Human Genetics

, Volume 118, Issue 6, pp 695–707 | Cite as

Phylogenetic relationship of the populations within and around Japan using 105 short tandem repeat polymorphic loci

  • Shi-Lin Li
  • Toshimichi Yamamoto
  • Takashi Yoshimoto
  • Rieko Uchihi
  • Masaki Mizutani
  • Yukihide Kurimoto
  • Katsushi Tokunaga
  • Feng Jin
  • Yoshinao Katsumata
  • Naruya Saitou
Original Investigation


We have analyzed 105 autosomal polymorphic short tandem repeat (STR) loci for nine East and South-eastern Asian populations (two Japanese, five Han Chinese, Thai, and Burmese populations) and a Caucasian population using a multiplex PCR typing system. All the STR loci are genomewide tetranucleotide repeat markers of which the total number of observed alleles and the observed heterozygosity were 756 and 0.743, respectively, for Japanese populations. Phylogenetic analysis for these allele frequency data suggested that the Japanese populations are more closely related with southern Chinese populations than central and/or northern ones. STRUCTURE program analysis revealed the almost clearly divided and accountable population structure at K=2–6, that the two Japanese populations always formed one group separated from the other populations and never belong to different groups at K≥3. Furthermore, our new allele frequency data for 91 loci were analyzed with those for 52 worldwide populations published by previous studies. Phylogenetic and multidimensional scaling (MDS) analyses indicated that Asian populations with large population size (six Han Chinese, three Japanese, two Southeast Asia) formed one distinct cluster and are closer to each other than other ethnic minorities in east and Southeast Asia. This pattern may be the caviar of comparing populations with greatly differing population sizes when STR loci were analyzed.


Short tandem repeat Population genetics East Asian Japanese Phylogenetic tree Polymorphism 



We are grateful to Prof. Sirirurg Songsivilai, Dr. Hla Hla Htay, and Dr. Yuri E. Dubrova for providing Thais, Burmese, and Caucasian DNA samples, respectively. We also thank Dr. Naoko Takezaki for helpful technical assistance and comments. This work was in part supported by Grants-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science, and Technology of Japan (12012204 to TY and 11307008 to YK).


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Copyright information

© Springer-Verlag 2005

Authors and Affiliations

  • Shi-Lin Li
    • 1
  • Toshimichi Yamamoto
    • 1
  • Takashi Yoshimoto
    • 1
  • Rieko Uchihi
    • 1
  • Masaki Mizutani
    • 1
  • Yukihide Kurimoto
    • 1
  • Katsushi Tokunaga
    • 2
  • Feng Jin
    • 4
  • Yoshinao Katsumata
    • 1
  • Naruya Saitou
    • 3
  1. 1.Department of Legal Medicine and Bioethics, Graduate School of MedicineNagoya UniversityNagoyaJapan
  2. 2.Department of Human Genetics, Graduate School of MedicineThe University of TokyoTokyoJapan
  3. 3.Division of Population Genetics, National Institute of GeneticsMishimaJapan
  4. 4.Chinese Academy of SciencesInstitute of Genetics and Developmental BiologyBeijingChina

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