Choice 3

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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.

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Phylogeny is a quest for evolutionary clues. The aim of this module is to recall the existence of gene phylogenies within species phylogenies, the ways in which evolutionary histories can be represented in tree form, and the challenge of positional molecular homology through sequence alignment. The principles of phylogenetic inference methods are at the heart of this course. Distance methods highlight the difficulties of separating homology and homoplasy, and the need to build models of character evolution. The maximum parsimony cladistic approach illustrates the use of bootstrapping to estimate the strength of phylogeny nodes, and the impact of taxonomic sampling in detecting multiple substitutions.

Probabilistic approaches are presented and explored in greater depth. The attraction artifact of long branches leads to an introduction to probabilistic reasoning. The maximum likelihood method is used to calculate likelihood, to estimate model parameters by optimality, to construct different character evolution models, and to compare models. Bayesian inference introduces the distinction between density-based and optimality-based approaches. It then shows the a priori use of probability densities, the data-driven estimation of a posteriori distributions of model parameters, their approximation by Markov chains with Monte Carlo techniques and Metropolis coupling (MCMCMC), the ignition and convergence phases, and the calculation and interpretation of tree and clade posterior probabilities. 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 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? 

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"All teaching is carried out in English.

The courses present 4 aspects of Conservation Biology, based on current scientific research in this discipline:

1. Introduction to biodiversity conservation (BC): Conservation Biology definition. 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. Does conservation work? Importance of social acceptability and political commitment. Need for biodiversity indicators and to measure the impact of conservation.

Students also complete a group assignment in which they present a BC project, around the questions: why, what, where, how, how much it costs and how to know if it's effective."

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