Molecular clocks are used to estimate the time of divergence of genes and species and have helped illuminate the evolutionary history of life. In a recent article, Graur and Martin raised concerns regarding confidence intervals of molecular time estimates and fossil calibrations. Although our past work was singled out, their concerns apply generally to the field, including their own previous studies. We believe that those concerns are unfounded. Graur and Martin use ad hoc methods for estimating confidence intervals and for the interpretation of fossil evidence, which led them to calculate overly wide confidence intervals and to make erroneous conclusions. In a separate article, Reisz and Müller propose that the bird-mammal fossil calibration used by us, and others, should be abandoned in favor of a bird-lizard calibration. However, other paleontologists disagree, and Reisz and Müller have failed to provide robust fossil evidence or to consider sequence availability. Molecular clocks have great potential but must be calibrated carefully.
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