Chrono-Environments and Paleoecology (CEPAGE)

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

General properties viewed through regression and one-factor ANOVA (R2, F, ddl, least squares, likelihood, diagnosis, validation, goodness of fit, interpretation of effect sizes); nested and crossed factor ANOVA, multiple regression (concept of parameters and effects, and interaction)

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

See the full page

The overall objective is to consolidate the foundations in ecology acquired by students and to give them the tools they need to apply them in an integrated way to interpret the functioning of ecological systems. The course includes: 1) lectures on ecological concepts from the population scale to the macroecological scale, using examples of applications that place the discipline in the current ecological and societal context; 2) practical and supervised work focused on tools (sampling strategies, modeling, data analysis); 3) field teaching, during which students are encouraged to ask relevant scientific questions based on their observations in the field and to use their knowledge to answer them in a reasoned manner.

Summary of EU content:

- CM: History of the emergence of concepts in ecology; Population dynamics/metapopulations; Biotic interactions and food webs; Community ecology, metacommunities; Ecosystem ecology/functional ecology; Concepts of macroecology/biogeography; Global change and ecosystem functioning;

- Field: Integrative analysis of ecosystem functioning in situ;

- TD/TP: sampling and experimentation strategies in ecology; modeling in population dynamics/metapopulations, community ecology/metacommunities, food webs; biodiversity measures (alpha, beta, etc.).

See the full page

The overall objective is to consolidate students' foundations in evolutionary biology by addressing both (i) macroevolutionary phenomena and the general methods used to analyze them, and (ii) microevolutionary processes with an emphasis on the population genetics approach. This course unit aims to provide a solid foundation of knowledge in evolutionary biology and to illustrate the applications of the discipline to students' future areas of specialization. The course includes: 1) lectures on the concepts of evolution; 2) practical work in two main forms: 2a. sessions focused on the use of tools (phylogeny) and the mathematical formalization of evolutionary processes (population genetics); and 2b: sessions built around group work, allowing students, depending on their background and professional goals, to explore a particular topic in depth (fundamental question or application of evolutionary biology).

See the full page

English tutorial courses aimed at developing professional autonomy in the English language.

See the full page

See the full page

Generalized linear mixed models + methodology and experimental protocols to account for biological reality: non-normal distribution and pseudo-replication

Protocol optimization, power, and uncontrolled type I risk: variable transformation, polynomial regression, link function, likelihood, model selection

Deviance and goodness-of-fit analysis

Incorporation of blocks, repeated measurements over time, consideration of spatial and temporal correlation, over-dispersion

Graphical representation of predictions.

See the full page

The objective of this course unit is to provide the necessary statistical foundations for following the more advanced modules in the curriculum; it is therefore a general refresher course. Descriptive statistics are reviewed (quantiles, cumulative frequency polygons, sample estimators), simple tests are presented, essential graphs for univariate and multivariate data are presented, and the general principle of a statistical test, hypothesis testing, the concept of p-value, and Type I and Type II errors are presented. In practical work, students are also brought up to speed in the R environment.

See the full page

Based on ecological concepts and methods, this course unit aims to introduce students to historical ecology (the study of interactions between humans and their environment over varying periods of time) and its main applications in paleoecology and environmental sciences: climate change, fluctuations in biodiversity, vegetation transformation, forest dynamics, disturbance ecology, bioarchaeology, etc. ORPAL is an APP course (1/3 fieldwork and 2/3 laboratory work). The work, carried out in pairs or groups of three under the supervision of a mentor, covers the entire research process, from defining the problem field sampling, 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 the academic year. This course unit begins with a three-day field school (24 hours - integration course) and continues with a mini laboratory course (24 hours). The course unit ends with the writing of a popular science article and an oral presentation of the results.

