Phylogenetic relationship of the populations within and around Japan using 105 short tandem repeat polymorphic loci
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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.
KeywordsShort 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).
- Aikens CM, Higuchi T (1982) Prehistory of Japan. Academic Press, New YorkGoogle Scholar
- Chakraborty R, Fornage M, Gueguen R, Boerwinkle E (1991) Population genetics of hypervariable loci: analysis of PCR based VNTR polymorphism within a population. In: Burke T, Dolf G, Jeffreys AJ, Wolff R (eds) DNA fingerprinting: approaches and applications. Birkhauser Verlag, Berlin, pp 127–143Google Scholar
- Felsenstein J (1995) Phylogeny Inference Package (PHYLIP).v.3.57c. Universuty of Washington, SeattleGoogle Scholar
- Hanihara K (1991) Dual structure model for the formation of the Japanese. Jpn Rev 2:1–33Google Scholar
- Lines M (1999) The Kalasha people of north-western Pakistan. Emjay books International, PeshawarGoogle Scholar
- Nei M (1995) The origins of human populations: genetic, linguistic, and archeological data. In: Brenner S, Hanihara K (eds) The origin and past of modern humans as viewed from DNA. World Scientific, Singapore, pp 71–91Google Scholar
- Rogers JS (1972) Measures of genetic similarity and genetic distance. In: Wheeler MR (ed) Studies in genetics VII. University of Texas, Austin, TX, pp 145–153Google Scholar
- Roubinet F, Despiau S, Calafell F, Jin F, Bertanpetit J, Saitou N, Blancher A (2004) Evolution of the O alleles of the human ABO blood group gene. Immunohematology 44:707–715Google Scholar
- Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:404–425Google Scholar
- Saitou N, Omoto K, Du C, Du R (1994) Population genetic study in Hainan Island, China II Genetic affinity analyses. Anthropol Sci 102:129–147Google Scholar
- Saitou N, Tokunaga K, Omoto K (1992) Genetic affinities of human populations. In: Roberts DL, Fujiki N, Torizuka K (eds) Society for the study of human biology symposium series 33: isolation and migration. Cambridge University Press, Cambridge, pp 118–129Google Scholar