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Mysterious Denisovans interbred with modern humans more than once

Neanderthals, Denisovans and our ancestors were mixing and mingling a long time ago -- and some of our genetics can be traced back to these archaic humans.

Neanderthals, Denisovans and our ancestors were mixing and mingling a long time ago — and some of our genetics can be traced back to these archaic humans.

In Asians, as much as 3% of an individual’s DNA may be Neanderthal. For Europeans, it’s as much as 2%. A new study has found that our ancestors interbred with two distinct Denisovan populations, increasing the probability of the presence in modern populations of DNA inherited from this ancient and mysterious people.

The study, using a new genome-analysis method to compare whole genomes of humans with Denisovans, was published in the journal Cell on Thursday.

“It is amazing that we can look into human history via current-day human genetic data, and determine some of the events that happened in the past,” study author Sharon Browning wrote in an email. Browning is a research professor with the University of Washington’s Department of Biostatistics.

“In particular, in this study we found two distinct episodes of Denisovan admixture, which adds to what was previously known about the contribution of Neanderthals and Denisovans to our genomes today.”

Denisovans pose questions

Denisovans pose particular questions for scientists because researchers have only a few bones that even point to their existence: a finger bone, toe bone and a couple of teeth. Fossilized DNA sequenced from those bones, recovered in Siberia, has allowed us to learn more about them. But we still don’t know what these extinct hominins looked like.

Neanderthal and Denisovan DNA was sequenced completely for the first time in 2010, which led to the initial discovery that they were interbreeding with our ancestors. Studies found that the population of Oceania and Papua New Guinea received the most DNA from Denisovans, around 5%.

Fifty thousand years ago, as modern humans moved out of Africa, they encountered Neanderthals and Denisovans, and the “admixing” happened. But pinning down exactly where it happened has proved difficult.

It was especially puzzling given that the fossils were found in Siberia, but Denisovans are most strongly connected to Oceania.

Denisovan ancestry was also present in Asia, although researchers believed that this occurred through migration from Oceania.

Comparing the Denisovan genome to that of 5,600 Europeans, Asians, Americans and Oceanians painted a different picture.

The data showed that Denisovans were even more closely related to modern East Asians, specifically Han Chinese, Chinese Dai and Japanese, than those from Papua New Guinea. And this second set of Denisovan ancestry was different from Oceanians and Papuans.

“It makes it clear that there were distinct populations of Denisovans, rather than a single population,” Browning said. “The fact that these populations had diverged somewhat from each other suggests that the two populations were not mixing very often with each other, perhaps due to geographical separation.”

A possible explanation is that our Oceanian ancestors encountered a southern group of Denisovans, while East Asians met a northern group.

“(This) led people to suspect that Denisovans did not just live in Siberia, but also lived elsewhere in Asia, somewhere south along the likely routes that the ancestors of Oceanians may have taken to get to Oceania,” Browning said. “This study makes this hypothesis look very likely.”

This could also mean that there were more than two distinct episodes of Denisovans mixing with modern humans, which Browning believes future analysis could reveal.

“A major novel finding is that some populations (East Asians) have evidence of multiple introgression related to Denisovans while a few others (South Asians, Papuans) have evidence of a single Denisovan introgression,” Sriram Sankararaman said in an email. “The Denisovan ancestry in South Asians is quite diverged from the sequence Denisovan while the additional component in East Asians is quite close. This suggests a complex interaction pattern of the Denisovans and modern human populations in mainland Asia.”

Sankararaman, who was not involved in the study, has worked on Denisovan research and is an assistant professor at the University of California, Los Angeles, in the department of computer science and the department of human genetics.

Going forward, Browning and her colleagues plan to study other populations to look for signatures of admixture with archaic humans besides Neanderthals and Denisovans.

“I’d love to delve further into Neanderthal ancestry, and understand why East Asians have a higher rate of Neanderthal ancestry — around 3% — compared to Europeans — around 2%,” Browning said.

“It has been hypothesized that the extra Neanderthal ancestry in East Asians is due to an additional admixture event, but we didn’t find a clear sign of that in our study. That doesn’t rule out this possibility — we might need to dig a little deeper to find it.”