Denisovan DNA may have aided Pacific migration

An international team of scientists has delved into the genetics of the Pacific population to trace the history of human settlement across the vast region – with a few surprising results.

By examining the genomes of 317 present-day individuals from 20 populations, the team found that the ancestors of modern-day Pacific populations interbred with little-understood ancient hominins called Denisovans. This genetic mixture seems to have bolstered the immune system and helped these early explorers adapt to living on isolated islands. The results may have implications for the health of Pacific populations today.

The paper is published in Nature.

What do we know about the peopling of the Pacific?

The population of the Pacific is one of the most impressive feats of exploration in human history. The Pacific Ocean is the single largest feature on the planet, sprinkled with islands that are fairly close together in the west but separated by larger and larger gaps towards the east, until there are thousands of kilometres between landmasses.

This enormous region is divided into Near Oceania (including Papua New Guinea, the Bismarck Archipelago and the Solomon Islands) and Remote Oceania (Micronesia, Santa Cruz, Vanuatu, New Caledonia, Fiji and Polynesia).

Our current understanding is that after humans migrated out of Africa, they flowed down through South East Asia, hopping across narrow straights and between islands. From Timor, they used rudimentary rafts or dugout canoes to cross to Papua New Guinea, then headed down the scythed curve of the Bismarck Archipelago, and reached the far edge of the Solomon Islands by around 40,000 years ago. There, nothing but the open ocean lay ahead of them, and so these people – the Near Oceanians – stopped, and Remote Oceania remained uninhabited.

Then some 5,000 years ago, a group of humans from what is now Taiwan left their home shores and journeyed south through the Philippines and Indonesia into Near Oceania. Called Austronesians, they brought with them sophisticated maritime technology and seafaring skills. They mixed with populations of the Near Oceanians, forging a new people – the Lapita – who then struck out to populate the rest of the Pacific.

What does this new study add?

The new genetic analysis suggests that the gene pool of the ancestors of Near Oceanians underwent a drastic reduction just before they settled in the region, with an effective population size of 214. The study also dated the settlement of Near Oceania to around 40,000 years ago, confirming archaeological records, and found evidence that after settling, the populations of different islands generally kept to themselves.

“Our results confirm that humans were able to cross the seas to reach new lands from an early stage,” explains co-author Etienne Patin, from the French National Centre for Scientific Research. “However, they also suggest that these voyages were relatively infrequent at this distant period in history.”

The study sheds light on the expansion of the Austronesian people out of Taiwan, suggesting that their dispersal wasn’t followed by a single event of mixing with Near Oceanian populations, but rather involved several recurring episodes.

“Our analyses suggest that humans left Taiwan more than 5,000 years ago, and that admixture between the Austronesian incomers and the populations of Near Oceania started only 2,000 years later,” Patin says. “The expansions from Taiwan therefore took some time, and may have involved a maturation phase in the Philippines or Indonesia.”

The study also revealed the percentage of ancient human DNA present in modern-day Pacific populations. While all humans outside of Africa have inherited Neanderthal DNA (2-3%), some Pacific populations also have inherited up to 3% of their genomes from Denisovans.

But surprisingly, as co-author Lluis Quintana-Murci from the Collège de France notes, “the Denisovan legacy varies considerably between populations, from virtually 0% in Taiwan and the Philippines to up to 3.2% in Papua New Guinea and Vanuatu”.

Previous work has shown that Neanderthal DNA has improved the adaptive capacity of modern humans, with beneficial mutations including those related to skin pigmentation, metabolism, and neural development. This new study now shows that admixture with Denisovans bolstered the immune system of Pacific populations, which may have helped humans adapt to and survive local pathogens when they spread into isolated island environments.

Plus, the mixing between humans and Denisovans didn’t occur just once – at least four independent mixing events occurred with at least two different lineages of Denisovans, as recently as 21,000 years ago. Two of these mixing events occurred after the emergence of the Lapita culture.

“Collectively, our analyses show that interbreeding between modern humans and highly structured groups of archaic hominins was a common phenomenon in the Asia-Pacific region,” the authors write in their paper.

Quintana-Murci notes that this also improves our understanding of the elusive Denisovans, a species for which we have very little fossil evidence.

“One of the strengths of these analyses is that, by studying the 3% of archaic heritage present in the genomes of modern humans, one can ‘resurrect’ Denisovans’ genomes, and thus show that they presented high levels of genetic diversity,” he says.

According to Murray Cox, a computational genomics researcher from Massey University in New Zealand, this is a “fascinating” result.

“The field has long held an implicit assumption that modern human admixture with Denisovans occurred in much the same way it did with Neanderthals,” explains Cox, who was not involved in the study but has worked on similar research. “This paper clearly shows that assumption is unfounded.

“Mixing between modern humans and archaic groups was much more structured, and occurred much later, in the Asia-Pacific region. It appears that Denisovans persisted in Oceania long after modern humans arrived, and sharing territory with archaic hominins was part of the modern human story for a long period of our history.”

The team also found that in the ancestors of modern-day Pacific populations, genes associated with lipid metabolism were selected for, which may further our understanding of why Pacific populations have been observed to suffer a high burden of metabolic disease, including obesity and type 2 diabetes.

“Large genomic studies in the Pacific region are required to understand the causal links between past genetic adaptation and present-day disease risk, and to promote the translation of medical genomic research in understudied populations,” the authors conclude.