Who We Are and How We Got Here
This book is inspired by a visionary, Luca Cavalli-Sforza, the founder of genetic studies of our past. I was trained by one of his students, and so it is that I am part of his school, inspired by his vision of the genome as a prism for understanding the history of our species.
The high-water mark of Cavalli-Sforza’s career came in 1994 when he published The History and Geography of Human Genes, which synthesized what was then known from archaeology, linguistics, history, and genetics to tell a grand story about how the world’s peoples got to be the way they are today.1 The book offered an overview of the deep past. But it was based on what was known at the time and was therefore handicapped by the paucity of genetic data then available, which were so limited as to be nearly useless compared to the far more extensive information from archaeology and linguistics. The genetic data of the time could sometimes reveal patterns consistent with what was already known, but the information they provided were not rich enough to demonstrate anything truly new. In fact, the few major new claims that Cavalli-Sforza did make have essentially all been proven wrong. Two decades ago, everyone, from Cavalli-Sforza to beginning graduate students such as myself, was working in the dark ages of DNA.
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.2
Through study after study over the subsequent five decades, Cavalli-Sforza seemed to be well on the path to making good on his bet. When he started his work, the technology for studying human variation was so poor that the only possibility was to measure proteins in the blood, using variations like the A, B, and O blood types that are tested by physicians to match blood donors to recipients. By the 1990s, he and his colleagues had assembled data from more than one hundred such variations in diverse populations. Using these data they were able to reliably cluster individuals by continent based on how often they matched each other at these variations: for example, Europeans have a high rate of matching to other Europeans, East Asians to East Asians, and Africans to Africans. In the 1990s and 2000s, they brought their work to a new level by moving beyond protein variation and directly examining DNA, our genetic code. They analyzed a total of about one thousand individuals from around fifty populations spread across the planet, examining variation at more than three hundred positions in the genome.3 When they told their computer—which had no knowledge of the population labels—to cluster the individuals into five groups, the results corresponded uncannily well to commonly held intuitions about the deep ancestral divisions among humans (West Eurasians, East Asians, Native Americans, New Guineans, and Africans).
Cavalli-Sforza was especially interested in interpreting the genetic clusters among present-day people in terms of population history. He and his colleagues analyzed their blood group data by using a technique that identifies combinations of biological variations that are most efficient at summarizing differences across individuals. Plotting these combinations of blood group types onto a map of West Eurasia, they found that the one summarizing the most variation across individuals reached its extreme value in the Near East, and declined along a southeast-to-northwest gradient into Europe.4 They interpreted this as a genetic footprint of the migration of farmers into Europe from the Near East, known from archaeology to have occurred after nine thousand years ago. The declining intensity suggested to them that after arriving in Europe, the first farmers mixed with local hunter-gatherers, accumulating more hunter-gatherer ancestry as they expanded, a process they called “demic diffusion.”5 Until recently, many archaeologists viewed the demic diffusion model as an exemplary merging of insights from archaeology and genetics.
The model that Cavalli-Sforza and colleagues proposed to describe the data was intellectually attractive, but it was wrong. Its flaws became apparent beginning in 2008, when John Novembre and colleagues demonstrated that gradients like those observed in Europe can arise without migration.6 They then showed that a Near Eastern farming expansion into Europe might counter-intuitively cause the mathematical technique that Cavalli-Sforza used to produce a gradient perpendicular to the direction of migration, not parallel to it as had been seen in the real data.7
It took the revolution wrought by the ability to extract DNA from ancient bones—the “ancient DNA revolution”—to drive a nail into the coffin of the demic diffusion model. The ancient DNA revolution documented that the first farmers even in the most remote reaches of Europe—Britain, Scandinavia, and Iberia—had very little hunter-gatherer-related ancestry. In fact, they had less hunter-gatherer ancestry than is present in diverse European populations today. The highest proportion of early farmer ancestry in Europe is today not in Southeast Europe, the place where Cavalli-Sforza thought it was most common based on the blood group data, but instead is in the Mediterranean island of Sardinia to the west of Italy.8
The example of Cavalli-Sforza’s maps shows why his Sforza’s grand bet went sour. He was correct in his assumption that the present-day genetic structure of populations echoes some of the great events in the human past. For example, the lower genetic diversity of non-Africans compared to Africans reflects the reduced diversity of the modern human population that expanded out of Africa and the Near East after around fifty thousand years ago. But the present-day structure of human populations cannot recover the fine details of ancient events. The problem is not just that people have mixed with their neighbors, blurring the genetic signatures of past events. It is actually far more difficult, in that we now know, from ancient DNA, that the people who live in a particular place today almost never exclusively descend from the people who lived in the same place far in the past.9 Under these circumstances, the power of any study that attempts to reconstruct past population movements from present-day populations is limited. In The History and Geography of Human Genes, Cavalli-Sforza wrote that he was excluding from his analysis populations known to be the product of major migrations, such as those of European and African ancestry in the Americas that owe their origin to transatlantic migrations in the last five hundred years, or European minorities such as Roma and Jews. His bet was that the past was a much simpler place than the present, and that by focusing on populations today that are not affected by major migrations in their recorded history, he might be studying direct descendants of people who lived in the same places long before. But what the study of ancient DNA has now shown is that the past was no less complicated than the present. Human populations have repeatedly turned over.
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