M2 - Integrative Study of Parasitic and Infectious Outbreaks (EI-EPI)

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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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Phylogeny is a search for evolutionary clues. The goal of this module is to highlight the existence of gene phylogenies within species phylogenies, the methods for representing evolutionary histories as trees, and the concept of positional molecular homology through sequence alignment. The principles of phylogenetic inference methods are at the core of this course unit. Distance-based methods highlight the difficulties in distinguishing between homology and homoplasy, as well as the need to construct models of character evolution. The cladistic approach based on maximum parsimony illustrates, on the one hand, the use of bootstrapping to estimate the robustness of phylogenetic nodes and, on the other hand, the impact of taxonomic sampling on the detection of multiple substitutions.

Probabilistic approaches are introduced and then explored in greater depth. The long-branch attraction artifact leads to the introduction of probabilistic reasoning. The maximum likelihood method allows us to address the calculation of likelihood, the estimation of model parameters using optimality criteria, the construction of various models of character evolution, and the comparison of models. Bayesian inference, in turn, introduces the distinction between density-based and optimality-based approaches. It then covers the a priori use of probability densities, the estimation of posterior distributions of model parameters based on the data, their approximation using Markov chains with Monte Carlo and Metropolis coupling (MCMCMC), the initialization and convergence phases, and the calculation and interpretation of posterior probabilities for trees and clades. The importance of evolutionary models for DNA, RNA, and protein sequences and their refinement is emphasized.

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The module aims to provide theoretical and practical knowledge of statistical analyses of spatial and temporal constraints: classification and ordination under constraints, "two-table ordination methods and statistical tests: canonical analyses (AFD, CCA, RDA, CAP)," "statistical tests on distance matrices, and matrix comparisons (PERMANOVA, Mantel, Procrustes)."

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The courses cover four aspects of conservation biology, drawing on current scientific research in this field:  

1. Introduction to Biodiversity Conservation(BC): Definition of Conservation Biology. Why conserve biodiversity? Who are the key players in BC, and what is the role of science in BC? 
2. Species Conservation: Which species are priorities? How can we conserve species? How do we know if a species is “well conserved”? 
3. Conservation of Areas: Which areas are priorities? How can we conserve these areas? 
4. Does Conservation Work?The Importance of Social Acceptance and Political Commitment. The Need for Biodiversity Indicators and for Measuring the Impact of Conservation. 

Students also work in groups to present a community library project, addressing the following questions: Why, what, where, how, how much does it cost, and how can we tell if it’s effective? 

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"All instruction is conducted in English.

The courses cover four aspects of conservation biology, drawing on current scientific research in this field:

1. Introduction to Biodiversity Conservation (BC): Definition of Conservation Biology. Why conserve biodiversity? Who are the key players in BC, and what is the role of science in BC?

2. Species conservation: Which species are priorities? How can we conserve species? How do we know if a species is “well conserved”?

3. Conservation of Areas: Which areas are priorities? How can we conserve these areas?

4. Does conservation work? The importance of social acceptance and political commitment. The need for biodiversity indicators and for measuring the impact of conservation.

Students also complete a group project in which they present a BC proposal, addressing the following questions: why, what, where, how, how much it costs, and how to determine if it is effective."

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