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      An enhanced MITOMAP with a global mtDNA mutational phylogeny

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          Abstract

          The MITOMAP ( http://www.mitomap.org) data system for the human mitochondrial genome has been greatly enhanced by the addition of a navigable mutational mitochondrial DNA (mtDNA) phylogenetic tree of ∼3000 mtDNA coding region sequences plus expanded pathogenic mutation tables and a nuclear-mtDNA pseudogene (NUMT) data base. The phylogeny reconstructs the entire mutational history of the human mtDNA, thus defining the mtDNA haplogroups and differentiating ancient from recent mtDNA mutations. Pathogenic mutations are classified by both genotype and phenotype, and the NUMT sequences permits detection of spurious inclusion of pseudogene variants during mutation analysis. These additions position MITOMAP for the implementation of our automated mtDNA sequence analysis system, Mitomaster.

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          MEGA2: molecular evolutionary genetics analysis software.

          S. Kumar, K Tamura, I. Jakobsen … (2001)
          We have developed a new software package, Molecular Evolutionary Genetics Analysis version 2 (MEGA2), for exploring and analyzing aligned DNA or protein sequences from an evolutionary perspective. MEGA2 vastly extends the capabilities of MEGA version 1 by: (1) facilitating analyses of large datasets; (2) enabling creation and analyses of groups of sequences; (3) enabling specification of domains and genes; (4) expanding the repertoire of statistical methods for molecular evolutionary studies; and (5) adding new modules for visual representation of input data and output results on the Microsoft Windows platform. http://www.megasoftware.net. s.kumar@asu.edu
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            Mitochondrial genome variation and the origin of modern humans.

            M Ingman, H Kaessmann, S Pääbo … (2000)
            The analysis of mitochondrial DNA (mtDNA) has been a potent tool in our understanding of human evolution, owing to characteristics such as high copy number, apparent lack of recombination, high substitution rate and maternal mode of inheritance. However, almost all studies of human evolution based on mtDNA sequencing have been confined to the control region, which constitutes less than 7% of the mitochondrial genome. These studies are complicated by the extreme variation in substitution rate between sites, and the consequence of parallel mutations causing difficulties in the estimation of genetic distance and making phylogenetic inferences questionable. Most comprehensive studies of the human mitochondrial molecule have been carried out through restriction-fragment length polymorphism analysis, providing data that are ill suited to estimations of mutation rate and therefore the timing of evolutionary events. Here, to improve the information obtained from the mitochondrial molecule for studies of human evolution, we describe the global mtDNA diversity in humans based on analyses of the complete mtDNA sequence of 53 humans of diverse origins. Our mtDNA data, in comparison with those of a parallel study of the Xq13.3 region in the same individuals, provide a concurrent view on human evolution with respect to the age of modern humans.
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              Natural selection shaped regional mtDNA variation in humans.

              Dan Mishmar, Eduardo Ruiz-Pesini, Pawel Golik … (2003)
              Human mtDNA shows striking regional variation, traditionally attributed to genetic drift. However, it is not easy to account for the fact that only two mtDNA lineages (M and N) left Africa to colonize Eurasia and that lineages A, C, D, and G show a 5-fold enrichment from central Asia to Siberia. As an alternative to drift, natural selection might have enriched for certain mtDNA lineages as people migrated north into colder climates. To test this hypothesis we analyzed 104 complete mtDNA sequences from all global regions and lineages. African mtDNA variation did not significantly deviate from the standard neutral model, but European, Asian, and Siberian plus Native American variations did. Analysis of amino acid substitution mutations (nonsynonymous, Ka) versus neutral mutations (synonymous, Ks) (kaks) for all 13 mtDNA protein-coding genes revealed that the ATP6 gene had the highest amino acid sequence variation of any human mtDNA gene, even though ATP6 is one of the more conserved mtDNA proteins. Comparison of the kaks ratios for each mtDNA gene from the tropical, temperate, and arctic zones revealed that ATP6 was highly variable in the mtDNAs from the arctic zone, cytochrome b was particularly variable in the temperate zone, and cytochrome oxidase I was notably more variable in the tropics. Moreover, multiple amino acid changes found in ATP6, cytochrome b, and cytochrome oxidase I appeared to be functionally significant. From these analyses we conclude that selection may have played a role in shaping human regional mtDNA variation and that one of the selective influences was climate.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (iso-abbrev): Nucleic Acids Res
                Journal ID (pmc): nar
                Journal ID (publisher-id): Nucleic Acids Research
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date (Print): January 2007
                Publication date (Electronic): 18 December 2006
                Publication date PMC-release: 18 December 2006
                Volume: 35
                Issue: Database issue
                Pages: D823-D828
                Affiliations
                1Center for Molecular and Mitochondrial Medicine and Genetics (MAMMAG) and Departments of Biological Chemistry, Ecology and Evolutionary Biology, and Pediatrics, University of California Irvine, CA 92697-3900, USA
                2Departamento de Bioquimica, Biologia Molecular y Celula, Universidad de Zaragoza Zaragoza, Spain
                3School of Information and Computer Science, University of California Irvine, CA 92697-3425, USA
                4Institute for Genomics and Bioinformatics, University of California Irvine, CA 92697-2025, USA
                5Department of Life Sciences, Building 40 Ben Gurion University, Beer Sheva, Israel
                Author notes
                *To whom correspondence should be addressed: Tel: +1 949 824 3490; Fax: +1 949 824 6388; Email: dwallace@ 123456uci.edu
                Article
                DOI: 10.1093/nar/gkl927
                PMC ID: 1781213
                PubMed ID: 17178747
                SO-VID: 0550457b-bc6a-4ee3-bae6-3b19528d6f5d
                Copyright © © 2006 The Author(s)
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 14 September 2006
                Date revision received : 12 October 2006
                Date accepted : 17 October 2006
                Categories
                Subject: Articles

                ScienceOpen disciplines: Genetics
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                ScienceOpen disciplines: Genetics

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