Publications by authors named "Mathieu Basille"

13 Publications

  • Page 1 of 1

Sex-specific effects of wind on the flight decisions of a sexually dimorphic soaring bird.

J Anim Ecol 2020 08 19;89(8):1811-1823. Epub 2020 Jun 19.

School of Environmental Sciences, University of Liverpool, Liverpool, UK.

In a highly dynamic airspace, flying animals are predicted to adjust foraging behaviour to variable wind conditions to minimize movement costs. Sexual size dimorphism is widespread in wild animal populations, and for large soaring birds which rely on favourable winds for energy-efficient flight, differences in morphology, wing loading and associated flight capabilities may lead males and females to respond differently to wind. However, the interaction between wind and sex has not been comprehensively tested. We investigated, in a large sexually dimorphic seabird which predominantly uses dynamic soaring flight, whether flight decisions are modulated to variation in winds over extended foraging trips, and whether males and females differ. Using GPS loggers we tracked 385 incubation foraging trips of wandering albatrosses Diomedea exulans, for which males are c. 20% larger than females, from two major populations (Crozet and South Georgia). Hidden Markov models were used to characterize behavioural states-directed flight, area-restricted search (ARS) and resting-and model the probability of transitioning between states in response to wind speed and relative direction, and sex. Wind speed and relative direction were important predictors of state transitioning. Birds were much more likely to take off (i.e. switch from rest to flight) in stronger headwinds, and as wind speeds increased, to be in directed flight rather than ARS. Males from Crozet but not South Georgia experienced stronger winds than females, and males from both populations were more likely to take-off in windier conditions. Albatrosses appear to deploy an energy-saving strategy by modulating taking-off, their most energetically expensive behaviour, to favourable wind conditions. The behaviour of males, which have higher wing loading requiring faster speeds for gliding flight, was influenced to a greater degree by wind than females. As such, our results indicate that variation in flight performance drives sex differences in time-activity budgets and may lead the sexes to exploit regions with different wind regimes.
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http://dx.doi.org/10.1111/1365-2656.13267DOI Listing
August 2020

Analysis of movement recursions to detect reproductive events and estimate their fate in central place foragers.

Mov Ecol 2020 3;8:24. Epub 2020 Jun 3.

Department of Wildlife Ecology and Conservation, Fort Lauderdale Research and Education Center, University of Florida, 3205 College Ave, Davie, FL 33314 USA.

Background: Recursive movement patterns have been used to detect behavioral structure within individual movement trajectories in the context of foraging ecology, home-ranging behavior, and predator avoidance. Some animals exhibit movement recursions to locations that are tied to reproductive functions, including nests and dens; while existing literature recognizes that, no method is currently available to explicitly target different types of revisited locations. Moreover, the temporal persistence of recursive movements to a breeding location can carry information regarding the fate of breeding attempts, but it has never been used as a metric to quantify recursive movement patterns. Here, we introduce a method to locate breeding attempts and estimate their fate from GPS-tracking data of central place foragers. We tested the performance of our method in three bird species differing in breeding ecology (wood stork ( lesser kestrel () Mediterranean gull ()) and implemented it in the R package 'nestR'.

Methods: We identified breeding sites based on the analysis of recursive movements within individual tracks. Using trajectories with known breeding attempts, we estimated a set of species-specific criteria for the identification of nest sites, which we further validated using non-reproductive individuals as controls. We then estimated individual nest survival as a binary measure of reproductive fate (success, corresponding to fledging of at least one chick, or failure) from nest-site revisitation histories during breeding attempts, using a Bayesian hierarchical modeling approach that accounted for temporally variable revisitation patterns, probability of visit detection, and missing data.

Results: Across the three species, positive predictive value of the nest-site detection algorithm varied between 87 and 100% and sensitivity between 88 and 92%, and we correctly estimated the fate of 86-100% breeding attempts.

Conclusions: By providing a method to formally distinguish among revisited locations that serve different ecological functions and introducing a probabilistic framework to quantify temporal persistence of movement recursions, we demonstrated how the analysis of recursive movement patterns can be applied to estimate reproduction in central place foragers. Beyond avian species, the principles of our method can be applied to other central place foraging breeders such as denning mammals. Our method estimates a component of individual fitness from movement data and will help bridge the gap between movement behavior, environmental factors, and their fitness consequences.
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http://dx.doi.org/10.1186/s40462-020-00201-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7268620PMC
June 2020

Evaluating the data quality of iNaturalist termite records.

