In recent years, advances in ancient DNA sequencing have redefined our understanding of human evolution, revealing that our species did not emerge in isolation but repeatedly interbred with close evolutionary relatives like Neanderthals and Denisovans.
Yet one of the field’s greatest mysteries has remained unanswered: What if some of our ancestors also encountered extinct human groups whose DNA has never been recovered from fossils? Now, a recent study published in Science suggests researchers may finally have found a way to detect those long-lost relatives.
Instead of relying on ancient bones or preserved genomes, researchers developed a powerful computational approach capable of identifying genetic traces of previously unknown archaic humans using only the genomes of living people.
Applying the technique to modern populations around the world, the researchers uncovered evidence that an unidentified “ghost” hominin contributed DNA to the ancestors of all living humans before the great migration out of Africa.
Researchers also found new evidence providing evidence for the existence of an even older “super-archaic” human lineage whose genetic legacy may survive today through Denisovan ancestry in Oceania.
“Admixture between modern humans and extinct hominins has shaped the genomes of present-day individuals, but reconstructing this history has been constrained by the scarcity of archaic samples and unadmixed outgroup populations,” researchers write. “We introduce TRACE, a reference- and outgroup-free approach that uses features of ancestral recombination graphs to identify archaic ancestry.”
Past research has sequenced only a handful of high-quality archaic human genomes, all from Eurasia. While those genomes have revealed that most people outside Africa carry roughly 1 to 2 percent Neanderthal DNA and that many Asian and Oceanian populations also inherited Denisovan ancestry, scientists have long suspected those known groups represented only part of humanity’s evolutionary history.
Previous genetic studies had hinted that modern humans, especially African populations, contained fragments of DNA from unidentified archaic relatives. However, because no fossil genomes exist for those populations, proving their existence has been extraordinarily difficult.
The new method, called TRACE, short for “TRacking Archaic Contributions via ARG Estimation,” takes a fundamentally different approach. Rather than comparing modern DNA against known Neanderthal or Denisovan genomes, it reconstructs ancestral recombination graphs. These enormous evolutionary family trees trace how pieces of DNA have been inherited over hundreds of thousands of years.
These ancestral graphs preserve signatures left behind when deeply divergent human lineages interbred. Such events create unusually long branches and distinctive genetic patterns that can persist in descendants for hundreds of thousands of years. By searching for those signatures, TRACE can identify archaic ancestry even when no reference genome exists.
To test the system, the researchers first ran extensive computer simulations modeling ancient human populations and known episodes of Neanderthal interbreeding. The method consistently revealed high accuracy while producing very low false-positive rates.
The team then applied TRACE to genomes from the 1000 Genomes Project, encompassing hundreds of individuals representing populations across Africa, Europe, Asia, and elsewhere.
The program successfully recovered well-established Neanderthal ancestry in Europeans and Asians, along with Denisovan ancestry concentrated primarily in Asian populations. More intriguing, however, was the discovery of an additional category of DNA that matched neither Neanderthals nor Denisovans.
TRACE identified between roughly 0.5 and 1.1 percent “ghost” ancestry across all modern populations examined. The genetic evidence suggests these segments originated from an unknown archaic human lineage that diverged from our ancestors roughly 830,000 years ago, before later contributing DNA to the ancestors of modern humans.
Perhaps most surprising was where that ancestry appeared.
Rather than being confined to African populations, as several earlier hypotheses proposed, the researchers found remarkably similar ghost ancestry in both Africans and non-Africans.
Most of the segments detected outside Africa were shared with African populations, suggesting the interbreeding event occurred before modern humans started dispersing across the globe roughly 50,000 to 70,000 years ago.
The findings point toward a previously unrecognized chapter of human evolution in which an unidentified human population mixed with the common ancestors of everyone alive today.
The researchers also explored where these ancient genetic fragments survive in the modern genome.
They found ghost ancestry spread across more than 70 percent of the accessible human genome, although it was far from evenly distributed. Some regions contained unusually high concentrations of ghost DNA, including genes involved in immune function and metabolism.
Even more unexpectedly, ghost ancestry persisted inside genomic regions previously believed to be largely devoid of archaic DNA.
These regions, known as “Neanderthal and Denisovan ancestry deserts,” have often been interpreted as places where natural selection eliminated archaic genetic variants because uniquely modern human versions proved advantageous.
The presence of ghost ancestry inside many of those same regions suggests the story may be more complicated. Rather than rejecting all archaic DNA equally, natural selection may have acted differently depending on which ancient human lineage contributed the genes.
The study also ventured even farther back in evolutionary time.
Focusing on genomes from Papua New Guinea, Vanuatu, and the Santa Cruz Islands, the researchers searched for evidence of “super-archaic” ancestry—genetic contributions from a lineage that diverged long before Neanderthals, Denisovans, and modern humans separated.
Previous studies had suggested Denisovans themselves may have inherited DNA from such an ancient population. TRACE now provides additional support for that hypothesis.
The team identified deeply divergent genetic segments embedded explicitly within Denisovan-derived DNA in Oceanian populations. Based on their analyses, those ancient lineages may have split from the ancestors of modern humans approximately 1.77 million years ago.
While the researchers stress this represents a conservative estimate of surviving super-archaic ancestry, the findings strengthen the idea that modern humans indirectly inherited DNA from a much older human lineage through Denisovan interbreeding.
The identity of both the ghost lineage and the super-archaic population remains unknown.
The ghost population may represent Middle Pleistocene human groups or African populations of Homo heidelbergensis that encountered the ancestors of modern humans before the Out-of-Africa migration. For the older super-archaic lineage, the researchers note that Homo erectus remains one plausible candidate given its estimated divergence time and broad geographic distribution.
Although the new method cannot yet identify specific fossil species, it provides researchers with an entirely new tool for investigating chapters of human evolution that may never yield recoverable ancient DNA.
Because DNA older than roughly one million years is extraordinarily unlikely to survive outside permanently frozen environments, computational approaches like TRACE are becoming increasingly important for reconstructing humanity’s deepest evolutionary history.
“We find evidence for at least one ghost introgression predating the OOA expansion that contributed ancestry to all present-day populations,” researchers write. “These results point to multiple layers of introgression—both direct and mediated through other archaic groups—shaping modern human genomes.”
The study, “Recovering signatures of archaic hominin introgression using ancestral recombination graphs,” was published in the journal Science.
Tim McMillan is a retired law enforcement executive, investigative reporter and co-founder of The Debrief. His writing typically focuses on defense, national security, the Intelligence Community and topics related to psychology. You can follow Tim on Twitter: @LtTimMcMillan. Tim can be reached by email: tim@thedebrief.org or through encrypted email: LtTimMcMillan@protonmail.com
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