International Journal of Legal Medicine

, Volume 125, Issue 3, pp 367–375 | Cite as

Y-STR diversity in the Himalayas

  • Tenzin Gayden
  • Shilpa Chennakrishnaiah
  • Joel La Salvia
  • Sacha Jimenez
  • Maria Regueiro
  • Trisha Maloney
  • Patrice J. Persad
  • Areej Bukhari
  • Annabel Perez
  • Oliver Stojkovic
  • Rene J. Herrera
Original Article


Linguistic and ethnic diversity throughout the Himalayas suggests that this mountain range played an important role in shaping the genetic landscapes of the region. Previous Y-chromosome work revealed that the Himalayas acted as a biased bidirectional barrier to gene flow across the cordillera. In the present study, 17 Y-chromosomal short tandem repeat (Y-STR) loci included in the AmpFlSTR® Yfiler kit were analyzed in 344 unrelated males from three Nepalese populations (Tamang, Newar, and Kathmandu) and a general collection from Tibet. The latter displays the highest haplotype diversity (0.9990) followed by Kathmandu (0.9977), Newar (0.9570), and Tamang (0.9545). The overall haplotype diversity for the Himalayan populations at 17 Y-STR loci was 0.9973, and the corresponding values for the extended (11 loci) and minimal (nine loci) haplotypes were 0.9955 and 0.9942, respectively. No Y-STR profiles are shared across the four Himalayan collections at the 17-, 11-, and nine-locus resolutions considered, indicating a lack of recent gene flow among them. Phylogenetic analyses support our previous findings that Kathmandu, and to some extent Newar, received significant genetic influence from India while Tamang and Tibet exhibit limited or no gene flow from the subcontinent. A median-joining network of haplogroup O3a3c-M134 based on 15 Y-STR loci from our four Himalayan populations suggests either a male founder effect in Tamang, possibly from Tibet, or a recent bottleneck following their arrival south of the Himalayas from Tibet leading to their highly reduced Y single-nucleotide polymorphism and Y-STR diversity. The genetic uniqueness of the four Himalayan populations examined in this study merits the creation of separate databases for individual identification, parentage analysis, and population genetic studies.


Himalayas Nepal Tibet Y-STR 



The authors gratefully acknowledge Sheyla Mirabal and Kristian J. Herrera for their constructive criticism of the manuscript.

Supplementary material

414_2010_485_MOESM1_ESM.xls (104 kb)
Supplementary Table 1 Y-STR data of the four Himalayan populations studied. (XLS 104 kb)
414_2010_485_MOESM2_ESM.doc (58 kb)
Supplementary Table 2 Allele frequencies of the 17 Y-STR loci studied for Tamang, Newar, Kathmandu, and Tibet populations. (DOC 58 kb)
414_2010_485_MOESM3_ESM.doc (71 kb)
Supplementary Table 3 Allele frequencies of the 17 Y-STR loci studied for Tamang, Newar, Kathmandu, and Tibet populations. (DOC 71 kb)
414_2010_485_MOESM4_ESM.doc (78 kb)
Supplementary Table 4 Allele frequencies of the 17 Y-STR loci studied for Tamang, Newar, Kathmandu, and Tibet populations. (DOC 77 kb)
414_2010_485_MOESM5_ESM.doc (102 kb)
Supplementary Table 5 Allele frequencies of the 17 Y-STR loci studied for Tamang, Newar, Kathmandu, and Tibet populations. (DOC 102 kb)


