The study cited above is the most recent (published 2011). There are two astonishing results from the study i.e.,

• the north population (non-Pashtuns) and south population (Pashtuns) are genetically distinct with the northern group exihibiting more genetic diversity than the southern group. The authors ascribe the higher diversity to the impact of Silk route which facilitated population interaction. The southern population (Pashtuns) were relatively isolated and so have less gene diversity. Furthermore, the authors attribute gene segregation between the two population to the role of Hindukush which formed a barrier to gene flow between north and south populations. The authors even propose assiging different population ids to the two population based on the genetic differences between the two.
• another interesting result is the degree to which contributions have been made to the two population by other genetically similar populations. According to authors, population of the northern Afghanistan is genetically more close to South Central Asian population compared to the southern population, which is genetically more close to two populations i.e., Lipezkaja and Penzenskaja in Southwest Russia. According to authors, Southwestern Russian population has made 94.4% contribution to Southern Population whereas to the northern population, it has made some 62% contribution (26% of the northern pop gene pool comes from South Central Asia).

Pashtun are not pure either.  There is some Haplogroup J among them (evidence of Arabic genetic contributions in Iran, Afghanistan, northern India areas).  They also found a couple percent Haplogroup O among them (East Asian or Central Asian influence).