International Journal of Legal Medicine

, Volume 126, Issue 4, pp 589–599 | Cite as

Understanding the Y chromosome variation in Korea—relevance of combined haplogroup and haplotype analyses

  • Myung Jin Park
  • Hwan Young Lee
  • Woo Ick Yang
  • Kyoung-Jin Shin
Original Article


We performed a molecular characterization of Korean Y-chromosomal haplogroups using a combination of Y-chromosomal single nucleotide polymorphisms (Y-SNPs) and Y-chromosomal short tandem repeats (Y-STRs). In a test using DNA samples from 706 Korean males, a total of 19 different haplogroups were identified by 26 Y-SNPs including the newly redefined markers (PK4, KL2, and P164) in haplogroup O. When genotyping the SNPs, phylogenetic nonequivalence was found between SNPs M117 and M133, which define haplogroup O3a3c1 (O3a2c1a according to the updated tree of haplogroup O by Yan et al. (European Journal of Human Genetics 19:1013–1015, 2011)), suggesting that the position of the M133 marker should be corrected. We have shown that the haplotypes consisted of DYS392, DYS393, DYS437, DYS438, DYS448, and DYS388 loci, which exhibit a relatively lower mutation rate, can preserve phylogenetic information and hence can be used to roughly distinguish Y-chromosome haplogroups, whereas more rapidly mutating Y-STRs such as DYS449 and DYS458 are useful for differentiating male lineages. However, at the relatively rapidly mutating DYS447, DYS449, DYS458, and DYS464 loci, unusually short alleles and intermediate alleles with common sequence structures are informative for elucidating the substructure within the context of a particular haplogroup. In addition, some deletion mutations in the DYS385 flanking region and the null allele at DYS448 were associated with a single haplogroup background. These high-resolution haplogroup and haplotype data will improve our understanding of regional Y-chromosome variation or recent migration routes and will also help to infer haplogroup background or common ancestry.


Y chromosome Haplogroup Single nucleotide polymorphism Short tandem repeat Atypical allele Korean 



The authors would like to thank the anonymous reviewers for their valuable comments and suggestions on our paper.

This research was supported by Future-based Technology Development Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (No. 2010-0020631).

Supplementary material

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ESM 1 (PDF 518 kb)
414_2012_703_MOESM2_ESM.pdf (117 kb)
ESM 2 (PDF 117 kb)
414_2012_703_MOESM3_ESM.xls (441 kb)
ESM 3 (XLS 441 kb)


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Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Myung Jin Park
    • 1
  • Hwan Young Lee
    • 1
    • 2
  • Woo Ick Yang
    • 1
  • Kyoung-Jin Shin
    • 1
    • 2
  1. 1.Department of Forensic Medicine and Brain Korea 21 Project for Medical ScienceYonsei University College of MedicineSeoulSouth Korea
  2. 2.Human Identification Research CenterYonsei UniversitySeoulSouth Korea

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