Multiple modes of positive selection shaping the patterns of incomplete selective sweeps over african populations of drosophila melanogaster

Ha My T. Vy, Yong Jin Won, Yuseob Kim

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12 Scopus citations


It remains a challenge in evolutionary genetics to elucidate how beneficial mutations arise and propagate in a population and how selective pressures on mutant alleles are structured over space and time. By identifying “sweeping haplotypes (SHs)” that putatively carry beneficial alleles and are increasing (or have increased) rapidly in frequency, and surveying the geographic distribution of SH frequencies, we can indirectly infer how selective sweeps unfold in time and thus which modes of positive selection underlie those sweeps. Using population genomic data from African Drosophila melanogaster, we identified SHs from 37 candidate loci under selection. At more than half of loci, we identify single SHs. However, many other loci harbor multiple independent SHs, namely soft selective sweeps, either due to parallel evolution across space or a high beneficial mutation rate. At about a quarter of the loci, intermediate SH frequencies are found across multiple populations, which cannot be explained unless a certain form of frequency-dependent positive selection, such as heterozygote advantage, is invoked given the reasonable range of migration rates between African populations. At one locus, many independent SHs are observed over multiple populations but always together with ancestral haplotypes. This complex pattern is compatible with a large number of mutational targets in a gene and frequency-dependent selection on new variants. We conclude that very diverse modes of positive selection are operating at different sets of loci in D. melanogaster populations.

Original languageEnglish
Pages (from-to)2792-2807
Number of pages16
JournalMolecular Biology and Evolution
Issue number11
StatePublished - 1 Nov 2017

Bibliographical note

Funding Information:
We greatly appreciate comments by two anonymous reviewers and Daven Presgraves that allowed us to improve this manuscript significantly. This research was supported by the National Research Foundation of Korea (NRF) grants funded by the Korean government (grant no. 2015R1A4A1041997).

Publisher Copyright:
© The Author 2017.


  • Adaptation
  • Drosophila
  • Heterozygote advantage
  • Population genomics
  • Selective sweep


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