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Mathieu Basille
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University of Florida

Mathieu Basille

Never let your sense of morals prevent you from doing what is right! Salvor Hardin's epigram

Résumé

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Current situation

Assistant Professor in Landscape Ecology at the University of Florida's Fort Lauderdale Research and Education Center (Fort Lauderdale, FL, USA), since May 2015.

Contact information

University of Florida
Ft Lauderdale Research and Education Center
3205 College Avenue
Fort Lauderdale, FL 33314
USA

Phone : +1.954.577.6314
E-mail:

Research profile

I am primarily interested in the determinism of the spatial distributions of animal species, from a fine scale (movement models) to a large scale (distribution in the landscape) in relation to the habitat and other species. My work lies on a strong theoretical and methodological basis using the concept of ecological niche, and allows applied achievements in the context of animal population management, as well as basic developments at the intersection of evolutionary ecology and behavioural ecology. My main study species are large vertebrates, such as lynx in Norway, caribou in Québec, and wood stork and sea turtles in Florida.

Teaching profile

I was responsible of more than 400 hours of statistics classes (2004–2009, bachelor degree), and 14 hours in habitat selection (2008–2009, master degree). In parallel, I offered 2 workshops on habitat selection and the use of PostGIS in spatial ecology at Laval University, Quebec City, Canada (2010–2011).

Academic achievements and professional positions

Since 2015 Assistant Professor in Landscape Ecology at the University of Florida (Fort Lauderdale, FL, USA).
2012–2014 Postdoctoral Associate at the University of Florida (Fort Lauderdale, FL, USA), under the supervision of James Watling.
2009–2012 Postdoctoral Associate at Laval University (Quebec City, QC, Canada) for 30 months, under the supervision of Daniel Fortin.
2007–2009 Part-time Teaching Fellow at Université Lyon 2 (Lyon, France), part-time Research Fellow at Université Lyon 1 (Lyon, France).
2004–2008 PhD thesis (Biology) at the Université Claude Bernard Lyon 1 (Lyon, France), available here (in English).
Title "Habitat selection by lynx (Lynx lynx) in a human-dominated landscape—From theory to application"
PhD supervisor Jean-Michel Gaillard, Université Claude Bernard Lyon 1 (Lyon, France) and Reidar Andersen, Norwegian University of Science and Technology (NTNU, Trondheim, Norway).
Jury Dominique Allainé, Éric Marboutin, Evelyn Merrill, Eloy Revilla & Nigel Gilles Yoccoz.
Defense July 7th juillet 2008, in Lyon, presentation available here (in English).
2004–2007 Teaching Assistant at Université Lyon 2 (France).
2002–2004 MSc. in Biology (Analysis and modelling of biological systems), Université Claude Bernard Lyon I (France), under the supervision of Jean-Michel Gaillard : "Modelling predator-prey relationships. Reviews of the wolf-ungulates system in North America" (bibliographical report, in French) and "Lynx, ENFA and SIG. A story of habitat selection." (technical report, in French), with high honours, rank 4th/27.
1999–2002 BSc. in Organismal Biology, Université Claude Bernard Lyon 1 (France), with high honours.

Research experience

I began conducting international research in 2003. Since then, I primarily focused on space use of large mammals at multiple scales, and related impact on fitness, with a special interest in predator-prey interactions. In particular, I intensively studied the Eurasian lynx (Lynx lynx)–roe deer (Capreolus capreolus) system in France and Norway, with the addition of human as a top predator, and a multi-predator multi-prey system involving woodland caribou (Rangifer tarandus caribou), moose (Alces alces), grey wolves (Canis lupus) and black bears (Ursus americanus) in Quebec, Canada. I give also a strong interest in habitat selection and ecological niche theories. In particular, I rely on a robust and consistent approach of the habitat concept, to connect it eventually to animal performance. There have been recently several studies that investigated the relationship between habitat selection and fitness components, which are opening new opportunities to understand the relationship between demography and space use. I strongly believe in the principles of open science and open research. To be specific, I think that science should be open from both a philosophical and a practical perspective, which is then a strong basis for improved collaborations. Practically, this is the main reason why I use intensively free software (from GNU/Linux to R and PostGIS) and try to publish methods and code to enable anyone to reproduce my analyses.

Past and current work

My work primarily revolves around three complementary axes:

A framework for the study of the ecological niche

Ecological niche
Ecological niche

Part of my past work aimed at developing a statistical exploratory framework for the ecological niche, defined as the geometric space in which a species can persist indefinitely, i.e. maintain viable populations. The "General niche-environment system factor analysis" (GNESFA), developed in close collaboration with Clément Calenge, allows for the comparison of the used habitat to the available habitat, at the population level. The GNESFA actually integrates three complementary analyses: the Mahalanobis distance factor analysis (MADIFA), the Factor analysis of the niche, taking the environment as the reference (FANTER), and the commonly used Ecological-niche factor analysis (ENFA). This work required strong statistical and R programming skills, with a set of ENFA-related methods developed for the adehabitat package, as well as a solid theoretical background to formulate the framework, and collaborative and integrative assets necessary for an effective pair work. This work actually led to three publications in international journals (Basille et al. 2008, Calenge et al. 2008, Calenge et Basille 2008, see below). Our framework also open new research avenues for a number of researchers, in various fields such as the study of the effects of food and water in large ungulates, the study of historic and current distributions of animal species, and the study of climate change on animal species distribution, and gave rise to new ideas on ecological specialization as well as new methodological developments.

Predator-prey systems

Eurasian lynx
© Scandlynx

The ecological-niche framework described above made possible a detailed study of space use patterns and their effect on fitness in the Eurasian lynx (Lynx lynx)–roe deer (Capreolus capreolus) system, in a human-dominated landscape in Norway. In this system, most lynx death are caused by humans (due mainly to legal hunting and poaching), while roe deer are both preyed upon by lynx and hunted by humans. This study demonstrated that lynx were present in areas with relatively high roe deer densities, but that they avoided the most disturbed areas. This comes in support of the hypothesis of a food-safety trade-off characterized by a search for a high prey abundance and an avoidance of human activities. The joint effect of lynx and climatic conditions on roe deer populations was very strong, as demonstrated by lower growth rates in roe deer populations in areas with both presence of their predator and harsh climatic conditions, as compared to areas without lynx and/or milder climatic conditions. Finally, at fine scale, lynx strongly avoided areas with lots of roads within their home ranges, where they were subject to a higher human-based mortality rate, which demonstrates a compensatory mechanism to mitigate at fine scale the impact of large-scale disturbances. Throughout this work, I enhanced my statistical skills (e.g. with the use of Cox models or Generalized additive models in R), and also improved my competence in analyzing data at several nested scales. This work led to three publications in international journals (Basille et al. 2009, Melis et al. 2010, Basille et al. 2013, see below).

Movement

Woodland caribou
© Daniel Fortin

I spent 30 months on a postdoc project at Laval University (Quebec City, Canada), in the lab of Daniel Fortin. This work focused on animal movement in a multi-predator multi-prey system in Quebec, including woodland caribou (Rangifer tarandus caribou), moose (Alces alces), grey wolves (Canis lupus) and black bears (Ursus americanus). With this project, I further improved my skills in studying fine-scale space use processes, such as movement-based Step selection functions (SSF, based on conditional logistic regressions). In particular, this study highlighted a temporal variation in movement patterns along the year related to movement constraints and limiting resources in caribou, moose and wolves. Moreover, the risk that caribou faced was not only a function of niche overlap with wolves, but also a function of relative niche overlap between moose and wolves during the same period of time, reflecting the strength of trophic interactions along the year. At a finer scale, a detailed analysis of anti-predator behaviour revealed a high flexibility in anti-predator behavior of the prey regarding food acquisition and search for cover when predators were in the vicinity. For example, when wolves were closer than 2.5 km), caribou strongly avoided areas associated to a higher probability of wolf encounter. However, the immediate proximity of wolves (< 1 km) triggered a strong avoidance of foraging areas in favour of a better cover. This work also led to the development of general individual-based modelling framework, able to replicate the behavior of real individuals in order to artifically generate the data required for an explicit modelling ot the real system. This work led to two publications in international journals (Basille et al. 2013, see below, Latombe et al. en révision), as well as two manuscripts currently in prep. (Basille et al. in prep, Labbé et al. in prep).

