by David Reich
But even if genetic changes—through coordinated natural selection on combinations of many mutations simultaneously—did enable new cognitive capacities, this is a very different scenario from Klein’s idea of a genetic switch. Genetic changes in this scenario are not a creative force abruptly enabling modern human behavior, but instead are responsive to nongenetic pressures imposed from the outside. In this scenario, it is not the case that the human population was unable to adapt because no one carried a mutation that allows a biological capability not previously present. Instead, the genetic formula that may have been necessary to drive the striking advances in human behavior and capacities that occurred during the Upper Paleolithic and Later Stone Ages is not particularly mysterious. The mutations necessary to facilitate modern human behavior were already in place, and many alternative combinations of these mutations could have increased in frequency together due to natural selection in response to changing needs imposed by the development of conceptual language or new environmental conditions. This in turn could have enabled further changes in lifestyle and innovation, in a self-reinforcing cycle. Thus, even if it is true that increases in the frequency of mutations were important in allowing modern humans to match their biology to new conditions during the Upper Paleolithic and Later Stone Age transition, what we now know about the nature of natural selection in humans and about the genetic encoding of many biological traits means it is unlikely that the first occurrence of these mutations triggered the great changes that followed. If we search for answers in a small number of mutations that arose shortly before the time of the Upper Paleolithic and Later Stone Age transitions, we are unlikely to find satisfying explanations of who we are.
How the Genome Can Explain Who We Are
It was molecular biologists who first focused the power of the genome onto the study of human evolution. Perhaps because of their background—and their track record of using reductionist approaches to solve great mysteries of life like the genetic code—molecular biologists were motivated by the hope that genetics would provide insights into the biological nature of how humans differ from other animals. Excitement about this prospect has also been shared by archaeologists and the public. But this research program, important as it is, is still at its very beginning because the answer is not going to be simple.
It is in the area of shedding light on human migrations—rather than in explaining human biology—that the genome revolution has already been a runaway success. In the last few years, the genome revolution—turbocharged by ancient DNA—has revealed that human populations are related to each other in ways that no one expected. The story that is emerging differs from the one we learned as children, or from popular culture. It is full of surprises: massive mixtures of differentiated populations; sweeping population replacements and expansions; and population divisions in prehistoric times that did not fall along the same lines as population differences that exist today. It is a story about how our interconnected human family was formed, in myriad ways never imagined.
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Encounters with Neanderthals
The Meeting of Neanderthals and Modern Humans
Today, the particular subgroup of humans to which we belong—modern humans—is alone on our planet. We outcompeted or exterminated other humans, mostly during the period after around fifty thousand years ago when modern humans expanded throughout Eurasia and when major movements of humans likely happened within Africa too. Today, our closest living relatives are the African apes: the chimpanzees, bonobos, and gorillas, all incapable of making sophisticated tools or using conceptual language. But until around forty thousand years ago, the world was inhabited by multiple groups of archaic humans who differed from us physically but walked upright and shared many of our capabilities. The question that the archaeological record cannot answer—but the DNA record can—is how those archaic people were related to us.
For no archaic group has the answer to this question seemed more urgent than for the Neanderthals. In Europe after four hundred thousand years ago, the landscape was dominated by these large-bodied people with brains slightly bigger on average than those of modern humans. The specimen that gave its name to Neanderthals was found in 1856 by miners in a limestone quarry in the Neander Valley (the German word for valley is Thal or Tal). For years, debate raged over whether these remains came from a deformed human, a human ancestor, or a human lineage that is extremely divergent from our own. Neanderthals became the first archaic humans to be recognized by science. In The Descent of Man, published in 1871, Charles Darwin argued that humans are like other animals in that they are also the products of evolution.1 Although Darwin didn’t himself appreciate their significance, Neanderthals were eventually acknowledged to be from a population more closely related to modern humans than to living apes, providing evidence for Darwin’s theory that such populations must have existed in the past.
Over the next century and a half there were discoveries of many additional Neanderthal skeletons. These studies revealed that Neanderthals had evolved in Europe from even more archaic humans. In popular culture, they garnered a reputation as beastly—much more different from us than they in fact were. The primitive reputation of Neanderthals was fueled in large part by a slouched reconstruction of the Neanderthal skeleton from La Chapelle-aux-Saints, France, made in 1911. But from all the evidence we have, before about one hundred thousand years ago, Neanderthals were behaviorally just as sophisticated as our own ancestors—anatomically modern humans.
Both Neanderthals and anatomically modern humans made stone tools using a technique that has become known as Levallois, which requires as much cognitive skill and dexterity as the Upper Paleolithic and Later Stone Age toolmaking techniques that emerged among modern humans after around fifty thousand years ago. In this technique, flakes are struck off carefully prepared rock cores that have little resemblance to the resulting tools, so that craftspeople must hold in their minds an image of what the finished tool will look like and execute the complex steps by which the stone must be worked to achieve that goal.
