The power of relative rates tests depends on the data

One of the most useful features of molecular phylogenetic analyses is the p otential for estimating dates of divergence of evolutionary lineages from t he DNA of extant species. But lineage-specific variation in rate of molecul ar evolution complicates molecular dating, because a calibration rate estim ated from one lineage may not be an accurate representation of the rate in other lineages. Many molecular dating studies use a "clock test" to identif y and exclude sequences that vary in rate between lineages. However, these clock tests should not be relied upon without a critical examination of the ir effectiveness at removing rate variable sequences from any given data se t, particularly with regard to the sequence length and number of variable s ites. As an illustration of this problem we present a power test of a frequ ently employed triplet relative rates test. We conclude that (1) relative r ates tests are unlikely to detect moderate levels of lineage-specific rate variation (where one lineage has a rate of molecular evolution 1.5 to 4.0 t imes the other) for most commonly used sequences in molecular dating analys es, and (2) this lack of power is likely to result in substantial error in the estimation of dates of divergence. As an example, we show that the well -studied rate difference between murid rodents and great apes will not be d etected for many of the sequences used to date the divergence between these two lineages and that this failure to detect rate variation is likely to r esult in consistent overestimation the elate of the rodent-primate split.