In the early 1980s a magazine asked me to report on a long-running legal battle over Pacific Northwest salmon. A coalition of Indian tribes had taken Washington State to court over a treaty it had signed with them in 1854, when the state was still part of the Oregon Territory. In the treaty, the territory promised to respect the Indians’ “right of taking fish, at all usual and accustomed grounds and stations,” which the tribes interpreted as guaranteeing them a share of the annual salmon harvests. Washington State said that the treaty did not mean what the Indians claimed, and in any case that circumstances had changed too much for it still to be binding. The courts repeatedly endorsed the Indian view and the state repeatedly appealed, twice reaching the U.S. Supreme Court. As the Indians approached final victory, tension rose in the fishing industry, then almost entirely controlled by whites. The magazine wanted me to write about the fight.

To learn more about the dispute, I visited the delta of the Nisqually River, at the southern tip of Puget Sound. Housing the Nisqually tribe, the sliver of land that is their reservation, and the riverbank meadow on which the treaty was signed, the delta is passed through, unnoticed, every day by the thousands of commuters on the interstate highway that slices through the reservation. At the time of my visit, the Nisqually had been annoying state authorities for decades, tenaciously pursuing what they believed to be their right to fish on their ancestral fishing grounds. I met the Franks, the stubborn, charismatic father-and-son team who then more or less ran the tribe, in a cluttered office that in my recollection occupied half of a double-wide trailer. Both had been arrested many times for “protest fishing”—fishing when the state said they couldn’t—and were the guiding spirits behind the litigation. After we spoke, Billy Frank, the son, told me I should visit Medicine Creek, where the Nisqually and eight other tribes had negotiated the treaty. And he asked someone who was hanging around to give me a tour.

That someone introduced himself as Denny. He was slim and stylish with very long black hair that fell unbound over the shoulders of his Levi jacket. Sewn on the back of the jacket was a replica of the American eagle on the dollar bill. A degree in semiotics was not required to see that I was in the presence of an ironist. He was not a Nisqually, he said, but from another Northwest group—at this remove, I can’t recall which. We clambered into an old truck with scraped side panels. As we set off, Denny asked, “Are you an archaeologist?”

Journalist, I told him.

“Good,” he said, slamming the truck into gear.

Because journalists rarely meet with such enthusiasm, I guessed—correctly—that his approval referred to my non-archaeological status. In this way I learned that archaeologists have aroused the ire of some Native American activists.

We drove to a small boat packed with fishing gear that was tied down on the edge of the Nisqually. Denny got the motor running and we puttered downstream, looking for harbor seals, which he said sometimes wandered up the river. Scrubby trees stood out from gravel banks, and beneath them, here and there, were the red-flushed, spawned-out bodies of salmon, insects happy around them. Freeway traffic was clearly audible. After half an hour we turned up a tributary and made land on a muddy bank. A hundred yards away was a tall snag, the dead stalk of a Douglas fir, standing over the meadow like a sentinel. The treaty negotiations had been conducted in its shelter. From under its branches the territorial governor had triumphantly emerged with two sheets of paper which he said bore the X marks of sixty-two Indian leaders, some of whom actively opposed the treaty and apparently were not at the signing.

Throughout our little excursion Denny talked. He told me that the claw holding the arrows on the back of the one-dollar bill was copied by Benjamin Franklin from an incident in Haudenosaunee lore; that the army base next door sometimes fired shells over the reservation; that Billy Frank once had been arrested with Marlon Brando; that a story Willie Frank, Billy’s father, had told me about his grandparents picking up smallpox-infected blankets on the beach was probably not true, but instead was an example of Willie’s fondness for spoofing gullible journalists; that Denny knew a guy who also had an eagle on the back of his jean jacket, but who, unlike Denny, could make the eagle flex its wings by moving his shoulders in a certain way that Denny admired; that most Indians hate the Internal Revenue Service even more than they hate the Bureau of Indian Affairs, because they believe that they paid taxes for all time when the federal government forced them to give up two billion acres of land; and that if I really wanted to see a crime against nature, I should visit the Quinault reservation, on the Olympic Peninsula, which had been plundered by loggers in the 1950s (I did, a few weeks afterward; Denny was right). He also explained to me why he and some other Indians had it in for archaeologists. The causes were many, in his telling, but two of them seemed especially pertinent: Aleš Hrdliimageka and the overkill hypothesis.