Current work

Crocodylus actilus niche in 2080

Between October 2012 and December 2014, I conducted a second postdoc at the University of Florida (Fort Lauderdale, USA), in the lab of James Watling, which integrates my research interests. James Watling's lab works collaboratively with researchers from several branches of the federal government to create niche models able to forecast species responses to changing climate. In particular, the project focuses on developing climate envelope models and associated prediction maps for 26 federally threatened and endangered (T&E) terrestrial vertebrate species occurring in peninsular Florida. My work is primarily dedicated to the development of mechanistic niche models integrating movement data and spatially-explicit population processes, using the wood stork (Mycteria americana) as a study case. These niche models are a first step towards the development of effective decision support tools for endangered species management in the face of climate change.

Other research activities

My involvement at each university was not strictly limited to my research activities. I particularly endeavor to share my work and methodological developments, in order to benefit the greatest number of scientists (and others). This means a participation in various duties such as mentoring students, consulting activities towards wildlife management institutions, or sharing code on-line.

Mentoring student

Right after my PhD, I co-supervised a bachelor student (Jonathan Rolland in 2009-2010) with Dr. Jean-Michel Gaillard (Université Lyon I, France), and more recently supervised a MSc student (Marie-Claude Labbé in 2010-2012) with Dr. Daniel Fortin (Université Laval, Canada). These two projects were tightly connected to my studies, and allowed me to learn about effective mentoring and collaborating with developing and active students in the context of international research. The work of J. Rolland culminated in a publication in a peer-reviewed journal (see below), while the work of M.C. Labbé was presented in November 2012 at the Wildlife Society 18th Annual Conference (Hawaii, USA) while a manuscript is actually in prep. for submission in an international ecology journal.

Consulting

I worked as a consultant for the Office national de la chasse et de la faune sauvage (ONCFS, the French wildlife services), for which I assessed the feasibility of a photo-detection monitoring study of lynx in the Alps (2003) and conducted a wolf howling program to detect wolf presence throughout the Alps (2003). I also worked for the Norwegian Institute for Nature Research (NINA, 2007 & 2008) to help them setting up a sampling design and the monitoring of moose and roe deer from faeces collection in three different areas of Norway (2007–2008).

Statistical programming

R logo

I was involved in the programming of functions included in the statistical package adehabitat (now adehabitatHS) for R, led by Clément Calenge. These functions include habitat selection methods centred around the ENFA (Ecological-niche factor analysis) and other utilities for the description of habitat selection. I also help on a regular basis in reviewing and correcting other functions of the package. Finally, I generally release the statistical code required to reproduce my work on-line, with the aim of making it as generally applicable as possible. In this context, I developed a R package for the study of seasonality from telemetry data, another one for the study of movement (e.g. Step Selection Functions) together with habitat selection utilities, and one for the interaction between R and PostGIS.

Field experience

I acquired a limited field experience throughout the various projects in which I was involved:

Community responsibilities

Last but not least, I try to reach an active position in the scientific community by leading and participating in research groups, or developing collaborative works between institutes or universities. I am also an active reviewer for international scientific journals, which I find essential in a healthy and balanced modern science.

Research groups

During the course of my PhD thesis, I created and coordinated a "Habitat group" within the Laboratoire de Biométrie et Biologie Évolutive. This group met once or twice per month to discuss new and innovative papers or ideas, and to share resources (presentations, meeting reports, etc.). This group was further enhanced by a dedicated website which I administrated. The core of the Habitat group later evolved into the Animal Spatial Ecology group, of which I am still the administrator, which focuses on animals' space use in relation to their environment using relocation data. Notably, the group published a book chapter about the opportunities offered, and the statistical challenges raised, by GPS technology in habitat selection and movement studies in order to gain new insights into the proximal mechanisms and evolutionary causes of animals' space use (see below).

Inter-institute collaborations

As soon as 2007, I was largely involved in the early steps that lead to the EURODEER project (called ISAMUD^2 at the time), by sharing resources and data between France and Italy (collaboration between the Laboratoire de Biométrie et Biologie Évolutive and the Center of Alpine Ecology in Italy). EURODEER later became an international group of researchers committed to roe deer monitoring with GPS collars. The project is still led by Francesca Cagnacci (Italy), and is based on an international platform to manage and analyze GPS data, already developed at the time of ISAMUD^2. However, owing to my research activities in Quebec and then in Florida, I am no longer an active member of the EURODEER network, but I keep a watchful eye on its constant evolution, which completely matches my point of view on international collaborative science.

Peer-reviewing

I am an active reviewer for the following peer-reviewed journals: Basic and Applied Ecology, Biological Conservation, the Canadian Journal of Zoology, Diversity and Distributions, Ecography, Écoscience, the International Journal of Biodiversity Science, Ecosystem Services & Management, the Journal of Animal Ecology, the Journal of Applied Ecology, the Journal of Herpethology, the Journal of Wildlife Management, Mammalian Biology, Methods in Ecology and Evolution, le Naturaliste Canadien (fr), Oecologia, Oikos, Oryx, the Philosophical Transactions of the Royal Society (B.), PLOS One, Wildlife Biology. I also reviewed a chapter of the Encyclopedia of Inland Waters, edited by Elsevier. Total: 29 reviews.

See my peer-review record on Publons.

Teaching experience

Teaching Fellow and Teaching Assistant

From 2004 to 2007, I was a Teaching Fellow at the Statistics and Data Processing department (in French STID) of the IUT Lumière (Université Lyon 2). During these 3 years, I was responsible of about 200 hours. I was then hired as a Teaching Assistant for 2 years (2007–2009) at the same department, which represent another 200 hours, including teaching and other responsibilities (department activity, administrative management, etc.). Here is a detailed description of these activities (which do not include defenses and mentoring):

I was primarily responsible of teaching descriptive and inferential statistics at the bachelor degree. I had to organize a program of seminars and practical works to follow lectures given by Anne Viallefont and Sabine Loudcher (professors at the IUT Lumière) to 1st-year students. The classes addressed the study of categorical variables, synthetic parameters of position and dispersion of a statistical distribution, graphs suitable for the display of univariate and bivariate statistics, and then the relationship between two variables (categorical or continuous).

This idea was later improved by the concept of statistical test in the second year. I proposed seminars and practical works that went along the lectures from Jean-Claude Oriol (professor at the IUT Lumière). The methodology introduced a variety of statistical tests, such as the comparison of means and variances, using parametric or non-parametric approaches, and also covered correlation and linear regression tests. Finally, I was responsible of a whole teaching module (lectures, seminars and practical works) addressing the analysis of variance, with a global statistical approach (description of the data sample, null and alternative hypotheses, conditions of the test, result and interpretation) of one-way and two-ways ANOVA, and multiple comparisons among means.

