PT - JOURNAL ARTICLE AU - Anna Maria Langmüller AU - Marlies Dolezal AU - Christian Schlötterer TI - Fine mapping without phenotyping: Identification of selection targets in secondary Evolve and Resequence experiments AID - 10.1101/2021.01.27.428395 DP - 2021 Jan 01 TA - bioRxiv PG - 2021.01.27.428395 4099 - http://biorxiv.org/content/early/2021/01/28/2021.01.27.428395.short 4100 - http://biorxiv.org/content/early/2021/01/28/2021.01.27.428395.full AB - Evolve and Resequence (E&R) studies investigate the genomic selection response of populations in an Experimental Evolution (EE) setup. Despite the popularity of E&R, empirical studies typically suffer from an excess of candidate loci due to linkage, and single gene or SNP resolution is the exception rather than the rule. Recently, a secondary E&R design – where unevolved founder genotypes are added to a primary E&R study - has been suggested as promising experimental procedure to confirm putative selection targets. Furthermore, secondary E&R provides 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 crossing scheme, population size, experimental duration, and number of replicates on the power, and resolution of secondary E&R. We find that the crossing scheme, population size, and the experimental duration are crucial factors for the 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 5 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 towards improved experimental designs aiming to characterize causative SNPs in EE studies.Competing Interest StatementThe authors have declared no competing interest.