Hrdliimageka’s zeal for completeness made him accumulate as many Indian skeletons as possible. Unfortunately, his fascination with the bones of old Indians was not matched by an equivalent interest in the sensibilities of living Native Americans. Both his zeal and his indifference were gaudily on display on Kodiak Island, Alaska, where he exhumed about a thousand skeletons between 1932 and 1936 at Larsen Bay, a village of Alutiiq Indians. Many of the dead were two thousand years old, but some were ripped from recent Alutiiq graves, and a few were not Alutiiq at all—the wife of a local salmon-cannery manager, eager to help Science, shipped Hrdliimageka the cadavers of Chinese workers when they died.

Larsen Bay was the single most productive excavation of Hrdliimageka’s long career. Confronted with what he viewed as an intellectual treasure trove, this precise, meticulous, formal man was to all appearances overcome by enthusiasm and scholarly greed. In his pop-eyed hurry to pull bones out of the ground, he tore open the site with a bulldozer and didn’t bother taking notes, sketching maps, or executing profile drawings. Without documentation, Hrdliimageka was unable afterward to make head or tail of the houses, storage pits, hearths, and burial wells he uncovered. He pored through old Russian and American accounts of the area to find answers, but he never asked the people in Larsen Bay about their own culture. Perhaps his failure to approach the Alutiiq was a good thing. Hrdliimageka’s excavation, made without their permission, so angered them that they were still steaming when Denny was there on a salmon boat fifty years later. (In 1991 the Smithsonian gave back the skeletons, which the townspeople reburied.)

Overkill was part of the same mindset, Denny told me. As the environmental movement gathered steam in the 1960s, he said, white people had discovered that Indians were better stewards of the land. Indigenous peoples were superior to them—horrors! The archies—that was what Denny called archaeologists—had to race in and rescue Caucasian self-esteem. Which they did with the ridiculous conceit that the Indians had been the authors of an ecological mega-disaster. Typical, Denny thought. In his view, archaeologists’ main function was to make white people feel good about themselves—an opinion that archaeologists have learned, to their cost, is not Denny’s alone.

“Archaeologists are trapped in their own prejudices,” Vine Deloria Jr., the Colorado political scientist, told me. The Berkeley geographer Carl Sauer first brought up overkill in the 1930s, he said. “It was immediately knocked down, because a lot of shellfish and little mammals also went extinct, and these mythical Pleistocene hit men wouldn’t have wiped them out, too. But the supposedly objective scientific establishment likes the picture of Indians as ecological serial killers too much to let go of it.”

To Deloria’s way of thinking, not only overkill but the entire Clovis-first theory is a theoretical Rube Goldberg device. “There’s this perfect moment when the ice-free corridor magically appears just before the land bridge is covered by water,” he said. “And the paleo-Indians, who are doing fine in Siberia, suddenly decide to sprint over to Alaska. And then they sprint through the corridor, which just in time for them has been replenished with game. And they keep sprinting so fast that they overrun the hemisphere even faster than the Europeans did—and this even though they didn’t have horses, because they were so busy killing them all.” He laughed. “And these are the same people who say traditional origin tales are improbable!”

Activist critiques like those from Denny and Deloria have had relatively little impact on mainstream archaeologists and anthropologists. In a sense, they were unnecessary: scientists themselves have launched such a sustained attack on the primacy of Clovis, the existence of the ice-free corridor, and the plausibility of overkill that the Clovis consensus has shattered, probably irrecoverably.

In 1964, the year Haynes announced the Clovis-first model, archaeologist Alex D. Krieger listed fifty sites said to be older than Clovis. By 1988 Haynes and other authorities had shot them all down with such merciless dispatch that victims complained of persecution by the “Clovis police.” Haynes, the dissenters said, was a new Hrdliimageka (minus the charge of insensitivity to living Native Americans). As before, archaeologists became gun-shy about arguing that Indians arrived in the Americas before the canonical date. Perhaps as a result, the most persuasive scientific critiques on Clovis initially came from fields that overlapped archaeology, but were mainly outside of it: linguistics, molecular biology, and geology.

