Clues emerging from DNA could reveal the mystery of human ancestors missing from the fossil record but present in the genes of people living today. Years ago, scientists found evidence that our species, Homo sapiens, had interbred with now-extinct human relatives, including Neanderthals and Denisovans. But some lineages have been difficult to identify because, unlike Neanderthals and Denisovans, whose DNA has been recovered from prehistoric remains, they are essentially genetic “ghosts,” with no DNA evidence of their existence that can be compared to the clues detected in our genomes. While previous studies have uncovered remains of ghost lineages, they were unable to determine when interbreeding occurred or to what extent these lineages diverged from the ancestors of modern humans. Now, researchers have developed a new method for analyzing modern human genomes and have discovered evidence of two previously unknown ancestral lineages working backwards from the DNA of living people to reconstruct missing parts of the human family tree. One of the lineages appears to have interbred directly with Homo sapiens in Africa more than 50,000 years ago, while the other was an even older group that passed some of its DNA to humans indirectly through the Denisovans. The researchers reported their findings July 30 in the journal Science. The scientists’ method reconstructs genealogies, or maps that show where different pieces of DNA came from and how they were passed down, revealing branches of our evolutionary past. “The most fundamental question most of us have is: ‘Why are we here? Where do we come from?’ And these genealogies really allow us to look back in a way that we haven’t been able to before,” said Priya Moorjani, a co-author of the study and an associate professor in the department of molecular and cellular biology at the University of California, Berkeley. Moorjani added that the discovery allows us to continue investigating why some groups of hominids survived while others disappeared. Understanding the genetic contributions of our diverse ancestors can help answer that question while also revealing how humans adapted to their environments and why certain diseases affect us today, he said. Modern humans first left Africa about 50,000 years ago. This migration of Homo sapiens is what led to interbreeding with Neanderthals and Denisovans in Eurasia. However, the newly detected lineages add more to the story. One of the unknown ghost ancestors described in the new study likely interbred with humans in Africa before the migration event. Researchers estimate that the DNA inherited from this lineage makes up about 0.5% to 1% of the genomes of people living today, about the same percentage as the Neanderthal DNA currently found in many modern humans. The second lineage is much older. Researchers refer to it as a “superarchaic” ancestor because it dates back to a branch of the human family tree that split about 1.8 million years ago. This hominid appears to have interbred with Denisovans in Eurasia more than 200,000 years ago, and some of its DNA eventually reached modern humans through our interbreeding with Denisovans. To uncover these ghost ancestors, researchers developed a new computational method, called TRACE, that can search contemporary human genomes for clues left by long-lost populations. “Our genomes are mosaics of small DNA fragments from all our ancestors, so in different parts of our genome we have a different family tree,” Moorjani explained. Some branches of those family trees are relatively recent, while others go back much further into the past. DNA inherited from ancient relatives like Neanderthals, for example, is found in these deeper branches. TRACE searches the entire genome for distant lineages that may indicate ancestry from previously unknown populations. The researchers tested TRACE on more than 500 modern human genomes from current populations in Africa, Europe and Asia. They found traces of the most recent ghost ancestry in every population they studied, pointing to a lineage that must have contributed DNA to the ancestors of modern humans before our species’ great migration out of Africa. “If we think about going even beyond humans, gene flow and mixing between groups is quite widespread across populations, so it’s not very surprising that we harbor DNA from different groups of hominids,” Moorjani said. “The thing is that until recently it was not possible to extract this DNA from people who lived in the past.” While researchers can’t yet say which hominid populations these lineages belonged to, they have narrowed down possible candidates based on when the lineages diverged in the hominid family tree. The estimated divergence time of one lineage is consistent with Middle Pleistocene Homo populations in Africa, suggesting it could be Homo heidelbergensis, the researchers wrote in the study. Homo heidelbergensis lived about 700,000 to 200,000 years ago in Africa and Europe. The other, much older lineage, the researchers speculate, could be related to Homo erectus of Eurasia. To date, no DNA has been recovered from any of the hominid groups. “The super-archaic find is particularly exciting because it reveals genetic contributions from a human lineage that lived more than a million years ago, despite the absence of sequenced DNA from that population,” Arjun Biddanda, a postdoctoral researcher at Johns Hopkins University and co-first author of the study, said in a statement. Modern human genomes are largely similar, but vary from individual to individual in small part because of these deep ancestral lineages, which have contributed some rare but notable differences to the genomes, explained John Hawks, a paleoanthropologist and professor at the University of Wisconsin-Madison. Hawks was not involved in the new study. “Today we tend to focus on differences between people that seem big, but are actually superficial, such as skin color or facial appearance,” Hawks said in an email. “These differences between living people are actually very small compared to the ancestors we all evolved from, and those ancestors found ways to interact and survive with each other. That’s our heritage, and it’s one that matters even more than ever.” The discovery of the younger ghost lineage “places the time of admixture well before admixture with Neanderthals, and shows that it affects all populations living today,” Hawks added. The researchers said they hope the TRACE method will uncover more hidden lineages in our species, as well as other animal species. But researchers agree that the best new evidence will come from DNA extracted directly from ancient fossils. For now, however, the clues left in modern DNA are the closest scientists can get to these long-lost ancestors. “Randomly, two people in the world could inherit the same piece of DNA from an ancestor that we previously had no idea about, but now actually know,” said the study’s co-first author, Yulin Zhang, a doctoral student in computational biology at UC Berkeley. “From this mysterious ancestor, we have something in common from another angle.” Taylor Nicioli is a freelance journalist based in New York. Subscribe to CNN’s Wonder Theory science newsletter. Explore the universe with news about fascinating discoveries, scientific breakthroughs and more.
