Science & Tech

Humanity’s Genes Reveal Its Tangled History

David Reich
Reality, it turns out, is more complex and interesting than scientists ever imagined.

In the early 19th century, Jean-Fraconnçois Champollion used the Rosetta Stone to begin the process of deciphering the hieroglyphics of ancient Egypt. We already knew Egypt through the Bible and the histories of the Greeks, but even Herodotus wrote 2,000 years after the beginning of the Old Kingdom. With the translation of hieroglyphics, the legend of Egypt came to life. What had been cloudy became clear.

In Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past, David Reich, a geneticist at Harvard’s Medical School and the Broad Institute, introduces us to the 21st-century Rosetta Stone: ancient DNA, which will do more for our understanding of prehistory than radiocarbon dating did. Where the latter allowed archaeologists to create a timeline based on the material objects they excavated, DNA sequencing allows scholars to explore the genetics of the people who created those material cultures. We may never see the face of Agamemnon, but we already have the DNA of the warlords of Mycenaean Greece, and in the future we could reconstruct their features from genes alone.

Reich operates at the intersection of a multiplicity of fields: archaeology to retrieve samples, molecular biology to extract genetic material, genomics to turn that material into data, and cluster computing to analyze the data generated. His team also includes a former cryptographer and zoologists, and his collaborators include linguists, anthropologists, and historians.

All these specialized skills brought together result in an incredibly productive scientific operation. Reich frankly admits that he transformed his laboratory into a data-generation factory. In five years the field of ancient DNA reduced the price of extracting genetic material from samples 1,000-fold. While genomics has destroyed the standard set by Moore’s law — a doubling of processing power every two years — ancient DNA has arguably shattered even the breakneck pace of genomics.

Reich’s initiation into the discipline began about ten years ago, when Svante Pääbo, the doyen of the field, invited him to his laboratory in Germany. Reich and his senior collaborator Nick Patterson had established their names as skilled analysts of population genetic data. Pääbo had pioneered the exploration of historical questions through extracting genetic material from ancient remains. And his lab had just returned data from the sequence of an ancient Neanderthal.

As recounted in Who We Are and How We Got Here, when Reich first saw the results he was surprised. The orthodoxy within the scientific community was that Neanderthals were an evolutionary dead end — but his colleagues found that Neanderthals had contributed to the ancestry of most humans alive today. Around 2 percent of the genetic ancestry of humans outside of Africa derive from Neanderthal people who probably lived in the Middle East 50,000 years ago.

Initially, Reich was skeptical. He and his colleagues checked every which way. But the data always gave the same result. He admits that even today he has nightmares that his analysis is somehow wrong, though all subsequent publications have confirmed the initial result.

Soon after this startling finding, researchers discovered that a fossil in Siberia’s Denisova cave came from an ancient human lineage we had previously not known of. Distantly related to Neanderthals, these “Denisovans” turn out to have contributed around 5 percent of the ancestry of modern people in Melanesia, as well as much smaller fractions to the ancestry of people from India through Southeast Asia and up into China.

And this wasn’t just a matter of fun and games. One of the main genetic paths that Tibetans use to adapt to high altitudes came from Denisovans. Genes from Neanderthals that are very common in populations today relate to immune response, hair and skin development, and pigmentation.

Who We Are and How We Got Here buries the classic “Out of Africa” theory that had emerged out of the notion of “mitochondrial Eve.” In this framework, humanity was born 50,000 years ago in East Africa, fully formed like Athena from the head of Zeus, and went on to conquer the rest of the continent and the world while leaving our cousins to be footnotes in prehistory. Both the fossil evidence and human genomics no longer support that idea. Our species does have roots in the African continent that go back hundreds of thousands of years — but other populations that contributed to our ancestry, at a minimum including the Neanderthals and the Denisovans, were already present when modern humans were expanding out of Africa 50,000 years ago. The ancestors of these groups had left Africa over half a million years ago. And modern humans were present within Africa for hundreds of thousands of years before one small branch fatefully migrated out of that continent 50,000 years ago. Rather than being created in an instant, modern humans were evolving, changing, and interacting within Africa as distinct populations for hundreds of thousands of years before a few left. So an “Out of Africa” thesis still holds, but it’s hard to pack into a few concise sentences.