PLoS One 2020 4;15(5):e0226534. Epub 2020 May 4.

University of Florida, Fort Lauderdale Research and Education Center Davie, Florida, United States of America.

Citizen science (CS) contributes to the knowledge about species distributions, which is a critical foundation in the studies of invasive species, biological conservation, and response to climatic change. In this study, we assessed the value of CS for termites worldwide. First, we compared the abundance and species diversity of geo-tagged termite records in iNaturalist to that of the University of Florida termite collection (UFTC) and the Global Biodiversity Information Facility (GBIF). Second, we quantified how the combination of these data sources affected the number of genera that satisfy data requirements for ecological niche modeling. Third, we assessed the taxonomic correctness of iNaturalist termite records in the Americas at the genus and family level through expert review based on photo identification. Results showed that iNaturalist records were less abundant than those in the UFTC and in GBIF, although they complemented the latter two in selected world regions. A combination of GBIF and the UFTC led to a significant increase in the number of termite genera satisfying the abundance criterion for niche modeling compared to either of those two sources alone, whereas adding iNaturalist observations as a third source only had a moderate effect on the number of termite genera satisfying that criterion. Although research grade observations in iNaturalist require a community-supported and agreed upon identification (ID) below the family taxonomic rank, our results indicated that iNaturalist data do not exhibit a higher taxonomic classification accuracy when they are designated research grade. This means that non-research grade observations can be used to more completely map the presence of termite locations in certain geographic locations without significantly jeopardizing data quality. We concluded that CS termite observation records can, to some extent, complement expert termite collections in terms of geographic coverage and species diversity. Based on recent data contribution patterns in CS data, the role of CS termite contributions is expected to grow significantly in the near future.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0226534PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7197788PMC
September 2020

Navigating through the r packages for movement.

J Anim Ecol 2020 01 28;89(1):248-267. Epub 2019 Oct 28.

Department of Wildlife Ecology and Conservation, Fort Lauderdale Research and Education Center, University of Florida, Fort Lauderdale, FL, USA.

The advent of miniaturized biologging devices has provided ecologists with unprecedented opportunities to record animal movement across scales, and led to the collection of ever-increasing quantities of tracking data. In parallel, sophisticated tools have been developed to process, visualize and analyse tracking data; however, many of these tools have proliferated in isolation, making it challenging for users to select the most appropriate method for the question in hand. Indeed, within the r software alone, we listed 58 packages created to deal with tracking data or 'tracking packages'. Here, we reviewed and described each tracking package based on a workflow centred around tracking data (i.e. spatio-temporal locations (x, y, t)), broken down into three stages: pre-processing, post-processing and analysis, the latter consisting of data visualization, track description, path reconstruction, behavioural pattern identification, space use characterization, trajectory simulation and others. Supporting documentation is key to render a package accessible for users. Based on a user survey, we reviewed the quality of packages' documentation and identified 11 packages with good or excellent documentation. Links between packages were assessed through a network graph analysis. Although a large group of packages showed some degree of connectivity (either depending on functions or suggesting the use of another tracking package), one third of the packages worked in isolation, reflecting a fragmentation in the r movement-ecology programming community. Finally, we provide recommendations for users when choosing packages, and for developers to maximize the usefulness of their contribution and strengthen the links within the programming community.
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http://dx.doi.org/10.1111/1365-2656.13116DOI Listing
January 2020

Life histories and conservation of long-lived reptiles, an illustration with the American crocodile (Crocodylus acutus).

J Anim Ecol 2017 Sep 31;86(5):1102-1113. Epub 2017 Jul 31.

Department of Wildlife Ecology and Conservation, Fort Lauderdale Research and Education Center, University of Florida, Fort Lauderdale, FL, USA.

