Profile: Biology and Ecology

Students will be required to conduct a literature review on a topic of their choice, which must be approved by the course instructors. Under the guidance of a faculty member, students must address the research question they have identified through an analysis of the available literature. They must provide a review of the current state of the art in their field, identifying areas of uncertainty, controversy, and unresolved questions. They must conduct a genuine critical scientific analysis of the available literature, rather than merely summarizing it. They must adhere to the conventions for writing a scientific article, including citing sources, synthesizing information through illustrations, framing the research question, and synthesizing scientific results.

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This unit builds on the "Basics of Evolution" unit to introduce the main concepts in evolutionary ecology, with the aim of understanding and formally describing, in a straightforward manner, the evolutionary and ecological mechanisms that shape biodiversity at various levels of integration.

This course unit is designed as a coherent whole in which lectures, tutorials, and lab sessions complement one another. Concepts are introduced through examples and then formalized using mathematical models, which are then tested against experimental results and real-world data.

It will cover population dynamics (intra- and interspecific competition) and ecological niches, and will detail the mechanisms of evolution and their genetic consequences at the population level: natural selection (including sexual selection), the influence of reproductive strategies, and genetic drift. The tutorials will enable students to master the mathematical formalization of concepts covered in class, their simple computer modeling, and the analysis of datasets. The lab sessions will involve conducting and analyzing, in small groups, two experiments lasting one month each (including the writing of a report and an oral presentation) in order to develop scientific methodology and reasoning.

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The EU is organized into five major areas:

Topic 1: Genetic mapping and recombination. Concepts in molecular biology related to gene expression, DNA repair, and epigenetic processes.

Topic 2: Introduction to Molecular Evolution: Measuring the intensity of selection in genetic divergence. The molecular clock and variation in evolutionary rates caused by natural selection. The neutral theory of evolution.

Topic 3: Introduction to Genomics: Composition and Size of Genomes. Importance of Repeated Elements. Concepts of Genetic Linkage and Local Selection Effects. Influence of Demographics.

Topic 4: Molecular Tools for Biodiversity: Barcoding, eDNA, metabarcoding. Molecular taxonomy. Limitations related to hybridization. Applications in conservation.

Topic 5: Extranuclear inheritance . Symbiosis, parasitism, and coevolution (intracellular: e.g., Wolbachia). The concept of the extended phenotype.

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This course will cover the concepts necessary for understanding the way of life of the major groups of single-celled organisms that form the basis of ecosystem functioning (viruses, bacteria, archaea, and single-celled eukaryotes, etc.). The lectures will cover the biological organization of each type of organism, their modes of reproduction, and their diversity, leading to an understanding of ecological concepts. We will examine the role of these microorganisms in the functioning and dynamics of ecosystems, considering the interactions these organisms have with other living beings (the concept of “symbiosis” in all its forms).

The hands-on exercises will allow students to:

 - the implementation of techniques for bacterial counting (CFU) and the identification of a specific strain from an environmental sample

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

 - identifying the unique characteristics of interactions between bacteria and bacteriophages

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The main objective is to learn the basics of the comparative anatomy of chordates so that we can compare and classify them, before tracing the key stages of their evolutionary history. The course is integrative in that it draws on both extant organisms and the fossil record to document the evolutionary history of the clade in its entirety and from all angles. Anatomical, biomechanical, phylogenetic, and ecomorphological approaches will be covered in lectures to illustrate the diversity and major characteristics of chordates. The lab sessions (and tutorials) will illustrate the evolution of diversity in the integument, skeleton, musculature, and digestive and respiratory systems over long time scales.

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This course is a natural continuation of the course “Quantification of Randomness” (HAV424B) offered in Semester 4. It is designed to provide students with the concepts needed to develop experimental protocols that address biological questions and to apply appropriate models for analyzing variability. The first part will focus on designing experimental protocols capable of addressing a wide range of questions in the life sciences, specifically by taking into account the inevitable dependencies among statistical individuals, such as kinship and the spatial or temporal structure of populations. This section will thus provide an opportunity to address the concepts of fluctuation, replication, and pseudo-replication, which will be incorporated into the models developed in the second part of the course. The second part will focus on demonstrating the link between the experimental protocol implemented and the modeling of the variability of a quantitative response variable, through the development of models that include several qualitative or quantitative variables. Particular attention will be paid to the conditions under which these methods are applicable, to Type I and Type II errors, to methods for estimating the parameters of the constructed models (including likelihood), and to the interpretation of the estimated parameters. Each concept will be illustrated through the analysis of real biological data from various fields, thereby helping students discover not only current and common biological questions but also the tools developed to address them. Hands-on exercises using R will enable students to independently perform analyses on published biological case studies.

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