Eastern Indonesia is an interesting and complicated place, in genetic terms, and I'd like to go over some of the implications of the genetic material. It isn't my intention to detail the haplogroups involved, here at least, but rather to point out the implications of the trends shown in the data. My principal source for this is a 2009 paper for which my former tutor collected the data, which can be found (for free!) here on PubMed. Here's the abstract:
Eastern Indonesia possesses more linguistic diversity than any other region in Southeast Asia, with both Austronesian (AN) languages that are of East Asian origin, as well as non-Austronesian (NAN) languages of likely Melanesian origin. Here, we investigated the genetic history of human populations from seven eastern Indonesian islands, including AN and NAN speakers, as well as the relationship between languages and genes, by means of nonrecombining Y-chromosomal (NRY) and mitochondrial DNA (mtDNA) analysis. We found that the eastern Indonesian gene pool consists of East Asian as well as Melanesian components, as might be expected based on linguistic evidence, but also harbors putative indigenous eastern Indonesian signatures that perhaps reflect the initial occupation of the Wallacea by aboriginal hunter-gatherers already in Palaeolithic times. Furthermore, both NRY and mtDNA data showed a complete lack of correlation between linguistic and genetic relationships, most likely reflecting genetic admixture and/or language shift. In addition, we noted a small fraction of the NRY and mtDNA data shared between eastern Indonesians and Australian Aborigines likely reflecting an ancient link between Asia and Australia. Our data thus provide insights into the complex genetic ancestry history of eastern Indonesian islanders characterized by several admixture episodes and demonstrate a clear example of the lack of the often-assumed correlation between the genes and languages of human populations.
The abstract, you'll note, is incorrect in its assertion that eastern Indonesia is the most linguistically diverse place in southeast Asia - there are many more than two language families in Vietnam, for instance, including Austronesian, Austroasiatic, Daic (Tai-Kadai), and Sino-Tibetan; in eastern Indonesia, though, there are probably only two (unless you count Dutch and Portuguese, which are Indo-European languages): Austronesian and non-Austronesian ('Papuan') languages, likely related to one another but less probably related to languages on New Guinea (the Trans-New Guinea languages). In any case, it's a worthwhile paper and it tells us a lot about eastern Indonesian genetics, and the conclusions are interesting.
The first point to be made is that Nusa Tenggara Timur is largely genetically 'non-Austronesian'. Now, this requires clarification: 'Austronesian' is a linguistic term, so it shouldn't refer to anything other than language. But language spreads with people, and along with people come plenty of other things: technologies, ideas, social structural principles, parasites, and haplotypes. Outrigger canoes are an 'Austronesian' technology, if anything is; certain haplogroups are 'Austronesian' haplogroups. They aren't exclusively Austronesian, and we shouldn't 'essentialise' Austronesian people, as the jargon goes (i.e, we shouldn't treat them as if speaking an Austronesian language automatically predisposes you to certain types of society or technology, or that these things are inevitably Austronesian and cannot spread beyond Austronesian speakers). Nonetheless, the genetic component associated with the spread of Austronesian languages is in the minority in eastern Indonesian communities, although this varies by location.
Secondly, there isn't a significant correlation between speaking an Austronesian language and having 'East Asian'/'Austronesian' DNA (in Nusa Tenggara Timur, at least). A person on Timor who speaks a non-Austronesian language is just as likely to possess genetic material associated with the Austronesian expansion as someone speaking an Austronesian language. The implication of this is that it is possible to take up new traits, including genetic ones, associated with the arrival of a new population without taking them all up. Language is just one of the many things 'the Austronesians' brought with them.
The anthropologist Andrew McWilliam, a specialist on Timor (whose work is, incidentally, excellent), has done research among Fataluku (non-Austronesian) speakers in Timor Leste and concluded, to paraphrase, that while they speak a non-Austronesian language, they practice an Austronesian way of life. This view makes the mistake of essentialising Austronesians, as if only speakers of Austronesian languages should be expected to exhibit traits associated with their expansion, but of course it's easy to see what he means, and he's right (assuming we're right about the prehistory of the area). Clearly, the migrants from the north brought more than just language, and gave what they had to people who didn't speak their languages. And, of course, linguists have long known that eastern Indonesian Austronesian languages (i.e, those formerly classified as 'Central Malayo-Polynesian') display the presence of a non-Austronesian substrate, so there has evidently been considerable mutual influence.
Third, the data suggest that some (very few, but some) people in eastern Indonesia exhibit haplogroups whose closest relatives are found among indigenous Australians. In the paper, IIRC, this is interpreted as evidence that eastern Indonesian populations are the ancestors of people who migrated into the area deep in the Pleistocene, which is a reasonable interpretation. Alternatively, it could also be evidence of mid-to-late-Holocene contact between Australians and eastern Indonesians, which is not particularly difficult to imagine (especially as there are some technological overlaps in lithic technology from northern Australia and eastern Indonesia, including the well-studied site of Ulu Leang in Sulawesi, c. 8-5,000 BP, indicating almost certainly pre-Austronesian contacts). Either way, this is quite interesting stuff.
Fourth, the cultural continuities listed in the previous post, among others, point to a continuum of activity and thought among people throughout Nusa Tenggara Timur and Maluku. They are typically associated with Austronesian speakers, which is in many cases entirely sensible.
Headhunting is doubtless of Austronesian origin, and is not autochthonous to the region; headhunting was once practiced almost throughout the entirety of western Austronesia, and it is notable that headhunters in New Guinea are found in those societies whose languages show the greatest Austronesian impact.
Textiles, likewise, were brought along with Austronesian languages. The word for loom-weaving (as opposed to basket weaving or other non-textile-based activities) is reconstructible to proto-Austronesian (*tenun), and there are obvious technological similarities between looms in Taiwan (the putative origin of Austronesian) and looms in eastern Indonesia and elsewhere in the Austronesian-speaking world. It is also notable that Alor, an island with an almost entirely non-Austronesian-speaking population, used to be textile-free apart from those woven by Austronesian speakers. The outrigger canoe is doubtless also an Austronesian innovation, as is (in this part of the world) the sail, which is probably also related to the textile arts. (As far as I'm aware, sails have only been invented independently in two locations: the Red Sea and the South China Sea, with all other examples being derivative. I'm not entirely sure of this, however.) So clearly the Austronesian speakers had a major impact on the technology, lifestyle, and thought of eastern Indonesia, even despite their genetic minority.
I suspect that much else comes from Austronesian precedents, actually. I was once convinced that some features of eastern Indonesian kinship came from a non-Austronesian source, including the dominant form of marriage alliance, matrilateral cross-cousin marriage (more about that later - I promise!). But in fact, despite its rarity, matrilateral cross-cousin marriage is found outside eastern Indonesia in Austronesian-speaking communities, including among the Batak in Sumatra, among whom the mother's brother is considered exceptionally spiritually and temporally powerful, as he is in eastern Indonesia. So even this may have been brought by Austronesian speakers, in some sense (which nevertheless leaves us with the mystery of why Bataks and eastern Indonesians would preserve an archaic form lost elsewhere, if that is what it is).
All of which is very interesting. It tells us that eastern Indonesia is genetically diverse despite displaying considerable continuities in activity. More importantly, it tells us that while 'Austronesian' (and, for that matter, 'Indo-European') is first and foremost a linguistic problem, it has repercussions in other areas of life. The true importance of the linguistics is highlighting the spread of lots of other objects, including people, parasites, and ideas about the cosmos. This comes out especially clearly in eastern Indonesia.