Lineage-specific selection in human mtDNA: lack of polymorphisms in a segment of MTND5 gene in haplogroup J.

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Moilanen JS, Finnila S, Majamaa K

Lineage-specific selection in human mtDNA: lack of polymorphisms in a segment of MTND5 gene in haplogroup J.

Mol Biol Evol. 2003 Dec;20(12):2132-42. Epub 2003 Aug 29.

PubMed ID
12949126 [ View in PubMed
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Abstract

Human mitochondrial DNA (mtDNA) is a nonrecombining genome that codes for 13 subunits of the mitochondrial oxidative phosphorylation system, 2 rRNAs, and 22 tRNAs. Mutations have accumulated sequentially in mtDNA lineages that diverged tens of thousands of years ago. The genes in mtDNA are subject to different functional constraints and are therefore expected to evolve at different rates, but the rank order of these rates should be the same in all lineages of a phylogeny. Previous studies have indicated, however, that specific regions of mtDNA may have experienced different histories of selection in different lineages, possibly because of lineage-specific interactions or environmental factors such as climate. We report here on a survey for lineage-specific patterns of nucleotide polymorphism in human mtDNA. We calculated molecular polymorphism indices and neutrality tests for classes of functional sites and genes in 837 human mtDNA sequences, compared the results between continent-specific mtDNA lineages, and used two sliding window methods to identify differences in the patterns of polymorphism between haplogroups. A general correlation between nucleotide position and the level of nucleotide polymorphism was identified in the coding region of the mitochondrial genome. Nucleotide diversity in the protein-coding sequence of mtDNA was generally not much higher than that found for many genes in nuclear DNA. A comparison of nonsynonymous/synonymous rate ratios in the 13 protein-coding genes suggested differences in the relative levels of selection between haplogroups, including the European haplogroup clusters. Interestingly, a segment of the MTND5 gene was found to be almost void of segregating sites and nonsynonymous mutations in haplogroup J, which has been associated with susceptibility to certain complex diseases. Our results suggest that there are haplogroup-specific differences in the intensity of selection against particular regions of the mitochondrial genome, indicating that some mutations may be non-neutral within specific phylogenetic lineages but neutral within others.

DrugBank Data that Cites this Article

Polypeptides
NameUniProt ID
NADH-ubiquinone oxidoreductase chain 3P03897Details
NADH-ubiquinone oxidoreductase chain 4LP03901Details
Cytochrome c oxidase subunit 1P00395Details
NADH-ubiquinone oxidoreductase chain 6P03923Details
NADH-ubiquinone oxidoreductase chain 1P03886Details
NADH-ubiquinone oxidoreductase chain 4P03905Details
NADH-ubiquinone oxidoreductase chain 5P03915Details
NADH-ubiquinone oxidoreductase chain 2P03891Details
Cytochrome c oxidase subunit 2P00403Details
ATP synthase subunit aP00846Details