Mysterious archaic humans left clues in a surprising place

The genetic legacy of two extinct human species persists to this day in our own genes, say scientists.

Sankararaman et al./Current Biology 2016
This map shows the proportion of the genome inferred to be Denisovan in ancestry in diverse non-Africans. The color scale is not linear to allow saturation of the high Denisova proportions in Oceania (bright red) and better visualization of the peak of Denisova proportion in South Asia.

Tens of thousands of years ago, our species, Homo sapiens, interbred with two different archaic human species, Neanderthals and Denisovans. The evidence for these interspecies interactions is in our genes. But the details are still fuzzy.

So teams of scientists have been combing over that genetic evidence searching for clues. And recently, researchers have worked to separate the Neanderthal from Denisovan ancestry in modern human genomes to better understand their influence. 

A new study that does just that finds that some non-African modern humans today could have Denisovans to thank for 3 to 6 percent of their DNA, whereas Neanderthals contributed just about 2 percent. That new paper published Monday in the journal Current Biology focuses in on Denisovan DNA in the modern human genome.

"We weren't the only humans in the world 50,000 years ago. There were these other humans that we not only met but interbred with," study author David Reich, a geneticist at Harvard Medical School, tells The Christian Science Monitor. "And those humans contributed a lot to who we are today."

The scenario went something like this: As H. sapiens began spreading out of Africa and into Eurasia and beyond, they would have encountered archaic human species that had already made the trek out of Africa. 

Of those other humans, Neanderthals and Denisovans would have been the most closely related species to our own and therefore most compatible. The ancestors of Neanderthals and modern humans are thought to have diverged some 500,000 to 700,000 years ago and those of Denisovans diverged from those of Neanderthals some 350,000 to 420,000 years ago, Dr. Reich says. 

But as those other human species went extinct tens of thousands of years ago, scientists must rely on the fossil record and the DNA they left behind in our own bodies for insights. The genetic clues may seem to be sparse hints at a complex, dynamic human history, but they actually could tell us a lot.

This new paper "allows a disambiguation between DNA from Denisovans and DNA from Neanderthals in modern human genomes,"  Rasmus Nielsen, a researcher at the Center for Theoretical Evolutionary Genomics at the University of California-Berkeley who was not part of this study, writes in an e-mail to the Monitor. "By doing so, they are able to date the time of the Neanderthal and Denisovan introgression events independently."

And separating out when the different species interbred with our own could tell us more about the mysterious human species, Denisovans.

Denisovans are only identified by a few fossilized remains and their DNA. The new study finds that Denisovans and modern humans interbred around 50,000 years ago, which adds a data point. Previously, some scientists had suggested that Denisvoans may have gone extinct before modern humans spread into their more easterly range. But, says Reich, this DNA evidence "tells you that the Denisovans were present in southeast Asia around 50,000 years ago."

Not only were these archaic humans in the region then, their DNA is concentrated in a surprising place, too. Although present-day humans from Oceania have the most Denisovan DNA, "there's more Denisovan ancestry today in South Asians than you would expect from existing models of history," Reich says. And that means that either there was a separate interbreeding event between the two species or more breeding among the hybrids that resulted from the interspecies match.

How many times did the human species intermingle?

A study published earlier this month suggested archaic humans (both Neanderthal and Denisovan) intermingled with H. sapiens remarkably frequently. But, as Reich says, "the genetic data are actually consistent with as few as one Denisovan admixture event into modern humans and as few as one Neanderthal admixture event into modern humans."

"The number of interbreeding events is highly debated among evolutionary biologists," Dr. Nielsen says.

And it could hinge on how scientists are interpreting the data. "There are an infinite number of models that you could imagine to explain the data," explains Joshua Akey, a co-author on the paper published earlier this month and a geneticist at the University of Washington in Seattle, in a phone interview with the Monitor. 

Dr. Akey's view is that the best model is one of multiple interbreeding events, but he admits there is a lot of uncertainty.

Reich says perhaps the same data could be explained simply by the way that the hybrid populations then interbred with other H. sapiens populations outside of Africa. In this model, the genetics would have been diluted differently as different H. sapiens and hybrid populations met across the globe.

"It could be that there was a single mixture event followed by dilution, or it could be that it was multiple independent events," Reich says.

What did we get from our extinct forefathers?

"We're trying to understand the biological effect of this mixture with archaic humans and modern humans," Reich says. Was archaic human DNA beneficial to our own ancestors or detrimental?

Perhaps those genes that stuck around to end up in present-day humans were beneficial from an evolutionary standpoint. For example, some people living at high altitudes in Tibet may have inherited a gene from Denisovans to survive under those conditions.

It's possible that, thanks to this interbreeding, "certain genetic changes were introduced into the modern human populations that allowed them to live better in the new environments that they were moving into in which these archaic humans were already adapted because they had lived there for hundreds of thousands of years," says Reich.

Likewise, those genes that didn't make it through to present-day human genomes meant the archaic human versions were probably not advantageous. These regions of the genome devoid of archaic human DNA are thought to be associated in particular with language development. 

Another segment of modern human DNA that doesn't have much Neanderthal or Denisovan DNA has to do with male fertility, says Reich. 

"This tells us that when Denisovans and Neanderthals and modern humans met and mixed, they were on the edge of biological compatibility," Reich says. "They produced offspring and many people today are descended from those offspring, but it was clear that the offspring had to overcome some challenges in order to be able to establish themselves as a successful population."

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