Please use this identifier to cite or link to this item: http://hdl.handle.net/2440/34231
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Type: Journal article
Title: Time dependency of molecular rate estimates and systematic overestimation of recent divergence times
Author: Ho, S.
Phillips, M.
Cooper, A.
Drummond, A.
Citation: Molecular Biology and Evolution, 2005; 22(7):1561-1568
Publisher: Oxford Univ Press
Issue Date: 2005
ISSN: 0737-4038
1537-1719
Statement of
Responsibility: 
Simon Y. W. Ho, Matthew J. Phillips, Alan Cooper and Alexei J. Drummond
Abstract: Studies of molecular evolutionary rates have yielded a wide range of rate estimates for various genes and taxa. Recent studies based on population-level and pedigree data have produced remarkably high estimates of mutation rate, which strongly contrast with substitution rates inferred in phylogenetic (species-level) studies. Using Bayesian analysis with a relaxed-clock model, we estimated rates for three groups of mitochondrial data: avian protein-coding genes, primate protein-coding genes, and primate d-loop sequences. In all three cases, we found a measurable transition between the high, short-term (< 1-2 Myr) mutation rate and the low, long-term substitution rate. The relationship between the age of the calibration and the rate of change can be described by a vertically translated exponential decay curve, which may be used for correcting molecular date estimates. The phylogenetic substitution rates in mitochondria are approximately 0.5% per million years for avian protein-coding sequences and 1.5% per million years for primate protein-coding and d-loop sequences. Further analyses showed that purifying selection offers the most convincing explanation for the observed relationship between the estimated rate and the depth of the calibration. We rule out the possibility that it is a spurious result arising from sequence errors, and find it unlikely that the apparent decline in rates over time is caused by mutational saturation. Using a rate curve estimated from the d-loop data, several dates for last common ancestors were calculated: modern humans and Neandertals (354 ka; 222-705 ka), Neandertals (108 ka; 70-156 ka), and modern humans (76 ka; 47-110 ka). If the rate curve for a particular taxonomic group can be accurately estimated, it can be a useful tool for correcting divergence date estimates by taking the rate decay into account. Our results show that it is invalid to extrapolate molecular rates of change across different evolutionary timescales, which has important consequences for studies of populations, domestication, conservation genetics, and human evolution.
Keywords: mutation rate; substitution rate; rate calibration; purifying selection
Description: © The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved.
RMID: 0020063659
DOI: 10.1093/molbev/msi145
Appears in Collections:Earth and Environmental Sciences publications
Australian Centre for Ancient DNA publications
Environment Institute Leaders publications

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