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In that year Peter Wilhelm Lund, a Danish botanist, found thirty skeletons in caves twenty miles north of Belo Horizonte. The caves were named Lagoa Santa, after a nearby village. Inside them were a jumble of remains from people and big, extinct beasts. If the human and animal bones were from the same time period, as their proximity suggested, the implication was that people had been living in the Americas many thousands of years ago, much longer than most scientists then believed. Who were these ancient hunters? Regarding Europe as the world’s intellectual capital, the intrigued Lund sent most of the skeletons to a museum in his native Copenhagen. He was certain that researchers there would quickly study and identify them. Instead the bones remained in boxes, rarely disturbed, for more than a century.

Scientists finally examined the Lagoa Santa skeletons in the 1960s. Laboratory tests showed that the bones could be fifteen thousand years old—possibly the oldest human remains in the Western Hemisphere. Lund had noted the skulls’ heavy brows, which are rare in Native Americans. The new measurements confirmed that oddity and suggested that these people were in many ways physically quite distinct from modern Indians, which indicated, at least to some Brazilian archaeologists, that the Lagoa Santa people could not have been the ancestors of today’s native populations. Instead the earliest inhabitants of the Americas must have been some other kind of people.

North American researchers tended to scoff at the notion that some mysterious non-Indians had lived fifteen thousand years ago in the heart of Brazil, but South Americans, Pena among them, were less dismissive. Pena had studied and worked for twelve years overseas, mainly in Canada and the United States. He returned in 1982 to Belo Horizonte, a surging, industrial city in the nation’s east-central highlands. In Brazilian terms, it was like abandoning a glamorous expatriate life in Paris to come back to Chicago. Pena had become interested while abroad in using genetics as a historical tool—studying family trees and migrations by examining DNA. At Belo Horizonte, he joined the university faculty and founded, on the side, Brazil’s first DNA-fingerprinting company, providing paternity tests for families and forensic studies for the police. He taught, researched, published in prestigious U.S. and European journals, and ran his company. In time he became intrigued by the Lagoa Santa skeletons.

The most straightforward way to discover whether the Lagoa Santa people were related to modern Indians, Pena decided, would be to compare DNA from their skeletons with DNA from living Indians. In 1999 his team tried to extract DNA from Lagoa Santa bones. When the DNA turned out to be unusable, Pena came up with a second, more unorthodox approach: he decided to look for Lagoa Santa DNA in the Botocudo.

The Botocudo were an indigenous group that lived a few hundred miles north of what is now Rio de Janeiro. (The name comes from
botoque,
the derogatory Portuguese term for the big wooden discs that the Botocudo inserted in their lower lips and earlobes, distending them outward.) Although apparently never numerous, they resisted conquest so successfully that in 1801 the Portuguese colonial government formally launched a “just war against the cannibalistic Botocudo.” There followed a century of intermittent strife, which slowly drove the Botocudo to extinction.

With their slightly bulging brows, deepset eyes, and square jaws, the Botocudo were phenotypically different (that is, different in appearance) from their neighbors—a difference comparable to the difference between West Africans and Scandinavians. More important, some Brazilian scientists believe, the Botocudo were phenotypically similar to the Lagoa Santa people. If the similarity was due to a genetic connection—that is, if the Botocudo were a remnant of an early non-Indian population at Lagoa Santa—studying Botocudo DNA should provide clues to the genetic makeup of the earliest Americans. To discover whether that genetic connection existed, Pena would first have to obtain some Botocudo DNA. This requirement would have seemed to doom the enterprise, because the Botocudo no longer exist. But Pena had an idea—innovative or preposterous, depending on the point of view—of how one might find some Botocudo DNA anyway.

