Book Summary: “Who We Are and How We Got Here” by David Reich

Title: Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past
Author: David Reich
Scope: 4 stars
Readability: 3.5 stars
My personal rating: 5 stars
See more on my book rating system.

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Topic of Book

Reich explores how recent whole-genome studies are revolutionizing our understanding of ancient human history.

My Comments

I believe that we are just at the beginning of a revolutionary change in our understanding of human history being led by genetic studies. This book is a great introduction to both the science driving the changes as well as some preliminary conclusions from that research.

Key Take-aways

  • Since 2009 inexpensive whole-genome data studies are upending many of our current views.
  • The long-held academic consensus that humans populations do not vary genetically is becoming impossible to align with genetic studies.
  • Recent whole-genome tests are far more accurate than previous genetic tests that relied exclusively on the Y-chromosome (i.e. the all-male lineage) and Mitochondrial DNA (i.e. the all-female lineage).
  • The ability to recover and test DNA samples from archeological digs has identified a number of ancient “ghost populations:” Genetic populations that existed in the past, who do have no relatively pure ancestors today.
  • Previously it was thought that once humans migrated from Africa, they settled down in regions for tens of thousands of years. Now we can trace migrations of ghost populations within and across continents. They created far more genetic mixing than had previously been known.
  • Many of these migrations are associated with farmers and herders expanding into areas that were previously dominated by Hunter Gatherers. The farmers and herders largely displaced the original population, but there was some interbreeding.
  • Modern European populations were created from at least five separate migrations:
    • Three from Hunter-Gatherers.
    • One from farmers in Anatolia (bringing agriculture to the continent)
    • One from Yamnaya herders from the steppe (bringing the Ind-European language)
  • Modern India populations were created from at least four separate migrations, each of which was very similar to the European migrations described above.
  • Modern Native American populations were created by at least four separate groups; one of which came before the well-known Clovis migration. This migration of a ghost population left only scattered remnants in Amazonia.
  • Modern Chinese populations were created by a merging of a Yangtze River Ghost population, who grew rice in Southern China, and Yangtze River Ghost population, who grew millet in Northern China.

Important Quotes from Book

This book is inspired by a visionary, Luca Cavalli-Sforza, the founder of genetic studies of our past.

Cavalli-Sforza made a grand bet in 1960 that would drive his entire career. He bet that it would be possible to reconstruct the great migrations of the past based entirely on the genetic differences among present-day peoples.

Cavalli- Sforza saw before anyone else the full potential of genetics for revealing the human past, but his vision predated the technology needed to fulfill it. Today, however, things are very different. We have several hundred thousand times more data, and in addition we have access to the rich lode of information contained in ancient DNA, which has become a more definitive source of information about past population movements than the traditional tools of archaeology and linguistics.

The resolution with which this revolution has allowed us to reconstruct events in the human past is stunning.

These days, human genome variation has surpassed the traditional toolkit of archaeology—the study of the artifacts left behind by past societies—in what it can reveal of changes in human populations in the deep past. This has come as a surprise to nearly everyone.

This book is about the genome revolution in the study of the human past. This revolution consists of the avalanche of discoveries based on data taken from the whole genome—meaning, the entire genome analyzed at once instead of just small stretches of it such as mitochondrial DNA. The revolution has been made far more powerful by the new technologies for extracting whole genomes’ worth of DNA from ancient humans.

Yet genetic evidence before around 2009 was mostly incidental to studies of the human past in other fields, a poor handmaiden to the main business of archaeology. Since 2009, though, whole-genome data have begun to challenge long-held views in archaeology, history, anthropology, and even linguistics—and to resolve controversies in those fields.

A great surprise that emerges from the genome revolution is that in the relatively recent past, human populations were just as different from each other as they are today, but that the fault lines across populations were almost unrecognizably different from today.

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.

The number of ancestors you have doubles every generation back in time. However, the number of stretches of DNA that contributed to you increases by only around seventy-one per generation. This means that if you go back eight or more generations, it is almost certain that you will have some ancestors whose DNA did not get passed down to you. Go back fifteen generations and the probability that any one ancestor contributed directly to your DNA becomes exceedingly small.

In 2001, the human genome was sequenced for the first time—which means that the great majority of its chemical letters were read.

By 2006, companies began selling robots that reduced the cost of reading DNA letters by more than ten thousand-fold and soon by one hundred thousand-fold, making it economical to map the genomes of many more people. It thus became possible to compare sequences not just from a few isolated locations, such as mitochondrial DNA, but from the whole genome. That made it possible to reconstruct each person’s tens of thousands of ancestral lines of descent. This revolutionized the study of the past. Scientists could gather orders of magnitude more data.

