The signature of strong positive selection in natural populations.

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When a positively selected mutation goes to fixation in a population, neutral variants in the neighbourhood of the selected locus that are initially associated with the beneficial allele also increase in frequency. They reach fixation unless recombination breaks the association. This fortuitous frequency increase of linked neutral alleles was coined genetic hitchhiking by Maynard Smith and Haigh (Maynard Smith J., J. Haigh. The hitch-hiking effect of a favorable gene. Genet. Res. 23: 23-35, 1974), who first described the phenomenon. As a result of the hitchhiking effect, the neutral nucleotide diversity around the site of directional selection is reduced. The genealogy underlying a sample of a neutral allele linked to a selected one can be described by a marked Yule process (Etheridge et al. 2006). The resulting marked genealogical tree allows for efficient numerical methods, which outperform existing approximations of the genealogy under hard selective sweeps (Pfaffelhuber et al. 2006). Besides reducing sequence diversity, selective sweeps change the association of alleles, i.e., patterns of linkage disequilibrium. Both a starlike and a Yule process approximation of the genealogy at the selected site were used to predict standardized linkage disequilibrium at the end of a selective sweep (Pfaffelhuber et al. 2008). The Yule process approximation gives more accurate results, while the star-like approximation allows for more explicit calculations. Recent developments are dealing with sweeps for alleles of arbitrary dominance (Ewing et al., 2011) and linkage disequilibrium under soft sweeps (Borck, 2011).

Additional information: http://www.stochastik.uni-freiburg.de
Phone: 0761/203-5667
Email: peter.pfaffelhuber@stochastik.uni-freiburg.de

Start of project: 2006
End of project: (unlimited)

Albert-Ludwigs-University Freiburg
Prof. Dr. Peter Pfaffelhuber
Abteilung für Mathematische Stochastik
Prof. Dr. Peter Pfaffelhuber
Ernst-Zermelo-Straße 1
79104 Freiburg
Germany

Phone: 0761/203-5664
Fax: 0761/203-5661
Email: sekretariat@stochastik.uni-freiburg.de
http://www.stochastik.uni-freiburg.de/pfaffelhuber
Actual Research Report

• Borck C

• DFG

• Borck C: The effect of recurrent mutation on the linkage disequilibrium under a selective sweep. J Math Biol, 2011. (in Druck)
• Ewing G, Hermisson J, Pfaffelhuber P, Rudolf J: Selective sweeps for recessive alleles and for other modes of dominance J Math Biol, 2011; 63 (3): 399-431. : https://doi.org/10.1007/s00285-010-0382-4 (download: https://arxiv.org/abs/1005.5536)
• Hermisson J, Pfaffelhuber P: The pattern of genetic hitchhiking under recurrent mutation. Electron J Probab, 2008; 13 (68) (online): 2069-2106. : http://arxiv.org/abs/0807.3167
• Pfaffelhuber P, Studeny A: Approximating genealogies for partially linked neutral loci under a selective sweep. J Math Biol, 2007; 55: 299-330. : http://arxiv.org/abs/q-bio/0611029
• Etheridge A, Pfaffelhuber P, Wakolbinger A: An approximate sampling formula under genetic hitchhiking. Ann Appl Probab, 2006; 16 (2): 685-729. (download: http://arxiv.org/abs/math/0503485)
• Pfaffelhuber P, Haubold B, Wakolbinger A: Approximate genealogies under genetic hitchhiking. Genetics, 2006; 174: 1995-2008.