  1. 1.
    Willuweit S, Roewer L, International Forensic Y Chromosome User Group (2007) Y chromosome haplotype reference database (YHRD): update. Forensic Sci Int Genet 1:83–87PubMedCrossRefGoogle Scholar
  2. 2.
    Jobling MA, Tyler-Smith C (1993) The human Y chromosome: an evolutionary marker comes of age. Nat Rev Genet 8:598–612Google Scholar
  3. 3.
    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 Leg Med 119:195–201CrossRefGoogle Scholar
  4. 4.
    Gayden T, Regueiro M, Martinez L, Cadenas AM, Herrera RJ (2008) Human Y-chromosome haplotyping by allele-specific polymerase chain reaction. Electrophoresis 29:2419–2423PubMedCrossRefGoogle Scholar
  5. 5.
    Iida R, Kishi K (2005) Identification, characterization and forensic application of novel Y-STRs. Leg Med 7:255–258CrossRefGoogle Scholar
  6. 6.
    Hanson EK, Ballantyne J (2007) An ultra-high discrimination Y chromosome short tandem repeat multiplex DNA typing system. PLoS ONE 8:e688CrossRefGoogle Scholar
  7. 7.
    Budowle B, Ge J, Low J, Lai C, Yee WH, Law G, Tan WF, Chang YM, Perumal R, Keat PY, Mizuno N, Kasai K, Sekiguchi K, Chakraborty R (2009) The effects of Asian population substructure on Y STR forensic analyses. Leg Med 11:64–69CrossRefGoogle Scholar
  8. 8.
    Alves C, Gusmão L, Barbosa J, Amorim A (2003) Evaluating the informative power of Y-STRs: a comparative study using European and new African haplotype data. Forensic Sci Int 34:126–133CrossRefGoogle Scholar
  9. 9.
    Roewer L, Croucher PJ, Willuweit S, Lu TT, Kayser M, Lessig R, de Knijff P, Jobling MA, Tyler-Smith C, Krawczak M (2005) Signature of recent historical events in the European Y-chromosomal STR haplotype distribution. Hum Genet 116:279–291PubMedCrossRefGoogle Scholar
  10. 10.
    Immel UD, Krawczak M, Udolph J, Richter A, Rodig H, Kleiber M, Klintschar M (2006) Y-chromosomal STR haplotype analysis reveals surname-associated strata in the East-German population. Eur J Hum Genet 14:577–582PubMedCrossRefGoogle Scholar
  11. 11.
    Rebała K, Mikulich AI, Tsybovsky IS, Siváková D, Dzupinková Z, Szczerkowska-Dobosz A, Szczerkowska Z (2007) Y-STR variation among Slavs: evidence for the Slavic homeland in the middle Dnieper basin. J Hum Genet 52:406–414PubMedCrossRefGoogle Scholar
  12. 12.
    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 Leg Med 123:137–141CrossRefGoogle Scholar
  13. 13.
    Roewer L, Krawczak M, Willuweit S et al (2001) Online reference database of European Y-chromosomal short tandem repeat (STR) haplotypes. Forensic Sci Int 118:106–113PubMedCrossRefGoogle Scholar
  14. 14.
    Kayser M, Brauer S, Willuweit S et al (2002) Online Y-chromosomal short tandem repeat haplotype reference database (YHRD) for U.S. populations. J Forensic Sci 47:513–519PubMedGoogle Scholar
  15. 15.
    Lessig R, Willuweit S, Krawczak M et al (2003) Asian online Y-STR haplotype reference database. Leg Med 5:S160–S163CrossRefGoogle Scholar
  16. 16.
    Gayden T, Cadenas AM, Regueiro M, Singh NB, Zhivotovsky LA, Underhill PA, Cavalli-Sforza LL, Herrera RJ (2007) The Himalayas as a directional barrier to gene flow. Am J Hum Genet 80:884–894PubMedCrossRefGoogle Scholar
  17. 17.
    Gayden T, Mirabal S, Cadenas AM, Lacau H, Simms TM, Morlote D, Chennakrishnaiah S, Herrera RJ (2009) Genetic insights into the origins of Tibeto-Burman populations in the Himalayas. J Hum Genet 54:216–223PubMedCrossRefGoogle Scholar
  18. 18.
    Thangaraj K, Chaubey G, Kivisild T et al (2008) Maternal footprints of Southeast Asians in North India. Hum Hered 66:1–6PubMedCrossRefGoogle Scholar
  19. 19.
    Fornarino S, Pala M, Battaglia V, Maranta R, Achilli A, Modiano G, Torroni A, Semino O, Santachiara-Benerecetti SA (2009) Mitochondrial and Y-chromosome diversity of the Tharus (Nepal): a reservoir of genetic variation. BMC Evol Biol 9:154PubMedCrossRefGoogle Scholar
