Evolution in the News - January 2019
by Do-While Jones

Prehistoric Mating

Did Neanderthals Date Denisovans?

New Scientist and Nature both thought the speculation about “Denny” (the fictional offspring of a Denisovan and a Neanderthal) was one of the top stories of 2018, so let’s tell the whole story from the beginning.

Svante Pääbo

Denny is fictional—but Svante Pääbo is the real person at the center of the story. He first appeared on the scene in 1985 when he published an article about ancient Egyptian mummy DNA. 1 This led to his work on molecular cloning and enzymatic amplification which allowed him to extract DNA from a frozen mammoth carcass in 1994. 2 He kept trying to extract DNA from older and older sources, and turned his attention to Neanderthals in 1997.

Munich-based ancient-DNA pioneer Svante Pääbo and his colleagues, described DNA extracted from the bones of the first ever Neanderthal to be discovered, the historic 'Feldhofer' Neanderthal, found in Germany in 1856. That benchmark study was published in the journal Cell in 1997. 3

He has been a recognized expert in extracting DNA from ancient sources for over 30 years.

Those of us who watched the O.J. Simpson murder trial (in 1994) remember the expert testimony about how quickly DNA degrades, so we might reasonably dispute the accuracy of analysis of DNA from old bones—but we won’t. That argument would be too boring and technical. Let’s just assume the DNA analysis is accurate—even if it might not be.

Svante Pääbo, a palaeogeneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, began his Neanderthal Genome Project about two years ago [that is, 2004]. He and his team have probed 60 Neanderthal specimens from museums for hints that the DNA might have survived millennia of degradation. 4

Svante Pääbo has been analyzing ancient DNA for a long time, and his peers trust his analysis.

The Denisovan Theory

The Denisovan speculation began in 2010.

In the summer of 2008, Russian researchers dug up a sliver of human finger bone from an isolated Siberian cave. The team stored it away for later testing, assuming that the nondescript fragment came from one of the Neanderthals who left a welter of tools in the cave between 30,000 and 48,000 years ago. Nothing about the bone shard seemed extraordinary.

Its genetic material told another story. When German researchers extracted and sequenced DNA from the fossil, they found that it did not match that of Neanderthals — or of modern humans, which were also living nearby at the time. The genetic data, published online in Nature, reveal that the bone may belong to a previously unrecognized, extinct human species that migrated out of Africa long before our known relatives.

"This really surpassed our hopes," says Svante Pääbo, senior author on the international study and director of evolutionary genetics at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. "I almost could not believe it. It sounded too fantastic to be true." 5

The fossil in question is a tiny bone fragment which is assumed to be a fingertip of an unknown human species. In the past, new species were based upon a distinctive “type fossil,” usually a tooth or skull. In this case, the new species is based on DNA that doesn’t match modern human or Neanderthal DNA.

It must not match any known ape DNA, either, or they would have identified it as an ape finger. We are told ape DNA is 98% the same as human DNA. If the unknown DNA is close to (but not exactly like) human DNA, it must be close to ape DNA, too Why assume it came from an unknown human rather than an unknown ape? Is a sliver of a human finger that much different from a sliver of an ape finger?

Apparently they were hoping to find something that could be construed to be a new human species because, "This really surpassed our hopes," says Svante Pääbo. Could hope have biased their analysis?

Although a Neanderthal mtDNA genome differs from that of Homo sapiens at 202 nucleotide positions on average, the Denisova Cave sample differed at an average of 385 positions.

The differences imply that the Siberian ancestor branched off from the human family tree a million years ago, well before the split between modern humans and Neanderthals. If so, the proposed species must have left Africa in a previously unknown migration, between that of Homo erectus 1.9 million years ago and that of the Neanderthal ancestor Homo heidelbergensis, 300,000 to 500,000 years ago. 6

They are making a vast conclusion based on half-vast data. Reasonable people should question the existence of an unknown species that had to have made an unknown migration without any supporting evidence other than DNA that doesn’t match Neanderthal DNA.

That was the background from about a decade ago. Let’s move on from that ancient history to the new discovery.

The New Fossil Evidence

Here is Ian R. Cartwright’s photo of the new discovery (shown larger than actual size):

The bone is only 26 mm (about 1 inch) long, so it is shorter than a toothpick. How do they know it is from a Denisovan? We are glad you asked!

Skeletal puzzle
Archaeologists are usually pretty good at distinguishing between the bones of ancient humans and those of other animals. But tiny, crumbled fragments with no clear features pose a challenge.

These fragments often make up a significant portion of the remains recovered from archaeological sites, says Tom Higham, an archaeologist at the University of Oxford, UK.

At Denisova Cave, for example, most bone material has been broken up over time by animals such as hyenas, rendering identification by eye impossible. “So it just basically sits in storage not doing anything,” he says,.

But even these tiny bone fragments contain tell-tale molecular signals that can be used to identify which animal group they belong to.

Using a technique called zooarchaeology by mass spectrometry, or ZooMS, researchers can extract collagen — a tough, fibrous protein that forms connective tissue — from a bone and break it down into its constituent units, called peptides. They then look for characteristic ‘fingerprints’ that differentiate the peptides of a hominin from those of, for example, a bear or mammoth.

Denny’s bone fragment was the first to be classified as hominin using this technique, described in a 2016 paper before her DNA had been extracted and sequenced.

