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MBE Advance Access first published online on October 20, 2006
This version published online on October 24, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl149
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted October 11, 2006

Letter

A Comparative Analysis of Numt Evolution in Human and Chimpanzee

Einat Hazkani-Covo 1 and Dan Graur 2 *

1 Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel; Present address: National Evolutionary Synthesis Center, Durham, North Carolina 27705, USA
2 Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel; Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA

* To whom correspondence should be addressed.
Dan Graur, E-mail: dgraur{at}uh.edu


  Abstract

Mitochondrial DNA sequences are frequently transferred into the nuclear genome, giving rise to numts (nuclear DNA sequences of mitochondrial origin). So far, the evolutionary history of numts has largely been studied by using single genomes. Here, we present the first attempt to study numt evolution in a comparative manner by using a pairwise genomic alignment. The total number of numts was estimated to be 452 in human and 469 in chimpanzee. Numts that were found in both genomes at identical loci were deemed to be orthologous; 391 numts (>80%) were classified as such. The preponderance of orthologous numts is due to the very short divergence time between the two hominoids. The rest of numts were deemed to be nonorthologous. Nonorthologous numts were subdivided into (a) ancestral numts that have lost an ortholog in one species through deletion (12 in human and 11 in chimpanzee), (b) new numts acquired by the insertion of a mitochondrial sequence after the divergence of the two species (34 in human and 46 in chimpanzee), and (c) paralogous numts created by the tandem duplication of a pre-existing numt (2 in human). This approach also enabled us to reconstruct the numt repertoire in the common ancestor of humans and chimpanzees (409 numts). Our comparative approach is also useful in identifying the exact boundaries of numts.

Dan Graur's last name has been corrected.


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