A New Species of Ancient Human Was Uncovered in the DNA of Living Papuans

In 1864, our understanding of what it means to be human changed when Neanderthals were identified as a distinct species of hominin. At the time, it was immensely scandalous to presume Homo sapiens weren’t uniquely human; now it’s obvious that we are one of many. On Thursday, scientists report in Cell that it may be time to add another member to our list of ancient kin.

The new human species, they posit, might actually be one that we grouped together with the Denisovans, a relatively recent addition to the human family tree. The first evidence of this distinct line was a fossilized pinkie bone found in a southern Siberian cave in 2008. But they were especially dynamic far away from the cold north: The DNA of modern humans shows that, from East Asia across to Oceania, Denisovan DNA fragments still persist — evidence that modern humans encountered Denisovans when they dispersed out of Africa and mated with them.

For a long time, Denisovans were thought to be a single group that existed in three geographically dispersed units: the Siberian and East Asian Denisovans, those apparently restricted to Papua New Guinea and nearby islands, and those who lived to a lesser extent across Asia and Oceania.

The scientists behind the paper propose that the latter group, labeled D2, is a new and separate archaic hominin species.

Murray Cox, Ph.D., a University of New Zealand professor who co-authored this study, tells Inverse that the D2 individuals are as genetically different from the other Denisovan groups as they are from Neanderthals — suggesting they are a new species.

“Naming is a contentious issue, but if we are going to call Neanderthals and Denisovans by special names, as we do, then D2 should get its own name too,” Cox says.

What Makes D2 a New Species?

The word “species” here is used tentatively. The exact number of human species — and what counts as a species — is up for debate. Jeremy DeSilva, Ph.D., an anthropologist unaffiliated with this new study, tells Inverse he refers to them all as different populations of humans, rather as different species or subspecies because “it appears that both Neanderthals and Denisovans had split from the human lineage and from one another before being reabsorbed to various degrees back into the gene pool.”

Human evolution, the scientist concludes, was complicated “and much more interesting that we once thought.”

The D2 group’s existence was not gleaned from an unearthed trove of bones but from DNA samples from living humans, collected by the Indonesian Genome Diversity Project over the past decade to collect a representative sample of genomic diversity across the Indonesian archipelago and neighboring regions.

This area is immensely diverse and important to our understanding of ancient human history, but it’s deeply understudied and underrepresented in modern genetic surveys. While hundreds of thousands of European genomes have been sequenced, only a handful of Indonesian genomes had been sequenced prior to this study, thanks to a 2016 global survey.

This set of complete genomes from 161 people in Indonesia and Papua New Guinea showed that many individuals in this group carried ancestry from both Neanderthals and Denisovans, but the Papuan populations of New Guinea and tropical eastern Indonesia carried groups of genes from two Denisovan groups — one seemingly unique to Oceania.

That Oceania-specific group, D2, may represent a different group of humans altogether. It’s so different from the other Denisovan group that the team thinks that modern Papuans carry gene variants from lineages that separated over 350,000 years ago.

How the Ancient Past Affects the Present

This ancient discovery has a more pressing application: Improving the healthcare of the individuals who still carry this lineage today. “We don’t think that people have really grasped just how much of a bias this puts on medical research,” says Cox, noting that the scientific community already acknowledges the lack of global representation in genome data.

"…they may have implications for modern issues like obesity."

Modern-day Papuans and people with Papuan ancestry, like many Hawaiians, inherited hundreds of genes from ancient humans that influence their health today. Papuans inherited about 400 genes from the D2 group alone, including immune and fat metabolism genes.

“While we still need to find out exactly what these gene variants do, they may have implications for modern issues like obesity,” Cox says. “Other genes are heavily involved in triggering the immune system, and appear to be associated with better and faster responses to infectious diseases.”

It’s been a busy week for research on ancient life in South East Asia and Oceania. Just Wednesday, scientists announced the discovery of another new species of ancient humans, known as Homo luzonensis, after discovering 12 bones in a cave in the Philippines — a rare feat in the tropics, since the heat and moisture makes preservation difficult. Attempts to extract DNA from H. luzonensis have failed because DNA in bones usually doesn’t survive in tropical environments for more than a few thousand years.

A Tropical Research Bias

The poorly preserved remains of ancient humans in tropical regions have contributed to research bias, causing scientific eyes to turn toward colder areas. Advances in genetic technology, however, are helping make up for lost time. In particular, the genetic record of modern humans is proving to be a reliable way to learn more about ancient humans in this region without having to find their bones.

"We need to stop caring so much about Europe and start looking where all the diversity is — Asia!"

“If you look at modern human diversity, and biological diversity in general, most diversity is in the tropics,” Cox says. “This study — and the Luzon hominin — fits into a much bigger body of scientific findings that show that this was also true for archaic hominins; their center of gravity was in the tropics too.”

In other words, he explains, “we need to stop caring so much about Europe and start looking where all the diversity is — Asia!”

Over the past 15 years, scientists have learned about hobbits on Flores, Denisovans, Homo naledi, Ardipthecus ramidus, a new species of Australopithecus, and now Homo luzonensis. One thing is clear: the evolution of our own species is messy — and is only likely to get messier as more discoveries are made.

“If we have found these fossils in just the last few decades,” DeSilva says, “can you imagine how much more must be out there waiting to be discovered?”

Abstract:

Genome sequences are known for two archaic hominins—Neanderthals and Denisovans—which interbred with anatomically modern humans as they dispersed out of Africa. We identified high-confidence archaic haplotypes in 161 new genomes spanning 14 island groups in Island Southeast Asia and New Guinea and found large stretches of DNA that are inconsistent with a single introgressing Denisovan origin. Instead, modern Papuans carry hundreds of gene variants from two deeply divergent Denisovan lineages that separated over 350 thousand years ago. Spatial and temporal structure among these lineages suggest that introgression from one of these Denisovan groups predominantly took place east of the Wallace line and continued until near the end of the Pleistocene. A third Denisovan lineage occurs in modern East Asians. This regional mosaic suggests considerable complexity in archaic contact, with modern humans interbreeding with multiple Denisovan groups that were geographically isolated from each other over deep evolutionary time.