Here another chart from a scientific paper published in 2013, confirming the story again as well.
The Pakistani Pashtuns fall clear cut in the Indus Basin (South Asia) cluster, while the Afghan Pashtuns are extremely close to it. One sample lies deeper into the Central Asian cluster, most likely as a deviating example. However, even then, drawing a horizontal line on the axis it still makes them closer to the Indus Basin cluster, than the Caucasus or Middle East cluster, which is totally obivous as well looking at geography and history. Keep also in mind that the largest population of ethnic Pashtuns in the world live in Pakistan,
not in Afghanistan.
http://i62.tinypic.com/e0qqtx.png
Analysis from the paper the graph is from:
source: Afghan Hindu Kush: Where Eurasian Sub-Continent Gene Flows Converge. MC: Julie Di Cristofaro, Erwan Pennarun. Published October 18, 2013.
http://www.plosone.org/article/info%...l.pone.0076748