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In defense of statistical methods for detecting positive selection

In a highly publicized article, Nozawa et al. (1) claimed that the branch-site model (BSM) (2, 3) was unreliable because it produced excessive false positives in their simulation experiment. BSM uses a likelihood ratio test to detect positive selection that affects particular branches and codons in protein-coding genes, indicated by accelerated nonsynonymous substitution rates. The authors' conclusion, if true, would be important. But it is contradicted by their simulation results.