International Journal of Legal Medicine

, Volume 124, Issue 4, pp 295–300 | Cite as

Seventeen Y-chromosomal short tandem repeat haplotypes in seven groups of population living in Taiwan

  • Hsiao-Lin Hwa
  • Li-Hui Tseng
  • Tsang-Ming Ko
  • Yih-Yuan Chang
  • Hsiang-Yi Yin
  • Yi-Ning Su
  • James Chun-I Lee


The analysis of Y-chromosome short tandem repeat (Y-STR) loci is a powerful tool in forensic casework. The aim of this study was to present the 17 Y-STR loci haplotype distributions of groups of population living in Taiwan and to demonstrate genetic distances between the groups as well as multidimensional scaling plot based on Y-STR genotype data. Five hundred and fifteen DNA samples from unrelated males of seven groups of population, including Taiwanese Han, two groups of indigenous Taiwanese of Taiwan Island, Tao, mainland Chinese, Filipinos, and a group of people with European, Near Eastern, or South Asian ancestry, were analyzed using a commercial kit that co-amplifies 17 Y-STRs. A total of 471 different haplotypes with 440 unique haplotypes were identified. The overall haplotype diversity was 0.9995 ± 0.0002. High haplotype diversity was observed in six groups of population, except the Tao. These Y-STRs revealed a low discrimination capacity in the Tao population (36.84%), which should be considered in forensic practice. The multidimensional scaling plot of these seven groups of population constructed based on the genetic distances according to 17 Y-STR loci presented a clear patrilineal genetic substructure in the area. Partial Y-STRs profiling reduced the discrimination capacity in most groups of population and distorted the multidimensional scaling plot.


Y-chromosome Short tandem repeats Forensic genetics Multidimensional scaling plot 



We would like to thank Ms Hong-Ciao Wan, Ms Pi-Mei Hsu, and Ms Shwu-Fang Li for technical support on DNA extraction. This work was supported by a grant from the College of Medicine, National Taiwan University (NTUCM-9503).

Supplementary material

414_2010_425_MOESM1_ESM.doc (30 kb)
Supplementary Figure S1 The multidimensional scaling plot based on 13 Y-chromosome short tandem repeat loci (DYS385a/b, DYS389I, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS456, DYS458, and Y GATA H4) (DOC 33 kb)
414_2010_425_MOESM2_ESM.doc (29 kb)
Supplementary Figure S2 The multidimensional scaling plot based on seven Y-chromosome short tandem repeat loci (DYS389I, DYS391, DYS 393, DYS439, DYS456, DYS458, and Y GATA H4) (DOC 32 kb)
414_2010_425_MOESM3_ESM.doc (1.1 mb)
Supplementary Table S1 Y-chromosome short tandem repeat haplotypes of seven groups of population (DOC 743 kb)
414_2010_425_MOESM4_ESM.doc (358 kb)
Supplementary Table S2 Allele frequency patterns of 17 Y-chromosome short tandem repeat loci in seven groups of population (DOC 293 kb)