See the full page

The EU's objectives are twofold. On the one hand, it aims to retrace all the major stages in the history of organisms on Earth since its birth. Topics such as the emergence of life, the colonization of continents, the emergence of angiosperms, glacial/interglacial cycles, and the domestication of plants will be addressed. Secondly, it aims to show how paleoecology fits into the modern world, whether in terms of methodological developments (geochemistry, optical microscopy, electron microscopy, X-ray microscopy, etc.), climate change prediction models, ecosystem management in the context of global change, or developments in biotechnology.  The EU will mainly be organized into lectures (TD), each given by a specialist in the subject.

See the full page

The individual M1 internship lasts approximately three months and, depending on the program, must be completed in a research laboratory or a non-academic organization. It allows students to gain professional experience in the field of biodiversity, evolution, or ecology. It can be carried out in a local, national, or international organization, on a topic approved by the teaching team so as to fit in with the objectives specific to the program followed by the student.

Assessment: Preparation for the internship is assessed on the basis of a written document and a presentation of the internship project. The internship work is assessed during a public presentation before a panel, during which the content of the dissertation and the quality of the responses to the panel's questions are evaluated. The student's behavior and enthusiasm during the internship are assessed by the internship supervisor.

See the full page

See the full page

Teaching unit aimed at linking theoretical ecology, its operational implementation, and territorial issues as seen by societal actors. Built on a format combining theoretical courses covering the elements necessary for understanding field issues (ecosystem dynamics, anthropization, socio-ecosystem resilience, in situ conservation, etc.), this teaching unit includes several field blocks (each consisting of a preparatory tutorial/practical and an "active" field trip). The territories visited will provide an opportunity to meet members of society (managers, elected officials, associations, shepherds, etc.) whose position allows us to understand how ecological issues govern their actions and how, in turn, their actions impact biodiversity, its dynamics, and its distribution.

See the full page

How is biodiversity distributed across the Earth? What ecological, evolutionary, and historical factors determine these patterns of biodiversity distribution? What changes have human activities brought about in the global distribution of biodiversity? In this course, we will study the role of spatial and temporal variations in the environment on a global scale 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 on a planetary scale.

See the full page

This module presents table management and the link between multivariate and univariate analysis: matrix manipulation and common operations; the concepts of projection and distance; translation of descriptive and univariate statistics using multiple regression/ACP/AFD as examples; indices of (dis)similarity, distance; correlation.

See the full page

The objective of this course is to consolidate students' foundations in ecology and/or evolution by inviting them to define a research topic and question(s), formulate relevant hypotheses with supporting arguments, and justify a data acquisition and analysis strategy for testing them.

Summary of EU content:

- Independent work under supervision: identification of a relevant scientific question; bibliographic review to establish the state of the art and justify scientific hypotheses; proposal and justification of a methodological approach (materials and methods) to test the proposed hypotheses.

Types of topics:

Topics may cover any issue identified by students (in groups of 3/4) and approved by the teaching team, and may be based on different approaches to suit the requirements of different courses. For example, students may propose a field sampling or experimentation strategy, a meta-analysis of literature data, an analysis of sequences retrieved from GenBank, an analysis of occurrence data retrieved from GBIF, etc.

In all cases, projects must involve a genuine data acquisition strategy, identified, justified, and described by students in the materials and methods required for M1S2, with a provisional schedule 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. Projects must also be financially realistic and include a provisional budget, and must be able to be completed within the time available in M2S3.

Assessment methods:

Teaching is based on a problem-based learning approach. Students are assessed on how they progress in developing their approach (40% of the final grade), as well as on their ability to present and defend their project in a final oral exam (60% of the final grade).

See the full page

The objective of this EU is to enable the implementation of projects defined within the framework of the M1S2 EU project.

Summary of EU content:

- Independent work supervised by student groups: readjustment of project objectives and methodology if necessary, data acquisition, ecological and/or evolutionary analyses and interpretations according to the provisional schedule defined in M1S2, presentation of results at a joint symposium for the different courses.