All human beings have two genomes. The first is the genome of the DNA in chromosomes, the genome of the famous human genome project, which proclaimed its success with great fanfare in 2000. The second and much smaller genome is of the DNA in mitochondria; it was mapped, to little public notice, in 1981. Mitochondria are minute, bean-shaped objects, hundreds of which bob about like so much flotsam in the warm, salty envelope of the cell. The body’s chemical plants, they gulp in oxygen and release the energy-rich molecules that power life. Mitochondria are widely believed to descend from bacteria that long ago somehow became incorporated into one of our evolutionary ancestors. They replicate themselves independently of the rest of the cell, without using its DNA. To accomplish this, they have their own genome, a tiny thing with fewer than fifty genes, left over from their former existence as free-floating bacteria. Because sperm cells are basically devoid of mitochondria, almost all of an embryo’s mitochondria come from the egg. Children’s mitochondria are thus in essence identical to their mother’s.
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More than that, every woman’s mitochondrial DNA is identical not only to her mother’s mitochondrial DNA, but to that of her mother’s mother’s mitochondrial DNA, and her mother’s mother’s mother’s mitochondrial DNA, and so on down the line for many generations. The same is not true for men. Because fathers don’t contribute mitochondrial DNA to the embryo, the succession occurs only through the female line.

In the late 1970s several scientists realized that an ethnic group’s mitochondrial DNA could provide clues to its ancestry. Their reasoning was complex in detail, but simple in principle. People with similar mitochondria have, in the jargon, the same “haplogroup.” If two ethnic groups share the same haplogroup, it is molecular proof that the two groups are related; their members belong to the same female line. In 1990 a team led by Douglas C. Wallace, now at the University of California at Irvine, discovered that just four mitochondrial haplogroups account for 96.9 percent of Native Americans—another example of Indians’ genetic homogeneity, but one without any known negative (or positive) consequences. Three of the four Indian haplogroups are common in southern Siberia. Given the inheritance rules for mitochondrial DNA, the conclusion that Indians and Siberians share common ancestry seems, to geneticists, inescapable.

Wallace’s research gave Pena a target to shoot at. Even as the Brazilian government was wiping out the Botocudos, some Brazilian men of European descent were marrying Botocudo women. Generations later, the female descendants of those unions should still have mitochondria identical to the mitochondria of their female Botocudo ancestors. In other words, Pena might be able to find ancient American DNA hidden in Brazil’s European population.

Pena had blood samples from people who believed their grandparents or great-grandparents were Indians and who had lived in Botocudo territory. “I’m looking for, possibly, a very odd haplogroup,” he told me. “One that is not clearly indigenous or clearly European.” If such a haplogroup turned up in Pena’s assays, it could write a new chapter in the early history of Native Americans. He expected to be searching for a while, and anything he found would need careful confirmation.

Since the sixteenth century, the origins of Native Americans have been an intellectual puzzle.
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Countless amateur thinkers took a crack at the problem, as did anthropologists and archaeologists when those disciplines were invented. The professionals made no secret of their disdain for the amateurs, whom they regarded as annoyances, cranks, or frauds. Unfortunately for the experts, in the 1920s and 1930s their initial theories about the timing of Indians’ entrance into the Americas were proven wrong, and in a way that allowed the crackpots to claim vindication. Thirty years later a new generation of researchers put together a different theory of Native American origins that gained general agreement. But in the 1980s and 1990s a gush of new information about the first Americans came in from archaeological digs, anthropological laboratories, molecular biology research units, and linguists’ computer models. The discoveries once again fractured the consensus about the early American history, miring it in dispute. “It really does seem sometimes that scientific principles are going out the window,” the archaeologist C. Vance Haynes said to me, unhappily. “If you listen to [the dissenting researchers], they want to throw away everything we’ve established.”

Haynes was waxing rhetorical—the critics don’t want to jettison
everything
from the past. But I could understand the reason for his dour tone. Again the experts were said to have been proved wrong, opening a door that until recently was bolted against the crackpots. A field that had seemed unified was split into warring camps. And projects like Pena’s, which not long ago would have seemed marginal, even nutty, now might have to be taken seriously.

