UC Berkeley researchers announced on July 30 that they have identified regions of DNA in modern humans inherited from two previously unknown ancestors, following interbreeding among modern humans and at least four other archaic human relatives.
The study pinpoints areas of the genome inherited from these unidentified ancestors and establishes a timeline using a new computational technique. This method leverages hundreds of genomes from present-day humans to trace ancient genealogical relationships. One ancestor, referred to as a ghost ancestor, interbred with modern humans in Africa before 50,000 years ago, prior to the migration of Homo sapiens out of Africa into Europe and Asia. These genes make up about 1% of the genomes of modern humans, similar to the amount attributed to Neanderthal ancestry. The ghost lineage split off around 800,000 years ago but interbred with modern humans earlier.
A second mysterious ancestor—described as a super-archaic ancestor—was part of a hominin lineage that existed about 1.8 million years ago and interbred with Denisovans in Eurasia. Denisovans later passed some super-archaic DNA on to Homo sapiens through further interbreeding events.
"The super-archaic finding is particularly exciting because it reveals genetic contributions from a human lineage that lived over a million years ago, despite the absence of any sequenced DNA from that population," said Arjun Biddanda, postdoctoral researcher at Johns Hopkins University and co-first author.
Priya Moorjani, associate professor at UC Berkeley and co-author, said, "With ancient DNA from Neanderthals and Denisovans and with these new genealogical methods, we are learning that mixture among human populations has been very pervasive across time, and that this is also likely to be true at ancient time scales." Moorjani added, "We often think of human evolution as a branching tree, but new genomic data and analytical methods reveal a much more interconnected history—more like a complex web of populations connected by repeated episodes of migration and mixing."
The research team developed TRACE (TRacking Archaic Contributions via ARG Estimation), which analyzes complete genomes from living people only by reconstructing ancestral recombination graphs across the genome. This approach enabled them to identify regions whose ancestry extends unusually far back in time—even without access to ancient DNA samples—and uncover genetic contributions from extinct populations.
Biddanda said, "TRACE allowed us to contextualize how the ancestry segments from these previously uncharacterized hominins are distributed throughout the human genome. We found that these contributions are widespread throughout the genome, and ghost ancestry is detected even in regions previously thought to be intolerant of Neanderthal and Denisovan ancestry." Many archaic segments appear enriched in regions related to immunity or metabolic function.
Moorjani hopes future work will detect additional faint signals as global genome databases grow more diverse; sequencing more Denisovan genomes or protein sequences could help clarify who these ancestors were.
