More Information From Denisova

Nature News is reporting about some more evidence from Denisova, following up on the bombshell news last year that bones discovered there belonged to a person (who they named “Denny”) who's father was a Denisovan and mother a Neandertal. From the story:

In the years that followed the discovery of Denisovans, scientists used DNA sequencing to attribute a few molar teeth from the cave to the same group4. They have also found other remains that harboured Neanderthal DNA. The analysis of Denny fills in some important details about the two groups. “We knew that Denisovans and Neanderthals had been there. We just didn’t think they interacted this intimately,” says [Svante] Pääbo. “It was so amazing to find direct proof — to find these people in the act, almost, of mixing.”

Denny’s discovery has also convinced Pääbo and other scientists that the remains of similar individuals, with recent ancestry from two groups of hominin, will be found — perhaps also in Denisova Cave. Researchers who analysed Denny’s genome found signs that the chromosome set that was contributed by her father, although clearly Denisovan, harboured some Neanderthal ancestry, which hints at earlier encounters between the groups2. “We should be able to pick up these individuals,” says [Katerina] Douka.

The Denisova cave appears to have been occupied for several hundred thousand years, being originally settled by either Denisovans or Neandertals, no one is sure which. Subsequent to this, it is unclear how much interbreeding actually occurred. 

“It’s still a head scratcher,” adds Tom Higham, an archaeological scientist at the University of Oxford, UK, who works with Douka and Brown. “It’s either an incredible piece of luck, or interbreeding happens so frequently that we might expect to find these types of occurrence in the archaeological record.”

One thing becomes increasingly clear with each new discovery, however: the complete replacement model of modern human origins, as espoused by Stringer and Andrews, is dead.

Neandertal/Denisovan Hybrid?

As J. Lawrence Angel once said: “When two groups of people meet, they may fight, but they will always mate.”  A story is now coming out of Russia describing more research at the Denisova Cave, in the Altai Mountain region that recounts exactly what Angel was talking about.  From Richard Coniff, at Scientific American:

In a remarkable twist in the story line of early human evolution, scientists have announced the discovery of “Denisova 11”—a female who was at least 13 years old, lived more than 50,000 years ago and was a child of mixed parentage. Her parents were not just of different races, but two different and now-extinct early human types. Their exact taxonomic designations—whether they were separate species or subspecies—is still a matter of scientific debate. But the bottom line for Denisova 11 is that mom was a Neandertal and dad a Denisovan.

This is a remarkable claim, similar to the one that Erik Trinkaus made about the Lagar Velho child discovered in Portugal that is thought to be a Neandertal/modern human offspring. What evidence has been marshalled to support this claim?  In a word: genetics.  The evidence is taken from another bone fragment from the site.  From the abstract:

The father, whose genome bears traces of Neanderthal ancestry, came from a population related to a later Denisovan found in the cave. The mother came from a population more closely related to Neanderthals who lived later in Europe than to an earlier Neanderthal found in Denisova Cave, suggesting that migrations of Neanderthals between eastern and western Eurasia occurred sometime after 120,000 years ago. The finding of a first-generation Neanderthal–Denisovan offspring among the small number of archaic specimens sequenced to date suggests that mixing between Late Pleistocene hominin groups was common when they met.

So, if they interbred regularly (or regularly enough, anyway), why aren't they just one species?  Svante Paabo argues that it is because they simply did not come together very often.  To this, I would argue that they probably also had fairly distinct cultures. 

If this kind of information had come out a few decades back, there would have been quite a few squawks and naysayers but as the evidence piles up for hybridization between many different groups throughout the Pleistocene, researchers have become more accepting of it.  It is pretty clear that the evolutionary picture was a whole lot more complex than we thought. 

National Geographic Special on Denisova

National Geographic is running a special report on the importance of the Denisova hominin for later human evolution.  The timing is curious since this was big news two years ago, but “The Case of the Missing Human Ancestor” goes into the depths of the discovery, the tests done, the complex stratigraphy of the cave, and the significance of what the Max Planck Institute found.  Further, it is written by Jamie Shreeve, and he is always a good read.  He writes:

In the summer of 2010 a human toe bone had emerged, along with the enormous tooth, from Layer 11. In Leipzig a graduate student named Susanna Sawyer analyzed its DNA. At the symposium in 2011 she presented her results for the first time. To everyone’s shock, the toe bone had turned out to be Neanderthal, deepening the mystery of the place.

The green stone bracelet found earlier in Layer 11 had almost surely been made by modern humans. The toe bone was Neanderthal. And the finger bone was something else entirely. One cave, three kinds of human being. “Denisova is magical,” said Pääbo. “It’s the one spot on Earth that we know of where Neanderthals, Denisovans, and modern humans all lived.” All week, during breaks in the conference, he kept returning alone to the cave. It was as if he thought he might find clues by standing where the little girl may have stood and touching the cool stone walls she too may have touched.

Look for this site to continue to influence models of later human evolution. There seem to have been several locations at which there were both, at various times, Neandertals and modern humans.

