MASTER BIODIVERSITY, ECOLOGY AND EVOLUTION

"This EU will take the form of a series of a dozen lectures/seminars on current research topics in vertebrate paleontology and evolutionary biology; biodiversity and paleobiodiversity of continental ecosystems (animal); topographic and climatic barriers vs. dispersal and vicariance; community structuring, trophic chains through time and paleoguilds; role of Geodynamics and contingency (crises). The main objective is to acquire a good knowledge of the current research themes/axes in the paleontological/evolutionary community.

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This course will take place, as far as possible, in the form of a one-week on-site internship (with accommodation). The locations of the internship may change from one year to the next depending on the discoveries and/or partnership proposals (public/private). This internship can therefore take different directions, with a "prospecting" approach and therefore a travelling field or a more "excavation site" approach and therefore fixed. In all cases, the different objectives listed below will be addressed to perfect this week of fieldwork so that the different techniques are mastered as well as possible.

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In this course we will approach the main theoretical concepts of evolutionary processes through the fossil record. The aim is to reconcile microevolutionary mechanisms with macroevolution. The concepts addressed will be: species and intraspecific variability, speciation and evolutionary rhythms, adaptive radiation (ecological speciation) in the fossil record, targeted extinctions (migrant-autochthonous competition) or mass extinctions (major biological crises), evolutionary modalities (anagenesis and saltationism) observed in the fossil record and a comprehensive review of microevolutionary mechanisms.

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The objective of this course is to accompany the student in the construction of his professional project and his search for an internship, while beginning to prepare his integration into professional life by an exhaustive and personal vision of possible career paths.

In concrete terms, meetings with different speakers allow the presentation of the doctoral thesis (presentation of the GAIA doctoral school, presentations by thesis students) and the professional environment targeted by the different courses (research professions and the non-academic sector). Activities specific to each pathway then help to better target the scientific fields most closely related to the students' professional projects. Lastly, the course includes practical sessions designed to prepare students to write scientific articles in English.

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This course provides the necessary tools for data analysis in paleontology

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"The objective is to analyze the phylogenetic, developmental and functional constraints that may have governed the morphological changes discernible in the fossil record. The phylogenetic approach will be approached by reconstruction methods applicable to fossils (parsimony; cladistic analysis). Developmental and functional approaches (mainly odontology) will be illustrated by different methodologies developed on the Montpellier campus (notably X-ray microtomography). The critical review of reference articles in the considered field will give rise to an oral presentation followed by questions."

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Evo-devo is an evolutionary approach to developmental genetics. This discipline seeks to shed light on the changes in developmental mechanisms that explain present and past morphological diversity, and thus opens an important bridge between biology and paleontology.

During the module, we will discuss, based on articles, several evolutionary issues that are useful for Evo-Devo approaches: the question of homology, the question of the establishment and evolution of repeated structures, the genetic basis of development and the links between genome evolution and shape evolution. We will illustrate these notions from examples taken from metazoans and the green lineage, and will apply them to the scale of large current groups but also to populations.

See full page

Phylogeny is a quest for evolutionary clues. The aim of this module is to recall the existence of gene phylogenies in species phylogenies, the ways of representing evolutionary histories in the form of trees, and the challenge of positional molecular homology through sequence alignment. The principles of phylogenetic inference methods are at the heart of the knowledge of this course. The distance methods allow to underline the difficulties of separating homology and homoplasy, and the necessity to build models of character evolution. The cladistic approach with maximum parsimony allows to illustrate on the one hand the use of bootstrap to estimate the strength of the nodes of phylogenies, and on the other hand the impact of taxonomic sampling to detect multiple substitutions.

The probabilistic approaches are presented and further developed. The attraction artifact of long branches leads to the introduction of probabilistic reasoning. The maximum likelihood method allows us to approach the calculation of the likelihood, the estimation of the parameters of the models by optimality, the construction of different models of character evolution, as well as the comparison of models. Bayesian inference introduces the distinction between density and optimality approaches. It then shows the a priori use of probability densities, the estimation of a posteriori distributions of model parameters given the data, their approximation by Markov chains with Monte Carlo techniques and Metropolis coupling (MCMCMC), the ignition and convergence phases, and the computation and interpretation of the posterior probabilities of trees and clades. The importance of DNA, RNA and protein sequence evolution models and their improvement is stressed.

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The objective of this course is to help students finalize their professional projects and prepare for the post-master's program.

The EU is organized at the level of the course, with regular discussion sessions between the teaching staff and the students.

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The individual M2 internship lasts approximately 5 to 6 months and must be carried out, depending on the course, in a research laboratory or a structure in the non-academic sector. It allows the student to acquire in-depth professional experience in the field of biodiversity, evolution or ecology. It can be carried out in a local, national, or international structure, on a subject validated by the teaching staff in order to meet the objectives of the course followed by the student.

Evaluation: The internship is evaluated during a public defense before a jury during which the content of the thesis and the quality of the answers to the jury's questions are evaluated. The behavior and dynamism of the student during the internship are evaluated by the internship supervisor.

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"General linear models with 1 or more explanatory random variables: from translating the figure that answers the biological question to the statistical model, i.e., taking into account many effects and knowing how to interpret them

general properties seen through regression and 1-factor ANOVA (R2, F, ddl, least squares, likelihood, diagnosis, validation, goodness of fit, interpretation of effect sizes); nested and cross-factor ANOVA, multiple regression (notion of parameter and effects, and interaction)

incorporation of the dependence of explanatory random variables, confounding of effects (quantitative for multiple regression, and unbalanced designs for ANOVA)".

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The general objective is to consolidate the basic knowledge of ecology acquired by the students, and to give them the tools to mobilize it in an integrative way to interpret the functioning of ecological systems. The courses include: 1) lectures on the concepts of ecology from the population scale to macroecological scales, with examples of applications that place the discipline in the current ecological and societal context; 2) practical and directed work focused on tools (sampling strategies, modeling, data analysis); 3) field courses during which students are invited to ask themselves relevant scientific questions based on observation in a situation, and to mobilize their knowledge in order to respond to them in an argumentative manner.

Synthetic content of the EU :

- CM: History of the emergence of concepts in ecology; Population dynamics / metapopulations; Biotic interactions and food webs; Community ecology, meta-communities; Ecology of ecosystems / functional ecology; Notions of macroecology / biogeography; Global changes and ecosystem functioning;

- Field: Integrative Analysis of Ecosystem Functioning in Situations;

- TD/TP: sampling and experimental strategies in ecology; modeling in population/meta-population dynamics, community/meta-community ecology, food webs; biodiversity metrics (alpha, beta, etc)."

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"The general objective is to consolidate the students' bases in evolutionary biology, by approaching both (i) macro-evolutionary phenomena, and the general methods used for their analysis and (ii) micro-evolutionary processes by insisting on the population genetic approach. The objective of this course is to provide a common base of solid knowledge in evolutionary biology and to illustrate the applications of the discipline to the students' future fields of specialization. The teaching includes: 1) lectures on evolutionary concepts; 2) practical work in two main forms: 2a. sessions focused on the use of tools (phylogeny) and on the mathematical formalization of evolutionary processes (population genetics) as well as 2b: sessions built around group work, allowing students, depending on their career path and professional objectives, to go deeper into a particular theme (fundamental question or application of evolutionary biology)."

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English tutorials aimed at professional autonomy in the English language.

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"The phylogenetic tree is a central concept in biology for students in the fields of ""Biodiversity, Ecology & Evolution"", ""Biology Agrosciences"", and ""Eco-epidemiology"". To approach phylogeny, this UE is divided into two successive parts of 22,5h each: ""Phylogeny and Evolution (Basics)"" (HAB708B) and ""Phylogeny and Evolution (Advanced)"" (HAB714B).

The following knowledge will be taught:

(i) History of the notion of evolution [Basics].

(ii) Phylogenetic systematics (characters, rules of taxonomy, molecular barcoding, genomics, alignment, homology and homoplasy, orthology and paralogy) [half in Basic; half in Advanced].

(iii) Phylogenetic representation (networks, trees, root, dendrograms, topology, branch lengths) [Bases].

(iv) Phylogenetic inference methods by distances [Advanced].

(v) The cladistic approach and the maximum parsimony principle [Basics].

(vi) The probabilistic approach, the maximum likelihood principle, and sequence evolution models [Advanced].

(vii) Measures of phylogeny robustness (bootstrap, topology comparison, multigene corroboration, gene and species trees) [Advances].

(viii) Applications to the phylogeny of some major taxonomic groups (Mammals, Eukaryotes) [Advances]."

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Generalized linear mixed models + methodology and experimental protocols to take into account a biological reality: non-normal law and pseudo-replication

Protocol optimization, power and uncontrolled 1st order risk: variable transformation, polynomial regression, link function, likelihood, model selection

Deviance analysis and goodness of fit

Incorporation of blocks, repeated measurements over time, taking into account spatial and temporal correlation, over-dispersion

Graphical representation of predictions.

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The objective of this course is to provide the necessary basis in statistics to follow all the more elaborate modules of the curriculum, so it is a general refresher. Descriptive statistics are reviewed (quantile, polygon of cumulative frequencies, estimators from samples), simple tests are presented, essential graphs for univariate and multivariate data are presented, the general principle of a statistical test, the hypothesis plan, the notion of p-value, first and second species risk are presented. In practical exercises, students are also brought up to speed in the R environment.

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"The phylogenetic tree is a central concept in biology for students in the fields of ""Biodiversity, Ecology & Evolution"", ""Biology Agrosciences"", and ""Eco-epidemiology"". To approach phylogeny, this UE is divided into two successive parts of 22,5h each: ""Phylogeny and Evolution (Basics)"" (HAB708B) and ""Phylogeny and Evolution (Advanced)"" (HAB714B).

The following knowledge will be taught:

(i) History of the notion of evolution [Basics].

(ii) Phylogenetic systematics (characters, rules of taxonomy, molecular barcoding, genomics, alignment, homology and homoplasy, orthology and paralogy) [half in Basic; half in Advanced].

(iii) Phylogenetic representation (networks, trees, root, dendrograms, topology, branch lengths) [Bases].

(iv) Phylogenetic inference methods by distances [Advanced].

(v) The cladistic approach and the maximum parsimony principle [Basics].

(vi) The probabilistic approach, the maximum likelihood principle, and sequence evolution models [Advanced].

(vii) Measures of phylogeny robustness (bootstrap, topology comparison, multigene corroboration, gene and species trees) [Advances].

(viii) Applications to the phylogeny of some major taxonomic groups (Mammals, Eukaryotes) [Advances]."

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This EU has three objectives:

1) deepen knowledge of concepts in genetics and evolutionary genomics such as linkage disequilibrium, selection, coalescent theory, detection of natural selection and evolutionary forces acting on genome evolution and the process of genomic speciation.

2) To propose a panorama of research themes in evolutionary genomics in the form of pedagogical seminars: molecular evolution, evolutionary genomics of endosymbioses, chromosomal evolution and molecular evolution.

3) Finally, the EU proposes a project of bioanalysis of an empirical dataset to understand the analysis in evolutionary genomics and to rub shoulders with the bioinformatics aspects increasingly developed in the discipline.

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The individual internship in M1 lasts about three months and must be carried out, depending on the course, in a research laboratory or a structure in the non-academic sector. It allows the student to acquire professional experience in the field of biodiversity, evolution or ecology. It can be carried out in a local, national, or international structure, on a subject validated by the teaching staff in order to meet the objectives of the course followed by the student.

Evaluation: The preparation of the internship is a graded exercise based on a written document and a defense of the internship project. The internship work is evaluated during a public defense before a jury during which the content of the thesis and the quality of the answers to the jury's questions are evaluated. The behavior and dynamism of the student during the internship are evaluated by the internship supervisor.

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"The objective of this course is to consolidate the students' knowledge of ecology and/or evolution by inviting them to define a research topic and question(s), by defining relevant hypotheses in an arguable manner, and by justifying a strategy for acquiring and analyzing data to test them.

Synthetic content of the EU:

- Independent tutored work: identification of a relevant scientific question; bibliographic synthesis allowing to realize the state of the art and to justify the scientific hypotheses; proposal and justification of a methodological approach (material and methods) to test the proposed hypotheses.

Type of topics:

The topics can be on any question identified by the students (in groups of 3/4), and validated by the teaching staff, and can be based on different approaches allowing to adjust to the expectations of the different courses. For example, students can propose a sampling strategy in the field or in experiments, a meta-analysis of data from the literature, an analysis of sequences retrieved from GenBank, an analysis of occurrence data retrieved from GBIF, etc.

In all cases, the projects must involve a real data acquisition strategy, identified, justified and described by the students in the material and method requested in M1S2, with a provisional timetable for the project and identification of the tasks that each student will carry out within each group as part of the implementation of the project in M2S3 The projects must also be financially realistic and propose a provisional budget, and must be able to be finalized in the time available in M2S3.

Methods of control of knowledge:

The teaching is based on a problem-based learning approach, and students are evaluated on the way they progress in building their approach (40% of CC), as well as on their ability to present and defend their project during a final oral (60% of the overall grade)."

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"This module presents table management and the link between multivariate and univariate: matrix manipulation and common operations; notion of projection and distance; translation of descriptive and univariate statistics with multiple regression/ACP/AFD as an example; (dis)similarity indices, distance; correlation"

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"The objective of this course is to complete the first semester's teaching by developing the problems related to the evolution of phenotypes and the main associated methodological approaches. The lectures will address the evolution of different types of traits (life history traits, traits involved in reproductive strategies, traits involved in biotic interactions, quantitative traits). The main approaches covered include game theory formalization, adaptive dynamics, quantitative genetic approaches, and the work of confronting theoretical predictions with empirical data. Coursework includes:

1) lectures on the main concepts of evolutionary ecology;

2) tutorials focused on document studies and exercises".

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How is biodiversity distributed on Earth? What ecological, evolutionary and historical factors determine these patterns of biodiversity distribution? What are the changes induced by human activities on the global distribution of biodiversity? In this course, we will study the role of spatio-temporal variations in the global environment on the dynamics of biodiversity. In particular, we will examine the influence of long-term climate cycles on the past and present diversity of organisms. We will also address the impact of human activities and global changes on biodiversity at the planetary scale.

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- Firstly, to give students a base of knowledge and computer skills and thus provide them with a solid foundation for learning and using the bioinformatics tools used more specifically in evolution and ecology.

- Secondly, to make them aware of the need to produce reproducible results and to introduce them to the key concepts and tools for this.

- Thirdly, to make the students work on concrete examples that can be used during their master's course and their future professional life.

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"Darwin Field School" takes place over a week with the following objectives:

- Create a group dynamic and integration in the Master 2 DARWIN-BEE class.

- Analyze ecological issues in their technical, scientific and social dimensions (for example: reintroduction operations).

- To address the issues of biodiversity management in a humanized protected area.

