Muslims in India: Spread of people or spread of religion?

This paper in AJPA confirms an earlier study on Indian Muslims using Y-chromosomes, in that, for the most part, Muslims in India are not there because of movement of people from western Asian populations as much as it is due to the movement of ideas, beliefs. This one examines mtDNA and finds pretty much the same thing.

North Indian Muslims: Enclaves of foreign DNA or Hindu converts?

Maria C. Terreros, Diane Rowold, Javier R. Luis, Faisal Khan, Suraksha Agrawal, Rene J. Herrera

American Journal of Physical Anthropology; Volume 133, Issue 3 , Pages 1004 - 1012

Abstract: The mtDNA composition of two Muslim sects from the northern Indian province of Uttar Pradesh, the Sunni and Shia, have been delineated using sequence information from hypervariable regions 1 and 2 (HVI and HVII, respectively) as well as coding region polymorphisms. A comparison of this data to that from Middle Eastern, Central Asian, North East African, and other Indian groups reveals that, at the mtDNA haplogroup level, both of these Indo-Sunni and Indo-Shia populations are more similar to each other and other Indian groups than to those from the other regions. In addition, these two Muslim sects exhibit a conspicuous absence of West Asian mtDNA haplogroups suggesting that their maternal lineages are of Indian origin. Furthermore, it is noteworthy that the maternal lineage data indicates differences between the Sunni and Shia collections of Uttar Pradesh with respect to the relative distributions of Indian-specific M sub-haplogroups (Indo Shia > Indo Sunni) and the R haplogroup (Indo Sunni > Indo Shia), a disparity that does not appear to be related to social status or geographic regions within India. Finally, the mtDNA data integrated with the Y-chromosome results from an earlier study, which indicated a major Indian genetic (Y-chromosomal) contribution as well, suggests a scenario of Hindu to Islamic conversion in these two populations. However, given the substantial level of the African/Middle Eastern YAP lineage in the Indo-Shia versus its absence in the Indo-Sunni, it is likely that this conversion was somewhat gender biased in favor of females in the Indo-Shia.