Chrono-Environments and Paleoecology (CEPAGE)

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

general properties examined through regression and one-way ANOVA (R², F, ddl, least squares, likelihood, diagnostics, validation, goodness of fit, interpretation of effect sizes); ANOVA with nested and crossed factors, multiple regression (concepts of parameters, effects, and interactions)

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

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The overall objective is to reinforce the students’ foundational knowledge of ecology and to provide them with the tools to apply this knowledge in an integrated manner to interpret the functioning of ecological systems. The curriculum includes: 1) lectures covering ecological concepts ranging from the population level to macroecological scales, supported by practical examples that place the discipline within the current ecological and societal context; 2) practical and guided exercises focused on tools (sampling strategies, modeling, data analysis); 3) fieldwork sessions during which students are encouraged to ask relevant scientific questions based on in-situ observations and to apply their knowledge to answer these questions in a well-reasoned manner.

Summary of the learning unit:

- 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;

- Fieldwork: Integrative analysis of ecosystem functioning in real-world settings;

- Tutorials/Lab Sessions: sampling and experimental strategies in ecology; modeling of population dynamics/metapopulations, community/metacommunity ecology, and food webs; measures of biodiversity (alpha, beta, etc.)."

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"The overall objective is to strengthen students’ foundational knowledge of 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 both to provide a solid common foundation of knowledge in evolutionary biology and to illustrate the discipline’s applications to the students’ future fields of specialization. The course includes: 1) lectures on evolutionary concepts; 2) laboratory sessions in two main formats: 2a. sessions focused on the use of analytical tools (phylogenetics) and on the mathematical formalization of evolutionary processes (population genetics), as well as 2b: sessions structured around group work, allowing students—based on their academic background and career goals—to explore a specific topic in greater depth (a fundamental question or an application of evolutionary biology)."

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English tutorial courses designed to foster professional proficiency in English.

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Generalized Linear Mixed Models + Methodology and Experimental Protocols to Account for Biological Reality: Non-Normal Distributions and Pseudo-Replication

Protocol Optimization, Power, and Uncontrolled Type I Risk: Variable Transformation, Polynomial Regression, Link Function, Likelihood, Model Selection

Deviance Analysis and Goodness of Fit

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

Graphical representation of the predictions.

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The objective of this course unit is to provide the necessary foundation in statistics to follow the more advanced modules in the curriculum; it is therefore a general refresher course. Descriptive statistics are reviewed (quantiles, cumulative frequency polygons, sample-based estimators); simple tests are introduced; essential graphs for univariate and multivariate data are presented; and the general principles of statistical testing, hypothesis testing, the concept of the p-value, and Type I and Type II errors are covered. In lab sessions, students also receive training in the R environment.

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Drawing on concepts and methods from ecology, this course unit aims to introduce students to and provide hands-on experience with historical ecology (the study of interactions between humans and their environment over varying time periods) and its main applications in paleoecology and environmental sciences: climate change, fluctuations in biodiversity, vegetation changes, forest dynamics, disturbance ecology, bioarchaeology… ORPAL is a course taught through applied practical training (1/3 fieldwork and 2/3 laboratory practicals). The work, carried out in pairs or groups of three under the supervision of an instructor, covers the entire research process, from defining the research question, field sampling, and data collection, all the way through to interpretation, writing a scientific article (see https://biologie-ecologie.com/exemples-travaux/), and an oral presentation of the results. ORPAM takes place during the first few weeks of the semester. This course unit begins with a 3-day field school (24 hours—orientation workshop) and continues with a short laboratory workshop (24 hours). The course unit concludes with the writing of a popular science article and an oral presentation of the results.

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The objectives of this EU initiative are twofold. On the one hand, it aims to trace all the major milestones in the history of organisms on Earth since the planet’s formation. Thus, topics such as the origin of life, the colonization of the continents, the emergence of angiosperms, glacial and interglacial cycles, and the domestication of plants will be addressed. Second, the course aims to demonstrate how paleoecology is relevant to the modern world, whether through methodological advancements (geochemistry, optical microscopy, electron microscopy, X-ray microscopy, etc.), models for predicting climate change, ecosystem management in the context of global change, or developments in biotechnology.  The course will primarily consist of lecture-style sessions (TD), each led by a specialist in the relevant topic.

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The M1 individual internship lasts approximately three months and, depending on the student’s program track, must be completed in a research laboratory or a non-academic organization. It allows students to gain professional experience in the fields of biodiversity, evolution, or ecology. It may be carried out at a local, national, or international organization, on a topic approved by the faculty to ensure it aligns with the specific objectives of the student’s program.

Assessment: Preparation for the internship is a graded assignment based on a written document and a presentation of the internship proposal. The internship work is assessed during a public presentation before a panel, during which the content of the report and the quality of the student’s responses to the panel’s questions are evaluated. The student’s conduct and initiative during the internship are assessed by the internship supervisor.

