For ten thousand years, a cave on the northern tip of Prince of Wales Island in Alaskaⁱ served as a resting place for the remains of an ancient man. But on July 4, 1996, paleontologists uncovered his mandible mingled with the bones of seals, lemmings, birds, caribou, foxes, and bears (1).

The cave provided an extraordinary window into the past.ⁱⁱ Paleontologist Tim Heaton and colleagues were able to tell from the remains of animals dating back as far as 41,000 years agoⁱⁱⁱ that this region^iv and others along coastal Southeast Alaska may have served as a refuge for animals during the Last Glacial Maximum (LGM)—a period in which much of northern North America was covered by massive glaciers. As the Earth warmed and the glaciers receded, northern North America gradually was repopulated by animals from these refugia, as well as by species that had crossed the Bering Land Bridge (BLB), sometime toward the end of the last glaciation. The BLB connected the continents of Asia and North America until about 10,000 years ago.

The unexpected discovery of an ancient human presence within Shuká Káa Cave made it even more significant, particularly to the Tlingit and Haida peoples who have lived in the region for millennia. A flaked stone spearpoint had been found and reported to the island archaeologist Terry Fifield a week before, but it was assumed to be just a single isolated find. When the human mandible was found, however, Heaton immediately knew that there was much more to the site than previously expected. He stopped excavations and radioed Forest Service law enforcement to report it. The next morning, Fifield flew to the site by helicopter to assess the situation. Following the stipulations of the Native American Graves Protection and Repatriation Act (NAGPRA), Fifield brought the man’s remains back to the Forest Service and called the presidents of the Klawock and Craig tribal councils the next day to notify them of the discovery.

Over the following week, aided by the NAGPRA specialist at the Central Council of the Tlingit and Haida Indian Tribes of Alaska (CCTHTA), Fifield and tribal leaders set up a consultation session hosted by the Klawock tribe and invited five Tlingit and Haida tribes to help decide what should be done next.^v

The initial reaction from the communities was mixed. Some were reluctant to disturb the human bones any further. But other community members wanted to learn what information the ancient man could reveal about the history of the people in the region. “As I remember those initial talks,” Terry Fifield told me in an email, “council members wondered who this person might be, whether he was related to them, how he might have lived. It was that curiosity about the man that inspired the partnership at the beginning.”

After much discussion and debate, community members eventually agreed that the scientists could continue their dig and study the ancient remains. They stipulated that excavations would immediately cease if the cave turned out to be a sacred burial site. They also mandated that the scientists were to share their findings with them before they were published and consult with community leaders on all steps taken during the research—and the community members would rebury their ancestor following the work.

The scientists involved agreed to all of these stipulations and updated the tribes regularly on their findings as the work progressed. Terry Fifield attended tribal council meetings and sought permission from the council whenever a journalist or filmmaker wanted to do a story on the site. Archaeologist E. James Dixon from the Denver Museum of Natural History developed a National Science Foundation–funded research project to excavate the cave, which also funded internships for tribal citizens to participate directly in the excavations. In subsequent years Sealaska Corporation, the Alaska Native Regional Corporation for the area, provided additional funding for internships to students working with the project.

This partnership between community members, archaeologists, and the Forest Service was fruitful. Over five seasons of archaeological fieldwork, seven human bones and two human teeth were recovered from inside the cave. All belonged to a single man. His bones were scattered and damaged by carnivores and were distributed across approximately 50 feet of a passage in sediments that had been churned up by water from a small spring. It was clear to archaeologists and community members alike that this was not the site of a deliberate burial; excavating his remains would not only help people learn more about the past, but it would also allow the communities to provide him with a respectful burial.^vi

Archaeologists were able to determine from the shape of the man’s pelvis and teeth that he had been in his early 20s when he died. A chemical analysis of his teeth revealed that he had grown up on a diet of seafood. Artifacts at the site suggested that he (or someone else who had left them in the cave) engaged in long-distance trade of high-quality stone, which was used to make tools that were specially designed for hunting in the challenging Arctic environment. Radiocarbon dates from his bones revealed something astonishing: He was over 10,000 years old. These remains were from one of the oldest people in Alaska.^vii

The Tlingit maintain that their ancestors were a seafaring people who have lived in this region since the dawn of history. The discovery of this man, whom the Tlingit called Shuká Káa (“Man Ahead of Us”), was consistent with oral histories that they descend from an ancient, coastally adapted people who engaged in long-distance trade. As the project progressed, the idea that this man could be their ancestor—or at least lived in ways similar to those of their ancestors—grew increasingly plausible.

