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  1. The rate of genetic evolution is often too variable among lineages to be explained by a strict molecular clock, prompting alternative ecological and evolutionary hypotheses to explain this rate heterogeneity.
  2. One controversial hypothesis is that speciation provokes a burst of rapid genetic change, giving molecular evolution a punctuational component. The amount of root-to-tip genetic change therefore tends to increase with the number of identified speciation events (nodes) along the root-to-tip path in molecular phylogenies. The controversy arises because nodes on molecular phylogenies can typically only be counted if both descendants are extant.
  3. Here, using stratigraphic, phylogenetic and ecological data from the exceptional fossil record of Cenozoic macroperforate planktonic foraminifera, we test whether among-lineage rate heterogeneity is explained by ecological factors (abundance, life history and environment) and by the numbers of speciation events according to fossil lineage, fossil morphospecies and molecular species concepts.
  4. The number of nodes between root and tips on the fossil lineage phylogeny was a statistically significant correlate of the rate of molecular evolution over the same root-to-tip path. The speciation counts from other species concepts and hypothesized ecological drivers had considerably less support.
  5. Our results showcase how the fossil record contains signals of biological processes that drive genetic evolution, justifying calls to further marry fossil and molecular data when studying macroevolution over geological time-scales.