Coalescent tree imbalance and a simple test for selective sweeps based on microsatellite variation

Haipeng Li; Thomas Wiehe

doi:10.1371/journal.pcbi.1003060

Coalescent tree imbalance and a simple test for selective sweeps based on microsatellite variation

PLoS Comput Biol. 2013;9(5):e1003060. doi: 10.1371/journal.pcbi.1003060. Epub 2013 May 16.

Authors

Haipeng Li¹, Thomas Wiehe

Affiliation

¹ Department of Computational Genomics, CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.

Abstract

Selective sweeps are at the core of adaptive evolution. We study how the shape of coalescent trees is affected by recent selective sweeps. To do so we define a coarse-grained measure of tree topology. This measure has appealing analytical properties, its distribution is derived from a uniform, and it is easy to estimate from experimental data. We show how it can be cast into a test for recent selective sweeps using microsatellite markers and present an application to an experimental data set from Plasmodium falciparum.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology
Computer Simulation
Databases, Genetic
Genetic Variation / genetics*
Genetics, Population / methods*
Microsatellite Repeats / genetics*
Models, Genetic*
Plasmodium falciparum / classification
Plasmodium falciparum / genetics

Grants and funding

HL was supported by the National Key Basic Research Program of China (2012CB316505), the NSFC grants (31172073 and 91131010) and the Bairen Program, and through a grant to TW by the German Research Foundation (DFG-SFB680, www.dfg.de). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.