Other signs of the cognitive sophistication of Neanderthals include the evidence that they cared for their sick and elderly. An excavation at Shanidar Cave in Iraq has revealed nine skeletons, all apparently deliberately buried, one of which was a half-blind elderly man with a withered arm, suggesting that the only way he could have survived is if friends and family had lovingly cared for him.2 The Neanderthals also had an appreciation of symbolism, as revealed by jewelry made of eagle talons found at Krapina Cave in Croatia and dating to about 130,000 years ago,3 and stone circles built deep inside Bruniquel Cave in France and dating to around 180,000 years ago.4
Yet despite similarities between Neanderthals and modern humans, profound differences are evident. An article written in the 1950s claimed that a Neanderthal on the New York City subway would attract no attention, “provided that he were bathed, shaved, and dressed in modern clothing.”5 But in truth, his or her strangely projecting brow and impressively muscular body would be giveaways. Neanderthals were much more different from any human population today than present-day populations are from each other.
The encounter of Neanderthals and modern humans has also captured the imagination of novelists. In William Golding’s 1955 The Inheritors, a band of Neanderthals is killed by modern humans, who adopt a surviving Neanderthal child.6 In Jean Auel’s 1980 The Clan of the Cave Bear, a modern human woman is brought up by Neanderthals, and the conceit of the book is a dramatization of what close interaction of these two sophisticated groups of humans, so alien to each other and yet so similar, might have been like.7
There is hard scientific evidence that modern humans and Neanderthals met. The most direct is from western Europe, where Neanderthals disappeared around thirty-nine thousand years ago.8 The arrival of modern humans in western Europe was at least a few thousand years earlier, as is evident at Fumane in southern Italy where around forty-four thousand years ago, Neanderthal-type stone tools gave way to tools t
ypical of modern humans. In southwestern Europe, tools typical of modern humans, made in a style called Châtelperronian, have been found amidst Neanderthal remains that date to between forty-four thousand and thirty-nine thousand years ago, suggesting that Neanderthals may have imitated modern human toolmaking, or that the two groups traded tools or materials. Not all archaeologists accept this interpretation, though, and there is ongoing debate about whether Châtelperronian artifacts were made by Neanderthals or by modern humans.9
Meetings between Neanderthals and modern humans took place not only in Europe but almost certainly in the Near East as well. After around seventy thousand years ago, a strong and successful Neanderthal population expanded from Europe into central Asia as far as the Altai Mountains, and into the Near East. The Near East had already been inhabited by modern humans, as attested by remains at Skhul Cave on the Carmel Ridge in Israel and Qafzeh Cave in the Lower Galilee dating to between about 130,000 and 100,000 years ago.10 Later, Neanderthals moved into the region, with one skeleton at Kebara Cave on the Carmel Ridge dating to between sixty and forty-eight thousand years ago.11 Reversing the expectation we might have that modern humans displaced Neanderthals at every encounter, Neanderthals were advancing from their homeland (Europe) even as modern humans retreated. Sometime after sixty thousand years ago, though, modern humans began to predominate in the Near East. Now the Neanderthals were the losers in the encounter, and they went extinct not only in the Near East but eventually elsewhere in Eurasia as well. So it was that in the Near East there were at least two opportunities for encounters between Neanderthals and modern humans: when early modern humans first peopled the region before around one hundred thousand years ago and established a population that met the expanding Neanderthals, and when modern humans returned and displaced the Neanderthals there sometime around sixty or fifty thousand years ago.
Figure 6. After around 400,000 years ago, Neanderthals were the dominant humans in western Eurasia, eventually extending as far east as the Altai Mountains. They survived an initial influx of modern humans at least by 120,000 years ago. Then, after 60,000 years ago, modern humans made a second push out of Africa into Eurasia. Before long, the Neanderthals went extinct.
Did the two populations interbreed? Are the Neanderthals among the direct ancestors of any present-day humans? There is some skeletal evidence for hybridization. Erik Trinkaus identified remains such as those from Oase Cave in Romania that he argued were intermediate between modern humans and Neanderthals.12 However, shared skeletal features sometimes reflect adaptation to the same environmental pressures, not shared ancestry. This is why archaeological and skeletal records cannot determine the relatedness of Neanderthals to us. Studies of the genome can.
Neanderthal DNA
Early on, scientists studying ancient DNA focused almost exclusively on mitochondrial DNA, for two reasons. First, there are about one thousand copies of mitochondrial DNA in each cell, compared to two copies of most of the rest of the genome, increasing the chance of successful extraction. Second, mitochondrial DNA is information-dense: there are many more differences for a given number of DNA letters than in most other places in the genome, making it possible to obtain a more precise measurement of genetic separation time for every letter of DNA that is successfully analyzed. Mitochondrial data analysis confirmed that Neanderthals shared maternal-line ancestors with modern humans more recently than previously thought13—the best current estimate is 470,000 to 360,000 years ago.14 Mitochondrial DNA analysis also confirmed that the Neanderthals were highly distinctive. Their DNA type was outside the range of present-day variation in humans, sharing a common ancestor with us at a date several times more ancient than the time when “Mitochondrial Eve” lived.15
Neanderthal mitochondrial DNA provided no support for the theory that Neanderthals and modern humans interbred when they encountered each other, but at the same time the mitochondrial DNA evidence could not exclude up to around a 25 percent contribution of Neanderthals to the DNA of present-day non-Africans.16 There is a reason why we have so little power to make statements about the Neanderthal contribution to modern humans based only on mitochondrial DNA. Even if modern humans outside Africa today do have substantial Neanderthal ancestry, there are only one or few women who lived at that time and were lucky enough to pass down their mitochondrial DNA to present-day people, and if most of those women were modern humans, the patterns we see today would not be surprising. So the mitochondrial data were not conclusive, but nevertheless the view that Neanderthals and modern humans did not mix remained the scientific orthodoxy until Svante Pääbo’s team extracted DNA from the whole genome of a Neanderthal, making it possible to examine the history of all its ancestors, not just the exclusively maternal line.