Shuká Káa’s story didn’t end with the archaeological examination of his remains. Prior to his reburial in 2008, the tribes allowed geneticists to sample a small portion of his bones for DNA analysis. Initial tests showed that the man belonged to a maternal lineage that is very uncommon in present-day Indigenous communities, suggesting that contemporary people in the region may not be direct descendants of Shuká Káa’s population.

But there’s been another twist to this story over the last few years. A technological revolution has taken place within the field of paleogenomics—the study of ancestral genomes—allowing the reconstruction of an ancient person’s complete nuclear genome from small samples of bone or tissue. This development allowed researchers (again with permission from the tribes) to reexamine Shuká Káa’s DNA on a vastly more detailed level than the original study. His complete nuclear genome, which includes all the DNA in his chromosomes, showed that his people were the ancestors of present-day Northwest Coast tribes after all, again reaffirming their own oral histories (2).

Since the publication of Shuká Káa’s genome, the Tlingit have continued to use genetics as a tool for studying their clan and moiety systems,^viii finding additional places where their lineage (as revealed by DNA), archaeological evidence, and the clan histories preserved in their oral traditions (3) speak with a unified voice.

For archaeologists, Shuká Káa added a significant piece of evidence against an outdated theory: the idea that a human presence in the Americas was recent, resulting from an overland migration about 13,000 years ago. This may have been the story you learned in school.

But we have learned over the last few decades that this story is not accurate. It does not even come close to accounting for the piles of new evidence that have been amassed by archaeologists and geneticists.

The old theory is clearly out of date, but the history of how people first got to the Americas remains a mystery, a complex puzzle to be solved. In this book, we will follow archaeologists as they draw connections between different sites across the Americas. Looking at the genetic evidence, we will examine the ways in which DNA has challenged and changed our understanding of Native American history, with a special focus on the events that are only indirectly understandable with the archaeological record. We will join scholars of both disciplines in their struggles to integrate these different clues into new models for how humans first arrived in the Americas. As we’ll see later in this book, many archaeologists and geneticists now believe that people were present in the Americas far earlier than was previously thought: perhaps by 17,000–16,000 years ago, or even as early as 30,000–25,000 years ago, and that the peopling of the continents was a complex process.

At the same time as we discuss the results and models from Western^ix scientific approaches, it’s important to acknowledge that Indigenous peoples of the Americas have diverse oral histories of their own origins. These traditional knowledges—like the Tlingit’s understanding of their origins and their relationship to Shuká Káa—convey important lessons about the emergence of their identities as people and their ties to the land; they may or may not agree with the models presented in this book.

Histories of the Americas written by non-Native scholars tend to be dominated by the story of how Europeans colonized the continents. In the stories of Christopher Columbus reaching San Salvador, or the Pilgrims founding Plymouth Colony, or Hernán Cortés conquering the Aztecs, Native Americans are often relegated to marginal roles as supporting characters, bystanders, victims, or antagonists. Precontact histories of Indigenous peoples are given far less prominence, and many of those that do exist in popular culture are rife with outdated scholarship (at best) or blatant pseudoscience (4). With some notable exceptions, Native Americans preserved their histories in oral, rather than written, stories. European colonists did not view these oral traditions as equivalent to their own histories.

In these frameworks, Native peoples are marginalized or forgotten, excluded from public conversations, and portrayed as inhabitants of the past rather than contemporary members of society. Their own knowledge too often is ignored by non-Native scholars. This ultimately contributes to the erasure or marginalization of Indigenous peoples in society at large. The contributions of Native artists, politicians, writers, traditional knowledge keepers, and scholars are unappreciated. Indigenous knowledge, sacred practices, and regalia are appropriated and commodified by white people. In some cases, academics repackage and re-interpret traditional knowledge as their own scholarship without credit to Native experts.

