Abstract: Heritable phenotypic variation in natural populations exceeds the levels predicted under mutation-selection balance where purifying selection removes variation. Balancing selection, inefficient or weak selection, polygenic adaptation, and non-equilibrium populations are all possible explanations for excess variation. Yet, available genomic data indicate an abundance of directional selection. One potential explanation is that fleeting directional selection drives beneficial mutations to high frequency in rapid waves resulting in many intermediate frequency haplotypes. This hypothesis is supported by the genomic data from a panel of 170 D. simulans genotypes established from a single stable population which show evidence for an abundance of incomplete soft sweeps. Demography, admixture, and balancing selection cannot entirely explain the patterns in these data, while transient selective sweeps can account for all the patterns of variation observed in this population. One interpretation is that constant environmental shifts rapidly change the optimal phenotype within Drosophila populations, leaving a signature of adaptive responses. Material type: Text files of pairwise linkage disequilibrium (LD) calculations from Plink (v). Larger Body of Work: Pervasive incomplete selective sweeps in D. simulans account for excess variation. Related publications and datasets: Drosophila simulans VCF, LD results from chromosomes 2L, 2R, 3R, 4, and X

LD calculated for all possible pairwise combinations of SNPs. Performed for each chromosome separately. This file contains only data for chromosome 3L.