- Oral presentation and confrontation of results to an assembly; assessment of the course.

Activities in Florac :

- Discover the landscapes of the Causse Méjean.

- Understand the specificities of the missions of the Cevennes National Park and its scientific policy of knowledge acquisition.

- Study the example of vultures in the Causses, the capercaillie and the beaver in the PNC, and the chamois in the Gorges du Tarn.

- Practice personal work in 3 sub-groups on different scientific and ethical themes.

Activities around Montpellier :

- To study bird migration and the ecosystems of the Mediterranean coastline.

- Practicing urban ecology.

- Discover the fauna of the Mediterranean scrublands, with daytime hikes along the Buèges (discovery of entomofauna) and evening hikes (bat and/or moth and nocturnal orthopterans evening)."

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The module covers the following fundamental topics in evolutionary biology: Micro evolution -Macro evolution, Fitness, Natural and sexual selves, Speciation. Other topics (mutation, epigenetics, evo-devo ...) are presented by the students themselves.

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The objective of this course is to accompany the student in the construction of his professional project and his search for an internship, while beginning to prepare his integration into professional life by an exhaustive and personal vision of possible career paths.

In concrete terms, meetings with different speakers allow the presentation of the doctoral thesis (presentation of the GAIA doctoral school, presentations by thesis students) and the professional environment targeted by the different courses (research professions and the non-academic sector). Activities specific to each pathway then help to better target the scientific fields most closely related to the students' professional projects. Lastly, the course includes practical sessions designed to prepare students to write scientific articles in English.

See full page

The objective of this course is to design a research project on one of the major themes in ecology such as ecological niche, biogeography, networks of ecological interactions or functional diversity. A short reminder of the major theories and concepts in these major themes in ecology is presented by specialists in these themes. This review is followed by one or more examples illustrating the conceptual bases for formulating a relevant and new research question and how to answer it with different methodologies, especially experimental, from the speakers' research. After choosing one of these major themes, each student develops an original research project (of the size of an M2 internship), by conducting a bibliographic search and proposing a coherent experimental plan to test the hypotheses. This project is presented to the lecturers and the other students.

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The objective of this EU is to show that biological diversity is functional:

1) for different groups of organisms: plants, insects, aquatic organisms, vertebrates, and

2) at different scales of organization (from organisms to the ecosystem). The lessons aim to explain how to approach this functional facet of diversity for the 10+ million organisms present on the surface of the planet, by taking examples in very or slightly anthropized environments.

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The module addresses the theoretical and empirical advances of recent research in evolutionary genetics through some major issues:

- theme 1: genetic burden and evolution of reproductive systems: recombination, sex/sex, auto/allo fertilization

- theme 2 : Matching structures and their evolutionary consequences : kinship selection, group selection, evolution of cooperation, sex ratios

- theme 3: sustainable interactions between species: parasitism, mutualism, coevolution

- theme 4: traces of evolutionary history in genomes, genomics of adaptation.

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The main objective of this course is to provide the necessary skills to understand and use the concepts and methods on which the quantitative study of population phenomena is based. The main methods of analysis and modelling of these phenomena will be approached both from a theoretical point of view (formal calculations) and from a practical point of view (statistics, simulations), by means of examples exploring the different phylogenetic scales (microbial dynamics, invasive species, human demography), spatial (from local to global) and temporal (transient and permanent regimes, eco-evolutionary coupling), with a particular attention to heterogeneity (spatial, genetic or phenotypic) and randomness (stochasticity, uncertainties) characteristic of populations or inherent to their study.

See full page

Evo-devo is an evolutionary approach to developmental genetics. This discipline seeks to shed light on the changes in developmental mechanisms that explain present and past morphological diversity, and thus opens an important bridge between biology and paleontology.

During the module, we will discuss, based on articles, several evolutionary issues that are useful for Evo-Devo approaches: the question of homology, the question of the establishment and evolution of repeated structures, the genetic basis of development and the links between genome evolution and shape evolution. We will illustrate these notions from examples taken from metazoans and the green lineage, and will apply them to the scale of large current groups but also to populations.

See full page

Phylogeny is a quest for evolutionary clues. The aim of this module is to recall the existence of gene phylogenies in species phylogenies, the ways of representing evolutionary histories in the form of trees, and the challenge of positional molecular homology through sequence alignment. The principles of phylogenetic inference methods are at the heart of the knowledge of this course. The distance methods allow to underline the difficulties of separating homology and homoplasy, and the necessity to build models of character evolution. The cladistic approach with maximum parsimony allows to illustrate on the one hand the use of bootstrap to estimate the strength of the nodes of phylogenies, and on the other hand the impact of taxonomic sampling to detect multiple substitutions.

The probabilistic approaches are presented and further developed. The attraction artifact of long branches leads to the introduction of probabilistic reasoning. The maximum likelihood method allows us to approach the calculation of the likelihood, the estimation of the parameters of the models by optimality, the construction of different models of character evolution, as well as the comparison of models. Bayesian inference introduces the distinction between density and optimality approaches. It then shows the a priori use of probability densities, the estimation of a posteriori distributions of model parameters given the data, their approximation by Markov chains with Monte Carlo techniques and Metropolis coupling (MCMCMC), the ignition and convergence phases, and the computation and interpretation of the posterior probabilities of trees and clades. The importance of DNA, RNA and protein sequence evolution models and their improvement is stressed.

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1. Bayesian inference: Motivation and simple example. 

2. The likelihood. 

3. A detour to explore priors. 

4. Markov chains Monte Carlo methods (MCMC)

5. Bayesian analyses in R with the Jags software.  

6. Contrast scientific hypotheses with model selection (WAIC).

7. Heterogeneity and multilevel models (aka mixed models. 

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The general objective is to present human evolutionary biology, proposing to mobilize the tools of evolutionary biology in order to better understand human behaviors and those observed in non-human primates in the context of their evolutionary history. Whether it be health, sociality, culture, local adaptations, language, morality, reproduction or sexual preferences, the themes are approached within the theoretical framework of evolutionary biology and ecology. Synthetic content of the course: Anthropology, human sciences and evolutionary biology / Evolution of cooperation / Cultural evolution / Evolution of food / Evolution of sociality in primates / Family ecology / Medicine, public health and evolution / Evolution of language / Evolutionary demography / The origins of equity.

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1. Bayesian inference: Motivation and simple example. 

2. The likelihood. 

3. A detour to explore priors. 

4. Markov chains Monte Carlo methods (MCMC)

5. Bayesian analyses in R with the Jags software.  

6. Contrast scientific hypotheses with model selection (WAIC).

7. Heterogeneity and multilevel models (aka mixed models. 

See full page

The courses present 4 aspects of Conservation Biology based on current scientific research in this discipline:  

1. Introduction to Biodiversity Conservation(BC): Definition of Conservation Biology Why conserve biodiversity? Who are the main actors in CB and the role of science in CB. 
2. Species conservation: What are the priority species? How to conserve species? How do you know if a species is "well conserved"? 
3. Space conservation: What are the priority spaces? How to conserve spaces? 
4. Does conservation work?Importance of social acceptability and political commitment. Need for biodiversity indicators and measuring the impact of conservation. 

Students also complete a group assignment in which they present a SA project around the questions: why, what, where, how, how much does it cost and how do we know if it is effective? 

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The goals of this course are to deepen the key concepts related to climate change, to illustrate important concepts in ecology and evolution in the light of climate change, in many different ecosystems, and to synthesize the different scientific and societal questions and issues raised by CC.

See full page

Quantitative genetics is a discipline born at the beginning of the 20th century to understand the heredity of continuous traits, i.e. the majority of traits of agronomic (yield...) or evolutionary interest (life history traits, morphology). It is therefore an essential tool for understanding, modeling and predicting natural or artificial selection and the evolution of natural systems or cultivated plants/animals. Its relevance is more relevant than ever at the beginning of the 21st century, with the advent of genomics (a factor of scientific progress provided that all evolutionary problems are not reduced to the fiction of a few Mendelian alleles with a strong effect), and the return in force of alternative models of heredity (epigenetics) that go beyond the sequence-centric vision inherited from classical molecular biology.

The aim of the module is to provide a culture of quantitative genetics sufficient to (i) understand the classical foundations of the discipline, manipulate the key quantities (genetic variances, heritabilities, genetic correlations) and the statistical techniques for estimating these parameters (ii) understand the power of this technique for posing and understanding fundamental or applied evolutionary problems (agronomic improvement) (iii) understand how this formalization of heredity fits in with the classical Mendelian view.

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The general objective is to present human evolutionary biology, proposing to mobilize the tools of evolutionary biology in order to better understand human behaviors and those observed in non-human primates in the context of their evolutionary history. Whether it be health, sociality, culture, local adaptations, language, morality, reproduction or sexual preferences, the themes are approached within the theoretical framework of evolutionary biology and ecology. Synthetic content of the course: Anthropology, human sciences and evolutionary biology / Evolution of cooperation / Cultural evolution / Evolution of food / Evolution of sociality in primates / Family ecology / Medicine, public health and evolution / Evolution of language / Evolutionary demography / The origins of equity.

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Behavioral Ecology approaches the study of behavior from an evolutionary perspective to study the mechanisms, function, and contribution of behavior to evolutionary and ecological processes. The work carried out in Behavioral Ecology helps to understand other phenomena observed in other disciplines of life biology, because all animals, from unicellulars to the most complex vertebrates, exhibit behaviors.

The module allows students to be exposed to the different basic concepts, as well as to the multitude of tools that can be used (observations and experiments in natural populations or on captive individuals, comparative analyses, use of tools from modeling, ecophysiology, molecular biology, biochemistry, embedded electronics...). Part of the training is based on specific discussions on the research approaches that can be used, the tools used and the limits of inferences that can be made. An active participation of the students will be required at these different levels, notably through critical discussions of articles.

The topics covered range from the exploration of food procurement strategies, mate choice, habitat choice, investment in reproduction, to the study of animal communication and the reasons for living in groups. The historical dimension of the discipline is addressed in the introduction, but also according to the sensibility of the speakers and the themes addressed (meaning and relations between 'Animal Behaviour', 'Ethology', Behavioral Ecology etc...).

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The module addresses the theoretical and empirical advances of recent research in evolutionary genetics through some major issues:

- theme 1: genetic burden and evolution of reproductive systems: recombination, sex/sex, auto/allo fertilization

- theme 2 : Matching structures and their evolutionary consequences : kinship selection, group selection, evolution of cooperation, sex ratios

- theme 3: sustainable interactions between species: parasitism, mutualism, coevolution

- theme 4: traces of evolutionary history in genomes, genomics of adaptation.

See full page

The main objective of this course is to provide the necessary skills to understand and use the concepts and methods on which the quantitative study of population phenomena is based. The main methods of analysis and modelling of these phenomena will be approached both from a theoretical point of view (formal calculations) and from a practical point of view (statistics, simulations), by means of examples exploring the different phylogenetic scales (microbial dynamics, invasive species, human demography), spatial (from local to global) and temporal (transient and permanent regimes, eco-evolutionary coupling), with a particular attention to heterogeneity (spatial, genetic or phenotypic) and randomness (stochasticity, uncertainties) characteristic of populations or inherent to their study.

See full page

The objective of this EU is to show that biological diversity is functional:

1) for different groups of organisms: plants, insects, aquatic organisms, vertebrates, and

2) at different scales of organization (from organisms to the ecosystem). The lessons aim to explain how to approach this functional facet of diversity for the 10+ million organisms present on the surface of the planet, by taking examples in very or slightly anthropized environments.

See full page

Phylogeny is a quest for evolutionary clues. The aim of this module is to recall the existence of gene phylogenies in species phylogenies, the ways of representing evolutionary histories in the form of trees, and the challenge of positional molecular homology through sequence alignment. The principles of phylogenetic inference methods are at the heart of the knowledge of this course. The distance methods allow to underline the difficulties of separating homology and homoplasy, and the necessity to build models of character evolution. The cladistic approach with maximum parsimony allows to illustrate on the one hand the use of bootstrap to estimate the strength of the nodes of phylogenies, and on the other hand the impact of taxonomic sampling to detect multiple substitutions.

The probabilistic approaches are presented and further developed. The attraction artifact of long branches leads to the introduction of probabilistic reasoning. The maximum likelihood method allows us to approach the calculation of the likelihood, the estimation of the parameters of the models by optimality, the construction of different models of character evolution, as well as the comparison of models. Bayesian inference introduces the distinction between density and optimality approaches. It then shows the a priori use of probability densities, the estimation of a posteriori distributions of model parameters given the data, their approximation by Markov chains with Monte Carlo techniques and Metropolis coupling (MCMCMC), the ignition and convergence phases, and the computation and interpretation of the posterior probabilities of trees and clades. The importance of DNA, RNA and protein sequence evolution models and their improvement is stressed.

See full page

Evo-devo is an evolutionary approach to developmental genetics. This discipline seeks to shed light on the changes in developmental mechanisms that explain present and past morphological diversity, and thus opens an important bridge between biology and paleontology.

During the module, we will discuss, based on articles, several evolutionary issues that are useful for Evo-Devo approaches: the question of homology, the question of the establishment and evolution of repeated structures, the genetic basis of development and the links between genome evolution and shape evolution. We will illustrate these notions from examples taken from metazoans and the green lineage, and will apply them to the scale of large current groups but also to populations.

See full page

See full page

1. Bayesian inference: Motivation and simple example. 

2. The likelihood. 

3. A detour to explore priors. 

4. Markov chains Monte Carlo methods (MCMC)

5. Bayesian analyses in R with the Jags software.  

6. Contrast scientific hypotheses with model selection (WAIC).

7. Heterogeneity and multilevel models (aka mixed models. 

See full page

The courses present 4 aspects of Conservation Biology based on current scientific research in this discipline:  

1. Introduction to Biodiversity Conservation(BC): Definition of Conservation Biology Why conserve biodiversity? Who are the main actors in CB and the role of science in CB. 
2. Species conservation: What are the priority species? How to conserve species? How do you know if a species is "well conserved"? 
3. Space conservation: What are the priority spaces? How to conserve spaces? 
4. Does conservation work?Importance of social acceptability and political commitment. Need for biodiversity indicators and measuring the impact of conservation. 

Students also complete a group assignment in which they present a SA project around the questions: why, what, where, how, how much does it cost and how do we know if it is effective? 

See full page

The goals of this course are to deepen the key concepts related to climate change, to illustrate important concepts in ecology and evolution in the light of climate change, in many different ecosystems, and to synthesize the different scientific and societal questions and issues raised by CC.

See full page

Quantitative genetics is a discipline born at the beginning of the 20th century to understand the heredity of continuous traits, i.e. the majority of traits of agronomic (yield...) or evolutionary interest (life history traits, morphology). It is therefore an essential tool for understanding, modeling and predicting natural or artificial selection and the evolution of natural systems or cultivated plants/animals. Its relevance is more relevant than ever at the beginning of the 21st century, with the advent of genomics (a factor of scientific progress provided that all evolutionary problems are not reduced to the fiction of a few Mendelian alleles with a strong effect), and the return in force of alternative models of heredity (epigenetics) that go beyond the sequence-centric vision inherited from classical molecular biology.

