The Other Neanderthal

Meet the first human-related species to be identified with more than fossil records.
A girl looks through the replica of a neanderthal skull. ( Nikola Solic/Reuters )

We don’t know what the Denisovan looked like. We don’t know how it lived, what tools it used, how tall it was, what it ate, or if it buried its dead. 

But from only two teeth and a piece of finger bone smaller than a penny, we’ve been able to extract the rich history of a species that split off from Homo sapiens approximately 600,000 years ago. We know they’re more closely related to Neanderthals than humans—though still distantly. We know they made their way to Southeast Asian islands, interbreeding with indigenous modern human groups in New Guinea and Australia. We know their interspecies mingling with modern humans in mainland Asia was brief, but enough to impart a few genes. And we know Denisovan genes reveal evidence of interbreeding with Neanderthals and an even more archaic hominin species.

It’s the first human cousin species identified with more than fossil records. Instead, scientists used the DNA it left behind. There’s now a mystery on our hands: Who were the Denisovans, and where did they go?

* * * 

“We still don’t know what the Denisovans look like morphologically,” says David Reich, a Harvard University geneticist. “We have two teeth right now and a finger bone, all of which have [Denisovan] DNA. But we don’t have anything else that we can firmly connect to the Denisovans.”

The Denisovan gets its name from the Denisova Cave, tucked away in the Altai Mountains in Siberia, near where the borders of Russia, Mongolia, and China intersect. The Denisovan pinky bone was found in 2008. (The teeth were found eight years before that but weren’t initially identified.) Archaeologists from the Institute of Archaeology and Ethnology of Novosibirsk stumbled upon these fragments as they searched for Neanderthal tools. Despite the presence of tools from the mid-Stone Age Mousterian Neanderthal culture, the finger bone found in Denisova showed mitochondrial DNA (mtDNA) different from Neanderthals or humans. Mitochondrial DNA is exclusively derived matrilineally—that is, tracing descent through the mother’s genetic line—with no information about any admixture deriving from males anywhere along the line. Further analysis of the nuclear genome showed Denisovans are more closely tied to Neanderthals, splitting off some 400,000 years ago.

“The mDNA is only one line of descent; it’s only one part of one’s ancestry, so It’s not a reflection of all your ancestors,” Reich, who worked on the Denisova project, says. “It’s your mother’s mother’s mother’s mother’s mother and you have many ancestors. And your mother’s mother’s mother’s mother’s mother could have lived in a very different population or had a very different history than your mother’s father’s father’s mother’s mother’s mother.” 

In other words, mtDNA is only part of the story.

Reich had previously worked with Denisovan project lead Svante Pääbo of the Max Planck Institute tracing the DNA of Neanderthals. Pääbo and his team knew there was something different about the original mtDNA extracted, which showed 1 million years separation from Neanderthals and modern humans. Reich found more clues in the nuclear genome.

The genome is extracted from the nucleus of the gene rather than the mitochondria organelles, and shows traits inherited from male ancestors—a process that provides a more complete genetic picture of our distant cousin species. As researchers zeroed in on this genome, a picture began to emerge of a separate human lineage. With that, we had a new hominin cousin species hiding in plain sight in East Asia.

Denisovans are an example of—in my mind—how mitochondrial DNA can lead you wrong, and only the nuclear genome tells the full story,” Pääbo said. “The mtDNA of the Denisovans diverge before modern human and Neandertal mtDNA [break off] from each other, yet the nuclear genome shows that they share a common ancestor with Neandertals, but far back in time. Perhaps they even got the mtDNA by gene flow from some other hominin in Asia.”

So the mother’s mother’s mother (ad infinitum) of the Denisovan showed a more ancient lineage than the nuclear genome, which revealed a hominin with a more recent branch of evolution with Neanderthals. The Denisovans split off from the lineage of Neanderthals 200,000 years after humans had already had their split from the species.   

The team found a DNA match for the mysterious human cousin in the islands of Southeast Asia, thousands of years removed from the Siberian Population. It wasn’t through fossil records, but through the DNA of their human descendants. 

Denisovan DNA was compared with modern human populations, matching with the Melanesian people of Papua New Guinea and the Aborigines of Australia. Some—but not all—indigenous populations in the Philippines show evidence of Denisovan ancestry. Melanesians and Aborigines share 5 percent of their DNA with the Denisovan hominin; Filipino indigenous groups like the Mamanwa and the Manobo share as much, if not more. Comparatively, European humans share only between 1 percent and 4 percent of DNA with the Neanderthals. The genetic evidence showed the Siberian Denisovan was distantly related to the Denisovan group that interbred with the island populations of Southeast Asia. The lines between the two Denisovans diverged 280,000 to 400,000 years ago.

The concentration was less in continental Asia. Mainland Asia shows just a fraction—around one-twenty-fifth—of Denisovan ancestry compared to islanders. While the Siberian Denisovan populations lived near the border of modern day China and Mongolia, their genetics didn’t hang around for long. Around the time the Siberian Denisovan was alive 40,000 years ago, the species had already dispersed far and wide, and already interbred with human populations. The Siberian Denisovan first identified in 2010 was a distant relative to her cousins in Southeast Asia.

“What’s quite clear is that 40,000 years ago, Southeast Asia was already a patchwork of peoples with and without Denisovan ancestry,” Reich said. The limited interbreeding that took place on the main Asian continent still shows up in populations there today as a small piece of the Denisovan hominin puzzle.  

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John Wenz is a writer based in Philadelphia.

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