This experience allowed me to deal from beginning to end with the management of a complete teaching module, from a theoretical as well as a practical perspective. I learned how to articulate my classes with other classes of the two years of the diploma. My talks in these other modules allowed me to offer an approach more integrated in the department and more consistent for the students, and participated in my self-assertion as a teacher. The next two years as a Teaching Assistant further reinforced the quality of my classes and their articulation with other classes, while strongly enhancing my implication in the department's everyday life.

Finally, I was also in charge of refresher courses in linear algebra and function analyses, and descriptive statistics (40 hours) for new bachelor students coming from a variety of horizons, which gave me the opportunity to challenge and reinforce my adaptability according to the audience.

Student projects

In parallel of teaching, I took charge of several long-term student projects involving professionals from the private sector, with precise targets to reach. This is for me an essential step in the training of students, in addition to their classes, in order to put them in direct touch with the business community.

In particular, I was in charge a statistical project of a group of 4 students. This project, planned over several months (about 45 hours), was made in collaboration with the Music and Dance Agency Rhône-Alpes (AMDRA, now the NACRe). The goal was to prepare and manage an on-line form with its data base to monitor the future of former students of music academies of the county. The AMDRA, as the prime contractor, defined the objectives, which had to be adjusted to both the possibilities of the students and the requirements of the IUT.

During 3 years, I was also strongly involved in a long-term partnership between the IUT and Kéolis Lyon, the company in charge of the public transportation in Lyon (France). The goal of this partnership was to administer a customer satisfaction survey, from the field survey to the processing of the data, through a dedicated data base. This project (about 80 hours over 3 years) associated a work experience in a real professional context (the survey is required by law) to a validation of the knowledge they earned at the IUT.

Department daily life

My commitment in the IUT was, however, not limited to my academic activities. During the 5 years I worked in this department, I was involved in mentoring students, for instance as a supervisor on several study projects, or as a department tutor for student internships in private companies. In particular, I monitored one student during two years in the laboratory Merial in Lyon (6 weeks for her first-year internship, and then apprenticeship for the second year), and a second one for her apprenticeship in the statistics department of the French register of cancers in Mulhouse.

I was also particularly involved in the daily life and operation of the department. First, I participated in all committees and defenses of the students I supervised as well as other students, and also joined all graduation and semester juries. I was also able to get a better understanding of the department recruitment, since I was given the charge of evaluating a couple of potential students' applications for one of the degrees in the department. Lastly, I represented the IUT Lumière at a national level by participating in a survey sponsored by the French Education Ministry and carried out by all STID departments in France. This survey aimed at taking an inventory of and analyzing the use of audiovisual tools in the university. This allowed me to involve students in a large-scale professional project, but at the same time required a strong commitment with, e.g. several meetings in Paris or Metz, and the preparation of a final report, presented at the International Conference "The University at the Digital Era" (22–24 May 2006, Paris).

Master teaching

More recently, I had the chance to return to the students the knowledge acquired during my PhD and my academic training, through a course that mixed theory, methods and applications in the field of habitat selection. This second-year master class tackled habitat selection and its application at several scales, based on real data analyzed using the R software. This allowed me to measure the potential of such a training, as well as the challenge of giving back my research knowledge through teaching. This class was part of the second year of the "Ecosciences and microbiology" Master at the Université Claude Bernard Lyon 1 (16 hours).

During my previous postdoc at Laval University (Quebec City, Canada), I was also involved in one of the classes of Daniel Fortin ("Quantitative evaluation of animal behaviour"). In March 2012, I took charge of a 2-hour lecture presented at graduate students on the topic of niche analyses in habitat selection. This lecture was largely based on the Master class described above.

Training

I conducted a 1-day training course entitled "An introduction to the study of habitat selection by wildlife" (in French) at University Laval (CFR: Centre for Forest Research) in June 2010. The course used the adehabitat package for R to tackle multivariate analyses based on the concept of ecological niche, at different ecological and spatial scales. I also conducted a second 2-days training course entitled "An introduction to the use of PostGIS in spatial ecology" (in French) at the Université du Québec à Rimouski in September 2011. Through a series of practical exercices, the course tackled concepts of relational databases and basic spatial functions of PostGIS, including intersects of points, buffers and steps with raster maps, and how to connect PostGIS to different clients (QGIS, R, pgAdmin).

Publication list

Peer-reviewed articles

  1. Beyer H.L., Gurarie E., Börger L., Panzacchi M., Basille M., Herfindal I., Van Moorter B., Lele S. & Matthiopoulos J. (2016) "You shall not pass!": quantifying barrier permeability and proximity avoidance by animals. Journal of Animal Ecology, 85: 43–53. 10.1111/1365-2656.12275 manuscript abstract

    abstract: 1. 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.
    2. 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.
    3. 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.
    4. 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 reindeer avoided areas near roads and that roads are semi-permeable barriers to movement. There was strong avoidance of roads extending up to approximately 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%).
    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. hide

  2. Van Moorter B., Rolandsen C. M., Basille M. & Gaillard J.-M. (2016) Movement is the glue connecting home ranges and habitat selection. Journal of Animal Ecology, 85: 21–31. 10.1111/1365-2656.12394 manuscript abstract

    abstract: 1. Animal space use has been studied by focusing either on geographic (e.g., home ranges, species’ distribution) or 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.
    2. Individuals increase their use of a given area by adjusting two key movement components: the duration of their visit, and/or the frequency of re-visits. 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 9 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.
    3. 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.
    4. 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., 2nd-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 to higher selectivity among habitat types (i.e., 3rd-order habitat selection).
    5. 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. hide

  3. Basille M., Fortin D., Dussault C., Bastille-Rousseau G., Ouellet J.-P. & Courtois R. (2015) Plastic response of fearful prey to the spatio-temporal dynamics of predator distribution. Ecology, 96:2622–2631. 10.1890/14-1706.1 manuscript abstract

    abstract: Ecological theory predicts that the intensity of anti-predator responses is dependent upon the spatio-temporal 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 the predator proximity. We collected spatially explicit data on predator and prey simultaneously to investigate acute responses of a threatened forest ungulate, the boreal caribou (Rangifer tarandus), to the spatio-temporal 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 towards 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 anti-predator tactics in response to predator proximity. hide

  4. Chouvenc T., Basille M. & Su N.-Y. (2015) The production of soldiers and the maintenance of caste proportions delay the growth of termite incipient colonies. Insectes Sociaux (International Journal for the Study of Social Arthropods), 62:23–29. 10.1007/s00040-014-0369-z manuscript abstract

    abstract: In a termite colony, the incipient phase is the most critical part of the life of the colony. The quality of the investment in the first offspring by the primary reproductives may determine the rate of success of the colony to survive the first year and its growth rate in the following years. However, termite colonies possess a physiological constraint, forcing the group to maintain a relatively fixed caste proportion. During the development of the incipient colony, there is therefore a conflict for the group on the developmental pathways of larvae into workers or soldiers. On the one hand, the more workers produced, the more work forces would be available to provide for the primary reproductives, the brood and the nest maintenance (overall nurturing capacity). On the other hand, some larvae must develop into soldiers to maintain the caste proportion, reducing the potential number of workers. Using incipient colonies of Coptotermes gestroi (Wasmann) we investigated the cost of maintaining the soldier proportion over the growth of the colony within the first year. Our results showed that an incipient colony maintains a stable soldier proportion regardless of the stress imposed. The resources redirected into the replacement of soldiers not only reduced the total number of workers, it also reduced the overall growth of the colony by delaying the development of the remaining eggs. Our observations suggest that in termite incipient colonies, because of physiological constraints, the maintenance of the soldier proportion overrides the development of the colony. hide