The aim of the module is to provide a culture of quantitative genetics sufficient to (i) understand the classical foundations of the discipline, manipulate the key quantities (genetic variances, heritabilities, genetic correlations) and the statistical techniques for estimating these parameters (ii) understand the power of this technique for posing and understanding fundamental or applied evolutionary problems (agronomic improvement) (iii) understand how this formalization of heredity fits in with the classical Mendelian view.

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The general objective is to present human evolutionary biology, proposing to mobilize the tools of evolutionary biology in order to better understand human behaviors and those observed in non-human primates in the context of their evolutionary history. Whether it be health, sociality, culture, local adaptations, language, morality, reproduction or sexual preferences, the themes are approached within the theoretical framework of evolutionary biology and ecology. Synthetic content of the course: Anthropology, human sciences and evolutionary biology / Evolution of cooperation / Cultural evolution / Evolution of food / Evolution of sociality in primates / Family ecology / Medicine, public health and evolution / Evolution of language / Evolutionary demography / The origins of equity.

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Behavioral Ecology approaches the study of behavior from an evolutionary perspective to study the mechanisms, function, and contribution of behavior to evolutionary and ecological processes. The work carried out in Behavioral Ecology helps to understand other phenomena observed in other disciplines of life biology, because all animals, from unicellulars to the most complex vertebrates, exhibit behaviors.

The module allows students to be exposed to the different basic concepts, as well as to the multitude of tools that can be used (observations and experiments in natural populations or on captive individuals, comparative analyses, use of tools from modeling, ecophysiology, molecular biology, biochemistry, embedded electronics...). Part of the training is based on specific discussions on the research approaches that can be used, the tools used and the limits of inferences that can be made. An active participation of the students will be required at these different levels, notably through critical discussions of articles.

The topics covered range from the exploration of food procurement strategies, mate choice, habitat choice, investment in reproduction, to the study of animal communication and the reasons for living in groups. The historical dimension of the discipline is addressed in the introduction, but also according to the sensibility of the speakers and the themes addressed (meaning and relations between 'Animal Behaviour', 'Ethology', Behavioral Ecology etc...).

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1. Bayesian inference: Motivation and simple example. 

2. The likelihood. 

3. A detour to explore priors. 

4. Markov chains Monte Carlo methods (MCMC)

5. Bayesian analyses in R with the Jags software.  

6. Contrast scientific hypotheses with model selection (WAIC).

7. Heterogeneity and multilevel models (aka mixed models. 

See full page

The general objective is to present human evolutionary biology, proposing to mobilize the tools of evolutionary biology in order to better understand human behaviors and those observed in non-human primates in the context of their evolutionary history. Whether it be health, sociality, culture, local adaptations, language, morality, reproduction or sexual preferences, the themes are approached within the theoretical framework of evolutionary biology and ecology. Synthetic content of the course: Anthropology, human sciences and evolutionary biology / Evolution of cooperation / Cultural evolution / Evolution of food / Evolution of sociality in primates / Family ecology / Medicine, public health and evolution / Evolution of language / Evolutionary demography / The origins of equity.

See full page

1. Bayesian inference: Motivation and simple example. 

2. The likelihood. 

3. A detour to explore priors. 

4. Markov chains Monte Carlo methods (MCMC)

5. Bayesian analyses in R with the Jags software.  

6. Contrast scientific hypotheses with model selection (WAIC).

7. Heterogeneity and multilevel models (aka mixed models. 

See full page

The courses present 4 aspects of Conservation Biology based on current scientific research in this discipline:  

1. Introduction to Biodiversity Conservation(BC): Definition of Conservation Biology Why conserve biodiversity? Who are the main actors in CB and the role of science in CB. 
2. Species conservation: What are the priority species? How to conserve species? How do you know if a species is "well conserved"? 
3. Space conservation: What are the priority spaces? How to conserve spaces? 
4. Does conservation work?Importance of social acceptability and political commitment. Need for biodiversity indicators and measuring the impact of conservation. 

Students also complete a group assignment in which they present a SA project around the questions: why, what, where, how, how much does it cost and how do we know if it is effective? 

See full page

The goals of this course are to deepen the key concepts related to climate change, to illustrate important concepts in ecology and evolution in the light of climate change, in many different ecosystems, and to synthesize the different scientific and societal questions and issues raised by CC.

See full page

Quantitative genetics is a discipline born at the beginning of the 20th century to understand the heredity of continuous traits, i.e. the majority of traits of agronomic (yield...) or evolutionary interest (life history traits, morphology). It is therefore an essential tool for understanding, modeling and predicting natural or artificial selection and the evolution of natural systems or cultivated plants/animals. Its relevance is more relevant than ever at the beginning of the 21st century, with the advent of genomics (a factor of scientific progress provided that all evolutionary problems are not reduced to the fiction of a few Mendelian alleles with a strong effect), and the return in force of alternative models of heredity (epigenetics) that go beyond the sequence-centric vision inherited from classical molecular biology.

The aim of the module is to provide a culture of quantitative genetics sufficient to (i) understand the classical foundations of the discipline, manipulate the key quantities (genetic variances, heritabilities, genetic correlations) and the statistical techniques for estimating these parameters (ii) understand the power of this technique for posing and understanding fundamental or applied evolutionary problems (agronomic improvement) (iii) understand how this formalization of heredity fits in with the classical Mendelian view.

See full page

The general objective is to present human evolutionary biology, proposing to mobilize the tools of evolutionary biology in order to better understand human behaviors and those observed in non-human primates in the context of their evolutionary history. Whether it be health, sociality, culture, local adaptations, language, morality, reproduction or sexual preferences, the themes are approached within the theoretical framework of evolutionary biology and ecology. Synthetic content of the course: Anthropology, human sciences and evolutionary biology / Evolution of cooperation / Cultural evolution / Evolution of food / Evolution of sociality in primates / Family ecology / Medicine, public health and evolution / Evolution of language / Evolutionary demography / The origins of equity.

See full page

Behavioral Ecology approaches the study of behavior from an evolutionary perspective to study the mechanisms, function, and contribution of behavior to evolutionary and ecological processes. The work carried out in Behavioral Ecology helps to understand other phenomena observed in other disciplines of life biology, because all animals, from unicellulars to the most complex vertebrates, exhibit behaviors.

The module allows students to be exposed to the different basic concepts, as well as to the multitude of tools that can be used (observations and experiments in natural populations or on captive individuals, comparative analyses, use of tools from modeling, ecophysiology, molecular biology, biochemistry, embedded electronics...). Part of the training is based on specific discussions on the research approaches that can be used, the tools used and the limits of inferences that can be made. An active participation of the students will be required at these different levels, notably through critical discussions of articles.

The topics covered range from the exploration of food procurement strategies, mate choice, habitat choice, investment in reproduction, to the study of animal communication and the reasons for living in groups. The historical dimension of the discipline is addressed in the introduction, but also according to the sensibility of the speakers and the themes addressed (meaning and relations between 'Animal Behaviour', 'Ethology', Behavioral Ecology etc...).

See full page

The module addresses the theoretical and empirical advances of recent research in evolutionary genetics through some major issues:

- theme 1: genetic burden and evolution of reproductive systems: recombination, sex/sex, auto/allo fertilization

- theme 2 : Matching structures and their evolutionary consequences : kinship selection, group selection, evolution of cooperation, sex ratios

- theme 3: sustainable interactions between species: parasitism, mutualism, coevolution

- theme 4: traces of evolutionary history in genomes, genomics of adaptation.

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The main objective of this course is to provide the necessary skills to understand and use the concepts and methods on which the quantitative study of population phenomena is based. The main methods of analysis and modelling of these phenomena will be approached both from a theoretical point of view (formal calculations) and from a practical point of view (statistics, simulations), by means of examples exploring the different phylogenetic scales (microbial dynamics, invasive species, human demography), spatial (from local to global) and temporal (transient and permanent regimes, eco-evolutionary coupling), with a particular attention to heterogeneity (spatial, genetic or phenotypic) and randomness (stochasticity, uncertainties) characteristic of populations or inherent to their study.

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The objective of this EU is to show that biological diversity is functional:

1) for different groups of organisms: plants, insects, aquatic organisms, vertebrates, and

2) at different scales of organization (from organisms to the ecosystem). The lessons aim to explain how to approach this functional facet of diversity for the 10+ million organisms present on the surface of the planet, by taking examples in very or slightly anthropized environments.

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Phylogeny is a quest for evolutionary clues. The aim of this module is to recall the existence of gene phylogenies in species phylogenies, the ways of representing evolutionary histories in the form of trees, and the challenge of positional molecular homology through sequence alignment. The principles of phylogenetic inference methods are at the heart of the knowledge of this course. The distance methods allow to underline the difficulties of separating homology and homoplasy, and the necessity to build models of character evolution. The cladistic approach with maximum parsimony allows to illustrate on the one hand the use of bootstrap to estimate the strength of the nodes of phylogenies, and on the other hand the impact of taxonomic sampling to detect multiple substitutions.

The probabilistic approaches are presented and further developed. The attraction artifact of long branches leads to the introduction of probabilistic reasoning. The maximum likelihood method allows us to approach the calculation of the likelihood, the estimation of the parameters of the models by optimality, the construction of different models of character evolution, as well as the comparison of models. Bayesian inference introduces the distinction between density and optimality approaches. It then shows the a priori use of probability densities, the estimation of a posteriori distributions of model parameters given the data, their approximation by Markov chains with Monte Carlo techniques and Metropolis coupling (MCMCMC), the ignition and convergence phases, and the computation and interpretation of the posterior probabilities of trees and clades. The importance of DNA, RNA and protein sequence evolution models and their improvement is stressed.

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Evo-devo is an evolutionary approach to developmental genetics. This discipline seeks to shed light on the changes in developmental mechanisms that explain present and past morphological diversity, and thus opens an important bridge between biology and paleontology.

During the module, we will discuss, based on articles, several evolutionary issues that are useful for Evo-Devo approaches: the question of homology, the question of the establishment and evolution of repeated structures, the genetic basis of development and the links between genome evolution and shape evolution. We will illustrate these notions from examples taken from metazoans and the green lineage, and will apply them to the scale of large current groups but also to populations.

See full page

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1. Bayesian inference: Motivation and simple example. 

2. The likelihood. 

3. A detour to explore priors. 

4. Markov chains Monte Carlo methods (MCMC)

5. Bayesian analyses in R with the Jags software.  

6. Contrast scientific hypotheses with model selection (WAIC).

7. Heterogeneity and multilevel models (aka mixed models. 

See full page

The general objective is to present human evolutionary biology, proposing to mobilize the tools of evolutionary biology in order to better understand human behaviors and those observed in non-human primates in the context of their evolutionary history. Whether it be health, sociality, culture, local adaptations, language, morality, reproduction or sexual preferences, the themes are approached within the theoretical framework of evolutionary biology and ecology. Synthetic content of the course: Anthropology, human sciences and evolutionary biology / Evolution of cooperation / Cultural evolution / Evolution of food / Evolution of sociality in primates / Family ecology / Medicine, public health and evolution / Evolution of language / Evolutionary demography / The origins of equity.

See full page

1. Bayesian inference: Motivation and simple example. 

2. The likelihood. 

3. A detour to explore priors. 

4. Markov chains Monte Carlo methods (MCMC)

5. Bayesian analyses in R with the Jags software.  

6. Contrast scientific hypotheses with model selection (WAIC).

7. Heterogeneity and multilevel models (aka mixed models. 

See full page

The courses present 4 aspects of Conservation Biology based on current scientific research in this discipline:  

1. Introduction to Biodiversity Conservation(BC): Definition of Conservation Biology Why conserve biodiversity? Who are the main actors in CB and the role of science in CB. 
2. Species conservation: What are the priority species? How to conserve species? How do you know if a species is "well conserved"? 
3. Space conservation: What are the priority spaces? How to conserve spaces? 
4. Does conservation work?Importance of social acceptability and political commitment. Need for biodiversity indicators and measuring the impact of conservation. 

Students also complete a group assignment in which they present a SA project around the questions: why, what, where, how, how much does it cost and how do we know if it is effective? 

See full page

The goals of this course are to deepen the key concepts related to climate change, to illustrate important concepts in ecology and evolution in the light of climate change, in many different ecosystems, and to synthesize the different scientific and societal questions and issues raised by CC.

See full page

Quantitative genetics is a discipline born at the beginning of the 20th century to understand the heredity of continuous traits, i.e. the majority of traits of agronomic (yield...) or evolutionary interest (life history traits, morphology). It is therefore an essential tool for understanding, modeling and predicting natural or artificial selection and the evolution of natural systems or cultivated plants/animals. Its relevance is more relevant than ever at the beginning of the 21st century, with the advent of genomics (a factor of scientific progress provided that all evolutionary problems are not reduced to the fiction of a few Mendelian alleles with a strong effect), and the return in force of alternative models of heredity (epigenetics) that go beyond the sequence-centric vision inherited from classical molecular biology.

The aim of the module is to provide a culture of quantitative genetics sufficient to (i) understand the classical foundations of the discipline, manipulate the key quantities (genetic variances, heritabilities, genetic correlations) and the statistical techniques for estimating these parameters (ii) understand the power of this technique for posing and understanding fundamental or applied evolutionary problems (agronomic improvement) (iii) understand how this formalization of heredity fits in with the classical Mendelian view.

See full page

The general objective is to present human evolutionary biology, proposing to mobilize the tools of evolutionary biology in order to better understand human behaviors and those observed in non-human primates in the context of their evolutionary history. Whether it be health, sociality, culture, local adaptations, language, morality, reproduction or sexual preferences, the themes are approached within the theoretical framework of evolutionary biology and ecology. Synthetic content of the course: Anthropology, human sciences and evolutionary biology / Evolution of cooperation / Cultural evolution / Evolution of food / Evolution of sociality in primates / Family ecology / Medicine, public health and evolution / Evolution of language / Evolutionary demography / The origins of equity.

See full page

Behavioral Ecology approaches the study of behavior from an evolutionary perspective to study the mechanisms, function, and contribution of behavior to evolutionary and ecological processes. The work carried out in Behavioral Ecology helps to understand other phenomena observed in other disciplines of life biology, because all animals, from unicellulars to the most complex vertebrates, exhibit behaviors.

The module allows students to be exposed to the different basic concepts, as well as to the multitude of tools that can be used (observations and experiments in natural populations or on captive individuals, comparative analyses, use of tools from modeling, ecophysiology, molecular biology, biochemistry, embedded electronics...). Part of the training is based on specific discussions on the research approaches that can be used, the tools used and the limits of inferences that can be made. An active participation of the students will be required at these different levels, notably through critical discussions of articles.

