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Detecting Selective Sweeps with Haplotype Tests

Hitchhiking and Haplotype Tests

  • Chapter
Selective Sweep

Part of the book series: Molecular Biology Intelligence Unit ((MBIU))

Abstract

In this chapter, neutrality tests based on haplotype distribution are evaluated as a way of detecting selective sweeps. Several kinds of haplotype tests are reviewed, including haplotype number, haplotype diversity and haplotype partition tests. We focus on incomplete sweeps, where recombination between the selected locus and a given marker allows for several preexisting neutral lineages to survive the sweep and for some preexisting genetic variation to remain in a sample. Several problems are addressed, including the distinction between possible alternative hypotheses, the effect of sampling strategy, of conditioning the statistics on the population mutational parameter θ and/or the observed number of polymorphic sites S and, finally, the effect of intragenic recombination together with the choice of one- vs. two-tailed tests. Corresponding guidelines are proposed. To compare the power of haplotype tests and of other classical tests to detect selective sweeps, we use a simple selective sweep model with a deterministic approximation, allowing for genetic exchange between the selected locus and a given neutral marker. We conclude that there are ways of overcoming the difficulties in applying the tests, which are powerful means for revealing incomplete selective sweep effects.

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Author information

Authors and Affiliations

  1. Laboratoire d’Ecologie EPHE-CNRS UMR, Université Pierre-et-Marie Curie, Paris, France

    Frantz Depaulis, Sylvain Mousset & Michel Veuille

Authors
  1. Frantz Depaulis
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  2. Sylvain Mousset
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  3. Michel Veuille
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Editor information

Editors and Affiliations

  1. Department of Anatomy and Cellular Biology, Tufts University School of Medicine, Boston, Massachusetts, USA

    Dmitry Nurminsky Ph.D.

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Depaulis, F., Mousset, S., Veuille, M. (2005). Detecting Selective Sweeps with Haplotype Tests. In: Nurminsky, D. (eds) Selective Sweep. Molecular Biology Intelligence Unit. Springer, Boston, MA. https://doi.org/10.1007/0-387-27651-3_4

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