Good things come in pairs, so a little after the recent publication of a paper on the Y chromosomes of Afghanistan, there is yet another paper on the same topic. There is some quite useful information in the open access supplementary material, including a table of haplogroup R-M198 and R-M198*(xM458) frequencies in a wide range of human populations.
Unfortunately, this paper too was probably written before the current developments in the R1a world, and did not take advantage of the newer discovered SNPs. Hopefully the DNA samples can be eventually tested in more phylogenetic detail.
European Journal of Human Genetics advance online publication 18 April 2012; doi: 10.1038/ejhg.2012.59
Afghanistan from a Y-chromosome perspective
Harlette Lacau et al.
Central Asia has served as a corridor for human migrations providing trading routes since ancient times. It has functioned as a conduit connecting Europe and the Middle East with South Asia and far Eastern civilizations. Therefore, the study of populations in this region is essential for a comprehensive understanding of early human dispersal on the Eurasian continent. Although Y- chromosome distributions in Central Asia have been widely surveyed, present-day Afghanistan remains poorly characterized genetically. The present study addresses this lacuna by analyzing 190 Pathan males from Afghanistan using high-resolution Y-chromosome binary markers. In addition, haplotype diversity for its most common lineages (haplogroups R1a1a*-M198 and L3-M357) was estimated using a set of 15 Y-specific STR loci. The observed haplogroup distribution suggests some degree of genetic isolation of the northern population, likely due to the Hindu Kush mountain range separating it from the southern Afghans who have had greater contact with neighboring Pathans from Pakistan and migrations from the Indian subcontinent. Our study demonstrates genetic similarities between Pathans from Afghanistan and Pakistan, both of which are characterized by the predominance of haplogroup R1a1a*-M198 (>50%) and the sharing of the same modal haplotype. Furthermore, the high frequencies of R1a1a-M198 and the presence of G2c-M377 chromosomes in Pathans might represent phylogenetic signals from Khazars, a common link between Pathans and Ashkenazi groups, whereas the absence of E1b1b1a2-V13 lineage does not support their professed Greek ancestry.