From today’s vantage, the attack seems to have begun, paradoxically, with the publication in 1986 of a landmark pro-Clovis paper in Current Anthropology by a linguist, a physical anthropologist, and a geneticist. The linguistic section attracted special attention. Students of languages had long puzzled over the extraordinary variety and fragmentation of Indian languages. California alone was the home of as many as 86 tongues, which linguists have classified into between 5 and 15 families (the schemes disagree with one another). No one family was dominant. Across the Americas, Indians spoke some 1,200 separate languages that have been classified into as many as 180 linguistic families. By contrast, all of Europe has just 4 language families—Indo-European, Finno-Ugric, Basque, and Turkic—with the great majority of Europeans speaking an Indo-European tongue. Linguists had long wondered how Indians could have evolved so many languages in the thirteen thousand years since Clovis when Europeans had ended up with many fewer in the forty thousand years since the arrival of humans there.

In the first part of the 1986 article, Joseph H. Greenberg, a linguist at Stanford, proclaimed that the profusion of idioms was more apparent than real. After four decades of comparing Native American vocabularies and grammars, he had concluded that Indian languages belonged to just three main linguistic families: Aleut, spoken by northern peoples in a broad band from Alaska to Greenland; NaDené, spoken in western Canada and the U.S. Southwest; and Amerind, much the biggest family, spoken everywhere else, including all of Central and South America. “The three linguistic stocks,” Greenberg said, “represent separate migrations.”

According to Greenberg’s linguistic analysis, paleo-Indians had crossed over Beringia not once, but thrice. Using glottochronology he estimated that the ancestors of Aleuts had crossed the strait around 2000 B.C. and that the ancestors of Na-Dené had made the journey around 7000 B.C. As for Amerind, Greenberg thought, “we are dealing with a time period probably greater than eleven thousand years.” But it was not that much greater, which indicated that the ancestors of Amerind-speaking peoples came over at just about the time that Clovis showed up in the archaeological record. Clovis-first, yes, but Clovis the first of three.

In the same article, Christy G. Turner II, a physical anthropologist at Arizona State, supported the three-migrations scheme with dental evidence. All humans have the same number and type of teeth, but their characteristics—incisor shape, canine size, molar root number, the presence or absence of grooves on tooth faces—differ slightly in ways that are consistent within ethnic groups. In a fantastically painstaking process, Turner measured “28 key crown and root traits” in more than 200,000 Indian teeth. He discovered that Indians formed “three New World dental clusters” corresponding to Greenberg’s Aleut, Na-Dené, and Amerind. By comparing tooth variation in Asian populations, Turner estimated the approximate rate at which the secondary characteristics in teeth evolved. (Because these factors make no difference to dental function, anthropologists assume that any changes reflect random mutation, which biologists in turn assume occurs at a roughly constant rate.) Applying his “worldwide rate of dental microevolution” to the three migrations, Turner came up with roughly similar dates of emigration. Amerinds, he concluded, had split off from northeast Asian groups about fourteen thousand years ago, which fit well “with the widely held view that the first Americans were the Clovis-culture big-game-hunting paleo-Indians.”

The article provoked vigorous reaction, not all of the sort that its authors wished. In hindsight, a hint of what was to come lay in its third section, in which Arizona State geneticist Stephen L. Zegura conceded that the “tripartite division of modern Native Americans is still without strong confirmation” from molecular biology. To the authors’ critics, the lack of confirmation had an obvious cause: the whole three-migrations theory was wrong. “Neither their linguistic classification nor their dental/genetic correlation is supported,” complained Lyle Campbell, of the State University of New York at Buffalo. Greenberg’s three-family division, Campbell thought, “should be shouted down in order not to confuse nonspecialists.” The Amerind-language family was so enormous, Berkeley linguist Johanna Nichols complained, that the likelihood of being able to prove it actually existed was “somewhere between zero and hopeless.”