Reality, it turns out, is more complex and interesting than scientists ever imagined.

But Who We Are and How We Got Here only begins by exploring our relationship to ancient lineages of humans gone by. The meat of the book deals with the human populations that are present today and how they — we — got here.

Work on this question also upended Reich’s expectations. He figured that after their migration out of Africa, humans mostly settled down and left descendants in place. The human family tree then split generation after generation into disparate branches — as small groups trickled out of their homelands to explore new territory — which could then be overlaid on a map of the world, tracing out distinct migrations. This assumption had already allowed researchers to use the genetics of modern populations to open a window onto the past.

The ancestors of the modern British arrived 4,500 years ago and did not, in fact, raise up Stonehenge.

Or so we thought. New methods reveal that modern people are mostly unrelated to those who lived in the same area in the past. The ancestors of the modern British, for example, arrived 4,500 years ago and did not, in fact, raise up Stonehenge.

At the end of the last Ice Age, Europe was dominated by hunter-gatherers, who carried the genes for blue eyes but not the ones modern Europeans have for light skin. Modern Europeans have very little ancestry from these people. Rather, they descended in Southern Europe from farmers who left the Middle East nearly 10,000 years ago and were as genetically distinct from the hunter-gatherers as the Chinese are from modern Europeans. Eventually these farmers and hunter-gatherers mixed, but in Northern Europe they were replaced and absorbed by a third population from the east, Eurasian pastoralists, who share ancestry with Native Americans and ancient peoples in Iran, as well as Pleistocene Europeans.

A similar dynamic of replacement or mixture applies to Africa, the Middle East, South Asia, and Southeast Asia. In other words, the vast majority of the world’s populations date to migrations and mixing within the last 10,000 years. Even characteristics that we think to be fundamental and primal, such as the fair complexion of modern Northern Europeans, are likely a recent phenomenon, driven by the mixing of disparate genes 4,000 to 5,000 years ago and reshaped by natural selection over the next few thousand years.

Who We Are and How We Got Here is less than 300 pages of text, but it is packed with startling facts and novel revelations that overturn the conventional expectations of both science and common sense. And after chapter upon chapter of dense scientific results, Reich concludes by making some observations about the social history of our species that is implied by ancient DNA.

The massive mixture events that occurred in the recent past to give rise to Europeans and South Asians, to name just two groups, were likely “male mediated.” That’s another way of saying that men on the move took local women as brides or concubines. In the New World there are many examples of this, whether it be among African Americans, where most European ancestry seems to come through men, or in Latin America, where conquistadores famously took local women as paramours. Both of these examples are disquieting, and hint at the deep structural roots of patriarchal inequality and social subjugation that form the backdrop for the emergence of many modern peoples.

Who We Are and How We Got Here then addresses the reality that large numbers of public intellectuals are extremely hostile to the idea that humans can be grouped together into distinct population clusters. In other words, since race is a pernicious social construction, population geneticists need to tread very carefully. Reich is frank that the time may have come to break the alliance geneticists have made with academics who declare that all differences between groups are trivial. He suggests that science is advancing at such a rate that we will soon understand the genetic basis of complex behaviors in exquisite detail — and that researchers should be prepared for the possibility that some findings will be discomfiting to contemporary sensibilities.

In short, Reich delivers the sword to cut through many orthodoxies. But still, the ultimate moral is that our common humanity remains. Modern populations are bound together by many distinct threads, and thus are connected together in ways that we may never have imagined. Modern Native Americans and modern Europeans both descend in part from Pleistocene Siberians, with one population migrating west and another east until they met again tens of thousands of years later. What we may term “races” are not primordial or fundamental, but recent specific instances of a general tapestry of human variation. Our species is ancient, and did not emerge just recently. Neanderthals and other humans were not animals, but people with whom we produced offspring.

Who we are is humanity. And how we got here is interesting, astounding, but at the end of the day incidental. We are here, and have been for a very long time.

Razib Khan — Razib Khan is a geneticist. His blog is Gene Expression (gnxp.com).

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