One of these ghost lineages left its DNA scattered in all present-day people. The other, a "super-archaic" lineage, dates back nearly 2 million years, researchers reported Thursday (July 30) in the journal Science.
For decades, experts have found DNA evidence that our species, Homo sapiens, once mated with now-extinct relatives such as Neanderthals and Denisovans. Most people not of sub-Saharan ancestry living today possess about 1% to 2.4% Neanderthal ancestry, and Asians and Oceanians (people from the island nations of the Pacific Ocean) harbor about 0.1% to 6% Denisovan ancestry. But scientists have suspected that modern humans may have interbred with other now-extinct human groups that have not been identified yet. However, the scarcity of ancient DNA samples makes it challenging to identify what these unidentified groups, often called ghost lineages, might have contributed to our species.
In the new study, Moorjani and her colleagues reasoned that everyone's genome contains a record of their ancestry. They investigated whether it was possible to uncover signs of "long-extinct ancestors preserved within the genomes of present-day people," Moorjani said.
"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."
The researchers experimentally tested the new method, which correctly identified Neanderthal and Denisovan ancestors in modern-human genomes. However, it also uncovered previously unknown instances of interbreeding with now-extinct groups.
"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."
Ghost candidates
One possible candidate for the ghost lineage is Homo heidelbergensis, the researchers wrote in the study. This human species lived from about 700,000 to 200,000 years ago in Africa and Europe.
The scientists also found evidence that people from Oceania inherited traces of a "super-archaic" human lineage that diverged from the ancestors of modern humans about 1.8 million years ago, before the emergence of the common ancestor of modern humans, Neanderthals and Denisovans. This super-archaic DNA, on average, made up about 0.002% of the Oceanian genomes investigated and appeared within regions of Denisovan DNA, suggesting that the super-archaic DNA got into modern humans through interbreeding with Denisovans.
The study's findings highlight that modern humans are the product of multiple species and that "hybridization is the norm and not the exception," Villanea said. "We see hybridization 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."
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Stringer agreed, adding that this new technique provides "indirect ways of reconstructing parts of the genomes of more primitive species like H. erectus and H. heidelbergensis."
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