Although the three-migrations theory was widely attacked, it spurred geneticists to pursue research into Native American origins. The main battleground was mitochondrial DNA, the special DNA with which Pena, the Brazilian geneticist, hoped to find the Botocudo. As I mentioned before, a scientific team led by Douglas Wallace found in 1990 that almost all Indians belong to one of four mitochondrial haplogroups, three of which are common in Asia (mitochondria with similar genetic characteristics, such as a particular mutation or version of a gene, belong to the same haplogroup). Wallace’s discovery initially seemed to confirm the three-migrations model: the haplogroups were seen as the legacy of separate waves of migration, with the most common haplogroup corresponding to the Clovis culture. Wallace came up with further data when he began working with James Neel, the geneticist who studied the Yanomami response to measles.

In earlier work, Neel had combined data from multiple sources to estimate that two related groups of Central American Indians had split off from each other eight thousand to ten thousand years before. Now Neel and Wallace scrutinized the two groups’ mitochondrial DNA. Over time, it should have accumulated mutations, almost all of them tiny alterations in unused DNA that didn’t affect the mitochondria’s functions. By counting the number of mutations that appeared in one group and not the other, Neel and Wallace determined the rate at which the two groups’ mitochondrial DNA had separately changed in the millennia since their separation: .2 to .3 percent every ten thousand years. In 1994 Neel and Wallace sifted through mitochondrial DNA from eighteen widely dispersed Indian groups, looking for mutations that had occurred since their common ancestors left Asia. Using their previously calculated rate of genetic change as a standard, they estimated when the original group had migrated to the Americas: 22,414 to 29,545 years ago. Indians had come to the Americas ten thousand years before Clovis.

Three years later, Sandro L. Bonatto and Francisco M. Bolzano, two geneticists at the Federal University of Rio Grande do Sul, in the southern Brazilian city of Pôrto Alegre, analyzed Indian mitochondrial DNA again—and painted a different picture. Wallace and Neel had focused on the three haplogroups that are also common in Asia. Instead, the Brazilians looked at the fourth main haplogroup—Haplogroup A is its unimaginative name—which is almost completely absent from Siberia but found in every Native American population. Because of its rarity in Siberia, the multiple-migrations theory had the implicit and very awkward corollary that the tiny minority of people with Haplogroup A just happened to be among the small bands that crossed Beringia—not just once, but several times. The two men argued it was more probable that a single migration had left Asia, and that some people in Haplogroup A were in it.

By tallying the accumulated genetic differences in Haplogroup A members, Bonatto and Bolzano calculated that Indians had left Asia thirty-three thousand to forty-three thousand years ago, even earlier than estimated by Wallace and Neel. Not only that, the measurements by Bonatto and Bolzano suggested that soon after the migrants arrived in Beringia they split in two. One half set off for Canada and the United States. Meanwhile, the other half remained in Beringia, which was then comparatively hospitable. The paleo-Indians who went south would not have had a difficult journey, because they arrived a little bit before the peak of the last Ice Age—before, that is, the two glacial sheets in Canada merged together. When that ice barrier closed, though, the Indians who stayed in Beringia were stuck there for the duration: almost twenty thousand years. Finally the temperatures rose, and some of them went south, creating a second wave and then, possibly, a third. In other words, just one group of paleo-Indians colonized the Americas, but it did so two or three times.

As other measurements came in, the confusion only increased. Geneticists disagreed about whether the totality of the data implied one or more migrations; whether the ancestral population(s) were small (as some measure of mitochondrial DNA diversity suggested) or large (as others indicated); whether Indians had migrated from Mongolia, the region around Lake Baikal in southern Siberia, or coastal east Asia, even possibly Japan.

Everything seemed up for grabs—or, anyway, almost everything. In the welter of contradictory data, University of Hawaii geneticist Rebecca L. Cann reported in 2001, “only one thing is certain”: scientists may argue about everything else, she said, but they all believe that “the ‘Clovis First’ archaeological model of a late entry of migrants into North America is unsupported by the bulk of new archaeological and genetic evidence.”

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