Male ancestors of the vast majority of present-day South Asians (Indians, Pakistanis, Bangladeshis) came from West Eurasia, Central Asia and Iran, according to the latest DNA research led by Harvard geneticist Dr. David Reich. Reich's team came to this conclusion after studying the Y-chromosomes of present-day Indians. Some Hindu Indian scientists have used mitochondrial DNA (mtDNA) samples, extracted from the bones of recently discovered ancient skeletal remains of a couple in Rakigarhi in Haryana, to claim the local indigenous origins of all Hindus. Y-chromosomes are passed from father to son while mitochondrial DNA is passed from mother to children. The Harvard team's findings thoroughly debunk Hindu Nationalists' "racial purity" myth similar to that promoted by White Supremacist racists in the West.  Reich writes: "The Hindutva ideology that there was no major contribution to Indian culture from migrants from outside South Asia is undermined by the fact that approximately half of the ancestry of Indians today is derived from multiple waves of mass migration from Iran and the Eurasian steppe within the last five thousand years". 

David Reich's "Who We Are"

Reich's Indian counterparts were highly resistant to the Harvard team findings of foreign origins of modern-day South Asians. Here's an excerpt from David Reich's "Who We Are and How We Got Here":     

"Based on their own mitochondrial DNA studies, it was clear to them (Indians) that the great majority of mitochondrial DNA lineages present in India today had resided in the subcontinent for many tens of thousands of years.They did not want to be part of a study that suggested a major West Eurasian incursion into India without being absolutely certain as to how the whole-genome data could be reconciled with their mitochondrial DNA findings. They also implied that the suggestion of a migration from West Eurasia would be politically explosive. They did not explicitly say this, but it had obvious overtones of the idea that migration from outside India had a transformative effect on the (South Asian) subcontinent". 

"To keep up the purity of the Race and its culture, Germany shocked the world by her purging the country of the Semitic races -- the Jews. Race pride at its highest has been manifested here. Germany has also shown how well-nigh impossible it is for races and cultures, having differences going to the root, to be assimilated into one united whole, a good lesson for us in Hindusthan to learn and profit by." 

"Groups of traditionally higher social status in the Indian caste system typically have a higher proportion of ANI ancestry than those of traditionally lower social status, even within the same state of India where everyone speaks the same language. For example, Brahmins, the priestly caste, tend to have more ANI ancestry than the groups they live among, even those speaking the same language. Although there are groups in India that are exceptions to these patterns, including well-documented cases where whole groups have shifted social status, the findings are statistically clear, and suggest that the ANI-ASI mixture in ancient India occurred in the context of social stratification".

South Asian Ancestry. Source: Arain Gang

1901 Indian Census of UP Muslims

Light Skin Gene Distribution. Source: PLOS Genetics

1901 India Census UP Hindu Population By Castes