None of this marginalization is accidental. Since the beginning of colonialism in the Americas, Native peoples have been removed, enslaved, or eliminated from their lands in order to make way for settlers. One way for colonizers to justify their claims to Native lands was to portray them as empty. The Native peoples who did remain were characterized as “savage” and backward, in need of the “civilizing” that the settler nation could provide. Disregarding or expunging Native histories from the broader narrative has been a crucial part of the larger strategy to discount the validity of age-old Native rights to lands the settlers wanted. Sadly, this practice of historical marginalization continues into the present day; as we shall see later in this book, DNA has been increasingly used as a tool for promoting narratives that disenfranchise Native peoples.

A greater awareness of the histories of Indigenous peoples on the American continents—that gives as much weight to the time before 1492 as after it—won’t fix these issues alone. But it is an important step in itself.

This book covers a small but exciting piece of the vast and complex arc of Indigenous histories in the Americas: the very beginning, when people first came to these continents. Thanks to information we have learned both from the archaeological record and the genomes of ancient peoples like Shuká Káa, the way scientists think about this event has changed radically in recent years.

We are living through a revolution in the scientific study of human history. Geneticists and archaeologists have been working together for decades to learn from the histories archived in DNA of both present-day and ancient peoples. But because of recent technical developments in approaches for recovering and analyzing that DNA, our ability to ask and answer questions about the past has improved dramatically. New results—some surprising, others that confirm long-standing ideas about the past—are piling up at a rate so fast it’s hard even for experts to keep up with each new discovery.

In the Americas the revolution has upended a long-standing model that describes the final steps that humans took on their journey from Africa across the globe. As I mentioned earlier, scientists once thought that the peopling of the Americas occurred around 13,000 years ago, following the last ice age, when a small group of people crossed the Bering Land Bridge from northeast Asia to northwestern Alaska. From Alaska they were thought to have traveled southward through a corridor that had opened up between the two massive ice sheets that blanketed northern North America. On their journey, these intrepid travelers invented new stone tool technologies for surviving in the novel environments they encountered. These technologies, which include a distinctive kind of stone spearpoint called a Clovis point, appear widely across the North American continent 13,000 years ago. The conventional model for explaining their appearance suggested that the people who made them migrated very quickly across the Americas once they passed the ice sheets.

We know today that this scenario—which dominated American archaeology for decades—is wrong. People had already been in the Americas for thousands of years by the time Clovis tools made their appearance. The updated story of how humans arrived here is still being assembled piece by piece, from clues left all over the continent: deep below the surface of a muddy pond in Florida, within the genome recovered from a tooth in Siberia, in layers of dirt baked by the hot Texas sun.

But as in the movie Clue, where the same events could be explained by multiple narratives, these pieces of evidence seem to tell different stories to different groups of scholars. In this book, we will examine these pieces of evidence and the various ways in which they are interpreted. We will focus our discussion primarily on the clues written in DNA, and how they support or cast doubt on interpretations of the archaeological record. A picture is gradually coming into focus, but there are still many unanswered questions.

The story of Shuká Káa and the other ancient peoples who were the first inhabitants of the Americas is not just ancient history. It’s also a story about the present: Shuká Káa became the nexus of an extraordinary collaboration between different groups of people who came together to study him. This shows us how much a collaboration between Indigenous peoples, scientists, and government agencies can achieve when following an approach respectful of tribal sovereignty and values, Indigenous knowledge, and scientific curiosity. But in the story of American anthropology and genetics, this partnership has historically been the exception, not the rule. Fortunately, as we shall see, this is changing.

So while this book is about how scientific understandings of the origins of Native Americans have changed, we cannot tell that story without also scrutinizing how scientists have arrived at these understandings. This is not a pleasant history to recount. The Indigenous inhabitants of the Americas have been treated with disrespect, condescension, and outright brutality by a number of scientists who have benefitted at the expense of the people they were so curious about. This is the legacy that contemporary anthropologists, archaeologists, and geneticists need to confront head-on; there can be no honest progress in the scientific study of the past without acknowledging those threads of human history we have dismissed, neglected, or erased in the past. The journey to knowledge has to involve self-scrutiny; scientific progress cannot be divorced from the social context in which it takes place.

These three themes—the histories reconstructed from genetics and archaeology, the story of how we achieved this knowledge, and the broader cultural questions that are raised by the research conducted in the field—are inexorably intertwined; you can’t understand the whole story by examining any one of them in isolation. But just as our revolution in ancient DNA methodologies has allowed us to understand new histories written within the strands of DNA, it’s my hope that by looking at the example of Shuká Káa, listening to scientists and Indigenous scholars and community leaders, we can transform our approaches to investigating the past.

