The Recalibration of the Molecular Clock: Ancient DNA Falsifies the Constant-Rate Hypothesis

The molecular clock hypothesis—that genetic substitutions accumulate at a constant rate proportional to time—has anchored evolutionary chronology for sixty years. We report the first direct test of this hypothesis using ancient DNA time series spanning 10,000 years of European human evolution. The clock predicts continuous, gradual fixation of alleles at approximately the mutation rate. Instead, we observe that 99.8% of fixation events occurred within a single 2,000-year window (8000-10000 BP), with essentially zero fixations in the subsequent 7,000 years. This represents a 400-fold deviation from the predicted constant rate. The substitution process is not continuous—it is punctuated, with discrete events followed by stasis. We further demonstrate that two independent lines of evidence—the Real Rate of Molecular Evolution (RRME) and time-averaged census population analysis—converge on the same conclusion: the effective population size inferred from the molecular clock is an artifact of a miscalibrated substitution rate, not a measurement of actual ancestral demography. The molecular clock measures genetic distance, not time. Its translation into chronology is assumption, not measurement, and that assumption is now empirically falsified.