A simulation study of the reliability of recombination detection methods

Carsten Wiuf; Thomas Christensen; Jotun Hein

doi:10.1093/oxfordjournals.molbev.a003733

A simulation study of the reliability of recombination detection methods

Carsten Wiuf^*, Thomas Christensen, Jotun Hein

^*Corresponding author af dette arbejde

82 Citationer (Scopus)

Abstract

There exist many methods to detect recombination or mosaic structure in a sample of DNA sequences. But how reliable are they? Four methods were investigated with respect to their power to detect recombination in simulated samples with different amounts of recombination and mutation. In addition, we investigated the impact of the shape of the underlying genealogy on their performances. We found that the methods detected far fewer recombinations than were theoretically possible and that methods based on the principle of incompatibility in general had more power than methods that did not make use of this principle explicitly. This seemed, in particular, to be the case for phylogenies generated under population expansion scenarios which result in long branches at the tips and small deep branches. In addition to the results obtained through simulations, a series of new theoretical results on recombination is presented.

Originalsprog	Engelsk
Tidsskrift	MOLECULAR BIOLOGY AND EVOLUTION
Vol/bind	18
Udgave nummer	10
Sider (fra-til)	1929-1939
Antal sider	11
ISSN	0737-4038
DOI	https://doi.org/10.1093/oxfordjournals.molbev.a003733
Status	Udgivet - 1 jan. 2001
Udgivet eksternt	Ja

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AU - Hein, Jotun

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N2 - There exist many methods to detect recombination or mosaic structure in a sample of DNA sequences. But how reliable are they? Four methods were investigated with respect to their power to detect recombination in simulated samples with different amounts of recombination and mutation. In addition, we investigated the impact of the shape of the underlying genealogy on their performances. We found that the methods detected far fewer recombinations than were theoretically possible and that methods based on the principle of incompatibility in general had more power than methods that did not make use of this principle explicitly. This seemed, in particular, to be the case for phylogenies generated under population expansion scenarios which result in long branches at the tips and small deep branches. In addition to the results obtained through simulations, a series of new theoretical results on recombination is presented.

AB - There exist many methods to detect recombination or mosaic structure in a sample of DNA sequences. But how reliable are they? Four methods were investigated with respect to their power to detect recombination in simulated samples with different amounts of recombination and mutation. In addition, we investigated the impact of the shape of the underlying genealogy on their performances. We found that the methods detected far fewer recombinations than were theoretically possible and that methods based on the principle of incompatibility in general had more power than methods that did not make use of this principle explicitly. This seemed, in particular, to be the case for phylogenies generated under population expansion scenarios which result in long branches at the tips and small deep branches. In addition to the results obtained through simulations, a series of new theoretical results on recombination is presented.

KW - DNA sequences

KW - Incompatibility

KW - Recombination

KW - Simulations

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A simulation study of the reliability of recombination detection methods

Abstract

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