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

Year: 2021

Authors: Langmüller, AM; Dolezal, M; Schlötterer, C

Title: Fine mapping without phenotyping: Identification of selection targets in secondary Evolve and Resequence experiments.

Source: Genome Biol Evol. 2021; 13(8):evab154



Authors Vetmeduni Vienna:

Dolezal Marlies
Langmüller Anna Maria
Schlötterer Christian

Vetmed Research Units
Institute of Population Genetics
Platform Bioinformatics and Biostatistics


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

Population Genetics

Traits first: identification and characterization of adaptive traits


Abstract:
Evolve and Resequence (E&R) studies investigate the genomic selection response of populations in an Experimental Evolution setup. Despite the popularity of E&R, empirical studies in sexually reproducing organisms typically suffer from an excess of candidate loci due to linkage disequilibrium, and single gene or SNP resolution is the exception rather than the rule. Recently, so-called "secondary E&R" has been suggested as promising experimental follow-up procedure to confirm putatively selected regions from a primary E&R study. Secondary E&R provides also the opportunity to increase mapping resolution by allowing for additional recombination events, which separate the selection target from neutral hitchhikers. Here, we use computer simulations to assess the effect of different crossing schemes, population size, experimental duration, and number of replicates on the power and resolution of secondary E&R. We find that the crossing scheme and population size are crucial factors determining power and resolution of secondary E&R: A simple crossing scheme with few founder lines consistently outcompetes crossing schemes where evolved populations from a primary E&R experiment are mixed with a complex ancestral founder population. Regardless of the experimental design tested, a population size of at least 4,800 individuals, which is roughly five times larger than population sizes in typical E&R studies, is required to achieve a power of at least 75%. Our study provides an important step toward improved experimental designs aiming to characterize causative SNPs in Experimental Evolution studies.© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.


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