The Y-chromosomal lineages and their frequencies in the Greeks, Burusho, Kalash, Pathan and the rest of the Pakistani population are shown in . The combination of biallelic markers identified 12 Y-chromosomal haplogroups or lineages in the Greeks, 17 in the Burusho and 15 in the Pathan populations. Only 8 Y lineages were found in the Kalash population. Principal component analysis of Y haplogroup frequencies incorporating published data from European17
and West Asian 18, 19
populations (data not shown) revealed that the Pakistani populations cluster together, separately from the Europeans, consistent with the previous conclusion that none of the Pakistani populations had a large male contribution from Greece, and demonstrating that this conclusion was not an artifact of the low phylogenetic resolution used before. The genetic distances between the populations were then calculated using measures that are more sensitive to recent events (). Pakistani-Greek population pairwise ΦST
values based on the variation of STRs within haplogroups 6
ranged from 0.131 to 0.213, with the lowest value between the Pathan and the Greeks. Pairwise ρ genetic distances (the number of steps between a haplotype in one population and the closest haplotype in the second population, averaged over all comparisons) 15
ranged from 4.3 to 8.1, with the lowest value again between the Pathan and the Greeks. These results therefore suggest that there might have been a low degree of recent Pathan-Greek admixture. To investigate this possibility further, we have examined individual lineages.
Figure 1 A. rooted maximum-parsimony tree of Y lineages found in the Greek, Burusho, Kalash, Pathan and Pakistan. The lineages were defined by binary markers whose designations and population frequencies are given below each branch. The YCC lineage names 10 are (more ...)
Weighted population pairwise rho genetic distances (below diagonal) and ΦST values (above diagonal) based on STR variation within haplogroups
Clade E lineages were more frequent in the Greeks (21%) as compared to Pakistan (4%). The majority of haplogroup E chromosomes belonged to clade E3b and all Greek and Pakistani samples were resolved into the branches E3b1 (M78) and E3b3 (M123). Among the three Pakistani populations claiming Greek descent, this clade was observed only in the Pathans. The Pathan samples belonged to clade E3b1 which constituted 17% of the Greek samples.
A median-joining network of clade E Y chromosomes was constructed in order to examine the genetic relationship between these Greek and Pathan samples. A duplication of 10 and 13 repeat units was observed in the clade-E-derived Y chromosomes for the trinucleotide repeat DYS425 and this locus was, therefore, excluded from the network. The most striking feature of this network was the sharing of haplotypes between the Pathan and Greek samples (). One Pathan individual shared the same Y-STR haplotype with three Greek individuals, and the other Pathan sample was separated from this cluster by a single mutation at the DYS436 locus. This demonstrates a very close relationship between the Pathan and Greek E lineages, but how surprising is this?
Median-Joining network of clade E lineages in Pakistan (open circles) and Greece (hatched circles). Circles represent haplotypes and have an area proportional to frequency. The Pathan individuals are shown in black.
Worldwide data for the 16-element haplotype are not available, but a subset of nine of the STRs are included in by the Y-STR Haplotype Reference Database (YHRD) 20
and were used to search this. The haplotype DYS19=13; 389I=13; 389II=30; 390=24; 391=10; 392=11; 393=13; 438=10; 439=12 was found in 53 individuals in a worldwide population sample of 7,897 haplotypes and was highly specific for the Balkans (). The contour map shows a major concentration around Macedonia and Greece, with a low scattering in other European countries, Tunisia, West Africa and the Pathans. This gives a strong indication of a European, possibly Greek, origin of these Pathan Y chromosomes.
Contour map showing the 9 Y-STR haplotype frequency distribution in Eurasia and northern Africa. This haplotype was shared between three Greeks and a Pathan individual belonging to clade E3b1.