  5. Bucklin D.N., Basille M., Benscoter A.M., Brandt L.A. , Mazzotti F.J., Romañach S.S., Speroterra C. & Watling J.I. (2015) Comparing species distribution models constructed with different subsets of environmental predictors. Diversity and Distributions, 21:23–35. 10.1111/ddi.12247 manuscript abstract

    abstract: Aim: To assess the usefulness of combining climate predictors with additional types of environmental predictors in species distribution models for range-restricted species, using common correlative species distribution modelling approaches.
    Location: Florida, USA.
    Methods: We used five different algorithms to create distribution models for 14 vertebrate species, using seven different predictor sets: two with bioclimate predictors only, and five "combination" models using bioclimate predictors plus "additional" predictors from groups representing: human influence, land cover, extreme weather, or noise (spatially random data). We use a linear mixed-model approach to analyse the effects of predictor set and algorithm on model accuracy, variable importance scores, and spatial predictions.
    Results: Regardless of modelling algorithm, no one predictor set produced significantly more accurate models than all others, though models including human influence predictors were the only ones with significantly higher accuracy than climate-only models. Climate predictors had consistently higher variable importance scores than additional predictors in combination models, though there was variation related to predictor type and algorithm. While spatial predictions varied moderately between predictor sets, discrepancies were significantly greater between modelling algorithms than between predictor sets. Furthermore, there were no differences in the level of agreement between binary "presence–absence" maps and independent species range maps related to the predictor set used.
    Main conclusions: Our results indicate that additional predictors have relatively minor effects on the accuracy of climate-based species distribution models and minor to moderate effects on spatial predictions. We suggest that implementing species distribution models with only climate predictors may provide an effective and efficient approach for initial assessments of environmental suitability. hide

  6. Chouvenc T., Basille M., Li H.-F., Su N.-Y. (2014) Developmental instability in incipient colonies of social insects. PLOS ONE, 9:e113949. 10.1371/journal.pone.0113949 manuscript abstract

    abstract: 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 suggested 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. hide

  7. Latombe G., Parrott L., Basille M. & Fortin D. (2014) Uniting statistical and individual-based approaches for animal movement modelling. PLOS ONE, 9:e99938. 10.1371/journal.pone.0099938 manuscript abstract

    abstract: 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. hide

  8. Basille M., Van Moorter B., Herfindal I., Martin J., Linnell J.D.C., Odden J., Andersen R. & Gaillard J.-M. (2013) Selecting habitat to survive: the impact of road density on survival in a large carnivore. PLOS ONE, 8:e65493. 10.1371/journal.pone.0065493 manuscript abstract

    abstract: 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. hide

  9. Van Moorter B., Visscher D., Herfindal I., Basille M. & Mysterud A. (2013) Inferring behavioural mechanisms in habitat selection studies – getting the null-hypothesis right for functional and familiarity responses. Ecography, 36:323–330. 10.1111/j.1600-0587.2012.07291.x manuscript|supplementary material abstract

    abstract: Recent studies of animal habitat selection are inferring more detail regarding the behavioural mechanisms involved, like functional responses and familiarity effects. Changes in animals' use or selection of a habitat type with changing availability are commonly interpreted as a functional response in habitat preference. Studies of familiarity inferred preference for familiar locations from selection for previously visited locations after accounting for habitat-related preference. We simulated movement paths on discrete landscapes using random walk models with known habitat selection behaviour to assess emergent properties related to habitat selection in the context of functional and familiarity responses. The behavioural interpretation of functional responses relies on the relationship between habitat use and preference. Unfortunately, this relationship is not unique and depends upon the habitat choice mechanism: habitat use can be proportional to preference or proportional to availability (called respectively, hierarchical and simultaneous choice). We found that when the analytical method did not match the choice mechanism, strong functional responses were observed in habitat selection, even though habitat preference was kept constant. Therefore, functional responses need to be discussed in the context of an animal's habitat choice mechanism. In the absence of familiarity-related preference, we found no familiarity effect while accounting for all habitat variables. However, when habitat models were incomplete (e.g. lack of information about resources and habitats in the landscape) – as in all field studies – spurious preference for familiar locations arose. Our study aids the interpretation of behavioural mechanisms in habitat selection studies, but also calls for a more thorough study of the approaches used to infer behavioural mechanisms in habitat selection studies. hide

  10. Basille M., Fortin D., Dussault C., Ouellet J.-P. & Courtois R. (2013) Ecologically based definition of seasons clarifies predator-prey interactions. Ecography, 36: 220–229. 10.1111/j.1600-0587.2011.07367.x manuscript|supplementary material|R package abstract

    abstract: Species interactions within food webs are driven by multiple constraints, including those imposed by seasonal changes in the environment. Ecologically sound definitions of seasons may therefore be a prerequisite for clarifying predator prey interactions. Most studies define biological seasons based on fixed schedules or on temporal changes in a single movement measurement. We used a novel clustering approach based on homogeneous space-use patterns of GPS-collared animals to reveal 7 biological seasons for caribou Rangifer tarandus caribou, and 5 for both moose Alces alces and grey wolves Canis lupus interacting in a boreal ecosystem. Subsequent evaluation of niche overlap showed that, as predicted, wolves had a stronger spatio-temporal connection with moose, its main prey, than with caribou. Movement constraints and limiting resource distributions similarly affected all species in some instances, but also caused temporal changes in the extent of niche overlap between wolves and its two prey. The risk that caribou faced was not only linked to the niche overlap with wolves, but also to the extent of wolf-moose niche overlap during the same period. Food-web properties emerged from the analysis, with temporal changes in relative niche overlap reflecting the strength of trophic interactions during the year. Our study demonstrates how the study of trophic interactions can benefit from comprehensive definitions of biological seasons. hide

  11. Rolland J., Basille M., Marboutin É. & Gaillard J.-M. (2011) Comparing profile methods and site-occupancy modeling for the study of occurrence of an elusive species. European Journal of Wildlife Research, 57:1115–1118. 10.1007/s10344-011-0549-3 manuscript abstract

    abstract: Based on 1,053 signs of presence collected between 2002 and 2006 by a network of well-trained observers, we modelled the occurrence of the Eurasian lynx (Lynx lynx) in France using two methods. The Mahalanobis distance factor analysis (MADIFA) provided a measure of habitat suitability based on environmental covariates, and site-occupancy modelling provided estimates of both presence and detection probabilities over time. Environmental covariates included in the site-occupancy modelling markedly improved the fit of the lynx presence model. We found a strong correlation between habitat suitability scores estimated from the MADIFA and probabilities of presence estimated from the site-occupancy modelling, indicating that both methods provided a convergent assessment of lynx potential occurrence. hide

  12. Martin, J., Basille M., Kindberg J., Van Moorter B., Allainé D. & Swenson J.E. (2010) Coping with human disturbance: Spatial and temporal tactics of brown bear. Canadian Journal of Zoology, 88:875–883. 10.1139/Z10-053 manuscript abstract

    abstract: In human-dominated landscapes, species with large spatial requirements, such as large carnivores, have to deal with human infrastructure and activities within their home ranges. This is the case for the brown bear (Ursus arctos L., 1758) in Scandinavia, which is colonizing more human-dominated landscapes, leading inevitably to an overlap between their home ranges and anthropogenic structures. In this study, we investigated fine-scale habitat selection by brown bears to examine how they deal with this potential disturbance. Using Global Positioning System (GPS) data, we studied (i) habitat selection of female brown bears within their home range and (ii) the influence of diurnal variation in human disturbance on fine-scale habitat use. As expected, females selected habitats within their home range that provided abundant food resources and minimized human-caused disturbance. In addition, our temporal analysis of habitat selection revealed an avoidance of disturbed areas and a selection of slopes by bears during periods of highest human activities, i.e., during daylight hours. We clearly demonstrate the importance of considering the fluctuations in human activity when studying habitat selection, especially at fine spatial scales. Failing to do so may considerably reduce the power to detect important fine-scale habitat-selection behaviors. hide

