There are two versions of the thesis of the paper: 1. The one as paraphrased by Sri Mohit M Rao, the journalist of the Hindu:

" For most upper-caste communities, endogamy (that is marrying within one’s caste) started nearly 70 generations ago, or around the time of the Hindu Gupta period around 1,500 years ago."

The title of the paper in PNAS is :

Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure.

The Hindu report limits the generalization of 'endogamy (that is marrying within one’s caste) started nearly 70 generations ago, or around the time of the Hindu Gupta period around 1,500 years ago' 'For most upper-caste communities' only. 

Whereas the title gives the impression that it is about the entire 'extant populations of India'. 

Given the extremely decentralized power structure of the premodern Indian society, it is implausible for endogamy to be 'enforced through the powerful state machinery ' across the  entire ' populations of India'. 

To believe that social institutions like endogamy can be enforced through powerful state machinery itself is a proposition to be viewed sceptically.

Reich et al whose work is referred to as the one over which the present one is an improvement has the following words: 

"Strong endogamy must have applied since then (average gene flow less than 1 in 30 per generation) to prevent the genetic signatures of founder events from being erased by gene flow. Some historians have argued that “caste” in modern India is an “invention” of colonialism in the sense that it became more rigid under colonial rule. However, our results suggest that many current distinctions among groups are ancient and that strong endogamy must have shaped marriage patterns in India for thousands of years " (highlighting mine).

Is the sentence “Some historians have argued that “caste” in modern India is an “invention” of colonialism in the sense that it became more rigid under colonial rule.” An example for social science arguments being poorva paksha for natural science research?