M2 - Paleontology (PAL)

"This course will take the form of a series of about a dozen lectures/seminars on current research topics in vertebrate paleontology and evolutionary biology; biodiversity and paleobiodiversity of continental (animal) ecosystems; topographic and climatic barriers versus dispersal and vicariance; community structure, food webs over time, and paleoguilds; and the role of geodynamics and contingency (crises). The main objective is to gain a solid understanding of the current research themes and areas of focus within the paleontological and evolutionary biology communities."

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This course unit will take the form, as far as possible, of a one-week field internship on-site (with accommodations provided). The internship locations may change from year to year depending on new discoveries and/or partnership proposals (public/private). This internship may therefore take different forms, ranging from a “survey” approach—involving travel to various sites—to a more “excavation site” approach—which is stationary. In all cases, the various objectives listed below will be addressed to ensure the success of this field week, so that students can master the various techniques as thoroughly as possible.

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In this course unit, we will explore the main theoretical concepts of evolutionary processes as reflected in the fossil record. We will focus on reconciling microevolutionary and macroevolutionary mechanisms. The concepts covered will include: species and intraspecific variability, speciation and the rates of evolution, adaptive radiations (ecological speciation) in the fossil record, targeted extinctions (competition between migrants and native species) or mass extinctions (major biological crises), evolutionary modes (anagenesis and saltationism) observed in the fossil record, and a comprehensive review of microevolutionary mechanisms.

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The goal of this course unit is to support students in developing their career plans and searching for internships, while helping them begin to prepare for their transition into the workforce by providing a comprehensive yet personalized overview of possible career paths.

Specifically, sessions with various stakeholders provide an opportunity to present the doctoral thesis (a presentation by the GAIA doctoral school, presentations by doctoral students) and to explore the professional opportunities targeted by the different tracks (research careers and the non-academic sector). Activities specific to each track then help students better identify the scientific fields most closely aligned with their career goals. Finally, tutorial sessions are designed to prepare students for writing scientific articles in English.

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This course provides the tools needed 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). The developmental and functional approaches (primarily odontology) will be illustrated using various methodologies developed on the Montpellier campus (notably X-ray microtomography). A critical review of key articles in the field will be presented orally, followed by 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 changes in developmental mechanisms that explain current and past morphological diversity, thereby bridging the gap between biology and paleontology.

Throughout this module, we will use articles to discuss several evolutionary topics relevant to Evo-Devo approaches: the concept of homology, the origin and evolution of repetitive structures, the genetic basis of development, and the links between genomic evolution and morphological evolution. We will illustrate these concepts using examples from metazoans and the green lineage, and apply them at the level of major modern groups as well as at the population level.

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Phylogeny is a search for evolutionary clues. The goal of this module is to highlight the existence of gene phylogenies within species phylogenies, the methods for representing evolutionary histories as trees, and the concept of positional molecular homology through sequence alignment. The principles of phylogenetic inference methods are at the core of this course unit. Distance-based methods highlight the difficulties in distinguishing between homology and homoplasy, as well as the need to construct models of character evolution. The cladistic approach based on maximum parsimony illustrates, on the one hand, the use of bootstrapping to estimate the robustness of phylogenetic nodes and, on the other hand, the impact of taxonomic sampling on the detection of multiple substitutions.

Probabilistic approaches are introduced and then explored in greater depth. The long-branch attraction artifact leads to the introduction of probabilistic reasoning. The maximum likelihood method allows us to address the calculation of likelihood, the estimation of model parameters using optimality criteria, the construction of various models of character evolution, and the comparison of models. Bayesian inference, in turn, introduces the distinction between density-based and optimality-based approaches. It then covers the a priori use of probability densities, the estimation of posterior distributions of model parameters based on the data, their approximation using Markov chains with Monte Carlo and Metropolis coupling (MCMCMC), the initialization and convergence phases, and the calculation and interpretation of posterior probabilities for trees and clades. The importance of evolutionary models for DNA, RNA, and protein sequences and their refinement is emphasized.

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The goal of this course unit is to support students as they finalize their career plans and prepare for life after the master’s program.

The EU is organized around the entire program, with regular discussion sessions between the teaching staff and students.

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The M2 individual internship lasts approximately 5 to 6 months and, depending on the student’s track, must be completed 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 may be conducted at a local, national, or international organization on a topic approved by the faculty to ensure it aligns with the specific objectives of the student’s track of study.

Evaluation: The internship is evaluated during a public defense before a panel, during which the content of the thesis and the quality of the student’s responses to the panel’s questions are assessed. The student’s conduct and initiative during the internship are evaluated by the internship supervisor.

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