Description du sujet de thèse

Understanding how and how often asexual lineages emerge within sexual species is essential for unlocking the mysteries of sex-asex transitions during evolution. A better understanding of these transitions is a key factor in solving the evolutionary enigma of sexual reproduction. These transitions are poorly understood, both empirically and theoretically. The aims of this PhD project are to develop this theory, to develop and apply new methods to analyze the genomes of asexuals, and to study these transitions in the test case of the brine shrimp Artemia parthenogenetica.

Asexuality can spread 'by transmission' from existing asexual lineages to new ones through various types of crosses, including cryptic sex and transmission via males that are rarely produced by certain asexual lineages. As a consequence, extant asexual lineages are often the result of repeated and nested hybridization and back-crossing event, and they may present ploidy variations and recombination within asexual lineages. These patterns may further be complicated by evolution within asexual lineages, involving mechanisms similar to those involved in the evolution of sex-chromosomes, in particular degeneration, recombination suppression, and dosage compensation.

On the empirical side, classical phylogenetic methods and standard measures of genetic distance are not suitable for analyzing evolutionary histories involving repeated and nested hybridization. In this project we aim at overcoming these challenges by developing new approaches to study the origin of the different asexual lineages of Artemia (small crustaceans that live in hypersaline environments). We will study the genomes of a large number of asexual lineages, including all known polyploids and their potential sexual relatives. Preliminary analyses suggest that all asexual Artemia, diploid as well as polyploid, have arisen as a result of successive and nested hybridization events, involving backcrosses with different sexual species (1). All asexual Artemia would have the same common ancestor and would therefore probably carry the same asexuality gene(s). However, we know little or nothing about the impact of hybridization on the evolution of the genomes of these lineages and the possible scenarios remain largely hypothetical.

From a theoretical side, multilocus models for the evolution of asexual genome, with and without the evolution of regulators of gene expression, will be used to investigate sex-asex transitions. Both the initial fitness of neo-asexuals, as well as their subsequent evolution (degeneration, recombination suppression, dosage compensation) will be addressed. These models will build on the recent development of chromosome-scale simulations developed for the study of sex chromosomes (2–5).

References:
1. N. O. Rode, R. Jabbour-Zahab, L. Boyer, É. Flaven, F. Hontoria, G. V. Stappen, F. Dufresne, C. Haag, T. Lenormand, The origin of asexual brine shrimps. The American Naturalist 200, E52–E76 (2022).
2. T. Lenormand, F. Fyon, E. Sun, D. Roze, Sex chromosome degeneration by regulatory evolution. Current Biology 30, 3001-3006.e5 (2020).
3. T. Lenormand, D. Roze, Y recombination arrest and degeneration in the absence of sexual dimorphism. Science 375, 663–666 (2022).
4. T. Lenormand, D. Roze, Can mechanistic constraints on recombination reestablishment explain the long-term maintenance of degenerate sex chromosomes? Peer Community Journal 4, e17 (2024).
5. F. Fyon, T. Lenormand, Cis-regulator runaway and divergence in asexuals. Evolution 72, 426–439 (2018).

Contexte de travail

The students will receive comprehensive training in state-of-the-art evolutionary genomics and theoretical population genetics. The students will spend most of their time in the Genetic and Evolutionary Ecology group (GEE) at the Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), a large, ecology and evolution-focused research institute in Montpellier, Southern France, with possible visits of project partners elsewhere in France. Montpellier is a lively student town with a beautiful historic center, located about 10 km from the Mediterranean Sea. The PhD will be part of an advanced ERC project ('RegEvol', Thomas Lenormand), addressing novel ideas and theoretical predictions on the role of regulatory evolution for several important fundamental topics in evolutionary biology (sex chromosomes, maintenance of sex, complexity of gene networks, etc.). The students will join the team working on this project, including Aline Muyle, Denis Roze, Sylvain Glémin, Christoph Haag and Thomas Lenormand as well as other people recruited on the project. Chistoph Haag and Thomas Lenormand will co-supervise the PhD.

Candidate requirements:
(1) Enthusiasm and genuine curiosity for evolutionary genetics, genomics, and evolutionary biology.
(2) An undergraduate degree in the subject area of evolutionary biology. Experience with genomics and/or population genetics and/or evolutionary theory is desirable.
(3) Strong quantitative skills. Experience with programming or bioinformatics is desirable.
(3) Strong oral and written communication skills in English (the work language for science at the CEFE is English).
(4) Ability to work both independently and in a highly collaborative environment.
(5) Well organized and highly motivated.

Contraintes et risques

There is no specific risk associated with the position