Y-chromosomal binary haplogroups in the Japanese population and their relationship to 16 Y-STR polymorphisms

Annals of Human Genetics

Volumn 71, Issue 4, 2007, Pages 480-495

  Nonaka, I ^a   Minaguchi, K ^a   Takezaki, N ^b  

^a TOKYO DENTAL COLLEGE   (Japan)

^b KAGAWA UNIVERSITY   (Japan)

Author keywords

Binary haplogroups; Japanese population; Y chromosome; Y STR haplotypes

Indexed keywords

ARTICLE; CLADISTICS; CONTROLLED STUDY; GENE FREQUENCY; GENE LOCUS; GENETIC MARKER; GENETIC POLYMORPHISM; GENETIC VARIABILITY; HAPLOTYPE; HUMAN; HUMAN CELL; JAPAN; JAPANESE; KOREA; MALE; POPULATION GENETICS; PRIORITY JOURNAL; SHORT TANDEM REPEAT; TAIWAN; Y CHROMOSOME;

ASIAN CONTINENTAL ANCESTRY GROUP; CHROMOSOMES, HUMAN, Y; GENETICS, POPULATION; HAPLOTYPES; HUMANS; MICROSATELLITE REPEATS; POLYMORPHISM, GENETIC; TANDEM REPEAT SEQUENCES;

EID: 34249908667     PISSN: 00034800     EISSN: 14691809     Source Type: Journal    
DOI: 10.1111/j.1469-1809.2006.00343.x     Document Type: Article

References (35)

