A New History of the First Peoples in the Americas

The miracle of modern genetics has revolutionized the story anthropologists tell about how humans spread out across the Earth.

A plastic cast of a skull
A plastic cast of Kennewick Man's skull (Elaine Thompson / AP)

Europeans arriving in the New World met people all the way from the frozen north to the frozen south. All had rich and mature cultures and established languages. The Skraeling were probably a people we now call Thule, who were the ancestors of the Inuit in Greenland and Canada and the Iñupiat in Alaska. The Taíno were a people spread across multiple chiefdoms around the Caribbean and Florida. Based on cultural and language similarities, we think that they had probably separated from earlier populations from South American lands, now Guyana and Trinidad. The Spanish brought no women with them in 1492, and raped the Taíno women, resulting in the first generation of “mestizo”—mixed ancestry people.

Immediately upon arrival, European alleles began to flow, admixed into the indigenous population, and that process has continued ever since: European DNA is found today throughout the Americas, no matter how remote or isolated a tribe might appear to be. But before Columbus, these continents were already populated. The indigenous people hadn’t always been there, nor had they originated there, as some of their traditions state, but they had occupied these American lands for at least 20,000 years.

It’s only because of the presence of Europeans from the 15th century onward that we even have terms such as Indians or Native Americans. How these people came to be is a subject that is complex and fraught, but it begins in the north. Alaska is separated from Russian land by the Bering Strait. There are islands that punctuate those icy waters, and on a clear day U.S. citizens of Little Diomede can see Russians on Big Diomede, just a little over two miles and one International Date Line away. Between December and June, the water between them freezes solid.

From 30,000 years ago until around 11,000 B.C., the earth was subjected to a cold snap that sucked up the sea into glaciers and ice sheets extending from the poles. This period is known as the Last Glacial Maximum, when the reach of the most recent Ice Age was at its fullest. By drilling mud cores out of the seabed, we can reconstruct a history of the land and the seas, notably by measuring concentrations of oxygen, and looking for pollen, which would have been deposited on dry ground from the flora growing there. We think therefore that sea level was somewhere between 60 and 120 meters lower than today. So it was terra firma all the way from Alaska to Russia, and all the way down south to the Aleutians—a crescent chain of volcanic islands that speckle the north Pacific.

The prevailing theory about how the people of the Americas came to those lands is via that bridge. We refer to it as a land bridge, though given its duration and size, it was simply continuous land, thousands of miles from north to south; it’s only a bridge if we view it in comparison to today’s straits. The area is called Beringia, and the first people across it the Beringians. These were harsh lands, sparse with shrubs and herbs; to the south, there were boreal woodlands, and where the land met the sea, kelp forests and seals.

Though these were still tough terrains, according to archaeological finds Western Beringians were living near the Yana River in Siberia by 30,000 B.C. There’s been plenty of debate over the years as to when exactly people reached the eastern side, and therefore at what point after the seas rose they became isolated as the founding peoples of the Americas. The questions that remain—and there are many—concern whether they came all at once or in dribs and drabs. Sites in the Yukon that straddle the U.S.-Alaskan border with Canada give us clues, such as the Bluefish Caves, 33 miles southwest of the village of Old Crow.

The latest radio-dating analysis of the remnants of lives in the Bluefish Caves indicates that people were there 24,000 years ago. These founding peoples spread over 12,000 years to every corner of the continents and formed the pool from which all Americans would be drawn until 1492. I will focus on North America here, and what we know so far, what we can know through genetics, and why we don’t know more.

Until Columbus, the Americas were populated by pockets of tribal groups distributed up and down both north and south continents. There are dozens of individual cultures that have been identified by age, location, and specific technologies—and via newer ways of knowing the past, including genetics and linguistics. Scholars have hypothesized various patterns of migration from Beringia into the Americas. Over time, it has been suggested that there were multiple waves, or that a certain people with particular technologies spread from north all the way south.