  1. 1.
    Jobling MA, Pandya A, Tyler-Smith C (1997) The Y chromosome in forensic analysis and paternity testing. Int J Legal Med 110:118–124CrossRefPubMedGoogle Scholar
  2. 2.
    Sibille I, Duverneuil C, de la Grandmaison L, Guerrouache K, Teissière F, Durigon M, de Mazancourt P (2002) Y-STR DNA amplification as biological evidence in sexually assaulted female victims with no cytological detection of spermatozoa. Forensic Sci Int 125:212–216CrossRefPubMedGoogle Scholar
  3. 3.
    Tsai LC, Yuen TY, Hsieh HM, Lin M, Tzeng CH, Huang NE, Linacre A, Lee JC (2002) Haplotype frequencies of nine Y-chromosome STR loci in the Taiwanese Han population. Int J Legal Med 116:179–183CrossRefPubMedGoogle Scholar
  4. 4.
    Kwak KD, Jin HJ, Shin DJ, Kim JM, Roewer L, Krawczak M, Tyler-Smith C, Kim W (2005) Y-chromosomal STR haplotypes and their applications to forensic and population studies in east Asia. Int J Legal Med 119:195–201CrossRefPubMedGoogle Scholar
  5. 5.
    Huang TY, Hsu YT, Li JM, Chung JH, Shun CT (2008) Polymorphism of 17 Y-STR loci in Taiwan population. Forensic Sci Int 174:249–254CrossRefPubMedGoogle Scholar
  6. 6.
    Palo JU, Pirttimaa M, Bengs A, Johnsson V, Ulmanen I, Lukka M, Udd B, Sajantila A (2008) The effect of number of loci on geographical structuring and forensic applicability of Y-STR data in Finland. Int J Legal Med 122:449–456CrossRefPubMedGoogle Scholar
  7. 7.
    Rodríguez V, Tomàs C, Sánchez JJ, Castro JA, Ramon MM, Barbaro A, Morling N, Picornell A (2009) Genetic sub-structure in western Mediterranean populations revealed by 12 Y-chromosome STR loci. Int J Legal Med 123:137–141CrossRefPubMedGoogle Scholar
  8. 8.
    Brinkmann B, Junge A, Meyer E, Wiegand P (1998) Population genetic diversity in relation to microsatellite heterogeneity. Hum Mutat 11:135–144CrossRefPubMedGoogle Scholar
  9. 9.
    de Knijff P, Kayser M, Caglià A et al (1997) Chromosome Y microsatellites: population genetic and evolutionary aspects. Int J Legal Med 110:134–140CrossRefPubMedGoogle Scholar
  10. 10.
    Kayser M, Caglià A, Corach D et al (1997) Evaluation of Y-chromosomal STRs: a multicenter study. Int J Legal Med 110:125–133CrossRefPubMedGoogle Scholar
  11. 11.
    Forster P, Röhl A, Lünnemann 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 Genet 67:182–196CrossRefPubMedGoogle Scholar
  12. 12.
    Gusmão L, Sánchez-Diz P, Alves C, Beleza S, Lopes A, Carracedo A, Amorim A (2003) Grouping of Y-STR haplotypes discloses European geographic clines. Forensic Sci Int 134:172–179CrossRefPubMedGoogle Scholar
  13. 13.
    Roewer L, Willuweit S, Krüger C et al (2008) Analysis of Y chromosome STR haplotypes in the European part of Russia reveals high diversities but non-significant genetic distances between populations. Int J Legal Med 122:219–223CrossRefPubMedGoogle Scholar
  14. 14.
    Schultes T, Hummel S, Herrmann B (1999) Amplification of Y-chromosomal STRs from ancient skeletal material. Hum Genet 104:164–166CrossRefPubMedGoogle Scholar
  15. 15.
    Park MJ, Lee HY, Chung U, Kang SC, Shin KJ (2007) Y-STR analysis of degraded DNA using reduced-size amplicons. Int J Legal Med 121:152–157CrossRefPubMedGoogle Scholar
  16. 16.
    Council of Indigenous Peoples, Executive Yuan, Taiwan, ROC. Accessed on 11 May 2009
  17. 17.
    Trejaut JA, Kivisild T, Loo JH, Lee CL, He CL, Hsu CJ, Li ZY, Lin M (2005) Traces of archaic mitochondrial lineages persist in Austronesian-speaking Formosan populations. PLoS Biology 3:e247CrossRefPubMedGoogle Scholar
  18. 18.
    Chow RA, Caeiro JL, Chen SJ, Garcia-Bertrand RL, Herrera RJ (2005) Genetic characterization of four Austronesian-speaking populations. J Hum Genet 50:550–559CrossRefPubMedGoogle Scholar
  19. 19.