  13. Gaillard J.-M., Hebblewhite M., Loison A., Fuller M., Powell R., Basille M. & Van Moorter B. (2010) Habitat-Performance Relationships: Finding the right metric at a given spatial scale. Philosophical Transactions of the Royal Society B., 365:2255–2265. 10.1098/rstb.2010.0085 manuscript abstract

    abstract: 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. hide

  14. Melis C., Basille M., Herfindal I., Linnell J.D.C., Odden J., Gaillard J.-M., Høgda K. & Andersen R. (2010) Roe deer population growth and lynx predation along a gradient of environmental productivity and climate in Norway. Ecoscience, 17:166–174. 10.2980/17-2-3314 manuscript abstract

    abstract: The extent to which large carnivores compete with hunters for harvestable populations of wild ungulates is a topic of widespread controversy in many areas of the world where carnivore populations are recovering or are reintroduced. Theory predicts that predation impacts should vary with prey density and environmental conditions. To test this prediction, we analyzed trends in an index of population abundance of roe deer (Capreolus capreolus) over 9 y in 144 Norwegian municipalities. The municipalities span a wide range of landscapes and climatic conditions and were associated with a varying degree of Eurasian lynx (Lynx lynx) presence. There was a wide variation in trends of roe deer abundance (estimated long-term average λ ranging from 0.69 to 1.23) among municipalities. Roe deer population growth rates were lower in the municipalities with lynx and harsh climatic conditions than in municipalities with mild climatic conditions and/or without lynx. Thus, lynx presence appears to be having a negative impact on roe deer populations; this was especially evident in areas with unfavourable environmental conditions. Our finding that estimated long-term average values of λ were less than 1 in many municipalities indicates that roe deer populations in Norway may not be able to sustain current combined mortality from hunters and lynx, especially in marginal areas. hide

  15. Basille M., Herfindal I., Santin-Janin H., Linnell J.D.C., Odden J., Andersen R., Høgda K. A., & Gaillard J.-M. (2009) What shapes Eurasian lynx distribution in human dominated landscapes: selecting prey or avoiding people? Ecography, 32:683–691. 10.1111/j.1600-0587.2009.05712.x manuscript abstract

    abstract: In the multi-use landscape of southern Norway, the distribution of lynx is likely to be determined both by the abundance of their favoured prey – the roe deer – and the risk associated with the presence of humans because most lynx mortalities are caused by humans (recreational harvest, poaching, vehicle collisions). We described the distribution of the reproductive portion of the lynx population based on snow-track observations of females with dependent kittens collected over 10 yr (1997–2006) in southern Norway. We used the ecological-niche factor analysis to examine how lynx distribution was influenced by roe deer, human activity, habitat type, environmental productivity and elevation. Our first prediction that lynx should be found in areas of relatively high roe deer abundance was supported. However, our second prediction that lynx should avoid human activity was rejected, and lynx instead occupied areas more disturbed in average than those available (with the exception of the most densely occupied areas). Lynx, however, avoided the most disturbed areas and our third prediction of a trade-off between abundance of prey and avoidance of human activity was supported. On the one hand, roe deer in the most disturbed areas benefit to a large extent from current human land use practices, potentially allowing them to escape predation from lynx. On the other hand, the situation is not so favourable for the predators who are restricted in competition refuges with medium to low prey densities. The consequence is that lynx conservation will have to be achieved in a human modifed environment where the potential for a range of conflicts and high human-caused mortality will remain a constant threat. hide

  16. Saint-Andrieux C., Bonenfant C., Toïgo C., Basille M. & Klein F. (2009) Factors affecting beech bark stripping by red deer (Cervus elaphus) in a mixed forest. Wildlife Biology, 15:187–196. 10.2981/07-100 manuscript abstract

    abstract: Bark stripping by large herbivores is widespread, yet poorly understood. Our study was carried out in a 2000-ha area situated in the Vosges Mountains, France, where beech Fagus sylvatica bark is heavily bark stripped by red deer Cervus elaphus. We tested whether the seasonal variation in the frequency of beech bark stripping by red deer was correlated with bark nutritive value or bark mechanical properties (using an index of bark detachability). We also evaluated whether red deer selected beech trees based on the chemical composition of their bark (e.g. carbohydrates and minerals). Bark-stripped trees had slightly higher carbohydrate contents than non-stripped trees, but this difference resulted from a physiological reaction of the tree to bark stripping. Bark composition was similar between stripped and non-stripped trees spring and summer, but was easier to detach during these periods than during autumn and winter. Therefore, beech bark stripping by red deer in the Vosges Mountains does not appear to be driven by nutritional needs, but it may help deer in improving digestion efficiency. hide

  17. Calenge C. & Basille M. (2008) A general framework for the statistical exploration of the ecological niche. Journal of Theoretical Biology, 252:674–685. 10.1016/j.jtbi.2008.02.036 manuscript abstract

    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. hide

  18. Calenge C., Darmon G., Basille M., Loison A. & Jullien J.-M. (2008) The factorial decomposition of the Mahalanobis distances in niche analysis. Ecology, 89:555–566. 10.1890/06-1750.1 manuscript abstract

    abstract: The Mahalanobis distances have been introduced in habitat selection studies for the estimation of environmental suitability maps (ESMs). The pixels of raster maps of a given area correspond to points in the multidimensional space defined by the mapped environmental variables (ecological space). The Mahalanobis distances measure the distances in this space between these points and the mean of the ecological niche (i.e., the hypothesized optimum for the species) regarding the structure of the niche. The map of these distances over the area of interest is an estimated ESM. Several authors recently noted that the use of a single optimum for the niche of a species may lead to biased predictions of animal occurrence. They proposed to use instead a minimum set of basic habitat requirements, found by partitioning the Mahalanobis distances into a restricted set of biologically meaningful axes. However, the statistical approach they proposed does not take into account the environmental conditions on the area where the niche was sampled (i.e., the environmental availability), and we show that including this availability is necessary. We used their approach as a basis to develop a new exploratory tool, the Mahalanobis distance factor analysis (MADIFA), which performs an additive partitioning of the Mahalanobis distances taking into account this availability. The basic habitat requirements of a species can be derived from the axes of the MADIFA. This method can also be used to compute ESMs using only this small number of basic requirements, therefore including only the biologically relevant information. We also prove that the MADIFA is complementary to the commonly used ecological-niche factor analysis (ENFA). We used the MADIFA method to analyze the niche of the chamois Rupicapra rupicapra in a mountainous area. This method adds to the existing set of tools for the description of the niche. hide

