DFG FOR 1078 Natural Selection in Structured Populations

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T2 - Competing selective sweeps

Project leader

Peter Pfaffelhuber
University of Freiburg, Faculty of Mathematics and Physics

bildhupfaThe fixation of a positively selected allele reduces linked neutral sequence diversity, an effect known as a “selective sweep”. The literature on recurrent selective sweeps has so far mainly focused on the non-overlapping case where at most a single beneficial allele sweeps to fixation at any time. In this project, we study competing selective sweeps where further beneficial mutations arise at different recombining loci during the time-course of the first selective sweep. For example, such a scenario is realistic for a structured population with low migration rates or with previously isolated demes (subpopulations). Recombination events can then bring beneficial alleles to the same genetic background. If such recombination events happen more than once, we expect that competing selective sweeps leave the following distinct genetic footprint: Between selected loci, there is a strong haplotype structure; outside the selected loci, there is a severe reduction of genetic diversity, similar to the case of a single selective sweep.

We analyze and apply this model of competing selective sweeps in three steps:

  1. The genealogy at a neutral locus, linked to the beneficial alleles, can be studied using the ancestral selection graph. Using this genealogical picture we will quantify the genetic footprint.
  2. Using simulation techniques based on the recently developed software MSMS (Ewing and Hermisson 2010) and its proposed extension (project J. Hermisson), we establish and analyze the distinct genetic footprint of competing sweeps in panmictic and structured populations. In particular, we explore possible sources of a strong haplotype structure.
  3. In collaboration with empirical groups of the research unit, we scan for the signature of competing sweeps in SNP data of Drosophila melanogaster and in SNP data of Solanum chilense and Solanum peruvianum.