MBE Advance Access published online on November 4, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn244
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Research Article |
Characterizing the Time-Dependency of Human Mitochondrial DNA Mutation Rate Estimates
,2
Research institutions and current affiliations
* Departments of Anthropology, Stanford University, Stanford, California, United States of America
Biological Sciences, Stanford University, Stanford, California, United States of America
23andMe, Inc., Bayshore Parkway, Mountain View, California, United States of America
1 Corresponding author: Brenna M. Henn, Department of Anthropology, Bldg. 50, Stanford University, Stanford CA 94035-2117. Work: 650-269-6535. E-mail: bmhenn{at}stanford.edu
Received for publication August 19, 2008. Revision received October 10, 2008. Accepted for publication October 21, 2008.
Previous research has established a discrepancy of nearly an order of magnitude between pedigree-based and phylogeny-based (human vs. chimpanzee) estimates of the mitochondrial (mtDNA) control region mutation rate. We characterize the time-dependency of the human mitochondrial hypervariable region one (HVRI) mutation rate by generating fourteen new phylogeny-based mutation rate estimates using within-human comparisons and archaeological dates. Rate estimates based on population events between 15,000 and 50,000 years ago are at least twofold lower than pedigree-based estimates. These within-human estimates are also higher than estimates generated from phylogeny-based human-chimpanzee comparisons. Our new estimates establish a rapid decay in evolutionary mutation rate between approximately 2,500 and 50,000 years ago, and a slow decay from 50,000 to 6 million years ago. We then extend this analysis to the mtDNA coding region. Our within-human coding region mutation rate estimates display a similar, though less rapid, time-dependent decay. We explore the possibility that multiple hits explain the discrepancy between pedigree-based and phylogeny-based mutation rates. We conclude that while nucleotide substitution models incorporating multiple-hits do provide a possible explanation for the discrepancy between pedigree-based and human-chimpanzee mutation rate estimates, they do not explain the rapid decline of within-human rate estimates. We propose that demographic processes such as serial bottlenecks prior to the Holocene could explain the difference between rates estimated before and after 15,000 years ago. Our findings suggest that human mitochondrial DNA estimates of dates of population and phylogenetic events should be adjusted in light of this time-dependency of the mutation rate estimates.
Key Words: mutation rate • time dependency • mitochondria • human evolution • calibration
2 Present address: Program in Pharmaceutical Sciences and Pharmacogenomics, University of California San Francisco, San Francisco, California, United States of America.
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