1. ¹Biomedical and Genetic Engineering Division, Dr. AQ Khan Research Laboratories, Islamabad, Pakistan
2. ²Unit of Prenatal Diagnosis, Center for Thalassemia, Laiko General Hospital, Athens, Greece
3. ³The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
4. ⁴Department of Genetics, Stanford University, Stanford, CA, USA

Correspondence: Dr Q Ayub, Biomedical and Genetic Engineering Division, Dr AQ Khan Research Laboratories, GPO Box 2891, Islamabad 44000, Pakistan. Tel: +92 51 926 1142; Fax: +92 51 926 1144; E-mail:qayub@comsats.net.pk

Received 16 November 2005; Revised 9 August 2006; Accepted 1 September 2006; Published online 18 October 2006.

Abstract

Three Pakistani populations residing in northern Pakistan, the Burusho, Kalash and Pathan claim descent from Greek soldiers associated with Alexander's invasion of southwest Asia. Earlier studies have excluded a substantial Greek genetic input into these populations, but left open the question of a smaller contribution. We have now typed 90 binary polymorphisms and 16 multiallelic, short-tandem-repeat (STR) loci mapping to the male-specific portion of the human Y chromosome in 952 males, including 77 Greeks in order to re-investigate this question. In pairwise comparisons between the Greeks and the three Pakistani populations using genetic distance measures sensitive to recent events, the lowest distances were observed between the Greeks and the Pathans. Clade E3b1 lineages, which were frequent in the Greeks but not in Pakistan, were nevertheless observed in two Pathan individuals, one of whom shared a 16 Y-STR haplotype with the Greeks. The worldwide distribution of a shortened (9 Y-STR) version of this haplotype, determined from database information, was concentrated in Macedonia and Greece, suggesting an origin there. Although based on only a few unrelated descendants, this provides strong evidence for a European origin for a small proportion of the Pathan Y chromosomes.