1.8 Mn years old: Scientists discover two mysterious 'ghost ancestors' hidden in human genome - More details inside

A new study has revealed that a trail of two "ghost lineages" of extinct human populations lies hidden within our genome. But one of these ghost lineages left its DNA dispersed in all present-day people. Meanwhile, researchers reported Thursday (July 30) in the journal Science that the other, a "super-archaic" lineage, dates back nearly 2 million years.

"These extinct populations may have lived hundreds of thousands, or even more than a million, years ago, yet traces of their genetic legacy remain preserved in our genomes today," said study co-author Priya Moorjani, a human evolutionary geneticist at the University of California, Berkeley.

For more than ten years, scientists have discovered that DNA evidence indicates our species, Homo sapiens, once mated with now-extinct relatives such as Neanderthals and Denisovans. Most of the population not a part of sub-Saharan ancestry living today have nearly 1 per cent to 2.4 per cent Neanderthal ancestry, and Asians and Oceanians (people from the island nations of the Pacific Ocean) harbour approximately 0.1 per cent to 6 per cent Denisovan ancestry.

However, scientists have speculated that contemporary humans may have crossbred with other now-extinct human groups that have not been detected yet. But the lack of ancient DNA samples makes it difficult to find out what these unidentified groups, often called ghost lineages, might have provided to our species.

"Ancient DNA has transformed our understanding of human evolution, but it can only tell us about populations for which DNA has been preserved," Moorjani said. "DNA survives only under very specific conditions — typically in cold, dry environments, which means that much of our evolutionary history, particularly in Africa, other tropical regions, and at very deep timescales, remains inaccessible."

Long-extinct ancestors

In the new finding, Moorjani and her team members explained that everyone's genome has a record of their ancestry. They also investigated possibilities to uncover signs of "long-extinct ancestors preserved within the genomes of present-day people." They also developed a new technique to scan and compare over 500 complete genomes of present-day humans from around the world.

Drawing on this data, researchers reconstructed detailed genealogies for individual segments of each person's genome, building family trees that traced ancestral lineages back through every point of divergence and merging. Their focus centred on ancestors whose genetic makeup differed significantly from modern humans, an indicator that these lineages had branched off from the modern human line long ago.

"Most regions of our genome share a common ancestor relatively recently in our evolutionary history," Moorjani said. "Occasionally, however, we find stretches of DNA whose common ancestor lies much farther back in time, indicating they originated from a long-separated human lineage," she added.

What sets this method apart from earlier techniques is that it doesn't rely on fossil DNA to detect ancient genetic sequences within modern-human genomes. According to Moorjani, scientists no longer need to depend on rare, well-preserved fossils to learn about extinct human populations. Instead, the genomes of people alive today carry remnants of these ancient ancestors, and genealogical analysis can help uncover that concealed history.

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To validate the approach, researchers tested it experimentally, and it successfully identified Neanderthal and Denisovan ancestry within modern-human genomes. Beyond confirming known lineages, the method also revealed previously undocumented cases of interbreeding with extinct groups. Notably, the researchers found DNA from one "ghost lineage" present across all modern humans — evidence suggesting this group interbred with modern humans in Africa more than 50,000 years ago, predating the most recent wave of Homo sapiens migration out of Africa and into the rest of the world.

"Previous publications suggested that there might be ghost ancestry, ancestry from unknown archaic lineages in modern humans, but they hadn't concluded whether this unknown ancestry is present only in Africans or not, and when this introgression event happened," study co-author Yulin Zhang, a computational biologist at UC Berkeley, said in a statement. "We were actually able to find and map genomic locations in modern humans that are from this ghost lineage and show that this ghost ancestry is in all modern humans, not only in Africans."

This new DNA contains around 0.5 per cent to 1 per cent of the genomes of modern humans, comparable to the amount of Neanderthal DNA. It has been estimated that about 800,000 years ago this ghost lineage diverged from the ancestors of modern humans, about the same time Neanderthals and Denisovans did. The possible ghost lineage was found to be Homo heidelbergensis, which lived from about 700,000 to 200,000 years ago in Africa and Europe.

"I agree with their speculation that this ghost could have been the species Homo heidelbergensis, which was present in Africa as recently as 300,000 years ago," Chris Stringer, a paleoanthropologist at the Natural History Museum in London who was not involved in the study, said.

‘Super-archaic’ human lineage

Researchers also discovered that people from Oceania carry traces of a "super-archaic" human lineage that split from modern humans' ancestors roughly 1.8 million years ago, well before the common ancestor of modern humans, Neanderthals, and Denisovans emerged. This ancient DNA accounted for approximately 0.002% of the Oceanian genomes studied and was found embedded within regions of Denisovan ancestry, indicating it likely entered modern humans through interbreeding with Denisovans.

Fernando Villanea, a population geneticist at the University of Colorado Boulder uninvolved in the study, suggested the DNA's age points to Homo erectus as its likely original source, passed first into Denisovans and then into modern humans. This theory gains support from Yunxian skull fossils in China, which share certain features with Denisovan remains, though limited H. erectus genetic material has been analysed so far. "We see hybridisation being a common trait in the evolution of many other species, and these findings help us reframe our scientific thinking away from a mentality of human exceptionalism," Villanea said.

According to Villanea, these findings underscore that modern humans descend from multiple ancient species, making hybridisation the norm rather than the exception. These newly identified DNA segments cluster most densely in genome regions tied to immune function and metabolism, a pattern Moorjani says reflects how adapting to new pathogens and food sources has consistently driven human evolutionary pressure.