Indian ancestry maritime Southeast Asia

In the comments, people keep asking about Indonesia, and Java in particular. The reason is pretty simple: before wholesale conversion to Islam maritime Southeast Asia was dominated at the elite level by Indic social and religious forms. I say “Indic” because unlike mainland Southeast Asia Theravada Buddhism did not supplant other Indian religions, and in fact, while indigenous Buddhism that led to the Borobudur temple complex in the 9th-century went extinct, Hinduism persisted for quite a bit longer and persists to this day. Not only are there long-standing Hindu traditions in Bali, but far eastern Java remained a Hindu kingdom until 1770, and there remain Javanese Hindus (some of them are recent converts).

As several mainland Southeast Asian groups seem to have Indian admixture, what is the evidence for Indonesia? (the Singapore genome data offers up some Malays, and though some show recent Indian admixture, all of them have some Indian admixture). Luckily, there is a paper and data, Complex Patterns of Admixture across the Indonesian Archipelago. It uses the GLOBETROTTER framework, so I decided to reanalyze the data in a simpler manner, adding the Cambodians as a check (since from my previous posts you know a fair amount about that as a baseline).

Three points.

1) Definitely gene flow. But on the whole less than mainland Southeast Asia?

2) Lots of heterogeneity. Not surprising. The Sumatra samples seem to be taken from Aceh. This may matter a great deal.

3) In mainland Southeast Asia east of Burma there hasn’t been lots of colonial migration of Indians, nor a great deal of trade. The opportunities within maritime Southeast Asia for contact with outsiders are far greater. The inspection of results from Malaysia indicates continuous gene flow over a long period of time. In contrast, the results from Thailand and Cambodia indicate an early pulse.