The earliest seafaring ancestors of people living in South Pacific islands such as Vanuatu and Tonga arrived from Asia, an analysis of ancient DNA from four skeletons reveals.

A wealth of archaeological evidence, including intricate pottery, indicates people associated with the Lapita culture were the first to colonise the remote islands in the Pacific in the last major dispersal of people to unpopulated lands 3,000 years ago.

But until this analysis we did not know who these people were, the study's co-author Professor Matthew Spriggs of the Australian National University said.

"Now that we've got the DNA of the ancient Lapita people, the big shock is that they are really like [Aboriginal] people from Taiwan," Professor Spriggs said.

Today, all south Pacific Islanders have a heritage that includes DNA from both a Papuan and an East Asian population to varying degrees.

The relationship between the Lapita people and Papuan people, which dominated the region for 50,000 years, has been long debated.

Linguistically and culturally the Lapita were similar to Asian groups.

But many archaeologists thought the Lapita mixed with the Papuan population as they travelled down through New Guinea and the Solomon Islands before setting out towards the remote islands 3,000 years ago.

Analysis of skeletons shows first Lapita did not mix

To uncover the origins of the Lapita people, Professor Spriggs and his colleague Dr Stuart Bedford worked closely with the Vanuatu Cultural Centre to excavate and extract DNA from skeletons from the Teouma burial ground in Vanuatu.

"This is in fact the fourth attempt to extract ancient DNA over the last decade," Professor Spriggs said.

Finally, a genetic analysis by a team led by Dr David Reich at Harvard University revealed three skeletons aged between 3,100 years and 2,700 years contained no traces of Papuan DNA.

A fourth Lapita skeleton aged between 2,700 and 2,300 years that was excavated in Tonga by a second team, led by Dr Geoffrey Clark of the Australian National University, and analysed at a different lab in Germany, also contained no Papuan DNA.

An additional analysis of DNA volunteered by 778 present day people from East Asia and Oceania shows all four skeletons contain unique DNA that no longer exists, but is similar to that found in Aboriginal groups from Taiwan and some northern Philippine populations.

"The first people who got to Vanuatu were not these people who'd been in the region for 50,000 years ... they were these Asian populations," Professor Spriggs said.

The analysis also showed that the Asian genes in today's Pacific people came from these first remote Oceanians.

"What we've been able to say is that Asian inheritance comes from Lapita," Professor Spriggs said.

He said the finding, reported in the journal Nature, challenged the use of labels such as Melanesian and Polynesian to describe peoples from different parts of the Pacific.

"The variation is simply the percentage of the genetic inheritance from the first people who got out to these islands 3,000 years ago."

Second wave of Papuan men mixed with Lapita

Not only did the genetic data show the Asian ancestry in today's South Pacific Islanders comes from the Lapita, but that it was more likely to come from women than men.

This indicated the first wave of Lapita seafarers was soon followed by a second wave of Papuan people — mainly men.

Just when the two lineages came across each other on the islands spread across the Pacific is unclear.

"We think for Vanuatu it is in late Lapita times 2,800 to 2,700 years ago when populations were small," Professor Spriggs said.

But he said it may have happened much later for places such as Fiji and Polynesia.

"For Fiji we just don't know. But for Polynesia we have an absolute date by which it must have occurred which is 1,000 years ago."

At that time, the population started moving out from Tonga and Samoa to the eastern Pacific Islands of Hawaii and Tahiti, then 700 years ago travelled south to become the Maori population in New Zealand.

"When they leave 1,000 years ago that mixture has already happened."

But more work with ancient DNA from skeletons of different ages would be needed to clarify exactly when the mixes happened in various locations, Professor Spriggs said.

Clues and questions about Pacific ancestry

Commenting on the study, director of the Australian Centre for Ancient DNA Professor Alan Cooper said the paper provided a lot more information about the Pacific and Polynesian origins "that was just conjecture before".

He said the study also raised questions about when the Papuan mix happened in Tonga and subsequently in Polynesia, whose people today have 26 per cent Papuan DNA.

"The Tongan individual carried little or no Papuan ancestry providing confirmation the ancestral population of Polynesians was not yet fully formed or widespread by the end of the Lapita," he said.

"So how long before [the Papuans] catch up? That's a long way out in the Pacific.

"You figure that the genetic mix that generated the Polynesians happened before they went out voyaging to the islands."

He said it also raised questions about the identity of the ancient Papuan people, who had a mix of Australian Aboriginal and Papuan DNA.

"I'm intrigued by who that Australian-Papuan group was — where do they come from?

"I'm going to guess off the top of my head Torres Strait Islands or some coastal group, possibly trading with the Lapita group."

DNA reveals Lapita ancestors of Pacific Islanders came from Asia - ABC News