People on These Pacific Islands Have the Most Ancient Genome of All Humans (and a Lot of Denisovan Genes)

Researchers found the people of Near Oceania carry some of the oldest human genetics.

The people of Near Oceania carry a genetic legacy that stretches back almost to the beginning of humanity’s expansion across the globe.

This legacy comes, at least partly, from some of the earliest settlers to reach the Pacific more than 42,000 years ago. Their ancestors remained largely isolated for millennia, preserving a record of ancient migrations, population bottlenecks, and encounters with now-extinct human relatives. A new study has now uncovered that record in unprecedented detail, revealing the richest catalog yet of Denisovan DNA and evidence that the ancestors of present-day Oceanians interbred with at least three distinct Denisovan-like groups.

A Missing Chapter in Human Genomics

Some 42,000 years ago, people reached the far edge of the human world.

They crossed into Near Oceania, reaching New Guinea, the Bismarck Archipelago, and the Solomon Islands. Then, for thousands of years, most of their descendants lived in deep isolation. The sea surrounded them, and moving away was really hard. The mountains only added to this division. Multiple languages blossomed as populations drifted apart. But inside their genomes, another story quietly endured: the DNA of extinct human relatives.

In a new study in Science, researchers sequenced 177 high-coverage genomes from 12 Near Oceanian populations, spanning multiple communities. They then compared those genomes to more than a thousand others from around the world.

Near Oceania’s genomes turned out to be different. Its people carry some of the highest known levels of archaic DNA in the world. In this study, Oceanian genomes carried about 2.5 times more archaic sequence per person than European genomes, and far more Denisovan sequence than East Asian genomes. One group carried roughly 25 times more Denisovan legacy than the average East Asian genome.

But it gets even weirder.

The Denisovan Connection

Denisovans are an extinct group of ancient humans, close relatives of Neanderthals. We know them mostly from DNA rather than from many fossils. Their remains were first identified from Denisova Cave in Siberia. But, while scientist have uncovered very few fossils, genetic studies show that they ranged far beyond that site.

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Unlike Neanderthals, whose bones have been found across Europe and western Asia, Denisovans remain physically mysterious. Yet they left a lasting mark in the genomes of living people, especially in parts of Asia and Oceania, where inherited Denisovan DNA can still influence traits such as immunity and adaptation.

In this case, the Denisovan story was not simple. The researchers found evidence that ancestors of Near Oceanians inherited DNA from three distinct Denisovan-like groups. This suggests that the ancestors of Near Oceanians did not encounter Denisovans just once. Instead, they appear to have inherited genes from several Denisovan-like populations, hinting at a long and complicated history of contact whose social details remain unknown.

Not all inherited archaic DNA is helpful. Much of it was probably neutral, some may have been harmful and removed over generations by natural selection. But some of it appears to have stuck around because it helped.

The study identified several candidate regions where archaic variants seem to have risen to high frequency because they offered an advantage. These included genes linked to immunity, metabolism, fertility, and skeletal development. One of the most intriguing signals appeared near TRPS1, a gene involved in bone development and craniofacial traits. The Denisovan-derived variant near this gene was found mainly in Oceania and Island Southeast Asia, reaching high frequency in some Near Oceanian groups.

That doesn’t mean Denisovan DNA “gave” people a particular face or body type. Genetics is rarely that simple. But it does suggest that variation near a skeletal-development gene may have been favored in certain environments.

The immune system story is even more notable. Using a lab method that tests whether genetic variants change gene activity, the researchers identified 3,127 high-frequency archaic variants that altered expression. Many were linked to immune pathways.

Why This Matters

The study changes the scale of the Denisovan story.

Scientists mostly know Denisovans from scraps: a finger bone, teeth, fragments of DNA from Siberia and Tibet. Yet their genetic legacy reaches deep into Oceania. The new study suggests that “Denisovan” may not describe one tidy group, but several related populations that mixed with modern humans at different times. We still don’t truly understand who these Denisovans were.

Then, this matters for human evolution. It means our species did not simply replace other humans as it expanded. We met them, we had children with them. Their genes entered ours and then selection sorted through that inheritance.

This also matters for medicine.

Many global biobanks still underrepresent Oceanian peoples. Many Denisovan-derived variants found in Oceania are absent or poorly represented in existing clinical datasets. That means researchers may miss variants relevant to disease risk, immune function, or drug response.

The study does not claim that archaic DNA determines health outcomes on its own. Environment, infectious disease, diet, colonial history, access to care, and social conditions all matter enormously. But genetics is one part of the picture, and for too long, that picture has been drawn from too narrow a slice of humanity.

The study was published in Science.