François Gillet

Bio: François Gillet is an academic researcher from Centre national de la recherche scientifique. The author has contributed to research in topics: Vegetation & Species richness. The author has an hindex of 33, co-authored 111 publications receiving 5813 citations. Previous affiliations of François Gillet include University of Neuchâtel & University of Franche-Comté.

Numerical Ecology with R

Abstract: Numerical Ecology with R provides a long-awaited bridge between a textbook in Numerical Ecology and the implementation of this discipline in the R language. After short theoretical overviews, the authors accompany the users through the exploration of the methods by means of applied and extensively commented examples. Users are invited to use this book as a teaching companion at the computer. The travel starts with exploratory approaches, proceeds with the construction of association matrices, then addresses three families of methods: clustering, unconstrained and canonical ordination, and spatial analysis. All the necessary data files, the scripts used in the chapters, as well as the extra R functions and packages written by the authors, can be downloaded from a web page accessible through the Springer web site(http://adn.biol.umontreal.ca/ numericalecology/numecolR/). This book is aimed at professional researchers, practitioners, graduate students and teachers in ecology, environmental science and engineering, and in related fields such as oceanography, molecular ecology, agriculture and soil science, who already have a background in general and multivariate statistics and wish to apply this knowledge to their data using the R language, as well as people willing to accompany their disciplinary learning with practical applications. People from other fields (e.g. geology, geography, paleoecology, phylogenetics, anthropology, the social and education sciences, etc.) may also benefit from the materials presented in this book. The three authors teach numerical ecology, both theoretical and practical, to a wide array of audiences, in regular courses in their Universities and in short courses given around the world. Daniel Borcard is lecturer of Biostatistics and Ecology and researcher in Numerical Ecology at Universite de Montreal, Quebec, Canada. Francois Gillet is professor of Community Ecology and Ecological Modelling at Universite de Franche-Comte, Besancon, France. Pierre Legendre is professor of Quantitative Biology and Ecology at Universite de Montreal, Fellow of the Royal Society of Canada, and ISI Highly Cited Researcher in Ecology/Environment.

Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns

Abstract: Technical developments in molecular biology have found extensive applications in the field of microbial ecology. Among these techniques, fingerprinting methods such as denaturing gel electrophoresis (DGE, including the three options: DGGE, TGGE and TTGE) has been applied to environmental samples over this last decade. Microbial ecologists took advantage of this technique, originally developed for the detection of single mutations, for the analysis of whole bacterial communities. However, until recently, the results of these high quality fingerprinting patterns were restricted to a visual interpretation, neglecting the analytical potential of the method in terms of statistical significance and ecological interpretation. A brief recall is presented here about the principles and limitations of DGE fingerprinting analysis, with an emphasis on the need of standardization of the whole analytical process. The main content focuses on statistical strategies for analysing the gel patterns, from single band examination to the analysis of whole fingerprinting profiles. Applying statistical method make the DGE fingerprinting technique a promising tool. Numerous samples can be analysed simultaneously, permitting the monitoring of microbial communities or simply bacterial groups for which occurrence and relative frequency are affected by any environmental parameter. As previously applied in the fields of plant and animal ecology, the use of statistics provides a significant advantage for the non-ambiguous interpretation of the spatial and temporal functioning of microbial communities.

A comparative framework for broad‐scale plot‐based vegetation classification

Abstract: Aims: Classification of vegetation is an essential tool to describe, understand, predict and manage biodiversity. Given the multiplicity of approaches to classify vegetation, it is important to develop international consensus around a set of general guidelines and purpose-specific standard protocols. Before these goals can be achieved, however, it is necessary to identify and understand the different choices that are made during the process of classifying vegetation. This paper presents a framework to facilitate comparisons between broad-scale plot-based classification approaches. -- Results: Our framework is based on the distinction of four structural elements (plot record, vegetation type, consistent classification section and classification system) and two procedural elements (classification protocol and classification approach). For each element we describe essential properties that can be used for comparisons. We also review alternative choices regarding critical decisions of classification approaches; with a special focus on the procedures used to define vegetation types from plot records. We illustrate our comparative framework by applying it to different broad-scale classification approaches. -- Conclusions: Our framework will be useful for understanding and comparing plot-based vegetation classification approaches, as well as for integrating classification systems and their sections.

