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

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.

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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)

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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 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...).

See full page

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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