M2 - Functional ecology and conceptualization of terrestrial and aquatic ecosystems (EcoSystèmes)

The aim of this course is to implement the projects defined in the M1S2 project course.

Synthetic content of the EU:

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

Assessment of knowledge:

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

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

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Ecophysiology is a discipline at the interface between organismal biology and ecology. Integrative ecophysiology focuses in particular on the question of change of scale. In other words, the aim of this course is to illustrate how the study of acclimatization/adaptation mechanisms on an 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 micro-organisms will be considered, and different types of approach will be illustrated: field observations, in situ or laboratory experiments.

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

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

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The aim 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 ecosystems). The aim of the lessons is to explain how to approach this functional facet of diversity for the 10+ million organisms present on the planet's surface, taking examples from both highly and less anthropized environments.

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

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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 players in BC and the role of science in BC. 
2. Species conservation: What are the priority species? How can species be conserved? How do you know if a species is "well conserved"? 
3. Space conservation: What are the priority spaces? How to conserve spaces? 
4. Theimportance of social acceptability and political commitment. Need for biodiversity indicators and to measure the impact of conservation. 

Students also carry out group work in which they present a BC project, based on the questions: why, what, where, how, how much does it cost and how do we know if it's effective? 

See full page

The aim of this course is to deepen understanding of key concepts relating to climate change, to illustrate important concepts in ecology and evolution in the light of climate change, in many different ecosystems, and to produce a synthesis of the various 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 Coastal and marine law; 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 highly multidisciplinary perspective. The physical structure of these ecosystems will be addressed through courses on their geomorphology and hydrology, with a particular focus on hydric couplings with the open sea and their watersheds. Their biogeochemistry will be addressed, in particular to describe carbon and nutrient flows through the water and sediment compartments. Several aspects of their biodiversity will be illustrated to describe the importance of these ecosystems as living environments for the species they support, and in particular the role of this biodiversity in their functioning. The coastal zone is densely populated by man (40% of the world's population). Particular attention will be paid to human uses (e.g. aquaculture) and their territorial planning, including the evaluation of their ecosystem services in an economic context, management and protection measures (e.g. Marine Protected Areas, Natura 2000), and professionals involved in the management of these environments will present practical feedback. Finally, the implications of the Law of the Sea for the management of coastal zones will be discussed. "

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

See full page

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

The module exposes students to the various basic concepts, as well as to the multitude of tools likely to be used (observations and experiments on natural populations or captive individuals, comparative analyses, use of modeling tools, ecophysiology, molecular biology, biochemistry, on-board electronics, etc.). Part of the training is based on specific discussions of the research approaches likely to be employed, the tools used and the limits of the inferences that can be made. Students will be expected to play an active role at all these levels, in particular through critical discussions of articles.

Topics range from the exploration of strategies for food provisioning, mate choice, habitat selection and investment in reproduction, to the study of animal communication and the reasons for group living. The historical dimension of the discipline is addressed in the introduction, but also according to the sensibilities of the contributors and the themes addressed (meaning and relationships between 'Animal Behaviour', 'Ethology', Behavioral Ecology etc.).

See full page

The aim of this resolutely trans-disciplinary course is to provide the skills needed to effectively manage and exploit data of various origins and types, particularly those with a spatial component. The course is divided into three complementary sections. The first deals with the issues inherent in data compilation and the solutions provided by database management systems (DBMS): from database design to queries. The second covers geographic information systems (GIS): from cartographic representation to geoprocessing. Finally, the third axis presents the diversity of spatial analysis tools for quantitative exploitation of spatial data, from metrics to statistical tests.

See full page

See full page

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

See full page

Ecophysiology is a discipline at the interface between organismal biology and ecology. Integrative ecophysiology focuses in particular on the question of change of scale. In other words, the aim of this course is to illustrate how the study of acclimatization/adaptation mechanisms on an 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 micro-organisms will be considered, and different types of approach will be illustrated: field observations, in situ or laboratory experiments.

See full page

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

See full page

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

See full page

The aim 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 ecosystems). The aim of the lessons is to explain how to approach this functional facet of diversity for the 10+ million organisms present on the planet's surface, taking examples from both highly and less anthropized environments.

See full page

The aim of this resolutely trans-disciplinary course is to provide the skills needed to effectively manage and exploit data of various origins and types, particularly those with a spatial component. The course is divided into three complementary sections. The first deals with the issues inherent in data compilation and the solutions provided by database management systems (DBMS): from database design to queries. The second covers geographic information systems (GIS): from cartographic representation to geoprocessing. Finally, the third axis presents the diversity of spatial analysis tools for quantitative exploitation of spatial data, from metrics to 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 to provide theoretical and practical knowledge of statistical analysis of spatial and temporal constraints: classification and ordering under constraints, '2-table ordering 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 players in BC and the role of science in BC. 
2. Species conservation: What are the priority species? How can species be conserved? How do you know if a species is "well conserved"? 
3. Space conservation: What are the priority spaces? How to conserve spaces? 
4. Theimportance of social acceptability and political commitment. Need for biodiversity indicators and to measure the impact of conservation. 

Students also carry out group work in which they present a BC project, based on the questions: why, what, where, how, how much does it cost and how do we know if it's effective? 

