Book Excerpt: Bigfoot—A Neanderthal Connection?

Human DNA and the Hunt for an Ape-Man

The two most promising candidates as the source of our anomalous primate, be it ‘yeti’ or ‘Bigfoot,’ are the giant ape Gigantopithecus and other human species, like Neanderthals, favored by Belgian biologist Bernard Heuvelmans and Russian hominologist, Boris Porchnev. There are several books that debate these two themes, often in great detail and with great passion, but which tend to forget that they have no convincing evidence for either. Both species are generally held to be extinct, though, as we have seen, the hope among cryptozoologists is that there are surviving pockets in remote parts of the world. Until very recently, there was no serious intellectual platform to support either theory. While nothing has happened to enhance the pros­pects of Gigantopithecus as the biological incarnation of yeti or Bigfoot, there has been spectacular progress in discovering the complexity of our own human evolution. It now seems as though our Homo sapiens ancestors shared the planet with several other human species and even interbred with them. The notion that there could be parts of the earth where these other humans survive to this day, either as a completely separate species or as a type of genetic hybrid, does not seem anywhere near as ridicu­lous as it once did.

The currents of thought in the matter of human evolution have flowed back and forth ever since Darwin convinced the world (or most of it) that we evolved from other species over a very long period rather than being created in our present form. The discovery, which began our appreciation that we have not always been the only human species on the planet, was made in 1856 when a very odd skull was found in a limestone cave near Dusseldorf, Germany. Among other unusual features, it had a receding forehead and very prominent brow ridges. At first it was dismissed as a freak, a mutant with some sort of deformity. However, when other very similar skulls began to turn up from excavations, first in Gibraltar, France, and Belgium, and later in the Middle East, it slowly dawned on antiquarians, the nineteenth­ century predecessors of today’s paleontologists, that these were not diseased skulls at all, but, they belonged to another type of human, eventually called Neanderthal after the Neander Valley (Thai in German) where the first skull, the type specimen as it is called, was discovered. There followed over a century of often-acrimonious debate as to whether Neanderthals were our own ancestors or whether they belonged to a different species now extinct. Judging by the age and distribution of Neanderthal and Homo sapiens fossils, the two species did share the same geographical range in Europe as well as further east. The long debate was finally settled in the 1980s when both genetic and careful anatom­ical analyses concluded that Neanderthals were a completely separate species and that our own ancestors, ‘newly’ arrived in Europe from Africa 40,000 to 50,000 years ago, had replaced them.

The argument appeared to be settled after the successful recovery of DNA from the Neanderthal-type specimen in 1997, which showed that its mitochondrial DNA sequence was quite unlike that of any modern human. The intellectual dominance of the ‘Recent Out of Africa’ camp lasted until 2010, when the same German team that had published the first Neanderthal mitochondrial DNA in 1997 declared, to an astonished and admiring world, that they had succeeded in sequencing the entire genome (more or less) from a particularly well-preserved set of Neanderthal bone fragments from Vindija cave in Croatia. The 2010 paper did not entirely reverse the earlier conclusion that we are the descendants of a separate species rather than merely modified Neanderthals, but it did add an intriguing twist. After comparing the Neanderthal DNA sequence with modern Homo sapiens genomes from Europe and Africa, the authors concluded that Europeans, though not Africans, were partly descended from Neanderthals rather than being genetically entirely separate. All Europeans tested, then and since, have inherited between 2% and 4% of their nuclear DNA from a Neanderthal ancestor. The ex­planation given was that this could only have occurred through interbreeding. This shocking news, for it was a shock to all concerned, has taken time to digest. Even the principal investi­gator, Svante Paabo, didn’t believe it at first, instructing his colleagues to double-check the data and the calculations.

The reasoning is complex and depends on three-way compari­sons of the sequences from Neanderthal, European, African, and also Asian genomes. This is not something one can do on the back of an envelope, and it required the pooled expertise of many of the world’s top brains in the new field of bioinformatics, assisted by a cluster of 256 computers, to score and compare the sequences of the billions of DNA fragments streaming from the new generation of DNA sequencing machines. The basic ques­tion asked of each of the Neanderthal DNA fragments was this: is it more similar to the same fragment in a modern European, or a modern African, genome? The null hypothesis was that the Neanderthal DNA fragments would most closely resemble an African Homo sapiens sequence 50% of the time and a European Homo sapiens sequence 50% of the time. This would indicate that there was no interbreeding. This hypothesis is based on the assumption that Neanderthals shared a common ancestor with all Homo sapiens, so any changes in the DNA sequences between humans and Neanderthals must have occurred since that split from the common ancestor. As the time elapsed since the split from the common ancestor is the same for all modern humans, whether Africans or Europeans, and changes accumulate at a steady rate, the null hypothesis predicts that the matches scored in Neanderthal vs. African and Neanderthal vs. European sequence comparisons would be equal.

