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| The role of selection in the evolution of human mitochondrial genomes |
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| Author(s): Kivisild T, Shen PD, Wall DP, Do B, Sung R, Davis K, Passarino G, Underhill PA, Scharfe C, Torroni A, Scozzari R, Modiano D, Coppa A, de Knijff P, Feldman M, Cavalli-Sforza LL, Oefner PJ |
| Source: GENETICS Volume: 172 Issue: 1 Pages: 373-387 Published: JAN 2006 |
| Times Cited: 145 References: 60 |
| Abstract: High mutation rate in mammalian mitochondrial DNA generates a highly divergent pool of alleles even within species that have dispersed and expanded in size recently. Phylogenetic analysis of 277 human mitochondrial genomes revealed a significant (P < 0.01) excess of rRNA and nonsynonymous base substitutions among hotspots of recurrent mutation. Most hotspots involved transitions from guanine to adenine that, with thymine-to-cytosine transitions, illustrate the asymmetric bias in codon usage at synonymous sites on the heavy-strand DNA. The mitochondrion-encoded tRNA(Thr) varied significantly more than any other tRNA gene. Threonine and valine codons were involved in 259 of the 414 amino acid replacements observed. The ratio of nonsynonymous changes from and to threonine and valine differed significantly (P = 0.003) between populations with neutral (22/58) and populations with significantly negative Tajima's D values (70/76), independent of their geographic location. In contrast to a recent suggestion that the excess of nonsilent mutations is characteristic of Arctic populations, implying their role in cold adaptation, we demonstrate that the Surplus of nonsynonymous mutations is a general feature of the Young branches of the phylogenetic tree, affecting also those that are found only in Africa. We introduce a new calibration method of the mutation rate of synonymous transitions to estimate the coalescent times of mtDNA haplogroups. |
| Document Type: Article |
| Language: English |
| Reprint Address: Kivisild, T (reprint author), Univ Tartu, Dept Evolutionary Biol, Riia 23, EE-51010 Tartu, Estonia |
Addresses:
1. Stanford Univ, Dept Genet, Stanford, CA 94305 USA
2. Stanford Genome Technol Ctr, Palo Alto, CA 94304 USA
3. Stanford Univ, Dept Biol Sci, Stanford, CA 94305 USA
4. Univ Calabria, Dipartimento Biol Cellulare, I-87036 Arcavacata Di Rende, Italy
5. Univ Pavia, Dipartimento Genet & Microbiol, I-27100 Pavia, Italy
6. Univ Roma La Sapienza, Dipartimento Genet & Biol Mol, I-00185 Rome, Italy
7. Univ Roma La Sapienza, Dipartimento Sci Sanita Pubbl, Sez Parassitol, I-00185 Rome, Italy
8. Univ Roma La Sapienza, Dipartimento Biol Anim & Uomo, I-00185 Rome, Italy
9. Leiden Univ, Med Ctr, Dept Human & Clin Genet, NL-2333 AL Leiden, Netherlands |
| Publisher: GENETICS, 428 EAST PRESTON ST, BALTIMORE, MD 21202 USA |
| Subject Category: Genetics & Heredity |
| IDS Number: 010MB |
| ISSN: 0016-6731 |
| DOI: 10.1534/genetics.105.043901 |
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