  19. Basille M., Calenge C., Marboutin É., Andersen R. & Gaillard J.-M. (2008) Assessing habitat selection using multivariate statistics: Some refinements of the Ecological-Niche Factor Analysis. Ecological Modelling, 211:233–240. 10.1016/j.ecolmodel.2007.09.006 manuscript abstract

    abstract: We propose here some refinements of the ecological-niche factor analysis (ENFA) to describe precisely one organism's habitat selection. The ENFA is based on the concept of the ecological niche, and provides a measure of the realised niche within the available space from the computation of two parameters, the marginality and the specialization. By measuring the departure of the ecological niche from the average available habitat, the marginality identifies the preference of the individual, population, or species for specific conditions of the environment among the whole set of possibilities. The specialization appears as a consequence of the narrowness of the niche on some environmental variables. The ENFA is a factorial analysis that extracts one axis of marginality and several axes of specialization. We present here the use of biplots (i.e., the projection of both the pixels of the map and the environmental variables in the subspace extracted by the ENFA) as a way to identify the key-variables for management, assessing which habitat features are of prime importance and should be preserved or reinforced. With the help of this tool, we are now able to describe much more precisely the habitat selection of the organism under focus. In our application to the lynx in the Vosges mountains, based on sightings as well as other indices of lynx presence, we thus underlined a strong avoidance of agricultural areas by the lynx. We also highlighted the relative indifference of the lynx to the proximity of artificial areas and at the opposite, the sensitivity to the proximity of highways. The ENFA provides a suitable way to measure habitat use/selection under a large range of ecological contexts and should be used to define precisely the ecological niche and therefore identify the characteristics searched for by the organism under study. hide

Book chapters

  1. Basille M., Urbano F. & Conway J. (2014) A Step Further in the Integration of Data Management and Analysis: Pl/R. In Spatial Database for GPS Wildlife Tracking Data (eds Urbano F. & Cagnacci F.), Springer International Publishing, Switzerland, pp. 213–229. 10.1007/978-3-319-03743-1_11 manuscript abstract

    Abstract: This chapter introduces the Pl/R extension, a very powerful alternative to integrate the features offered by R in the database in a gapless workflow. Pl/R is a loadable procedural language that allows the use of the R engine and libraries directly inside the database, thus embedding R scripts into SQL statements and database functions and triggers. Among many advantages, Pl/R avoids unnecessary data replication, allows the use of a single SQL interface for complex scripts involving R queries and offers a tight integration of data analysis and management processes into the database. In this chapter, you will have a basic overview of the potential of Pl/R for the study of GPS locations. You will be introduced to the use of Pl/R, starting with exercises involving simple calculations in R (logarithms, median and quantiles), followed by more elaborated exercises designed to compute the daylight times of a given location at a given date, or to compute complex home range methods. hide

  2. Urbano F., Basille M. & Racine P. (2014) Exploring Tracking Data: Representations, Methods, and Tools in a Spatial DB. In Spatial Database for GPS Wildlife Tracking Data (eds Urbano F. & Cagnacci F.), Springer International Publishing, Switzerland, pp. 139–180. 10.1007/978-3-319-03743-1_9 manuscript abstract

    Abstract: The objects of movement ecology studies are animals whose movements are usually sampled at more-or-less regular intervals. This spatiotemporal sequence of locations is the basic, measured information that is stored in the database. Starting from this data set, animal movements can be analysed (and visualised) using a large set of different methods and approaches. These include (but are not limited to) trajectories, raster surfaces of probability density, points, (home range) polygons and tabular statistics. Each of these methods is a different representation of the original data set that takes into account specific aspects of the animals’ movement. The database must be able to support these multiple representations of tracking data. In this chapter, a wide set of methods for implementing many GPS tracking data representations into a spatial database (i.e. with SQL code and database functions) are introduced. The code presented is based on the database created in Chaps. 2, 3, 4, 5, 6, 7 and 8. hide

  3. Urbano F., Basille M. & Cagnacci F. (2014) Data Quality: Detection and Management of Outliers. In Spatial Database for GPS Wildlife Tracking Data (eds Urbano F. & Cagnacci F.), Springer International Publishing, Switzerland, pp. 115–137. 10.1007/978-3-319-03743-1_8 manuscript abstract

    Abstract: Tracking data can potentially be affected by a large set of errors in different steps of data acquisition and processing. Erroneous data can heavily affect analysis, leading to biased inference and misleading wildlife management/conservation suggestions. Data quality assessment is therefore a key step in data management. In this chapter, we especially deal with biased locations, or ‘outliers’. While in some cases incorrect data are evident, in many situations, it is not possible to clearly identify locations as outliers because although they are suspicious (e.g. long distances covered by animals in a short time or repeated extreme values), they might still be correct, leaving a margin of uncertainty. In this chapter, different potential errors are identified and a general approach to managing outliers is proposed that tags records rather than deleting them. According to this approach, practical methods to find and mark errors are illustrated on the database created in Chaps. 2, 3, 4, 5, 6 and 7. hide

  4. Basille M., Urbano F., Racine P., Capecchi V. & Cagnacci F., (2014) Tracking Animals in a Dynamic Environment: Remote Sensing Image Time Series. In Spatial Database for GPS Wildlife Tracking Data (eds Urbano F. & Cagnacci F.), Springer International Publishing, Switzerland, pp. 95–114. 10.1007/978-3-319-03743-1_7 manuscript abstract

    Abstract: This chapter looks into the spatiotemporal dimension of both animal tracking data sets and the dynamic environmental data that can be associated with them. Typically, these geographic layers derive from remote sensing measurements, commonly those collected by sensors deployed on earth-orbiting satellites, which can be updated on a monthly, weekly or even daily basis. The modelling potential for integrating these two levels of ecological complexity (animal movement and environmental variability) is huge and comes from the possibility to investigate processes as they build up, i.e. in a full dynamic framework. This chapter’s exercise will describe how to integrate dynamic environmental data in the spatial database and join to animal locations one of the most used indices for ecological productivity and phenology, the normalised difference vegetation index (NDVI) derived from MODIS. The exercise is based on the database built so far in Chaps. 2, 3, 4, 5 and 6. hide

  5. Urbano F., Basille M. & Racine P. (2014) From Points to Habitat: Relating Environmental Information to GPS Positions. In Spatial Database for GPS Wildlife Tracking Data (eds Urbano F. & Cagnacci F.), Springer International Publishing, Switzerland, pp. 75–93. 10.1007/978-3-319-03743-1_6 manuscript abstract

    Abstract: Animals move in and interact with complex environments that can be characterised by a set of spatial layers containing environmental data. Spatial databases can manage these different data sets in a unified framework, defining spatial and non-spatial relationships that simplify the analysis of the interaction between animals and their habitat. A large set of analyses can be performed directly in the database with no need for dedicated GIS or statistical software. Such an approach moves the information content managed in the database from a ‘geographical space’ to an ‘animal’s ecological space’. This more comprehensive model of the animals’ movement ecology reduces the distance between physical reality and the way data are structured in the database, filling the semantic gap between the scientist’s view of biological systems and its implementation in the information system. This chapter shows how vector and raster layers can be included in the database and how you can handle them using (spatial) SQL. The database built so far in Chaps. 2, 3, 4 and 5 is extended with environmental ancillary data sets and with an automated procedure to intersect these layers with GPS positions. hide

  6. Urbano F. & Basille M. (2014) Spatial is Not Special: Managing Tracking Data in a Spatial Database. In Spatial Database for GPS Wildlife Tracking Data (eds Urbano F. & Cagnacci F.), Springer International Publishing, Switzerland, pp. 53–73. 10.1007/978-3-319-03743-1_5 manuscript abstract

    Abstract: A wildlife tracking data management system must include the capability to explicitly deal with the spatial properties of movement data. GPS tracking data are sets of spatiotemporal objects (locations), and the spatial component must be properly managed. You will now extend the database built in Chaps. 2, 3 and 4, adding spatial functionalities through the PostgreSQL spatial extension called PostGIS. PostGIS introduces spatial data types (both vector and raster) and a large set of SQL spatial functions and tools, including spatial indexes. This possibility essentially allows you to build a GIS using the capabilities of relational databases. In this chapter, you will start to familiarise yourself with spatial SQL and implement a system that automatically transforms the GPS coordinates generated by GPS sensors from a pair of numbers into spatial objects. hide