The advance to sequencing the whole Neanderthal genome was made possible by a huge leap in the efficiency of the technology for studying ancient DNA in the decade after the sequencing of Neanderthal mitochondrial DNA.
The mainstay of ancient DNA research prior to 2010 was a technique called polymerase chain reaction (PCR). This involved selecting a stretch of DNA to be targeted, and then synthesizing approximately twenty-letter-long fragments of DNA that match the genome on each side of the targeted segment. These unique fragments pick out the targeted part of the genome, which is then duplicated many times over by enzymes. The effect is to take a tiny fraction of all the DNA in the sample and make it the dominant sequence. This method throws away the vast majority of DNA (the part that is not targeted). Nevertheless, it can extract at least some DNA that is of interest.
The new approach for extracting ancient DNA was radically different. It relied on sequencing all of the DNA in the sample, regardless of the part of the genome it comes from, and without preselecting the DNA based on targeting sequences. It took advantage of the brute power of new machines, which from 2006 to 2010 reduced the cost of sequencing by at least about ten thousandfold. The data could be analyzed by a computer to piece together most of a genome, or alternatively to pick out a gene of interest.
To make the new approach work, Pääbo’s team needed to overcome several challenges. First, they needed to find a bone from which they could extract enough DNA. Anthropologists often work with fossils—bones completely mineralized into rocks. But it is impossible to get any DNA from a true fossil. Pääbo was therefore looking for bones that were not completely mineralized but contained organic material, including stretches of well-preserved DNA. Second, supposing the team could find a “golden sample” with well-preserved DNA, they still had to overcome the problem of contamination of the sample by microbial DNA, which comes from the bacteria and fungi that embed themselves in bone after an individual’s death. These contribute the overwhelming majority of DNA in most ancient samples. Finally, the team had to consider the likelihood of contamination by the researchers—archaeologists or molecular biologists—who handled the samples and chemicals and may have left traces of their own DNA on them.
Contamination is a huge danger for studies of ancient human DNA. Contaminated sequences can mislead analysts because the modern humans handling the bone are related, even if very distantly, to the individual being sequenced. A typical Neanderthal ancient DNA fragment from a well-preserved sample is only about forty letters long, while the rate of differences between modern humans and Neanderthals is about one per six hundred letters, so it is sometimes impossible to tell whether a particular stretch of DNA comes from the bone or from someone who handled it. Contamination has bedeviled ancient DNA researchers time and again. For example, in 2006 Pääbo’s group sequenced about a million letters of DNA from Neanderthals as a trial run prior to whole-genome sequencing.17 A high fraction of the sequences were modern human contaminants, compromising interpretation of the data.18
Modern measures to minimize the possibility of contamination in ancient DNA analysis, which had already begun to be implemented in the 2006 study and which became even more elaborate afterward, involve an obsessive set of precautions. For the
2010 study in which Pääbo and his team successfully sequenced an uncontaminated Neanderthal genome, they took each of the bones they screened into a “clean room,” which they adapted from the blueprints of the clean spaces used in microchip fabrication facilities in the computer industry. There was an overhead ultraviolet (UV) light of the same type used in surgical operating suites that was turned on whenever researchers were not present, in order to convert contaminating DNA into a form that cannot be sequenced (the light also destroys ancient DNA on the outside of samples, but researchers drill beneath the surface and so are able to access DNA that is not destroyed). The air was ultra-filtered to remove tiny dust particles—anything more than one thousand times smaller than the width of a human hair—that might contain DNA. The suite was pressurized so that air flowed from inside to outside, to protect the samples from any contaminating DNA wafting in from outside the lab.
There were three separate rooms in the suite. In the first, the researchers donned full-body clean suits, gloves, and face masks. In the second, they placed the bones chosen for sampling into a chamber where they were exposed to high-energy UV radiation, again with the goal of converting the contaminating DNA that might be lying on the surface into a form that cannot be sequenced. The researchers then cored the bones using a sterilized dental drill, collected tens or hundreds of milligrams of powder onto UV-irradiated aluminum foil, and deposited this powder into a UV-irradiated tube. In the third chamber, they immersed the powder into chemical solutions that removed bone minerals and protein, and ran the solution over pure sand (silicon dioxide), which under the right conditions binds the DNA while removing the compounds that poison the chemical reactions used for sequencing.