Rates of DNA Duplication and Mitochondrial DNA Insertion in the Human Genome
- 179 Downloads
The hundreds of mitochondrial pseudogenes in the human nuclear genome sequence (numts) constitute an excellent system for studying and dating DNA duplications and insertions. These pseudogenes are associated with many complete mitochondrial genome sequences and through those with a good fossil record. By comparing individual numts with primate and other mammalian mitochondrial genome sequences, we estimate that these numts arose continuously over the last 58 million years. Our pairwise comparisons between numts suggest that most human numts arose from different mitochondrial insertion events and not by DNA duplication within the nuclear genome. The nuclear genome appears to accumulate mtDNA insertions at a rate high enough to predict within-population polymorphism for the presence/absence of many recent mtDNA insertions. Pairwise analysis of numts and their flanking DNA produces an estimate for the DNA duplication rate in humans of 2.2 × 10−9 per numt per year. Thus, a nucleotide site is about as likely to be involved in a duplication event as it is to change by point substitution. This estimate of the rate of DNA duplication of noncoding DNA is based on sequences that are not in duplication hotspots, and is close to the rate reported for functional genes in other species.
KeywordsNumt numtDNA Segmental duplication Human population genetic markers
Many thanks for helpful discussion, advice, and comments on the manuscript go to Aviv Bergman, Casey M. Bergman, Krista K. Ingram, and Dennis P. Wall, and to Jeffrey L. Boore for support in the later stages of this work. The comments of two anonymous reviewers substantially improved the manuscript. This work was partly funded by the Center for Computational Genetics and Biological Modeling.
- 1.Bailey, JA, Gu, Z, Clark, RA, Reinert, K, Samonte, RV, Schwatz, S, Adams, MD, Myers, EW, Li, PW, Eichler, EE 2002aRecent segmental duplications in the human genome.Science29710031007Google Scholar
- 2.Bailey, JA, Yavor, AM, Viggiano, L, Misceo, D, Horvath, JE, Archidiacono, N, Shchwartz, S, Rocchi, M, Eichler, EE 2002bHuman-specific duplication and mosaic transcripts: The recent paralogous structure of chromosome 22.Am J Hum Gene7083100Google Scholar
- 11.Hall, TA 1999BioEdit: A user-friendly biological sequence alignment editor and analysis (program for windows 95/98/NT).Nucleic Acids Symp Ser419598Google Scholar
- 16.Li, W-H 1997Molecular evolution.Sinauer AssociatesSunderland, MAGoogle Scholar
- 20.Mourier, T, Hansen, AJ, Willerslev, E, Arctander, P 2001The human genome project reveals a continuous transfer of large mitochondrial fragments to the nucleus.Mol Biol Evol1818331837Google Scholar
- 29.Swofford, DL 2002PAUP*: Phylogenetic analysis using parsimony (* and other methods).Sinauer AssociatesSunderland, MAGoogle Scholar