DOI: 10.5061/dryad.rr137kn
title: Data from: Genetic redundancy fuels polygenic adaptation in Drosophila

description: The genetic architecture of adaptive traits is of key importance to
 predict evolutionary responses. Most adaptive traits are polygenic—i.e.,
 result from selection on a large number of genetic loci—but most
 molecularly characterized traits have a simple genetic basis. This
 discrepancy is best explained by the difficulty in detecting small allele
 frequency changes (AFCs) across many contributing loci. To resolve this,
 we use laboratory natural selection to detect signatures for selective
 sweeps and polygenic adaptation. We exposed 10 replicates of a Drosophila
 simulans population to a new temperature regime and uncovered a polygenic
 architecture of an adaptive trait with high genetic redundancy among
 beneficial alleles. We observed convergent responses for several
 phenotypes—e.g., fitness, metabolic rate, and fat content—and a strong
 polygenic response (99 selected alleles; mean s = 0.059). However, each of
 these selected alleles increased in frequency only in a subset of the
 evolving replicates. We discerned different evolutionary paradigms based
 on the heterogeneous genomic patterns among replicates. Redundancy and
 quantitative trait (QT) paradigms fitted the experimental data better than
 simulations assuming independent selective sweeps. Our results show that
 natural D. simulans populations harbor a vast reservoir of adaptive
 variation facilitating rapid evolutionary responses using multiple
 alternative genetic pathways converging at a new phenotypic optimum. This
 key property of beneficial alleles requires the modification of testing
 strategies in natural populations beyond the search for convergence on the
 molecular level.
description: phenotypic
 dataphenotypic_data.zipJaccard indicesJaccard.zipreplicate frequency spectrumRFS.zipTE insertions and frequencies at F60This file contains the frequency of TE insertions in 10 hot-evolved replicates at generation 60. Format specification of this file can be found in manual of PopoolationTE2 (Kofler R, Gomez-Sanchez D, Schlötterer C. PoPoolationTE2: Comparative Population Genomics of Transposable Elements Using Pool-Seq. Mol Biol Evol. 2016;33(10):2759–64.). Column 1: 1-10 since it’s a joint analysis of 10 replicates, column 2: chromosome, column3 : position, column 4: strand of the TE insertion; plus (sense), minus (antisense) or point (unknown), column 5: TE family, column 6: order, column 7: support for the TE insertions; either a single forward signature (F) or a single reverse signature (R) or a matching pair of forward and reverse signatures (FR), column 8: comment (empty or "-" in newer versions), column 9-18: the population frequency of the TE in replicate 1 to 10 respectively.F60_10Reps.teinsertionsF0-F60 sync file, CMH and FET pvalues, haplotype block IDsF0-F60SNP_CMH_FET_blockID.sync.zipevolved haplotypesevolved_haplos.zipselection coefficients and starting allele frequenciesS_SAF.zipnumber of selected alleleThis file has 10 columns which correspond to the number of allele that have &gt;=0.1 frequency change (method 1) in 10 replicates respectively. For a description of method 1, see Materials and Methods: Different approaches to determine the presence of selected alleles and their frequencies.allele_num_perReplicate.txt