  20. 20.
    Qian Y, Qian B, Su B et al (2000) Multiple origins of Tibetan Y chromosomes. Hum Genet 106:453–454PubMedCrossRefGoogle Scholar
  21. 21.
    Su B, Xiao C, Deka R et al (2000) Y chromosome haplotypes reveal prehistorical migrations to the Himalayas. Hum Genet 107:582–590PubMedCrossRefGoogle Scholar
  22. 22.
    Hammer MF, Karafet TM, Park H, Omoto K, Harihara S, Stoneking M, Horai S (2006) Dual origins of the Japanese: common ground for hunter–gatherer and farmer Y chromosomes. J Hum Genet 51:47–58PubMedCrossRefGoogle Scholar
  23. 23.
    Zhang Q, Yan J, Tang H, Jiao Z, Liu Y (2006) Genetic polymorphisms of 17 Y-STRs haplotypes in Tibetan ethnic minority group of China. Leg Med 8:300–305CrossRefGoogle Scholar
  24. 24.
    Zhu B, Liu S, Ci D et al (2006) Population genetics for Y-chromosomal STRs haplotypes of Chinese Tibetan ethnic minority group in Tibet. Forensic Sci Int 161:78–83PubMedCrossRefGoogle Scholar
  25. 25.
    Kang LL, Liu K, Ma Y (2007) Y chromosome STR haplotypes of Tibetan living Tibet Lassa. Forensic Sci Int 172:79–83PubMedCrossRefGoogle Scholar
  26. 26.
    Zhu B, Wu Y, Shen C et al (2008) Genetic analysis of 17 Y-chromosomal STRs haplotypes of Chinese Tibetan ethnic group residing in Qinghai province of China. Forensic Sci Int 175:238–243PubMedCrossRefGoogle Scholar
  27. 27.
    Parkin EJ, Kraaijenbrink T, Opgenort JRML, van Driem GL, Tuladhar NM, de Knijff P, Jobling MA (2007) Diversity of 26-locus Y-STR haplotypes in a Nepalese population sample: isolation and drift in the Himalayas. Forensic Sci Int 166:176–181PubMedCrossRefGoogle Scholar
  28. 28.
    Antunez de Mayolo G, Antúñez de Mayolo A, Antúñez de Mayolo P (2002) Phylogenetics of worldwide human populations as determined by polymorphic Alu insertions. Electrophoresis 23:3346–3356PubMedCrossRefGoogle Scholar
  29. 29.
    Applied Biosystems (2006) AmpFlSTR Yfiler PCR amplification kit user’s manual. Applied Biosystems, Foster CityGoogle Scholar
  30. 30.
    Gusmão L, Butler JM, Carracedo A, Gill P, Kayser M, Mayr WR, Morling N, Prinz M, Roewer L, Tyler-Smith C, Schneider PM, DNA Commission of the International Society of Forensic Genetics (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. Forensic Sci Int 157:187–197PubMedCrossRefGoogle Scholar
  31. 31.
    Y Chromosome Consortium (2002) A nomenclature system for the tree of human Y-chromosomal binary haplogroups. Genome Res 12:339–348CrossRefGoogle Scholar
  32. 32.
    Karafet TM, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, Hammer MF (2008) New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Res 18:830–838PubMedCrossRefGoogle Scholar
  33. 33.
    Excoffier L, Laval LG, Schneider S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50PubMedGoogle Scholar
  34. 34.
    Brinkmann C, Forster P, Schürenkamp M, Horst J, Rolf B, Brinkmann B (1999) Human Y-chromosomal STR haplotypes in a Kurdish population sample. Int J Leg Med 112:181–183CrossRefGoogle Scholar
  35. 35.
    Pfeiffer H, Brinkmann B, Hühne J, Rolf B, Morris AA, Steighner R, Holland MM, Forster P (1999) Expanding the forensic German mitochondrial DNA control region database: genetic diversity as a function of sample size and microgeography. Int J Leg Med 112:291–298CrossRefGoogle Scholar
  36. 36.
    Hashiyada M, Umetsu K, Yuasa I et al (2008) Population genetics of 17 Y-chromosomal STR loci in Japanese. Forensic Sci Int Genet 2:e69–e70PubMedCrossRefGoogle Scholar
  37. 37.
    Yan J, Tang H, Liu Y et al (2007) Genetic polymorphisms of 17 Y-STRs haplotypes in Chinese Han population residing in Shandong province of China. Leg Med 94:196–202CrossRefGoogle Scholar
  38. 38.
