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Assistant Professor in Landscape Ecology at the University of Florida’s Fort Lauderdale Research and Education Center (Fort Lauderdale, FL, USA), since May 2015.
University of Florida
Ft Lauderdale Research and Education Center
3205 College Avenue
Fort Lauderdale, FL 33314
Phone : +1.954.577.6314
E-mail: [email protected]
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.
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
|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.|
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
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.
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).
© 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).
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.
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.
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).
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.
I acquired a limited field experience throughout the various projects in which I was involved:
- Setting up and monitoring snow probes (1 week in 2010, Quebec, Canada);
- Collecting roe deer, moose and hare feces (2 weeks in 2007, Akershus county, Norway);
- Monitoring lynx and red fox using VHF telemetry (6 weeks in 2005, Akershus county, Norway);
- Captures and behavioural observations of Alpine marmots (1 week in 2004, La Grande Sassière, France).
- Conducting a wolf howling program throughout the Alps with the ONCFS (6 weeks in 2003, France);
- Behavioural observations of feral cats (1 month in 2003, Lyon, France).
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.
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).
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.
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, Movement Ecology, 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: 45 reviews.
See my peer-review record on Publons.