Two Ghost Lineages Mapped in Human DNA, No Fossils
A method called TRACE, built at the University of California, Berkeley, pinned down stretches of DNA in living people that came from two archaic human lineages nobody has ever dug up.
Geneticists at the University of California, Berkeley published a paper in Science on July 30 that, for the first time, points to specific stretches of the modern human genome inherited from two previously unidentified archaic lineages. No DNA has ever been extracted from either population, and no bone belonging to them sits in any collection. The lineages surfaced indirectly, from the genealogical relationships written into the genomes of hundreds of living people. The paper is titled Recovering signatures of archaic hominin introgression using ancestral recombination graphs, DOI 10.1126/science.aef8874.
For the past fifteen years the field has worked the other way around. The first draft of the Neanderthal genome appeared in 2010, the same year a finger bone from Denisova Cave in the Altai yielded a population science had not known existed and later named after the cave. Everything we knew about archaic interbreeding came down to whether someone had a bone preserved well enough to sequence. The new method removes that dependency.
How does TRACE work?
TRACE stands for TRacking Archaic Contributions via ARG Estimation. Rather than comparing a modern genome against a reference archaic one, it reconstructs an ancestral recombination graph, a map that shows, segment by segment, how lines of inheritance branch backwards through time. Segments whose ancestry runs unusually deep betray an ancestral population that split off long before the rest.
The co-first authors are Yulin Zhang, a graduate student at Berkeley, and Arjun Biddanda, a postdoctoral researcher at Johns Hopkins University. The work is led by Priya Moorjani, associate professor of molecular and cell biology at Berkeley. Sarah Johnson of Berkeley’s Center for Computational Biology and Colm O’Dushlaine of 54Gene, based in Washington, D.C., are also on the team.
Two lineages, two different routes into us
The first split from the ancestors of modern humans roughly 800,000 years ago, around the same window in which Neanderthals and Denisovans parted ways, and interbred with humans in Africa more than 50,000 years ago, before the main exit of Homo sapiens from the continent. It accounts for 0.5 to 1 percent of an individual genome, comparable to the roughly 1 percent that is Neanderthal.
“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.”
That is how Zhang described the result in a statement from the University of California, Berkeley. African and non-African populations alike carry the signal.
The second lineage is labelled super-archaic and descends from a line about 1.8 million years old. It reached us the long way round. According to the Berkeley statement, it interbred with Denisovans in Eurasia more than 200,000 years ago and makes up 3 to 5 percent of the Denisovan genome; only later mixing between Denisovans and Homo sapiens carried a sliver of that material into us.
“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.”
Biddanda said that in the same statement. Archaic hominins account for about 2 percent of the modern human genome overall, with the Denisovan share reaching 4 percent in populations across Oceania.
What is new here, and what is not
A ghost ancestor lurking in African genomes is not a new idea. Work by Arun Durvasula and Sriram Sankararaman, published in Science Advances in 2020, already made a statistical case for archaic ancestry in West African populations, but could not place that ancestry at particular coordinates. The Berkeley paper moves the line exactly there: instead of an estimate of how much, it yields a map of where.
The archaic segments cluster in regions tied to immunity and metabolism, the authors report.
“Adaptation to new pathogens and food sources has been one of the strongest selective pressures in human evolution. Interbreeding with other human groups introduced new genetic variation, providing additional raw material for natural selection.”
Moorjani said that in the university statement. Read alongside the four interbreeding events the team dates, it points to mixing between human groups as a recurring pattern rather than an exception.
The limits
The method cannot say which species these two lineages belonged to, or where they lived. It produces a genetic signature, not a fossil, and no site can be named on the strength of this paper. The authors themselves note that fainter signals, and any attempt to trace the origin of the super-archaic lineage, will require larger genome databases and more sequenced Denisovan samples; only one has been published so far. The split and admixture dates are model-derived estimates with error ranges, not measured years. Until the result is replicated on independent genome panels, TRACE remains one group’s finding, however detailed the map it draws.
