Skip to main content

Y-STR loci diversity in native Alaskan populations


Y chromosome short tandem repeat (Y-STR) loci are important genetic markers for forensic biological evidence analyses. However, paternal inheritance, reduced effective population size, and lack of independence between loci can reduce Y-STR diversity and may yield greater population substructure effects on a locus-by-locus basis compared with the autosomal STR loci. Population studies are necessary to assess the genetic variation of forensically relevant markers so that proper inferences can be made about the rarity of DNA profiles. This study examined 16 Y-STRs in three sampled populations of Native Americans from Alaska: Inupiat, Yupik, and Athabaskan. Population genetic and statistical issues addressed were: (1) the degree of diversity at locus and haplotype levels, (2) determination of the loci that contribute more so to haplotype diversity, and (3) the effects of population substructure on forensic statistical calculations of the rarity of a Y-STR profile. All three population samples were highly polymorphic at the haplotype level for the 16 Y-STR markers; however, the Native Americans demonstrated reduced genetic diversity compared with major US populations. The degree of substructure indicated that the three populations were related and admixed in terms of paternal lineage. The examination of more polymorphic loci may be needed to increase the power of discrimination of Y-STR systems in these populations.

This is a preview of subscription content, access via your institution.

Fig. 1


  1. 1.

    Huntley K, Long J (2005) Gene flow across linguistic boundaries in Native North American populations. PNAS 102:1312–1317

    Article  Google Scholar 

  2. 2.

    Budowle B, Chidambaram A, Strickland L, Beheim C, Taft G, Chakraborty R (2002) Population studies on three Native Alaska population groups using STR loci. Forensic Sci Int 129:51–57

    PubMed  Article  CAS  Google Scholar 

  3. 3.

    Burch ES Jr (1979) Indians and Eskimos in North Alaska, 1816–1977: a study in changing ethnic relations. Arct Anthropol 16(2):123–151

    Google Scholar 

  4. 4.

    Hammond HA, Jin L, Zhong Y, Caskey CK, Chakraborty R (1994) Evaluation of 13 short tandem repeat loci for use in personal identification application. Am J Hum Genet 55(1):175–189

    PubMed  CAS  Google Scholar 

  5. 5.

    Szathmary E (1993) Genetics of aboriginal North Americans. Evol Anthropol 1(6):202–220

    Article  Google Scholar 

  6. 6.

    Hallenberg C, Tomas C, Simonsen B, Morling N (2009) Y-chromosome STR haplotypes in males from Greenland. Forensic Sci Int Genet 3(4):e145–e146

    PubMed  Article  CAS  Google Scholar 

  7. 7.

    Bosch E, Calafell F, Rosser Z, Nǿrby S, Lynnerup N, Hurles M, Jobling M (2003) High level of male-biased Scandinavian admixture in Greenlandic Inuit shown by Y-chromosomal analysis. Hum Genet 112:353–363

    PubMed  Google Scholar 

  8. 8.

    Budowle B, Adamowicz M, Aranda X, Barna C, Chakraborty R, Eisenberg AJ, Frappier R, Gross AM, Lee HS, Milne S, Prinz M, Saldanha G, Krenke BE (2005) Twelve short tandem repeat loci Y chromosome haplotypes: genetic analysis on populations residing in North America. Forensic Sci Int 150(1):1–15

    PubMed  Article  CAS  Google Scholar 

  9. 9.

    Budowle B, Ge J, Chakraborty R (2007) Basic principles for estimating the rarity of Y-STR haplotypes derived from forensic evidence. Eighteenth International Symposium on Human Identification 2007, Promega Corporation, Madison, Wisconsin. Available from:

  10. 10.

    Budowle B, Ge J, Aranda X, Planz J, Eisenberg A, Chakraborty R (2009) Texas population substructure and its impact on estimating the rarity of Y-STR haplotypes from DNA evidence. J Forensic Sci 54(5):1016–1021

    PubMed  Article  CAS  Google Scholar 

  11. 11.

    Budowle B, Ge J, Aranda X, 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 11:64–69

    Article  CAS  Google Scholar 

  12. 12.

    Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370

    Article  Google Scholar 

  13. 13.

    Nei M (1975) Molecular population genetics and evolution. North-Holland, Amsterdam, pp 149–150

    Google Scholar 

  14. 14.

    Slatkin M (1995) A measure of population subdivision based on microsatellite allele frequencies. Genetics 139:457–462

    PubMed  CAS  Google Scholar 

  15. 15.

    Matlab. Available from: Accessed on 10 Feb 2011

  16. 16.

    Ge J, Budowle B, Planz J, Eisenberg A, Ballantyne J, Chakraborty R (2010) US forensic Y chromosome short tandem repeats database. Leg Med 12(6):289–295

    Article  CAS  Google Scholar 

  17. 17.

    National Research Council (1996) The evaluation of forensic DNA evidence. National Academy Press, Washington

    Google Scholar 

  18. 18.

    Balding DJ, Nichols RA (1994) DNA profile match probability calculation: how to allow for population stratification, relatedness, database selection and single bands. Forensic Sci Int 64:125–140

    PubMed  Article  CAS  Google Scholar 

  19. 19.

    Ballantyne KN, Goedbloed M, Fang R, Schaap O, Lao O, Wollstein A, Choi Y, van Duijn K, Vermeulen M, Brauer S, Decorte R, Poetsch M, von Wurmb-Schwark N, de Knijff P, Labuda D, Vézina H, Knoblauch H, Lessig R, Roewer L, Ploski R, Dobosz T, Henke L, Henke J, Furtado MR, Kayser M (2010) Mutability of Y-chromosomal microsatellites: rates, characteristics, molecular bases, and forensic implications. Am J Hum Genet 87(3):341–353

    PubMed  Article  CAS  Google Scholar 

Download references

Author information



Corresponding author

Correspondence to Bruce Budowle.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Table 1

(XLS 102 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Davis, C., Ge, J., Chidambaram, A. et al. Y-STR loci diversity in native Alaskan populations. Int J Legal Med 125, 559–563 (2011).

Download citation


  • Forensic DNA analysis
  • Y chromosome
  • STR
  • Haplotype
  • Native American