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The Cave Where It Happened: The Daughter of a Neanderthal Mom and a Denisovan Dad

Once upon a time, in a cave in the Altai Mountains of southern Siberia, different types of ancient peoples were having sex.

A new report in Nature from Svante Pääbo, the Max Planck Institute for Evolutionary Anthropology superstar, and his team introduces the young teen “Denisova 11.” I’ll call her Eleven, in honor of the beloved character in the TV show Stranger Things. She was a type of archaic human called a Denisovan, pronounced “Denise-o-van.”

The title of the new paper tells the whole tale: “The genome of the offspring of a Neandertal mother and a Denisovan father.”

The valley above the cave where it happened (with apologies to the score of Hamilton). (Credit: Bence Viola, Max Planck Institute for Evolutionary Anthropology)

Introducing Denise

The research team introduced the first Denisovan, named Denise, in 2010, based on a preliminary genome sequence from her finger bone, discovered in 2008 in the cave. Denise lived 32,000 to 50,000 years ago and had dark skin and brown eyes and hair. Her genome included some Neanderthal sequences, so it was clear there’d been some mixing of genomes going on.

A few other Denisovans emerged from the collection of 2,000 or so bone fragments collected from the cave. “The Denisova Genome and Guys Banging Rocks,” which I wrote for Scientific American blogs awhile back, fleshes out the story.

We only have evidence of Denisovans from that one cave, but abundant bones indicate that Neanderthals roamed western Eurasia. Modern human genomes replaced both by about 40,000 years ago, with some Neanderthal DNA remaining in today’s European genomes and Denisovan DNA in Northern Island Melanesians and in Papua New Guineans. Australian aborigine genomes harbor sequences from Neanderthals and Denisovans.

Neanderthals Spread Their Seed

DNA evidence is collected nondestructively, from bits of dust shaved from the bones. Then gene and genome comparisons can fill in some of the blanks, along with traditional types of evidence.

  • Calculating backwards from DNA sequence differences, using a molecular clock based on mutation rates, reveals that Neanderthals and Denisovans diverged from a shared ancestor more than 390,000 years ago.
  • Eleven’s mitochondrial DNA was Neanderthal, and therefore so was her mother.
  • The thickness of a bone fragment indicates that she was at least 13 when she died.
  • Radiocarbon dating places her time in the cave to more than 50,000 years ago.

Svante Pääbo, director of the Department of Evolutionary Genetics at the Max Planck Institute for Evolutionary Anthropology in Leipzig, and a friend.

The researchers found that 38.6% of Eleven’s DNA pieces hailed from a Neanderthal and 42.3% from a Denisovan. That’s about equal, considering that the parents did share a distant ancestor, so some sites in the genome are identical in both chromosomes, and therefore parental origin obscured. The explanation most consistent with shared sequences approaching 50:50 is that Eleven had one Neanderthal parent and one Denisovan parent, rather than being the product of a population with many N-D couplings over time.

The teen’s genome also harbors at least five million-base-long stretches, identical on both chromosomes of a pair, that are totally Neanderthal. That would mean that the Denisovan dad had some Neanderthal DNA himself. Plus, his Neanderthal DNA sequences don’t quite match those from Eleven’s mom, suggesting that Neanderthal DNA might have entered a few times, as far back as 300-600 or so generations. Those guys got around.

For some reason I’m picturing hordes of Harvey Weinsteins traipsing across Asia and impregnating Neanderthals and Denisovans and whomever else was around and walked erect, a little like Genghis Khan spreading his Y chromosome far and wide a thousand years ago. Whatever the DNA sequences say, these folks from what anthropologists are deeming different groups presumably looked and smelled enough alike to mate and leave children. And of course I’m wondering whether the sex was consensual or forced. That’s fodder for another post …


Those sexy Neanderthals may have been around even more recently than Eleven’s time of 50,000 years ago. DNA from a jaw bone from “An early modern human from Romania with a recent Neanderthal ancestor,” also published in Nature from Pääbo’s team, deduces an encounter with a Neanderthal who may have lived just four to six generations before the date of the jaw bone, about 40,000 years ago.

The Future of Humanity

The new report glimpses the sorting out of genomes – sex – that led to us, even as lineages yet unknown branched off from the path to modern humanity. But imagining what actually went on in that cave is a little like trying to reconstruct the story of the wizard of Oz solely from the wicked witch’s feet curling up under the house that crushed her. Still, any paper on the fascinating Neanderthals and Denisovans, whether they hooked up or not, makes me think about the future of our species

Things could go either of two ways.

People might continue to mix and blend, destroying the notion of races that never had a basis in human biology anyway. Or hatred of those perceived as “other” might prevail, fueling a splintering of humanity.

How far will the “us and them” mindset go?

The current divisiveness is so unrelenting that even when I read technical articles about our deep past, I can’t help but imagine humanity in a time before our advanced brains invented the idea of “otherness.”


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