Both ideas have now fallen from grace. The multiple-waves theory has failed as a model because the linguistic similarities used to show patterns of migration are just not that convincing. And the second theory fails because of timing. Cultures are often named and known by the technology that they left behind. In New Mexico there is a small town called Clovis, population 37,000. In the 1930s, projectile points resembling spearheads and other hunting paraphernalia were found in an archaeological site nearby, dating from around 13,000 years ago. These were knapped on both sides—bifaced with fluted tips. It had been thought that it was the inventors of these tools who had been the first people to spread up and down the continents. But there’s evidence of humans living in southern Chile 12,500 years ago without Clovis technology. These people are too far away to show a direct link between them and the Clovis in such a way that indicates the Clovis being the aboriginals of South America.

Today, the emerging theory is that the people up in the Bluefish Caves some 24,000 years ago were the founders, and that they represent a culture that was isolated for thousands of years up in the cold north, incubating a population that would eventually seed everywhere else. This idea has become known as Beringian Standstill. Those founders had split from known populations in Siberian Asia some 40,000 years ago, come across Beringia, and stayed put until around 16,000 years ago.

Analysis of the genomes of indigenous people show 15 founding mitochondrial types not found in Asia. This suggests a time when genetic diversification occurred, an incubation lasting maybe 10,000 years. New gene variants spread across the American lands, but not back into Asia, as the waters had cut them off. Nowadays, we see lower levels of genetic diversity in modern Native Americans—derived from just those original 15—than in the rest of the world. Again, this supports the idea of a single, small population seeding the continents, and—unlike in Europe or Asia—these people being cut off, with little admixture from new populations for thousands of years, at least until Columbus.

In Montana, 20 miles or so off Highway 90, lies the minuscule conurbation of Wilsall, population 178 as of 2010. Though stacks of material culture in the Clovis tradition have been recovered throughout North America, only one person from this time and culture has risen from his grave. He’s acquired the name Anzick-1, and was laid to rest in a rock shelter in what would become—around 12,600 years later—Wilsall. He was a toddler, probably less than two years old, judging from the unfused sutures in his skull. He was laid to rest surrounded by at least 100 stone tools, and 15 ivory ones. Some of these were covered in red ochre, and together they suggest Anzick was a very special child who had been ceremonially buried in splendor. Now he’s special because we have his complete genome.

And there’s the woeful saga of Kennewick Man. While attending a hydroplane race in 1996, two locals of Kennewick, Washington, discovered a broad-faced skull inching its way out of the bank of the Columbia River. Over the weeks and years, more than 350 fragments of bone and teeth were eked out of this 8,500-year-old grave, all belonging to a middle-aged man, maybe in his 40s, deliberately buried, with some signs of injuries that had healed over his life—a cracked rib, an incision from a spear, a minor depression fracture on his forehead. There were academic squabbles about his facial morphology, with some saying it was most similar to Japanese skulls, some arguing for a link with Polynesians, and some asserting he must have been European.

With all the toing and froing about his morphology, DNA should be a rich source of conclusive data for this man. But the political controversies about his body have severely hampered his value to science for 20 years. For Native Americans, he became known as the Ancient One, and five clans, notably the Confederated Tribes of the Colville Reservation, wanted to have him ceremonially reburied under guidelines determined by the Native American Graves Protection and Repatriation Act (NAGPRA), which affords custodial rights to Native American artifacts and bodies found on their lands. Scientists sued the government to prevent his reburial, some claiming that his bones suggested he was European, and therefore not connected with Native Americans.

To add an absurd cherry on top of this already distasteful cake, a Californian pagan group called the Asatru Folk Assembly put in a bid for the body, claiming Kennewick Man might have a Norse tribal identity, and if science could establish that the body was European, then he should be given a ceremony in honor of Odin, ruler of the mythical Asgard, though what that ritual entails is not clear.

