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Human Molecular Genetics Advance Access published online on May 19, 2006
Human Molecular Genetics, doi:10.1093/hmg/ddl130
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© The Author 2006. Published by Oxford University Press. All rights reserved
Received April 7, 2006
Revised May 14, 2006
Accepted May 14, 2006

Article

Updating the East Asian mtDNA Phylogeny: A Prerequisite for the Identification of Pathogenic Mutations

Qing-Peng Kong 1 *, Hans-Jürgen Bandelt 2, Chang Sun 3, Yong-Gang Yao 4, Antonio Salas 5, Alessandro Achilli 6, Cheng-Ye Wang 3, Li Zhong 7, Chun-Ling Zhu 4, Shi-Fang Wu 4, Antonio Torroni 6, and Ya-Ping Zhang 8 *

1 Laboratory of Cellular and Molecular Evolution, and Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yannan 650223, China; Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming 650091, China; Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
2 Department of Mathematics, University of Hamburg, 20146 Hamburg, Germany
3 Laboratory of Cellular and Molecular Evolution, and Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming 650091, China; Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
4 Laboratory of Cellular and Molecular Evolution, and Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
5 Unidad de Genética, Instituto de Medicina Legal, Facultad de Medicina, Universidad de Santiago de Compostela, 15782, and Centro Nacional de Genotipado (CeGen), Hospital Clínico Universitario, 15706 Galicia, Spain
6 Dipartimento di Genetica e Microbiologia, Università di Pavia, 27100 Pavia, Italy
7 Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming 650091, China
8 Laboratory of Cellular and Molecular Evolution, and Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming 650091, China

* To whom correspondence should be addressed.
Qing-Peng Kong, E-mail: kongqp{at}yahoo.com.cn
Ya-Ping Zhang, E-mail: zhangyp1{at}263.net.cn


  Abstract

Knowledge about the world phylogeny of human mitochondrial DNA (mtDNA) is essential not only for evaluating the pathogenic role of specific mtDNA mutations but also for performing reliable association studies between mtDNA haplogroups and complex disorders. In the past few years, the main features of the East Asian portion of the mtDNA phylogeny have been determined based on complete sequencing efforts, but representatives of several basal lineages were still lacking. Moreover, some recently published complete mtDNA sequences did apparently not fit into the known phylogenetic tree and conflicted with the established nomenclature. To refine the East Asian mtDNA tree and resolve data conflicts, we first completely sequenced 20 carefully selected mtDNAs - likely representatives of novel subhaplogroups - and then, in order to distinguish diagnostic mutations of novel haplogroups from private variants, we applied a "motif-search" procedure to a large sample collection. The novel information was incorporated into an updated East Asian mtDNA tree encompassing more than 1000 (near-) complete mtDNA sequences. A reassessment of the mtDNA data from a series of disease studies testified to the usefulness of such a refined mtDNA tree in evaluating the pathogenicity of mtDNA mutations. In particular, the claimed pathogenic role of mutations G3316A, T3394C, A4833G, and G15497A appears to be most questionable as those initial claims were derived from anecdotal findings rather than association studies. Following a guideline based on the phylogenetic knowledge as proposed here could help avoiding similar problems in the future.


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