    National Immigration Agency, Ministry of the Interior, Taiwan, ROC. Accessed on 28 Dec 2009
  20. 20.
    Gusmão L, Butler JM, Carracedo A et al (2006) DNA Commission of the International Society of Forensic Genetics (ISFG): an update of the recommendations on the use of Y-STRs in forensic analysis. Int J Legal Med 120:191–200CrossRefPubMedGoogle Scholar
  21. 21.
    Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New YorkGoogle Scholar
  22. 22.
    Gené M, Borrego N, Xifró A, Piqué E, Moreno P (1999) Haplotype frequencies of eight Y-chromosome STR loci in Barcelona (north-east Spain). Int J Legal Med 112:403–405CrossRefPubMedGoogle Scholar
  23. 23.
    Excoffier L, Smouse P, Quattro J (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491PubMedGoogle Scholar
  24. 24.
    Excoffier L, Smouse P (1994) Using allele frequencies and geographic subdivision to reconstruct gene trees within a species: molecular variance parsimony. Genetics 136:343–359PubMedGoogle Scholar
  25. 25.
    Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50PubMedGoogle Scholar
  26. 26.
    Reynolds J, Weir BS, Cockerham CC (1983) Estimation of the coancestry coefficient: basis for a short-term genetic distance. Genetics 105:767–779PubMedGoogle Scholar
  27. 27.
    Felsenstein J (1986) PHYLIP (Phylogeny Inference Package) Version 3.5c. University of Washington, SeattleGoogle Scholar
  28. 28.
    He M, Gitschier J, Zerjal T, de Knijff P, Tyler-Smith C, Xue Y (2009) Geographical affinities of the HapMap samples. PLoS ONE 4:e4684CrossRefPubMedGoogle Scholar
  29. 29.
    Roewer L, Croucher PJP, Willuweit S et al (2005) Signature of recent historical events in the European Y-chromosomal STR haplotype distribution. Hum Genet 116:279–291CrossRefPubMedGoogle Scholar
  30. 30.
    Frank WE, Ellinger ER, Krishack PA (2006) Y chromosome STR haplotypes and allele frequencies in Illinois Caucasian, African American, and Hispanic males. J Forensic Sci 51:1207–1215CrossRefPubMedGoogle Scholar
  31. 31.
    Berger B, Lindinger A, Niederstatter H, Grubwieser P, Parson W (2005) Y-STR typing of an Austrian population sample using a 17-loci multiplex PCR assay. Int J Legal Med 119:241–246CrossRefPubMedGoogle Scholar
  32. 32.
    Miranda JJ, Benecke M, Hidding M, Schmitt C (2001) Y-chromosomal short tandem repeat haplotypes at the loci DYS393, DYS19, DYS392, and DYS385-I/II, DYS390, DYS389-I/II, and DYS391 in a Filipino population sample. J Forensic Sci 46:1250–1253PubMedGoogle Scholar
  33. 33.
    Chang YM, Perumal R, Keat PY, Kuehn DLC (2007) Haplotype diversity of 16 Y-chromosomal STRs in three main ethnic populations (Malays, Chinese and Indians) in Malaysia. Forensic Sci Int 167:70–76CrossRefPubMedGoogle Scholar
  34. 34.
    Pakendorf B, Morar B, Tarskaia LA, Kayser M, Soodyall H, Rodewald A, Stoneking M (2002) Y-chromosomal evidence for a strong reduction in male population size of Yakuts. Hum Genet 110:198–200CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Hsiao-Lin Hwa
    • 1
    • 2
    • 3
  • Li-Hui Tseng
    • 3
  • Tsang-Ming Ko
    • 4
  • Yih-Yuan Chang
    • 4
  • Hsiang-Yi Yin
    • 1
  • Yi-Ning Su
    • 3
  • James Chun-I Lee
    • 1
    • 5
  1. 1.Department and Graduate Institute of Forensic Medicine, College of MedicineNational Taiwan UniversityTaipeiTaiwan
  2. 2.Department of Obstetrics and GynecologyNational Taiwan University Hospital and College of Medicine, National Taiwan UniversityTaipeiTaiwan
  3. 3.Department of Medical GeneticsNational Taiwan University HospitalTaipeiTaiwan
  4. 4.Genephile Bioscience LaboratoryTaipeiTaiwan
  5. 5.Institute of Forensic MedicineMinistry of JusticeTaipeiRepublic of China

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