Dataset Information

Phylogeographic differentiation of mitochondrial DNA in Han Chinese.

ABSTRACT: To characterize the mitochondrial DNA (mtDNA) variation in Han Chinese from several provinces of China, we have sequenced the two hypervariable segments of the control region and the segment spanning nucleotide positions 10171-10659 of the coding region, and we have identified a number of specific coding-region mutations by direct sequencing or restriction-fragment-length-polymorphism tests. This allows us to define new haplogroups (clades of the mtDNA phylogeny) and to dissect the Han mtDNA pool on a phylogenetic basis, which is a prerequisite for any fine-grained phylogeographic analysis, the interpretation of ancient mtDNA, or future complete mtDNA sequencing efforts. Some of the haplogroups under study differ considerably in frequencies across different provinces. The southernmost provinces show more pronounced contrasts in their regional Han mtDNA pools than the central and northern provinces. These and other features of the geographical distribution of the mtDNA haplogroups observed in the Han Chinese make an initial Paleolithic colonization from south to north plausible but would suggest subsequent migration events in China that mainly proceeded from north to south and east to west. Lumping together all regional Han mtDNA pools into one fictive general mtDNA pool or choosing one or two regional Han populations to represent all Han Chinese is inappropriate for prehistoric considerations as well as for forensic purposes or medical disease studies.

SUBMITTER: Yao YG

PROVIDER: S-EPMC384943 | biostudies-other | 2002 Mar

REPOSITORIES: biostudies-other

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Phylogeographic differentiation of mitochondrial DNA in Han Chinese.

Yao Yong-Gang YG Kong Qing-Peng QP Bandelt Hans-Jürgen HJ Kivisild Toomas T Zhang Ya-Ping YP

American journal of human genetics 20020208 3

To characterize the mitochondrial DNA (mtDNA) variation in Han Chinese from several provinces of China, we have sequenced the two hypervariable segments of the control region and the segment spanning nucleotide positions 10171-10659 of the coding region, and we have identified a number of specific coding-region mutations by direct sequencing or restriction-fragment-length-polymorphism tests. This allows us to define new haplogroups (clades of the mtDNA phylogeny) and to dissect the Han mtDNA poo ...[more]

PMID: 11836649

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Project description:ObjectiveAcute exposure to hypobaric hypoxia can trigger acute mountain sickness (AMS), while the exact mechanism has not been fully revealed. The role of genetic factors in the susceptibility of various high-altitude diseases has also gained much interest. Previous studies have provided evidence for the link between AMS and certain nuclear genes or mitochondrial haplogroup. The correlation between point mutations of mitochondrial DNA (mtDNA) and AMS was further explored in the present study.MethodsA total of 84 young Han males residing at low altitude were taken to an elevation of 4,000 m within 40 h. We collected data of their heart rate, blood pressure, peripheral oxygen saturation (SaO2), and obtained blood samples, at sea level and at high altitude. AMS was diagnosed using the revised version of the Lake Louise Questionnaire Score. Sequencing was utilized to identify the association between mtDNA alleles and the occurrence of AMS. We also assessed the association between the presence of AMS and physiological variables, and provided a preliminary discussion of the association between genotypic and phenotypic variation.ResultsThe percentage of neutrophils [Odds ratio (OR): 1.06, 95% confidence interval (CI): 1.01-1.12, P = 0.034) and SaO2 level (OR: 0.87, 95% CI: 0.79-0.95, P = 0.004) were independently associated with the development of AMS. A4576G was a risk factor for AMS (OR: 6.27, 95% CI: 1.2-32.7). T11613C (OR: 0.10, 95% CI: 0.01-0.83), A8923G (OR: 0.15, 95% CI: 0.03-0.76), and T5543C (OR: 0.19, 95% CI: 0.04-0.95) were protective factors for AMS. The level of SaO2 was significantly lower in the individual with A4576G mutation as compared with the individual without A4576G mutation (68.1 ± 7.9 vs. 75.8 ± 6.1, P = 0.001). The level of serum sodium was significantly higher in the individual with A8923G mutation as compared to the individual without A8923G mutation (144.6 ± 1.9 vs. 143.2 ± 1.9, P = 0.027).ConclusionsThe increase in neutrophils and the disability to preserve oxygen saturation may be associated with the high altitude intolerance in young Chinese Han males. A4576G is the risk factor for AMS. T11613C, A8923G, and T5543C are protective factors for AMS. The role of A8923G mutation may correlate with the sodium and water balance and the role of the A4576G mutation may be related to the disability to maintain blood oxygen level after quickly entering the plateau.

Project description:I examined mitochondrial ND2 sequences in species of tits (genus Parus) to determine whether substitutions were neutral or under selection. Haplotype trees in these species are shallow and geographically unstructured, which could be a signature of recent demographic expansion or purifying selection. McDonald-Kreitman tests revealed a pattern of excess replacement polymorphisms for closely related taxa. Replacement substitutions tended to be less common in the basal parts of haplotype trees, suggesting that they are selected against over evolutionary time. Thus, the pattern of selection is consistent with a model of mildly deleterious haplotypes. To investigate the significance of this selection, the ND2 gene was subdivided into surface and transmembrane portions, and synonymous-non-synonymous sites, and F(ST)-values (the amount of variance distributed among populations) computed for each. Among sampling localities in P. major, both partitions gave similar estimates of F(ST), which is consistent with demographic expansion as the cause of the shallow trees. In P. montanus, two localities contained high percentages of individuals that had a single replacement substitution in the transmembrane portion of the gene, which inflated F(ST)-values relative to the surface sites. Thus, the interpretation of the genetic differentiation of these two sites could be either geographical isolation or selection. Given that the sole substitution causing the high F(ST)-values was a replacement one, selection is implicated. However, this substitution occurred in only 2 of 12 localities, revealing that overall the phylogeographic pattern was not biased by selection, once the cause of the two high pairwise F(ST)-comparisons was recognized. Investigators should consider the source of significant genetic heterogeneity within species, to determine if the variation is likely caused by demographic isolation or selection. However, it seems unlikely that most phylogeographic analyses are invalidated by the effects of natural selection.

Dataset Information

Phylogeographic differentiation of mitochondrial DNA in Han Chinese.

Publications

Phylogeographic differentiation of mitochondrial DNA in Han Chinese.

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