Coalescent Tree Imbalance and a Simple Test for Selective Sweeps Based on Microsatellite Variation

Haipeng Li and Thomas Wiehe

PLOS Computational Biology, 2013, vol. 9, issue 5, 1-14

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.Author Summary: It is one of the major interests in population genetics to contrast the properties and consequences of neutral and non-neutral modes of evolution. As is well-known, positive Darwinian selection and genetic hitchhiking drastically change the profile of genetic diversity compared to neutral expectations. The present-day observable genetic diversity in a sample of DNA sequences depends on events in their evolutionary history, and in particular on the shape of the underlying genealogical tree. In this paper we study how the shape of coalescent trees is affected by the presence of positively selected mutations. We define a measure of tree topology and study its properties under scenarios of neutrality and positive selection. We show that this measure can reliably be estimated from experimental data, and define an easy-to-compute statistical test of the neutral evolution hypothesis. We apply this test to data from a population of the malaria parasite Plasmodium falciparum and confirm the signature of recent positive selection in the vicinity of a drug resistance locus.

Date: 2013
References: View references in EconPapers View complete reference list from CitEc
Citations: View citations in EconPapers (3)

Downloads: (external link)
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003060 (text/html)
https://journals.plos.org/ploscompbiol/article/fil ... 03060&type=printable (application/pdf)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:plo:pcbi00:1003060

DOI: 10.1371/journal.pcbi.1003060

Access Statistics for this article

More articles in PLOS Computational Biology from Public Library of Science
Bibliographic data for series maintained by ploscompbiol ().