Etched in DNA: Decoding the secrets of the past

What does it mean to be human? Paleoanthropologists have long wrestled with this question. Ancient DNA analysis has enabled them to probe new depths of our ancestral past.

DECEMBER 30, 2019 - Over the past decade, the study of ancient DNA has enriched our evolving tale of early human history. In the field, it’s resolved long-standing debates, raised new questions, and added nuance to our perpetual quest to answer what it means to be human. 

A visitor sizes up a reconstruction of a Homo neanderthalensis in a business suit at the Neanderthal Museum in Mettmann, Germany, July 3, 2019.Martin Meissner/AP 

“I can’t tell you how many times I’ve had to rewrite lectures” because of new paleogenetics revelations, says Jennifer Raff, an anthropological geneticist at the University of Kansas. “I can’t wait to see what the next decade brings.”

Human origins research. The phrase probably evokes an image of dusty scientists hunched over in the sun, combing the ground for scraps left behind by people of millennia past. The field has long been the realm of stones and bones, with test tube-filled laboratories playing second fiddle. 

But that’s changing. Paleoanthropology has found a second home in the lab, as geneticists have joined the field, extracting DNA from fossils in search of new insights into early human history.

“It’s white coat science,” says John Shea, a professor of archaeology at Stony Brook University. “It’s not bluejeans and khaki shirt science.”

A turning point

Ancient DNA, or aDNA, was just beginning to catch on when Dr. Raff finished her dual Ph.D. in anthropology and genetics in 2008. Fragments of ancient genomes were being sequenced, analyzed, and discussed. But Dr. Raff was unsure if science could ever recover full genomes from long back in time. 

But then it happened. The following year, a team of scientists announced that they had pieced together the full genome of a 38,000-year-old Neanderthal. They published their findings in May 2010 in the journal Science, ushering in a new decade of discovery and understanding.

The sequence was not only a marvel of this new technology; it shed light on a long-standing debate about how these archaic humans may have interacted with our direct ancestors. 

The two had interbred. The idea had circulated in some circles, but had long been considered the musings of a “lunatic fringe” by many in the field. But now, there it was, etched in the DNA.

For decades, scientists categorized hominins based on the differences in the shape of their bones. But DNA has brought a faster way to get more definitive answers about the identities of ancient peoples. 

“I’m done with ‘who’ questions,” Dr. Shea says. “Ancient DNA is freeing archaeologists up to start looking at the really interesting questions. And the most interesting question is ‘how.’” How did a group of ancient people move across a forbidding landscape? How did they survive through frigid winters? 

Those questions can help to animate our view of the past, and deepen our understanding of where we come from. Paleogeneticists are digging into ancient genomes looking for biological answers to those questions, too, but piecing together a fuller story will take a multidisciplinary approach, says Dr. Raff.

“There’s a whole field of anthropology that talks about what makes us human, and that’s not just our biology,” she says. “It’s also culture and technology and behavior and ecology. There’s just so much that goes into understanding the past.”

One of us?

The revelation that Neanderthals interbred with early Homo sapiens has raised some fundamental questions about what it means to be human. 

Traditionally, the line between species is defined by whether they can interbreed and produce viable offspring that can, in turn, produce viable offspring. But, due to similarities in the bones and now the genetic evidence, some anthropologists have labeled Neanderthals as Homo sapiens neanderthalensis and anatomically modern humans as Homo sapiens sapiens.

One such researcher is Fred Smith, professor emeritus of anthropology and biology at Illinois State University. He argues it from a morphological point of view, too.

“You would never mistake a Neanderthal for anything but a human,” Dr. Smith says. “It might not be a human that you’d like to go on a blind date with, but if you saw one, you wouldn’t think of it as not being human.”

By that logic, many researchers refer to other members of the genus Homo as “human,” too. But some say it might be our understanding of speciation that needs revising, not the distinctions among species in the genus. 

“The pattern of evolutionary thinking is that you have a point in time where two lineages diverge,” after which they do not cross again, says Rick Potts, director of the Smithsonian National Museum of Natural History’s Human Origins Program. 

But that branching model of evolution and speciation is proving to be too simplistic across biology, with hybridizing appearing among present-day creatures, too. “Evolution and the formation of species are a process, not an event,” he says.

Regardless of whether we can call Neanderthals one of us, the revelation of prehistoric trysts between the two peoples has changed our perception of those other humans. 

Before ancient DNA came on the scene, “Neanderthal” was often lobbed as an insult – and sometimes still is. When archaeologists suggested that they had found Neanderthal art and musical instruments, they were dismissed quickly, as the logic went that only Homo sapiens could have the cognitive abilities for that level of creativity. But with the revelation that we are similar enough to them that we could interbreed, that kind of research has been entertained and discussed more frequently. 

“I think it gives a very important correction on those who would see the Neanderthal simply as incapable of thought, incapable of being clever,” Dr. Potts says. “And it also, I think, gives a bit of humility to ourselves for those who are willing to look at it.” 

A decade of discovery

Our species is the only creature (that we know of) to have colonized the entire terrestrial globe. Why is that? There were a lot of other hominins at one point in time; what makes us so special? Over the past decade, the story of early human history has had chapters added and edits made, adding nuance to those questions.

The human family tree has sprouted new branches. In 2010, scientists introduced the world to Denisovans after finding a finger bone in a Siberian cave that resembled – but was clearly distinct from – that of a Neanderthal. Ancient DNA analysis confirmed that it was indeed a new species.

Hundreds of fossils that appeared distinct from any known hominin were discovered in a cave in South Africa in 2013. When the discovery was announced two years later, the new species was given the name Homo naledi. And this past April, researchers announced that bones of yet another previously unknown hominin had been unearthed in the Philippines. They named it Homo luzonensis after the island of Luzon where the fossils were found. 

In the final weeks of 2019, another finding altered the human timeline. Researchers reported on Dec. 11 that they’d found cave art on the Indonesian island of Sulawesi dating back at least 43,900 years, depicting a hunting scene with mythical beings – the earliest such storytelling found. Other dates have also been pushed back. For example, fossils found outside Africa have suggested that some Homo sapiens spread into other continents more than 100,000 years ago – much earlier than previously thought.

These new players and shifts in the human timeline are simply the latest chapters in our understanding of the human story. What revelations will the next decade bring?