Time Dependency of Molecular Rate Estimates and Systematic Overestimation of Recent Divergence Times
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- 6 April 2005
- journal article
- Published by Oxford University Press (OUP) in Molecular Biology and Evolution
- Vol. 22 (7), 1561-1568
- https://doi.org/10.1093/molbev/msi145
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
This publication has 42 references indexed in Scilit:
- Is there a universal mtDNA clock for birds?Journal of Avian Biology, 2004
- Tracing the Decay of the Historical Signal in Biological Sequence DataSystematic Biology, 2004
- Precision of molecular time estimatesTrends in Genetics, 2004
- Patterns of Intra- and Interhost Nonsynonymous Variation Reveal Strong Purifying Selection in Dengue VirusJournal of Virology, 2003
- Estimation of Divergence Times for Major Lineages of Primate SpeciesMolecular Biology and Evolution, 2003
- Effects of Models of Rate Evolution on Estimation of Divergence Dates with Special Reference to the Metazoan 18S Ribosomal RNA PhylogenySystematic Biology, 2002
- Preponderance of slightly deleterious polymorphism in mitochondrial DNA: nonsynonymous/synonymous rate ratio is much higher within species than between species.Molecular Biology and Evolution, 1998
- Evolution on a volcanic conveyor belt: using phylogeographic reconstructions and K–Ar‐based ages of the Hawaiian Islands to estimate molecular evolutionary ratesMolecular Ecology, 1998
- Dating of the human-ape splitting by a molecular clock of mitochondrial DNAJournal of Molecular Evolution, 1985
- Rapid evolution of animal mitochondrial DNA.Proceedings of the National Academy of Sciences, 1979