African and Levantine origins of Pakistani YAP(+) Y chromosomes

We surveyed 9 Pakistani subpopulations for variation on the nonrecombining portion of the Y chromosome. The polymorphic systems examined were the Y-ch romosome Alu insertion polymorphism (YAP) at DYS287, 5 single nucleotide po lymorphisms, and the tetranucleotide microsatellite DYS19. Y chromosomes ca rrying the YAP element (YAP(+)) were found in populations from southwestern Pakistan at frequencies ranging from 2% to 8%, whereas northeastern popula tions appeared to lack YAP(+) chromosomes. In contrast to other South Asian populations, several Pakistani subpopulations had a high frequency of the DYS19*B allele, the most frequent allele in West Asian, North African, and European populations. The combination of alleles at all poly morphic sites gave rise to 9 YAP-DYS19 combination haplotypes in Pakistani populations, i ncluding 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 migrat ory routes to Pakistan: YAP(+) haplotype 5 may have entered Pakistan from t he Arabian Peninsula by means of migrations across the Gulf of Oman, wherea s males possessing YAP(+) haplotype 4 may have traveled over land from the Middle East. These inferences are consistent with ethnohistorical data sugg esting that Pakistan's ethnic groups have been influenced by migrations fro m both African and Levantine source populations.