Why was New Guinea not colonized by Austronesians the way Indonesia was?
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I think the vital piece of information you were missing that made this appear to be a mystery was that, unlike a lot of the rest of Indonesia, the native inhabitants of New Guinea that the Austronesians found living there were not a thin population of hunter-gatherers. Rather the Paupuans of the interior were one of the world's densely populated agricultural societies. In fact, the island highlands were one of the many worldwide independent loci of the discovery of agriculture when the current interglacial started around 10,000 years ago.
The Austronesians would have reached the shores of New Guinea around 1300BC. McEvedy & Jones estimate there were probably around a quarter of a million Paupans living there at that time. That isn't a lot by today's standards (currently the island supports on the order of 40x that), but was a very respectable number at the time, and clearly far more than a few boatloads of Austronesians were capable of wiping out. Austronesian farming techniques weren't significantly better, they weren't more organized, and once you got inland a bit past the reach of their boats, the military logistics weren't in their favor.
That doesn't mean they had 0 impact though. There are in fact today widespread Austronesian-speaking enclaves near the coasts (where one would expect to see them), circumstantially the Austronesians clearly went through the area, and ongoing trade with their society is one reasonable explanation of how the South American domesticated Sweet Potato got added to the Paupuan crop package (if indeed that happened pre-Magellan).
(A good map of the Asmat-Kamrau (Paupuan) language distribution, useful here as it also shows the actually somewhat extensive distribution of Austronesian languages in New Guinea)
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