East Asian mtDNA haplogroup determination in Koreans: Haplogroup-level coding region SNP analysis and subhaplogroup-level control region sequence analysis

Lee, Hwan Young; Yoo, Jieun; Park, Myung Jin; Chung, Ukhee; Kim, Jaehyup; Shin, Kyoung Jin

doi:10.1002/elps.200600151

Cited by 42 publications

(50 citation statements)

References 26 publications

(38 reference statements)

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“…Frequencies of mtDNA haplogroups are inferred from published data as follows: Hokkaido Jomon (Adachi et al, 2011); Okhotsk (Sato et al, 2009); Modern Ainu (Tajima et al, 2004);.Mainland Japanese (Maruyama et al, 2003); Ryukyu Islanders (Sekiguchi et al, 2008); Koreans (Lee et al, 2006); Han Chinese (Xu & Hu, 2015; Yao et al, 2002);.Nivkhi, Udegey, Negidal (Starikovskaya et al, 2005); Ulchi, Even (Sukernik et al, 2012); Koryak, Itel'men (Schurr et al, 1999). All populations except for the Edo Ainu, Okhotsk, and.…”

Section: Resultsmentioning

confidence: 99%

“…Mainland Japanese (Maruyama et al, 2003); Ryukyu Islanders (Sekiguchi et al, 2008); Koreans (Lee et al, 2006); Han Chinese (Xu & Hu, 2015; Yao et al, 2002);.…”

Section: Resultsmentioning

confidence: 99%

“…and K.S. To clarify the biological relationships between the Edo Ainu and other populations, their haplogroup frequencies were compared with those of 14 ancient and modern‐day East Asian and Siberian populations obtained from previously published data (Adachi et al, 2011; Lee et al, 2006; Maruyama, Minaguchi, & Saitou, 2003; Sato et al, 2009; Schurr, Sukernik, Starikovskaya, & Wallace, 1999; Sekiguchi et al, 2008; Starikovskaya, Sukernik, Schurr, Kogelnik, & Wallace, 1998; Starikovskaya et al, 2005; Sukernik et al, 2012; Tajima et al, 2004; Xu & Hu, 2015; Yao, Kong, Bandelt, Kivisild, & Zhang, 2002). The approximate locations of these populations are shown in Figure 1.…”

Section: Methodsmentioning

confidence: 99%

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Ethnic derivation of the Ainu inferred from ancient mitochondrial DNA data

Adachi

Kakuda

Takahashi

et al. 2017

American J Phys Anthropol

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ObjectivesThe Ainu, the indigenous people living on the northernmost island of Japan, Hokkaido, have long been a focus of anthropological interest because of their cultural, linguistic, and physical identity. A major problem with genetic studies on the Ainu is that the previously published data stemmed almost exclusively from only 51 modern‐day individuals living in Biratori Town, central Hokkaido. To clarify the actual genetic characteristics of the Ainu, individuals who are less influenced by mainland Japanese, who started large‐scale immigration into Hokkaido about 150 years ago, should be examined. Moreover, the samples should be collected from all over Hokkaido.Materials and methodsMitochondrial DNA haplogroups of 94 Ainu individuals from the Edo era were successfully determined by analyzing haplogroup‐defining polymorphisms in the hypervariable and coding regions. Thereafter, their frequencies were compared to those of other populations.ResultsOur findings indicate that the Ainu still retain the matrilineage of the Hokkaido Jomon people. However, the Siberian influence on this population is far greater than previously recognized. Moreover, the influence of mainland Japanese is evident, especially in the southwestern part of Hokkaido that is adjacent to Honshu, the main island of Japan.DiscussionOur results suggest that the Ainu were formed from the Hokkaido Jomon people, but subsequently underwent considerable admixture with adjacent populations. The present study strongly recommends revision of the widely accepted dual‐structure model for the population history of the Japanese, in which the Ainu are assumed to be the direct descendants of the Jomon people.

