Tag Archives: Denisovans

An unknown ancestor mated with ancient humans. Its DNA is found in living people to this day

The unidentified ancient human relative may have been Homo erectus. Credit: flowcomm, Flickr.

To say the sex lives of our ancestors was complicated would be an understatement. After they migrated out of Africa into Eurasia, humans interbred with Neanderthals, Denisovans, and at least one other group of archaic people belonging to our genus. Evidence of this latter interbreeding lives on in our genes, according to a new study by researchers in the United States. The identity of this group is still shrouded in mystery.

When Homo sapiens migrated in large numbers out of Africa through the Middle East into Europe and Asia, they came in contact with the Neanderthals, who had been masters of their domains for thousands of years prior to the arrival of anatomically modern humans. The two species interbred, the effects of which are still seen in the genomes of people alive today who are not of Sub-Saharan heritage. About 2% of the DNA in the genomes of modern-day people with Eurasian ancestry is Neanderthal in origin.

But the gene flow goes both ways, of course. In a new study, Melissa Hubisz and Amy Williams of Cornell University and Adam Siepel of Cold Spring Harbor Laboratory performed a complex genomic analysis of the DNA of two Neanderthals, a Denisovan and two living African humans. The latter have no Neanderthal DNA in their genomes, as opposed to Caucasians, which helped the researchers differentiate patterns of ancient interbreeding.

The team of researchers employed a computational method that enabled them to identify recombination events, in which segments of the chromosomes from one individual become incorporated into the chromosomes of another. This clever method can map out the tree of relationships among individuals at every position along the genome.

In more practical terms, this approach enabled the researchers to uncover previous instances of mating nested in the genomes of living or extant species. For instance, if Neanderthals mated with some other human species, and later these descendants mated with modern humans, this method can uncover that initial instance of ancient interbreeding.

As it turned out, the study revealed some amazing instances of such nested insections of DNA. For instance, 3% of the Neanderthal genomes came from ancient humans, estimated to have occurred 200,000 to 300,000 years ago. This is additional evidence supporting the fact that humans left Africa in multiple waves before making a huge leap out of the continent primarily 50-60,000 years ago. These early migratory waves of humans were likely assimilated by Neanderthals or were wiped out one way or the other.

But the most striking finding was that 1% of the Denisovan DNA came from a yet unidentified species of ancient humans. The interbreeding occurred roughly one million years ago, a timeline that suggests the lover may have been Homo erectus. Sadly, no Homo erectus DNA has ever been found, so this hypothesis remains speculation at this point. It may very well have been some different, yet to be identified species altogether.

In any event, both interbreeding events have been passed down to living modern humans. About 15% of the interbreeding sequences found in the Denisovans are present in living people today, the researchers reported in the journal PLoS Genetics.

Given the sheer number of gene exchanges between ancient humans and their extinct relatives, it’s very likely that genetic exchange took place whenever two distinct groups of humans overlapped in time and space. The same algorithm employed by the study could be used to study gene flow in other species where interbreeding occurred in the distant past, such as between wolves and dogs.

“What I think is exciting about this work is that it demonstrates what you can learn about deep human history by jointly reconstructing the full evolutionary history of a collection of sequences from both modern humans and archaic hominins,” Siepel said in a statement. “This new algorithm that Melissa has developed, ARGweaver-D, is able to reach back further in time than any other computational method I’ve seen. It seems to be especially powerful for detecting ancient introgression.”

Two waves of Denisovan ancestry have shaped present-day humans. Credit: Browning et al./Cell.

Modern humans and Denisovans interbred at least twice in history

In 2010, scientists announced the discovery of an extinct species of Ice Age humans called Denisovans, known only from bits of DNA taken from a sliver of bone in the Denisova Cave in Siberia. Recent research suggests that our Homo sapiens ancestors were intimately in contact with Denisovans. According to a new paper published by researchers at the University of Washington in Seattle, there were at least two distinct episodes of Denisovan genetic intermixing between the two species.

Two waves of Denisovan ancestry have shaped present-day humans. Credit: Browning et al./Cell.

Two waves of Denisovan ancestry have shaped present-day humans. Credit: Browning et al./Cell.

It was first shown that humans interbred with Neanderthals 50,000 years ago100,000 years ago. Later, a 2016 study found that Oceanic individuals hold substantial amounts of not only Neanderthal, but also Denisovan DNA. For instance, the inhabitants of Melanesia, a subregion of Oceania, have between 4% and 6% Denisovan DNA. This fact itself is intriguing because we’re talking about an isolated population on a relatively inaccessible island, thousands of miles away from the Altai Mountains in Siberia.

Sharon Browning, a research professor of biostatistics at the University of Washington School of Public Health, along with colleagues studied 5,600 whole-genome sequences analyzed from individuals from Europe, Asia, America, and Oceania, then compared them to the Denisovan genome.

