Julien Dutheil
Please refer to <https://www.evolbio.mpg.de/2996577/group_molsysevolution> or contact Julien Dutheil via <dutheil@evolbio.mpg.de> for further information on the project after having read the publications stated below.
To apply for the position please write an email to <imprs-application@evolbio.mpg.de> for attention of Ms. Ellen Karl from the MPI personnel department. Your application documents have to be compiled in one PDF including a short motivational statement, a short CV (biosketch), bachelor and master degrees/transcripts of records and contact information for two academic references. Name the PDF as follows: Lastname_Firstname_Lastnamesupervisor.pdf.
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The evolution of the recombination landscape and its impact across eukaryotic genomes
The recombination rate influences the patterns of genetic diversity across populations and along genomes. In most species, recombination is heterogeneous across the genome, defining a "recombination landscape". This project aims to study the evolution of some properties of the recombination landscape across Eukaryotes.
Population genomic modeling offers a powerful and cost-efficient way to infer recombination rates. State-of-the-art methods achieve high accuracy by explicitly incorporating population demographics. Inference methods based on the sequentially Markov coalescent (SMC) process even permit joint inference of the demographic history and the recombination landscape with as little as a single diploid, unphased genome, provided the assembly is of chromosome-level quality.
The goal of this project is to apply the iSMC method to a large sample of species with available population-genomic datasets to provide an unprecedented picture of the recombination landscape and to map the evolution of its features along the eukaryotic phylogeny. The resulting recombination maps will be further correlated with other molecular features, such as the rate of (adaptive) evolution, the occurrence of compensatory mutations, GC content, and the strength of these correlations will be assessed throughout the phylogeny.
The project will require to (1) establish with the help of simulations, which genome data features are necessary for the obtention of unbiased recombination rates using SMC approaches; (2) generate a dataset of genomes throughout the Eukaryote tree, and conduct a phylogenetic comparative analysis of the inferred recombination landscapes; (3) for each genome, obtain proxies of the fitness landscape and assess how the recombination landscape impacts them. A particular focus will be given to epistatic interactions and the rate of compensatory mutations.
Recommended reading:
1) Dutheil, J. Y. (2024). On the estimation of genome-average recombination rates. Genetics, 227(2). https://doi.org/10.1093/genetics/iyae051
2) V. Barroso G, Puzović N, Dutheil JY (2019). Inference of recombination maps from a single pair of genomes and its application to ancient samples. PLoS Genet 15(11): e1008449. https://doi.org/10.1371/journal.pgen.1008449
3) Chaurasia S, Dutheil JY (2022). The Structural Determinants of Intra-Protein Compensatory Substitutions. Mol Biol Evol 39(4):msac063. https://doi.org/10.1093/molbev/msac063.