M2 - Integrative Study of Parasitic and Infectious Emergencies EI-EPI

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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.

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Phylogeny is a quest for evolutionary clues. The aim of this module is to highlight the existence of gene phylogenies within species phylogenies, the methods used to represent evolutionary histories in the form of trees, and the challenge of positional molecular homology through sequence alignment. The principles of phylogenetic inference methods are at the heart of this course unit. Distance methods highlight the difficulties of separating homology and homoplasy, and the need to construct models of character evolution. The cladistic approach with maximum parsimony illustrates, on the one hand, the use of bootstrapping to estimate the robustness of phylogeny nodes and, on the other hand, the impact of taxonomic sampling on the detection of multiple substitutions.

Probabilistic approaches are presented and explored in depth. The artifact of attraction to long branches leads to the introduction of probabilistic reasoning. The maximum likelihood method allows us to address likelihood calculation, model parameter estimation by optimality, the construction of different character evolution models, and model comparison. Bayesian inference introduces the distinction between density-based and optimality-based approaches. It then shows the a priori use of probability densities, the estimation of the posterior distributions of model parameters based on the data, their approximation by Markov chains with Monte Carlo techniques and Metropolis coupling (MCMCMC), the ignition and convergence phases, and the calculation and interpretation of the posterior probabilities of trees and clades. The importance of DNA, RNA, and protein sequence evolution models and their improvement 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, '2-table ordination methods and statistical tests: canonical analyses (AFD, CCA, RDA, CAP), 'statistical tests on distance matrices, matrix comparison (PERMANOVA, Mantel, Procrustes)

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The courses present four 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 what role does science play in BC? 
2. Species conservation: Which species are priorities? How can species be conserved? How can we tell if a species is "well conserved"? 
3. Conserving spaces: Which spaces are priorities? How can spaces be conserved? 
4. Does conservation work?The importance of social acceptability and political commitment. The need for biodiversity indicators and measuring the impact of conservation. 

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

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All instruction is conducted in English.

The courses present four 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 BC and what is the role of science in BC?

2. Species conservation: Which species are priorities? How can species be conserved? How can we know if a species is "well conserved"?

3. Conservation of spaces: Which spaces are priorities? How can spaces be conserved?

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

Students also work in groups to present a BC project, addressing the following questions: why, what, where, how, how much does it cost, and how can we tell if it is effective?

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