Paleontology (PAL)

"This EU will take the form of a series of a dozen lectures/seminars on current research topics in vertebrate paleontology and evolutionary biology; biodiversity and paleobiodiversity of continental ecosystems (animal); topographic and climatic barriers vs. dispersal and vicariance; community structuring, trophic chains through time and paleoguilds; role of Geodynamics and contingency (crises). The main objective is to acquire a good knowledge of the current research themes/axes in the paleontological/evolutionary community.

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This course will take place, as far as possible, in the form of a one-week on-site internship (with accommodation). The locations of the internship may change from one year to the next depending on the discoveries and/or partnership proposals (public/private). This internship can therefore take different directions, with a "prospecting" approach and therefore a travelling field or a more "excavation site" approach and therefore fixed. In all cases, the different objectives listed below will be addressed to perfect this week of fieldwork so that the different techniques are mastered as well as possible.

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In this course we will approach the main theoretical concepts of evolutionary processes through the fossil record. The aim is to reconcile microevolutionary mechanisms with macroevolution. The concepts addressed will be: species and intraspecific variability, speciation and evolutionary rhythms, adaptive radiation (ecological speciation) in the fossil record, targeted extinctions (migrant-autochthonous 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 course is to accompany the student in the construction of his professional project and his search for an internship, while beginning to prepare his integration into professional life by an exhaustive and personal vision of possible career paths.

In concrete terms, meetings with different speakers allow the presentation of the doctoral thesis (presentation of the GAIA doctoral school, presentations by thesis students) and the professional environment targeted by the different courses (research professions and the non-academic sector). Activities specific to each pathway then help to better target the scientific fields most closely related to the students' professional projects. Lastly, the course includes practical sessions designed to prepare students to write 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 discernible in the fossil record. The phylogenetic approach will be approached by reconstruction methods applicable to fossils (parsimony; cladistic analysis). Developmental and functional approaches (mainly odontology) will be illustrated by different methodologies developed on the Montpellier campus (notably X-ray microtomography). The critical review of reference articles in the considered field will give rise to an oral presentation followed by questions."

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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 present and past morphological diversity, and thus opens an important bridge between biology and paleontology.

During the module, we will discuss, based on articles, several evolutionary issues that are useful for Evo-Devo approaches: the question of homology, the question of the establishment and evolution of repeated structures, the genetic basis of development and the links between genome evolution and shape evolution. We will illustrate these notions from examples taken from metazoans and the green lineage, and will apply them to the scale of large current groups but also to populations.

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Phylogeny is a quest for evolutionary clues. The aim of this module is to recall the existence of gene phylogenies in species phylogenies, the ways of representing 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 the knowledge of this course. The distance methods allow to underline the difficulties of separating homology and homoplasy, and the necessity to build models of character evolution. The cladistic approach with maximum parsimony allows to illustrate on the one hand the use of bootstrap to estimate the strength of the nodes of phylogenies, and on the other hand the impact of taxonomic sampling to detect multiple substitutions.

The probabilistic approaches are presented and further developed. The attraction artifact of long branches leads to the introduction of probabilistic reasoning. The maximum likelihood method allows us to approach the calculation of the likelihood, the estimation of the parameters of the models by optimality, the construction of different models of character evolution, as well as the comparison of models. Bayesian inference introduces the distinction between density and optimality approaches. It then shows the a priori use of probability densities, the estimation of a posteriori distributions of model parameters given the data, their approximation by Markov chains with Monte Carlo techniques and Metropolis coupling (MCMCMC), the ignition and convergence phases, and the computation and interpretation of the posterior probabilities of trees and clades. The importance of DNA, RNA and protein sequence evolution models and their improvement is stressed.

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The objective of this course is to help students finalize their professional projects and prepare for the post-master's program.

The EU is organized at the level of the course, with regular discussion sessions between the teaching staff and the students.

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The individual M2 internship lasts approximately 5 to 6 months and must be carried out, depending on the course, in a research laboratory or a structure in the non-academic sector. It allows the student to acquire in-depth professional experience in the field of biodiversity, evolution or ecology. It can be carried out in a local, national, or international structure, on a subject validated by the teaching staff in order to meet the objectives of the course followed by the student.

Evaluation: The internship is evaluated during a public defense before a jury during which the content of the thesis and the quality of the answers to the jury's questions are evaluated. The behavior and dynamism of the student during the internship are evaluated by the internship supervisor.

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