Y Chromosomal DNA Variation and the Peopling of Japan

Overview

Journal Am J Hum Genet

Publisher Cell Press

Specialty Genetics

Date 1995 Apr 1

PMID 7717406

Citations 108

Authors

M F Hammer

S Horai

Affiliations

Soon will be listed here.

Abstract

Four loci mapping to the nonrecombining portion of the Y chromosome were genotyped in Japanese populations from Okinawa, the southernmost island of Japan; Shizuoka and Aomori on the main island of Honshu; and a small sample of Taiwanese. The Y Alu polymorphic (YAP) element is present in 42% of the Japanese and absent in the Taiwanese, confirming the irregular distribution of this polymorphism in Asia. Data from the four loci were used to determine genetic distances among populations, construct Y chromosome haplotypes, and estimate the degree of genetic diversity in each population and on different Y chromosome haplotypes. Evolutionary analysis of Y haplotypes suggests that polymorphisms at the YAP (DYS287) and DXYS5Y loci originated a single time, whereas restriction patterns at the DYS1 locus and microsatellite alleles at the DYS19 locus arose more than once. Genetic distance analysis indicated that the Okinawans are differentiated from Japanese living on Honshu. The data support the hypotheses that modern Japanese populations have resulted from distinctive genetic contributions involving the ancient Jomon people and Yayoi immigrants from Korea or mainland China, with Okinawans experiencing the least amount of admixture with the Yayoi. It is suggested that YAP+ chromosomes migrated to Japan with the Jomon people > 10,000 years ago and that a large infusion of YAP- chromosomes entered Japan with the Yayoi migration starting 2,300 years ago. Different degrees of genetic diversity carried by these two ancient chromosomal lineages may be explained by the different life-styles (hunter-gatherer versus agriculturalist). of the migrant groups, the size of the founding populations, and the antiquities of the founding events.

Citing Articles

The evolving Japanese: the dual structure hypothesis at 30.

Hudson M, Nakagome S, Whitman J Evol Hum Sci. 2023; 2:e6.

PMID: 37588379 PMC: 10427290. DOI: 10.1017/ehs.2020.6.

Japan considered from the hypothesis of farmer/language spread.

de Boer E, Yang M, Kawagoe A, Barnes G Evol Hum Sci. 2023; 2:e13.

PMID: 37588377 PMC: 10427481. DOI: 10.1017/ehs.2020.7.

Kazak mitochondrial genomes provide insights into the human population history of Central Eurasia.

Askapuli A, Vilar M, Garcia-Ortiz H, Zhabagin M, Sabitov Z, Akilzhanova A PLoS One. 2022; 17(11):e0277771.

PMID: 36445929 PMC: 9707748. DOI: 10.1371/journal.pone.0277771.

Cultural transmission of traditional songs in the Ryukyu Archipelago.

Nishikawa Y, Ihara Y PLoS One. 2022; 17(6):e0270354.

PMID: 35749479 PMC: 9231793. DOI: 10.1371/journal.pone.0270354.

Geographic variation in the polygenic score of height in Japan.

Isshiki M, Watanabe Y, Ohashi J Hum Genet. 2021; 140(7):1097-1108.

PMID: 33900438 DOI: 10.1007/s00439-021-02281-4.

References

Richards B, Skoletsky J, Shuber A, Balfour R, Stern R, Dorkin H . Multiplex PCR amplification from the CFTR gene using DNA prepared from buccal brushes/swabs. Hum Mol Genet. 1993; 2(2):159-63. DOI: 10.1093/hmg/2.2.159. View

Rogers A, Jorde L . Genetic evidence on modern human origins. Hum Biol. 1995; 67(1):1-36. View

Saitou N, Nei M . The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987; 4(4):406-25. DOI: 10.1093/oxfordjournals.molbev.a040454. View

Cann R, Stoneking M, Wilson A . Mitochondrial DNA and human evolution. Nature. 1987; 325(6099):31-6. DOI: 10.1038/325031a0. View