The topics covered range from the exploration of food procurement strategies, mate choice, habitat choice, investment in reproduction, to the study of animal communication and the reasons for living in groups. The historical dimension of the discipline is addressed in the introduction, but also according to the sensibility of the speakers and the themes addressed (meaning and relations between 'Animal Behaviour', 'Ethology', Behavioral Ecology etc...).

See full page

The module addresses the theoretical and empirical advances of recent research in evolutionary genetics through some major issues:

- theme 1: genetic burden and evolution of reproductive systems: recombination, sex/sex, auto/allo fertilization

- theme 2 : Matching structures and their evolutionary consequences : kinship selection, group selection, evolution of cooperation, sex ratios

- theme 3: sustainable interactions between species: parasitism, mutualism, coevolution

- theme 4: traces of evolutionary history in genomes, genomics of adaptation.

See full page

The main objective of this course is to provide the necessary skills to understand and use the concepts and methods on which the quantitative study of population phenomena is based. The main methods of analysis and modelling of these phenomena will be approached both from a theoretical point of view (formal calculations) and from a practical point of view (statistics, simulations), by means of examples exploring the different phylogenetic scales (microbial dynamics, invasive species, human demography), spatial (from local to global) and temporal (transient and permanent regimes, eco-evolutionary coupling), with a particular attention to heterogeneity (spatial, genetic or phenotypic) and randomness (stochasticity, uncertainties) characteristic of populations or inherent to their study.

See full page

The objective of this EU is to show that biological diversity is functional:

1) for different groups of organisms: plants, insects, aquatic organisms, vertebrates, and

2) at different scales of organization (from organisms to the ecosystem). The lessons aim to explain how to approach this functional facet of diversity for the 10+ million organisms present on the surface of the planet, by taking examples in very or slightly anthropized environments.

See full page

Phylogeny is a quest for evolutionary clues. The aim of this module is to recall the existence of gene phylogenies in species phylogenies, the ways of representing evolutionary histories in the form of trees, and the challenge of positional molecular homology through sequence alignment. The principles of phylogenetic inference methods are at the heart of the knowledge of this course. The distance methods allow to underline the difficulties of separating homology and homoplasy, and the necessity to build models of character evolution. The cladistic approach with maximum parsimony allows to illustrate on the one hand the use of bootstrap to estimate the strength of the nodes of phylogenies, and on the other hand the impact of taxonomic sampling to detect multiple substitutions.

The probabilistic approaches are presented and further developed. The attraction artifact of long branches leads to the introduction of probabilistic reasoning. The maximum likelihood method allows us to approach the calculation of the likelihood, the estimation of the parameters of the models by optimality, the construction of different models of character evolution, as well as the comparison of models. Bayesian inference introduces the distinction between density and optimality approaches. It then shows the a priori use of probability densities, the estimation of a posteriori distributions of model parameters given the data, their approximation by Markov chains with Monte Carlo techniques and Metropolis coupling (MCMCMC), the ignition and convergence phases, and the computation and interpretation of the posterior probabilities of trees and clades. The importance of DNA, RNA and protein sequence evolution models and their improvement is stressed.

See full page

Evo-devo is an evolutionary approach to developmental genetics. This discipline seeks to shed light on the changes in developmental mechanisms that explain present and past morphological diversity, and thus opens an important bridge between biology and paleontology.

During the module, we will discuss, based on articles, several evolutionary issues that are useful for Evo-Devo approaches: the question of homology, the question of the establishment and evolution of repeated structures, the genetic basis of development and the links between genome evolution and shape evolution. We will illustrate these notions from examples taken from metazoans and the green lineage, and will apply them to the scale of large current groups but also to populations.

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The objective of this course is to help students finalize their professional projects and prepare for the post-master's program.

The EU is organized at the level of the course, with regular discussion sessions between the teaching staff and the students.

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The individual M2 internship lasts approximately 5 to 6 months and must be carried out, depending on the course, in a research laboratory or a structure in the non-academic sector. It allows the student to acquire in-depth professional experience in the field of biodiversity, evolution or ecology. It can be carried out in a local, national, or international structure, on a subject validated by the teaching staff in order to meet the objectives of the course followed by the student.

Evaluation: The internship is evaluated during a public defense before a jury during which the content of the thesis and the quality of the answers to the jury's questions are evaluated. The behavior and dynamism of the student during the internship are evaluated by the internship supervisor.

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https://www.evobio.eu/summer-school

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Each year, teachers will suggest a number of topics, from which students will choose (the list will be neither binding nor exhaustive: any topic that relates to evolution is fair game). Working in groups of two or three people, the students will be responsible for presenting the topic they have chosen. Each person in a group should participate equally in these presentations. Each group will be given a small selection of recent papers that they will use to begin to explore the topic, or the groups will themselves propose pertinent papers. Among these, the group will distribute (one week before the class session) one-two papers that everyone should read before class. The group will be responsible for presenting the topicto the rest of the class and leading discussion of it. The group presentation should explain why the topic is interesting and present the state of the art, outlining points ofcontroversy and defining big open questions. The presentation format will be defined by the group, keeping in mind that it should open discussions. For the last session(s) at the end of the course, students will give short individual presentations providing a recap of some aspect(s) of another group's topic. In addition to the main hot topic presentations, there will be a brief 'writing summaries' exercise at the beginning of the course, and regular "news & views" briefings of recent articles picked by the students from journals of their choice.

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https://www.umontpellier.fr/en/research

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Starting from scratch for analysing biological data: describing, testing and modelling simple experimental protocols;

Getting to know fundamental properties of linear models dealing with simple regressions and simple ANOVAs;

Incorporating into models the essence of biological data: co-linearity, dependence, spatial structure, laws that are not normal....

Representing data and results from models.

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Modelling is a methodology that is frequently used in biological sciences nowadays, in particular in ecological and evolutionary studies. However, models usually frighten students. The aim of this initiation is to show that modelling is by no means more inaccessible than other techniques in biology. The goal is to give students a feel of how a model is constructed, to be able to spot the key assumptions behind a result, and to test their validity. The course will seek to familiarize the students with several basic modelling techniques and tools.

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This one week course will be offered at least in winter 2020 (and in following years if independent funding can be secured). It will be organized as a retreat during which students will write in small groups grant proposals on Evolutionary Biology topics.

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The course discusses cases where evolutionary biology based implementations provide invaluable insight in applied issues such as vector control, conservation biology or fish stock management.

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"The objectives of this course are threefold: (i) to remind students of the theoretical bases of some essential concepts of population genetics theory; (ii) to detail some "classical" inference methods (e.g., F-statistics) and more "modern" approaches (based, e.g., on coalescent theory); (iii) to show how demographic history may be inferred from the analysis of genetic polymorphisms."

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The objective of this course is to provide the theoretical background for understanding, and potentially being able to use and apply the principles of how selection will affect the evolution of populations. Y. Michalakis describes the basics of selection theory and shows with elementary algebra that it is possible to derive some fundamental results in Population Genetics, such as Fisher's Fundamental Theorem. He also gives an introduction to mutation-_selection balance and two--locus theory. The latter topics are put in perspective in the courses by T. Lenormand on the evolution of sexual reproduction, migration and local adaptation. T. Lenormand also presents the theory that allows understanding the dynamics of adaptation. G. Martin's courses explain how stochastic effects interact with selection to influence the fate of adaptive mutations.

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https://www.evobio.eu/semester-3-4

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https://www.evobio.eu/summer-school

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"General linear models with 1 or more explanatory random variables: from translating the figure that answers the biological question to the statistical model, i.e., taking into account many effects and knowing how to interpret them

general properties seen through regression and 1-factor ANOVA (R2, F, ddl, least squares, likelihood, diagnosis, validation, goodness of fit, interpretation of effect sizes); nested and cross-factor ANOVA, multiple regression (notion of parameter and effects, and interaction)

incorporation of the dependence of explanatory random variables, confounding of effects (quantitative for multiple regression, and unbalanced designs for ANOVA)".

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The general objective is to consolidate the basic knowledge of ecology acquired by the students, and to give them the tools to mobilize it in an integrative way to interpret the functioning of ecological systems. The courses include: 1) lectures on the concepts of ecology from the population scale to macroecological scales, with examples of applications that place the discipline in the current ecological and societal context; 2) practical and directed work focused on tools (sampling strategies, modeling, data analysis); 3) field courses during which students are invited to ask themselves relevant scientific questions based on observation in a situation, and to mobilize their knowledge in order to respond to them in an argumentative manner.

Synthetic content of the EU :

- CM: History of the emergence of concepts in ecology; Population dynamics / metapopulations; Biotic interactions and food webs; Community ecology, meta-communities; Ecology of ecosystems / functional ecology; Notions of macroecology / biogeography; Global changes and ecosystem functioning;

- Field: Integrative Analysis of Ecosystem Functioning in Situations;

- TD/TP: sampling and experimental strategies in ecology; modeling in population/meta-population dynamics, community/meta-community ecology, food webs; biodiversity metrics (alpha, beta, etc)."

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"The general objective is to consolidate the students' bases in evolutionary biology, by approaching both (i) macro-evolutionary phenomena, and the general methods used for their analysis and (ii) micro-evolutionary processes by insisting on the population genetic approach. The objective of this course is to provide a common base of solid knowledge in evolutionary biology and to illustrate the applications of the discipline to the students' future fields of specialization. The teaching includes: 1) lectures on evolutionary concepts; 2) practical work in two main forms: 2a. sessions focused on the use of tools (phylogeny) and on the mathematical formalization of evolutionary processes (population genetics) as well as 2b: sessions built around group work, allowing students, depending on their career path and professional objectives, to go deeper into a particular theme (fundamental question or application of evolutionary biology)."

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English tutorials aimed at professional autonomy in the English language.

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ORPAL is an APP course (1/3 field and 2/3 laboratory work). The work carried out in pairs or in triples under the responsibility of a referee, covers the whole research chain, from the definition of the problem, the sampling in the field, the acquisition of data to the interpretation, the writing of a scientific article (see https://biologie-ecologie.com/exemples-travaux/) and the oral presentation of the results.

The ORPAM course takes place during the first weeks of teaching. This UE starts with a 3 days field school (24h - integration internship) and continues with a mini internship in laboratory (24h). The UE ends with the writing of a scientific article and an oral presentation of the results.

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Generalized linear mixed models + methodology and experimental protocols to take into account a biological reality: non-normal law and pseudo-replication

Protocol optimization, power and uncontrolled 1st order risk: variable transformation, polynomial regression, link function, likelihood, model selection

Deviance analysis and goodness of fit

Incorporation of blocks, repeated measurements over time, taking into account spatial and temporal correlation, over-dispersion

Graphical representation of predictions.

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The objective of this course is to provide the necessary basis in statistics to follow all the more elaborate modules of the curriculum, so it is a general refresher. Descriptive statistics are reviewed (quantile, polygon of cumulative frequencies, estimators from samples), simple tests are presented, essential graphs for univariate and multivariate data are presented, the general principle of a statistical test, the hypothesis plan, the notion of p-value, first and second species risk are presented. In practical exercises, students are also brought up to speed in the R environment.

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The individual internship in M1 lasts about three months and must be carried out, depending on the course, in a research laboratory or a structure in the non-academic sector. It allows the student to acquire professional experience in the field of biodiversity, evolution or ecology. It can be carried out in a local, national, or international structure, on a subject validated by the teaching staff in order to meet the objectives of the course followed by the student.

Evaluation: The preparation of the internship is a graded exercise based on a written document and a defense of the internship project. The internship work is evaluated during a public defense before a jury during which the content of the thesis and the quality of the answers to the jury's questions are evaluated. The behavior and dynamism of the student during the internship are evaluated by the internship supervisor.

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The aim of this course is to understand the adaptive biology of organisms by considering individual and population responses to environmental variation. Concrete examples in animal evolutionary ecophysiology will be discussed in the context of global change. The responses of organisms and populations to abiotic parameters (such as temperature, salinity, oxygen availability, pollutants) will be considered as well as their interactive effects. The course will show the implication of physiological mechanisms in ecology, from phenotypic and cognitive processes at the intra-individual level to functional variants between individuals and between species. Intraspecific variability, phenotypic plasticity and transgenerational effects will also be discussed. This course will be illustrated by examples of phenotypic trait analysis (including behavior) within populations. Links with genetic and epigenetic markers will also be discussed. Different approaches (-omics vs. target gene/protein), several experimental setups and various scales of organization of living organisms will be considered (molecule, gene, phenotype, individual, population, species).

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The teaching of this module is an introduction to ethnobotany and ethnoecology in order to understand the material and immaterial dimensions of the relationships between humans and their environment, with a particular focus on the plant world. We will be particularly interested in local systems of nomenclature and classification, perceptions and representations of nature, uses and management practices of resources, biocultural, ecological and evolutionary interactions. Ethnobotany and ethnoecology are disciplines at the interface of anthropology, botany and ecology, which can also borrow tools and concepts from linguistics, archaeology, geography and agronomy. This module complements the "Ethnoecology and Sustainable Development" module (Master 2) by providing the theoretical and methodological bases of ethnobotany.

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"The objective of this course is to complete the first semester's teaching by developing the problems related to the evolution of phenotypes and the main associated methodological approaches. The lectures will address the evolution of different types of traits (life history traits, traits involved in reproductive strategies, traits involved in biotic interactions, quantitative traits). The main approaches covered include game theory formalization, adaptive dynamics, quantitative genetic approaches, and the work of confronting theoretical predictions with empirical data. Coursework includes:

1) lectures on the main concepts of evolutionary ecology;

2) tutorials focused on document studies and exercises".

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"The objective of this course is to consolidate the students' knowledge of ecology and/or evolution by inviting them to define a research topic and question(s), by defining relevant hypotheses in an arguable manner, and by justifying a strategy for acquiring and analyzing data to test them.

Synthetic content of the EU:

- Independent tutored work: identification of a relevant scientific question; bibliographic synthesis allowing to realize the state of the art and to justify the scientific hypotheses; proposal and justification of a methodological approach (material and methods) to test the proposed hypotheses.

Type of topics:

The topics can be on any question identified by the students (in groups of 3/4), and validated by the teaching staff, and can be based on different approaches allowing to adjust to the expectations of the different courses. For example, students can propose a sampling strategy in the field or in experiments, a meta-analysis of data from the literature, an analysis of sequences retrieved from GenBank, an analysis of occurrence data retrieved from GBIF, etc.

In all cases, the projects must involve a real data acquisition strategy, identified, justified and described by the students in the material and method requested in M1S2, with a provisional timetable for the project and identification of the tasks that each student will carry out within each group as part of the implementation of the project in M2S3 The projects must also be financially realistic and propose a provisional budget, and must be able to be finalized in the time available in M2S3.

