Dienekes points to a new paper which attempts to quantify the genetic ancestry of South Asian Muslims into indigenous and exogenous components:
Islam is the second most practiced religion in India, next to Hinduism. It is still unclear whether the spread of Islam in India has been only a cultural transformation or is associated with detectable levels of gene flow. To estimate the contribution of West Asian and Arabian admixture to Indian Muslims, we assessed genetic variation in mtDNA, Y-chromosomal and LCT/MCM6 markers in 472, 431 and 476 samples, respectively, representing six Muslim communities from different geographical regions of India. We found that most of the Indian Muslim populations received their major genetic input from geographically close non-Muslim populations. However, low levels of likely sub-Saharan African, Arabian and West Asian admixture were also observed among Indian Muslims in the form of L0a2a2 mtDNA and E1b1b1a and J*(xJ2) Y-chromosomal lineages. The distinction between Iranian and Arabian sources was difficult to make with mtDNA and the Y chromosome, as the estimates were highly correlated because of similar gene pool compositions in the sources. In contrast, the LCT/MCM6 locus, which shows a clear distinction between the two sources, enabled us to rule out significant gene flow from Arabia. Overall, our results support a model according to which the spread of Islam in India was predominantly cultural conversion associated with minor but still detectable levels of gene flow from outside, primarily from Iran and Central Asia, rather than directly from the Arabian Peninsula.
This is entirely predictable; there’s a reason that during communal riots men are forced to expose their penises, aside from dress distinguishing a Muslim from a Hindu is not really possible. A small number of very high status Muslims are obviously predominantly non-South Asian, they look different. This stratum still intermarries internationally, e.g., Benazir Bhutto’s mother was Kurdish (one reason she looked so white). When the British first arrived in the Indian subcontinent they distinguished between white and black Muslims just as the local elite Muslims did. Nevertheless, there was a great deal of intermarriage. Even at the commanding heights of the white Muslim aristocracy, the Mughals, there was outmarriage. Shah Jahan was 3/4 Rajput. Compare Shah Jahan to his grandfather, Akbar (a contemporary portrait).* The Mughals were not the best record keepers (they were a rentier state par excellence), but the composition of their military and civil service is known because of differential grants of income to categories of service elites. Foreign Muslims, those born outside India, were at a premium, and often comprised a significant proportion every generation (Persians being siphoned to the civilian bureaucracy, Turks and Pathans to the military). This is in keeping with a tendency among the Turkic Muslim dynasties in general, from the Mamlukes to the Ottomans, who replenished their non-hereditary elite from without. Where did the offspring of these newcomers go? Likely they descended down the class hierarchy, intermarrying with local Muslim converts (or, even facilitating the conversion of a high status Hindu family through intermarriage), who would be eager to acquire Persian or Turkic ancestry for their descendants and so a higher heritable status.
But these data do show an exception. The Bohra. Unlike the other Muslim groups, there is basically no evidence of significant (i.e., above expectation) Middle Eastern lineages among them. Why? You need to know a little history and ethnography. The Bohras are an Ismaili group, a minority sect within Shiism, and very marginal due to their peculiar history and theology. Recent works of religious history suggest that Ismailis were extremely influential in spreading Islamic ideas among the populations of South Asia. These researchers suggest that Ismaili Islam served as a “gateway” to Sunni Islam for many South Asians. Additionally, it may be that many Hindu groups (Hussaini Brahmins and the Megh for example) were influenced by this variant of Islam. The Ismaili flavor of South Asian Islam was eclipsed by the rise of the institutional structure of Sunni orthodoxy (which included the state, as well as Sufi orders), most prominently among the late Mughals such as Aurangzeb. It was during this period when there were massive shifts from Ismailism to Sunni Islam, and some suggestions that many Hindu groups moved away from syncretism with Islam lest they be labelled heretics by the state, a far worse position than simply being heathen. The Bohras are one group of Ismailis who did not convert to Sunni Islam. Some scholars assert that before the Mughal period the majority of Muslims in Gujarat were Ismaili, while after only a minority were. Like South Asian Muslims in general the origin of Ismailism was among converts from what became Hinduism, in particular the trader castes in the instance of the Bohras. These data give tentative support to that contention, the mix of lineages is what is common among Indian upper castes. I speculate that there is a possibility that there was selective conversion to Sunni Islam, and that those from mercantile backgrounds were the least incentivized to switch to the “orthodox” confession. In contrast, those reliant on state beneficence, or those who had Sunni landlords, were probably more likely to switch. There is some suggestion that the Parsis, who were the remnants of Iranian Zoroastrianism which emigrated to India, were mostly from priestly families. This group obviously had least incentive to convert to Islam because many of their privileges were bundled up with a Zoroastrian religious identity. In any case, this can be tied back up to the intermarriage of Iranian and Central Asian Muslims with local Muslim elites: there would be no incentive for non-South Asian Muslims to marry into Ismaili families who were on the wrong side of the Mughal state which had served as their initial patrons. Rather, it would be contingent upon any native Muslim family who wished to intermarry with a more prestigious Persian or Central Asian lineage to toe the line of religious orthodoxy, whether that be Sunnism, or, the less heterodox Twelver Shiism (there were Twelver Shia polities in India). An alternative hypothesis is that the scholars who claim many more Ismailis in the past are misreading the textual evidence, and that Ismailism was a much smaller sect than they envisage. That is never went much beyond the trader castes, and so the possibility for intermarriage with prestigious non-South Asian lineages was already minimized because of that group’s preference for wealth based on land rents. Note: Though the authors dismiss this, I suspect that Dienekes’ is correct in observing that the Mapplas of Kerala do have Arab ancestry, which other South Asian Muslims do not. This is culturally expected, the Mappla form of Islam owes much more to South Arabian exemplars than Sunni Islam in the rest of the subcontinent, which is Turkic or Persian in flavor. Citation: Traces of sub-Saharan and Middle Eastern lineages in Indian Muslim populations, European Journal of Human Genetics, doi: 10.1038/ejhg.2009.168 * The portraits may be idealizations, but from what I have read Akbar didlook much more Mongolian than his descendants. Aurangzeb, Shah Jahan’s half-Persian son, was noted to have particularly fair skin, likely in contrast with his father who was mostly South Asian in ancestry.