African and Levantine origins of Pakistani YAP+ Y chromosomes

R. Qamar, Q. Ayub, S. Khaliq, A. Mansoor, T. Karafet, S. Q. Mehdi, M. F. Hammer

Research output: Contribution to journalArticlepeer-review

23 Scopus citations


We surveyed 9 Pakistani subpopulations for variation on the nonrecombining portion of the Y chromosome. The polymorphic systems examined were the Y-chromosome Alu insertion polymorphism (YAP) at DYS287, 5 single nucleotide polymorphisms, and the tetranucleotide microsatellite DYS19. Y chromosomes carrying the YAP element (YAP+) were found in populations from southwestern Pakistan at frequencies ranging from 2% to 8%, whereas northeastern populations appeared to lack YAP+ chromosomes. In contrast to other South Asian populations, several Pakistani subpopulations had a high frequency of the DYSJ9*B allele, the most frequent allele in West Asian, North African, and European populations. The combination of alleles at all polymorphic sites gave rise to 9 YAP-DYS19 combination haplotypes in Pakistani populations, including YAP+ haplotypes 4-A, 4-B, 5-C, and 5-E. We hypothesize that the geographic distributions of YAP+ haplotypes 4 and 5 trace separate migratory routes to Pakistan: YAP+ haplotype 5 may have entered Pakistan from the Arabian Peninsula by means of migrations across the Gulf of Oman, whereas males possessing YAP+ haplotype 4 may have traveled over land from the Middle East. These inferences are consistent with ethnohistorical data suggesting that Pakistan's ethnic groups have been influenced by migrations from both African and Levantine source populations.

Original languageEnglish (US)
Pages (from-to)745-755
Number of pages11
JournalHuman biology
Issue number5
StatePublished - Oct 1999


  • Male migration
  • Pakistan
  • Y-chromosome haplotypes

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Genetics(clinical)


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