Methods of control of knowledge:

The teaching is based on a problem-based learning approach, and students are evaluated on the way they progress in building their approach (40% of CC), as well as on their ability to present and defend their project during a final oral (60% of the overall grade)."

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The objective of this UE is to allow the implementation of projects defined in the framework of the UE project of M1S2.

Synthetic content of the EU:

- Tutor-led autonomous work by groups of students: readjustment of the project's objectives and methodology if necessary, acquisition of data, ecological and/or evolutionary analyses and interpretations according to the provisional schedule defined in M1S2, restitution of results in the framework of a conference common to the different courses.

Methods of control of knowledge:

As for the M1 project UE, the UE is based on a problem-based learning approach. Students are therefore evaluated as they go along on how they are progressing with their project (40% CC), and then at the end of the semester on their ability to present the results of their project and discuss them in an oral presentation at a general restitution conference (60% of the overall mark).

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The pedagogical objective of this course is to reposition the main types of soil on a global scale, to explain their formation and to identify the mineral phases or the main abiotic factors likely to regulate the biological activity of soils. Based on this analysis, the different soil organisms (micro-organisms, micro-, meso- and macro-fauna) will be presented as well as their relationships in order to reposition the cycle of organic matter and mineral elements in the soil at different temporal and spatial scales. The notions of recycling, looping of biogeochemical cycles and community assembly rules will also be addressed. The organization of this course is based on lectures and conferences as well as fieldwork.

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Ecophysiology is a discipline at the interface between organismal biology and ecology. Integrative ecophysiology focuses more particularly on the issue of scale change. In other words, the objective of this course is to illustrate how the study of acclimation/adaptation mechanisms at the individual (or even sub-individual) scale can explain the structure of populations, the distribution of species and the functioning of ecosystems. The responses of organisms and populations to the main abiotic structuring parameters (such as temperature, salinity, oxygen availability, pollutants) will be considered as well as their interactive effects. The role of interactions between organisms will also be addressed. In this course, animals, plants and microorganisms will be considered and different types of approaches will be illustrated: field observations, in situ or laboratory experiments.

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The main objective of this course is to provide the necessary skills to understand and use the concepts and methods on which the quantitative study of population phenomena is based. The main methods of analysis and modelling of these phenomena will be approached both from a theoretical point of view (formal calculations) and from a practical point of view (statistics, simulations), by means of examples exploring the different phylogenetic scales (microbial dynamics, invasive species, human demography), spatial (from local to global) and temporal (transient and permanent regimes, eco-evolutionary coupling), with a particular attention to heterogeneity (spatial, genetic or phenotypic) and randomness (stochasticity, uncertainties) characteristic of populations or inherent to their study.

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This course aims at better understanding the main types of pollutants (organic vs. inorganic), their source(s), their fate in the environment and the way they interact with living organisms (bioaccumulation, biotransformation, effects). The methods used in depollution and bioremediation will be discussed. A particular focus will be made on the contribution of terrestrial and aquatic plants in phytoremediation as well as on the role of microorganisms (bacteria, fungi) in the mechanisms of biodegradation, biotransformation or biosequestration. This course will be illustrated through different case studies through which examples of chronic and acute/accidental pollution of water, air and soil will be discussed. In particular, the treatment of pollution related to mining, petroleum, plastics and phyto-pharmaceutical industries as well as the treatment of liquid effluents (wastewater, industrial effluents) will be discussed. A field trip to Saint-Laurent-Le-Minier will illustrate a current project of phytoremediation of a former mining site.

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The objective of this EU is to show that biological diversity is functional:

1) for different groups of organisms: plants, insects, aquatic organisms, vertebrates, and

2) at different scales of organization (from organisms to the ecosystem). The lessons aim to explain how to approach this functional facet of diversity for the 10+ million organisms present on the surface of the planet, by taking examples in very or slightly anthropized environments.

See full page

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1. Bayesian inference: Motivation and simple example. 

2. The likelihood. 

3. A detour to explore priors. 

4. Markov chains Monte Carlo methods (MCMC)

5. Bayesian analyses in R with the Jags software.  

6. Contrast scientific hypotheses with model selection (WAIC).

7. Heterogeneity and multilevel models (aka mixed models. 

See full page

The module aims at providing theoretical and practical knowledge of statistical analysis of spatial and temporal constraints: classification and ordering under constraints, '2-table ordinations methods and statistical tests: canonical analyses (AFD, CCA, RDA, CAP), 'statistical tests on distance matrices, comparison of matrices (PERMANOVA, Mantel, Procrustes)

See full page

The courses present 4 aspects of Conservation Biology based on current scientific research in this discipline:  

1. Introduction to Biodiversity Conservation(BC): Definition of Conservation Biology Why conserve biodiversity? Who are the main actors in CB and the role of science in CB. 
2. Species conservation: What are the priority species? How to conserve species? How do you know if a species is "well conserved"? 
3. Space conservation: What are the priority spaces? How to conserve spaces? 
4. Does conservation work?Importance of social acceptability and political commitment. Need for biodiversity indicators and measuring the impact of conservation. 

Students also complete a group assignment in which they present a SA project around the questions: why, what, where, how, how much does it cost and how do we know if it is effective? 

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The goals of this course are to deepen the key concepts related to climate change, to illustrate important concepts in ecology and evolution in the light of climate change, in many different ecosystems, and to synthesize the different scientific and societal questions and issues raised by CC.

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"I - Physical characterization and biogeochemical cycles of coastal marine ecosystems II - Biodiversity and functioning of coastal marine ecosystems III - Law of the coast and the sea; Uses, conflicts and integrated management of the coastal zone. This course offers students a systemic approach to the study of coastal marine ecosystems from a multidisciplinary perspective. The physical structure of these ecosystems will be addressed through courses on their geomorphology and hydrology with a particular interest in the hydric couplings with the open sea and their watersheds. Their biogeochemistry will be addressed in particular to describe the fluxes of carbon and nutrients through the water and sediment compartments. Several aspects of their biodiversity will be illustrated to describe the importance of these ecosystems as a living environment for the species they support and in particular the role of this biodiversity in their functioning will be discussed. The coastal zone is densely populated by humans (40% of the world population). Particular interest will be given to human uses (e.g. aquaculture) and their territorial planning and in particular the evaluation of their ecosystem services in an economic context, management and protection measures (e.g. Marine Protected Areas, Natura 2000) and professionals in the management of these environments will present feedback from concrete experiences. Finally, the implications of the law of the sea for the management of the coastal zone will be taught. "

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The module presents lessons around the identification, quantification and modeling of interactions between climate, marine species and their exploitation.

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Behavioral Ecology approaches the study of behavior from an evolutionary perspective to study the mechanisms, function, and contribution of behavior to evolutionary and ecological processes. The work carried out in Behavioral Ecology helps to understand other phenomena observed in other disciplines of life biology, because all animals, from unicellulars to the most complex vertebrates, exhibit behaviors.

The module allows students to be exposed to the different basic concepts, as well as to the multitude of tools that can be used (observations and experiments in natural populations or on captive individuals, comparative analyses, use of tools from modeling, ecophysiology, molecular biology, biochemistry, embedded electronics...). Part of the training is based on specific discussions on the research approaches that can be used, the tools used and the limits of inferences that can be made. An active participation of the students will be required at these different levels, notably through critical discussions of articles.

The topics covered range from the exploration of food procurement strategies, mate choice, habitat choice, investment in reproduction, to the study of animal communication and the reasons for living in groups. The historical dimension of the discipline is addressed in the introduction, but also according to the sensibility of the speakers and the themes addressed (meaning and relations between 'Animal Behaviour', 'Ethology', Behavioral Ecology etc...).

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The objective of this resolutely transdisciplinary course is to provide skills useful for an effective management and a relevant exploitation of data of various origins and nature, and in particular with spatial component. The UE is composed of three successive complementary axes. The first one deals with the issues inherent to data compilation and the solutions provided by database management systems (DBMS): from database design to queries. The second deals with geographic information systems (GIS): from cartographic representation to geoprocessing. Finally, the third axis presents the diversity of spatial analysis tools that allow the quantitative exploitation of spatial data, whether it be metrics or statistical tests.

See full page

See full page

The pedagogical objective of this course is to reposition the main types of soil on a global scale, to explain their formation and to identify the mineral phases or the main abiotic factors likely to regulate the biological activity of soils. Based on this analysis, the different soil organisms (micro-organisms, micro-, meso- and macro-fauna) will be presented as well as their relationships in order to reposition the cycle of organic matter and mineral elements in the soil at different temporal and spatial scales. The notions of recycling, looping of biogeochemical cycles and community assembly rules will also be addressed. The organization of this course is based on lectures and conferences as well as fieldwork.

See full page

Ecophysiology is a discipline at the interface between organismal biology and ecology. Integrative ecophysiology focuses more particularly on the issue of scale change. In other words, the objective of this course is to illustrate how the study of acclimation/adaptation mechanisms at the individual (or even sub-individual) scale can explain the structure of populations, the distribution of species and the functioning of ecosystems. The responses of organisms and populations to the main abiotic structuring parameters (such as temperature, salinity, oxygen availability, pollutants) will be considered as well as their interactive effects. The role of interactions between organisms will also be addressed. In this course, animals, plants and microorganisms will be considered and different types of approaches will be illustrated: field observations, in situ or laboratory experiments.

See full page

The main objective of this course is to provide the necessary skills to understand and use the concepts and methods on which the quantitative study of population phenomena is based. The main methods of analysis and modelling of these phenomena will be approached both from a theoretical point of view (formal calculations) and from a practical point of view (statistics, simulations), by means of examples exploring the different phylogenetic scales (microbial dynamics, invasive species, human demography), spatial (from local to global) and temporal (transient and permanent regimes, eco-evolutionary coupling), with a particular attention to heterogeneity (spatial, genetic or phenotypic) and randomness (stochasticity, uncertainties) characteristic of populations or inherent to their study.

See full page

This course aims at better understanding the main types of pollutants (organic vs. inorganic), their source(s), their fate in the environment and the way they interact with living organisms (bioaccumulation, biotransformation, effects). The methods used in depollution and bioremediation will be discussed. A particular focus will be made on the contribution of terrestrial and aquatic plants in phytoremediation as well as on the role of microorganisms (bacteria, fungi) in the mechanisms of biodegradation, biotransformation or biosequestration. This course will be illustrated through different case studies through which examples of chronic and acute/accidental pollution of water, air and soil will be discussed. In particular, the treatment of pollution related to mining, petroleum, plastics and phyto-pharmaceutical industries as well as the treatment of liquid effluents (wastewater, industrial effluents) will be discussed. A field trip to Saint-Laurent-Le-Minier will illustrate a current project of phytoremediation of a former mining site.

See full page

The objective of this EU is to show that biological diversity is functional:

1) for different groups of organisms: plants, insects, aquatic organisms, vertebrates, and

2) at different scales of organization (from organisms to the ecosystem). The lessons aim to explain how to approach this functional facet of diversity for the 10+ million organisms present on the surface of the planet, by taking examples in very or slightly anthropized environments.

See full page

The objective of this resolutely transdisciplinary course is to provide skills useful for an effective management and a relevant exploitation of data of various origins and nature, and in particular with spatial component. The UE is composed of three successive complementary axes. The first one deals with the issues inherent to data compilation and the solutions provided by database management systems (DBMS): from database design to queries. The second deals with geographic information systems (GIS): from cartographic representation to geoprocessing. Finally, the third axis presents the diversity of spatial analysis tools that allow the quantitative exploitation of spatial data, whether it be metrics or statistical tests.

See full page

See full page

1. Bayesian inference: Motivation and simple example. 

2. The likelihood. 

3. A detour to explore priors. 

4. Markov chains Monte Carlo methods (MCMC)

5. Bayesian analyses in R with the Jags software.  

6. Contrast scientific hypotheses with model selection (WAIC).

7. Heterogeneity and multilevel models (aka mixed models. 

See full page

The module aims at providing theoretical and practical knowledge of statistical analysis of spatial and temporal constraints: classification and ordering under constraints, '2-table ordinations methods and statistical tests: canonical analyses (AFD, CCA, RDA, CAP), 'statistical tests on distance matrices, comparison of matrices (PERMANOVA, Mantel, Procrustes)

See full page

The courses present 4 aspects of Conservation Biology based on current scientific research in this discipline:  

1. Introduction to Biodiversity Conservation(BC): Definition of Conservation Biology Why conserve biodiversity? Who are the main actors in CB and the role of science in CB. 
2. Species conservation: What are the priority species? How to conserve species? How do you know if a species is "well conserved"? 
3. Space conservation: What are the priority spaces? How to conserve spaces? 
4. Does conservation work?Importance of social acceptability and political commitment. Need for biodiversity indicators and measuring the impact of conservation. 

Students also complete a group assignment in which they present a SA project around the questions: why, what, where, how, how much does it cost and how do we know if it is effective? 

See full page

The goals of this course are to deepen the key concepts related to climate change, to illustrate important concepts in ecology and evolution in the light of climate change, in many different ecosystems, and to synthesize the different scientific and societal questions and issues raised by CC.

See full page

"I - Physical characterization and biogeochemical cycles of coastal marine ecosystems II - Biodiversity and functioning of coastal marine ecosystems III - Law of the coast and the sea; Uses, conflicts and integrated management of the coastal zone. This course offers students a systemic approach to the study of coastal marine ecosystems from a multidisciplinary perspective. The physical structure of these ecosystems will be addressed through courses on their geomorphology and hydrology with a particular interest in the hydric couplings with the open sea and their watersheds. Their biogeochemistry will be addressed in particular to describe the fluxes of carbon and nutrients through the water and sediment compartments. Several aspects of their biodiversity will be illustrated to describe the importance of these ecosystems as a living environment for the species they support and in particular the role of this biodiversity in their functioning will be discussed. The coastal zone is densely populated by humans (40% of the world population). Particular interest will be given to human uses (e.g. aquaculture) and their territorial planning and in particular the evaluation of their ecosystem services in an economic context, management and protection measures (e.g. Marine Protected Areas, Natura 2000) and professionals in the management of these environments will present feedback from concrete experiences. Finally, the implications of the law of the sea for the management of the coastal zone will be taught. "

See full page

The module presents lessons around the identification, quantification and modeling of interactions between climate, marine species and their exploitation.

See full page

Behavioral Ecology approaches the study of behavior from an evolutionary perspective to study the mechanisms, function, and contribution of behavior to evolutionary and ecological processes. The work carried out in Behavioral Ecology helps to understand other phenomena observed in other disciplines of life biology, because all animals, from unicellulars to the most complex vertebrates, exhibit behaviors.

The module allows students to be exposed to the different basic concepts, as well as to the multitude of tools that can be used (observations and experiments in natural populations or on captive individuals, comparative analyses, use of tools from modeling, ecophysiology, molecular biology, biochemistry, embedded electronics...). Part of the training is based on specific discussions on the research approaches that can be used, the tools used and the limits of inferences that can be made. An active participation of the students will be required at these different levels, notably through critical discussions of articles.

