Somehow I can't open the article suggested in the OP. However recent genetic studies suggest that Most of the Indians carry two distinct lines of genetic pool known as Ancestral north Indian (ANI) and Ancestral south Indian (ASI). Now generally the proportion of ASI is higher in south Indians in comparision to north Indians and same is true for the ANI. (however this is just generalization and not the rule) Besides ANI has also been found to be associated with the Europeans. However this intermixing of ANI and ASI has occured for almost 10000 years ago which predates the supposed time period of Aryan invasion theory for a long interval which is around 1500 BCE. So higher proportion of ANI in north Indians doesn't support the Aryan invasion theory, as the population has already been present in the subcontinent for atleast 10000 years.
Now castes like UP brahmins and Punjabi Khatris do have much higher proportion of the R1a1 haplotype than the rest of the population (which is also seen in some European population). but then again many south Indian tribes like Chenchus also have the higher proportion of R1a1!!! So R1a1 mutation doesn't go in favour of Aryan invasion theory either.
Besides European population which carries the R1a1 mutation also carries M458 mutation which isn't seen in Indian population. And again this mutation is estimated to have occured around 8000 years ago. which again not only suggests that the two population seperated a long time ago before the proposed date of Aryan invasion theory but it also suggests that original population cotaining R1A1 actuaaly migrated from Indian subcontinent to the Europe as M458 mutation is seen only in the European population.