Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past

by David Reich

chromosomes themselves are mosaics of even smaller tiles. For example, the first third of a chromosome a woman passes down to her egg might come from her father and the last two-thirds from her mother, the result of a splicing together of her father’s and mother’s copies of that chromosome in her ovaries. Females create an average of about forty-five new splices when producing eggs, while males create about twenty-six splices when producing sperm, for a total of about seventy-one new splices per generation.

Twenty generations in the past, the number of ancestors is almost a thousand times greater than the number of ancestral stretches of DNA in a person’s genome, so it is a certainty that each person has not inherited any DNA from the great majority of his or her actual ancestors.

These calculations mean that a person’s genealogy, as reconstructed from historical records, is not the same as his or her genetic inheritance.

Queen Elizabeth II of England almost certainly inherited no DNA from William of Normandy, who conquered England in 1066 and who is believed to be her ancestor twenty-four generations back in time.21 This does not mean that Queen Elizabeth II did not inherit DNA from ancestors that far back, just that it is expected that only about 1,751 of her 16,777,216 twenty-fourth-degree genealogical ancestors contributed any DNA to her.

Tracing back fifty thousand years in the past, our genome is scattered into more than one hundred thousand ancestral stretches of DNA, greater than the number of people who lived in any population at that time, so we inherit DNA from nearly everyone in our ancestral population who had a substantial number of offspring at times that remote in the past.

At each place in the genome, if we trace back our lineages far enough into the past, we reach a point where everyone descends from the same ancestor, beyond which it becomes impossible to obtain any information about deeper time from comparison of the DNA sequences of people living today. From this perspective, the common ancestor at each point in the genome is like a black hole in astrophysics, from which no information about deeper time can escape. For mitochondrial DNA this black hole occurs around 160,000 years ago, the date of “Mitochondrial Eve.” For the great majority of the rest of the genome the black hole occurs between five million and one million years ago, and thus the rest of the genome can provide information about far deeper time than is accessible through analysis of mitochondrial DNA.22 Beyond this, everything goes dark.

When an African American person is said to have 80 percent West African and 20 percent European ancestry, for example, a statement is being made that about five hundred years ago, prior to the population migrations and mixtures precipitated by European colonialism, 80 percent of the person’s ancestral threads probably resided in West Africa and the remainder probably lived in Europe.

An equally valid perspective is that one hundred thousand years ago, the vast majority of lineages of African American ancestors, like those of everyone today, were in Africa.

times in the past when the population size was low can be identified based on the periods in the past when a disproportionate fraction of lineages have evidence of sharing common ancestors.

after the separation of non-African and African populations, there was an extended period in the shared history of non-Africans when populations were small, as reflected in evidence for many shared ancestors spread over tens of thousands of years.

the common ancestor of everyone living today (that is, the person in whom modern humanity’s shared copy of FOXP2 last occurred), lived more than one million years ago.

Expanding our analysis to the whole genome, we could not find any location—apart from mitochondrial DNA and the Y chromosome—where all people living today share a common ancestor less than about 320,000 years ago.

only a small fraction of evolution in humans has likely involved intense natural selection for advantageous mutations that had not previously been present in the population.32 Thus, intense and easily detectable episodes of natural selection such as those that have facilitated the digestion of cow’s milk into adulthood are an exception.

identifying more than ten thousand individual mutations that occur at significantly elevated frequency in people with particular traits, including height.

made stone tools using a technique that has become known as Levallois,

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.

Meetings between Neanderthals and modern humans took place not only in Europe but almost certainly in the Near East as well.

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

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 test we developed is now called the “Four Population Test,” and it has become a workhorse for comparing populations. The test takes as its input the DNA letters seen at the same position in four genomes: for example, two modern human genomes, the Neanderthal, and a chimpanzee. It examines whether, at positions where there is a mutation distinguishing the two modern human genomes that is also observed in the Neanderthal genome—which must reflect a mutation that occurred prior to the final separation of Neanderthals and modern humans—the Neanderthal matches the second human population at a different rate from the first. If the two modern humans descend from a common ancestral population that separated earlier from the ancestors of Neanderthals, there is no reason why the mutation is more likely to have been passed down one modern human line than another, and thus the rate of matching of each of the two modern human genomes to Neanderthal is expected to be equal. In contrast, if Neanderthals and some modern humans interbred, the modern human population descended from the interbreeding will share more mutations with Neanderthals.

When we tested diverse present-day human populations, we found Neanderthals to be about equally close to Europeans, East Asians, and New Guineans, but closer to all non-Africans than to all sub-Saharan Africans, including populations as different as West Africans and San hunter-gatherers from southern Africa.

