Three Pakistani populations claim descent from Greek soldiers during the time of Alexander the Great of Macedonia's conquest of the Greek world and eastward to India in the 4th century BC. The authors of this paper investigated these claims using Y-chromosome single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs).
These claims had been investigated previously, finding no evidence in one case and ambiguous data in another. The present study provides strong evidence that a minority of the Pathan men do show Y-chromosomes similar to those in Greek populations, these being in the E3b1 subclade. One Pathan 16-loci Y-STR haplotype was shared with three Greeks.
The authors searched the Y-STR Haploytpe Reference Database for this nine-loci haplotype: DYS19=13, DYS389i=13, DYS389ii=30, DYS390=24, DYS391=10, DYS392=11, DYS393=13, DYS438=10, DYS439=12. They found 53 individuals with this haploype which maps to the Balkans and is concentrated around Macedonia and Greece.
In addition to the the army of Alexander the Great as the source of E3b1 chromosomes in some Pathan men, Greek slaves were also imported into the Persian Empire during the reign of Xerxes (about 150 years before Alexander) and this source cannot be eliminated as a possible source found in this study.
Reference: Firasat, Sadaf et al. , Y-chromosomal evidence for a limited Greek contribution to the Pathan population of Pakistan, European Journal of Human Genetics (2006), 1–6