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New Information from Ancient Genomes

High-tech sequencing teams up with creative scientific thinking to help resolve a few nagging questions from prehistoric times.

Sandra J. Ackerman

2014-09SpotlightAckermanFA.jpgClick to Enlarge ImageAt the Euroscience Open Forum meeting this June, one intriguing session addressed the topic of what can or cannot be learned from ancient DNA. Eske Willerslev, director of the Centre for GeoGenetics at the Natural History Museum of Denmark, discussed research published earlier this year in Nature. His recent studies reaffirm the truth of the old saying, “One man’s trash is another man’s treasure.” Or, to put it in terms of evolutionary genomics, “One research project’s contamination is another project’s trove of information.”

Two of the recently published papers discuss a find that has excited great interest ever since it came to light in 1968 in western Montana: the remains of an infant boy dating back about 13,000 years, when a people known as the Clovis inhabited wide swaths of the North American plains. Despite many findings of Clovis blades and worked stone, physical traces of the Clovis people themselves have been hard to come by. In fact, this site in western Montana is the only one in all of the Americas where human remains were found in direct association with Clovis tools. The site was remarkable in its elaborate construction, as well: In Willerslev‘s words, “The roof was more than a meter thick with spear points stacked on top of one another. These points were some of the Clovis people’s most prized possessions; it’s as if we were to find today a gravesite with a meter-thick roof of iPads and tablets stacked on top of it.”

Clearly this was the work of a complex society—but who were the Clovis people, and where did they come from? Archaeologists, anthropologists, and others have argued for decades over when Clovis people first appeared in the Americas and how they may or may not be related to the nations of Native America today.

Evolutionary genomics has much to say on this point. Ancient DNA is notoriously difficult to read because as an organism decomposes after death, its DNA gradually comes to be replaced by the DNA of the microbes and other organisms that feed on it. Ultimately, the genome of the original organism survives only in very short fragments.

The first, painfully slow attempts to study ancient genomes could be used only on mitochondrial DNA, but in the mid-2000s the advent of next-generation sequencing gave researchers the ability to sequence all the molecules of a genome in parallel, saving enormous amounts of time and expense. With this technology, Willerslev’s lab has found evidence that the Native Americans of today share their ancestry with western Eurasians, through the migration of a late Paleolithic population from Siberia into the Americas.

Ludovic Orlando, associate professor at the University of Copenhagen and also at the Centre for GeoGenetics, says, “With ancient DNA, often you don’t know where to start looking, because the DNA molecules of the guy you’re trying to sequence are mixed in with the DNA of microbes that are active in decomposition.” Then again, next-generation sequencing can target extremely short pieces of DNA, allowing scientists to test extremely complex models of migrations, divergence, and admixtures of genes.

The Centre for GeoGenetics has also turned its attention to the “mixed-in” DNA that Orlando describes—the genetic material that is normally discounted as contamination. The scientists’ aim here is to bring a fresh approach to the nagging question of what killed off the great megafauna of the Arctic many millennia ago.

Large-bodied mammals such as the woolly mammoth, the mastodon, and the giant sloth all vanished 10,000 to 12,000 years ago, for reasons that have not yet become clear. The most popular theory is that the Clovis peoples hunted these animals to extinction. Another possible explanation, however, is climate change. According to this line of reasoning, humans were not the main culprits in the extinction. Instead, the warming climate caused irreversible changes in vegetation that led to the extinction of the herbivores, which led in turn to the extinction of the carnivores.

Willerslev and his colleagues decided to examine how the vegetation, rather than the animal populations, had changed over the past 50,000 years. To do this, they brought their sequencing expertise to bear on the plant and animal DNA preserved in the sediment itself.

As Willerslev tells it: ”We retrieved from the permafrost the DNA of plants, animals, discarded cells, feces, and urine preserved in sediments, and we found that 50,000 years ago the landscape was dominated not by grasses but by forbs, a kind of plant that contains large amounts of protein. However, 20,000 years ago came the last glacial maximum (or Little Ice Age), with the record showing a massive drop in plant diversity. Although a warmer climate returned 10,000 years ago, the ecosystem no longer had the same elements in place that had favored the diverse and abundant growth of forbs.”

The genomic data of feces from the large-bodied mammals over 50 millennia constitute a strong case that climate change—not hunting—caused the last great extinction. Because the main food of the large mammals was protein-rich forbs, when those became less abundant, the animal populations that depended on them dwindled away.

“Based on the comments I received after the session,” says Willerslev, “I think some in the audience were surprised about the level of information that can now be retrieved from studying ancient genetics and genomics. I believe that over the next few years we will witness a rewriting of our past, both in deep time and in more recent times, due to recent developments in genetics.”

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