Assuming -as is likely- that J*(xJ2) is mostly J1, here are some observations:
- J1 far exceeds J2 in Arabia
- In Muslim Iran J1/J2 is much lower (about half in this sample)
- Indian non-Muslims have a low J1/J2 ratio (near zero)
Some Bohras' ancestors were converts from Hinduism to Islam in Gujarat, India. Their conversion was the result of the work of Fatimid missionaries from Egypt and Yemen before the seclusion of the 21st Fatimid Imām, some time during the reign of Caliph-Imām al-Mustansir. The converted were largely from the higher castes, many of whom were engaged in trade and commerce.A zero J1/J2 ratio with a sizeable J2 presence is indeed reminiscent of Indian upper-caste populations.
Indian Shia/Sunni populations from Uttar Pradesh have a sizeable J1 presence which, given its absence in Indian non-Muslims is likely of exogenous Middle Eastern origin.
The absence of J1 in Iranian Shia from Andhra Pradesh is interesting. I have not been able to find more information on this population, but presumably they originate from an Iranian group that settled in India prior to experiencing admixture and hence does not exhibit the mixed J1/J2 ratio as in the current general Iranian population.
The Mappla from South India show a balanced J1/J2 ratio. From Wikipedia:
The long-standing Arab and Jewish contact with the coastal areas of India has left its permanent mark in the form of several communities. These communities came into existence through the marriage of local women to Arab sailors (The Muslim Mappilas) and traders and conversion of early Jews to Christianity (Nasrani Christians).European Journal of Human Genetics doi:10.1038/ejhg.2009.168
Traces of sub-Saharan and Middle Eastern lineages in Indian Muslim populations
Muthukrishnan Eaaswarkhanth et al.
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.