As genetic studies continue to expand in scope, one of the things they're revealing is the complexity of humanity's shared legacy. Rather than a clean expansion out of Africa, we've found that the ancestors of Europeans and Asians mated with Neanderthals, while the group that populated Australia and New Guinea later went on to mate with Denisovans—a group we didn't even know existed a decade ago.

The native population of Australia and New Guinea is also exceptional as it appears to be one of the earliest branches off the group that migrated out of Africa; initial studies suggested that it had been isolated for nearly 40,000 years, since the groups first crossed from Indonesia to an area called the Sahul, which includes Australia, New Guinea, and the areas between them that would be above sea level during the peak of ice ages. But a new study has done a more detailed analysis and found an indication that the supposedly isolated population received a genetic (and possibly cultural) infusion about 4,000 years ago. And that it came not from the nearby islands of Indonesia, but from the Indian subcontinent.

The authors were using a genome-wide scan for places where human populations are known to have single-base differences in their DNA (termed SNPs, for single-nucleotide polymorphisms). They used a panel of samples that covered area of interest, along with some from other islands lying between there and the Asian mainland. In addition, they included African, European, and mainland Asian samples.

One of the first surprises was that the people of the Sahul shared a close genetic affinity for a group called the Mamanwa, who inhabit the Philippines. That's somewhat surprising, given that the Philippines are on the opposite side of the Wallace Line, the area of deep water that separates Australia and New Guinea from mainland Asia and helped to keep their population largely isolated.

Closely linked SNPs are likely to be inherited together and only become randomized with time. The extent to which they're inherited together can thus be used as a measure of separation time. The authors performed this analysis, and came up with a figure of 36,000 years. That's notably lower than the 40,000 years of most other estimates, although the authors discuss a number of factors that can potentially distort the results. Still, it's consistent with the general idea that the ancestors of native Australians split off shortly after the departure of modern humans from Africa, and took a southern route to their eventual home, where they lived in isolation.

What wasn't consistent with that was an affinity that turned up with populations native to the Indian subcontinent. The authors tried a variety of tests, and it kept showing up, and several of the tests produced a consistent number: 11 percent of the genomes of Australia and New Guinea seems to have been derived from Indians.

This could have been the result of events that happened after European contact, so the authors did the math to estimate when the DNA entered the current population. They came up with an estimate of 141 generations, which (based on a typical human generation time) would place the arrival of the Indians at over 4,000 years ago. Clearly that predates European contact, but the authors note that a number of changes in stone tool use took place in Australia around this time; it's also the first time that the dingo appears in the fossil record.

The authors note that their sample of Australians is limited to those from the Northern Territory, so they don't know whether this influence extends throughout the continent. (The New Guinea population was limited to those who live in the highlands, as they're a distinct population.) What they can say is that a similar Indian input seems to be lacking from any of the 11 populations they sampled from islands in Southeast Asia. That suggests that, either the Indians went directly to Australia (which would have been an impressive feat) or their travels through the islands on the way were very limited.

The study highlights how higher resolution data and more extensive sampling is changing our perspective on human history. The initial human genome studies saw no indication of any interbreeding with Neanderthals; more detailed studies were just starting to hint at it when the completion of the Neanderthal genome first confirmed it. In a similar way, the initial study of a native Australian genome suggested something was a bit off with some of the DNA, but couldn't identify a source. This study finally has.

I cant wait to see what other surprises might be lurking as genomic information becomes ever more widespread.

PNAS, 2013. DOI: 10.1073/pnas.1211927110 (About DOIs).