Gene admixture in the Silk Road region of China: Evidence from mtDNA and melanocortin 1 receptor polymorphism.

Yao, Yong‐Gang; Lu, Xuemei; Luo, Huai‐Rong; Li, Wen-Hsiung; Zhang, Yaping

doi:10.1266/ggs.75.173

Cited by 80 publications

(72 citation statements)

References 15 publications

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“…The three sequences with this motif that appear in the Korean data of Snäll et al (2002), however, tested positively for the RFLP site +4830 HaeII (recognizing a transition at nt 4833) of haplogroup G. We additionally found the 4833 transition (confirmed by +4831 HhaI) in four mtDNAs from China (Table 2). Because all of these mtDNA sequences that belong to haplogroup G have (near-)matches with sequences sampled in Japan (Horai et al 1996;Imaizumi et al 2002;Koyama et al 2002), Korea (Pfeiffer et al 1998;Lee et al 1997Lee et al , 2002, and China (Tsai et al 2001;Yao et al 2000Yao et al , 2003a, it appears that these sequences also belong to haplogroup G. The vast majority of these HVS-I and HVS-II sequences share the 150 polymorphism. In particular, eleven HVS-I and HVS-II sequences from the Korean sample of Lee et al (1997) carry the partial motif 16223-16325; seven of them have the additional part 16362-150 of the motif, Yao et al (2003a) and the data underlying figure 1 of Mishmar et al (2003), respectively; 2 n.d. = not determined.…”

Section: Distinguishing Asian From Native American Mtdnasmentioning

confidence: 78%

Identification of Native American Founder mtDNAs Through the Analysis of Complete mtDNA Sequences: Some Caveats

Bandelt

Herrnstadt²,

Yao

et al. 2003

Annals of Human Genetics

104

116

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SummaryIn this study, a detailed analysis of both previously published and new data was performed to determine whether complete, or almost complete, mtDNA sequences can resolve the long-debated issue of which Asian mtDNAs were founder sequences for the Native American mtDNA pool. Unfortunately, we now know that coding region data and their analysis are not without problems. To obtain and report reasonably correct sequences does not seem to be a trivial task, and to discriminate between Asian and Native American mtDNA ancestries may be more complex than previously believed. It is essential to take into account the effects of mutational hot spots in both the control and coding regions, so that the number of apparent Native American mtDNA founder sequences is not erroneously inflated. As we report here, a careful analysis of all available data indicates that there is very little evidence that more than five founder mtDNA sequences entered Beringia before the Last Glacial Maximum and left their traces in the current Native American mtDNA pool.

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Section: Distinguishing Asian From Native American Mtdnasmentioning

confidence: 78%

Identification of Native American Founder mtDNAs Through the Analysis of Complete mtDNA Sequences: Some Caveats

Bandelt

Herrnstadt²,

Yao

et al. 2003

Annals of Human Genetics

104

116

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“…A homology search (BLAST search) was conducted using the mtDNA data samples obtained from the East-Asian populations in [59][60][61][62][63][64][65][66][67][68][69][70][71][72] The sequence type of individual no. 913 did not correspond to that of the modern East-Asian populations.…”

Section: Resultsmentioning

confidence: 99%

Mitochondrial DNA analysis of Yayoi period human skeletal remains from the Doigahama site

et al. 2009

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We analyzed the mitochondrial DNA extracted from 14 human skeletal remains from the Doigahama site in Japan to clarify the genetic structure of the Doigahama Yayoi population and the relationship between burial style and kinship among individuals. The sequence types obtained in this study were compared with those of the modern Japanese, northern Kyushu Yayoi and ancient Chinese populations. We found that the northern Kyushu Yayoi populations belonged to the groups that include most of the modern Japanese population. In contrast, most of the Doigahama Yayoi population belonged to the group that includes a small number of the modern Japanese population. These results suggest that the Doigahama Yayoi population might have contributed less to the formation of the modern Japanese population than the northern Kyushu Yayoi populations. Moreover, when we examined the kinship between individuals in the Doigahama site, we found that the vicinal burial of adult skeletons indicated a maternal kinship, although that of juvenile skeletons did not. The vicinal burial style might have been influenced by many factors, such as paternal lineages, periods and geographical regions, as well as maternal lineages. In addition, skeletons considered to be those of shamans or leaders had the same sequence types. Their crucial social roles may have been inherited through maternal lineage.

