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

by David Reich

But the 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.20 So it is that as we trace each generation back further into the past, a person’s genome is derived from an ever-increasing number of spliced-together ancestral fragments. This means that our genomes hold within them a multitude of ancestors. Any person’s genome is derived from 47 stretches of DNA corresponding to the chromosomes transmitted by mother and father plus mitochondrial DNA. One generation back, a person’s genome is derived from about 118 (47 plus 71) stretches of DNA transmitted by his or her parents. Two generations back, the number of ancestral stretches of DNA grows to around 189 (47 plus 71 plus another 71) transmitted by four grandparents. Look even further back in time, and the additional increase in ancestral stretches of DNA every generation is rapidly overtaken by the doubling of ancestors. Ten generations back, for example, the number of ancestral stretches of DNA is around 757 but the number of ancestors is 1,024, guaranteeing that each p...

The Bible and the chronicles of royal families record who begat whom over dozens of generations. Yet even if the genealogies are accurate, 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. This is such a small fraction that the only way William could plausibly be her genetic ancestor is if he was her genealogical ancestor in thousands of different lineage paths, which seems unlikely even considering the high level of inbreeding in the British royal family.

Going back deeper in time, a person’s genome gets scattered into more and more ancestral stretches of DNA spread over ever-larger numbers of ancestors. 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. There is a limit, though, to the information that comparison of genome sequences provides about deep time. 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.

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.

The problems faced by modern humans with Neanderthal ancestry went beyond reduced fertility, as it turns out that Neanderthal ancestry is not just reduced on the X chromosome and around genes important in male reproduction, but is also reduced around the great majority of genes (there is far more Neanderthal ancestry in “junk” parts of the genome with few biological functions). The clearest evidence for this came from a study in 2016, in which we published a genome-wide ancient DNA dataset from more than fifty Eurasians spread over the last forty-five thousand years.41 We showed that Neanderthal ancestry decreased continually from 3 to 6 percent in most of the samples we analyzed from earlier times to its present-day value of around 2 percent at later times and that this was driven by widespread natural selection against Neanderthal DNA.

The problematic mutations in the Neanderthal genome form a sharp contrast with more recent mixtures of divergent modern human populations where there is no evidence for such effects. For example, among African Americans, in studies of about thirty thousand people, we have found no evidence for natural selection against African or European ancestry.43 One explanation for this is that when Neanderthals and modern humans mixed they had been separated for about ten times longer than had West Africans and Europeans, giving that much more time for biological incompatibilities to develop. A second explanation relates to the observation, from studies of many species, that when infertility arises between populations, it is often due to interactions between two genes in different parts of the genome. Since two changes are required to produce such an incompatibility, the rate of infertility increases with the square of population separation time, so a ten-times-larger population separation translates to one hundred times more genetic incompatibility. In light of this the lack of infertility in hybrids of present-day humans may no longer seem so surprising.

The fusion of these highly different populations into today’s West Eurasians is vividly evident in what might be considered the classic northern European look: blue eyes, light skin, and blond hair. Analysis of ancient DNA data shows that western European hunter-gatherers around eight thousand years ago had blue eyes but dark skin and dark hair, a combination that is rare today.33 The first farmers of Europe mostly had light skin but dark hair and brown eyes—thus light skin in Europe largely owes its origins to migrating farmers.34 The earliest known example of the classic European blond hair mutation is in an Ancient North Eurasian from the Lake Baikal region of eastern Siberia from seventeen thousand years ago.35 The hundreds of millions of copies of this mutation in central and western Europe today likely derive from a massive migration into the region of people bearing Ancient North Eurasian ancestry, an event that is related in the next chapter.

It is tempting to argue that genetic influence on bodily dimensions is one thing, but that cognitive and behavioral traits are another. But this line has already been crossed. Often when a person participates in a genetic study of a disease, he or she fills out a form providing information on height, weight, and number of years of education. By compiling the information on the number of years of education for over four hundred thousand people of European ancestry whose genomes have been surveyed in the course of various disease studies, Daniel Benjamin and colleagues identified seventy-four genetic variations each of which has overwhelming evidence of being more common in people with more years of education than in people with fewer years even after controlling for such possibly confounding factors as heterogeneity in the study population.25 Benjamin and colleagues also showed that the power of genetics to predict number of years of education is far from trivial, even though social influences surely have a greater average influence on this behavior than genetics. They showed that in the European ancestry population in which they carried out their study, it should be possible to build a genetic predictor in which the probability of completing twelve years of education is 96 percent for the twentieth of people with the highest prediction compared to 37 percent for the lowest.

How do these genetic variations influence educational attainment? The obvious guess is that they have a direct effect on academic abilities, but that is probably wrong. A study of more than one hundred thousand Icelanders showed that the variations also increase the age at which a woman has her first child, and that this is a more powerful effect than the one on the number of years of education. It is possible that these variations exert their effect indirectly, by nudging people to defer having children, which makes it easier for them to complete their education.27 This shows that when we discover biological differences governing behavior, they may not be working in the way we naively assume.

We truly have no idea right now what the nature or direction of genetically encoded differences among populations will be. An example is the extreme overrepresentation of people of West African ancestry among elite sprinters. All the male finalists in the Olympic hundred-meter race since 1980, even those from Europe and the Americas, had recent West African ancestry.46 The genetic hypothesis most often invoked to explain this is that there has been an upward shift in the average sprinting ability of people of West African ancestry due to natural selection. A small increase in the average might not sound like much, but it can make a big difference at the extremes of high ability—for example, a 0.8-standard-deviation increase in the average sprinting ability in West Africans would be expected to lead to a hundredfold enrichment in the proportion of people above the 99.9999999th percentile point in Europeans. But an alternative explanation that would predict the same magnitude of effect is that there is simply more variation in sprinting ability in people of West African ancestry—with more people of both very high and very low abilities.47 A wider spread of abilities around the same mean and a hundredfold enrichment in West Africans in the proportion of people above the 99.9999999th percentile point seen in Europeans is in fact exactly what is expected given the approximately 33 percent higher genetic diversity in West Africans than in Europeans.48 Whether or not this explain...

Beyond the imperative to give everyone equal respect, it is also important to keep in mind that there is a great diversity of human traits, including not just cognitive and behavioral traits, but also areas of athletic ability, skill with one’s hands, and capacity for social interaction and empathy. For most traits, the degree of variation among individuals is so large that any one person in any population can excel at any trait regardless of his or her population origin, even if particular populations have different average values due to a mixture of genetic and cultural influences. For most traits, hard work and the right environment are sufficient to allow someone with a lower genetically predicted performance at some task to excel compared to people with a higher genetically predicted performance. Because of the multidimensionality of human traits, the great variation that exists among individuals, and the extent to which hard work and upbringing can compensate for genetic endowment, the only sensible approach is to celebrate every person and every population as an extraordinary realization of our human genius and to give each person every chance to succeed, regardless of the particular average combination of genetic propensities he or she happens to display.

As a white person in the United States with its history of forcible deprivation of peoples of their roots, I feel that everyone—African Americans and Native Americans especially—has the right to try to use genetic data to help fill in missing pieces in his or her family history. Nevertheless, for those who assume that personal ancestry testing results have the authority of science, it is important to keep in mind that many of the results are easily misinterpreted and rarely include the warnings that scientists attach to tentative findings.