Assessment methods:

As with the EU M1 project, the EU uses a problem-based learning approach. Students are therefore assessed on an ongoing basis on their progress in completing their project (40% of the final grade), then at the end of the semester on their ability to present the results of their project and discuss them during an oral presentation at a general feedback symposium (60% of the final grade).

See the full page

This EU focuses on analyzing the impact of humans on the climate and the environment.

See the full page

Present different methodological approaches in an applied context, from data acquisition to interpretation. Each approach is covered in half a day (3 hours), addressing data acquisition methods (1.5 hours of practical work) and interpretation of results (1.5 hours of tutorials).

See the full page

"The aim of this EU is to present and explain the concepts, issues, operational approach in the field and in the laboratory, and methodological and analytical strategies used to infer and reconstruct fluctuations in wild and human-exploited biodiversity over time. It draws on empirical and modeled data sets covering ecology, paleoecology, paleobiogeography, archaeobiology, archaeology, and paleoethnobiology. Particular attention will be paid to:

- the functional role of ecological disturbances such as fires in vegetation cover transformations;

- the impact of changes in human societies on the dynamics of forest ecosystems;

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

See the full page

The objective of this EU is to support students in developing their career plans and searching for internships, while beginning to prepare for their integration into professional life by providing a comprehensive and personalized overview of possible career paths.

In practical terms, meetings with various stakeholders provide an opportunity to present the doctoral thesis (presentation of the GAIA doctoral school, presentations by doctoral students) and the professional network targeted by the various courses (research professions and non-academic sector). Activities specific to each course then enable students to better target the scientific fields most relevant to their professional projects. Finally, tutorial sessions are designed to prepare students for writing scientific articles in English.

See the full page

See the full page

In this course, we will address the main theoretical concepts of evolutionary processes through the fossil record. We will discuss how to reconcile microevolutionary and macroevolutionary mechanisms. The concepts covered will be: species and intraspecific variability, speciation and the pace of evolution, adaptive radiation (ecological speciation) in the fossil record, targeted extinctions (migrant-native competition) or mass extinctions (major biological crises), evolutionary modalities (anagenesis and saltationism) observed in the fossil record, and a comprehensive review of microevolutionary mechanisms.

See the full page

The objective of this resolutely transdisciplinary course is to provide students with the skills needed for the effective management and relevant use of data of various origins and types, particularly those with a spatial component. The course consists of three complementary and successive sections. The first addresses the challenges inherent in data compilation and the solutions provided by database management systems (DBMS): from database design to queries. The second focuses on geographic information systems (GIS): from cartographic representation to geoprocessing. Finally, the third axis presents the diversity of spatial analysis tools that enable the quantitative exploitation of spatial data, whether metrics or statistical tests.

See the full page

The educational objective of this teaching unit is to reposition the major soil types on a global scale, explain their formation, and identify the mineral phases or main abiotic factors likely to regulate biological activity in soils. Based on this analysis, the various soil organisms (microorganisms, micro-, meso- and macrofauna) will be presented, along with their relationships, in order to reposition the cycle of organic matter and mineral elements in the soil at different temporal and spatial scales. The concepts of recycling, biogeochemical cycles and community assembly rules will also be addressed. This course unit is organized around lectures and conferences, as well as tutorials and fieldwork.

See the full page

"The objective is to analyze the phylogenetic, developmental, and functional constraints that may have governed the morphological changes observable in the fossil record. The phylogenetic approach will be addressed using reconstruction methods applicable to fossils (parsimony; cladistic analysis). Developmental and functional approaches (mainly odontology) will be illustrated by various methodologies developed on the Montpellier campus (in particular X-ray microtomography). A critical review of reference articles in the field will be followed by an oral presentation and a question-and-answer session."

See the full page

See the full page

Land use changes are responsible for approximately 10% of anthropogenic carbon dioxide emissions. Tropical forest ecosystems can contribute to both pillars of addressing global warming, namely mitigation and adaptation:

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

-The ability of human societies that are still predominantly 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 intervention.

