MBE Advance Access published online on February 14, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msm271
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Research Article |
Geological Dates and Molecular Rates: Fish DNA Sheds Light on Time-Dependency
1 Department of Zoology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
2 Department of Geology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
3 Department of Mathematics and Statistics, University of Otago, PO Box 56, Dunedin 9054, New Zealand
* To whom correspondence should be addressed. E-mail: chris.burridge{at}stonebow.otago.ac.nz, Department of Zoology, University of Otago, PO Box 56, Dunedin 9054, New Zealand, Ph. +64 3 479 4039; Fax +64 3 479 7584
Received for publication September 1, 2007. Revision received November 15, 2007. Accepted for publication November 20, 2007.
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 spatio-temporal 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 persistence of timedependency observed here appears short 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
Key Words: molecular clock • mutation rate • calibration • time-dependency • purifying selection