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  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.*14

  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.*15 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.

  Contact with Indians caused Europeans considerably more consternation. Columbus went to his grave convinced that he had landed on the shores of Asia, near India. The inhabitants of this previously unseen land were therefore Asians—hence the unfortunate name “Indians.” As his successors discovered that the Americas were not part of Asia, Indians became a dire anthropogonical problem. According to Genesis, all human beings and animals perished in the Flood except those on Noah’s ark, which landed “upon the mountains of Ararat,” thought to be in eastern Turkey. How, then, was it possible for humans and animals to have crossed the immense Pacific? Did the existence of Indians negate the Bible, and Christianity with it?

  Among the first to grapple directly with this question was the Jesuit educator José de Acosta, who spent a quarter century in New Spain. Any explanation of Indians’ origins, he wrote in 1590, “cannot contradict Holy Writ, which clearly teaches that all men descend from Adam.” Because Adam had lived in the Middle East, Acosta was “forced” to conclude “that the men of the Indies traveled there from Europe or Asia.” For this to be possible, the Americas and Asia “must join somewhere.”

  If this is true, as indeed it appears to me to be,…we would have to say that they crossed not by sailing on the sea, but by walking on land. And they followed this way quite unthinkingly, changing places and lands little by little, with some of them settling in the lands already discovered and others seeking new ones. [Emphasis added]

  Acosta’s hypothesis was in basic form widely accepted for centuries. For his successors, in fact, the main task was not to discover whether Indians’ ancestors had walked over from Eurasia, but which Europeans or Asians had done the walking. Enthusiasts proposed a dozen groups as the ancestral stock: Phoenicians, Basques, Chinese, Scythians, Romans, Africans, “Hindoos,” ancient Greeks, ancient Assyrians, ancient Egyptians, the inhabitants of Atlantis, even straying bands of Welsh. But the most widely accepted candidates were the Lost Tribes of Israel.

  The story of the Lost Tribes is revealed mainly in the Second Book of Kings of the Old Testament and the apocryphal Second (or Fourth, depending on the type of Bible) Book of Esdras. At that time, according to scripture, the Hebrew tribes had split into two adjacent confederations, the southern kingdom of Judah, with its capital in Jerusalem, and the northern kingdom of Israel, with its capital in Samaria. After the southern tribes took to behaving sinfully, divine retribution came in the form of the Assyrian king Shalmaneser V, who overran Israel and exiled its ten constituent tribes to Mesopotamia (today’s Syria and Iraq). Now repenting of their wickedness, the Bible explains, the tribes resolved to “go to a distant land never yet inhabited by man, and there at last to be obedient to their laws.” True to their word, they walked away and were never seen again.

  Because the Book of Ezekiel prophesizes that in the final days God “will take the children of Israel from among the heathen…and bring them into their own land,” Christian scholars believed that the Israelites’ descendants—Ezekiel’s “children of Israel”—must still be living in some remote place, waiting to be taken back to their homeland. Identifying Indians as these “lost tribes” solved two puzzles at once: where the Israelites had gone, and the origins of Native Americans.

  Acosta weighed the Indians-as-Jews theory but eventually dismissed it because Indians were not circumcised. Besides, he blithely explained, Jews were cowardly and greedy, and Indians were not. Others did not find his refutation convincing. The Lost Tribes theory was endorsed by authorities from Bartolomé de Las Casas to William Penn, founder of Pennsylvania, and the famed minister Cotton Mather. (In a variant, the Book of Mormon argued that some Indians were descended from Israelites though not necessarily the Lost Tribes.) In 1650 James Ussher, archbishop of Armagh, calculated from Old Testament genealogical data that God created the universe on Sunday, October 23, 4004 B.C. So august was Ussher’s reputation, wrote historian Andrew Dickson White, that “his dates were inserted in the margins of the authorized version of the English Bible, and were soon practically regarded as equally inspired with the sacred text itself.” According to Ussher’s chronology, the Lost Tribes left Israel in 721 B.C. Presumably they began walking to the Americas soon thereafter. Even allowing for a slow passage, the Israelites must have arrived by around 500 B.C. When Columbus landed, the Americas therefore had been settled for barely two thousand years.

