A Simple and Robust Statistical Test for Detecting the Presence of Recombination

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ID: 294847
2006
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Abstract
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, Φw, that can be used to test for recombination. We show through simulation that our test can discriminate effectively between the presence and absence of recombination, even in diverse situations such as exponential growth (star-like topologies) and patterns of substitution rate correlation. A number of other tests, Max χ2, 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 strong population growth. Moreover, both Max χ2 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 Φw is one of the best approaches to distinguish recurrent mutation from recombination in a wide variety of circumstances.
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openalex_W2155645165 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Trevor C. Bruen, Hervé Philippe, David Bryant
Journal current genetics
Year 2006
DOI
10.1534/genetics.105.048975
URL
https://doi.org/10.1534/genetics.105.048975
Keywords Keywords not found

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