  7. Dettki H., Urbano F., Basille M. & Cagnacci F. (2014). Wildlife-Tracking Data Management: Chances Come from Difficulties. In Spatial Database for GPS Wildlife Tracking Data (eds Urbano F. & Cagnacci F.), Springer International Publishing, Switzerland, pp. 1–7. 10.1007/978-3-319-03743-1_1 manuscript abstract

    (none) In recent years, new wildlife tracking and telemetry technologies have become available, leading to substantial growth in the volume of wildlife tracking data. In the future, one can expect an almost exponential increase in collected data as new sensors are integrated into current tracking systems. A crucial limitation for efficient use of telemetry data is a lack of infrastructure to collect, store and efficiently share the information. Large data sets generated by wildlife tracking equipment pose a number of challenges: to cope with this amount of data, a specific data management approach is needed, one designed to deal with data scalability, automatic data acquisition, long-term storage, efficient data retrieval, management of spatial and temporal information, multi-user support and data sharing and dissemination. The state-of-the-art technology to meet these challenges are relational database management systems (DBMSs), with their dedicated spatial extension. DBMSs are efficient, industry-standard tools for storage, fast retrieval and manipulation of large data sets, as well as data dissemination to client programs or Web interfaces. In the future, we expect the development of tools able to deal at the same time with both spatial and temporal dimensions of animal movement data, such as spatiotemporal databases. hide

  8. Cagnacci F., Basille M., Berger A., Cain Davidson S., Dettki H., van Moorter B. & Urbano F. (2014) The Long and Winding Road to Movement Ecology: Let's put Things in Order First. In Spatial Database for GPS Wildlife Tracking Data (eds Urbano F. & Cagnacci F.), Springer International Publishing, Switzerland, pp. XVII–XXIII. manuscript

  9. Martin J., Tolon V., Van Moorter B., Basille M. & Calenge C. (2009) On the use of telemetry in habitat selection studies. In Telemetry: Research, Technology and Applications (eds Barculo D. & Daniels J.), Nova Science Publishers Inc., pp. 37–55 manuscript abstract

    Abstract: Understanding the relationships between organisms and their habitat is a central question in ecology. The study of habitat selection often refers to the static description of the pattern resulting from the selection process. However the very nature of this habitat selection process is dynamic, as it relies on individual movements, which are affected by both internal components (i.e. related to the animal itself, such as its behavior; foraging, resting, etc.) and external components (i.e. related to the composition of the environment). Coupling habitat selection and movement analyses should thus provide new insights into the proximal mechanisms and evolutionary causes of animals' space use. To achieve this, the introduction of GPS technology in the early 1990s showed great promise, as it facilitates tracking of animals with high fix frequency over long time periods. From a statistical point of view, this led to an increased temporal autocorrelation in the positions of successive locations. Whereas classic approaches of habitat selection often relied on the assumption of statistical independence between relocations, the development of newer methods has made possible the use of autocorrelation for more dynamic approaches. As several statistical tools are now available for researchers, autocorrelation can be incorporated successfully into the analysis, instead of being removed or even ignored. We emphasize the need to integrate individual behavioral mechanisms in habitat selection studies. The use of GPS technology in wildlife management issues is, however, often motivated by its technological advantage to produce large amounts of data, rather than biological questions. We warn users of GPS devices about the statistical and conceptual changes induced by this technology used for studying habitat selection. We encourage a solid biological reflection about the ecological characteristics of studied species and spatial and temporal scales considered, before deciding on which sampling protocol and which telemetry technology to use in accordance with the biological question of interest. hide

Popular articles & reports

  1. Basille M., Courtois R., Bastille-Rousseau G., Courbin N., Faille G., Dussault C., Ouellet J.-P. & Fortin D. (2010) Direct and indirect effects of boreal forest management on woodland caribou in Quebec (translated from French). The Canadian Naturalist (Le Naturaliste Canadien), 135:46–52. manuscript
  2. Melis C., Holmern T., Basille M., Herfindal I., Odden J. & Linnell J.D.C. (2009) From the fjord to the mountain: how the Scandinavian tiger affects roe deer populations? (translated from Norwegian). Wild deer (Hjorteviltet), 2009:20–22. manuscript
  3. Basille M., Calenge C., Marboutin É., Andersen R. & Gaillard J.-M. (2007) Characterization of habitat from presence data: the case of lynx in the Vosges (translated from French). ONCFS, scientific report, 2007:20–24. manuscript
  4. Bunnefeld N., Börger L., Nilsen E. B., Basille M., Hall R., Ezard T.H., Trierweiler C., Minderman J., Mangel M., Gaillard J.-M., Milner-Gulland E.J. & attendees of the Populations Under Pressure symposium (2007) Coming out of the ivory tower: how to ensure that ecological modelling research remains practical and applied. Bulletin of the British Ecological Society, 38:64–66. manuscript
  5. Marboutin É., Laurent A., Regazzi C., Léger F., Moisson P., Lambrech M., Balestra L., Henri J., Basille M., Touzain L. & Michallet D. (2004) Some insight into the new tools to monitor the French lynx population (translated from French). ONCFS, scientific report, 2004:18–21. manuscript

Oral communications

Invited seminars and workshops

  1. Cagnacci F., Urbano F., Basille M., Berger A., Campbell H., Giles T., Davidson S., Galea A., & Rocchini D. (2015) Next Generation Data Management in Movement Ecology. Summer School at the Fondazione Edmund Mach, San Michele all'Adige (Italy). material
  2. Basille M. (2015) Ecology on the Move: Using Wood Stork Movement to Enhance Conservation Efforts. Seminar for UNESCO-IHE, Fort Lauderdale (Florida, USA). presentation
  3. Basille M. (2014) Ecology on the Move: Using Wood Stork Movement to Enhance Conservation Efforts. Seminar at the University of Florida, Gainesville, then Fort Lauderdale (USA). presentation|transcript
  4. Basille M. (2014) Ecology on the move: New opportunities from modern tracking data. Seminar at the USGS Southeast Ecological Science Center, Gainesville (USA). presentation|video
  5. Basille M. (2012) Meanwhile in the taiga... Can large mammals deal with humans? Introductory seminar at University of Florida, Fort Lauderdale (USA). presentation
  6. Basille M. (2012) Niche analyses in habitat selection. Invited conference for the workshop "Stuck in motion? Reconnecting questions and tools in movement ecology", Evenstad (Norway). presentation
  7. Basille M., Fortin D., Dussault C., Ouellet J.-P., & Courtois R. (2012) Caribou under pressure: Spatio-temporal variation of caribou behaviour facing human disturbance and predation risk (translated from French). Invited seminar at the Laboratoire de Biométrie et Biologie Évolutive, Lyon (France). presentation
  8. Basille M., Fortin D., Dussault C., Ouellet J.-P., & Courtois R. (2011) From human to caribou: Spatio-temporal variations of forest-dwelling caribou behaviours in a managed landscape. Invited seminar for the CFR postdoc festival, Québec (Canada). presentation
  9. Basille M. et al. (2007) Characterization of the habitat of the lynx in southern Norway–Theory, Methodology & Application. Invited seminar at the Institute of Zoology, London (United Kingdom). presentation
  10. Basille M. & Calenge C., (2004) Ecological-niche multivariate analyses (translated from French). Statistical seminar at the ONCFS, Cléry Saint André (France). presentation