Successful species conservation is dependent on adequate estimates of population dynamics, but age-specific demographics are generally lacking for many long-lived iteroparous species such as large reptiles. Accurate demographic information allows estimation of population growth rate, as well as projection of future population sizes and quantitative analyses of fitness trade-offs involved in the evolution of life-history strategies. Here, a long-term capture-recapture study was conducted from 1978 to 2014 on the American crocodile (Crocodylus acutus) in southern Florida. Over the study period, 7,427 hatchlings were marked and 380 individuals were recaptured for as many as 25 years. We estimated survival to be strongly age dependent with hatchlings having the lowest survival rates (16%) but increasing to nearly 90% at adulthood based on mark-recapture models. More than 5% of the female population were predicted to be reproductive by age 8 years; the age-specific proportion of reproductive females steadily increased until age 18 when more than 95% of females were predicted to be reproductive. Population growth rate, estimated from a Leslie-Lefkovitch stage-class model, showed a positive annual growth rate of 4% over the study period. Using a prospective sensitivity analysis, we revealed that the adult stage, as expected, was the most critical stage for population growth rate; however, the survival of younger crocodiles before they became reproductive also had a surprisingly high elasticity. We found that variation in age-specific fecundity has very limited impact on population growth rate in American crocodiles. We used a comparative approach to show that the original life-history strategy of American crocodiles is actually shared by other large, long-lived reptiles: while adult survival rates always have a large impact on population growth, this decreases with declining increasing growth rates, in favour of a higher elasticity of the juvenile stage. Crocodiles, as a long-lived and highly fecund species, deviate from the usual association of life histories of "slow" species. Current management practices are focused on nests and hatchling survival; however, protection efforts that extend to juvenile crocodiles would be most effective for conservation of the species, especially in an ever-developing landscape.
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http://dx.doi.org/10.1111/1365-2656.12723DOI Listing
September 2017

Plastic response of fearful prey to the spatiotemporal dynamics of predator distribution.

Ecology 2015 Oct;96(10):2622-31

Ecological theory predicts that the intensity of antipredator responses is dependent upon the spatiotemporal context of predation risk (the risk allocation hypothesis). However, most studies to date have been conducted over small spatial extents, and did not fully take into account gradual responses to predator proximity. We simultaneously collected spatially explicit data on predator and prey to investigate acute responses of a threatened forest ungulate, the boreal caribou (Rangifer tarandus), to the spatiotemporal dynamics of wolf (Canis lupus) distribution during spring. Movement analysis of GPS-collared individuals from both species revealed high plasticity in habitat-selection decisions of caribou. Female caribou avoided open areas and deciduous forests and moved relatively fast and toward foraging areas when wolves were closer than 2.5 km. Caribou also avoided food-rich areas only when wolves were within 1 km. Our results bridge the gap between long-term perceived risk and immediate flight responses by revealing dynamic antipredator tactics in response to predator proximity.
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http://dx.doi.org/10.1890/14-1706.1DOI Listing
October 2015

Movement is the glue connecting home ranges and habitat selection.

J Anim Ecol 2016 Jan 30;85(1):21-31. Epub 2015 Jul 30.

Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, CNRS, Université Lyon 1, 69622, Villeurbanne, France.

Animal space use has been studied by focusing either on geographic (e.g. home ranges, species' distribution) or on environmental (e.g. habitat use and selection) space. However, all patterns of space use emerge from individual movements, which are the primary means by which animals change their environment. Individuals increase their use of a given area by adjusting two key movement components: the duration of their visit and/or the frequency of revisits. Thus, in spatially heterogeneous environments, animals exploit known, high-quality resource areas by increasing their residence time (RT) in and/or decreasing their time to return (TtoR) to these areas. We expected that spatial variation in these two movement properties should lead to observed patterns of space use in both geographic and environmental spaces. We derived a set of nine predictions linking spatial distribution of movement properties to emerging space-use patterns. We predicted that, at a given scale, high variation in RT and TtoR among habitats leads to strong habitat selection and that long RT and short TtoR result in a small home range size. We tested these predictions using moose (Alces alces) GPS tracking data. We first modelled the relationship between landscape characteristics and movement properties. Then, we investigated how the spatial distribution of predicted movement properties (i.e. spatial autocorrelation, mean, and variance of RT and TtoR) influences home range size and hierarchical habitat selection. In landscapes with high spatial autocorrelation of RT and TtoR, a high variation in both RT and TtoR occurred in home ranges. As expected, home range location was highly selective in such landscapes (i.e. second-order habitat selection); RT was higher and TtoR lower within the selected home range than outside, and moose home ranges were small. Within home ranges, a higher variation in both RT and TtoR was associated with higher selectivity among habitat types (i.e. third-order habitat selection). Our findings show how patterns of geographic and environmental space use correspond to the two sides of a coin, linked by movement responses of individuals to environmental heterogeneity. By demonstrating the potential to assess the consequences of altering RT or TtoR (e.g. through human disturbance or climatic changes) on home range size and habitat selection, our work sets the basis for new theoretical and methodological advances in movement ecology.
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http://dx.doi.org/10.1111/1365-2656.12394DOI Listing
January 2016

Developmental instability in incipient colonies of social insects.

