DNA research suggests large-scale collapse of Native American ancestors

Scientists have long looked to the archeological record to answer questions about the early population history of the Americas. A new study digs into different data: the human genome.

A new ancient DNA study bolsters accounts that European arrival in the Americas decimated indigenous populations. 

An international team of scientists has sequenced mitochondrial DNA from skeletons and mummies of indigenous Americans ranging from 8,600 to 500 years ago. They compared this new data to the DNA of modern Native American populations and found that the old sequences were mysteriously missing.

This doesn't mean that all indigenous Americans died off, study lead author Bastien Llamas points out. There still are Native Americans alive today across both continents. But of the 92 archaic individuals that the team looked at, none of their mitochondrial sequences survived to the present day.

It could have been disease, warfare, societal collapse or some other catastrophe, Dr. Llamas tells The Christian Science Monitor. What the study indicates is that something significant happened to reduce the genetic diversity of this population in the past 500 or so years. Christopher Columbus's expedition that brought him to the Americas was in 1492. 

But historical accounts suggested the European arrival coincided with a significant reduction of the populations already living in South, Central, and North America. Estimates have ranged from around 50 to 90 percent of the population died off at the time. "Even those low, low numbers, that's an incredible calamity," John Walker, an archeologist at the University of Central Florida who was not part of the study, tells the Monitor.

The study, published Friday in the journal Science Advances, wasn't about just one moment in the early history of the Americas. The research team also found clues into the initial peopling of the region.

"We knew that Native Americans living today have a relatively low genetic diversity," Llamas says. "Meaning it is highly likely that some time in the past, they lost some of their genetic diversity in what we call a bottleneck."

"Was it because of Europeans? Or was it because of the very early events that led to the peopling of the Americas?" he says. According to Llamas' research, "a combination of both" shaped Native American genomes.

Telling the tale of the peopling of the Americas

Llamas and his team combined their genetic data with archeological, geological and other evidence to model what might have happened. The story goes something like this:

During the last ice age, sea levels were significantly lower. At the time, there was a large swath of land where the Bering strait is now, between Alaska and Siberia. That region, called Beringia, formed a sort of land bridge connecting the two continents.

The genetic data shows the most recent population divergence between Siberians and Native Americans to be 24,900 years ago, suggesting that's around when people started moving into the far reaches of North America. There, these early Americans developed their own, unique, signature genetic lineage that persists among Native Americans today. 

But when they arrived, they would have been greeted by humongous ice sheets that covered what is now Canada. So these first Americans hunkered down in Beringia for awhile.

What happened next has been an issue of debate among researchers. For decades, the predominant explanation among researchers was the Clovis First Model, which suggested the Clovis people – a prehistoric culture known for their distinctive fluted stone spear points – were the first to move south, around 13,000 years ago. But many archeological finds have since shown that people were as far as Chile by 14,000 years ago.

These mitochondrial DNA findings are "more or less consistent with the archaeological data," Theodore Schurr, an anthropologist at the University of Pennsylvania who was not part of the study, tells the Monitor in a phone interview. According to the genes, people started leaving Beringia around 16,000 years ago, likely trekking along the Pacific coast where a corridor would have opened up.

Genetic diversity greatly increased after that time, says Llamas. That suggests a significant population increase. And Beringia, cold, stark, and confined, would likely not have supported a large population. 

As the people started moving south, some settled in groups along the way. As these separate groups established themselves, they too developed unique lineages. 

This model "seems to fit very nicely," Dennis L. Jenkins, an archeologist at the University of Oregon who was not part of the study, tells the Monitor. "Right now it does match what is commonly accepted among the majority of first colonization studiers." But, he cautions, the Clovis First Model seemed like a perfect fit at one time too. 

Does the DNA tell the whole story?

No. 

Mitochondrial DNA is just a portion of the human genetics. These genes are passed only from mother to child, so represent only maternal lineages, say scientists.

Furthermore, Llamas says, ancient specimens that the researchers can extract DNA from are limited. In this study, most of the ancient individuals are from Bolivia, Chile, and Peru. So, he says, "there may have been some kind of bias in our sampling."

As such, "The conclusions that we have drawn from this dataset may change in the future when we gather more data," he says. "It's an ongoing story."

Dr. Jenkins agrees that more research and more genetic data is necessary to fill out the picture. "I think that DNA in archeology is just going to get stronger as time goes on and I would hope that more archeologists would begin thinking and sampling in such ways that we can explore the genetic evidence that's around us all the time," he says. "It's going to become a really great tool for archeology."

"Ancient DNA is critical for understanding these details because it provides us with a direct snapshot of genetic diversity in the past, which can then be used to infer details about human history, including estimates of past population size, ancestor-descendent relationships, and population divergence.  These are details which aren’t necessarily obtainable from archaeological or paleo-climate data," Jennifer Raff, a biological anthropologist at the University of Kansas who was not part of this study, tells the Monitor in an email.

Dr. Walker adds, "The use of DNA from pre-Columbian people is very innovative, it makes a lot of sense."

And this research won't just inspire more ancient DNA research, "Speaking as an archaeologist, I would see it as a reason to do more archaeological research" to confirm their models, Walker says.