Data from: Genetic redundancy fuels polygenic adaptation in Drosophila
| Main Authors: | Barghi, Neda, Tobler, Raymond, Nolte, Viola, Jakšić, Ana Marija, Mallard, François, Otte, Kathrin Anna, Dolezal, Marlies, Taus, Thomas, Kofler, Robert, Schlötterer, Christian |
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| Format: | info dataset Journal |
| Terbitan: |
, 2019
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| Subjects: | |
| Online Access: |
https://zenodo.org/record/4991665 |
Daftar Isi:
- 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.
- 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 >=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