Cited by 448Evolution and Genetic DynamicsGenetic diversity and population structureGenetic and phenotypic traits in livestock

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Genome-wide analysis of a long-term evolution experiment with Drosophila

Burke, Molly K., Dunham, Joseph P., Shahrestani, Parvin, Thornton, Kevin R., Rose, Michael R., Long, Anthony D.·2010·Nature

DOI 10.1038/nature09352

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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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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.
ORCID: Burke, Molly K.
Shahrestani, Parvin
Thornton, Kevin R.
Rose, Michael R.
Long, Anthony D.
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2010-09
Volume: 467
Issue: 7315
Pages: 587-590
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature09352
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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Genome-wide analysis of a long-term evolution experiment with Drosophila

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