In another sense, though, Haynes’s unhappy view seemed off the mark. The rekindled dispute over Indian origins has tended to mask a greater archaeological accomplishment: the enormous recent accumulation of knowledge about the American past. In almost every case, Indian societies have been revealed to be older, grander, and more complex than was thought possible even twenty years ago. Archaeologists not only have pushed back the date for humanity’s entrance into the Americas, they have learned that the first large-scale societies grew up earlier than had been believed—almost two thousand years earlier, and in a different part of the hemisphere. And even those societies that had seemed best understood, like the Maya, have been placed in new contexts on the basis of new information.

At one point I asked Pena what he thought the reaction would be if he discovered that ancient Indians were, in fact, not genetically related to modern Indians. He was standing by a computer printer that was spewing out graphs and charts, the results of another DNA comparison. “It will seem impossible to believe at first,” he said, flipping through the printout. “But if it is true—and I am not saying that it is—people will ultimately accept it, just like all the other impossible ideas they’ve had to accept.”

LOST TRIBES

So various were the peoples of the Americas that continent-wide generalizations are risky to the point of folly. Nonetheless, one can say that for the most part the initial Indian-European encounter was less of an intellectual shock to Indians than to Europeans. Indians were surprised when strange-looking people appeared on their shores, but unlike Europeans they were not surprised that such strange people
existed.

Many natives, seeking to categorize the newcomers, were open to the possibility that they might belong to the realm of the supernatural. They often approached visitors as if they might be deities, possibly calculating, in the spirit of Pascal’s wager, that the downside of an erroneous attribution of celestial power was minimal. The Taino Indians, Columbus reported after his first voyage, “firmly believed that I, with my ships and men, came from the heavens…. Wherever I went, [they] ran from house to house, and to the towns around, crying out, ‘Come! come! and see the men from the heavens!’” On Columbus’s later voyages, his crew happily accepted godhood—until the Taino began empirically testing their divinity by forcing their heads underwater for long periods to see if the Spanish were, as gods should be, immortal.

Motecuhzoma, according to many scholarly texts, believed that Cortés was the god-hero Quetzalcoatl returning home, in fulfillment of a prophecy. What historian Barbara Tuchman called the emperor’s “wooden-headedness, in the special variety of religious mania” is often said to be why he didn’t order his army to wipe out the Spaniards immediately. But the anthropologist Matthew Restall has noted that none of the conquistadors’ writings mention this supposed apotheosis, not even Cortés’s lengthy memos to the Spanish king, which go into detail about every other wonderful thing he did. Instead the Quetzalcoatl story first appears decades later. True, the Mexica apparently did call the Spaniards
teteo,
a term referring both to gods and to powerful, privileged people. The ambiguity captures the indigenous attitude toward the hairy, oddly dressed strangers on their shores: recognition that their presence was important, plus a willingness to believe that such unusual people might have qualities unlike those of ordinary men and women.

Similarly, groups like the Wampanoag, Narragansett, and Haudenosaunee in eastern North America also thought at first that Europeans might have supernatural qualities. But this was because Indians north and south regarded Europeans as human beings exactly like themselves. In their view of the world, certain men and women, given the right circumstances, could wield more-than-human powers. If the Wampanoag and Mexica had shamans who could magically inflict sickness, why couldn’t the British? (The Europeans, who themselves believed that people could become witches and magically spread disease, were hardly going to argue.)

As a rule, Indians were theologically prepared for the existence of Europeans. In Choctaw lore, for example, the Creator breathed life into not one but many primeval pairs of human beings scattered all over the earth. It could not have been terribly surprising to Choctaw thinkers that the descendants of one pair should show up in the territory of another. Similarly, the Zuni took the existence of Spaniards in stride, though not their actions. To the Zuni, whose accounts of their origins and early history are as minutely annotated as those in the Hebrew Bible, all humankind arose from a small band that faded into existence in a small, dark, womb-like lower world. The sun took pity on these bewildered souls, gave them maize to eat, and distributed them across the surface of the earth. The encounter with Europeans was thus a meeting of long-separated cousins.