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Distinguishing between Selective Sweeps from Standing Variation and from a De Novo Mutation

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  • Benjamin M Peter
  • Emilia Huerta-Sanchez
  • Rasmus Nielsen

Abstract

An outstanding question in human genetics has been the degree to which adaptation occurs from standing genetic variation or from de novo mutations. Here, we combine several common statistics used to detect selection in an Approximate Bayesian Computation (ABC) framework, with the goal of discriminating between models of selection and providing estimates of the age of selected alleles and the selection coefficients acting on them. We use simulations to assess the power and accuracy of our method and apply it to seven of the strongest sweeps currently known in humans. We identify two genes, ASPM and PSCA, that are most likely affected by selection on standing variation; and we find three genes, ADH1B, LCT, and EDAR, in which the adaptive alleles seem to have swept from a new mutation. We also confirm evidence of selection for one further gene, TRPV6. In one gene, G6PD, neither neutral models nor models of selective sweeps fit the data, presumably because this locus has been subject to balancing selection. Author Summary: Considerable effort has been devoted to detecting genes that are under natural selection, and hundreds of such genes have been identified in previous studies. Here, we present a method for extending these studies by inferring parameters, such as selection coefficients and the time when a selected variant arose. Of particular interest is the question whether the selective pressure was already present when the selected variant was first introduced into a population. In this case, the variant would be selected right after it originated in the population, a process we call selection from a de novo mutation. We contrast this with selection from standing variation, where the selected variant predates the selective pressure. We present a method to distinguish these two scenarios, test its accuracy, and apply it to seven human genes. We find three genes, ADH1B, EDAR, and LCT, that were presumably selected from a de novo mutation and two other genes, ASPM and PSCA, which we infer to be under selection from standing variation.

Suggested Citation

  • Benjamin M Peter & Emilia Huerta-Sanchez & Rasmus Nielsen, 2012. "Distinguishing between Selective Sweeps from Standing Variation and from a De Novo Mutation," PLOS Genetics, Public Library of Science, vol. 8(10), pages 1-14, October.
  • Handle: RePEc:plo:pgen00:1003011
    DOI: 10.1371/journal.pgen.1003011
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    1. Pardis C. Sabeti & David E. Reich & John M. Higgins & Haninah Z. P. Levine & Daniel J. Richter & Stephen F. Schaffner & Stacey B. Gabriel & Jill V. Platko & Nick J. Patterson & Gavin J. McDonald & Han, 2002. "Detecting recent positive selection in the human genome from haplotype structure," Nature, Nature, vol. 419(6909), pages 832-837, October.
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    Cited by:

    1. Felix M Key & Benjamin Peter & Megan Y Dennis & Emilia Huerta-Sánchez & Wei Tang & Ludmila Prokunina-Olsson & Rasmus Nielsen & Aida M Andrés, 2014. "Selection on a Variant Associated with Improved Viral Clearance Drives Local, Adaptive Pseudogenization of Interferon Lambda 4 (IFNL4)," PLOS Genetics, Public Library of Science, vol. 10(10), pages 1-12, October.
    2. Roy Ronen & Glenn Tesler & Ali Akbari & Shay Zakov & Noah A Rosenberg & Vineet Bafna, 2015. "Predicting Carriers of Ongoing Selective Sweeps without Knowledge of the Favored Allele," PLOS Genetics, Public Library of Science, vol. 11(9), pages 1-27, September.
    3. Daniel R Schrider & Andrew D Kern, 2016. "S/HIC: Robust Identification of Soft and Hard Sweeps Using Machine Learning," PLOS Genetics, Public Library of Science, vol. 12(3), pages 1-31, March.

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