  The Lost Tribes theory held sway until the nineteenth century, when it was challenged by events. As Lund had in Brazil, British scientists discovered some strange-looking human skeletons jumbled up with the skeletons of extinct Pleistocene mammals. The find, quickly duplicated in France, caused a sensation. To supporters of Darwin’s recently published theory of evolution, the find proved that the ancestors of modern humans had lived during the Ice Ages, tens or hundreds of thousands of years ago. Others attacked this conclusion, and the skeletons became one of the casus belli of the evolution wars. Indirectly, the discovery also stimulated argument about the settlement of the Americas. Evolutionists believed that the Eastern and Western Hemispheres had developed in concert. If early humans had inhabited Europe during the Ice Ages, they must also have lived in the Americas at the same time. Indians must therefore have arrived before 500 B.C. Ussher’s chronology and the Lost Tribes scenario were wrong.

  The nineteenth century was the heyday of amateur science. In the United States as in Europe, many of Darwin’s most ardent backers were successful tradespeople whose hobby was butterfly or beetle collecting. When these amateurs heard that the ancestors of Indians must have come to the Americas thousands of years ago, a surprising number of them decided to hunt for the evidence that would prove it.

  “BLIND LEADERS OF THE BLIND”

  In 1872 one such seeker—Charles Abbott, a New Jersey physician—found stone arrowheads, scrapers, and axheads on his farm in the Delaware Valley. Because the artifacts were crudely made, Abbott believed that they must have been fashioned not by historical Indians but by some earlier, “ruder” group, modern Indians’ long-ago ancestors. He consulted a Harvard geologist, who told him that the gravel around the finds was ten thousand years old, which Abbott regarded as proof that Pleistocene Man had lived in New Jersey at least that far in the past. Indeed, he argued, Pleistocene Man had lived in New Jersey for so many millennia that he had probably evolved there. If modern Indians had migrated from Asia, Abbott said, they must have “driven away” these original inhabitants. Egged on by his proselytizing, other weekend bone hunters soon found similar sites with similar crude artifacts. By 1890 amateur scientists cl
aimed to have found traces of Pleistocene Americans in New Jersey, Indiana, Ohio, and the suburbs of Philadelphia and Washington, D.C.

  Unsurprisingly, Christian leaders rejected Abbott’s claims, which (to repeat) contradicted both Ussher’s chronology and the theologically convenient Lost Tribes theory. More puzzling, at least to contemporary eyes, was the equally vehement objections voiced by professional archaeologists and anthropologists, especially those at the Smithsonian Institution, which had established a Bureau of American Ethnology in 1879. According to David J. Meltzer, a Southern Methodist University archaeologist who has written extensively about the history of his field, the bureau’s founders were determined to set the new disciplines on a proper scientific footing. Among other things, this meant rooting out pseudoscience. The bureau dispatched William Henry Holmes to scrutinize the case for Pleistocene proto-Indians.

  C. C. Abbott

  William Henry Holmes

  Holmes was a rigorous, orderly man with, Meltzer told me, “no sense of humor whatsoever.” Although Holmes in no way believed that Indians were descended from the Lost Tribes, he was also unwilling to believe that Indians or anyone else had inhabited the Americas as far back as the Ice Ages. His determined skepticism on this issue is hard to fathom. True, many of the ancient skeletons in Europe were strikingly different from those of contemporary humans—in fact, they were Neanderthals, a different subspecies or species from modern humans—whereas all the Indian skeletons that archaeologists had seen thus far looked anatomically modern. But why did this lead Holmes to assume that Indians must have migrated to the Americas in the recent past, a view springing from biblical chronology? Underlying his actions may have been bureau researchers’ distaste for “relic hunters” like Abbott, whom they viewed as publicity-seeking quacks.