Paleontology (PAL)

This EU will take the form of a series of a dozen conferences/seminars on current research topics in vertebrate paleontology and evolutionary biology; biodiversity and paleobiodiversity of continental ecosystems (animal); topographic and climatic barriers vs. dispersion and vicariance; community structure, food chains over time, and paleoguilds; the role of geodynamics and contingency (crises). The main objective is to acquire a good understanding of the current research topics/areas in the paleontological/evolutionary community."

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This course will take the form of a one-week field internship on site (with accommodation provided), where possible. The internship locations may change from year to year depending on discoveries and/or partnership proposals (public/private). This internship may therefore take different forms, with a "prospecting" approach and therefore a mobile fieldwork component, or a more "excavation site" approach and therefore a fixed component. In all cases, the various objectives listed below will be addressed in order to make the most of this week in the field and ensure that the various techniques are mastered as well as possible.

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In this course, we will address the main theoretical concepts of evolutionary processes through the fossil record. We will discuss how to reconcile microevolutionary and macroevolutionary mechanisms. The concepts covered will be: species and intraspecific variability, speciation and the pace of evolution, adaptive radiation (ecological speciation) in the fossil record, targeted extinctions (migrant-native competition) or mass extinctions (major biological crises), evolutionary modalities (anagenesis and saltationism) observed in the fossil record, and a comprehensive review of microevolutionary mechanisms.

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The objective of this EU is to support students in developing their career plans and searching for internships, while beginning to prepare for their integration into professional life by providing a comprehensive and personalized overview of possible career paths.

In practical terms, meetings with various stakeholders provide an opportunity to present the doctoral thesis (presentation of the GAIA doctoral school, presentations by doctoral students) and the professional network targeted by the various courses (research professions and non-academic sector). Activities specific to each course then enable students to better target the scientific fields most relevant to their professional projects. Finally, tutorial sessions are designed to prepare students for writing scientific articles in English.

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This course provides the necessary tools for data analysis in paleontology.

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"The objective is to analyze the phylogenetic, developmental, and functional constraints that may have governed the morphological changes observable in the fossil record. The phylogenetic approach will be addressed using reconstruction methods applicable to fossils (parsimony; cladistic analysis). Developmental and functional approaches (mainly odontology) will be illustrated by various methodologies developed on the Montpellier campus (in particular X-ray microtomography). A critical review of reference articles in the field will be followed by an oral presentation and a question-and-answer session."

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Evo-devo is an evolutionary approach to developmental genetics. This discipline seeks to shed light on the changes in developmental mechanisms that explain current and past morphological diversity, thus forming an important bridge between biology and paleontology.

During the module, we will discuss several evolutionary issues relevant to Evo-Devo approaches based on articles: the question of homology, the establishment and evolution of repeated structures, the genetic basis of development, and the links between genome evolution and form evolution. We will illustrate these concepts using examples from metazoans and the green lineage, and apply them to both large modern groups and populations.

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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 objective of this EU is to support students in finalizing their professional projects and preparing for life after their master's degree.

The EU is organized on a course-wide basis, with regular discussion sessions between the teaching team and students.

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The individual M2 internship lasts approximately 5 to 6 months and must be carried out, depending on the course concerned, in a research laboratory or a non-academic organization. It allows students to gain in-depth professional experience in the field of biodiversity, evolution, or ecology. It can be carried out in a local, national, or international organization, on a topic approved by the teaching team so as to fit in with the specific objectives of the program followed by the student.

Assessment: The internship is assessed during a public defense before a jury, during which the content of the thesis and the quality of the responses to the jury's questions are evaluated. The student's behavior and enthusiasm during the internship are assessed by the internship supervisor.

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