CPES SV S5 profile Biology and ecology

Students will be asked to carry out a bibliographical analysis on a topic of their choice, validated by the UE supervisors. Under the tutelage of a teacher-researcher, students will have to answer the problem they have set themselves by analyzing the available bibliography. They will have to assess the state of the art in the field they are working on, identifying areas of uncertainty and controversy, and open questions that remain to be resolved. They will have to carry out a genuine critical scientific analysis of the available bibliography, and not simply report on it. They will have to follow the conventions of scientific article writing, involving citation of sources, synthesis of information through illustration, problematization and synthesis of scientific results.

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This course is an extension of the "Fundamentals of Evolution" course, and introduces the main concepts of evolutionary ecology in order to understand and formalize in a simple way the evolutionary and ecological mechanisms that shape biodiversity at different scales of integration.

This course is designed as a coherent whole, with lectures, tutorials and practical work complementing each other. Notions are approached by example, then formalized using mathematical models, which are compared with experience and real data.

It will deal with population dynamics (intra- and interspecific competition), ecological niches and will detail the mechanisms of evolution and their genetic consequences on a population scale: natural selection (including sexual selection), influence of reproductive regimes, genetic drift. The practical sessions will enable students to master the mathematical formalization of notions seen in class and their simple computer modeling, as well as the analysis of data sets. Practical work will enable students to carry out and analyze in small groups 2 experiments lasting 1 month each (with report writing and oral presentation), in order to develop methodology and scientific reasoning.

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The EU is organized into five main themes:

Theme 1: Gene mapping and recombination. Notions of molecular biology related to gene expression, DNA repair and epigenetic processes.

Theme 2: Introduction to molecular evolution: Measuring the intensity of selection in genetic divergence. Molecular clock and variation in evolutionary rates created by the action of natural selection. Neutralist theory of evolution.

Theme 3: Introduction to genomics: composition and size of genomes. Importance of repeated elements. Notion of genetic linkage and local effect of selection. Influence of demography.

Theme 4: Molecular tools for biodiversity: Barcoding, eDNA, metabarcoding. Molecular taxonomy. Limitations of hybridization. Conservation applications.

Theme 5: Extranuclear heredity. Symbiosis, parasitism and co-evolution (intra-cellular: e.g. Wolbachia). Notion of extended phenotype.

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This teaching unit will cover the elements needed to understand the way of life of the major groups of unicellular organisms at the basis of ecosystem functioning (viruses, bacteria, archaea and unicellular eukaryotes....). The course covers the biological organization of each type of organism, its modes of reproduction and diversity, leading to notions of ecology. We will look at the role of these microorganisms in the functioning and dynamics of ecosystems, considering the interactions that these organisms maintain with other living beings (the notion of "symbiosis" in all its variations).

Practical work will :

 - implementation of techniques for bacterial enumeration (CFU), identification of a particular strain from an environmental sample

 - highlighting the diversity of phytoplankton (unicellular algae) in aquatic environments (freshwater)

 - demonstrating the specificity of interactions between bacteria and bacteriophages

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The main objective is to learn the basics of comparative anatomy of chordates, so as to be able to compare and classify them, before tracing the key stages in their evolutionary history. Teaching is integrative in the sense that it draws on both present-day organisms and the fossil record, so as to document the evolutionary history of the clade in its entirety and in all its aspects. Anatomical, biomechanical, phylogenetic and ecomorphological approaches will be addressed in lectures to illustrate the diversity and major characteristics of chordates. Practical work (and practical sessions) will illustrate the evolution of the diversity of integuments, skeleton, musculature, digestive and respiratory systems over long time scales.

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This course is a natural continuation of the " Quantifying Hazards " course (HAV424B) presented in S4. It should provide the concepts for constructing experimental protocols that answer biological questions, and for associating appropriate models for analyzing variability. The first part will be devoted to the construction of experimental protocols that can answer a multitude of questions in the life sciences, i.e. taking into account the inevitable dependence of statistical individuals, such as pairing and the spatial or temporal structure of populations. This part of the course will also introduce the notion of fluctuation, replication and pseudo-replication, which will be taken into account in the models built in the second part of the course. The second part of the course will show the link between the experimental protocol and the modeling of the variability of a quantitative response variable, through the construction of models including several qualitative or quantitative variables. Particular attention will be paid to the conditions of application of these methods, to type I and type II errors, to methods for estimating the parameters of the models constructed (including likelihood) and to the interpretation of the estimated parameters. Each notion will be illustrated by the analysis of real biological data from a variety of themes, helping students to discover not only modern and current biological questions, but also the tools developed to answer them. Practical work in R will enable students to independently carry out analyses on published biological cases.

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