    Chang YM, Perumal R, Keat PY, Kuehn DL (2007) Haplotype diversity of 16 Y-chromosomal STRs in three main ethnic populations (Malays, Chinese and Indians) in Malaysia. Forensic Sci Int 167:70–76PubMedCrossRefGoogle Scholar
  39. 39.
    Huang TY, Hsu YT, Li JM, Chung JH, Shun CT (2008) Polymorphism of 17 Y-STR loci in Taiwan population. Forensic Sci Int 174:249–254PubMedCrossRefGoogle Scholar
  40. 40.
    Dobashi Y, Kido A, Fujitani N, Susukida R, Hara M, Oya M (2005) Y-chromosome STR haplotypes in a Bangladeshi population. Leg Med 7:122–126CrossRefGoogle Scholar
  41. 41.
    Nagy M, Henke L, Henke J et al (2007) Searching for the origin of Romanies: Slovakian Romani, Jats of Haryana and Jat Sikhs Y-STR data in comparison with different Romani populations. Forensic Sci Int 169:19–26PubMedCrossRefGoogle Scholar
  42. 42.
    Woźniak M, Derenko M, Malyarchuk B et al (2006) Allelic and haplotypic frequencies at 11 Y-STR loci in Buryats from South-East Siberia. Forensic Sci Int 164:271–275PubMedCrossRefGoogle Scholar
  43. 43.
    Parkin EJ, Kraayenbrink T, van Driem GL, Tshering Of Gaselô K, de Knijff P, Jobling MA (2006) 26-Locus Y-STR typing in a Bhutanese population sample. Forensic Sci Int 161:1–7PubMedCrossRefGoogle Scholar
  44. 44.
    Rohlf F (2002) NTSYSpc. Exter, SetauketGoogle Scholar
  45. 45.
    Felsentein J (2002) Phylogeny inference package (PHYLIP), version 3.6a3. Department of Genetics, University of Washington, Seattle, distributed by authorGoogle Scholar
  46. 46.
    Kayser M, Brauer S, Weiss G et al (2003) Reduced Y-chromosome, but not mitochondrial DNA, diversity in human populations from West New Guinea. Am J Hum Genet 72:281–302PubMedCrossRefGoogle Scholar
  47. 47.
    Polzin T, Daneschmand SV (2002) On Steiner trees and minimum spanning trees in hypergraphs. Oper Res Lett 31:12–20CrossRefGoogle Scholar
  48. 48.
    Ferri G, Robino C, Alù M et al. (2008) Molecular characterisation and population genetics of the DYS458.2 allelic variant. Forensic Sci Int Genet: Genetics Supplement Series, Progress in Forensic Genetics 12—Proceedings of the 22nd International ISFG Congress, vol. 1, pp 203–205Google Scholar
  49. 49.
    Cadenas AM, Regueiro M, Gayden T, Singh N, Zhivotovsky LA, Underhill PA, Herrera RJ (2007) Male amelogenin dropouts: phylogenetic context, origins and implications. Forensic Sci Int 166:155–163PubMedCrossRefGoogle Scholar
  50. 50.
    Thangaraj K, Reddy AG, Singh L (2002) Is the amelogenin gene reliable for gender identification in forensic casework and prenatal diagnosis? Int J Leg Med 116:121–123CrossRefGoogle Scholar
  51. 51.
    Santos FR, Pandya A, Tyler-Smith C (1998) Reliability of DNA-based sex tests. Nat Genet 18:103PubMedCrossRefGoogle Scholar
  52. 52.
    Wen B, Xie X, Gao S (2004) Analyses of genetic structure of Tibeto-Burman populations reveals sex-biased admixture in southern Tibeto-Burmans. Am J Hum Genet 74:856–865PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Tenzin Gayden
    • 1
    • 2
  • Shilpa Chennakrishnaiah
    • 2
    • 3
  • Joel La Salvia
    • 2
    • 3
  • Sacha Jimenez
    • 2
    • 3
  • Maria Regueiro
    • 2
  • Trisha Maloney
    • 1
    • 2
  • Patrice J. Persad
    • 1
    • 2
  • Areej Bukhari
    • 1
    • 2
  • Annabel Perez
    • 1
    • 2
  • Oliver Stojkovic
    • 4
  • Rene J. Herrera
    • 1
    • 2
  1. 1.Department of Biological SciencesFlorida International UniversityMiamiUSA
  2. 2.Department of Molecular and Human Genetics, College of MedicineFlorida International UniversityMiamiUSA
  3. 3.Department of Chemistry and BiochemistryFlorida International UniversityMiamiUSA
  4. 4.Institute of Forensic Medicine, Faculty of MedicineUniversity of BelgradeBelgradeSerbia

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