Identities Of Mysterious "Ghost Lineages" – Groups Of Ancient Hominins That Bred With Our Ancestors – Narrowed Down By New Technique

We've known for some time that modern human DNA contains contributions from other, long-extinct human lineages, including Neanderthals and their cousins the Denisovans – a group of hominins we think was closely related to Neanderthals and lived in East Asia up to perhaps 30,000 years ago. 

We're talking about populations separated from us by hundreds of thousands of years of evolution

Yulin Zhang

But there are also hints of other, more mysterious contributors with whom we must have had secret liaisons but whose identities are harder to pin down, hence the name "ghost lineages."

According to the new research, one of these unknown ancestors appears to have been a "super-archaic" hominin lineage that diverged from other humans around 1.8 million years ago and later interbred with Denisovans, 

The researchers also found another, younger lineage that interbred directly with modern humans in Africa prior to the most recent migration of Homo sapiens out of Africa into Eurasia more than 50,000 years ago.

“On relatedness, both were deeply divergent," Yulin Zhang, joint first author of the study and a PhD student at UC Berkeley, told IFLScience. 

"The [younger] ghost lineage separated from modern human ancestors around the time of the Neanderthal split, tracing back to a common ancestor roughly 0.8 million years ago; the super-archaic lineage is older, diverging close to 1.8 million years ago.” 

“So we're talking about populations separated from us by hundreds of thousands to well over a million years of independent evolution,” she added.

Despite never interbreeding with Homo sapiens directly, the extremely old DNA of the "super-archaic" group seems to have made its way into the genomes of modern Homo sapiens through our interbreeding with Denisovans.

That story lines up with research published earlier this year, where proteins recovered from Homo erectus teeth in China were found to carry distinguishing mutations also present in Denisovans and modern humans. 

Homo erectus is thought to have left Africa around 1.8 million years ago, so it's a probable candidate for the identity of this super-archaic ghost lineage – though without DNA evidence, we can't know for sure.

Ghost lineages in people beyond Africa

When it comes to the yonger ghost lineage, its age suggests its DNA entered the modern human genome before Homo sapiens dispersed out of Africa, meaning it can be found in people across the world, both Africans and non-Africans.

While previous work had turned up hints of ghost ancestry from ancient African hominins in modern humans, most of it suggested the interbreeding had occurred after the last migration of Homo sapiens out of Africa, meaning their legacy wouldn't be present in all people, only those with African ancestry. 

The same hallmarks are seen in Neanderthal and Denisovan segments, and are inconsistent with random noise

Yulin Zhang

Although our direct ancestors would have directly interbred with this ghost lineage at some point, according to the work, the exact nature of our relationship – exactly when, where, and for how long it continued – is unclear. 

“For the [younger] ghost lineage, we can say the mixing happened before the out-of-Africa migration, which is why its imprint is shared across all populations – but we didn't pin down the exact timing or test whether it was a single pulse or continuous gene flow,” Zhang explained.

“What's clear is the genetic contribution is about 0.5 to 1 percent per person,” she continued. This is similar to the contribution made by Neanderthals, which ranges between about 1 percent and 4 percent in non-African people.

Fingerprints in the genetic code

The findings come from a computational method called TRACE (TRacking Archaic Contributions via ARG Estimation), developed by a team of researchers at UC Berkeley led by population geneticist Priya Moorjani.

As well as uncovering these two episodes of interbreeding with archaic human groups, the technique picked up the known interbreeding events with Neanderthals and Denisovans, with whom modern humans had a well-documented "love affair."

This, the researchers say, helps confirm that these unusual genetic segments aren't just random noise, but real evidence of encounters with unknown hominins.

“Those segments also carry the fingerprints of a genuinely ancient lineage: they're long, unbroken stretches showing markedly higher divergence from present-day people than the rest of the genome, plus elevated heterozygosity – the same hallmarks seen in confirmed Neanderthal and Denisovan segments, and inconsistent with random noise,” Zhang explained.

The "super-archaic" hominin lineage linked to Denisovans was found by analyzing only genomes from populations in Oceania, where people are known to have high concentrations of Denisovan DNA, sometimes up to 4 percent of their genome.

That's no coincidence. Since this DNA is thought to have journeyed into modern humans via ancient interbreeding with Denisovans, it shows up most clearly in populations that carry the most Denisovan ancestry today.

The team believes future research may be able to pin down the identity of these ancient ancestors, especially as the world's genome databases become more diverse and begin incorporating a broader sample of humanity. 

The discovery of additional Denisovan genomes would also help, as would more protein sequences from Homo erectus fossils, they added. Of course, fossils showing unequivocal evidence of interbreeding would be the dream, but that would be a long shot. 

The new study is published in the journal Science.