Bishop C, Guellaen G, Geldwerth D, Voss R, Fellous M, Weissenbach J . Single-copy DNA sequences specific for the human Y chromosome. Nature. 1983; 303(5920):831-2. DOI: 10.1038/303831a0. View

Nakahori Y, Tamura T, Yamada M, NAKAGOME Y . Two 47z [DXYS5] RFLPs on the X and the Y chromosome. Nucleic Acids Res. 1989; 17(5):2152. PMC: 317578. DOI: 10.1093/nar/17.5.2152. View

Li W . Distribution of nucleotide differences between two randomly chosen cistrons in a finite population. Genetics. 1977; 85(2):331-7. PMC: 1213636. DOI: 10.1093/genetics/85.2.331. View

Mathias N, Bayes M, Tyler-Smith C . Highly informative compound haplotypes for the human Y chromosome. Hum Mol Genet. 1994; 3(1):115-23. DOI: 10.1093/hmg/3.1.115. View

Tuner 2nd C . Dental evidence on the origins of the Ainu and Japanese. Science. 1976; 193(4256):911-3. DOI: 10.1126/science.781841. View

10.

Bowcock A, Kidd J, Mountain J, Hebert J, Carotenuto L, Kidd K . Drift, admixture, and selection in human evolution: a study with DNA polymorphisms. Proc Natl Acad Sci U S A. 1991; 88(3):839-43. PMC: 50909. DOI: 10.1073/pnas.88.3.839. View

11.

Hammer M . A recent insertion of an alu element on the Y chromosome is a useful marker for human population studies. Mol Biol Evol. 1994; 11(5):749-61. DOI: 10.1093/oxfordjournals.molbev.a040155. View

12.

Feinberg A, Vogelstein B . "A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity". Addendum. Anal Biochem. 1984; 137(1):266-7. DOI: 10.1016/0003-2697(84)90381-6. View

13.

Hammer M, Silver L . Phylogenetic analysis of the alpha-globin pseudogene-4 (Hba-ps4) locus in the house mouse species complex reveals a stepwise evolution of t haplotypes. Mol Biol Evol. 1993; 10(5):971-1001. DOI: 10.1093/oxfordjournals.molbev.a040051. View

14.

Harihara S, Hirai M, Suutou Y, Shimizu K, Omoto K . Frequency of a 9-bp deletion in the mitochondrial DNA among Asian populations. Hum Biol. 1992; 64(2):161-6. View

15.

NAKAGOME Y, Young S, Akane A, NUMABE H, Jin D, Yamori Y . A Y-associated allele may be characteristic of certain ethnic groups in Asia. Ann Hum Genet. 1992; 56(4):311-4. DOI: 10.1111/j.1469-1809.1992.tb01158.x. View

16.

Horai S, Matsunaga E . Mitochondrial DNA polymorphism in Japanese. II. Analysis with restriction enzymes of four or five base pair recognition. Hum Genet. 1986; 72(2):105-17. DOI: 10.1007/BF00283927. View

17.

Spurdle A, Woodfield D, Hammer M, Jenkins T . The genetic affinity of Polynesians: evidence from Y chromosome polymorphisms. Ann Hum Genet. 1994; 58(3):251-63. DOI: 10.1111/j.1469-1809.1994.tb01889.x. View

18.

Tsuchida S, Ikemoto S . Further studies of salivary polymorphisms in the Japanese population. Hum Hered. 1989; 39(2):61-6. DOI: 10.1159/000153836. View

19.

Nei M . Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics. 1978; 89(3):583-90. PMC: 1213855. DOI: 10.1093/genetics/89.3.583. View

20.

Mountain J, Cavalli-Sforza L . Inference of human evolution through cladistic analysis of nuclear DNA restriction polymorphisms. Proc Natl Acad Sci U S A. 1994; 91(14):6515-9. PMC: 44233. DOI: 10.1073/pnas.91.14.6515. View