How Ancient DNA Is Rewriting Human History

We thought we knew how we'd been shaped by evolution. We were wrong.
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(Photo: Heartland Arts/Shutterstock)

(Photo: Heartland Arts/Shutterstock)

There are no written records of the most important developments in our history: the transition from hunting and gathering to farming, the initial colonization of regions outside Africa, and, most crucially, the appearance of modern humans and the vanishing of archaic ones. Our primary information sources about these "pre-historic" events are ancient tools, weapons, bones, and, more recently, DNA. Like an ancient text that has picked up interpolations over the millennia, our genetic history can be difficult to recover from the DNA of people alive today. But with the invention of methods to read DNA taken from ancient bones, we now have access to much older copies of our genetic history, and it's radically changing how we understand our deep past. What seemed like an episode of Lost turns out to be much more like Game of Thrones: instead of a story of small, isolated groups that colonized distant new territory, human history is a story of ancient populations that migrated and mixed all over the world.

There is no question that most human evolutionary history took place in Africa. But by one million years ago—long before modern humans evolved—archaic human species were already living throughout Asia and Europe. By 30,000 years ago, the archaic humans had vanished, and modern humans had taken their place. How did that happen?

From the results of early DNA studies in the late 1980s and early '90s, scientists argued that anatomically modern humans evolved in Africa, and then expanded into Asia, Oceania, and Europe, beginning about 60,000 years ago. The idea was that modern humans colonized the rest of the world in a succession of small founding groups—each one a tiny sampling of the total modern human gene pool. These small, isolated groups settled new territory and replaced the archaic humans that lived there. As a result, humans in different parts of the world today have their own distinctive DNA signature, consisting of the genetic quirks of their ancestors who first settled the area, as well as the genetic adaptations to the local environment that evolved later.

There are very few isolated branches of the human family tree. People in nearly every part of the world are a product of many different ancient populations, and sometimes surprisingly close relationships span a wide geographical distance.

This view of human history, called the "serial founder effect model," has big implications for our understanding of how we came to be who we are. Most importantly, under this model, genetic differences between geographically separated human populations reflect deep branchings in the human family tree, branches that go back tens of thousands of years. It also declares that people have evolutionary adaptations that are matched to their geographical area, such as lighter skin in Asians and Europeans or high altitude tolerance among Andeans and Tibetans. With a few exceptions, such as the genetic mixing after Europeans colonized the Americas, our geography reflects our deep ancestry.

Well, it's time to scrap this picture of human history. Looking over the stunning new data generated in just the last five years, geneticists Joseph Pickrell at the New York Genome Center and David Reich at Harvard University argue that the genetic record of the first modern humans leaving Africa has long been "overwritten" by later developments. "It is now clear that the data contradict any model in which the genetic structure of the world today is approximately the same as it was immediately following the out-of-Africa expansion," they write. Present-day geography of human genes is not a good guide to our ancestry.

Pickrell and Reich lay out the case for "a systematic reevaluation of human history" in light of the new genetic data collected with new technologies. Much of this new data comes from recent large-scale collections of human genomes, which provide a much more comprehensive picture of geographical patterns in the DNA of living human populations. But the truly revolutionary findings come from studies that look directly at ancient DNA. Instead of trying to reconstruct our ancient genetic record with only modern sources, scientists can now, in some cases, examine the original source itself. The Neanderthal genome, published in 2010, is the most famous case, but researchers have published many more ancient DNA studies since then. The results are clear: There are very few isolated branches of the human family tree. People in nearly every part of the world are a product of many different ancient populations, and sometimes surprisingly close relationships span a wide geographical distance.

One surprising finding, published in January, is that the traces of European DNA in contemporary Native Americans can't all be chalked up to the arrival of Christopher Columbus. A team of scientists led by Eske Willerslev at the University of Copenhagen sequenced DNA taken from the bones of a boy who died 24,000 years ago in south-central Siberia. Their results show that this boy was from an ancient population that contributed to the ancestry of both Europeans and Native Americans. Other ancient DNA studies published within the past year include analyses of Stone Age hunter-gatherers and farmers from Scandinavia and Spain, a Bronze-age population from the Ukrainian steppes, and a 12,000-year-old Native American that lived in what is now Western Montana. The story coming out of these genetic studies is still developing, but one feature is clear. As Pickrell and Reich put it, "Human history is not one of stasis." We can easily see this in written history, which tells why most African Americans and Latinos have a mixed ancestry. The genetic record shows that for the past tens of thousands of years, mixed human ancestry is the rule and not the exception.

This finding has implications for the role of evolution in shaping who we are. Genetic adaptations that first evolved in one environment were sometimes brought to other parts of the world with very different environments. This means that we need to be wary about accepting overly simple stories about how present-day people in a particular region carry genes that have evolved to fit their particular niche—those evolved genes may be recent arrivals from somewhere else.

Reading deep human history from the record of our DNA is a tricky business, but it's also a powerful way to answer some compelling questions about our past—a past that is more surprising and complex than we originally thought.

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