1. Ayub, Q., Mohyuddin, A., Qamar, R., Mazhar, K., Zerjal, T., Mehdi, S. Q. & Tyler-Smith, C. (2000) Identification and characterization of novel human Y-chromosomal microsatellites from sequence database information. Nucleic Acids Res 28, e8.
2. Bosch, E., Calafell, F., Santos, F. R., Perez-Lezaun, A., Comas, D., Benchemsi, N., Tyler-Smith, C. & Bertranpetit, J. (1999) Variation in short tandem repeats is deeply structured by genetic background on the human Y chromosome. Am J Hum Genet 65, 1623-1638.
3. Forster, P., Rohl, A., Lunnemann, P., Brinkmann, C., Zerjal, T., Tyler-Smith, C. & Brinkmann, B. (2000) A short tandem repeat-based phylogeny for the human Y chromosome. Am J Hum Gene 67, 182-196.
4. Fujita, T. & Kiyama, M. (1995) Identification of DNA polymorphism by asymmetric-PCR SSCP. Biotechniques 19, 532-534.
5. Gill, P., Brenner, C., Brinkmann, B., Budowle, B., Carracedo, A., Jobling, M. A., de Knijff, P., Kayser, M., Krawczak, M., Mayr, W. R., Morling, N., Olaisen, B., Pascali, V., Prinz, M., Roewer, L., Schneider, P. M., Sajantila, A. & Tyler-Smith, C. (2001) DNA commission of the International Society of Forensic Genetics: Recommendations on forensic analysis using Y-chromosome STRs. Int J Legal Med 114, 305-309.
6. Gusmao, L., Alves, C. & Amorim, A. (2001) Molecular characteristics of four human Y-specific microsatellites (DYS434, DYD437, DYS438, DYS439) for population and forensic studies. Ann Hum Genet 65, 285-291.
7. Gusmao, L., Alves, C., Costa, S., Amorim, A., Brion, M., Gonzalez-Neira, A., Sanchez-Diz, P. & Carracedo, A. (2002) Point mutations in the flanking regions of the Y-chromosome specific STRs DYS391, DYS437 and DYS438. Int J Legal Med 116, 322-326.
8. Haga, H., Yamada, R., Ohnishi, Y., Nakamura, Y. & Tanaka, T. (2002) Gene-based SNP discovery as part of the Japanese Millennium Genome Project: Identification of 190562 genetic variations in the human genome. Single-nucleotide polymorphism. J Hum Genet 47, 605-610.
9. Hammer, M. F. & Horai, S. (1995) Y chromosomal DNA and the peopling of Japan. Am J Hum Genet 56, 951-962.
10. Hammer, M. F., Karafet, T., Rasanayagam, A., Wood, E. T., Altheide, T. K., Jenkins, T., Griffiths, R. C., Templeton, A. R. & Zegura, S. L. (1998) Out of Africa and back again: Nested cladistic analysis of human Y chromosome variation. Mol Biol Evol 15, 427-441.
11. Hammer, M. F., Karafet, T. M., Redd, A. J., Jarjanazi, H., Santachiara-Benerecetti, S., Soodyall, H. & Zegura, S. L. (2001) Hierarchical patterns of global human Y-chromosome diversity. Mol Biol Evol 18, 1189-1203.
12. Hirakawa, M., Tanaka, T., Hashimoto, Y., Kuroda, M., Takagi, T. & Nakamura, Y. (2002) JSNP: A database of common gene variations in the Japanese population. Nucleic Acids Res 30, 158-162.
13. Hou, Y. P., Zhang, J., Li, Y. B., Wu, J., Zhang, S. Z. & Prinz, M. (2001) Allele sequences of six new Y-STR loci and haplotypes in the Chinese Han population. Forensic Sci Int 15, 147-152.
14. Jin, H. J., Kwak, K. D., Hammer, M. F., Nakahori, Y., Shinka, T., Lee, J. W., Jin, F., Jia, X., Tyler-Smith, C. & Kim, W. (2003) Y-chromosomal DNA haplogroups and their implications for the dual origins of the Koreans. Hum Genet 114, 27-35.
15. Jobling, M. A. & Tyler-Smith, C. (2000) New uses for new haplotypes the human Y chromosome, disease and selection. Trends Genet 16, 356-362.
16. Jobling, M. A. & Tyler-Smith, C. (2003) The human Y chromosome: An evolutionary marker comes of age. Nat Rev Genet 4, 598-612.
17. Karafet, T. M., Osipova, L. P., Gubina, M. A., Posukh, O. L., Zegura, S. L. & Hammer, M. F. (2002) High levels of Y-chromosome differentiation among native Siberian populations and the genetic signature of a boreal hunter-gatherer way of life. Hum Biol 74, 761-789.
18. Karafet, T., Xu, L., Du, R., Wang, W., Feng, S., Wells, R. S., Redd, A. J., Zegura, S. L. & Hammer, M. F. (2001) Paternal population history of East Asia: Sources, patterns, and microevolutionary processes. Am J Hum Genet 69, 615-628.
