Broad geographic sampling reveals the shared basis and environmental correlates of seasonal adaptation in Drosophila
- Wellcome Sanger Institute, United Kingdom
- University of Virginia, United States
- Stanford University, United States
- University of Pennsylvania, United States
- University of Georgia, United States
- University of Cambridge, United Kingdom
- University of Fribourg, Switzerland
- Institute of Evolutionary Biology, CSIC- Universitat Pompeu Fabra, Spain
- University of Utah, United States
- Taras Shevchenko National Univ Kyiv, Ukraine
- Cornell University, United States
- Laurentian University, Canada
- University of Wisconsin-Madison, United States
- University of Kansas, United States
- The Pennsylvania State University, United States
- Taras Shevchenko National University of Kyiv, Ukraine
Abstract
To advance our understanding of adaptation to temporally varying selection pressures, we identified signatures of seasonal adaptation occurring in parallel among Drosophila melanogaster populations. Specifically, we estimated allele frequencies genome-wide from flies sampled early and late in the growing season from 20 widely dispersed populations. We identified parallel seasonal allele frequency shifts across North America and Europe, demonstrating that seasonal adaptation is a general phenomenon of temperate fly populations. Seasonally fluctuating polymorphisms are enriched in large chromosomal inversions and we find a broad concordance between seasonal and spatial allele frequency change. The direction of allele frequency change at seasonally variable polymorphisms can be predicted by weather conditions in the weeks prior to sampling, linking the environment and the genomic response to selection. Our results suggest that fluctuating selection is an important evolutionary force affecting patterns of genetic variation in Drosophila.
Data availability
- All raw sequence data have been deposited to the NCBI short read archive (SRA; BioProject Accession #PRJNA308584; accession numbers for each sample can be found in Supplemental Table 1).- Code to conduct these analyses, primary results files, and code to reproduce the figures are available at https://github.com/machadoheather/dmel_seasonal_RTEC.- VCF files with the raw allele frequencies per population and a R-data file of allele frequencies and effective sample sizes (Nc; compatible with scripts) are available on DataDryad (https://datadryad.org/stash/dataset/doi:10.5061/dryad.4r7b826).
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Data from: Broad geographic sampling reveals predictable, pervasive, and strong seasonal adaptation in DrosophilaDryad Digital Repository, doi:10.5061/dryad.4r7b826.
Article and author information
Author details
Funding
NIH Office of the Director (R01GM100366)
- Dmitri A Petrov
NIH Office of the Director (R35GM118165)
- Dmitri A Petrov
NIH Office of the Director (R01GM100366,R01GM137430)
- Alan Bergland
NIH Office of the Director (F32GM097837,R35GM119686)
- Alan Bergland
European Commission (H2020-ERC-2014-CoG-647900)
- Josefa González
Natural Sciences and Engineering Research Council of Canada (RGPIN-2018-05551)
- Thomas Merritt
Canada Research Chairs (950-230113)
- Thomas Merritt
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2021, Machado et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Broad geographic sampling reveals the shared basis and environmental correlates of seasonal adaptation in Drosophila
eLife 10:e67577.
https://doi.org/10.7554/eLife.67577
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