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A course designed to link theoretical ecology, its practical application, and regional challenges as perceived by stakeholders in society. Built around a format that combines theoretical lectures covering the fundamentals necessary for understanding on-the-ground issues (ecosystem dynamics, anthropogenic impacts, socio-ecosystem resilience, in situ conservation, etc.), this course unit includes several field components (each consisting of a preparatory tutorial and an “active” field trip). Visits to these areas will provide opportunities to meet stakeholders (managers, elected officials, nonprofit organizations, shepherds, etc.) whose perspectives help students understand how ecological issues shape their actions and, in turn, how those actions impact biodiversity, its dynamics, and its distribution.

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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 unit, we will study the role of spatiotemporal 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 both past and present organism diversity. We will also address the impact of human activities and global changes on biodiversity on a global scale.

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"This module introduces array management and the relationship between multivariate and univariate analysis: matrix manipulation and common operations; the concepts of projection and distance; interpretation of descriptive and univariate statistics, using multiple regression, PCA, and AFD as examples; (dis)similarity indices, distance; and correlation."

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"The objective of this course is to strengthen students' foundations in ecology and/or evolution by encouraging them to identify a research topic and question(s), formulate well-reasoned and relevant hypotheses, and justify a strategy for collecting and analyzing data to test those hypotheses.

Summary of the learning unit:

- Supervised independent work: identifying a relevant scientific question; conducting a literature review to assess the state of the art and justify scientific hypotheses; proposing and justifying a methodological approach (materials and methods) to test the proposed hypotheses.

Topic types:

Topics may address any issue identified by the students (in groups of 3 or 4) and approved by the teaching staff, and may draw on various approaches to align with the learning objectives of the different programs. For example, students may propose a field sampling or experimental strategy, 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, projects must include a concrete data collection strategy—identified, justified, and described by the students in the “Materials and Methods” section required for the M1S2 course—along with a projected timeline for the project’s progress and a breakdown of the tasks each student will perform within each group as part of the project’s implementation during the M2S3 course. Projects must also be financially realistic and include a projected budget, and they must be capable of being completed within the time available during the M2S3 semester.

Assessment Procedures:

"The course is based on a problem-based learning approach; students are evaluated on their progress in developing their methodology (40% of the grade), as well as on their ability to present and defend their project during a final oral presentation (60% of the overall grade)."

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The objective of this course unit is to facilitate the implementation of the projects defined as part of the M1S2 course unit.

Summary of the learning unit:

- Independent work supervised by student groups: readjustment of project objectives and methodology as needed; data collection; ecological and/or evolutionary analyses and interpretations in accordance with the tentative schedule established in M1S2; presentation of results at a joint symposium for the various tracks.

Assessment Procedures:

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

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This unit focuses on analyzing the impact of human activity on the climate and the environment

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Present various methodological approaches in an applied context, from data collection through interpretation. Each approach is covered over half a day (3 hours), focusing on data collection methods (1.5 hours of lab work) and the interpretation of results (1.5 hours of tutorial).

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"The objective of this course is to present and explain the concepts, issues, operational approaches 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 datasets from the fields of ecology, paleoecology, paleobiogeography, archaeobiology, archaeology, and paleethnobiology. Particular attention will be paid to:

- the functional role of ecological disturbances, such as wildfires, in changes to vegetation cover;

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

- the use, cultivation, and domestication of plants and animals based on the analysis of modern and bioarchaeological data."

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The goal of this course unit is to support students in developing their career plans and searching for internships, while helping them begin to prepare for their transition into the workforce by providing a comprehensive yet personalized overview of possible career paths.

Specifically, sessions with various stakeholders provide an opportunity to present the doctoral thesis (a presentation by the GAIA doctoral school, presentations by doctoral students) and to explore the professional opportunities targeted by the different tracks (research careers and the non-academic sector). Activities specific to each track then help students better identify the scientific fields most closely aligned with their career goals. Finally, tutorial sessions are designed to prepare students for writing scientific articles in English.

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In this course unit, we will explore the main theoretical concepts of evolutionary processes as reflected in the fossil record. We will focus on reconciling microevolutionary and macroevolutionary mechanisms. The concepts covered will include: species and intraspecific variability, speciation and the rates of evolution, adaptive radiations (ecological speciation) in the fossil record, targeted extinctions (competition between migrants and native species) or mass extinctions (major biological crises), evolutionary modes (anagenesis and saltationism) observed in the fossil record, and a comprehensive review of microevolutionary mechanisms.

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The goal of this resolutely transdisciplinary course is to provide the skills necessary for the effective management and meaningful use of data from various sources and of various types, particularly data with a spatial component. The course consists of three complementary, sequential modules. 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 area presents the diversity of spatial analysis tools that enable the quantitative exploitation of spatial data, whether through metrics or statistical tests.