Denisovan DNA Sequenced

Science Insider is reporting that the entire genetic sequence of the Denisova Cave individual has been completed and posted on the web site at the Max Planck Institute for Evolutionary Anthropology. Ann Gibbons writes:

A year ago, researchers published the first rough draft of the genome of an archaic girl who lived in Denisova Cave, Siberia, at least 30,000 years ago. In January, Max Planck paleogeneticist Svante Pääbo was at a meeting in Sweden when he realized that researchers in other labs were poring over year-old sequence data that was far less complete than what his colleagues had obtained in the lab in the past year using sensitive, new methods to sequence ancient DNA. "I felt bad knowing that we had this very much better version of the same genome and that it would be a few months before it became available," says Pääbo.

I am curious to see what sorts of ERVs are present and if any are derived from the Neandertal condition. A wealth of studies are just waiting to be done.

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Dear Svante, I am a Neandertal

The Guardian's Notes and Theories has a column on the mail that Svante Pääbo received after delivering the revelation that Neandertals and Early modern humans interbred. They write:

In the months after the paper was published, Pääbo began to receive letters and emails from people who had read about the work. He decided to keep track of the correspondence, at least until September that year, to see if any trends appeared. He wasn't disappointed.

Some 45 men wrote in to declare themselves fully or partially Neanderthal and several asked if they should provide saliva samples for Pääbo to analyse. Over the same few months, only two women wrote in to declare themselves of Neanderthal stock.

I think that it was Dave Frayer who once said that, on an individual trait basis, you could see the remnants of Neandertals in the modern European populations but that if you took the whole suite of Neandertal traits, there wasn't a person alive who had them. I wonder what led the women to think they were Neandertals? “Evening vear. Svimvear. Very nice!”

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Answers in Genesis on the Neandertal Genome

I missed this a month back. AIG weighed in on the sequencing of the Neandertal Genome here. If you will recall, it was found by Svante Paabo and colleagues that Neandertals appear to have contributed at least 4% of their DNA to modern humans, thus strongly suggesting that the speciation event in sub-Saharan Africa that gave rise to modern humans was not total, with at least some interbreeding between the two groups. The article by Layman, reads thus:

The news doesn’t surprise young-earth creationists, who predicted overlap between modern human and Neanderthal genomes. Based on Scripture, creationists consider Neanderthals to have been fully human, descendants of Adam and Eve (through Noah), and therefore they would have lived in the same time and place as other humans. But factors related to both the dispersion at Babel and environmental pressures afterward resulted in people groups with different physical characteristics, including humans with “Neanderthal” characteristics.

Liberty University cell biologist (and creationist) David DeWitt called the research an “amazing feat” of science that supports creationist expectations. “Finding Neanderthal DNA in humans was not expected by evolutionists, but it was predicted from a creation standpoint because we have said all along that Neanderthals were fully human: descendants of Adam and Eve, just like us,” he told News to Note.

There is no explanation as to why this finding would "not be expected by evolutionists." There are quite a few models that would welcome this sort of explanation. It is only unexpected if you are unfamiliar with the data or the models. As for whether Neandertals were "fully human," there is a problem with that: Neandertals aren't fully human. That is the source of the controversy in the first place. Many anthropologists regard them as a separate species of human based on their distinctness from modern humans.

The Neandertals represented a distinct European and Near Eastern variant of what has become known as "archaic Homo sapiens." This is a grade of Homo sapiens that existed after Homo erectus/ergaster but before true Homo sapiens, which are decidedly different. As biological anthropologist Dave Frayer has pointed out, there is not a single person alive that has the full suite of Neandertal characteristics. For example, in the following diagram, it is clear that there are sharp differences between these two hominid forms.



Several things are immediately apparent in this comparison. The modern human individual has much reduced ridges over the eyes, a much more vaulted forehead, a smaller nose opening, a shorter, higher cranium, smaller teeth and more forward-placed cheek bones.

There are those that argue, however, that the earliest modern humans have traits that are holdovers from the preceding Neandertals. And for those of us that hold to this perspective, this finding was perfectly expected. The last Neandertals date to around 30 thousand years ago and this overlaps with the earliest modern humans, which date to between 34 and 37 thousand years. At the point of this overlap, the earliest moderns, which are likely migrants from the Near East, either mated with the Neandertals or replaced them. While there has been evidence from the crania of the earliest moderns that some degree of interpopulational mating has occurred, the DNA evidence has largely supported the replacement idea. Svante Paabo's evidence changes that.

Anthropologist Richard Klein has stated that he doesn't see how any modern human would have found a Neandertal attractive enough to mate with. What the findings from the Neandertal genome show us is that two very different groups of people met somewhere in Europe between 30 and 40 thousand years ago and that some of the moderns did find the Neandertals suitable as mates. But modern human the Neandertals certainly were not.

P.S. Why don't sites like AIG and the Discovery Institute allow comments by readers? It would have been nice to simply point this out on the AIG site.

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