UC Berkeley team identifies two unknown 'ghost' hominin lineages in modern human DNA

A team led by researchers at the University of California, Berkeley, has identified genetic traces of two previously unknown archaic human lineages—referred to as “ghost” ancestors—in the DNA of modern humans, according to a study published July 30 in the journal Science (science.org).

Using a new computational technique called TRACE (TRacking Archaic Contributions via ARG Estimation), the scientists analyzed high-coverage genomes from the 1000 Genomes Project and other modern populations. TRACE reconstructs ancestral recombination graphs to map deep genealogical relationships without requiring sequenced archaic reference genomes or unadmixed outgroups (news.berkeley.edu).

The method successfully recovered known Neanderthal and Denisovan introgression segments as a validation step. It then uncovered two additional signals. One ghost lineage diverged from the modern human line roughly around the same time as Neanderthals and Denisovans, about 800,000 years ago. This group interbred with modern humans in Africa more than 50,000 years ago, prior to the major out-of-Africa migration. Its DNA is present in both African and non-African populations at levels of approximately 0.5% to 1% per individual—comparable to typical Neanderthal ancestry in non-Africans—and is distributed widely across the genome (eurekalert.org).

“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,” said co-first author Yulin Zhang, a UC Berkeley graduate student, in a university release (news.berkeley.edu).

The second signal comes from a “super-archaic” lineage that split off about 1.8 million years ago. This group interbred with Denisovans in Eurasia, likely more than 200,000 years ago. Denisovans later passed a fraction of that super-archaic DNA to modern humans during known interbreeding events. The signal is most detectable in Oceanian populations, which carry higher Denisovan ancestry (livescience.com).

Overall, the researchers estimate that about 2% of the modern human genome derives from archaic hominins beyond or in addition to previously characterized sources. Ghost ancestry appears even in genomic regions previously described as deserts of Neanderthal or Denisovan DNA, suggesting those regions may have been intolerant specifically of Neanderthal/Denisovan variants rather than all archaic DNA (eurekalert.org).

Many of the archaic segments, including ghost contributions, are enriched in regions linked to immunity and metabolism. “Adaptation to new pathogens and food sources has been one of the strongest selective pressures in human evolution,” said senior author Priya Moorjani, associate professor of molecular and cell biology at Berkeley. “Interbreeding with other human groups introduced new genetic variation” (news.berkeley.edu).

The divergence times overlap with known Middle Pleistocene Homo groups in Africa and Homo erectus in Eurasia, though no fossils or ancient DNA have been directly linked to either ghost lineage. Co-first author Arjun Biddanda, now at Johns Hopkins University, noted that the super-archaic finding reveals contributions “from a human lineage that lived over a million years ago, despite the absence of any sequenced DNA from that population” (newscientist.com).

Independent experts, including Chris Stringer of the Natural History Museum in London, described the work as important for providing indirect ways to reconstruct genomes of more primitive species. The study was funded by the National Science Foundation and included co-authors from Berkeley’s Center for Computational Biology and 54Gene (aa.com.tr).

The results reinforce a view of human evolution as a web of repeated migrations and mixing rather than a simple branching tree, Moorjani said.