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“…All of the individuals were confirmed to be unrelated before sampling and were given informed consent. To better understand the phylogeny of haplogroup F2, the previously reported data sets (Yao et al 2000(Yao et al , 2002a(Yao et al ,c, 2003Tsai et al 2001;Kivisild et al 2002;Oota et al 2002;Yao and Zhang 2002;Kong et al 2003a;Tajima et al 2003) were also included. As a result, a total of 3,090 mtDNAs from 57 populations across China were examined, and their detailed information was illustrated in Table 1.…”

Section: Samplingmentioning

confidence: 99%

“…The haplogroup status was further confirmed by detecting additional variations in other regions as described in our previous studies (Yao et al 2002aKong et al 2003a). A segment covering region 10171-10659 of the rCRS, which was suggested to be informative in defining East Asian specific haplogroups (Yao et al 2002a), was adopted to specify the phylogenetic status of the F* or R9* mtDNAs (the asterisk attached to haplogroups indicates that the sample was not able to be further classified into the sub-clade(s) of the haplogroup) in our previous studies (Yao et al 2000(Yao et al , 2002a(Yao et al ,c, 2003Yao and Zhang 2002;Kong et al 2003a) and unpublished data. For those published data sets (not from our laboratory) with only HVS-I and/or HVS-II information available, we recognized the potential F2 types by matching and/or near-matching with the identified F2 types that have been tested for coding region information.…”

Section: Data Analysesmentioning

confidence: 99%

“…The nucleotide change was originally detected in two mtDNAs (GD7809 and QD8147) when we systematically surveyed mtDNAs belonging to all the major haplogroups specific to East Asian by complete mtDNA sequencing (Kong et al 2003b). To substantiate whether the T12338C change is specific to haplogroup F2 and to learn more about the origin of haplogroup F2, we performed an extensive search for F2 in more than 3,000 Chinese mtDNAs in reported studies (Yao et al 2000(Yao et al , 2002a(Yao et al ,c, 2003Tsai et al 2001;Kivisild et al 2002;Oota et al 2002;Yao and Zhang 2002;Kong et al 2003a;Tajima et al 2003) and our unpublished data by motif-searching and/or (near-)matching methods (Yao et al 2002a. Our phylogeographic study revealed that the T12338C change was specific to haplogroup F2 and occurred in normal individuals across China, thus suggesting a polymorphic change rather than a pathogenic mutation.…”

Section: Introductionmentioning

confidence: 99%

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Phylogeographic analysis of mitochondrial DNA haplogroup F2 in China reveals T12338C in the initiation codon of the ND5 gene not to be pathogenic

et al. 2004

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In this report, we studied on a homoplasmic T12338C change in mitochondrial DNA (mtDNA), which substituted methionine in the translational initiation codon of the NADH dehydrogenase subunit 5 gene (ND5) with threonine. This nucleotide change was originally identified in two mtDNAs belonging to haplogroup F2 by our previous complete sequencing of 48 mtDNAs. Since then, a total of 76 F2 mtDNAs have been identified by the variations occurring in the hypervariable segments and coding regions among more than 3,000 individuals across China. As the T12338C change was detected in 32 samples representing various sub-clades of the F2 haplogroup while not in 14 non-F2 controls, we believe that the T12338C change is specific to the F2 haplogroup. As F2 and its sub-clades were widely distributed in normal individuals of various Chinese populations, we conclude that T12338C is not pathogenic. In addition, based on the average distribution frequency, haplotype diversity and nucleotide diversity of haplogroup F2 in the populations across China, the T12338C nucleotide substitution seems to have been occurred in north China about 42,000 years ago. Our results provided a good paradigm for distinguishing a polymorphic change from a pathogenic mutation based on mtDNA phylogeny.

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Gene admixture in the Silk Road region of China: Evidence from mtDNA and melanocortin 1 receptor polymorphism.

Cited by 80 publications

References 15 publications

Identification of Native American Founder mtDNAs Through the Analysis of Complete mtDNA Sequences: Some Caveats

Identification of Native American Founder mtDNAs Through the Analysis of Complete mtDNA Sequences: Some Caveats

Mitochondrial DNA analysis of Yayoi period human skeletal remains from the Doigahama site

Phylogeographic analysis of mitochondrial DNA haplogroup F2 in China reveals T12338C in the initiation codon of the ND5 gene not to be pathogenic

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