When confronted with the diversity of life, evolutionary biologists are drawn to the metaphor of a tree.

The genome revolution has taught us that great mixtures of highly divergent populations have occurred repeatedly. Instead of a tree, a better metaphor may be a trellis, branching and remixing far back into the past.

The finding that several of the great populations outside of Africa today are profoundly mixed was at odds with what most scientists expected. Prior to the genome revolution, I, like most others, had assumed that the big genetic clusters of populations we see today reflect the deep splits of the past. But in fact the big clusters today are themselves the result of mixtures of very different populations that existed earlier. We have since detected similar patterns in every population we have analyzed: East Asians, South Asians, West Africans, southern Africans. There was never a single trunk population in the human past. It has been mixtures all the way down.

Analyzing our data, he found that about ten thousand years ago there were at least four major populations in West Eurasia—the farmers of the Fertile Crescent, the farmers of Iran, the hunter-gatherers of central and western Europe, and the hunter-gatherers of eastern Europe. All these populations differed from one another as much as Europeans differ from East Asians today.

Having migrated out of Africa and the Near East, modern human pioneer populations spread throughout Eurasia (1). By at least thirty-nine thousand years ago, one group founded a lineage of European hunter-gatherers that persisted largely uninterrupted for more than twenty thousand years (2). Eventually, groups derived from an eastern branch of this founding population of European hunter-gatherers spread west (3), displaced previous groups, and were eventually themselves pushed out of northern Europe by the spread of glacial ice… As the glaciers receded, western Europe was repeopled from the southwest (4) by a population that had managed to persist for tens of thousands of years and was related to an approximately thirty-five-thousand-year-old individual from far western Europe. A later human migration, following the first strong warming period, had an even larger impact, with a spread from the southeast (5) that not only transformed the population of western Europe but also homogenized the populations of Europe and the Near East.

The farmers in present-day Turkey expanded into Europe. The farmers in present-day Israel and Jordan expanded into East Africa, and their genetic legacy is greatest in present-day Ethiopia. Farmers related to those in present-day Iran expanded into India as well as the steppe north of the Black and Caspian seas. They mixed with local populations there and established new economies based on herding that allowed the agricultural revolution to spread into parts of the world inhospitable to domesticated crops. The different food-producing populations also mixed with one another… It is an extraordinary example of how technology—in this case, domestication—contributed to homogenization, not just culturally but genetically. It shows that what is happening with the Industrial Revolution and the information revolution in our own time is not unique in the history of our species.

A great lesson of the ancient DNA revolution is that its findings almost always provide accounts of human migrations that are very different from preexisting models, showing how little we really knew about human migrations and population formation prior to the invention of this new technology.

The people of India today are the outcome of mixtures between two highly differentiated populations, “Ancestral North Indians” (ANI) and “Ancestral South Indians” (ASI), who before their mixture were as different from each other as Europeans and East Asians are today. The ANI are related to Europeans, central Asians, Near Easterners, and people of the Caucasus, but we made no claim about the location of their homeland or any migrations. The ASI descend from a population not related to any present-day populations outside India. We showed that the ANI and ASI had mixed dramatically in India. The result is that everyone in mainland India today is a mix, albeit in different proportions, of ancestry related to West Eurasians, and ancestry more closely related to diverse East Asian and South Asian populations. No group in India can claim genetic purity.

We found that West Eurasian–related mixture in India ranges from as low as 20 percent to as high as 80 percent. This continuum of West Eurasian–related ancestry in India is the reason for the Indian Cline—the gradient we had seen on our principal components plots. No group is unaffected by mixing, neither the highest nor the lowest caste, including the non-Hindu tribal populations living outside the caste system.

Groups in India that speak Indo-European languages typically have more ANI ancestry than those speaking Dravidian languages, who have more ASI ancestry. This suggested to us that the ANI probably spread Indo-European languages, while the ASI spread Dravidian languages.

Groups of traditionally higher social status in the Indian caste system typically have a higher proportion of ANI ancestry than those of traditionally lower social status, even within the same state of India where everyone speaks the same language.

Remarkably, the patterns we observed were consistent with the hypothesis that all of the mixture of ANI and ASI ancestry that occurred in the history of some present-day Indian groups happened within the last four thousand years. This meant that the population structure of India before around four thousand years ago was profoundly different from what it is today. Before then, there were unmixed populations, but afterward, there was convulsive mixture in India, which affected nearly every group.