As part of the implementation of the United Nations Framework Convention on Climate Change, mechanisms such as the Clean Development Mechanism (CDM) and REDD+, voluntary markets, and ecosystem-based adaptation provide new opportunities for tropical forestry, as well as potential leverage for protecting or restoring tropical forests. The module provides an understanding of the basic concepts of climate change, the role of tropical ecosystems in the global carbon cycle, and technical, political, 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 political measures for mitigating and adapting to this change. The potential of tropical agroecosystems is assessed on the basis of scientific studies and existing operational projects.

Teaching and learning methods:

-Classes (18 hours)

-TD (3 hours).

See the full page

1. Bayesian inference: Motivation and simple example. 

2. The likelihood. 

3. A detour to explore priors. 

4. Markov chain Monte Carlo methods (MCMC)

5. Bayesian analyses in R with the Jags software.  

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

7. Heterogeneity and multilevel models (also known as mixed models). 

See the full page

1. "The way in which the modern West represents nature is the least well-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.

While Philippe Descola contributes to renewing questions about society-environment relations, he nevertheless draws on a long tradition in the humanities and social sciences. Numerous works already explore the various forms of knowledge and social organization to which these relations 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 attracts the interest of conservationists (biodiversity, natural resources, etc.) and industry (pharmacology). It also mobilizes so-called "indigenous" populations who are demanding, both locally and internationally, access to resources and the preservation of intangible heritage.

2. Located at the intersection of social sciences and 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 interrelationships between so-called "traditional" societies and their immediate environment. Subsequently, beginning in the 1970s, researchers reconsidered the distinction between so-called "traditional" and "modern" societies in order to better address new contemporary environmental and social transformations.

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

On the other hand, modern societies' relationship with their environment is being reconfigured in light of the fact that our planet is becoming increasingly "artificialized" and threatened by serious disruptions and crises. The place of fauna and flora is being reconsidered and is the subject of controversy regarding their rights. Furthermore, the dawn of a new geological era, the Anthropocene, is being invoked to challenge both the natural sciences and the humanities and social sciences on the need to take a different approach to the shared history of the environment and societies.

3. The work of scientists and engineers is being viewed in a new light. In this regard, a new scientific project in the humanities and social sciences aims to reconsider the role of "non-humans" and calls for the development of analytical categories other than those of Nature and Culture. New scales and methods of investigation are also being considered for analyzing global processes.

These recent changes in scale invite researchers in the humanities and social sciences to (re)consider their approach through a reflexive lens: they are no longer mere observers, but can also be active participants in processes, even when they are not directly involved in a social movement.

4. The objective of this module is to introduce these different scientific and operational fields. It aims to provide students with reference points and food for thought, enabling them to develop scientific questions on the relationship between society and the environment, with a view to reflecting on how to address current environmental and social issues. The varied geographical and disciplinary experiences of the speakers will illustrate the approach through a wide range of ecosystem types, sociocultural contexts, and themes. In the time available, we do not claim to cover all themes, approaches, and methods exhaustively. Any student wishing to study this field in greater depth will need to undertake more in-depth training.

See the full page

The objective of this EU is to support students in finalizing their professional projects and preparing for life after their master's degree.

The EU is organized on a course-wide basis, with regular discussion sessions between the teaching team and students.

See the full page

The individual M2 internship lasts approximately 5 to 6 months and must be carried out, depending on the course concerned, in a research laboratory or a non-academic organization. It allows students to gain in-depth professional experience in the field of biodiversity, evolution, or ecology. It can be carried out in a local, national, or international organization, on a topic approved by the teaching team so as to fit in with the specific objectives of the program followed by the student.

Assessment: The internship is assessed during a public defense before a jury, during which the content of the thesis and the quality of the responses to the jury's questions are evaluated. The student's behavior and enthusiasm during the internship are assessed by the internship supervisor.

See the full page