Skip to main content
Log in

Analysis of Y-chromosomal SNP haplogroups and STR haplotypes in an Algerian population sample

International Journal of Legal Medicine Aims and scope Submit manuscript

Abstract

The distribution of Y-chromosomal single nucleotide polymorphism (SNP) haplogroups and short tandem repeat (STR) haplotypes was determined in a sample of 102 unrelated men of Arab origin from northwestern Algeria (Oran area). A total of nine different haplogroups were identified by a panel of 22 binary markers. The most common haplogroups observed in the Algerian population were E3b2 (45.1%) and J1 (22.5%). Y-STR typing by a 17-loci multiplex system allowed 93 haplotypes to be defined (88 were unique). Striking differences in the allele distribution and gene diversity of Y-STR markers between haplogroups could be found. In particular, intermediate alleles at locus DYS458 specifically characterized the haplotypes of individuals carrying haplogroup J1. All the intermediate alleles shared a common repeat sequence structure, supporting the hypothesis that the variant originated from a single mutational event.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

References

  1. Gusmao 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 120:191–200

    Article  PubMed  CAS  Google Scholar 

  2. Willuweit S, Roewer L (2007) Y chromosome haplotype reference database (YHRD): Update. FSI: Genetics 1:83–87

    Google Scholar 

  3. Jobling MA (2001) Y-chromosomal SNP haplotype diversity in forensic analysis. Forensic Sci Int 118:158–162

    Article  PubMed  CAS  Google Scholar 

  4. Wetton JH, Tsang KW, Khan H (2005) Inferring the population of origin of DNA evidence within the UK by allele-specific hybridization of Y-SNPs. Forensic Sci Int 152:45–53

    Article  PubMed  CAS  Google Scholar 

  5. Brion M, Sanchez JJ, Balogh K et al (2005) Introduction of an single nucleodite polymorphism-based “Major Y-chromosome haplogroup typing kit” suitable for predicting the geographic origin of male lineages. Electrophoresis 26:4411–4420

    Article  PubMed  CAS  Google Scholar 

  6. Miller SA, Dykes DD, Polesky HF (1988) A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res 16:1215

    Article  PubMed  CAS  Google Scholar 

  7. Cinnioglu C, King R, Kivisild T et al (2004) Excavating Y-chromosome haplotype strata in Anatolia. Hum Genet 114:127–148

    Article  PubMed  Google Scholar 

  8. Oefner PJ, Underhill PA (1998) DNA mutation detection using denaturing high performance liquid chromatography (DHPLC). In: Dracopoli NC et al (eds) Current protocols in human genetics, Suppl 19. Wiley, NewYork, pp 7.10.1–7.10.12

    Google Scholar 

  9. Jobling MA, Tyler-Smith C (2003) The human Y chromosome: an evolutionary marker comes of age. Nat Rev Genet 4:598–612

    Article  PubMed  CAS  Google Scholar 

  10. Schoske R, Vallone PM, Kline MC, Redman JW, Butler JM (2004) High-throughput Y-STR typing of U.S. populations with 27 regions of the Y chromosome using two multiplex PCR assays. Forensic Sci Int 139:107–121

    Article  PubMed  CAS  Google Scholar 

  11. Schneider S, Roessli D, Excoffier L (2000) Arlequin Version 2.000: A Software for Population Genetics Data Analysis, Genetics and Biometry Laboratory, University of Geneva, Switzerland

  12. Felsenstein J (1989) PHYLIP: phylogeny inference package (version 3.2). Cladistics 5:164–166

    Google Scholar 

  13. Delfiner P (1976) Linear estimation of non-stationary spatial phenomena. In: Guarasio M, David M, Haijbegts C (eds) Advanced geostatistics in the mining industry. Reidel, Dordrecht, pp 49–68

    Google Scholar 

  14. Arredi B, Poloni ES, Paracchini S et al (2004) A predominantly neolithic origin for Y-chromosomal DNA variation in North Africa. Am J Hum Genet 75:338–345

    Article  PubMed  CAS  Google Scholar 

  15. Cruciani F, La Fratta R, Santolamazza P et al (2004) Phylogeographic analysis of haplogroup E3b (E-M215) Y chromosomes reveals multiple migratory events within and out of Africa. Am J Hum Genet 74:1014–1022

    Article  PubMed  CAS  Google Scholar 

  16. Semino O, Magri C, Benuzzi G et al (2004) Origin, diffusion, and differentiation of Y-chromosome haplogroups E and J: inferences on the neolithization of Europe and later migratory events in the Mediterranean area. Am J Hum Genet 74:1023–1034

    Article  PubMed  CAS  Google Scholar 

  17. Di Giacomo F, Luca F, Popa LO et al (2004) Y chromosomal haplogroup J as a signature of the post-neolithic colonization of Europe. Hum Genet 115:357–371

    Article  PubMed  CAS  Google Scholar 

  18. Quintana-Murci L, Bigham A, Rouba H, Barakat A, McElreavey K, Hammer M (2004) Y-chromosomal STR haplotypes in Berber and Arabic-speaking populations from Morocco. Forensic Sci Int 140:113–115

