupying mainly anthropogenic landscapes and areas with suitable habitat that are currently not legally protected, thus creating a new conservation reality for the species in Greece. This development dictates the re-evaluation of the national management and conservation priorities for brown bears in Greece by focusing in establishing new protected areas that will safeguard their recovery. Our conservation approach is a swift and cheap way of identifying priority conservation areas, while gaining important insights on the spatial processes associated with population recoveries. It will help prioritize conservation actions for brown bears in Greece and may serve as a model conservation approach to countries facing financial and logistic constraints in the monitoring of local biodiversity or facing challenges in managing rapid population recoveries. Our conservation approach appeared also to be better suited to identifying priority areas for conservation in areas with recovering wildlife populations and may therefore be used as an \"early-warning\" conservation system.

ecology↗

R2ucare: An R package to perform goodness-of-fit tests for capture-recapture models

O_LIAssessing the quality of fit of a statistical model to data is a necessary step for conducting safe inference.\nC_LIO_LIWe introduce R2ucare, an R package to perform goodness-of-fit tests for open single-and multi-state capture-recapture models. R2ucare also has various functions to manipulate capture-recapture data.\nC_LIO_LIWe remind the basics and provide guidelines to navigate towards testing the fit of capture-recapture models. We demonstrate the functionality of R2ucare through its application to real data.\nC_LI

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