PLoS One 2014 25;9(11):e113949. Epub 2014 Nov 25.

Department of Entomology and Nematology, Fort Lauderdale Research and Education Center, University of Florida, Institute of Food and Agricultural Sciences, Fort Lauderdale, Florida, United States of America.

Social insect colonies can provide homeostatic conditions that buffer the incidence of environmental fluctuations on individuals, which have contributed to their ecological success. Coptotermes (Isoptera: Rhinotermitidae) is a highly invasive termite genus and several species have important economic impact in many areas of the world. Mature Coptotermes colonies with millions of individuals can provide optimal environmental condition and nurturing capacity for the developing brood. However, it was previously suggested that contrary to mature colonies, incipient colonies may be exposed to critical stress, which may explain for the low success rate of establishment within the first year of the life of a termite colony. We here investigated the stress imposed on individuals of incipient colonies by comparing the developmental instability of individuals between incipient and mature colonies of two Coptotermes species, C. formosanus Shiraki and C. gestroi (Wasmann). We assessed the developmental instability by measuring the asymmetry of morphological traits from the head capsule of the soldier caste. Soldiers from incipient colonies of both species displayed strong asymmetrical traits in comparison to soldiers from mature colonies. We suggest that homeostatic conditions for optimal development are reached as the colony matures, and confirmed that the incipient colony remains a critical bottleneck where individuals are exposed to high developmental stress.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0113949PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4244189PMC
January 2016

'You shall not pass!': quantifying barrier permeability and proximity avoidance by animals.

J Anim Ecol 2016 Jan 25;85(1):43-53. Epub 2014 Aug 25.

Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK.

Impediments to animal movement are ubiquitous and vary widely in both scale and permeability. It is essential to understand how impediments alter ecological dynamics via their influence on animal behavioural strategies governing space use and, for anthropogenic features such as roads and fences, how to mitigate these effects to effectively manage species and landscapes. Here, we focused primarily on barriers to movement, which we define as features that cannot be circumnavigated but may be crossed. Responses to barriers will be influenced by the movement capabilities of the animal, its proximity to the barriers, and habitat preference. We developed a mechanistic modelling framework for simultaneously quantifying the permeability and proximity effects of barriers on habitat preference and movement. We used simulations based on our model to demonstrate how parameters on movement, habitat preference and barrier permeability can be estimated statistically. We then applied the model to a case study of road effects on wild mountain reindeer summer movements. This framework provided unbiased and precise parameter estimates across a range of strengths of preferences and barrier permeabilities. The quality of permeability estimates, however, was correlated with the number of times the barrier is crossed and the number of locations in proximity to barriers. In the case study we found that reindeer avoided areas near roads and that roads are semi-permeable barriers to movement. There was strong avoidance of roads extending up to c. 1 km for four of five animals, and having to cross roads reduced the probability of movement by 68·6% (range 3·5-99·5%). Human infrastructure has embedded within it the idea of networks: nodes connected by linear features such as roads, rail tracks, pipelines, fences and cables, many of which divide the landscape and limit animal movement. The unintended but potentially profound consequences of infrastructure on animals remain poorly understood. The rigorous framework for simultaneously quantifying movement, habitat preference and barrier permeability developed here begins to address this knowledge gap.
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http://dx.doi.org/10.1111/1365-2656.12275DOI Listing
January 2016

Uniting statistical and individual-based approaches for animal movement modelling.

PLoS One 2014 30;9(6):e99938. Epub 2014 Jun 30.

Chaire de recherche industrielle CRSNG-Université Laval en sylviculture et faune, Département de biologie, Université Laval, Québec, Québec, Canada.