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Section: Resultsmentioning

confidence: 99%

“…Mainland Japanese (Maruyama et al, 2003); Ryukyu Islanders (Sekiguchi et al, 2008); Koreans (Lee et al, 2006); Han Chinese (Xu & Hu, 2015; Yao et al, 2002);.…”

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Ethnic derivation of the Ainu inferred from ancient mitochondrial DNA data

Adachi

Kakuda

Takahashi

et al. 2017

American J Phys Anthropol

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“…The O2b subgroup is prominent in Korea, Japan, and Manchuria. (2) Fifteen mtDNA variations were annotated as the marker of ''D4'' haplogroup, which is prevalent in Korea (Umetsu et al 2005;Lee et al 2006). (3) A phylogenic tree drawn with 31,460 autosomal common SNPs within 93 individuals indicated that SJK has a common Korean autosomal makeup.…”

Section: Genetic Ancestry Of the Sjk Donormentioning

confidence: 99%

The first Korean genome sequence and analysis: Full genome sequencing for a socio-ethnic group

Ahn

Kim²,

Lee³

et al. 2009

Genome Res.

292

229

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We present the first Korean individual genome sequence (SJK) and analysis results. The diploid genome of a Korean male was sequenced to 28.95-fold redundancy using the Illumina paired-end sequencing method. SJK covered 99.9% of the NCBI human reference genome. We identified 420,083 novel single nucleotide polymorphisms (SNPs) that are not in the dbSNP database. Despite a close similarity, significant differences were observed between the Chinese genome (YH), the only other Asian genome available, and SJK: (1) 39.87% (1,371,239 out of 3,439,107) SNPs were SJK-specific (49.51% against Venter's, 46.94% against Watson's, and 44.17% against the Yoruba genomes); (2) 99.5% (22,495 out of 22,605) of short indels (< 4 bp) discovered on the same loci had the same size and type as YH; and (3) 11.3% (331 out of 2920) deletion structural variants were SJK-specific. Even after attempting to map unmapped reads of SJK to unanchored NCBI scaffolds, HGSV, and available personal genomes, there were still 5.77% SJK reads that could not be mapped. All these findings indicate that the overall genetic differences among individuals from closely related ethnic groups may be significant. Hence, constructing reference genomes for minor socio-ethnic groups will be useful for massive individual genome sequencing.

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“…mtDNA were classified into haplogroups based on D-loop motifs of the specific sequences described in recent studies (Tanaka et al, 2004;Lee et al, 2006;Uchiyama et al, 2007). The mtDNA sequenced by M13 without setting the inner primers.…”

Section: Dna Analysismentioning

confidence: 99%

Relationship between mitochondrial haplogroup and psychophysiological responses during cold exposure in a Japanese population

Nishimura

Motoi

Hoshi

et al. 2011

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The purpose of this study was to investigate the genetic factors responsible for individual differences in cold tolerance. Focusing on mitochondrial haplogroup D (D4) in Japanese subjects, differences in cold tolerance between haplogroup D subjects and other haplogroup subjects were investigated. The experiment was conducted in summer (August-September). Room temperature was decreased from 27 to 10°C in 30 min, and cold exposure was then maintained at 10°C for 60 min. During that time, measurements were made of physiological responses, including rectal temperature, skin temperature, oxygen consumption, blood pressure, and heart rate. A subjective evaluation was also made. It was found that, under cold exposure, the decrease in rectal temperature of haplogroup D subjects was significantly less than that in other groups (P < 0.001). There was no significant main group effect for oxygen consumption or mean skin temperature. In haplogroup D subjects, the thermal comfort sensation was judged to be significant discomfort at 20 and 30 min after the start of cold stimulation (P < 0.05). From the relation of oxygen consumption to rectal temperature, it is conjectured that the rectal temperature at which increased thermogenesis starts is higher in haplogroup D subjects. This study suggests that differences in mitochondrial haplogroup are one factor in individual differences in cold tolerance in Japanese.

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East Asian mtDNA haplogroup determination in Koreans: Haplogroup-level coding region SNP analysis and subhaplogroup-level control region sequence analysis

Cited by 42 publications

References 26 publications

Ethnic derivation of the Ainu inferred from ancient mitochondrial DNA data

Ethnic derivation of the Ainu inferred from ancient mitochondrial DNA data

The first Korean genome sequence and analysis: Full genome sequencing for a socio-ethnic group

Relationship between mitochondrial haplogroup and psychophysiological responses during cold exposure in a Japanese population

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