Genome-wide analysis of a long-term evolution experiment with Drosophila
Abstract
Experimental evolution systems allow the genomic study of adaptation, and so far this has been done primarily in asexual systems with small genomes, such as bacteria and yeast. Here we present whole-genome resequencing data from Drosophila melanogaster populations that have experienced over 600 generations of laboratory selection for accelerated development. Flies in these selected populations develop from egg to adult ∼20% faster than flies of ancestral control populations, and have evolved a number of other correlated phenotypes. On the basis of 688,520 intermediate-frequency, high-quality single nucleotide polymorphisms, we identify several dozen genomic regions that show strong allele frequency differentiation between a pooled sample of five replicate populations selected for accelerated development and pooled controls. On the basis of resequencing data from a single replicate population with accelerated development, as well as single nucleotide polymorphism data from individual flies from each replicate population, we infer little allele frequency differentiation between replicate populations within a selection treatment. Signatures of selection are qualitatively different than what has been observed in asexual species; in our sexual populations, adaptation is not associated with 'classic' sweeps whereby newly arising, unconditionally advantageous mutations become fixed. More parsimonious explanations include 'incomplete' sweep models, in which mutations have not had enough time to fix, and 'soft' sweep models, in which selection acts on pre-existing, common genetic variants. We conclude that, at least for life history characters such as development time, unconditionally advantageous alleles rarely arise, are associated with small net fitness gains or cannot fix because selection coefficients change over time.
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Re-sequencing of evolved outbred Drosophila melanogaster populations provides strong support for selection on thousands of variants being responsible for changes in body size and fecundity.
“re-sequencing of evolved outbred populations of Drosophila melanogaster has provided strong support for selection on thousands of variants being responsible for changes in the highly complex traits of body size and fecundity97,98.”
From Rare and common variants: twenty arguments (2012) · cites this paper as [97]
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Self-citation
- Authors
- Burke, M. K., Dunham, J. P., Shahrestani, P., Thornton, K. R., Rose, M. R., & Long, A. D.
- Affiliations
- University of California, Irvine (US)
- University of Southern California (US)
- Corresponding author
- Burke, Molly K.
- Long, Anthony D.
- Venue
- Nature
- Published
- 2010-09
- Volume
- 467
- Issue
- 7315
- Pages
- 587-590
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2072201802
- Cited by
- 448
- References
- 26
- Citations by year
- 2026: 17 · 2025: 15 · 2024: 17 · 2023: 17 · 2022: 23 · 2021: 28 · 2020: 28 · 2019: 30 · 2018: 20 · 2017: 28 · 2016: 32 · 2015: 38 · 2014: 33 · 2013: 40 · 2012: 41
- FWCI
- 21.92
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- University of Oregon
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Keywords
- experimental evolution, Drosophila melanogaster, accelerated development, soft sweeps, selection coefficients, allele frequency differentiation, single nucleotide polymorphisms, whole-genome resequencing, life history evolution, laboratory selection, correlated phenotypes, genome-wide association study
- MeSH terms
- Alleles, Animals, Drosophila melanogaster, Biological Evolution, Female, Gene Frequency, Heterozygote, Phenotype, Selection, Genetic, Sex, Polymorphism, Single Nucleotide, Genome, Insect, Genetic Fitness
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