The Invisible History of the Human Race (32 page)

Currently in the United States, according to Wagner, “minorities are overrepresented in forensic databases and underrepresented in biomedical research databases. Genetic and genomic technologies could either mitigate or exacerbate racial disparities. We must be mindful of that and do everything we can to ensure that every individual shares in the benefits of scientific knowledge.”

The big human family tree that Wagner will teach could have grown into thousands of different shapes, so why has it taken the particular shape it has? In part it is because of its biological machinery, and in part it is because of the events of history. Human choice, chance occurrence, and unpredictable contingency have all contributed to the tree’s growth. It would be impossible to identify all the factors that have shaped the genome, but we are beginning to have the ability to piece together the events that matter. What were the biggest shapers of the genome we have today?

Human beings are ultimately nothing but carriers—passageways—for genes. They ride us into the ground like racehorses from generation to generation. Genes don’t think about what constitutes good or evil. They don’t care whether we are happy or unhappy. We’re just means to an end for them. The only thing they think about is what is most efficient for them.

—Haruki Murakami,
1Q84

W
hen you visualize the human tree, picture its trunk firmly planted in African soil. Modern humans emerged there several hundred thousand years ago and lived only there from 250,000 years ago for at least 150,000 years—a much longer span of time than we have lived across the globe.

Working out what life was like when humans were an exclusively African species is probably one of our biggest scientific challenges. There are no written records and few fossils from that time, and handmade artifacts date back to only 70,000 years ago. Which is not to say that humans didn’t use tools or wear jewelry before then—it’s simply that, if there are any that remain, we haven’t yet found them. Still, while scientists have only begun to plumb these depths, with each year that passes our view into the past reaches further back as we find new evidence. While we often think of human history as a kind of reverse dimming, in which the light of our consciousness and intelligence grew ever brighter, the evidence that we were profoundly aware as early as 200,000 years ago is growing. In the last few years 60,000-year-old ostrich eggs with marks that appeared to be
intentional engraving were discovered. Dating of beads from Israel and Algeria suggests they are between 100,000 and 130,000 years old. Ancient tools found in Crete suggest that someone sailed there
more than 100,000 years ago. It looks as if there was
ocher processing in the Blombos Cave in South Africa 100,000 years ago, and in the same region people sharpened the tips of
their stone tools using heat—a technique that we used to think dated back only 20,000 years. In the history of science few people have dared to imagine that humans were as intelligent or as technologically adept so early in their history.

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For hundreds of thousands of years much of the African continent was inhabited by different family and tribal groups. Around sixty thousand years ago a small band of them—
perhaps not much more than one thousand to two thousand five hundred individuals—went traveling. We don’t know why they left or if they had any sense that they were going somewhere new, but we do know their decision kicked off one of the biggest events in the history of the human genome.

Those who remained are the ancestors of most of the one billion people who live in Africa today. The small band that left are the ancestors of everyone else in the world, and the suite of DNA they carried was only a small sample of the variety of human genomes that existed in Africa at the time of their departure. Indeed, we know the migration occurred because even now we can see that the genomes of everyone in the world outside of Africa is a subset of the genomic variation still found in Africa.

When a small sample of a species’s genome is isolated and then becomes the foundation for another group, it’s called a bottleneck. (In this analogy the neck of the bottle is the small founding group, and the expansion of the neck into the body is what happens when the population grows.) Bottlenecks can be caused by many things and are powerful examples of the role of chance in shaping the human genome. “Things
that happened a long time ago can constrain what can happen afterwards,” said Marcus Feldman, a professor of biological sciences at Stanford. “If there is a disaster that kills off 98 percent of the organisms of a certain type, then what happens to the rest of the animals is constrained by the fact that there are only 2 percent of this particular type that are left.”

As a group passes through a bottleneck, it becomes particularly vulnerable to drift. DNA diffuses more quickly within a small population, and it may not take too many generations before everyone’s genome starts to look a bit more like everyone else’s. There’s no rhyme or reason to drift; it’s a matter of chance. Bits of DNA may spread throughout a group for no reason other than that the people who carried them ended up with more children and therefore passed them on more often. DNA that has drifted throughout a group may have consequences for the people in it—like red hair or a protruding brow or a certain health issue—or it may not. It is equally possible that some bits of DNA will not come into prominence but instead float off into oblivion.

