A paleogenomic peek into the human history of the Americas — and all its complications

A “birdman” tablet unearthed at the Cahokia Mounds site in what is now Illinois, a massive earthworks that was the centerpiece of a community of tens of thousands at its peak in the 12 Century CE. (Flickr, Don Sniegowski)

The following is a guest post from Ellen Quinlan, a PhD Candidate in Biology at Wake Forest University. Ellen’s dissertation work studies the ecology and population genomics of altitudinal range limits in Andean trees. 

The Molecular Ecologist receives a small commission for purchases made on Bookshop.org via links from this post.

Who, when, and how the Americas were first peopled is one of the biggest mysteries in human history. If you’ve heard anything of this story, it’s likely the same one I learned in my college anthropology course and the same one that dominated the fields of archaeology and biological anthropology throughout the 20th century. Under this model, a small group of humans arrived in the Americas fairly recently (~13,000 ya), after walking across the Bering Land Strait, following animal and plant migrations as ice retreated. However, over the last two decades this narrative has been dismantled by new archaeological discoveries and, of course, modern paleogenomics, which have introduced new evidence and prompted the re-examination of old. Geneticist and anthropologist Jennifer Raff’s book Origin: A Genetic History of the Americas is a deep but accessible overview of the new insights yielded by paleogenomics to this rapidly evolving field. 

While I admittedly came to Origin for some cool paleogenomics (of which there are plenty), the book has stuck with me because it is about so much more. Through Origin, Raff eloquently tells both the history of the science as well as the history of how colonialism and misogyny have impacted scientists’ interpretations and harmed the communities involved for centuries. Further, she demonstrates how these stories are deeply intertwined and offers a clear roadmap (with examples from her own work and others) for how the fields of anthropology and human genomics can begin to repair that harm and develop more ethical approaches for the future. 

Part 1 of the book summarizes the history of archaeology and anthropology in the Americas, with an extensive analysis of the theories that have dominated the field, how well they are (or are not) supported by evidence, and the alternative models that have been proposed. The most significant of these was the Clovis First model of Native American origins, which governed archaeology for decades. “Clovis First” refers to a culture of people identified in the archaeological record by their use of Clovis points, a weapon developed for hunting megafauna. Under this model, they were the first humans to arrive in the Americas at the end of the Pleistocene and populations quickly exploded, spreading across North and South America within just a few hundred years. This model became so engrained in archaeology that as new sites and evidence arose that did not fit neatly within the model, leaders in the field brushed them off as distractions resulting from contaminated sites and sloppy work. For example, it took nearly three decades from the initial discovery of the Monte Verde site in Chile for it to be officially declared a pre-Clovis site, indicating that humans must have been in South America by at least 14,600 years ago (1,000 years before the first Clovis point). This acknowledgement opened the door for a complete rethinking of this history, and many other pre-Clovis sites have since been recognized from across the Americas. Unfortunately, this story is not uncommon in science, and as with other paradigm-shifting discoveries such as Wegner’s plate tectonics and Woese’s Archaea, fields can become so fixated on a specific idea that contradictory evidence is ignored and progress hindered for years. 

As a non-expert, and someone who came to this book for the genetics, this first section was a bit difficult to get into. I found myself flipping back to recall names and dates, just to try and keep up. However, I appreciate that Raff is careful not to cherry-pick from the data to build a single, cohesive narrative. Instead, with each discovery she presents the conflicting theories (if there are any), allowing the reader to decide for themselves which they subscribe to. Importantly, these chapters also examine how the fields of archaeology and anthropology in the Americas developed out of colonialism, misogyny, and fear, as the mere existence of Native Americans threatened colonialists’ belief systems and understanding of themselves. This resulted in the development of hypotheses and mythologies (such as Clovis First) that intentionally diminished Native Americans and their origins as the First Peoples. Rather than shy away from this reality, Raff addresses it head-on in the opening pages of the book and returns to it throughout, demonstrating that the two histories are so intertwined that they could not, and should not, be examined in isolation. 