See full page

The aim of this course is to deepen understanding of key concepts relating to climate change, to illustrate important concepts in ecology and evolution in the light of climate change, in many different ecosystems, and to produce a synthesis of the various 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 Coastal and marine law; 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 highly multidisciplinary perspective. The physical structure of these ecosystems will be addressed through courses on their geomorphology and hydrology, with a particular focus on hydric couplings with the open sea and their watersheds. Their biogeochemistry will be addressed, in particular to describe carbon and nutrient flows through the water and sediment compartments. Several aspects of their biodiversity will be illustrated to describe the importance of these ecosystems as living environments for the species they support, and in particular the role of this biodiversity in their functioning. The coastal zone is densely populated by man (40% of the world's population). Particular attention will be paid to human uses (e.g. aquaculture) and their territorial planning, including the evaluation of their ecosystem services in an economic context, management and protection measures (e.g. Marine Protected Areas, Natura 2000), and professionals involved in the management of these environments will present practical feedback. Finally, the implications of the Law of the Sea for the management of coastal zones will be discussed. "

See full page

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

See full page

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

The module exposes students to the various basic concepts, as well as to the multitude of tools likely to be used (observations and experiments on natural populations or captive individuals, comparative analyses, use of modeling tools, ecophysiology, molecular biology, biochemistry, on-board electronics, etc.). Part of the training is based on specific discussions of the research approaches likely to be employed, the tools used and the limits of the inferences that can be made. Students will be expected to play an active role at all these levels, in particular through critical discussions of articles.

Topics range from the exploration of strategies for food provisioning, mate choice, habitat selection and investment in reproduction, to the study of animal communication and the reasons for group living. The historical dimension of the discipline is addressed in the introduction, but also according to the sensibilities of the contributors and the themes addressed (meaning and relationships 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 to provide theoretical and practical knowledge of statistical analysis of spatial and temporal constraints: classification and ordering under constraints, '2-table ordering 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 players in BC and the role of science in BC. 
2. Species conservation: What are the priority species? How can species be conserved? How do you know if a species is "well conserved"? 
3. Space conservation: What are the priority spaces? How to conserve spaces? 
4. Theimportance of social acceptability and political commitment. Need for biodiversity indicators and to measure the impact of conservation. 

Students also carry out group work in which they present a BC project, based on the questions: why, what, where, how, how much does it cost and how do we know if it's effective? 

See full page

The aim of this course is to deepen understanding of key concepts relating to climate change, to illustrate important concepts in ecology and evolution in the light of climate change, in many different ecosystems, and to produce a synthesis of the various 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 Coastal and marine law; 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 highly multidisciplinary perspective. The physical structure of these ecosystems will be addressed through courses on their geomorphology and hydrology, with a particular focus on hydric couplings with the open sea and their watersheds. Their biogeochemistry will be addressed, in particular to describe carbon and nutrient flows through the water and sediment compartments. Several aspects of their biodiversity will be illustrated to describe the importance of these ecosystems as living environments for the species they support, and in particular the role of this biodiversity in their functioning. The coastal zone is densely populated by man (40% of the world's population). Particular attention will be paid to human uses (e.g. aquaculture) and their territorial planning, including the evaluation of their ecosystem services in an economic context, management and protection measures (e.g. Marine Protected Areas, Natura 2000), and professionals involved in the management of these environments will present practical feedback. Finally, the implications of the Law of the Sea for the management of coastal zones will be discussed. "

See full page

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

See full page

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

The module exposes students to the various basic concepts, as well as to the multitude of tools likely to be used (observations and experiments on natural populations or captive individuals, comparative analyses, use of modeling tools, ecophysiology, molecular biology, biochemistry, on-board electronics, etc.). Part of the training is based on specific discussions of the research approaches likely to be employed, the tools used and the limits of the inferences that can be made. Students will be expected to play an active role at all these levels, in particular through critical discussions of articles.

Topics range from the exploration of strategies for food provisioning, mate choice, habitat selection and investment in reproduction, to the study of animal communication and the reasons for group living. The historical dimension of the discipline is addressed in the introduction, but also according to the sensibilities of the contributors and the themes addressed (meaning and relationships between 'Animal Behaviour', 'Ethology', Behavioral Ecology etc.).

See full page

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

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The aim of this course is to help students build their career plans and find internships, while beginning to prepare for their integration into professional life through a comprehensive and personal vision of possible career paths.

In concrete terms, a series of meetings with various participants introduces the doctoral thesis (presentation of the GAIA doctoral school, presentations by thesis students) and the professional environment targeted by the different career paths (research careers and the non-academic sector). Activities specific to each pathway then enable students to better target the scientific fields most closely aligned with their career plans. Finally, TD sessions are designed to prepare students to write scientific articles in English.

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This course approaches the issues surrounding ecosystem management from a social science perspective, with a particular focus on science studies. It aims to help develop a general understanding of the relationship between ecological sciences and society, and to equip participants to analyze the 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 socio-scientific controversies, and illustrates this tool using current examples. Thematic presentations by ecology researchers illustrate a variety of issues surrounding the ecological sciences, and serve as the basis for students' application and acquisition of the reflexive analysis tool. Students are assessed on their ability to mobilize this analytical framework to position themselves individually and argumentatively in ecological science controversies.

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

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

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The individual M2 internship lasts approximately 5 to 6 months, and must be carried out in a research laboratory or a non-academic structure, depending on the course. It enables 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 structure, on a subject validated by the teaching team to fit in with the objectives of the course followed by the student.

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

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