Genetics. Published Articles Ahead of Print: February 19, 2006, Copyright © 2006
doi:10.1534/genetics.105.048975


A more recent version of this article appeared on April 1, 2006.

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A simple and robust statistical test to detect the presence of recombination

Trevor C Bruen 1*, Herve Philippe 2 and David Bryant 1

1 McGill University
2 Universite de Montreal

* To whom correspondence should be addressed. E-mail: trevor{at}mcb.mcgill.ca.

Submitted on July 30, 2005
Revised on November 3, 2005
Accepted on 3 February 2006


Abstract

Recombination is a powerful evolutionary force that merges historically distinct genotypes. But the extent of recombination within many organisms is unknown, and even determining its presence within a set of homologous sequences is a difficult question. Here we develop a new statistic, {varphi}w, that can be used to test for recombination. We show through simulation that our test can effectively discriminate between the presence and absence of recombination, even in diverse situations such as exponential growth (starlike topologies) and patterns of substitution rate correlation. A number of other tests, Max {chi}2, NSS, a coalescent based likelihood permutation test (from LDHat), and correlation of linkage disequilibrium (both r2 and |D'|) with distance, all tend to underestimate the presence of recombination under population growth. Moreover, both Max {chi}2 and NSS falsely infer the presence of recombination under a simple model of mutation rate correlation. Results on empirical data show that our test can be used to detect recombination between closely as well as distantly related samples, regardless of the suspected rate of recombination. The results suggest that {varphi}w is one of the best approaches to distinguish recurrent mutation from recombination in a wide variety of circumstances.

Key Words: compatibility, gene conversion, recombination, statistical test, virus




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