Data from: Late-glacial demographic expansion motivates a clock overhaul for population genetics

The molecular clock hypothesis is fundamental in evolutionary biology as
by assuming constancy of the molecular rate it provides a time frame for
evolution. However, increasing evidence shows time dependence of inferred
molecular rates with inflated values obtained using recent calibrations.
As recent demographic calibrations are virtually non-existent in most
species, older phylogenetic calibration points (>1 Ma) are commonly
used, which overestimate demographic parameters. To obtain more reliable
rates of molecular evolution for population studies, I propose the
Calibration of Demographic Transition (CDT) method, which uses the timing
of climatic changes over the late glacial warming period to calibrate
expansions in various species. Simulation approaches and empirical
datasets from a diversity of species (from mollusk to humans) confirm
that, when compared to other genealogy-based calibration methods, the CDT
provides a robust and broadly applicable clock for population genetics.
The resulting CDT rates of molecular evolution also confirm rate
heterogeneity over time and among taxa. Comparisons of expansion dates
with ecological evidence confirm the inaccuracy of phylogenetically
derived divergence rates when dating population-level events. The CDT
method opens opportunities for addressing issues such as demographic
responses to past climate change and the origin of rate heterogeneity
related to taxa, genes, time and genetic information content.