19. Kayser, M., Caglia, A., Corach, D., Fretwell, N., Gehrig, C., Graziosi, G., Heidorn, F., Herrmann, S., Herzog, B., Hidding, M., Honda, K., Jobling, M., Krawczak, M., Leim, K., Meuser, S., Meyer, E., Oesterreich, W., Pandya, A., Parson, W., Penacino, G., Perez- Lezaun, A., Piccinini, A., Prinz, M., Schmitt, C., Schneider, P. M., Szibor, R., Teifel-Greding, J., Weichhold, G., de Knijff, P. & Roewer, L. (1997) Evaluation of Y-chromosomal STRs: A multicenter study. Int J Legal Med 110, 125-133, 141-149.
20. Kayser, M., Roewer, L., Hedman, M., Henke, L., Henke, J., Brauer, S., Kruger, C., Krawczak, M., Nagy, M., Dobosz, T., Szibor, R., de Knijff, P., Stoneking, M. & Sajantila, A. (2000) Characteristics and frequency of germline mutations at microsatellite loci from the human Y chromosome, as revealed by direct observation in father/son pairs. Am J Hum Genet 66, 1580-1588.
21. Mitchell, R. J. & Hammer, M. F. (1996) Human evolution and the Y chromosome. Curr Opin Genet Dev 6, 737-742.
22. Nonaka, I. & Minaguchi, K. (2001) Allele frequencies and haplotype o ten Y-specific STRs in the Japanese population. J Forensic Sci 41, 179-182.
23. Santos, F. R., Pandya, A., Kayser, M., Mitchell, R. J., Liu, A., Singh, L., Destro-Bisol, G., Novelletto, A., Qamar, R., Mehdi, S. Q., Adhikari, R., de Knijff, P. & Tyler-Smith, C. (2000) A polymorphic L1 retroposon insertion in the centromere of the human Y chromosome. Hum Mol Genet 9, 421-430.
24. Sasaki, M. & Dahiya, R. (2000) The polymorphisms of various short tandem repeats on the Y chromosome in Japanese and German populations. Int J Legal Med 113, 181-188.
25. Seielstad, M. T., Minch, E. & Cavalli-Sforza, L. L. (1998) Genetic evidence for a higher female migration rate in humans. Nat Genet 20, 278-280.
26. Shin, D. J., Jin, H. J., Kwak, K. D., Choi, J. W., Han, M. S., Kang, P. W., Choi, S. K. & Kim, W. (2001) Y-chromosome multiplexes and their potential for the DNA profiling of Koreans. Int J Legal Med 115, 109-117.
27. Shinka, T., Tomita, K., Toda, T., Kotliarova, S. E., Lee, J., Kuroki, Y., Jin, D. K., Tokunaga, K., Nakamura, H. & Nakahori, Y. (1999) Genetic variations on the Y chromosome in the Japanese population and implications for modern human Y chromosome lineage. J Hum Genet 44, 240-245.
28. The Y Chromosome Consortium (2002) A nomenclature system for the tree of human Y-chromosomal binary haplogroups. Genome Research 12, 339-348.
29. Tsai, L. C., Yuen, T. Y., Hsieh, H. M., Lin, M., Tzeng, C. H., Huang, N. E., Linacre, A. & Lee, J. C. (2001) Haplotype frequencies of nine Y-chromosome STR loci in the Taiwanese Han population. Int J Legal Med 116, 179-183.
30. Uchihi, R., Yamamoto, T., Usuda, K., Yoshimoto, T., Tanaka, M., Tokunaga, S., Kurihara, R., Tokunaga, K. & Katsumata, Y. (2003) Haplotype analysis with 14 Y-STR loci using 2 multiplex amplification and typing systems in 2 regional populations in Japan. Int J Legal Med 117, 34-38.
31. Underhill, P. A., Jin, L., Lin, A. A., Mehdi, S. Q., Jenkins, T., Vollrath, D., Davis, R. W., Cavalli-Sforza, L. L. & Oefner, P. J. (1997) Detection of numerous Y chromosome biallelic polymorphisms by denaturing high-performance liquid chromatography. Genome Res 7, 996-1005.
32. Underhill, P. A., Passarino, G., Lin, A. A., Shen, P., Mirazon Lahr, M., Foley, R. A., Oefner, P. J. & Cavalli-Sforza, L. L. (2001) The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations. Ann Hum Genet 65, 43-62.
33. Underhill, P. A., Shen, P., Lin, A. A., Jin, L., Passarino, G., Yang, W. H., Kauffman, E., Bonne-Tamir, B., Bertranpetit, J., Francalacci, P., Ibrahim, M., Jenkins, T., Kidd, J. R., Mehdi, S. Q., Seielstad, M. T., Wells, R. S., Piazza, A., Davis, R. W., Feldman, M. W., Cavalli-Sforza, L. L. & Oefner, P. J. (2000) Y chromosome sequence variation and the history of human populations. Nat Genet 26, 358-361.
34. Zegura, S. L., Karafet, T. M., Zhivotovsky, L. A. & Hammer, M. F. (2004) High-resolution SNPs and microsatellite haplotypes point to a single, recent entry of Native American Y chromosomes into the Americas. Mol Biol Evol 21, 164-175.
35. Zerjal, T., Dashnyam, B., Pandya, A., Kayser, M., Roewer, L., Santos, F. R., Schiefenhovel, W., Fretwell, N., Jobling, M. A., Harihara, S., Shimizu, K., Semjidmaa, D., Sajantila, A., Salo, P., Crawford, M. H., Ginter, E. K., Evgrafov, O. V. & Tyler-Smith, C. (1997) Genetic relationships of Asians and Northern Europeans, revealed by Y-chromosomal DNA analysis. Am J Hum Genet 60, 1174-1183.