His reburial was successfully blocked in 2002, when a judge ruled that his facial bones suggested he was European, and therefore NAGPRA guidelines could not be invoked. The issue was batted back and forth for years, in a manner in which no one came out looking good. Nineteen years after this important body was found, the genome analysis was finally published.

Had he been European (or Japanese or Polynesian), it would’ve been the most revolutionary find in the history of U.S. anthropology, and all textbooks on human migration would have been rewritten. But of course he wasn’t. A fragment of material was used to sequence his DNA, and it showed that lo and behold, Kennewick Man—the Ancient One—was closely related to the Anzick baby. And as for the living, he was more closely related to Native Americans than to anyone else on Earth, and within that group, most closely related to the Colville tribes.

Anzick is firm and final proof that North and South America were populated by the same people. Anzick’s mitochondrial genome is most similar to people of central and south America today. The genes of the Ancient One most closely resemble those of tribes in the Seattle area today. These similarities do not indicate that either were members of those tribes or people, nor that their genes have not spread throughout the Americas, as we would expect over timescales of thousands of years. What they show is that the population dynamics—how ancient indigenous people relate to contemporary Native Americans—is complex and varies from region to region. No people are completely static, and genes less so.

In December 2016, in one of his last acts in office, President Barack Obama signed legislation that allowed Kennewick Man to be reburied as a Native American. Anzick was found on private land, so not subject to NAGPRA rules, but was reburied anyway in 2014 in a ceremony involving a few different tribes. We sometimes forget that though the data should be pure and straightforward, science is done by people, who are never either.

Anzick and Kennewick Man represent narrow samples—a tantalizing glimpse of the big picture. And politics and history are hampering progress. The legacy of 500 years of occupation has fostered profound difficulty in understanding how the Americas were first peopled. Two of the doyennes of this field—Connie Mulligan and Emőke Szathmáry—suggest that there is a long cultural tradition that percolates through our attempts to deconstruct the past.

Europeans are taught a history of migration from birth, of Greeks and Romans spreading over Europe, conquering lands, and interloping afar. Judeo-Christian lore puts people in and out of Africa and Asia, and the silk routes connect Europeans with the East and back again. Many European countries have been seafaring nations, exploring and sometimes belligerently building empires for commerce or to impose a perceived superiority over other people. Even though we have national identities, and pride and traditions that come with that sense of belonging, European culture is imbued with migration.

For Native Americans, this is not their culture. Not all believe they have always been in their lands, nor that they are a static people. But for the most part, the narrative of migration does not threaten European identity in the same way that it might for the people we called the Indians. The scientifically valid notion of the migration of people from Asia into the Americas may challenge Native creation stories. It may also have the effect of conflating early modern migrants from the 15th century onward with those from 24,000 years earlier, with the effect of undermining indigenous claims to land and sovereignty.

* * *

Deep among the lakes of the Grand Canyon are the Havasupai. Their name means “people of the blue-green waters,” and they’ve been there for at least 800 years. They’re a small tribe, around 650 members today, and they use ladders, horses, and sometimes helicopters to travel in and out of—or rather, up and down—the canyon. The tribe is rife with type 2 diabetes, and in 1990, the Havasupai people agreed to provide Arizona State University scientists with DNA from 151 individuals with the understanding that they would seek genetic answers to the puzzle of why diabetes was so common. Written consent was obtained, and blood samples were taken.

An obvious genetic link to diabetes was not found, but the researchers continued to use their DNA to test for schizophrenia and patterns of inbreeding. The data was also passed on to other scientists who were interested in migration and the history of Native Americans. The Havasupai only found this out years later, and eventually sued the university. In 2010, they were awarded $700,000 in compensation.

Therese Markow was one of the scientists involved, and insists that consent was on the papers they signed, and that the forms were necessarily simple, as many Havasupai do not have English as a first language, and many did not graduate from high school. But many in the tribe thought that they were being asked only about their endemic diabetes. A blood sample contains an individual’s entire genome, and with it, reams of data about that individual, their family, and evolution.

