Geological Dates and Molecular Rates: Fish DNA Sheds Light on Time Dependency
Burridge, CP and Craw, D and Fletcher, D and Waters, JM, Geological Dates and Molecular Rates: Fish DNA Sheds Light on Time Dependency, Molecular Biology and Evolution, 25, (4) pp. 624-633. ISSN 0737-4038 (2008) [Refereed Article]
Knowledge of DNA evolution is central to our understanding of biological history, but how fast does DNA change?
Previously, pedigree and ancient DNA studies—focusing on evolution in the short term—have yielded molecular rate
estimates substantially faster than those based on deeper phylogenies. It has recently been suggested that short-term,
elevated molecular rates decay exponentially over 1–2 Myr to long-term, phylogenetic rates, termed ‘‘time dependency of
molecular rates.’’ This transition has potential to confound molecular inferences of demographic parameters and dating of
many important evolutionary events. Here, we employ a novel approach—geologically dated changes in river drainages
and isolation of ﬁsh populations—to document rates of mitochondrial DNA change over a range of temporal scales. This
method utilizes precise spatiotemporal disruptions of linear freshwater systems and hence avoids many of the limitations
associated with typical DNA calibration methods involving fossil data or island formation. Studies of freshwater-limited
ﬁshes across the South Island of New Zealand have revealed that genetic relationships reﬂect past, rather than present,
drainage connections. Here, we use this link between drainage geology and genetics to calibrate rates of molecular
evolution across nine events ranging in age from 0.007 Myr (Holocene) to 5.0 Myr (Pliocene). Molecular rates of change
in galaxiid ﬁshes from calibration points younger than 200 kyr were faster than those based on older calibration points.
This study provides conclusive evidence of time dependency in molecular rates as it is based on a robust calibration
system that was applied to closely related taxa, and analyzed using a consistent and rigorous methodology. The time
dependency observed here appears short-lived relative to previous suggestions (1–2 Myr), which has bearing on the
accuracy of molecular inferences drawn from processes operating within the Quaternary and mechanisms invoked to
explain the decay of rates with time.
molecular clock, mutation rate, calibration, time dependency, purifying selection.