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The educational objective of this course unit is to provide an overview of the major soil types on a global scale, explain their formation, and identify the mineral phases or primary abiotic factors that may regulate biological activity in soils. Based on this analysis, the various soil organisms (microorganisms, micro-, meso-, and macrofauna) will be presented, along with their interactions, in order to contextualize the cycles of organic matter and mineral elements in the soil across different temporal and spatial scales. The concepts of recycling, the closure of biogeochemical cycles, and the principles governing community assembly will also be addressed. This course unit is organized around lectures and presentations, as well as tutorial sessions and fieldwork.

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"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). The developmental and functional approaches (primarily odontology) will be illustrated using various methodologies developed on the Montpellier campus (notably X-ray microtomography). A critical review of key articles in the field will be presented orally, followed by a question-and-answer session."

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Land-use changes account for approximately 10% of anthropogenic carbon dioxide emissions. Tropical forest ecosystems can contribute to both pillars of addressing climate change—namely, mitigation and adaptation:

-Tropical forests and plantations are significant 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—which 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 interventions.

As part of the implementation of the United Nations Framework Convention on Climate Change, mechanisms such as the Clean Development Mechanism (CDM) and REDD+, along with voluntary markets and ecosystem-based adaptation, provide new opportunities for tropical forestry, as well as a potential lever for the protection or restoration of tropical forests. This module provides an understanding of the basic concepts of climate change, the role of tropical ecosystems in the global carbon cycle, and the technical, political, and economic responses to the challenges of climate change.

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 measures for mitigating and adapting to climate change. The potential of tropical agroecosystems is assessed based on scientific studies and existing operational projects.

Teaching and Learning Methods:

-Course (18 hours)

-Tutorial (3 hours).

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1. Bayesian inference: Motivation and a simple example. 

2. The likelihood. 

3. A detour to explore priors. 

4. Markov chain Monte Carlo (MCMC) methods

5. Bayesian analyses in R using the Jags software.  

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

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

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1. “The way the modern West conceives of nature is the least widely shared view 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 a European invention that is merely one of the possibilities available to societies for accounting for the living and non-living beings that surround them.

While Philippe Descola helps to revitalize the discussion of the relationship between society and the environment, he nevertheless draws on a long tradition in the humanities and social sciences. Numerous studies have already explored the various forms of knowledge and social organization that arise from this relationship: ethnoscience, the anthropology of technology, economic anthropology, ethnoecology, the sociology of science and technology, and so on.

This issue is by no means confined to the academic sphere. It also attracts the interest of stakeholders in conservation (biodiversity, natural resources, etc.) and industry (pharmacology). It also mobilizes so-called “indigenous” peoples, who are advocating—both locally and internationally—for access to resources and the preservation of their intangible cultural heritage.

2. Situated at the intersection of the social sciences and the life sciences, these disciplines analyze how human societies use plants, animals, and other components of the environment, as well as how their conceptions and representations of their environment(s) shape 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 reevaluated 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 communities—even the most isolated ones—are affected by events that are decided and unfold at various levels (international agreements, economic crises). Their immediate environment is also affected by global phenomena (climate change, loss of biodiversity, etc.). Conversely, their actions can also have international ecological, social, and economic repercussions, for example, when these communities organize to voice their demands in international forums.

Furthermore, the relationship that modern societies have with their environment is being reshaped in light of the reality of an increasingly “artificialized” planet threatened by serious disruptions and crises. The role of flora and fauna is being reevaluated, and their rights are the subject of controversy. Furthermore, the onset of a new geological era—the Anthropocene—is cited to challenge both the natural sciences and the humanities and social sciences to reconsider how we view the shared history of the environment and societies.

3. The very work of scientists and engineers is being viewed in a new light. In this regard, a new research project in the humanities and social sciences aims to reexamine 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 to analyze global processes.

These recent shifts in scale prompt researchers in the humanities and social sciences to (re)examine their methodology through a reflective approach: they are no longer mere observers, but can also be active participants in these processes—even when they are not directly involved in a social movement.

4. The objective of this module is to introduce these various scientific and operational fields. It aims to provide students with points of reference and food for thought so that they can formulate scientific questions about the relationship between society and the environment, with a view to reflecting on how to address current environmental and social challenges. The instructors’ diverse geographical and disciplinary backgrounds will help illustrate this approach through a wide range of ecosystem types, sociocultural contexts, and themes. Given the time constraints, we do not intend to provide an exhaustive coverage of all topics, approaches, and methods. Any student wishing to delve deeper into this field should pursue more in-depth training.

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The goal of this course unit is to support students as they finalize their career plans and prepare for life after the master’s program.

The EU is organized around the entire program, with regular discussion sessions between the teaching staff and students.

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The M2 individual internship lasts approximately 5 to 6 months and, depending on the student’s track, must be completed 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 may be conducted at a local, national, or international organization on a topic approved by the faculty to ensure it aligns with the specific objectives of the student’s track of study.

Evaluation: The internship is evaluated during a public defense before a panel, during which the content of the thesis and the quality of the student’s responses to the panel’s questions are assessed. The student’s conduct and initiative during the internship are evaluated by the internship supervisor.

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