But they are not. The Neanderthal fragments were slightly more similar to their equivalent fragments in European than in African genomes. The null hypothesis predictions of 50/50 balance were shifted faintly in favor of a closer genetic match to Europeans than to Africans. In one comparison, for example, Neanderthal fragments had closer matches to a modern French genome 52.5% of the time, and to a Yoruba from Nigeria in 47.5% of comparisons. Though the difference is small, so many millions of comparisons were made for each analysis that the final result is highly statistically significant.

Less clear, though, are the alternative interpretations. For example, if Neanderthals were descended from an ancient African population in, say, East Africa that was also the source of later Homo sapiens dispersals that shared ancestry may have contri­buted to the closer genetic affinities to Europeans apparent in the sequence comparisons. Or could it be that the genome of Homo sapiens changed to meet the much colder conditions of Ice-Age Europe in the same way as the Neanderthal genome became adapted hundreds of thousands of years earlier? An intriguing paper published in 2011 noted that the DNA segment with one of the strongest similarities between Neanderthal and modern Europeans is located in the part of the genome that controls the immune response, vital for fighting infections. Having the same immune response genes as Neanderthals, perhaps through interbreeding or maybe through selection of pre-existing genetic variants, could well have been critical for the survival of Homo sapiens in Europe in the face of resident Neanderthal pathogens.

Svante Paabo, who led the Neanderthal Genome Project, has written a candid first-hand account, which covers all these possibilities, and reveals the excruciating complexity of the venture. It wasn’t only the bioinformatics that were difficult. Getting reliable data from the tiny percentage of Neanderthal DNA remaining in the Vindija bone fragments in the face of overwhelming amounts of bacterial and modern human contamination was a grueling business indeed, taking its toll on budgets, collaborations, and even on Paabos’ health.

One immediate puzzle that needed explaining was this. How is it that not a single Neanderthal mitochondrial DNA has ever been found in a modern European? Several hundreds of thousands, maybe even a million, Europeans have had their mito­chondrial DNA tested whether in research projects or as customers of genetic genealogy companies. Yet there has never been a whisper of Neanderthal mitochondrial DNA in any of them. Although mitochondrial DNA is inherited exclusively down the maternal line, all things being equal, we should expect the same proportion of mitochondrial DNA with a Neanderthal origin in modern Europeans and Asians as there is Neanderthal nuclear DNA. With the average amount of Neanderthal nuclear DNA in Europeans estimated to be 2.5%, then if a million Europeans have had their mitochondrial DNA analyzed, which is a reasonable estimate after two decades of widespread testing, 25,000 of them would have shown a Neanderthal result. There is not a single one.

This anomaly isn’t quite as hard to explain as it first seems, though it remains something of a puzzle to me. The solution offered by statisticians is centered on the fact that mitochondrial DNA is far more likely than its nuclear counterpart to be lost as it travels through the generations. For example, a woman will pass her nuclear DNA to both her sons and daughters. However, thanks to its strict matrilineal inheritance pattern, only her daugh­ters will pass on her mitochondrial DNA to the next generations. Although her nuclear DNA will live on in her sons’ children, her mitochondrial DNA dies with them. The upshot of all this is that, on average, four times less mitochondrial DNA is passed on to the next generation compared to nuclear DNA. This same equation applies to each generation, so very soon there are fewer and fewer different mitochondrial DNAs in circulation.

Mitochondrial DNA can never be lost entirely because it is vital for aerobic metabolism. Nevertheless, after a few hundred generations it is theoretically possible for Neanderthal nuclear DNA to have gotten through to the present day and for all the Neanderthal mitochondrial DNA to have been lost. This eradica­tion was never certain to happen, and the other scenario might have been that Neanderthal mitochondrial DNA did get through and lots of people had it. In The Seven Daughters of Eve I explain how I found that over 95% of native Europeans are matrilinear descendants of only seven ancestral clan mothers. If Neanderthal mitochondrial DNA had survived as well as its nuclear equivalent, at least one of these seven women might have been a Neanderthal. But that did not happen and, as the authors of the 2010 paper argued, it is just a matter of chance that no one these days carries the mitochondrial DNA of a Neanderthal.

The other solution was that the interbreeding which led to the Neanderthal DNA getting into the human genome in the first place was all between Neanderthal men and Homo sapiens women. In that frankly unlikely scenario, there would be no Neanderthal mitochondrial DNA in any of the offspring. This was diminished as an explanation when further work showed that there were no Neanderthal Y-chromosomes, which would have come from males, in modern Europeans either.

