Last year I posted The Genetics of the St. Thomas Christians. Recently I got some more samples. Of these, four were clearly self-identified as Southist/Knanaya Christians (as opposed to Northist Christians). The Knanaya are a bit different in their traditions than the broader much larger St. Thomas Christian community.
In the PCA above the bottom left are Middle Eastern groups. Druze and Yemeni Jews. Toward the top are Lithuanians. Green are Iranians. From the bottom right, up a diagonal axis, you see south-north Indian cline from low caste Telugu Christians, to Jatts from Punjab.
It does seem in relation to the other more generically labeled St. Thomas Christians the four Knanaya show some noticeable Middle Eastern shift.
Here’s an admixture plot:
The St. Thomas Christians have more yellow “Druze” cluster than other South Indians, with variation (the Knanaya have more).
I ran some Treemix. Didn’t detect major gene flow, but the Knanaya group was different from the other St. Thomas Christians, having a closer position to West Eurasians. When I ran a three-population test, it was the St. Thomas Christians (Nasrani above), and not the Knanaya, which registered admixture with Middle Eastern groups. It’s probably an artifact that the latter was not detected.
The Christians of Kerala are very similar to other peoples of Kerala. But, I now think it is more than 50% likely that they do have detectable Near Eastern ancestry above what you should expect.