Gene Conversion Among Paralogs Results in Moderate False Detection of Positive Selection Using Likelihood Methods |
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Authors: | Claudio Casola Matthew W Hahn |
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Institution: | (1) Department of Biology and School of Informatics, Indiana University, 1001 E. 3rd Street, Bloomington, IN 47405, USA |
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Abstract: | Previous studies have shown that recombination between allelic sequences can cause likelihood-based methods for detecting
positive selection to produce many false-positive results. In this article, we use simulations to study the impact of nonallelic
gene conversion on the specificity of PAML to detect positive selection among gene duplicates. Our results show that, as expected,
gene conversion leads to higher rates of false-positive results, although only moderately. These rates increase with the genetic
distance between sequences, the length of converted tracts, and when no outgroup sequences are included in the analysis. We
also find that branch-site models will incorrectly identify unconverted sequences as the targets of positive selection when
their close paralogs are converted. Bayesian prediction of sites undergoing adaptive evolution implemented in PAML is affected
by conversion, albeit in a less straightforward way. Our work suggests that particular attention should be devoted to the
evolutionary analysis of recent duplicates that may have experienced gene conversion because they may provide false signals
of positive selection. Fortunately, these results also imply that those cases most susceptible to false-positive results—i.e.,
high divergence between paralogs, long conversion tracts—are also the cases where detecting gene conversion is the easiest.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. |
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Keywords: | Recombination Adaptive evolution Gene duplicates PAML |
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