    Article  PubMed  CAS  Google Scholar 

  19. Cherni L, Pereira L, Goios A et al (2005) Y-chromosomal STR haplotypes in three ethnic groups and one cosmopolitan population from Tunisia. Forensic Sci Int 152:95–99

    Article  PubMed  CAS  Google Scholar 

  20. Frigi S, Pereira F, Pereira L et al (2006) Data for Y-chromosome haplotypes defined by 17 STRs (AmpFLSTR Yfiler) in two Tunisian Berber communities. Forensic Sci Int 160:80–83

    Article  PubMed  CAS  Google Scholar 

  21. Alves C, Gomes V, Prata MJ, Amorim A, Gusmao L (2007) Population data for Y-chromosome haplotypes defined by 17 STRs (AmpFlSTR YFiler) in Portugal. Forensic Sci Int DOI 10.1016/j.forsciint.2006.10.002

  22. Robino C, Inturri S, Gino S et al (2006) Y-chromosomal STR haplotypes in Sicily. Forensic Sci Int 159:235–240

    Article  PubMed  CAS  Google Scholar 

  23. Gonzalez-Neira A, Gusmao L, Brion M, Lareu MV, Amorim A, Carracedo A (2000) Distribution of Y-chromosome STR defined haplotypes in Iberia. Forensic Sci Int 110:117–126

    Article  PubMed  CAS  Google Scholar 

  24. Bosch E, Calafell F, Santos FR et al (1999) Variation in short tandem repeats is deeply structured by genetic background on the human Y chromosome. Am J Hum Genet 65:1623–1638

    Article  PubMed  CAS  Google Scholar 

  25. Mulero JJ, Chang CW, Calandro LM, Green RL, Li Y, Johnson CL, Hennessy LK (2006) Development and validation of the AmpFlSTR Yfiler PCR amplification kit: a male specific, single amplification 17 Y-STR multiplex system. J Forensic Sci 51:64–75

    Article  PubMed  CAS  Google Scholar 

  26. Onofri V, Alessandrini F, Turchi C, Fraternale B, Buscemi L, Pesaresi M, Tagliabracci A (2007) Y-chromosome genetic structure in sub-Apennine populations of Central Italy by SNP and STR analysis. Int J Legal Med 121:234–237

    Article  PubMed  Google Scholar 

  27. Sobrino B, Brion M, Carracedo A (2005) SNPs in forensic genetics: a review on SNP typing methodologies. Forensic Sci Int 154:181–194

    Article  PubMed  CAS  Google Scholar 

  28. Nebel A, Filon D, Brinkmann B, Majumder PP, Faerman M, Oppenheim A (2001) The Y chromosome pool of Jews as part of the genetic landscape of the Middle East. Am J Hum Genet 69:1095–1112

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgements

The continuing support of the Compagnia di San Paolo to C. Torre’s laboratory is gratefully acknowledged. We also thank Dr Boudjema A, Medienne Benchekor S and Meghoufel N for assistance in the collection of the samples.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to C. Robino.

Electronic supplementary material

Below is the link to the Electronic supplementary material.

Fig. S1

NJ tree forAlgerian Arabs “A-AR”(n = 102) and 11 reference populations: Algerian Berbers “A-B”(n = 16), northern “E-N”(n = 47) and southern Egyptians “E-S”(n = 50) [14]; Moroccan Arabs “M-AR”(n = 60), Moroccan Berbers “M-B”(n = 49) [18]; Andalusians“T-AN”(n = 132) and cosmopolitan (Tunisi) “T-T”Tunisians (n = 54) [19]; Tunisian Berbers “T-B”(n = 66) [20]; Portuguese “POR”(n = 250) [21]; Sicilians “SIC”(n = 255) [22]; Spaniards from Andalusia “SPA”(n = 56) [23] (PDF 14 KB)

Table S1

Complete Y-SNP typing results and haplogroups observed in the Algerian population sample (XLS 28 KB)

Table S2

Complete list of Y-chromosomal haplotypes observed in the Algerian population sample (XLS 32 KB)

Table S3

Pairwise distance (RST) between Algerian Arabs (A-AR) and eleven reference populations: Algerian Berbers “A-B” (n = 16), northern “E-N” (n = 47) and southern Egyptians “E-S” (n = 50) [14]; Moroccan Arabs “M-AR” (n = 60), Moroccan Berbers “M-B” (n = 49) [18]; Andalusians “T-AN” (n = 132) and cosmopolitan (Tunisi) “T-T” Tunisians (n = 54) [19]; Tunisian Berbers “T-B” (n = 66) [20]; Portuguese “POR” (n = 250) [21]; Sicilians “SIC” (n = 255) [22]; Spaniards from Andalusia “SPA” (n = 56) [23]. RST and p values are shown below and above the diagonal, respectively. Significant comparisons are shown in bold (PDF 30 KB)

Table S4

Most frequent Y-STR alleles within major haplogroups found in the Algerian population sample (unique alleles are underlined) (PDF 24 KB)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Robino, C., Crobu, F., Di Gaetano, C. et al. Analysis of Y-chromosomal SNP haplogroups and STR haplotypes in an Algerian population sample. Int J Legal Med 122, 251–255 (2008). https://doi.org/10.1007/s00414-007-0203-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00414-007-0203-5

Keywords

Navigation