International congresses

  1. Basille M., Borkhataria B., Benscoter A., Brandt L.A., Bucklin D., Mazzotti F.J., Romañach S.S., Speroterra C., & Watling J.I. (2015) Movement Ecology of Wood Stork Migration. Ecological Society of America: 2015 Meeting, Baltimore (Maryland, USA). presentation abstract

    abstract:
    Background/Question/Methods
    Movement is the primary behavioral adaptation to dynamic environments. Large-scale movements, and migration in particular, allow species to alter their distribution and range in response to seasonal environmental variation (e.g. photoperiod, temperature, rainfall). To understand the capacity of species to adapt to global change, it is thus essential to accurately determine migration routes and assess individual variation in migration performance (timing and location). We studied movement of wood storks (Mycteria americana), a threatened species in the Southeastern U.S., using GPS telemetry over 7 years. Wood storks are facultative migrants, with migration routes sometimes exceeding 1,000 km, ranging from Mississippi and North Carolina in the summer to South Florida in winter. We first trained a classification algorithm on a few individuals (representing 5 % of the whole data set) with typical movement trajectories throughout the year, to be able to predict movement modes (foraging, commuting, traveling and migrating) for the whole data set. We then used line density methods to identify migratory corridors. Finally, we investigated temporal and geographic variation of individual migration routes with respect to environmental conditions using linear regressions.
    Results/Conclusions
    Movement modes were classified correctly ≥ 90 % of the time, and migration accounted for less than 1 % of a total of nearly 500,000 wood stork locations. Of 56 adults monitored over at least one complete migration season, 33 (58 %) migrated at least once. Two main migration corridors were identified, along the eastern coastline of Florida during spring (northward migration) and western coastline during fall (southward migration). Although individual one-way migration typically lasts between 5 to 15 days, we highlighted a large temporal variation in the population, both within and between years; spring migration generally occurred during a four month period (February 25–June 20), and fall migration during a two month period (September 20–November 20). Individual adults, however, tended to be relatively consistent over the years, both in space (using the same route) and time (migrating at the same period), regardless of climatic conditions. In conclusion, we identified a minor portion of the data with high ecological importance, which are migratory movements. Wood storks migration revealed high temporal plasticity that may give room for adaptation, though constrained by low geographic variation.
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  2. Basille M., Fortin D., Dussault C., Ouellet J.-P., & Courtois R. (2010) Space use seasonality in a multi-predator and multi-prey system. Society for Conservation Biology: 2010 Congress, Edmonton (Alberta, Canada). presentation
  3. Basille M., Fortin D., Dussault C., Ouellet J.-P., & Courtois R. (2010) Space use seasonality in a multi-predator and multi-prey system. Canadian Society for Ecology and Evolution: 2010 Congress, Quebec City (Quebec, Canada). presentation
  4. Basille M., Herfindal I., Linnell J.D.C., Andersen R., Høgda K. A., & Gaillard J.-M., (2007) Eurasian lynx distribution in human dominated landscapes: selecting prey or avoiding people? 5th European Congress of Mammalogy, Sienna (Italy). presentation
  5. Basille M., Calenge C., Herfindal I., Linnell J.D.C., Andersen R. & Gaillard J.-M. (2007) Lynx and people: a possible coexistence? 8th European Roe deer Meeting, Velenje (Slovenia). presentation

Regional and local congresses

  1. Basille M., Benscoter A., Borkhataria B., Bucklin D., Brandt L.A., Mazzotti F.J., Romañach S.S., Speroterra C., & Watling J.I. (2015) Using Wood Stork Movement to Enhance Conservation Efforts. GEER 2015, Coral Springs (Florida, USA). presentation|presentation|transcript abstract

    abstract:
    Wood storks are iconic wading birds found in South Florida during wintertime. The distinct breeding population occurring in Florida and its neighboring states is currently classified as threatened under the Endangered Species Act, and as such, is of conservation concern. Wood storks are partially migratory, and individuals can migrate distances longer than 1000 km from South Florida in winter up to Mississippi and North Carolina during summertime. The objective of this project was to investigate detailed movement dynamics of wood stork, monitored using fine-scale GPS telemetry, and relate them to landscape features, such as urbanization and climate, to understand wood stork migrations at multiple spatio-temporal scales.
    At the individual level, we identified movement modes within individual GPS trajectories, to be able to disentangle between potential behaviors. We trained a classification algorithm to recognize four typical movement modes, including migration, and be able to predict the movement mode of any movement step. The algorithm was able to classify movement modes correctly 90 % of the time, and identified migration steps as less than 1 % of movements. This small portion of movements is however critical, as it is responsible for the rapid switch of wood storks from Northern summer areas to Southern nesting ranges.
    We then used migration data only to understand what shapes migration, and the environmental factors that affect it. We identified two main migration routes along the Eastern and Western coastlines of Florida, with the Eastern coastline being strongly used during the spring migration going northwards, while the Western coastline is more strongly used during the fall migration going southwards. We thus evaluated habitat selection along each migration path, which revealed that wood storks clearly selected for lower temperatures along their northwards migration in spring, while they preferred higher temperatures along their southwards migration in fall. In both seasons, wood storks strongly preferred wetlands, and cultivated areas, while they strongly avoided developed areas.
    By decomposing the mechanisms of movement during wood stork migration, we were able to identify migration corridors, and suitable conditions along migration paths. This work provides relevant information for wood stork conservation across the landscape, highlighting how current land use and climatic conditions influence wood stork movements, as a basis to integrate future climate projections and urbanization into a comprehensive conservation plan. hide

  2. Basille M., Fortin D., Dussault C., Ouellet J.-P., & Courtois R. (2011) Flee or hide when you're hunted? How woodland caribou evaluate predation risk. (translated from French). 5th annual congress of the CFR 2011, Quebec City (Quebec, Canada). presentation
  3. Basille M., Fortin D., Dussault C., Ouellet J.-P., & Courtois R. (2011) Flee or hide when you're hunted? How woodland caribou evaluate predation risk. (translated from French). 2011 congress of the Sylviculture and Wildlife Research Chair CRSNG-Laval University, Baie-Comeau (Quebec, Canada). intro|presentation
  4. Basille M., Fortin D., Dussault C., Ouellet J.-P., & Courtois R. (2010) Flee or hide when you're hunted? How woodland caribou evaluate predation risk. (translated from French). Congress "Woodland caribou: biodiversity and sustainable development stakes", Saguenay (Quebec, Canada). presentation
  5. Basille M. (2010) Space use seasonality in a complex predator-prey system (translated from French). Space use2010 congress of the Sylviculture and Wildlife Research Chair CRSNG-Laval University, Baie-Comeau (Quebec, Canada). presentation
  6. Basille M., Calenge C., Herfindal I., Linnell J.D.C., Andersen R. & Gaillard J.-M. (2007) The Niche of the Lynx in Norway. Symposium "Populations under pressure", London (United Kingdom). presentation
  7. Basille M., Linnell J.D.C., Andersen R. & Gaillard J.-M. (2006) Habitat Selection by the roe deer in Norway. Workshop France–Norway–United Kingdom, Doucy en Bauges (France). presentation
  8. Basille M., Marboutin E. & Gaillard J.-M. (2006) Habitat Selection by the Lynx in the Vosges Massif–A comparative study. Symposium "Fragmentation of habitats and lynx populations in Europe", Fischbach (Germany). presentation
  9. Gaillard J.-M., Loison A., & Basille M. (2004) Understanding population dynamics of ungulates: What do we know and what should we do? Workshop "Ungulates and large predators in Europe", Białowieża (Poland). presentation
[last update: 2016/01/29]