The topics covered range from the exploration of food procurement strategies, mate choice, habitat choice, investment in reproduction, to the study of animal communication and the reasons for living in groups. The historical dimension of the discipline is addressed in the introduction, but also according to the sensibility of the speakers and the themes addressed (meaning and relations between 'Animal Behaviour', 'Ethology', Behavioral Ecology etc...).

See full page

See full page

1. Bayesian inference: Motivation and simple example. 

2. The likelihood. 

3. A detour to explore priors. 

4. Markov chains Monte Carlo methods (MCMC)

5. Bayesian analyses in R with the Jags software.  

6. Contrast scientific hypotheses with model selection (WAIC).

7. Heterogeneity and multilevel models (aka mixed models. 

See full page

The module aims at providing theoretical and practical knowledge of statistical analysis of spatial and temporal constraints: classification and ordering under constraints, '2-table ordinations methods and statistical tests: canonical analyses (AFD, CCA, RDA, CAP), 'statistical tests on distance matrices, comparison of matrices (PERMANOVA, Mantel, Procrustes)

See full page

The courses present 4 aspects of Conservation Biology based on current scientific research in this discipline:  

1. Introduction to Biodiversity Conservation(BC): Definition of Conservation Biology Why conserve biodiversity? Who are the main actors in CB and the role of science in CB. 
2. Species conservation: What are the priority species? How to conserve species? How do you know if a species is "well conserved"? 
3. Space conservation: What are the priority spaces? How to conserve spaces? 
4. Does conservation work?Importance of social acceptability and political commitment. Need for biodiversity indicators and measuring the impact of conservation. 

Students also complete a group assignment in which they present a SA project around the questions: why, what, where, how, how much does it cost and how do we know if it is effective? 

See full page

The goals of this course are to deepen the key concepts related to climate change, to illustrate important concepts in ecology and evolution in the light of climate change, in many different ecosystems, and to synthesize the different scientific and societal questions and issues raised by CC.

See full page

"I - Physical characterization and biogeochemical cycles of coastal marine ecosystems II - Biodiversity and functioning of coastal marine ecosystems III - Law of the coast and the sea; Uses, conflicts and integrated management of the coastal zone. This course offers students a systemic approach to the study of coastal marine ecosystems from a multidisciplinary perspective. The physical structure of these ecosystems will be addressed through courses on their geomorphology and hydrology with a particular interest in the hydric couplings with the open sea and their watersheds. Their biogeochemistry will be addressed in particular to describe the fluxes of carbon and nutrients through the water and sediment compartments. Several aspects of their biodiversity will be illustrated to describe the importance of these ecosystems as a living environment for the species they support and in particular the role of this biodiversity in their functioning will be discussed. The coastal zone is densely populated by humans (40% of the world population). Particular interest will be given to human uses (e.g. aquaculture) and their territorial planning and in particular the evaluation of their ecosystem services in an economic context, management and protection measures (e.g. Marine Protected Areas, Natura 2000) and professionals in the management of these environments will present feedback from concrete experiences. Finally, the implications of the law of the sea for the management of the coastal zone will be taught. "

See full page

The module presents lessons around the identification, quantification and modeling of interactions between climate, marine species and their exploitation.

See full page

Behavioral Ecology approaches the study of behavior from an evolutionary perspective to study the mechanisms, function, and contribution of behavior to evolutionary and ecological processes. The work carried out in Behavioral Ecology helps to understand other phenomena observed in other disciplines of life biology, because all animals, from unicellulars to the most complex vertebrates, exhibit behaviors.

The module allows students to be exposed to the different basic concepts, as well as to the multitude of tools that can be used (observations and experiments in natural populations or on captive individuals, comparative analyses, use of tools from modeling, ecophysiology, molecular biology, biochemistry, embedded electronics...). Part of the training is based on specific discussions on the research approaches that can be used, the tools used and the limits of inferences that can be made. An active participation of the students will be required at these different levels, notably through critical discussions of articles.

The topics covered range from the exploration of food procurement strategies, mate choice, habitat choice, investment in reproduction, to the study of animal communication and the reasons for living in groups. The historical dimension of the discipline is addressed in the introduction, but also according to the sensibility of the speakers and the themes addressed (meaning and relations between 'Animal Behaviour', 'Ethology', Behavioral Ecology etc...).

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The objective is to master the modeling and statistical analysis of ecosystem data. Students should be able to model complex systems (e.g. plant of a cultivated ecosystem, population dynamics, lake ecosystem). They will also need to know what type of statistical model to use for ecological data processing, and how to interpret it.

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The objective of this course is to accompany the student in the construction of his professional project and his search for an internship, while beginning to prepare his integration into professional life by an exhaustive and personal vision of possible career paths.

In concrete terms, meetings with different speakers allow the presentation of the doctoral thesis (presentation of the GAIA doctoral school, presentations by thesis students) and the professional environment targeted by the different courses (research professions and the non-academic sector). Activities specific to each pathway then help to better target the scientific fields most closely related to the students' professional projects. Lastly, the course includes practical sessions designed to prepare students to write scientific articles in English.

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This course approaches the issues surrounding ecosystem management from the perspective of social sciences, and more particularly "science studies". It aims to contribute to the development of a general culture related to the relationship between ecological sciences and societies, and to equip participants to analyze social issues and underlying socio-scientific controversies. The first part of the course provides a conceptual and methodological framework for the presentation of a reflexive tool for analyzing the interplay of actors and arguments (epistemological, axiological) involved in socioscientific controversies, and illustrates this tool with current examples. Subsequently, thematic presentations by ecological researchers illustrate a variety of issues surrounding ecological sciences, and serve as a basis for the application and acquisition by students of the reflexive analysis tool. Students are evaluated on their ability to mobilize this analytical framework in order to position themselves in an individual and argued manner in controversies related to ecological sciences.

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The objective of this course is to help students finalize their professional projects and prepare for the post-master's program.

The EU is organized at the level of the course, with regular discussion sessions between the teaching staff and the students.

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The individual M2 internship lasts approximately 5 to 6 months and must be carried out, depending on the course, in a research laboratory or a structure in the non-academic sector. It allows the student to acquire in-depth professional experience in the field of biodiversity, evolution or ecology. It can be carried out in a local, national, or international structure, on a subject validated by the teaching staff in order to meet the objectives of the course followed by the student.

Evaluation: The internship is evaluated during a public defense before a jury during which the content of the thesis and the quality of the answers to the jury's questions are evaluated. The behavior and dynamism of the student during the internship are evaluated by the internship supervisor.

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"General linear models with 1 or more explanatory random variables: from translating the figure that answers the biological question to the statistical model, i.e., taking into account many effects and knowing how to interpret them

general properties seen through regression and 1-factor ANOVA (R2, F, ddl, least squares, likelihood, diagnosis, validation, goodness of fit, interpretation of effect sizes); nested and cross-factor ANOVA, multiple regression (notion of parameter and effects, and interaction)

incorporation of the dependence of explanatory random variables, confounding of effects (quantitative for multiple regression, and unbalanced designs for ANOVA)".

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The general objective is to consolidate the basic knowledge of ecology acquired by the students, and to give them the tools to mobilize it in an integrative way to interpret the functioning of ecological systems. The courses include: 1) lectures on the concepts of ecology from the population scale to macroecological scales, with examples of applications that place the discipline in the current ecological and societal context; 2) practical and directed work focused on tools (sampling strategies, modeling, data analysis); 3) field courses during which students are invited to ask themselves relevant scientific questions based on observation in a situation, and to mobilize their knowledge in order to respond to them in an argumentative manner.

Synthetic content of the EU :

- CM: History of the emergence of concepts in ecology; Population dynamics / metapopulations; Biotic interactions and food webs; Community ecology, meta-communities; Ecology of ecosystems / functional ecology; Notions of macroecology / biogeography; Global changes and ecosystem functioning;

- Field: Integrative Analysis of Ecosystem Functioning in Situations;

- TD/TP: sampling and experimental strategies in ecology; modeling in population/meta-population dynamics, community/meta-community ecology, food webs; biodiversity metrics (alpha, beta, etc)."

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"The general objective is to consolidate the students' bases in evolutionary biology, by approaching both (i) macro-evolutionary phenomena, and the general methods used for their analysis and (ii) micro-evolutionary processes by insisting on the population genetic approach. The objective of this course is to provide a common base of solid knowledge in evolutionary biology and to illustrate the applications of the discipline to the students' future fields of specialization. The teaching includes: 1) lectures on evolutionary concepts; 2) practical work in two main forms: 2a. sessions focused on the use of tools (phylogeny) and on the mathematical formalization of evolutionary processes (population genetics) as well as 2b: sessions built around group work, allowing students, depending on their career path and professional objectives, to go deeper into a particular theme (fundamental question or application of evolutionary biology)."

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English tutorials aimed at professional autonomy in the English language.

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Generalized linear mixed models + methodology and experimental protocols to take into account a biological reality: non-normal law and pseudo-replication

Protocol optimization, power and uncontrolled 1st order risk: variable transformation, polynomial regression, link function, likelihood, model selection

Deviance analysis and goodness of fit

Incorporation of blocks, repeated measurements over time, taking into account spatial and temporal correlation, over-dispersion

Graphical representation of predictions.

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The objective of this course is to provide the necessary basis in statistics to follow all the more elaborate modules of the curriculum, so it is a general refresher. Descriptive statistics are reviewed (quantile, polygon of cumulative frequencies, estimators from samples), simple tests are presented, essential graphs for univariate and multivariate data are presented, the general principle of a statistical test, the hypothesis plan, the notion of p-value, first and second species risk are presented. In practical exercises, students are also brought up to speed in the R environment.

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Based on concepts and methods of Ecology, this course aims at discovering and practicing historical ecology (study of the interactions between Man and his environment over variable chronological periods) and its main applications in paleoecology and environmental sciences: climatic changes, biodiversity fluctuations, vegetation transformation, forest dynamics, disturbance ecology, bioarchaeology. The work done in pairs or in triads under the responsibility of a referee, covers the entire research chain, from the definition of the problem, sampling in the field, data acquisition to interpretation, writing a scientific article (see https://biologie-ecologie.com/exemples-travaux/) and oral presentation of the results. ORPAM takes place during the first weeks of teaching. This UE starts with a 3-day field school (24h - integration internship) and continues with a mini internship in a laboratory (24h). The UE ends with the writing of a scientific article and an oral presentation of the results.

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The objectives of this EU are twofold. On the one hand, it is a question of placing all the major stages of the history of organisms on Earth since the birth of the latter. Thus, themes such as the appearance of life, the colonization of continents, the appearance of angiosperms, glacial/interglacial cycles and the domestication of plants will be covered. On the other hand, it will be shown how paleoecology is part of modernity, whether it is on methodological developments (geochemistry, optical, electron and X-ray microscopy, etc.), on prediction models of climate evolution, ecosystem management in the context of global change or on biotechnology developments. The course will be mainly organized in lectures, each of which will be given by a specialist in the field.

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The individual internship in M1 lasts about three months and must be carried out, depending on the course, in a research laboratory or a structure in the non-academic sector. It allows the student to acquire professional experience in the field of biodiversity, evolution or ecology. It can be carried out in a local, national, or international structure, on a subject validated by the teaching staff in order to meet the objectives of the course followed by the student.

Evaluation: The preparation of the internship is a graded exercise based on a written document and a defense of the internship project. The internship work is evaluated during a public defense before a jury during which the content of the thesis and the quality of the answers to the jury's questions are evaluated. The behavior and dynamism of the student during the internship are evaluated by the internship supervisor.

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This teaching unit aims to link theoretical ecology, its operational implementation and the issues of territories as seen by society's actors. Built on a format combining theoretical courses recalling the elements necessary for the understanding of field issues (ecosystem dynamics, anthropization, resilience of socio-ecosystems, in situ conservation, etc.), this UE includes several field blocks (each consisting of a preparatory TD/TP and an "active" field trip). The territories visited will allow the students to meet actors from society (managers, elected officials, associations, shepherds, etc.) whose position allows them to understand how ecological issues govern their actions, and how in return their actions impact biodiversity, its dynamics and its distribution.

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How is biodiversity distributed on Earth? What ecological, evolutionary and historical factors determine these patterns of biodiversity distribution? What are the changes induced by human activities on the global distribution of biodiversity? In this course, we will study the role of spatio-temporal variations in the global environment on the dynamics of biodiversity. In particular, we will examine the influence of long-term climate cycles on the past and present diversity of organisms. We will also address the impact of human activities and global changes on biodiversity at the planetary scale.

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"This module presents table management and the link between multivariate and univariate: matrix manipulation and common operations; notion of projection and distance; translation of descriptive and univariate statistics with multiple regression/ACP/AFD as an example; (dis)similarity indices, distance; correlation"

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"The objective of this course is to consolidate the students' knowledge of ecology and/or evolution by inviting them to define a research topic and question(s), by defining relevant hypotheses in an arguable manner, and by justifying a strategy for acquiring and analyzing data to test them.

Synthetic content of the EU:

- Independent tutored work: identification of a relevant scientific question; bibliographic synthesis allowing to realize the state of the art and to justify the scientific hypotheses; proposal and justification of a methodological approach (material and methods) to test the proposed hypotheses.

Type of topics:

The topics can be on any question identified by the students (in groups of 3/4), and validated by the teaching staff, and can be based on different approaches allowing to adjust to the expectations of the different courses. For example, students can propose a sampling strategy in the field or in experiments, a meta-analysis of data from the literature, an analysis of sequences retrieved from GenBank, an analysis of occurrence data retrieved from GBIF, etc.

In all cases, the projects must involve a real data acquisition strategy, identified, justified and described by the students in the material and method requested in M1S2, with a provisional timetable for the project and identification of the tasks that each student will carry out within each group as part of the implementation of the project in M2S3 The projects must also be financially realistic and propose a provisional budget, and must be able to be finalized in the time available in M2S3.

Methods of control of knowledge:

The teaching is based on a problem-based learning approach, and students are evaluated on the way they progress in building their approach (40% of CC), as well as on their ability to present and defend their project during a final oral (60% of the overall grade)."

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The objective of this UE is to allow the implementation of projects defined in the framework of the UE project of M1S2.

Synthetic content of the EU:

- Tutor-led autonomous work by groups of students: readjustment of the project's objectives and methodology if necessary, acquisition of data, ecological and/or evolutionary analyses and interpretations according to the provisional schedule defined in M1S2, restitution of results in the framework of a conference common to the different courses.

Methods of control of knowledge:

As for the M1 project UE, the UE is based on a problem-based learning approach. Students are therefore evaluated as they go along on how they are progressing with their project (40% CC), and then at the end of the semester on their ability to present the results of their project and discuss them in an oral presentation at a general restitution conference (60% of the overall mark).