The dynamic nature of their internal states and the environment directly shape animals' spatial behaviours and give rise to emergent properties at broader scales in natural systems. However, integrating these dynamic features into habitat selection studies remains challenging, due to practically impossible field work to access internal states and the inability of current statistical models to produce dynamic outputs. To address these issues, we developed a robust method, which combines statistical and individual-based modelling. Using a statistical technique for forward modelling of the IBM has the advantage of being faster for parameterization than a pure inverse modelling technique and allows for robust selection of parameters. Using GPS locations from caribou monitored in Québec, caribou movements were modelled based on generative mechanisms accounting for dynamic variables at a low level of emergence. These variables were accessed by replicating real individuals' movements in parallel sub-models, and movement parameters were then empirically parameterized using Step Selection Functions. The final IBM model was validated using both k-fold cross-validation and emergent patterns validation and was tested for two different scenarios, with varying hardwood encroachment. Our results highlighted a functional response in habitat selection, which suggests that our method was able to capture the complexity of the natural system, and adequately provided projections on future possible states of the system in response to different management plans. This is especially relevant for testing the long-term impact of scenarios corresponding to environmental configurations that have yet to be observed in real systems.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0099938PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4076191PMC
October 2015

Selecting habitat to survive: the impact of road density on survival in a large carnivore.

PLoS One 2013 10;8(7):e65493. Epub 2013 Jul 10.

Fort Lauderdale Research and Education Center, University of Florida, Fort Lauderdale, Florida, United States of America.

Habitat selection studies generally assume that animals select habitat and food resources at multiple scales to maximise their fitness. However, animals sometimes prefer habitats of apparently low quality, especially when considering the costs associated with spatially heterogeneous human disturbance. We used spatial variation in human disturbance, and its consequences on lynx survival, a direct fitness component, to test the Hierarchical Habitat Selection hypothesis from a population of Eurasian lynx Lynx lynx in southern Norway. Data from 46 lynx monitored with telemetry indicated that a high proportion of forest strongly reduced the risk of mortality from legal hunting at the home range scale, while increasing road density strongly increased such risk at the finer scale within the home range. We found hierarchical effects of the impact of human disturbance, with a higher road density at a large scale reinforcing its negative impact at a fine scale. Conversely, we demonstrated that lynx shifted their habitat selection to avoid areas with the highest road densities within their home ranges, thus supporting a compensatory mechanism at fine scale enabling lynx to mitigate the impact of large-scale disturbance. Human impact, positively associated with high road accessibility, was thus a stronger driver of lynx space use at a finer scale, with home range characteristics nevertheless constraining habitat selection. Our study demonstrates the truly hierarchical nature of habitat selection, which aims at maximising fitness by selecting against limiting factors at multiple spatial scales, and indicates that scale-specific heterogeneity of the environment is driving individual spatial behaviour, by means of trade-offs across spatial scales.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0065493PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3707854PMC
March 2014

Habitat-performance relationships: finding the right metric at a given spatial scale.

Philos Trans R Soc Lond B Biol Sci 2010 Jul;365(1550):2255-65

Unité Mixte de Recherche CNRS-Université Lyon 1 N degrees 5558 Biométrie et Biologie Evolutive, Bâtiment Gregor Mendel, 43 boulevard du 11 novembre 1918, 69622 Villeurbanne Cedex, France.

The field of habitat ecology has been muddled by imprecise terminology regarding what constitutes habitat, and how importance is measured through use, selection, avoidance and other bio-statistical terminology. Added to the confusion is the idea that habitat is scale-specific. Despite these conceptual difficulties, ecologists have made advances in understanding 'how habitats are important to animals', and data from animal-borne global positioning system (GPS) units have the potential to help this clarification. Here, we propose a new conceptual framework to connect habitats with measures of animal performance itself--towards assessing habitat-performance relationship (HPR). Long-term studies will be needed to estimate consequences of habitat selection for animal performance. GPS data from wildlife can provide new approaches for studying useful correlates of performance that we review. Recent examples include merging traditional resource selection studies with information about resources used at different critical life-history events (e.g. nesting, calving, migration), uncovering habitats that facilitate movement or foraging and, ultimately, comparing resources used through different life-history strategies with those resulting in death. By integrating data from GPS receivers with other animal-borne technologies and combining those data with additional life-history information, we believe understanding the drivers of HPRs will inform animal ecology and improve conservation.
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http://dx.doi.org/10.1098/rstb.2010.0085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2894964PMC
July 2010

A general framework for the statistical exploration of the ecological niche.

J Theor Biol 2008 Jun 3;252(4):674-85. Epub 2008 Mar 3.

Université de Lyon, F-69000, Lyon, France; Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622, Villeurbanne, France.

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.
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http://dx.doi.org/10.1016/j.jtbi.2008.02.036DOI Listing
June 2008