Tens of thousands of years ago, island South East Asia was the crucible of human diversity, with species such as Homo floresiensis (“Hobbits”) and Homo luzonensis living there, possibly beside Denisovans and Homo sapiens. The story in more recent times was considered to be much more boring, at least in regard to Wallacea – now part of eastern Indonesia – with a single wave of Austronesian farmers largely displacing previous hunter-gatherers. However, DNA collected from 2,600 to 250-year-old bones and teeth tells a very different story.

The region known as Wallacea is divided by deep water straits from both mainland Asia and Australia. Where other South East Asian Islands became connected to one continent or the other during periods of low sea level, the islands of Wallacea never did, thus developing ecosystems of plants and animals that could float, fly, or swim there. For the same reason, human occupation was challenging, and we still don't understand how the earliest inhabitants reached these islands.

More recently, however, a great migration of Austronesian-speaking peoples are known to have settled on the islands as part of arguably the greatest migration in human history, which took people as far as Easter Island and Madagascar. However, in Nature Ecology and Evolution, a team of scientists show this was just one of at least three settlements around the same time, each with distinctive characteristics.

Professor Sue O'Connor of the Australian National University conducts archeological digs on these islands. She told IFLScience that multiple institutions have tried to extract DNA from her older discoveries without success. That's not surprising, since tropical heat and humidity are not kind to DNA, but it has left big questions unanswered about the relationship between early human inhabitants of the area and ourselves.

However, when younger bones and teeth that O'Connor and colleagues found were sent to the Max Plank Institute the results were different. DNA from 16 inhabitants of Wallacea between 600 BCE and 1770 BC was successfully sequenced, and revealed what O'Connor called in a statement “a tremendous genetic melting pot.”

Before the Austronesians, DNA from mainland Southeast Asia appeared on the islands. “I suspect that we might be looking at small groups, perhaps of early farmers, who travelled a long way, left no archaeological or linguistic traces along the way, but who increased their population sizes after arrival," said ANU's Emeritus Professor Peter Bellwood. 

O'Connor told IFLScience that the Austronesian languages had come to dominate the area, but archaeologists suspected another culture settled on the islands based on two styles of pottery and tools, sometimes called Neolithic A and B. “Until recently there was no firm proof,” she said, “but the buck stops with DNA.”

Ancient DNA also proves that around the same time, Papuan people were coming to the islands from the opposite direction. On the other hand, there is no genetic evidence of Indigenous Australians visiting Wallacea, despite signs of trade having occurred.

The fact that advances in DNA processing mean so many specimens were successfully sequenced may raise hopes for even older samples. If so, it might help answer some of the deepest questions about the increasingly baffling human family tree – or perhaps entangled bush – in the region. But O'Connor is cautious, noting the repeated failure to find viable DNA in this climate more than 7,000 years old.