Abstract
The rate of change in DNA is an important parameter for understanding molecular evolution and hence for inferences drawn from studies of
phylogeography and phylogenetics. Most rate calibrations for mitochondrial coding regions in marine species have been made from divergence dating
for fossils and vicariant events older than 1–2 My and are typically 0.5–2% per lineage per million years. Recently, calibrations made with ancient DNA
(aDNA) from younger dates have yielded faster rates, suggesting that estimates of the molecular rate of change depend on the time of calibration,
decaying from the instantaneous mutation rate to the phylogenetic substitution rate. aDNA methods for recent calibrations are not available for most
marine taxa so instead we use radiometric dates for sea-level rise onto the Sunda Shelf following the Last Glacial Maximum (starting ∼18,000 years ago),
which led to massive population expansions for marine species. Instead of divergence dating, we use a two-epoch coalescent model of logistic
population growth preceded by a constant population size to infer a time in mutational units for the beginning of these expansion events. This model
compares favorably to simpler coalescent models of constant population size, and exponential or logistic growth, and is far more precise than estimates
from the mismatch distribution. Mean rates estimated with this method for mitochondrial coding genes in three invertebrate species are elevated in
comparison to older calibration points (2.3–6.6% per lineage per million years), lending additional support to the hypothesis of calibration time
dependency for molecular rates.