Super Archaic Action

Ancient humans had extremely complicated sex lives, evidence shows

The remains of a "super archaic" ancestor live on in modern humans.

Even today's digitally expanded world of modern dating has nothing on the ancient world.

Hundreds of thousands of years ago, there were roughly four species of ancient hominids getting it on with their contemporaries. Thanks to new genetic analysis algorithms, scientists have identified the vestiges of this free-wheeling ancient hookup scene, which lives on inside our DNA.

This includes material from a mysterious "super archaic" ancestor.

Analysis of two Neanderthal genomes, one Denisovan genome, and four modern human genomes revealed new evidence of gene flow between these species, further confirming previous work that suggests that they mated with one another.

The team found that three percent of the Neanderthal genome came from interbreeding with ancient humans. They estimate this intermixing happened between 200,000 and 300,000 years ago — far earlier than previous estimates indicated.

They also found that one percent of the Denisovan genome contained genetic material that came from an unexpected source – an "archaic human ancestor" that was neither human, nor Neanderthal, nor Denisovan.

The authors suggest that 15 percent of genetic regions that came from that archaic ancestor have been passed on to humans today, and there are a few theories as to who it came from and how it got baked into our genetic code.

The paper was published Thursday in PLOS Genetics.

New genetic analysis suggests that humans, Neanderthals, Denisovans and a super archaic ancestor all intermixed with one another. Getty Images

Who is the "archaic" human ancestor? – The team proposes that this archaic human ancestor could be Homo Erectus.

Homo Erectus was likely one of the first human ancestors to leave Africa, spreading to areas like the modern-day Republic of Georgia, China, and Indonesia. They looked much like we do today, but with elongated legs and shorter arms. They were also the most enduring of our ancestors and lasted until as recently as 117,000 years ago, as one fossil found in Java suggests.

This the guess partially thanks to a proposal put forth in a 2013 paper in Nature, which reported the complete genome of a Neanderthal from the Altai mountains in Mongolia. In that paper, the authors also report that there was evidence of "archaic" DNA in that Neanderthal genome, which they suggest got there through mating with Denisovans.

The Nature genetic analysis also suggests that this ancient ancestor split from Denisovans between 0.7 million and 1.3 million years ago. That date of the split, that study team writes, "is also compatible with the possibility that this unknown hominin was what is known from the fossil record as Homo Erectus."

The genetic analysis presented in this recent paper suggests that this super ancient ancestor split off from the lineage that would eventually become modern-day humans around 1 million years ago. That's within the window proposed by the 2013 paper suggesting that this super archaic DNA comes from Homo Erectus.

However, since we still don't have a genome sequenced for that particular ancient hominid, these results are still tenuous.

How did that "super archaic" DNA get there? – Previous studies indicate that there was certainly intermixing between humans, Neanderthals, and Denisovans.

The authors of this new study note that between one and three percent of the human genome in Europeans and East Asians comes from Neanderthals. Other studies posit that some present-day humans (notably in Oceania) can trace as much as five percent of their DNA back to Denisovans.

Intermixing events between Denisovans, Neanderthals, a "super archaic" hominin and Humans. Dotted lines represent new intermixing events proposed in the paper.

What about the DNA of that un-sequenced "super archaic" ancestor? Finding out how that DNA got into humans required following relatively thin genetic trails, and the team notes that their evidence isn't as powerful as it could be.

However, they suggest that a number of intermixing events could have helped sustain the presence of this super archaic DNA.

The most obvious mode of entry would have been through mating with Denisovans, who as the 2013 paper indicates, likely intermixed with "super archaic" humans. The team found that 15 percent of the genetic regions that came from that super archaic ancestor overlap with those that made their way into modern-day Asian and Oceanic individuals via Denisovans.

It's been proposed that Denisovans and ancient humans mated with one another until as recently as 15,000 years ago, so that's one direct way that we may have ended up with super archaic DNA.

It's also possible that the super ancient ancestor mated directly with humans – though the evidence for that was so scant that the authors suggest it may have been a false signal. Other studies, however, have suggested that humans did intermix with more archaic ancestors.

There was better evidence for a complicated triple-species love triangle between the archaic ancestor, Neanderthals, and humans.

The team found that 35 percent of the regions that overlapped between the super archaic ancestor and Neanderthals were present in the genome of one modern-day human from Africa. That suggests that the material was passed from the super archaic ancestor to Neanderthals, and then onward to humans.

The fact that there's currently no genome sequenced for the ancient hominin makes pinning down how intermingling happened quite tricky. But at this point the authors know one thing for sure: "it may be reasonable to assume that genetic exchange was likely whenever two groups overlapped in time and space," they write.

That is, if any two species found themselves in the same place at the same time, they were probably getting it on.

Abstract: The sequencing of Neanderthal and Denisovan genomes has yielded many new insights about interbreeding events between extinct hominins and the ancestors of modern humans. While much attention has been paid to the relatively recent gene flow from Neanderthals and Denisovans into modern humans, other instances of introgression leave more subtle genomic evidence and have received less attention. Here, we present a major extension of the ARGweaver algorithm, called ARGweaver-D, which can infer local genetic relationships under a user-defined demographic model that includes population splits and migration events. This Bayesian algorithm probabilistically samples ancestral recombination graphs (ARGs) that specify not only tree topologies and branch lengths along the genome, but also indicate migrant lineages. The sampled ARGs can therefore be parsed to produce probabilities of introgression along the genome. We show that this method is well powered to detect the archaic migration into modern humans, even with only a few samples. We then show that the method can also detect introgressed regions stemming from older migration events, or from unsampled populations. We apply it to human, Neanderthal, and Denisovan genomes, looking for signatures of older proposed migration events, including ancient humans into Neanderthal, and unknown archaic hominins into Denisovans. We identify 3% of the Neanderthal genome that is putatively introgressed from ancient humans, and estimate that the gene flow occurred between 200-300kya. We find no convincing evidence that negative selection acted against these regions. Finally, we predict that 1% of the Denisovan genome was introgressed from an unsequenced, but highly diverged, archaic hominin ancestor. About 15% of these “super-archaic” regions—comprising at least about 4Mb— were, in turn, introgressed into modern humans and continue to exist in the genomes of people alive today.

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