The analysis revealed that the genomes of two groups of modern humans with Denisovan ancestry are uniquely different, suggesting there were two separate episodes of Denisovan admixture. Specifically, the analysis showed that modern Papuan individuals contain approximately 5% Denisovan ancestry, while East Asians carry about 0.2% Denisovan DNA. It’s not yet clear what effects this Denisovan ancestry might pose to both populations, Browning told me.

“The major challenge was in developing a statistical method for detecting segments of archaic introgression in modern human genomes that would be sensitive (able to find such segments), specific (not yielding a lot of false positive results) and computationally efficient for analysis of thousands of modern human genomes. We spent a lot of time working on our method, testing it on simulated and real data, to address these challenges,” Browning told ZME Science.

Scientists were already aware that Papuans had significant amounts of Denisovan ancestry and that East Asians also bore signs of this admixture, but to a lesser degree. However, the assumption was that the Asian Denisovan ancestry was achieved from an admixture with an Oceanic population. The new work shows that this was not the case. Instead, East Asian populations must have interbred with Denisovans in a separate event, judging from the presence of a second set of Denisovan ancestry that could not be found in South Asians and Papuans. “This result was unexpected,” Browning said.

“When we compared pieces of DNA from the Papuans against the Denisovan genome, many sequences were similar enough to declare a match, but some of the DNA sequences in the East Asians, notably Han Chinese, Chinese Dai, and Japanese, were a much closer match with the Denisovan,” she said in a statement.

Browning thinks it’s possible that the ancestors of today’s Oceanians admixed with a southern group of Denisovans while the ancestors of East Asians admixed with a northern group. Perhaps upcoming studies of other Asian populations, as well as others throughout the world like Native Americans and Africans, might shed valuable new clues.

“We plan to apply our methodology to further worldwide populations, and see if we can find traces of introgression from archaic humans other than Neanderthals and Denisovans,” Browning told me, adding that “Our work helps to further reveal the complexity of human demographic history.”

Scientific reference: Cell, Browning, SR, et al: “Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture.

Modern humans lost some of their smoke-resistance genes and we don’t know why

Researchers peeking into our genetic code found that modern humans are less adept at handling smoke-borne toxins than the Neanderthals. We’re even worse at it than great apes, they add.

Smoke churning out of an US-issue green M18 grenade.
Image credits Lance Cpl. Jody Lee Smith / Released by the U.S. Marine Corps.

Modern human society can arguably trace its roots back to our mastery of fire. It not only let us prepare high-quality, energy-rich food, but provided protection against the cold, predators, and it underpinned early technology and industry.

But it’s not all rosy. Exposure to the toxic compounds released in smoke (such as like polycyclic aromatic hydrocarbons) can take a heavy toll on our bodies, increasing the risk for pneumonia as well as a host of other conditions and negatively impacting pregnancy development in women and sperm quality in males.

This double edge has sent researchers from the Leiden University and Wageningen University on a quest to find genetic markers for the use of fire in ancient humans.

It’s all about genes

Archeologists have quite a hard task in pinning the first use of fire, which has led to some pretty heated arguments in the past. Some argue that humans have been using it for as long as two million years, but most evidence found in Europe and the Near East suggest that we’ve learned to use fire somewhere around 350,000 years ago.

To bring new insight to this debate, the team looked at the biological adaptations of prehistoric and recent humans to toxic compounds in smoke. Since using fire involved heavy exposure to these compounds in breathed smoke and in cooked food, the team expected it to have an impact on the selection of human genes — specifically, that it would promote individuals who had a built-in resistance against them. They analyzed gene variants from Neanderthal, Denisovan, and prehistoric modern humans.

They tested single nucleotide variants in 19 genes that have been linked to increased risk of fertility and reproduction issues in tobacco smoke studies. These were compared to variants found in Neanderthal and Denisovan genetic material, and with DNA harvested from chimpanzees and gorillas as a control group — we’re closely related but they don’t use fire.

The results showed that Neanderthals and Denisonvans both had genetic variants which were better at handling smoke than we do. Surprisingly, even the apes had them — suggesting they were very old gene variants, inherited from a common ancestor.

Up in smoke

The less efficient variants were only observed from the earliest hunter-gatherers we have genetic information on, so from about 40,000 years ago up to the present. The team suspects the apes’ genes are involved in defending them from toxins in the plants they eat. Our own defenses apparently borrow heavily from those adaptations, being developed deep in our primate ancestry.

The findings show that our ancestors were well equipped to deal with smoke long before they made any fires for themselves. Somewhere along the line though, we traded these genes for their less efficient variants. Previous studies have discovered, however, that modern humans have developed a whole new set of mutations to help them cope with toxic smoke compounds, so maybe the genetic variants seen in Neanderthals and Denisovans didn’t have a big enough effect to apply selective pressure.

All of this will have to be answered by future research.

The full paper “Fire Usage and Ancient Hominin Detoxification Genes: Protective Ancestral Variants Dominate While Additional Derived Risk Variants Appear in Modern Humans” has been published in the journal PLOS ONE.