This was the pattern that would be expected if Neanderthals had interbred with the ancestors of non-Africans but not Africans.

But in 2012 we hadn’t yet proven that the interbreeding we had detected was with Neanderthals themselves.

Instead, the patterns could be the result of interbreeding with an as yet unknown archaic human in turn distantly related to Neanderthals.

non-African genomes today are around 1.5 to 2.1 percent Neanderthal in origin,24 with the higher numbers in East Asians and the lower numbers in Europeans, despite the fact that Europe was the homeland of the Neanderthals.25

interbreeding in the Near East provides a plausible explanation for the Neanderthal ancestry that is shared by Europeans and East Asians.

the Aurignacian, the first widespread modern human culture in Europe.

Excoffier argued that the only way that the modern human genome could have ended up with so little Neanderthal ancestry was if expanding modern humans had offspring with other modern humans at least fifty times more often than they did with the Neanderthals living in their midst.

the impact of Neanderthal interbreeding varied dramatically across the genome of non-African people today.

In more than half the genome, no Neanderthal ancestry has been detected in anyone. But in some unusual places in the genome, more than 50 percent of DNA sequences are from Neanderthals.

we found a particularly intense depletion of Neanderthal ancestry by natural selection in two parts of the genome known to be relevant to the fertility of hybrids.

when two populations are so separated that their offspring have reduced fertility, but nevertheless mix together to produce hybrids, it is expected that there will be intense natural selection to remove the factors contributing to reduced fertility.

there tends to be natural selection on chromosome X for stretches of DNA from the population that contributed most of the hybrid population’s ancestry. This causes the hybrid population to derive its chromosome X almost entirely from the majority population, leading to an anomalously low genetic divergence on chromosome X between the hybrid population and one of the hybridizing populations, consistent with the pattern seen in humans and chimpanzees.

when they applied the method to study humans and chimpanzees, they found evidence for an extended period of genetic interchange after population differentiation began, as expected for hybridization.

So in the half million years since Neanderthals and modern humans separated, Neanderthal genomes accumulated mutations that would prove detrimental when later, Neanderthal/modern human interbreeding occurred.

For a long time, many anthropologists favored multiregionalism, the theory that modern humans in any given place in the world descend substantially from archaic humans who lived in the same geographical region.

out-of-Africa theory.

modern humans everywhere derive from a relatively recent migration from Africa and the Near East beginning around fifty thousand years ago.

the out-of-Africa theory emphasizes the recent origin of the differences among present-day human populations, relative to the multimillion-year time depth of the human skeletal record.

This affirms a “mostly out-of-Africa” theory, and also reveals something profound about the culture of those modern humans who must have known Neanderthals intimately.

In 2008, Russian archaeologists dug up a pinky bone at Denisova Cave in the Altai Mountains of southern Siberia, named after an eighteenth-century Russian hermit named Denis who had made his home there.

There are around two hundred mutational differences separating the mitochondrial DNA of people living today from that of Neanderthals. The new mitochondrial DNA from the Denisova finger bone featured nearly four hundred differences from the mitochondrial DNA of both present-day humans and Neanderthals.

Based on the rate at which mutations accumulate, mitochondrial DNA sequences from present-day humans and Neanderthals are estimated to have separated from each other 470,000 to 360,000 years ago.3 The number of mutational differences found in the mitochondrial DNA from the Denisova finger bone suggested a separation time of roughly eight hundred thousand to one million years ago. This suggested that the finger bone might belong to a member of a never-before-sampled group of archaic humans.

Pääbo and his team had already been able to obtain more data on the whole genome (not just mitochondrial DNA) from this small bone than they had previously obtained from Neanderthals.

The invitation to analyze the Denisovan genome was the greatest piece of good fortune I have had in my scientific career.

For the Denisova finger bone, the whole genome painted a very different picture from what was recorded in the mitochondrial DNA.

Neanderthals and the new humans from Denisova Cave were more closely related to each other than either was to modern humans—a different pattern from what was observed in mitochondrial DNA.

separation between the Neanderthal and Denisovan ancestral populations to have occurred 470,000 to 380,000 years ago, and the separation between the common ancestral populations of both of these archaic groups and modern humans to have occurred 770,000 to 550,000 years ago.

Denisovans were cousins of Neanderthals, but were also very different, having separated from Neanderthal ancestors before many Neanderthal traits appeared in the fossil record.

Homo altaiensis is now used in a museum exhibit in Novosibirsk in Russia that describes the discovery at Denisova.