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The out-of-Africa bottleneck is one of the easiest to identify, but it’s far from the only one in human history. Around seventy thousand years ago one bottleneck may have taken the human race perilously close to extinction. A volcano erupted in Toba, Indonesia, causing abrupt climate change and leaving a layer of ash over a huge segment of the world. Some researchers have proposed that all of us today descend from a small number of Toba survivors. Indeed, if you wanted to summarize the myriad migrations, cataclysms, illnesses, innovations, and acts of love and hate that have changed the human genome, you could say that it’s been shaped by a series of bottlenecks, where a population shrinks, and fusions, where two or more populations come together and blend their genetic material. To be more precise, you’d have to throw in some Darwinian adaptation as well. Marcus Feldman, who has been comparing populations across the world for a long time, says that the differences between populations “are reflective of two processes. One is migration and the distance from Africa, and the other one, most of which happens after the origin of agriculture, is natural selection on some genes.”

Although the first big out-of-Africa migration was enormously significant, as it marked our transition from being a regional animal to being a global one, there have been many significant migrations since then. Indeed, the histories of most of the world’s large populations include a bottleneck of that first out-of-Africa population.

As they traveled, humans made their way through Asia and along the coast into the southeast. They passed through strange climates and terrains, stumbling upon fantastically colorful and unimagined wildlife, much of which tried to harm or eat them. Everywhere they stopped, they left descendants behind, and wherever the descendants stayed, they adapted to the local terrain and available food. Within a few generations these weird new worlds became a familiar landscape that the travelers’ descendants had always known. In the course of time, later generations of their descendants ultimately changed, becoming different colors, shapes, and sizes.

The wanderers and their descendants invented the taming of animals like dogs, goats, sheep, cats, and horses. They invented transport like sailing and
skating on ice. Some of the earlier groups of travelers met humanlike creatures, thickset survivors of an earlier exodus. Others who made it all the way to the landmass we think of as Indonesia may have discovered a group of people who were all the size of small children. On the first leg of the trip they traveled as far as possible, arriving in Australia, a land of two-ton wombats, ten-foot-tall kangaroos, and enormous marsupial lions, about fifty thousand years ago. The ancestors of modern humans began to spread through Europe only forty thousand years ago.

Less than 18,000 years ago humans arrived on a landmass now known as North America. (Only Antarctica has been free of humans for longer than the Americas.) It seems that almost the entire indigenous population of the Americas descends from a small group of perhaps eighty people, originally from Siberia, who followed a route that has now been covered over by the ocean. Over 32,000 years ago they took refuge in northwestern Beringia, a land bridge connecting what are now Alaska and Russia. Over the millennia that followed they moved into eastern Beringia, and then sometime before 14,000 years ago they moved into the North American continent, spreading along the
Pacific coastline and then eastward. Geneticists have found that Native Americans have only five kinds of mtDNA, and the first four are common in northeastern Asia. With this evidence and other genetic studies, it has become well-established that the small ancestral population of Native Americans can trace its genome back to Asia.

The picture got more complicated when a study by David Reich found an ancient connection between the modern Native American and European genomes, suggesting that there once existed a population in northern
Eurasia that was ancestral to both. The study was based on a comparison of modern genomes; no bones from such a population had been found. Yet in 2013 the remains of a young boy who lived 24,000 years ago were found in Mal’ta in south-central Siberia. Analysis of his DNA showed that he was related to modern Europeans and Native Americans. The finding confirmed that at least 14 percent and up to 38 percent of Native American DNA came from a
population in western Eurasia. Remarkably, a few months later the scientists who analyzed the Mal’ta boy’s DNA published the genome of another ancient boy, an infant who was buried in Montana more than 12,500 years ago. Anzick-1, as he was called, was covered in red ocher and placed in the earth with stone tools from the Clovis culture. He is the first ancient Native American whose genome has been sequenced. The people who buried Anzick-1 are ancestors of modern Native Americans (although he is more closely related to 44 groups from Central and South America than to
others from North America).

