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Type of publication: Journal Article
Type of document: Full Paper

Year: 2020

Authors: Burny, C; Nolte, V; Nouhaud, P; Dolezal, M; Schlötterer, C

Title: Secondary evolve and re-sequencing: an experimental confirmation of putative selection targets without phenotyping.

Source: Genome Biol Evol. 2020; 12(3):151-159

Authors Vetmeduni Vienna:

Burny Claire Delphine
Dolezal Marlies
Nolte Viola
Nouhaud Pierre
Schlötterer Christian

Vetmed Research Units
Institute of Population Genetics
Platform Bioinformatics and Biostatistics

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Project(s): ERC ADG: The architecture of adaptation

Population Genetics

Evolve and resequencing (E&R) studies investigate the genomic responses of adaptation during experimental evolution. Because replicate populations evolve in the same controlled environment, consistent responses to selection across replicates are frequently used to identify reliable candidate regions that underlie adaptation to a new environment. However, recent work demonstrated that selection signatures can be restricted to one or a few replicate(s) only. These selection signatures frequently have weak statistical support, and given the difficulties of functional validation, additional evidence is needed before considering them as candidates for functional analysis. Here, we introduce an experimental procedure to validate candidate loci with weak or replicate-specific selection signature(s). Crossing an evolved population from a primary E&R experiment to the ancestral founder population reduces the frequency of candidate alleles that have reached a high frequency. We hypothesize that genuine selection targets will experience a repeatable frequency increase after the mixing with the ancestral founders if they are exposed to the same environment (secondary E&R experiment). Using this approach, we successfully validate two overlapping selection targets, which showed a mutually exclusive selection signature in a primary E&R experiment of Drosophila simulans adapting to a novel temperature regime. We conclude that secondary E&R experiments provide a reliable confirmation of selection signatures that either are not replicated or show only a low statistical significance in a primary E&R experiment unless epistatic interactions predominate. Such experiments are particularly helpful to prioritize candidate loci for time-consuming functional follow-up investigations.© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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