Today, ANI ancestry in India derives more from males than from females. This pattern is exactly what one would expect from an Indo-European- speaking people taking the reins of political and social power after four thousand years ago and mixing with the local peoples in a stratified society, with males from the groups in power having more success in finding mates than those from the disenfranchised groups.

These results reveal a remarkably parallel trade of the prehistories  of two similarly sized subcontinents of Eurasia—Europe and India. In both regions, farmers migrating from the core region of the Near East after nine thousand years ago—in Europe from Anatolia, and in India from Iran—brought a transformative new technology, and interbred with the previously established hunter-gatherer populations to form new mixed groups between nine thousand and four thousand years ago. Both subcontinents were then also affected by a second later major migration with an origin in the steppe, in which Yamnaya pastoralists speaking an Indo-European language mixed with the previously established farming population they encountered along the way, in Europe forming the peoples associated with the Corded Ware culture, and in India eventually forming the ANI. These populations of mixed steppe and farmer ancestry then mixed with the previously established farmers of their respective regions, forming the gradients of mixture we see in both subcontinents today.

The genetic data could be giving evidence of early peopling of the Americas by a minimum of two very different groups moving in from Asia, perhaps along two different routes and at different times. If Population Y spread through parts of South America before the First Americans, then it seems likely that after this initial peopling, the First Americans advanced into nearly all of the territories the Population Y people had already visited, replacing them either completely or only partially, as in Amazonia. Population Y ancestry may have survived better in Amazonia than it did elsewhere because of the relative impenetrability of the Amazonian environment.

We found that in Southeast Asia and Taiwan, there are many populations that derive most or all of their ancestry from a homogeneous ancestral population. Since the locations of these populations strongly overlap with the regions where rice farming expanded from the Yangtze River valley, it is tempting to hypothesize that they descend from the people who developed rice agriculture. We do not yet have ancient DNA from the first farmers of the Yangtze River valley, but my guess is that they will match this reconstructed “Yangtze River Ghost Population,” the name that we have given the population that contributed the overwhelming majority of ancestry to present-day Southeast Asians.

But we found that the Han Chinese—the world’s largest group with a census size of more than 1.2 billion—is not consistent with descending directly from the Yangtze River Ghost population. Instead, the Han also have a large proportion of ancestry from another deeply divergent East Asian lineage.

Because of the combined evidence of archaeology, language, and genetics, we called this the “Yellow River Ghost Population,” hypothesizing that it developed agriculture in the north while spreading Sino-Tibetan languages.

Once the core agricultural populations of the Chinese plain—the Yangtze and Yellow River ghost populations—formed, they expanded in all directions, mixing with groups that had arrived in earlier millennia.

Between fifty thousand and ten thousand years ago, hunter-gatherer groups diversified and spread northeast toward the Americas and southeast toward Australia. By nine thousand years ago, two very divergent populations from this initial radiation—one centered on the northern Yellow River and one on the Yangtze River—independently developed agriculture, and then by five thousand years ago spread in all directions. In China, their collision created the gradient of northern and southern ancestry seen in the Han today.

The agriculturalist expansion that had the greatest impact on Africa is the one associated with people who speak languages of the Bantu family.14 Archaeological studies have documented how beginning around four thousand years ago, a new culture spread out of the region at the border of Nigeria and Cameroon in west-central Africa. People from this culture lived at the boundary of the forest and expanding savanna and developed a highly productive set of crops that was capable of supporting dense populations.15 By about twenty-five hundred years ago they had spread as far as Lake Victoria in eastern Africa and mastered iron toolmaking technology,16 and by around seventeen hundred years ago they had reached southern Africa.17 The consequence of this expansion is that the great majority of people in eastern, central, and southern Africa speak Bantu languages.

Another agricultural expansion that had a profound impact is the one that spread Nilo-Saharan languages, spoken by groups from Mali to Tanzania. Many Nilo-Saharan speakers are cattle herders, and a common view is that the Nilo-Saharan expansion was driven by the spread of farming and herding in Africa’s dry Sahel region during the expansion of the Sahara Desert over the last five thousand years. One important branch of Nilo-Saharan is the Nilotic languages, which are mostly spoken by cattle herders along the Nile River and in East Africa, including the Maasai and Dinka. The genetic data make it clear that Nilotic- speaking herders were not always socially disadvantaged relative to farmers in the frontier regions where they encountered each other.

The African language expansion whose origin is most unclear is the one associated with Afroasiatic languages.

The fourth great agriculturalist expansion in Africa is the one associated with the Khoe-Kwadi languages of southern Africa.