The Theory of Island Biogeography

Abstract: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201

Forest disturbances under climate change

Abstract: Forest disturbances are sensitive to climate. However, our understanding of disturbance dynamics in response to climatic changes remains incomplete, particularly regarding large-scale patterns, interaction effects and dampening feedbacks. Here we provide a global synthesis of climate change effects on important abiotic (fire, drought, wind, snow and ice) and biotic (insects and pathogens) disturbance agents. Warmer and drier conditions particularly facilitate fire, drought and insect disturbances, while warmer and wetter conditions increase disturbances from wind and pathogens. Widespread interactions between agents are likely to amplify disturbances, while indirect climate effects such as vegetation changes can dampen long-term disturbance sensitivities to climate. Future changes in disturbance are likely to be most pronounced in coniferous forests and the boreal biome. We conclude that both ecosystems and society should be prepared for an increasingly disturbed future of forests.

Defining the Anthropocene

Abstract: Time is divided by geologists according to marked shifts in Earth's state. Recent global environmental changes suggest that Earth may have entered a new human-dominated geological epoch, the Anthropocene. Here we review the historical genesis of the idea and assess anthropogenic signatures in the geological record against the formal requirements for the recognition of a new epoch. The evidence suggests that of the various proposed dates two do appear to conform to the criteria to mark the beginning of the Anthropocene: 1610 and 1964. The formal establishment of an Anthropocene Epoch would mark a fundamental change in the relationship between humans and the Earth system.

Quantifying Community Assembly Processes and Identifying Features that Impose Them

Abstract: Spatial turnover in the composition of biological communities is governed by (ecological) Drift, Selection and Dispersal. Commonly applied statistical tools cannot quantitatively estimate these processes, nor identify abiotic features that impose these processes. For interrogation of subsurface microbial communities distributed across two geologically distinct formations of the unconfined aquifer underlying the Hanford Site in southeastern Washington State, we developed an analytical framework that advances ecological understanding in two primary ways. First, we quantitatively estimate influences of Drift, Selection and Dispersal. Second, ecological patterns are used to characterize measured and unmeasured abiotic variables that impose Selection or that result in low levels of Dispersal. We find that (i) Drift alone consistently governs ∼25% of spatial turnover in community composition; (ii) in deeper, finer-grained sediments, Selection is strong (governing ∼60% of turnover), being imposed by an unmeasured but spatially structured environmental variable; (iii) in shallower, coarser-grained sediments, Selection is weaker (governing ∼30% of turnover), being imposed by vertically and horizontally structured hydrological factors;(iv) low levels of Dispersal can govern nearly 30% of turnover and be caused primarily by spatial isolation resulting from limited exchange between finer and coarser-grain sediments; and (v) highly permeable sediments are associated with high levels of Dispersal that homogenize community composition and govern over 20% of turnover. We further show that our framework provides inferences that cannot be achieved using preexisting approaches, and suggest that their broad application will facilitate a unified understanding of microbial communities.

The interdependence of mechanisms underlying climate-driven vegetation mortality

Abstract: Climate-driven vegetation mortality is occurring globally and is predicted to increase in the near future. The expected climate feedbacks of regional-scale mortality events have intensified the need to improve the simple mortality algorithms used for future predictions, but uncertainty regarding mortality processes precludes mechanistic modeling. By integrating new evidence from a wide range of fields, we conclude that hydraulic function and carbohydrate and defense metabolism have numerous potential failure points, and that these processes are strongly interdependent, both with each other and with destructive pathogen and insect populations. Crucially, most of these mechanisms and their interdependencies are likely to become amplified under a warmer, drier climate. Here, we outline the observations and experiments needed to test this interdependence and to improve simulations of this emergent global phenomenon.