Société Française de Bioinformatique

Mots-Clés

population genetics genome dynamics comparative genomics statistical modelling experimental evolution C. elegans.

Description

Structural Variations (SVs) at the chromosomal scale, including deletions, duplications, inversions and translocations encompass large DNA fragments. They are a major source of evolution and can have a greater phenotypic impact than single nucleotide variations. In humans, for example, it is estimated that SV occur at a higher rate than single nucleotide polymorphims. In this project we will study how varying recombination rates along the genome impacts natural selection on SVs during adaptation to a novel environment, using as a model system populations of the nematode Caenorhabditis elegans with standing genetic variation. The project has three main aims. The first aim is to describe SVs in a domesticated lab population of C. elegans that is ultimately derived from the hybridization of wild isolates. To accomplish this aim the student will perform a comparative analysis of published de novo genome sequences from at least two wild isolates and identify SV polymorphism from short-read resequencing data using existing programs as well as derive ad hoc bio-informatic tools if needed. The second aim is to follow SV evolution in an “evolve and resequencing” experiment. For this, the student will collect and analyze genome resequence data from populations adapting to a new lab environment under varying recombination rates along the genome. A third aim is to model the observed experimental evolution of SV as a function of recombination, natural selection and genetic drift. The student will develop individual-based simulations of the expected population genetics of SV.

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