The team has examined hundreds more bones since then, identifying the four further hominin specimens which they are currently analysing. 7

They have examined hundreds of tiny bone fragments like this one, and think Denny (and four others) might have come from a prehistoric human.

The denizens of Denisova also bred with contemporary humans, according to Pääbo and Reich's analysis. But the only traces of their DNA to be found in modern humans were in residents of Melanesia, thousands of miles away from Denisova, suggesting that the Denisovans had once lived across Asia. In 2008, Pääbo's team set up a lab in Beijing to screen fossils that might contain Denisovan DNA, in the hope of learning more about them and their interactions with modern humans. Currently, the bone that yielded the Denisovan genome, and a single molar from the same cave, are their only known fossil remains, but other archaic human fossils from Asia could bear traces of this group. 8

Since the only traces of Denisovan DNA found in modern humans comes from people living thousands of miles away, a more logical conclusion (than the speculation that Denisovans once lived all across Asia) is that the genetic similarity is a coincidence.

In 2011, the only “known” fossil remains of Denisovans were one bone and one molar. I could not find any reason for why they believe that molar came from a Denisovan; nor could I find any other reference to Denisovan fossils discovered before Denny. But there could be other fossils which will someday be discovered that “could bear traces” of Denisovan DNA—wishing might make it so!

The Fable

From this one tiny bone fragment they constructed this fable:

Neanderthals and Denisovans are extinct groups of hominins that separated from each other more than 390,000 years ago. Here we present the genome of ‘Denisova 11’, a bone fragment from Denisova Cave (Russia) and show that it comes from an individual who had a Neanderthal mother and a Denisovan father. 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.

Neanderthals and Denisovans inhabited Eurasia until they were replaced by modern humans around 40,000 years ago (40 ka). Neanderthal remains have been found in western Eurasia, whereas physical remains of Denisovans have thus far been found only in Denisova Cave, where Neanderthal remains have also been recovered. Although little is known about the morphology of Denisovans, their molars lack the derived traits that are typical of Neanderthals.

DNA recovered from individuals of both groups suggests that they diverged from each other more than 390 ka. The presence of small amounts of Neanderthal DNA in the genome of ‘Denisova 3’, the first Denisovan individual to be identified, indicates that the two groups mixed with each other at least once. It has also been shown that Neanderthals mixed with the ancestors of present-day non-Africans around 60 ka, and possibly with earlier ancestors of modern humans; and that Denisovans mixed with the ancestors of present-day Oceanians and Asians. Denisovans may furthermore have received gene flow from an archaic hominin that diverged more than a million years ago from the ancestors of modern humans. 9

Supposedly, an unknown human ancestor (the yellow circle in the diagram below) evolved into Neanderthals (blue) and Denisovans (red) about 415,000 years ago (not 1 million years ago as Dalton said in 2010). Then, a Neanderthal man and a Denisovan woman got together about 90,000 years ago to produce a girl who left a bone fragment designated Denisova 11 in a Russian cave.

It is an interesting story—but what’s the proof? The “proof” is nothing more than DNA that is like Neanderthal DNA in some respects, and like Denisovan DNA in some respects.

“The father, whose genome bears traces of Neanderthal ancestry” is purely speculative. Without a birth certificate (or the help of Maury Povich 10 ) they assume the father must have been Denisova 3. They didn’t analyze the DNA of the mother because they don’t know who she was, and don’t have any DNA from the mother to analyze. They just assume she must have been a Neanderthal.

Mixing Facts with Speculation

They think they have demonstrated that Neanderthals mixed with Denisovans. What they actually demonstrated is that they mixed a fact (a specific DNA sequence) with speculation (about how that sequence arose). The only reason they believe Neanderthals and Denisovans mated is because they think Neanderthals and Denisovans must have mated, and they have imagined the DNA of such a mating could have been like the DNA they analyzed.

That’s speculation—not science!

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1 Svante Pääbo, Nature, 18 April 1985, “Molecular cloning of Ancient Egyptian mummy DNA”, pp. 644–645
2 Matthias Hoss, Svante Pääbo, & N. K. Vereshchagin, Nature, 4 August 1994, “Mammoth DNA sequences”, p. 333
3 Henry Gee, Nature, 29 March 2000, “Neanderthal DNA confirms distinct history”, https://www.nature.com/news/2000/000330/full/news000030-8.html
4 Rex Dalton, Nature, 18 May 2006, “Neanderthal DNA yields to genome foray”, pp. 260–261
5 Rex Dalton, Nature, 24 March 2010, “Fossil finger points to new human species”, https://www.nature.com/news/2010/100324/full/464472a.html
6 ibid.
7 Matthew Warren, Nature, 20 September 2018, “Denisovan hybrid cave yields four more hominin bones”, https://www.nature.com/articles/d41586-018-06763-w
8 Ewen Callaway, Nature, 9 August 2011, “Ancient DNA reveals secrets of human history”, https://www.nature.com/news/2011/110809/full/476136a.html
9 Viviane Slon, et al., Nature, 22 August 2018, “The genome of the offspring of a Neanderthal mother and a Denisovan father”, https://www.nature.com/articles/s41586-018-0455-x
10 https://en.wikipedia.org/wiki/Maury_(talk_show)#Paternity_tests