Most of the present-day population structure of Africa is shaped by the agricultural expansions of the past few thousand years.

A great surprise that emerged from our ancient DNA analysis was that there was evidence of a ghost population dominating the eastern seaboard of sub-Saharan Africa that appears to have been largely displaced by the expansion of agriculturalists, which we called the “East African Foragers.

Ancestry currently restricted to San hunter- gatherers of southern Africa was once spread across eastern Africa at least to Tanzania. Ancestry currently restricted to the isolated Hadza huntergatherers of Tanzania was once widespread too.

The genome revolution has shown that we are not living in particularly special times when viewed from the perspective of the great sweep of the human past. Mixtures of highly divergent groups have happened time and again, homogenizing populations just as divergent from one another as Europeans, Africans, and Native Americans. And in many of these great admixtures, a central theme has been the coupling of men with social power in one population and women from the other.

Evidence of sex bias in the mixture of human populations is becoming commonplace. The male-biased European contribution to admixed populations in the Americas is stark in African Americans, but it is truly extraordinary in populations in South and Central America, reflecting stories like that of Hern.n Cort.s and La Malinche. Andr.s Ruiz-Linares and colleagues have documented how in the Antioquia region of Colombia, which was relatively isolated between the sixteenth and nineteenth centuries, about 94 percent of the Y chromosomes are European in origin, whereas about 90 percent of the mitochondrial DNA sequences are of Native American origin.

Through the collaboration of anthropologists and geneticists, a consensus was established that there are no differences among human populations that are large enough to support the concept of “biological race.”

But this consensus view of many anthropologists and geneticists has morphed, seemingly without questioning, into an orthodoxy that the biological differences among human populations are so modest that they should in practice be ignored—and moreover, because the issues are so fraught, that study of biological differences among populations should be avoided if at all possible.

But whether we like it or not, there is no stopping the genome revolution. The results that it is producing are making it impossible to maintain the orthodoxy established over the last half century, as they are revealing hard evidence of substantial differences across populations. I have deep sympathy for the concern that genetic discoveries about differences among populations may be misused to justify racism. But it is precisely because of this sympathy that I am worried that people who deny the possibility of substantial biological differences among populations across a range of traits are digging themselves into an indefensible position, one that will not survive the onslaught of science. In the last couple of decades, most population geneticists have sought to avoid contradicting the orthodoxy. When asked about the possibility of biological differences among human populations, we have tended to obfuscate. 

To understand why it is no longer an option for geneticists to lock arms with anthropologists and imply that any differences among human populations are so modest that they can be ignored, go no further than the “genome bloggers.” Since the genome revolution began, the Internet has been alive with discussion of the papers written about human variation, and some genome bloggers have even become skilled analysts of publicly available data.

What real differences do we know about? We cannot deny the existence of substantial average genetic differences across populations, not just in traits such as skin color, but also in bodily dimensions, the ability to efficiently digest starch or milk sugar, the ability to breathe easily at high altitudes, and susceptibility to particular diseases. These differences are just the beginning.

The indefensibility of the orthodoxy is obvious at almost every turn.

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

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.

For those who wish to argue against the possibility of biological differences across populations that are substantial enough to make a difference in people’s abilities or propensities, the most natural refuge might be to make the case that even if such differences exist, they will be small.  

But this argument doesn’t hold up either. The average time separation between pairs of human populations since they diverged from common ancestral populations, which is up to around fifty thousand years for some pairs of non-African populations, and up to two hundred thousand years or more for some pairs of sub-Saharan African populations, is far from negligible on the time scale of human evolution. If selection on height and infant head circumference can occur within a couple of thousand years,31 it seems a bad bet to argue that there cannot be similar average differences in cognitive or behavioral traits.

As recently as 2012, it still seemed reasonable to interpret human genetic data as pointing to immutable categories such as “East Asians,” “Caucasians,” “West Africans,” “Native Americans,” and “Australasians,” with each group having been separated and unmixed for tens of thousands of years.  

But ancient DNA discoveries have rendered the serial founder model untenable. We now know that the present-day structure of populations does not reflect the one that existed many thousands of years ago. Instead, the current populations of the world are mixtures of highly divergent populations that no longer exist in unmixed form—for example, the Ancient North Eurasians, who contributed a large amount of the ancestry of present-day Europeans as well as of Native Americans, and multiple ancient populations of the Near East, each as differentiated from the other as Europeans and East Asians are differentiated from each other today. Most of today’s populations are not exclusive descendants of the populations that lived in the same locations ten thousand years ago.

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