• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of ajhgLink to Publisher's site
Am J Hum Genet. Sep 1999; 65(3): 829–846.
PMCID: PMC1377990

Combined use of biallelic and microsatellite Y-chromosome polymorphisms to infer affinities among African populations.


To define Y-chromosome haplotypes, we studied seven biallelic polymorphic sites. We combined data with those from four dinucleotide-repeat polymorphisms, to establish Y-chromosome compound superhaplotypes. Eight biallelic haplotypes that matched the dendrogram proposed by other investigators were identified in 762 Y chromosomes from 25 African populations. For each biallelic site, coalescence time of lineages carrying the derived allele was estimated and compared with previous estimates. The "ancestral" haplotype (haplotype 1A) was observed among Ethiopians, "Khoisan" (!Kung and Khwe), and populations from northern Cameroon. Microsatellite distributions within this haplotype showed that the Khoisan haplotypes 1A are widely divergent from those of the other two groups. Populations from northern Africa and northern Cameroon share a haplotype (i.e., 1C), which is not observed in other African populations but represents a major Eurasian cluster. Haplotypes 1C of northern Cameroon are clearly distinct from those of Europe, whereas haplotypes 1C of northern African are well intermingled with those of the other two groups. Apportionment of diversity for the Y-chromosomal biallelic haplotypes was calculated after populations were clustered into different configurations. Despite some correspondence between language affiliation and genetic similarity, geographic proximity seems to be a better predictor of genetic affinity.