A few weeks before the Neanderthal genome paper was published in 2010, another astonishing genetic revelation found its way into the journal Nature: Here the same team that had sequenced the Neanderthal genome announced that they had identified a new human species. Mitochondrial DNA was extracted from a fragment of a little finger bone found alongside other human remains in Denisova Cave in the Altai Mountains of southern Siberia during an excavation in 2008. The sequence showed that this bone fragment belonged not to a Neanderthal, nor to a Homo sapiens but to an as yet unknown human species. Following the tradition of naming a species after the place where it was found, the authors were tempted to name this as Homo altaiensis. They wisely recanted, as all that remained on which to base a description of the new species was the fragment of finger bone, two molar teeth found nearby, and the DNA sequence. There are strict rules about naming new species, as Heuvelmans discovered to his cost when he tried to register the Minnesota Iceman as Homo pongoides (literally man-ape). Heuvelmans’ attempt to file his new species name without a type specimen so enraged traditional taxonomists that they lobbied, successfully, to have it struck off the official register of species.

Paabo wisely avoided any such controversy, so there is no Homo altaiensis, at least not yet. The new species is, for the moment, known simply as Denisovan.

Another great surprise was that the Denisovan bone was in such good condition. It was no bigger than two grains of rice, but contained more intrinsic DNA than all the Vindija Neanderthal fragments put together. Exactly why this should be is still a mystery. The sample is too small to be carbon-dated so we do not know how old it is. One possibility is that it is very much younger than the less-well-preserved Neanderthal fossils. Paabo even suggests, though not very seriously, that it might be from a modern alma. Now that would be something. It would also be vindication of a sort for Russian hominologists, from Porchnev onward, who always believed in the survival of Neanderthals. I am sure they would settle for Denisovans instead.

When the Denisovan sequence was compared to the same region in modern humans and in the six complete Neanderthal mitochondrial DNA sequences known by that time, there were twice as many differences between the Denisovan and Homo sapiens as there were between ourselves and Neanderthals. By this reckoning, the Denisovans were our considerably more distant relatives than the Neanderthals. An estimate can be made, based on the differences between the DNA sequences, of how much time has passed since two species last shared a common ancestor. There are many provisos in such estimates and nobody relies too much on the precision of the figures; but, roughly speaking, the last common ancestor we shared with the Denisovans lived about a million years ago while the same calculations split Homo sapiens from Neanderthals about half a million years back.

Thanks to the exceptional preservation of the Denisovan bone fragment, it did not take long to get a good genome sequence, and a much better one in terms of quality than the Neanderthal. However, there were more surprises in store. A comparison of the Neanderthal and Denisovan nuclear DNA showed that they were much more closely related than the mitochondrial DNA had suggested. One possible explanation for the discrepancy is that the mitochondrial DNA in the Denisovans was actually from yet another, earlier human species with whom their ancestors had interbred. Its survival through interbreeding in Denisovans was just as much a matter of chance as the apparent extinction of Neanderthal mitochondrial DNA in modern humans, where we have the reverse outcome. The matrilineal lineage of the other ancestral species survived in Denisovans whereas most or the entire nuclear DNA had come from the other hybridizing species.

There were yet more surprises to come when the signs of inter­breeding between Neanderthals and ourselves, at least in Europe, was also detected between Denisovans and ourselves. Denisovan nuclear DNA was found not in natives of Europe but of Papua New Guinea and, subsequently, in native Australians and Pacific Islanders, and at a slightly higher level, up to 4.8%. With some Neanderthal thrown in as well, the total percentage of non-sapiens DNA in modern Papuan genomes rises to the substantial total of 7.4 %. To explain the link between Denisovans living forty thousand years ago in Siberia and present-day occupants of Melanesian islands like Papua, New Guinea, the only logical interpretation is that the ancestors of both human species had interacted elsewhere, probably as the ancestors of today’s Papuans were en route to the islands of Melanesia. It is a remarkable story, completely unex­pected from classical palaeontology and the sure sign, if one were needed, of the real contribution ancient DNA is now making to the understanding of our own evolution. It is quite likely that there are more collateral hominids yet to be discovered. Interbreeding between different human species, once thought unlikely or impossible, is now all the rage, with DNA signals of mixing between the ancestors of modern Africans and some other archaic human species. Denisovan-like mitochondrial DNA was recently found in a 400,000 year-old ‘human’ bone excavated from a deep cave-shaft in northern Spain, making it look as though the ancestors of Europeans might have interbred first with Denisovans, then with Neanderthals! What exciting times. Who knows what will turn up next?

 

The above is an edited excerpt of Bigfoot, Yeti, and the Last Neanderthal, (Disinformation Books, 2016) by Bryan Sykes, Ph.D., DSc., a Professor of Human Genetics at the University of Oxford and a Fellow of Wolfson College. Sykes is best known outside the community of geneticists for his best-selling books on the investigation of human history and pre-history through studies of mitochondrial DNA. Visit him at: http://www.oxfordancestors.com.

By Bryan Sykes, Ph.D., D.Sc.