This isn’t the first time this has happened. In the 1980s, before the days of easy and cheap genomics, blood samples were taken with consent to analyze the unusually high levels of rheumatic disease in the Nuu-chah-nulth people of the Pacific Northwest of Canada. The project, led by the late Ryk Ward, then at the University of British Columbia, found no genetic link in their samples, and the project petered out. By the ’90s, though, Ward had moved to the University of Utah, and then Oxford in the U.K., and the blood samples had been used in anthropological and HIV/AIDS studies around the world, which turned into grants, academic papers, and a PBS–BBC jointly produced documentary.

The use of the samples for historical migration indicated that the origins of the Havasupai were from ancient ancestors in Siberia, which is in accordance with our understanding of human history by all scientific and archaeological methods. But it is in opposition to the Havasupai religious belief that they were created in situ in the Grand Canyon. Though nonscientific, it is perfectly within their rights to preclude investigations that contradict their stories, and those rights appear to have been violated. Havasupai Vice Chairman Edmond Tilousi told The New York Times in 2010 that “coming from the canyon ... is the basis of our sovereign rights.”

Sovereignty and membership of a tribe is a complex and hard-won thing. It includes a concept called “blood quantum,” which is effectively the proportion of one’s ancestors who are already members of a tribe. It’s an invention of European Americans in the 19th century, and though most tribes had their own criteria for tribal membership, most eventually adopted Blood Quantum as part of the qualification for tribal status.

DNA is not part of that mix. With our current knowledge of the genomics of Native Americans, there is no possibility of DNA being anywhere near a useful tool in ascribing tribal status to people. Furthermore, given our understanding of ancestry and family trees, I have profound doubts that DNA could ever be used to determine tribal membership. While mtDNA (which is passed down from mothers to children) and the Y chromosome (passed from fathers to sons) have both proved profoundly useful in determining the deep ancestral trajectory of the first peoples of the Americas into the present, these two chromosomes represent a tiny proportion of the total amount of DNA that an individual bears. The rest, the autosomes, comes from all of one’s ancestors.

Some genetic genealogy companies will sell you kits that claim to grant you membership to historical peoples, albeit ill-defined, highly romanticized versions of ancient Europeans. This type of genetic astrology, though unscientific and distasteful to my palate, is really just a bit of meaningless fantasy; its real damage is that it undermines scientific literacy in the general public.

Over centuries, people have been too mobile to have remained genetically isolated for any significant length of time. Tribes are known to have mixed before and after colonialism, which should be enough to indicate that some notion of tribal purity is at best imagined. Of the genetic markers that have been shown to exist in individual tribes so far, none is exclusive. Some tribes have begun to use DNA as a test to verify immediate family, such as in paternity cases, and this can be useful as part of qualification for tribal status. But on its own, a DNA test cannot place someone in a specific tribe.

That hasn’t stopped the emergence of some companies in the United States that sell kits that claim to use DNA to ascribe tribal membership. Accu-Metrics is one such company. On its web page, it states that there are “562 recognized tribes in the United States, plus at least 50 others in Canada, divided into First Nation, Inuit, and Metis.” For $125 the company claims that it “can determine if you belong to one of these groups.”

The idea that tribal status is encoded in DNA is both simplistic and wrong. Many tribespeople have non-native parents and still retain a sense of being bound to the tribe and the land they hold sacred. In Massachusetts, members of the Seaconke Wampanoag tribe identified European and African heritage in their DNA, due to hundreds of years of interbreeding with New World settlers. Attempting to conflate tribal status with DNA denies the cultural affinity that people have with their tribes. It suggests a kind of purity that genetics cannot support, a type of essentialism that resembles scientific racism.

The specious belief that DNA can bestow tribal identity, as sold by companies such as Accu-Metrics, can only foment further animosity—and suspicion—toward scientists. If a tribal identity could be shown by DNA (which it can’t), then perhaps reparation rights afforded to tribes in recent years might be invalid in the territories to which they were moved during the 19th century. Many tribes are effective sovereign nations and therefore not necessarily bound by the laws of the state in which they live.