The complex tales told by the ancient Siberian and Clovis children are echoed by what happened during the out-of-Africa exodus in the rest of the world. No matter where they stopped, even after a group of travelers settled in place, life—and the genome—kept changing. Some settlers were joined—or overrun—by others; sometimes a subgroup set off anew. It was thought that the Australian genome was isolated for tens of thousands of years before eighteenth-century colonization, but in 2013 it was discovered that roughly four thousand years ago a band from the Indian subcontinent traveled into Australia and contributed to the genome. Around the same time, there were changes in tools and in the way food was processed, and the dingo first appeared, suggesting that the Indian group may have brought the
wild canine in with them.

Of course, it’s not just the descendants of the out-of-Africa band who have changed; African populations have changed as well. Indeed, as far as the genome is concerned, the groups who remained were also small bands of travelers. There were genomic bottlenecks on the African continent long before the 60,000-year mark: In 2012 researchers announced that they had found one of the original branches of the human family tree. The Khoe-San, a tribe who live in southern Africa, split off from everyone else 100,000 years ago. In addition, many groups journeyed through the land and
blended with other groups. In many parts of the continent native Africans effectively journeyed through different environments even as they stayed in the same place. In all that time the climate changed, plants bloomed, and animals thrived, and then ice ages dried the land out.

Feldman and colleagues have counted the number of bottlenecks that different modern populations have passed through and have found that populations that have passed through the most bottlenecks have more deleterious mutations in their genome than populations that have passed through fewer. Yet even as they find ways to identify difference, their work still underlines the overwhelming commonality of all people. When you examine the human genome, Feldman told me, “The thing that strikes you is that people in different continents actually have very similar genomes and that the fraction of the genomes that are different is pretty small. I mean, you’re down to a tenth of a percent.”

When humans left Africa 60,000 years ago, it was almost certainly not the first journey they had attempted but merely the most successful one. The bones of modern-looking humans found in the Skhul and Qafzeh caves in Israel date to 120,000 years ago. These people are not our direct ancestors but were likely an earlier group who walked out of Africa. It may be the case that the out-of-Africa journey that led to the peopling of the world was more complicated too. A 2014 study that compared both DNA and the shapes of fossilized human skulls suggests that the ancestors of the Australian Aboriginal population actually left Africa 130,000 years ago and that there were at least two waves of the
modern human exodus from Africa. Stone tools found in the inland deserts and mountains of the Arabian peninsula that date to more than 100,000
years ago support this idea. Yet another kind of creature left Africa much earlier, almost 500,000 years ago, and founded a civilization that spread across much of the world.

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There’s another way we can tell that the human tree splits between people who come from Africa and people born elsewhere in the world. The traces of the split lead us back to an event that occurred just as the out-of-Africa diaspora began. When the small band of travelers was essentially standing on the doorstep of the continent, perhaps wondering where to turn, they met up with a group of Neanderthals and ended up making some human-Neanderthal babies together. All non-Africans today carry the mark of those encounters in their DNA.

In just the last few years we have learned that 85 percent of all people carry DNA from Neanderthals, an entirely different species that lived until 27,000 years ago. If the research on the human genome hasn’t completely destroyed the idea of genetic purity, our newly discovered Neanderthal ancestors show how truly absurd the notion is. Colin Groves, a professor of bioanthropology at the Australian National University, explained, “
Neanderthals and
Homo sapiens
are like lions and tigers. Genetically they are sharply distinct, but they can interbreed.”

A first-draft sequence of the Neanderthal genome was published in 2010 by an international team of scientists,
including David Reich at Harvard. I visited Reich’s lab in 2011 and asked him what that first meeting between our ancestors was like. He explained that it might have been a meeting of a few dozen humans and Neanderthals, or it could have been a blending of thousands of individuals. At the time I spoke with Reich, we didn’t know which parts of the human genome had come to us from Neanderthals. Since then the science of Neanderthal DNA has progressed faster than anyone imagined it would.