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This course focuses on the analysis of the impact of man on the climate and the environment

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To present different methodological approaches in an applied approach, from data acquisition to interpretation. Each approach is covered in a half-day (3h), addressing the methods of data acquisition (1.5h TP) and the interpretation of results (1.5h TD).

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"This course aims to present and explain the concepts, the problems, the operational approach in the field and in the laboratory, the methodological and analytical strategies that allow us to infer and reconstruct the fluctuations of wild and human-used biodiversity over time. It is based on empirical and modelled, ecological, palaeoecological, palaeobiogeographical, archaeobiological and palethnobiological data sets. Particular attention will be paid to:

- the functional role of ecological disturbances such as fire in the transformation of the vegetation cover;

- the impact of the evolution of human societies on the dynamics of forest ecosystems;

- exploitation, cultivation / breeding and domestication of plants and animals based on the study of modern and bioarchaeological data. "

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The objective of this course is to accompany the student in the construction of his professional project and his search for an internship, while beginning to prepare his integration into professional life by an exhaustive and personal vision of possible career paths.

In concrete terms, meetings with different speakers allow the presentation of the doctoral thesis (presentation of the GAIA doctoral school, presentations by thesis students) and the professional environment targeted by the different courses (research professions and the non-academic sector). Activities specific to each pathway then help to better target the scientific fields most closely related to the students' professional projects. Lastly, the course includes practical sessions designed to prepare students to write scientific articles in English.

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In this course we will approach the main theoretical concepts of evolutionary processes through the fossil record. The aim is to reconcile microevolutionary mechanisms with macroevolution. The concepts addressed will be: species and intraspecific variability, speciation and evolutionary rhythms, adaptive radiation (ecological speciation) in the fossil record, targeted extinctions (migrant-autochthonous competition) or mass extinctions (major biological crises), evolutionary modalities (anagenesis and saltationism) observed in the fossil record and a comprehensive review of microevolutionary mechanisms.

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The objective of this resolutely transdisciplinary course is to provide skills useful for an effective management and a relevant exploitation of data of various origins and nature, and in particular with spatial component. The UE is composed of three successive complementary axes. The first one deals with the issues inherent to data compilation and the solutions provided by database management systems (DBMS): from database design to queries. The second deals with geographic information systems (GIS): from cartographic representation to geoprocessing. Finally, the third axis presents the diversity of spatial analysis tools that allow the quantitative exploitation of spatial data, whether it be metrics or statistical tests.

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The pedagogical objective of this course is to reposition the main types of soil on a global scale, to explain their formation and to identify the mineral phases or the main abiotic factors likely to regulate the biological activity of soils. Based on this analysis, the different soil organisms (micro-organisms, micro-, meso- and macro-fauna) will be presented as well as their relationships in order to reposition the cycle of organic matter and mineral elements in the soil at different temporal and spatial scales. The notions of recycling, looping of biogeochemical cycles and community assembly rules will also be addressed. The organization of this course is based on lectures and conferences as well as fieldwork.

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"The objective is to analyze the phylogenetic, developmental and functional constraints that may have governed the morphological changes discernible in the fossil record. The phylogenetic approach will be approached by reconstruction methods applicable to fossils (parsimony; cladistic analysis). Developmental and functional approaches (mainly odontology) will be illustrated by different methodologies developed on the Montpellier campus (notably X-ray microtomography). The critical review of reference articles in the considered field will give rise to an oral presentation followed by questions."

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Land use change is responsible for about 10% of anthropogenic carbon dioxide emissions. Tropical forest ecosystems can participate in both pillars of addressing global warming, namely mitigation and adaptation:

-Tropical forests and plantations are important potential carbon sinks, their biomass can provide energy to replace fossil fuels, while reducing deforestation and forest degradation and improving forest management (REDD+) can significantly reduce anthropogenic GHG emissions

-The ability of human societies, which are still essentially rural, to adapt to climate change depends in part on the state of available natural resources, while the necessary adaptation of tropical ecosystems to climate change can be facilitated by human interventions.

In the context of the implementation of the United Nations Framework Convention on Climate Change, mechanisms such as the Sustainable Development Mechanism (SDM) and REDD+, and voluntary markets, as well as ecosystem-based adaptation to climate change, provide a new opportunity for tropical forestry, as well as a potential lever for tropical forest protection or restoration. The module provides an understanding of the basic concepts of climate change, the role of tropical ecosystems in the global carbon cycle, and the technical, policy and economic responses to climate change issues.

Module Content:

This module provides basic knowledge on topics such as the carbon cycle, the mechanisms and consequences of climate change, and the technical and policy frameworks for mitigation and adaptation to climate change. The potential of tropical agro-ecosystems is assessed based on scientific studies and existing operational projects.

Teaching and Learning Methods:

-Course (18 hours)

-TD (3 hours).

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1. Bayesian inference: Motivation and simple example. 

2. The likelihood. 

3. A detour to explore priors. 

4. Markov chains Monte Carlo methods (MCMC)

5. Bayesian analyses in R with the Jags software.  

6. Contrast scientific hypotheses with model selection (WAIC).

7. Heterogeneity and multilevel models (aka mixed models. 

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1 "The way in which the modern West represents nature is the least shared thing in the world" (Descola, 2005, p. 56). According to anthropologist Philippe Descola, the category of "Nature," as a reality separate from the human world, is an invention of Europeans that is only one of the possibilities available to societies to account for the living and non-living beings that surround them.

If Philippe Descola contributes to renewing questions about the relationship between society and the environment, he nevertheless draws on a long tradition in the human and social sciences. Numerous works have already explored the various forms of knowledge and social organization to which these relationships give rise: ethnoscience, anthropology of technology, economic anthropology, ethnoecology, sociology of science and technology, etc.

This issue is far from being confined to the academic sphere. It also arouses the interest of actors in conservation (biodiversity, natural resources, etc.) and industry (pharmacology). It also mobilizes so-called "indigenous" populations who claim, both locally and internationally, access to resources and the preservation of an intangible heritage.

2. Situated at the meeting point of the social sciences and the life sciences, these disciplines analyze how human societies use plants, animals, and other components of the environment, but also how their conceptions and representations of their environment(s) guide these uses. This research also explores how human societies organize themselves, perpetuate themselves, change to adapt to new contexts (globalization, global changes) and transmit knowledge about their relationships with nature.

For a long time, these disciplines focused more specifically on the interrelations between so-called "traditional" societies and their immediate environment. Subsequently, since the 1970s, researchers have reconsidered the distinction between so-called "traditional" and "modern" societies in order to better address new contemporary environmental and social transformations.

Indeed, on the one hand, local societies, even the most isolated, are affected by events that are decided and take place on different scales (international conventions, economic crises). Their immediate environment is also affected by global phenomena (climate change, erosion of biodiversity, etc.). In return, their actions can also have international ecological, social and economic repercussions, when, for example, these societies organize themselves to bring their claims to international arenas.

On the other hand, the relationship that modern societies have with their environment is being reconfigured in the face of the observation that the planet is increasingly "artificialized" and threatened by ruptures and serious crises. The place of fauna and flora is being reconsidered and is the subject of controversy as to their rights. Moreover, the entry into a new geological era, the Anthropocene, is invoked to challenge both the natural sciences and the human and social sciences on the need to consider differently a common history of the environment and societies.

3. The very work of scientists and engineers is apprehended in a new light. In this respect, a new scientific project in the humanities and social sciences aims at reconsidering the role of "non-humans" and calls for finding other analytical categories than those of Nature and Culture. New scales and methods of investigation are also envisaged to analyze global processes.

These recent changes in scale invite the researcher in the humanities and social sciences to (re)consider his or her approach through a reflexive approach: he or she is no longer a simple observer, but can also be a real actor in the processes, when not directly involved in a social movement.

4. The objective of this module is to introduce these different scientific and operational fields. It is to provide students with reference points and elements for reflection, in order to be able to construct scientific questions on the relationships between societies and the environment, in order to reflect on the ways in which current environmental and social issues can be dealt with. The varied geographical and disciplinary experiences of the speakers will make it possible to illustrate the approach through a wide range of ecosystem types, socio-cultural contexts and themes. In the time available, we will not pretend to cover all the themes, approaches and methods in an exhaustive manner. Any student wishing to delve deeper into this area will need to engage in a more in-depth training process.

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The objective of this course is to help students finalize their professional projects and prepare for the post-master's program.

The EU is organized at the level of the course, with regular discussion sessions between the teaching staff and the students.

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The individual M2 internship lasts approximately 5 to 6 months and must be carried out, depending on the course, in a research laboratory or a structure in the non-academic sector. It allows the student to acquire in-depth professional experience in the field of biodiversity, evolution or ecology. It can be carried out in a local, national, or international structure, on a subject validated by the teaching staff in order to meet the objectives of the course followed by the student.

Evaluation: The internship is evaluated during a public defense before a jury during which the content of the thesis and the quality of the answers to the jury's questions are evaluated. The behavior and dynamism of the student during the internship are evaluated by the internship supervisor.

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"General linear models with 1 or more explanatory random variables: from translating the figure that answers the biological question to the statistical model, i.e., taking into account many effects and knowing how to interpret them

general properties seen through regression and 1-factor ANOVA (R2, F, ddl, least squares, likelihood, diagnosis, validation, goodness of fit, interpretation of effect sizes); nested and cross-factor ANOVA, multiple regression (notion of parameter and effects, and interaction)

incorporation of the dependence of explanatory random variables, confounding of effects (quantitative for multiple regression, and unbalanced designs for ANOVA)".

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The general objective is to consolidate the basic knowledge of ecology acquired by the students, and to give them the tools to mobilize it in an integrative way to interpret the functioning of ecological systems. The courses include: 1) lectures on the concepts of ecology from the population scale to macroecological scales, with examples of applications that place the discipline in the current ecological and societal context; 2) practical and directed work focused on tools (sampling strategies, modeling, data analysis); 3) field courses during which students are invited to ask themselves relevant scientific questions based on observation in a situation, and to mobilize their knowledge in order to respond to them in an argumentative manner.

Synthetic content of the EU :

- CM: History of the emergence of concepts in ecology; Population dynamics / metapopulations; Biotic interactions and food webs; Community ecology, meta-communities; Ecology of ecosystems / functional ecology; Notions of macroecology / biogeography; Global changes and ecosystem functioning;

- Field: Integrative Analysis of Ecosystem Functioning in Situations;

- TD/TP: sampling and experimental strategies in ecology; modeling in population/meta-population dynamics, community/meta-community ecology, food webs; biodiversity metrics (alpha, beta, etc)."

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"The general objective is to consolidate the students' bases in evolutionary biology, by approaching both (i) macro-evolutionary phenomena, and the general methods used for their analysis and (ii) micro-evolutionary processes by insisting on the population genetic approach. The objective of this course is to provide a common base of solid knowledge in evolutionary biology and to illustrate the applications of the discipline to the students' future fields of specialization. The teaching includes: 1) lectures on evolutionary concepts; 2) practical work in two main forms: 2a. sessions focused on the use of tools (phylogeny) and on the mathematical formalization of evolutionary processes (population genetics) as well as 2b: sessions built around group work, allowing students, depending on their career path and professional objectives, to go deeper into a particular theme (fundamental question or application of evolutionary biology)."

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English tutorials aimed at professional autonomy in the English language.

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This teaching unit is part of a pre-professionalization framework. It aims to reflect on the professional integration project through meetings with scientific mediation professionals, involvement in scientific mediation work at the interface between the world of research and secondary education (assistance in carrying out environmental and sustainable development education projects by secondary school classes) and analysis of projects developed by Master 2 students.

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Generalized linear mixed models + methodology and experimental protocols to take into account a biological reality: non-normal law and pseudo-replication

Protocol optimization, power and uncontrolled 1st order risk: variable transformation, polynomial regression, link function, likelihood, model selection

Deviance analysis and goodness of fit

Incorporation of blocks, repeated measurements over time, taking into account spatial and temporal correlation, over-dispersion

Graphical representation of predictions.

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The objective of this course is to provide the necessary basis in statistics to follow all the more elaborate modules of the curriculum, so it is a general refresher. Descriptive statistics are reviewed (quantile, polygon of cumulative frequencies, estimators from samples), simple tests are presented, essential graphs for univariate and multivariate data are presented, the general principle of a statistical test, the hypothesis plan, the notion of p-value, first and second species risk are presented. In practical exercises, students are also brought up to speed in the R environment.

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The individual internship in M1 lasts about three months and must be carried out, depending on the course, in a research laboratory or a structure in the non-academic sector. It allows the student to acquire professional experience in the field of biodiversity, evolution or ecology. It can be carried out in a local, national, or international structure, on a subject validated by the teaching staff in order to meet the objectives of the course followed by the student.

Evaluation: The preparation of the internship is a graded exercise based on a written document and a defense of the internship project. The internship work is evaluated during a public defense before a jury during which the content of the thesis and the quality of the answers to the jury's questions are evaluated. The behavior and dynamism of the student during the internship are evaluated by the internship supervisor.

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The mediation (scientific or not) is more and more based on digital tools for the diffusion of information which allow to reach a large public very quickly. These tools are numerous and diversified and it is complicated to make the tour in a simple way. Nevertheless, in the vast majority of job offers or internships in the field of mediation, knowledge in the use of these digital mediation tools is required.

The objective of this course is to present the main tools of digital mediation and to initiate the use of these tools by students intending to work in scientific mediation. The EU will also discuss the importance of sourcing and verifying data in an era where untruths and even lies are increasingly visible.

The first part of the course will take place in the form of TD/TP allowing to approach the main digital tools of scientific mediation. Examples put online by different mediation organizations will be analyzed in order to detail the strong and weak points.

The second part of the course will be practical. The students will have to visit scientific mediation structures (temporary or permanent) and will have to make reports using digital tools of scientific mediation. In particular, one of the reports will be focused on the scientific activity of the Biology and Ecology teaching department and will be put online on the department's website.

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This teaching unit aims to link theoretical ecology, its operational implementation and the issues of territories as seen by society's actors. Built on a format combining theoretical courses recalling the elements necessary for the understanding of field issues (ecosystem dynamics, anthropization, resilience of socio-ecosystems, in situ conservation, etc.), this UE includes several field blocks (each consisting of a preparatory TD/TP and an "active" field trip). The territories visited will allow the students to meet actors from society (managers, elected officials, associations, shepherds, etc.) whose position allows them to understand how ecological issues govern their actions, and how in return their actions impact biodiversity, its dynamics and its distribution.

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How is biodiversity distributed on Earth? What ecological, evolutionary and historical factors determine these patterns of biodiversity distribution? What are the changes induced by human activities on the global distribution of biodiversity? In this course, we will study the role of spatio-temporal variations in the global environment on the dynamics of biodiversity. In particular, we will examine the influence of long-term climate cycles on the past and present diversity of organisms. We will also address the impact of human activities and global changes on biodiversity at the planetary scale.

