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  Detecting and characterizing sweeps using the frequency spectrum of rare haplotypes

Neher, R., & Messer, P. (2011). Detecting and characterizing sweeps using the frequency spectrum of rare haplotypes. In 13th Congress of the European Society for Evolutionary Biology (ESEB 2011) (pp. 762).

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Item Permalink: https://hdl.handle.net/21.11116/0000-000C-A41D-B Version Permalink: https://hdl.handle.net/21.11116/0000-000C-A41F-9
Genre: Meeting Abstract

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https://eseb.org/wp-content/uploads/2018/08/2011_Program_Abstracts.pdf (Abstract)
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 Creators:
Neher, RA1, Author                 
Messer, PW, Author
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1Research Group Evolutionary Dynamics and Biophysics, Max Planck Institute for Developmental Biology, Max Planck Society, ou_3377926              

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 Abstract: We present a method that allows to detect selective sweeps and estimate the selection coefficients driving individual sweeps. The method uses the frequency spectrum of rare haplotypes which arose during the sweep through mutation or recombination of the haplotype on which the beneficial mutation arose. The interplay of this diversification and the exponential amplification of the beneficial mutation results in a characteristic haplotype spectrum: The abundance of the ith most abundant haplotype is proportional to 1/i. The constant of proportionality is given by the ratio of the overall mutation/recombination rate in the haplotype and the coefficient of selection. Given an independent estimate of the mutation rate, we can therefore estimate the strength of selection. Furthermore, we present a statistic of the pairwise distances between rare haplotypes which allows us to detect sweeps and soft sweeps. We exemplify this method with deep sequencing data from HIV populations and discuss how it can be used to analyze data from population scale re-sequencing projects in other organisms such as the human 1000 Genomes project.

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 Dates: 2011-08
 Publication Status: Published online
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Title: 13th Congress of the European Society for Evolutionary Biology (ESEB 2011)
Place of Event: Tübingen, Germany
Start-/End Date: 2011-08-20 - 2011-08-25

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Title: 13th Congress of the European Society for Evolutionary Biology (ESEB 2011)
Source Genre: Proceedings
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Pages: - Volume / Issue: - Sequence Number: - Start / End Page: 762 Identifier: -