In part 2 of Origin, the focus shifts to paleogenomics and I realized that the detailed archaeological review in part 1 was critical for establishing why the new genomics work is so ground breaking. Specifically, which open questions the genomic data helps to fill and which theories it’s blowing up. For example, the sequencing of just a few ancient Mesoamerican individuals has completely reshaped our understanding of the movement of humans between North and South America. Researchers once thought that a single, recent migration accounted for the colonization of South America. Instead, the genomes of these individuals suggest it was much more complex, with multiple movements and interactions among distant groups. The genomes of an elderly Mayan woman and two men buried in the same rock shelter 2,000 years later point to one such migration, where a group now referred to as “Unsampled Population A” moved from North to Central America between 9000 and 7400 years ago. These genomes combined with evidence from contemporary Maya suggest that these populations intermarried, spreading not just DNA but also language and culture.  

Any molecular ecologist can relate to the struggles paleogenomicists have faced while attempting to reconstruct these histories – fragmented or degraded DNA and missing and under-sampled (or unsampled) populations, with the data often raising more questions than they answer. In the second half of part 2, Raff brings the reader into her highly restricted lab at the University of Kansas, to follow her through the DNA extraction and sequencing of a single tooth sample from a recently discovered individual. As someone who has done a few DNA extractions, I found the details of working with such ancient samples both captivating and daunting, and it made me extra grateful to be studying contemporary plants. However, this narrative serves as more than just a description of the sterile and meticulous extraction process. It also communicates the care and respect that is given to each specimen in her lab and the extent of their partnership with the responsible tribe, working for years to agree upon the questions to be studied and methods to be used before any work begins. 

The third and final part of the book synthesizes what we now know from ancient and modern genomes and how they agree or disagree with the models developed from archaeological evidence. Each chapter is dedicated to a specific region, taking the reader on a migratory journey from Asia and Beringia to North and South America and then finally to the North American Arctic and Caribbean. Throughout the book, but particularly in these chapters, Raff pairs narrative vignettes with important discoveries, which she describes as her imaginings of the ancient people that have been unearthed. While these vignettes help to illustrate what is known about these people and how they lived their lives, their true value is in their effectiveness in humanizing the remains and elevating them from specimens to ancestors. The final chapters return to the discussion of how scientists obtain data from these remains and how outdated models and practices can and do continue to cause harm to Indigenous communities. Raff then offers examples of how researchers can develop more ethical practices by not only consulting but partnering with Native American communities at every step of the scientific process. 

Both a success and frustration with this book is that it does not leave the reader with one clear story or conclusion at the end. Raff expertly presents the evidence from archaeology and ancient genomics as well as indigenous science and origin stories, pointing out where they align, where the stories they reconstruct diverge, and what questions are left to be answered. In doing so, she demonstrates how science really works – it’s messy, often there is not one clear solution, and conclusions must be re-evaluated each time a new piece of evidence is introduced. This is particularly true here, as constantly evolving methods in paleogenomics and the discovery of new sites means that the story of the peopling of the Americas is ever-changing. As a reader this may at times be frustrating, but I appreciated Raff’s restraint from the temptation to smooth over the story to make it easier to digest, as is common in many popular science books. Instead, she works to elevate the reader, making the story accessible while maintaining the truth of the scientific complexity. The result is a fascinating and rigorous retelling of our current understanding of the peopling of the Americas and the science that has helped to piece it together. 

With the current pace of scientific discovery, especially in fields that deal with big data like genomics, many of the new and exciting models proposed in this book will soon be out of date. What will remain is the framework it establishes for considering the impact of the legacies of colonialism, racism, misogyny, and bigotry in our science and how we can develop better approaches for the future. Raff is not herself indigenous, but it’s clear that she’s done the work of listening and learning from many who are, and thus has made specific choices throughout the writing of this book and within her own research program to not just avoid further harm but actively right past wrongs. This book is a bold and unapologetic reminder of the lasting impact of some of science’s darkest history and the responsibility we have to acknowledge and correct it in our respective fields. 


Raff J. 2022. Origin: A Genetic History of the Americas. United States: Grand Central Publishing, 368 pages. Find it on Bookshop.


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About Jeremy Yoder

Jeremy B. Yoder is an Associate Professor of Biology at California State University Northridge, studying the evolution and coevolution of interacting species, especially mutualists. He is a collaborator with the Joshua Tree Genome Project and the Queer in STEM study of LGBTQ experiences in scientific careers. He has written for the website of Scientific American, the LA Review of Books, the Chronicle of Higher Education, The Awl, and Slate.
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