Expansion Dating: Calibrating Molecular Clocks in Marine Species from Expansions onto the Sunda Shelf following the Last Glacial Maximum

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 million years, and are typically 0.5% - 2% per lineage per million years. Recently, calibrations made with ancient DNA 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. Ancient DNA 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