In part 1 of this book, I’ll examine the history of attempts by Europeans to understand the origins of Native Americans and explain how this fascination was born out of colonialism. Chapter 1 will discuss how Europeans grappled with the fact that the peoples they encountered in the Americas were not mentioned in the Bible. The Indigenous peoples of the Americas were an existential threat as well as an impediment to colonization; attempts to understand their origins were informed partially by curiosity and partially by a desire to subvert the threat they posed. The present-day disciplines of archaeology and biological anthropology in the United States emerged from those early attempts; ideas about racial categorization and eugenics have roots in the period as well. We will take an unflinching look at how these different roots are intertwined and their influence on subsequent research on Native American origins. We will also examine the Mound Builder hypothesis and other mythologies designed to obfuscate the truth about Native Americans as the first peoples of the Americas, as well as the other ways in which people start from the wrong place in thinking about Native American origins in the present day.

In chapter 2, I’ll tell you about the “Clovis First” model of Native American origins that dominated much of 20th-century archaeology, as well as the archaeological evidence that ultimately refuted it. We’ll then examine the evidence for alternative models for how people reached and dispersed through the Americas. In chapter 3, we’ll look closely at the early archaeological record of Alaska. Alaska is thought to have served as a gateway through which people entered North America, but the archaeological sites there that date to the late Pleistocene and early Holocene seem to contradict the story told by sites elsewhere in the Americas. Some archaeologists believe that the evidence from Alaska supports a new version of the Clovis First hypothesis; we will examine and evaluate this model.

In part 2 of this book, we will focus on how paleogenomics—the science of learning histories from ancient genomes—has changed our understanding of the past, beginning with new findings about Mesoamerican and South American histories from sequenced genomes in chapter 4. In chapter 5 I will take the reader into our laboratory at the University of Kansas and provide a glimpse into what it’s like to work with ancient DNA, explaining how we learn about population history from the fragments of ancient genomes that we coax out of samples.

In part 3, we will go through the stories that genetics has told us. I will describe what we’ve learned from the genomes of ancient and contemporary Indigenous peoples of the Americas and Asia, and how these stories may align with archaeological evidence for the peopling of the Americas. I’ll try to make the models produced by genetics and archaeological evidence more vivid with a series of narrative vignettes that illustrate what we know about the lives of ancient people in Asia and Beringia (chapter 6), North and South America (chapter 7), and the peopling of the North American Arctic and the Caribbean (chapter 8). We will then return to the theme of how scientists obtain data in chapter 9, with a focus on how outdated models and research approaches continue to cause harm to Indigenous communities. And finally we will close on a hopeful note, as we look at the efforts of Indigenous and non-Indigenous researchers to work together with communities in developing more ethical research approaches, as the story of the study of Shuká Káa exemplifies.

I am not myself Native American; I’m the great-great-grandchild of immigrants from Poland, Ireland, and England who came to the United States in the early 20th century in search of a better life for themselves and their children. I have no idea if my ancestors were aware of the long history of settlers dispossessing the Indigenous peoples of this place of their land and culture and even committing genocide… but I am. I’m also conscious of the equally long history of people in my profession declaring themselves the experts on other peoples’ origins, lives, cultures, and histories, sometimes using despicable methods to get the data they needed. It’s important that I acknowledge these two facts at the beginning of the book.

I am a scientist, and this book is about the past from a scientific perspective. The stories from genetics and archaeology offered here connect the Indigenous peoples of the Americas with the broader story of human evolution, adaptation, and movements across the globe. This view of migration, however ancient, conflicts with the understanding of some (though certainly not all) tribes of their own origins. They know that they have always existed in their lands; they did not travel from somewhere else. Some Indigenous people view their origin stories as metaphorical, useful for understanding one’s place in the universe and in relation to others, but still compatible with Western science. Indeed, some Native American archaeologists have demonstrated the importance of oral traditions in interpreting the archaeological record and call for careful and analytical study of these traditions and the integration of any clues they might give us to understanding the past (5). Others accept their origin stories as literal truth: They have always been on these lands; they didn’t come from anywhere (6). I acknowledge this conflict but will not attempt to resolve it (if it is possible—or necessary—to resolve it at all). I present history in this book from the perspective of a Western scientist, but for many Indigenous peoples this is not the whole story or the only story that should be told.