When coupled with cases such as that of the Havasupai, and centuries of racism, the relationship between Native Americans and geneticists is not healthy. After the legal battles over the remains of Kennewick Man were settled, and it was accepted that he was not of European descent, the tribes were invited to join in the subsequent studies. Out of five, only the Colville Tribes did. Their representative, James Boyd, told The New York Times in 2015, “We were hesitant. Science hasn’t been good to us.”

Data is supreme in genetics, and data is what we crave. But we are the data, and people are not there for the benefit of others, regardless of how noble one’s scientific aims are. To deepen our understanding of how we came to be and who we are, scientists must do better, and invite people whose genes provide answers to not only volunteer their data, but to participate, to own their individual stories, and to be part of that journey of discovery.

This is beginning to change. A new model of engagement with the first people of the Americas is emerging, albeit at a glacial pace. The American Society of Human Genetics meeting is the annual who’s who in genetics, and has been for many years, where all of the newest and biggest ideas in the study of human biology are discussed. In October 2016 they met in Vancouver, and it was hosted by the Squamish Nation, a First Nations people based in British Colombia. They greeted the delegates with song, and passed the talking stick to the president for the proceedings to begin.

The relationship between science and indigenous people has been one characterized by a range of behaviors from outright exploitation to casual insensitivity to tokenism and lip service. Perhaps this time is coming to an end and we might foster a relationship based on trust, genuine engagement, and mutual respect, so that we might work together and build the capacity for tribes to lead their own research into the histories of these nations.

* * *

Though the terms Native American and Indian are relative, the United States is a nation of immigrants and descendants of slaves who have overwhelmed the indigenous population. Less than 2 percent of the current population defines itself as Native American, which means that 98 percent of Americans are unable to trace their roots, genetic or otherwise, beyond 500 years on American soil. That is, however, plenty of time for populations to come and breed and mix and lay down patterns of ancestry that can be enlightened with living DNA as our historical text.

A comprehensive genetic picture of the people of postcolonial North America was revealed at the beginning of 2017, drawn from data submitted by paying customers to the genealogy company AncestryDNA. The genomes of more than 770,000 people born in the United States were filtered for markers of ancestry, and revealed a picture of mishmash, as you might expect from a country of immigrants.

Nevertheless, genetic clusters of specific European countries are seen. Paying customers supply spit harboring their genomes, alongside whatever genealogical data they have. By aligning these as carefully as possible, a map of post-Columbus America can be summoned with clusters of common ancestry, such as Finnish and Swedish in the Midwest, and Acadians—French-speaking Canadians from the Atlantic seaboard—clustering way down in Louisiana, close to New Orleans, where the word Acadian has mutated into Cajun. Here, genetics recapitulates history, as we know the Acadians were forcibly expelled by the British in the 18th century, and many eventually settled in Louisiana, then under Spanish control.

In trying to do something similar with African Americans, we immediately stumble. Most black people in the United States cannot trace their genealogy with much precision because of the legacy of slavery. Their ancestors were seized from West Africa, leaving little or no record of where they were born. In 2014, the genetic genealogy company 23andMe published its version of the population structure of the United States. In that portrait we see a similar pattern of European admixture, and some insights into the history of the postcolonial United States.

The Emancipation Proclamation—a federal mandate to change the legal status of slaves to free—was issued by President Lincoln in 1863, though the effects were not necessarily immediate. In the genomic data, there’s admixture between European DNA and African that begins in earnest around six generations ago, roughly in the mid-19th century. Within these samples we see more male European DNA and female African, measured by Y chromosome and mitochondrial DNA, suggesting male Europeans had sex with female slaves. Genetics makes no comment on the nature of these relations.

This post is adapted from Rutherford’s upcoming book, A Brief History of Everyone Who Ever Lived: The Human Story Retold Through Our Genes.