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Soft selective sweeps: Addressing new definitions, evaluating competing models, and interpreting empirical outliers

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  • Parul Johri
  • Wolfgang Stephan
  • Jeffrey D Jensen

Abstract

The ability to accurately identify and quantify genetic signatures associated with soft selective sweeps based on patterns of nucleotide variation has remained controversial. We here provide counter viewpoints to recent publications in PLOS Genetics that have argued not only for the statistical identifiability of soft selective sweeps, but also for their pervasive evolutionary role in both Drosophila and HIV populations. We present evidence that these claims owe to a lack of consideration of competing evolutionary models, unjustified interpretations of empirical outliers, as well as to new definitions of the processes themselves. Our results highlight the dangers of fitting evolutionary models based on hypothesized and episodic processes without properly first considering common processes and, more generally, of the tendency in certain research areas to view pervasive positive selection as a foregone conclusion.

Suggested Citation

  • Parul Johri & Wolfgang Stephan & Jeffrey D Jensen, 2022. "Soft selective sweeps: Addressing new definitions, evaluating competing models, and interpreting empirical outliers," PLOS Genetics, Public Library of Science, vol. 18(2), pages 1-12, February.
  • Handle: RePEc:plo:pgen00:1010022
    DOI: 10.1371/journal.pgen.1010022
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    References listed on IDEAS

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    1. Jeffrey D Jensen, 2014. "On the unfounded enthusiasm for soft selective sweeps," Nature Communications, Nature, vol. 5(1), pages 1-10, December.
    2. Jerome Kelleher & Alison M Etheridge & Gilean McVean, 2016. "Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes," PLOS Computational Biology, Public Library of Science, vol. 12(5), pages 1-22, May.
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    Cited by:

    1. Vivak Soni & John W. Terbot & Jeffrey D. Jensen, 2024. "Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data," Nature Communications, Nature, vol. 15(1), pages 1-5, December.

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