This is what I believe: The aggregate understanding of ancient history is akin to a forest with many trees. Each tree corresponds with a particular compounding set of ideas about the evidence you prioritize in building your understanding of the past (7).

There are deep differences in perspectives on the peopling of the Americas, even among scientists who nominally apply the same approaches to understanding the past. For example, as we will discuss later in this book, some archaeologists are quite conservative when it comes to evaluating evidence from early sites (those that predate 13,000 years ago). They apply an impressively rigorous standard for what constitutes a legitimate archaeological site. This framing produces a very particular view of the past. I admire their rigor, but their approach differs somewhat from my own. My own metaphorical tree is rooted in the evidence produced by genetics as a starting point.

And naturally, both of these systems of knowledge can be vastly different from that of a person who prioritizes Indigenous traditional knowledge and oral histories.

My colleague Savannah Martin, a member of the Confederated Tribes of Siletz Indians who studies health disparities and stress, explained her perspective to me this way: “As an Indigenous bioanthropologist with her own creation/origin stories, I balance the interdigitations of many different ways of knowing about my peoples’ histories.”

Just as the forest is healthier and more beautiful for having many different kinds of trees, I believe that these different perspectives can coexist in united appreciation of the past. And as you will see, there are places where the branches—and the roots—of the trees intersect.

How I Write about Indigenous Peoples in This Book

Before Christopher Columbus opened the floodgates for mass European colonization (and the atrocities that accompanied it), there were thousands of different nations in the Americas. There still are today. Within the United States alone, there are 574 federally recognized tribes, others who are recognized by individual states, others who don’t have “official” legal status but may (or may not) be seeking recognition (or reinstatement after termination) as sovereign entities, and many individuals who aren’t citizens of a tribe but who are connected to communities by kinship and culture. Many more nations, tribes, and communities exist without the benefit of recognized sovereignty or autonomy throughout the rest of the Americas, each with their own unique identity, traditions, and histories.

Genetically, Native Americans are not “a people” or “a race,” any more than they are a homogenous culture or speak one language. However, in talking about the peoples of the Americas, I am constrained by the limitations of the English language, and so I will frequently use the terms Native peoples, Native Americans, and Indigenous peoples. (Following convention, I capitalize Indigenous when referring to the Native peoples of the Americas, lowercase when using it as a more generalized term.) These names are themselves used by contemporary tribal members, who also refer to themselves in various places as “American Indians,” “Indians,” “Amerindigenous,” “Natives,” and “First Nations.” Archaeologists often write about the “First Americans” or the “Paleoamericans”; this usage is generally an attempt to avoid the term Indian, which was coined by Christopher Columbus in a vain attempt to support his initial claim that he had arrived in India. Many Indigenous peoples view that term as inaccurate and offensive. (It is important to note that some are fine with it and prefer the designation over Native American, which they view as a colonial term.) Some of my Indigenous colleagues are uncomfortable with the terms PaleoAmerican, PaleoIndian, and First Americans, and, at their advice, I tend to use First Peoples when I am talking about people living in the Western Hemisphere prior to European contact/colonialism. I will also use these terms to refer to the portions of the genomes of contemporary Native Americans that are inherited from those peoples. I will, without apology, change the usage of a particular term used in linguistics and archaeology to refer to an Arctic group that is viewed by many of my colleagues and community partners as a slur^x (8).

As we shall see, the genetic effects of European contact were profound. Today there is no “Native American genome.” Contemporary Indigenous peoples are diverse, with genetic ancestries from First Peoples, but also from populations around the world. We will discuss later in this book how genetics and ancestry testing does not give insights into the question, “Who is Native American?” today.

In general, the commonly preferred way to talk about living peoples in the Americas is to be as specific as possible: e.g., “member of X” or “citizen of Y,” where X or Y refers to tribe, nation, band, or group. I will do that as often as I can here.

The peopling of the Americas is not simply an esoteric bit of science and history, important to only scholars and intellectuals. It is a story of resilience, compassion, intrepidness, adventure, and loss. As the United States is engaged in a difficult conversation about its identity as a nation, the histories of the Indigenous peoples of the Western Hemisphere—and how they have been impacted by outsiders—need to be understood and acknowledged. One place to start is by understanding just how long the First Peoples have been here.