Australia might not have been as isolated for the 40,000 years before European colonisation as once thought.

A new study has found evidence of substantial gene flow between Indian populations and Australia about 4000 years ago.

The researchers also suggest the dingo might have arrived on Australian shores about that time, along with tool technology and food processing.

The study, published in the journal PNAS, says it was commonly assumed that Australia remained largely isolated following initial colonisation some 40,000 years ago - but genetic histories had not been explored in detail.

Irina Pugach, of the Max Planck Institute for Evolutionary Anthropology in Germany, joined colleagues in analysing large-scale genotyping data from Aboriginal Australians, New Guineans, island Southeast Asians and Indians that suggest a new possibility.

The authors found a common origin for populations in Australia, New Guinea and the Mamanwa (a Negrito group from the Philippines) and estimated these groups split from each other about 36,000 years ago.

The researchers say this supports the view that they represent the descendents of an ancient southwards migration out of Africa.

They also found a substantial gene flow from India to Australia 141 generations ago, or 4230 years ago assuming a generation span of 30 years.

"This is also approximately when changes in tool technology, food processing, and the dingo appear in the Australian archeological record, suggesting that these may be related to the migration from India," their paper says.

They said the Indian gene flow might not have come directly from India.

The researchers said the Australian samples came from a broad area of the Northern Territory but might not be representative of the indigenous population as a whole.