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"This module presents table management and the link between multivariate and univariate: matrix manipulation and common operations; notion of projection and distance; translation of descriptive and univariate statistics with multiple regression/ACP/AFD as an example; (dis)similarity indices, distance; correlation"

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The objectives of this EU are twofold. On the one hand, it is a question of placing all the major stages of the history of organisms on Earth since the birth of the latter. Thus, themes such as the appearance of life, the colonization of continents, the appearance of angiosperms, glacial/interglacial cycles and the domestication of plants will be covered. On the other hand, it will be shown how paleoecology is part of modernity, whether it is on methodological developments (geochemistry, optical, electron and X-ray microscopy, etc.), on prediction models of climate evolution, ecosystem management in the context of global change or on biotechnology developments. The course will be mainly organized in lectures, each of which will be given by a specialist in the field.

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"The objective of this course is to consolidate the students' knowledge of ecology and/or evolution by inviting them to define a research topic and question(s), by defining relevant hypotheses in an arguable manner, and by justifying a strategy for acquiring and analyzing data to test them.

Synthetic content of the EU:

- Independent tutored work: identification of a relevant scientific question; bibliographic synthesis allowing to realize the state of the art and to justify the scientific hypotheses; proposal and justification of a methodological approach (material and methods) to test the proposed hypotheses.

Type of topics:

The topics can be on any question identified by the students (in groups of 3/4), and validated by the teaching staff, and can be based on different approaches allowing to adjust to the expectations of the different courses. For example, students can propose a sampling strategy in the field or in experiments, a meta-analysis of data from the literature, an analysis of sequences retrieved from GenBank, an analysis of occurrence data retrieved from GBIF, etc.

In all cases, the projects must involve a real data acquisition strategy, identified, justified and described by the students in the material and method requested in M1S2, with a provisional timetable for the project and identification of the tasks that each student will carry out within each group as part of the implementation of the project in M2S3 The projects must also be financially realistic and propose a provisional budget, and must be able to be finalized in the time available in M2S3.

Methods of control of knowledge:

The teaching is based on a problem-based learning approach, and students are evaluated on the way they progress in building their approach (40% of CC), as well as on their ability to present and defend their project during a final oral (60% of the overall grade)."

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The objective of this UE is to allow the implementation of projects defined in the framework of the UE project of M1S2.

Synthetic content of the EU:

- Tutor-led autonomous work by groups of students: readjustment of the project's objectives and methodology if necessary, acquisition of data, ecological and/or evolutionary analyses and interpretations according to the provisional schedule defined in M1S2, restitution of results in the framework of a conference common to the different courses.

Methods of control of knowledge:

As for the M1 project UE, the UE is based on a problem-based learning approach. Students are therefore evaluated as they go along on how they are progressing with their project (40% CC), and then at the end of the semester on their ability to present the results of their project and discuss them in an oral presentation at a general restitution conference (60% of the overall mark).

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"The teaching takes the form of an interdisciplinary project (biology-ecology-geology) combining a field approach, bibliographical studies, meetings with professionals or resource persons and scientific mediation. The objective is to produce a synthetic scientific study of a territory, by relating the bio-ecological-geological characteristics of the area to its economic, social, historical and/or heritage specificities. Students work in small groups (generally 2; maximum 3), under the responsibility of a tutor. They must produce a written dissertation (scientific mediation book type) and a one-day field session, tested with a group of students and teachers. "

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The teaching takes the form of a project based on an essentially bibliographical approach. It is a study of the epistemology and history of science based on the work of a scientist in the fields of Life Sciences or Earth and Universe Sciences. The student must highlight the key points of the scientist's work, placing them in the scientific-historical-political context of his or her time, highlighting the advances and controversies, the contributions to science and the interests in scientific mediation. At the end of his or her work, carried out under the responsibility of a tutor, the student produces a written thesis, a poster and an oral presentation.

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The individual M2 internship lasts approximately 5 to 6 months and must be carried out, depending on the course, in a research laboratory or a structure in the non-academic sector. It allows the student to acquire in-depth professional experience in the field of biodiversity, evolution or ecology. It can be carried out in a local, national, or international structure, on a subject validated by the teaching staff in order to meet the objectives of the course followed by the student.

Evaluation: The internship is evaluated during a public defense before a jury during which the content of the thesis and the quality of the answers to the jury's questions are evaluated. The behavior and dynamism of the student during the internship are evaluated by the internship supervisor.

See full page

The objective of this course is to help students finalize their professional projects and prepare for the post-master's program.

The EU is organized at the level of the course, with regular discussion sessions between the teaching staff and the students.

See full page

"General linear models with 1 or more explanatory random variables: from translating the figure that answers the biological question to the statistical model, i.e., taking into account many effects and knowing how to interpret them

general properties seen through regression and 1-factor ANOVA (R2, F, ddl, least squares, likelihood, diagnosis, validation, goodness of fit, interpretation of effect sizes); nested and cross-factor ANOVA, multiple regression (notion of parameter and effects, and interaction)

incorporation of the dependence of explanatory random variables, confounding of effects (quantitative for multiple regression, and unbalanced designs for ANOVA)".

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Generalized linear mixed models + methodology and experimental protocols to take into account a biological reality: non-normal law and pseudo-replication

Protocol optimization, power and uncontrolled 1st order risk: variable transformation, polynomial regression, link function, likelihood, model selection

Deviance analysis and goodness of fit

Incorporation of blocks, repeated measurements over time, taking into account spatial and temporal correlation, over-dispersion

Graphical representation of predictions.

See full page

The objective of this course is to provide the necessary basis in statistics to follow all the more elaborate modules of the curriculum, so it is a general refresher. Descriptive statistics are reviewed (quantile, polygon of cumulative frequencies, estimators from samples), simple tests are presented, essential graphs for univariate and multivariate data are presented, the general principle of a statistical test, the hypothesis plan, the notion of p-value, first and second species risk are presented. In practical exercises, students are also brought up to speed in the R environment.

See full page

The general objective is to consolidate the basic knowledge of ecology acquired by the students, and to give them the tools to mobilize it in an integrative way to interpret the functioning of ecological systems. The courses include: 1) lectures on the concepts of ecology from the population scale to macroecological scales, with examples of applications that place the discipline in the current ecological and societal context; 2) practical and directed work focused on tools (sampling strategies, modeling, data analysis); 3) field courses during which students are invited to ask themselves relevant scientific questions based on observation in a situation, and to mobilize their knowledge in order to respond to them in an argumentative manner.

Synthetic content of the EU :

- CM: History of the emergence of concepts in ecology; Population dynamics / metapopulations; Biotic interactions and food webs; Community ecology, meta-communities; Ecology of ecosystems / functional ecology; Notions of macroecology / biogeography; Global changes and ecosystem functioning;

- Field: Integrative Analysis of Ecosystem Functioning in Situations;

- TD/TP: sampling and experimental strategies in ecology; modeling in population/meta-population dynamics, community/meta-community ecology, food webs; biodiversity metrics (alpha, beta, etc)."

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"The general objective is to consolidate the students' bases in evolutionary biology, by approaching both (i) macro-evolutionary phenomena, and the general methods used for their analysis and (ii) micro-evolutionary processes by insisting on the population genetic approach. The objective of this course is to provide a common base of solid knowledge in evolutionary biology and to illustrate the applications of the discipline to the students' future fields of specialization. The teaching includes: 1) lectures on evolutionary concepts; 2) practical work in two main forms: 2a. sessions focused on the use of tools (phylogeny) and on the mathematical formalization of evolutionary processes (population genetics) as well as 2b: sessions built around group work, allowing students, depending on their career path and professional objectives, to go deeper into a particular theme (fundamental question or application of evolutionary biology)."

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English tutorials aimed at professional autonomy in the English language.

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The objective of this course is to introduce students to the diversity of plants in tropical environments, from a botanical, morphological and functional point of view. Lessons include an introduction to tropical biodiversity and its observation, the taxonomic and phylogenetic diversity of the major tropical families, the life forms of tropical plants (morphology and anatomy, architecture), their ecophysiology (diversity of phenolic compounds, link with adaptation and distribution), functional ecology (general notions, responses to environmental gradients, specializations, plant succession), the diversity of biotic interactions, notions of coevolution (symbioses, reproductive systems, dispersion).

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The individual internship in M1 lasts about three months and must be carried out, depending on the course, in a research laboratory or a structure in the non-academic sector. It allows the student to acquire professional experience in the field of biodiversity, evolution or ecology. It can be carried out in a local, national, or international structure, on a subject validated by the teaching staff in order to meet the objectives of the course followed by the student.

Evaluation: The preparation of the internship is a graded exercise based on a written document and a defense of the internship project. The internship work is evaluated during a public defense before a jury during which the content of the thesis and the quality of the answers to the jury's questions are evaluated. The behavior and dynamism of the student during the internship are evaluated by the internship supervisor.

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This teaching unit aims to link theoretical ecology, its operational implementation and the issues of territories as seen by society's actors. Built on a format combining theoretical courses recalling the elements necessary for the understanding of field issues (ecosystem dynamics, anthropization, resilience of socio-ecosystems, in situ conservation, etc.), this UE includes several field blocks (each consisting of a preparatory TD/TP and an "active" field trip). The territories visited will allow the students to meet actors from society (managers, elected officials, associations, shepherds, etc.) whose position allows them to understand how ecological issues govern their actions, and how in return their actions impact biodiversity, its dynamics and its distribution.

See full page

How is biodiversity distributed on Earth? What ecological, evolutionary and historical factors determine these patterns of biodiversity distribution? What are the changes induced by human activities on the global distribution of biodiversity? In this course, we will study the role of spatio-temporal variations in the global environment on the dynamics of biodiversity. In particular, we will examine the influence of long-term climate cycles on the past and present diversity of organisms. We will also address the impact of human activities and global changes on biodiversity at the planetary scale.

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The teaching of this module is an introduction to ethnobotany and ethnoecology in order to understand the material and immaterial dimensions of the relationships between humans and their environment, with a particular focus on the plant world. We will be particularly interested in local systems of nomenclature and classification, perceptions and representations of nature, uses and management practices of resources, biocultural, ecological and evolutionary interactions. Ethnobotany and ethnoecology are disciplines at the interface of anthropology, botany and ecology, which can also borrow tools and concepts from linguistics, archaeology, geography and agronomy. This module complements the "Ethnoecology and Sustainable Development" module (Master 2) by providing the theoretical and methodological bases of ethnobotany.

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"The objective of this course is to consolidate the students' knowledge of ecology and/or evolution by inviting them to define a research topic and question(s), by defining relevant hypotheses in an arguable manner, and by justifying a strategy for acquiring and analyzing data to test them.

Synthetic content of the EU:

- Independent tutored work: identification of a relevant scientific question; bibliographic synthesis allowing to realize the state of the art and to justify the scientific hypotheses; proposal and justification of a methodological approach (material and methods) to test the proposed hypotheses.

Type of topics:

The topics can be on any question identified by the students (in groups of 3/4), and validated by the teaching staff, and can be based on different approaches allowing to adjust to the expectations of the different courses. For example, students can propose a sampling strategy in the field or in experiments, a meta-analysis of data from the literature, an analysis of sequences retrieved from GenBank, an analysis of occurrence data retrieved from GBIF, etc.

In all cases, the projects must involve a real data acquisition strategy, identified, justified and described by the students in the material and method requested in M1S2, with a provisional timetable for the project and identification of the tasks that each student will carry out within each group as part of the implementation of the project in M2S3 The projects must also be financially realistic and propose a provisional budget, and must be able to be finalized in the time available in M2S3.

Methods of control of knowledge:

The teaching is based on a problem-based learning approach, and students are evaluated on the way they progress in building their approach (40% of CC), as well as on their ability to present and defend their project during a final oral (60% of the overall grade)."

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This EU has three objectives:

1) deepen knowledge of concepts in genetics and evolutionary genomics such as linkage disequilibrium, selection, coalescent theory, detection of natural selection and evolutionary forces acting on genome evolution and the process of genomic speciation.

2) To propose a panorama of research themes in evolutionary genomics in the form of pedagogical seminars: molecular evolution, evolutionary genomics of endosymbioses, chromosomal evolution and molecular evolution.

3) Finally, the EU proposes a project of bioanalysis of an empirical dataset to understand the analysis in evolutionary genomics and to rub shoulders with the bioinformatics aspects increasingly developed in the discipline.

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"This module presents table management and the link between multivariate and univariate: matrix manipulation and common operations; notion of projection and distance; translation of descriptive and univariate statistics with multiple regression/ACP/AFD as an example; (dis)similarity indices, distance; correlation"

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The aim of this course is to understand the adaptive biology of organisms by considering individual and population responses to environmental variation. Concrete examples in animal evolutionary ecophysiology will be discussed in the context of global change. The responses of organisms and populations to abiotic parameters (such as temperature, salinity, oxygen availability, pollutants) will be considered as well as their interactive effects. The course will show the implication of physiological mechanisms in ecology, from phenotypic and cognitive processes at the intra-individual level to functional variants between individuals and between species. Intraspecific variability, phenotypic plasticity and transgenerational effects will also be discussed. This course will be illustrated by examples of phenotypic trait analysis (including behavior) within populations. Links with genetic and epigenetic markers will also be discussed. Different approaches (-omics vs. target gene/protein), several experimental setups and various scales of organization of living organisms will be considered (molecule, gene, phenotype, individual, population, species).

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The objective of this UE is to allow the implementation of projects defined in the framework of the UE project of M1S2.

Synthetic content of the EU:

- Tutor-led autonomous work by groups of students: readjustment of the project's objectives and methodology if necessary, acquisition of data, ecological and/or evolutionary analyses and interpretations according to the provisional schedule defined in M1S2, restitution of results in the framework of a conference common to the different courses.

Methods of control of knowledge:

As for the M1 project UE, the UE is based on a problem-based learning approach. Students are therefore evaluated as they go along on how they are progressing with their project (40% CC), and then at the end of the semester on their ability to present the results of their project and discuss them in an oral presentation at a general restitution conference (60% of the overall mark).

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This course approaches the issues surrounding ecosystem management from the perspective of social sciences, and more particularly "science studies". It aims to contribute to the development of a general culture related to the relationship between ecological sciences and societies, and to equip participants to analyze social issues and underlying socio-scientific controversies. The first part of the course provides a conceptual and methodological framework for the presentation of a reflexive tool for analyzing the interplay of actors and arguments (epistemological, axiological) involved in socioscientific controversies, and illustrates this tool with current examples. Subsequently, thematic presentations by ecological researchers illustrate a variety of issues surrounding ecological sciences, and serve as a basis for the application and acquisition by students of the reflexive analysis tool. Students are evaluated on their ability to mobilize this analytical framework in order to position themselves in an individual and argued manner in controversies related to ecological sciences.

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