Full Text

The Full Text of this article is available as a PDF (351K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Altheide TK, Hammer MF. Evidence for a possible Asian origin of YAP+ Y chromosomes. Am J Hum Genet. 1997 Aug;61(2):462–466. [PMC free article] [PubMed]
  • Biondi G, Rickards O, Martinez-Labarga C, Taraborelli T, Ciminelli B, Gruppioni G. Biodemography and genetics of the Berba of Benin. Am J Phys Anthropol. 1996 Apr;99(4):519–535. [PubMed]
  • Bottema CD, Sommer SS. PCR amplification of specific alleles: rapid detection of known mutations and polymorphisms. Mutat Res. 1993 Jul;288(1):93–102. [PubMed]
  • Cooper G, Amos W, Hoffman D, Rubinsztein DC. Network analysis of human Y microsatellite haplotypes. Hum Mol Genet. 1996 Nov;5(11):1759–1766. [PubMed]
  • Destro-Bisol G, Battaggia C, Macchiarelli R, Bailly C, Scozzari MR, Spedini G. A bio-anthropological study on the Bakakas of Cameroon. Ann Hum Biol. 1992 Mar-Apr;19(2):185–195. [PubMed]
  • Excoffier L, Smouse PE, Quattro JM. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics. 1992 Jun;131(2):479–491. [PMC free article] [PubMed]
  • Fort M, de Stefano GF, Cambon-Thomsen A, Giraldo-Alvarez P, Dugoujon JM, Ohayon E, Scano G, Abbal M. HLA class II allele and haplotype frequencies in Ethiopian Amhara and Oromo populations. Tissue Antigens. 1998 Apr;51(4 Pt 1):327–336. [PubMed]
  • Goldstein DB, Reich DE, Bradman N, Usher S, Seligsohn U, Peretz H. Age estimates of two common mutations causing factor XI deficiency: recent genetic drift is not necessary for elevated disease incidence among Ashkenazi Jews. Am J Hum Genet. 1999 Apr;64(4):1071–1075. [PMC free article] [PubMed]
  • Goldstein DB, Ruiz Linares A, Cavalli-Sforza LL, Feldman MW. Genetic absolute dating based on microsatellites and the origin of modern humans. Proc Natl Acad Sci U S A. 1995 Jul 18;92(15):6723–6727. [PMC free article] [PubMed]
  • Goldstein DB, Zhivotovsky LA, Nayar K, Linares AR, Cavalli-Sforza LL, Feldman MW. Statistical properties of the variation at linked microsatellite loci: implications for the history of human Y chromosomes. Mol Biol Evol. 1996 Nov;13(9):1213–1218. [PubMed]
  • Hammer MF. A recent common ancestry for human Y chromosomes. Nature. 1995 Nov 23;378(6555):376–378. [PubMed]
  • Hammer MF, Horai S. Y chromosomal DNA variation and the peopling of Japan. Am J Hum Genet. 1995 Apr;56(4):951–962. [PMC free article] [PubMed]
  • Hammer MF, Karafet T, Rasanayagam A, Wood ET, Altheide TK, Jenkins T, Griffiths RC, Templeton AR, Zegura SL. Out of Africa and back again: nested cladistic analysis of human Y chromosome variation. Mol Biol Evol. 1998 Apr;15(4):427–441. [PubMed]
  • Hammer MF, Spurdle AB, Karafet T, Bonner MR, Wood ET, Novelletto A, Malaspina P, Mitchell RJ, Horai S, Jenkins T, et al. The geographic distribution of human Y chromosome variation. Genetics. 1997 Mar;145(3):787–805. [PMC free article] [PubMed]
  • Karafet TM, Zegura SL, Posukh O, Osipova L, Bergen A, Long J, Goldman D, Klitz W, Harihara S, de Knijff P, et al. Ancestral Asian source(s) of new world Y-chromosome founder haplotypes. Am J Hum Genet. 1999 Mar;64(3):817–831. [PMC free article] [PubMed]
  • Li H, Cui X, Arnheim N. Direct electrophoretic detection of the allelic state of single DNA molecules in human sperm by using the polymerase chain reaction. Proc Natl Acad Sci U S A. 1990 Jun;87(12):4580–4584. [PMC free article] [PubMed]
  • Malaspina P, Ciminelli BM, Viggiano L, Jodice C, Cruciani F, Santolamazza P, Sellitto D, Scozzari R, Terrenato L, Rocchi M, et al. Characterization of a small family (CAIII) of microsatellite-containing sequences with X-Y homology. J Mol Evol. 1997 Jun;44(6):652–659. [PubMed]
  • Malaspina P, Cruciani F, Ciminelli BM, Terrenato L, Santolamazza P, Alonso A, Banyko J, Brdicka R, García O, Gaudiano C, et al. Network analyses of Y-chromosomal types in Europe, northern Africa, and western Asia reveal specific patterns of geographic distribution. Am J Hum Genet. 1998 Sep;63(3):847–860. [PMC free article] [PubMed]
  • Mathias N, Bayés M, Tyler-Smith C. Highly informative compound haplotypes for the human Y chromosome. Hum Mol Genet. 1994 Jan;3(1):115–123. [PubMed]
  • Persichetti F, Blasi P, Hammer M, Malaspina P, Jodice C, Terrenato L, Novelletto A. Disequilibrium of multiple DNA markers on the human Y chromosome. Ann Hum Genet. 1992 Oct;56(Pt 4):303–310. [PubMed]
  • Poloni ES, Semino O, Passarino G, Santachiara-Benerecetti AS, Dupanloup I, Langaney A, Excoffier L. Human genetic affinities for Y-chromosome P49a,f/TaqI haplotypes show strong correspondence with linguistics. Am J Hum Genet. 1997 Nov;61(5):1015–1035. [PMC free article] [PubMed]
  • Reich DE, Goldstein DB. Genetic evidence for a Paleolithic human population expansion in Africa. Proc Natl Acad Sci U S A. 1998 Jul 7;95(14):8119–8123. [PMC free article] [PubMed]
  • Santos FR, Bianchi NO, Pena SD. Worldwide distribution of human Y-chromosome haplotypes. Genome Res. 1996 Jul;6(7):601–611. [PubMed]
  • Santos FR, Pandya A, Tyler-Smith C, Pena SD, Schanfield M, Leonard WR, Osipova L, Crawford MH, Mitchell RJ. The central Siberian origin for native American Y chromosomes. Am J Hum Genet. 1999 Feb;64(2):619–628. [PMC free article] [PubMed]
  • Santos FR, Pena SD, Tyler-Smith C. PCR haplotypes for the human Y chromosome based on alphoid satellite DNA variants and heteroduplex analysis. Gene. 1995 Nov 20;165(2):191–198. [PubMed]
  • Scozzari R, Cruciani F, Malaspina P, Santolamazza P, Ciminelli BM, Torroni A, Modiano D, Wallace DC, Kidd KK, Olckers A, et al. Differential structuring of human populations for homologous X and Y microsatellite loci. Am J Hum Genet. 1997 Sep;61(3):719–733. [PMC free article] [PubMed]
  • Seielstad MT, Hebert JM, Lin AA, Underhill PA, Ibrahim M, Vollrath D, Cavalli-Sforza LL. Construction of human Y-chromosomal haplotypes using a new polymorphic A to G transition. Hum Mol Genet. 1994 Dec;3(12):2159–2161. [PubMed]
  • Seielstad MT, Minch E, Cavalli-Sforza LL. Genetic evidence for a higher female migration rate in humans. Nat Genet. 1998 Nov;20(3):278–280. [PubMed]
  • Torroni A, Semino O, Scozzari R, Sirugo G, Spedini G, Abbas N, Fellous M, Santachiara Benerecetti AS. Y chromosome DNA polymorphisms in human populations: differences between Caucasoids and Africans detected by 49a and 49f probes. Ann Hum Genet. 1990 Oct;54(Pt 4):287–296. [PubMed]
  • Underhill PA, Jin L, Lin AA, Mehdi SQ, Jenkins T, Vollrath D, Davis RW, Cavalli-Sforza LL, Oefner PJ. Detection of numerous Y chromosome biallelic polymorphisms by denaturing high-performance liquid chromatography. Genome Res. 1997 Oct;7(10):996–1005. [PMC free article] [PubMed]
  • Weber JL, Wong C. Mutation of human short tandem repeats. Hum Mol Genet. 1993 Aug;2(8):1123–1128. [PubMed]
  • Whitfield LS, Sulston JE, Goodfellow PN. Sequence variation of the human Y chromosome. Nature. 1995 Nov 23;378(6555):379–380. [PubMed]

Articles from American Journal of Human Genetics are provided here courtesy of American Society of Human Genetics


Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


  • Cited in Books
    Cited in Books
    PubMed Central articles cited in books
  • PubMed
    PubMed citations for these articles

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...