Not just Neanderthals: Ghost lineage in Africa left its mark on our DNA

With enough genomic data, computers can be used to reconstruct what are called ancestral recombination graphs that try to reconstruct this history. For each base in the genome, ancestral recombination graphs estimate its history: How many generations back that particular base first appeared in the genome and when it has been involved with recombinations. Because of the randomness of some of these things and complexities like deletions, many of the individual inferences about history will be wrong. But those are likely to be the exceptions, and the average picture across the genome’s three billion bases should be informative. The Berkeley team made a few inferences about what these ancestral recombination graphs should look like in cases where a separate lineage contributed DNA to modern humans (a process called “introgression”). One is that there should be a cluster of sequences that look consistently old, since they shouldn’t have as many of the same variants that the modern human genomes have picked up while the lineages were separate. Normally, sequences that have been around for a while have more chances to be involved in a recombination. But these sequences were reintroduced to the human genome later in our history, so recombination should be far less frequent relative to a genome that’s been in the modern human lineage the whole time. So any part of the genome that introgressed from a separate lineage should have two properties: Many of its bases should look “old” in the sense of how far back their common ancestry can be traced, yet they should look “young” in terms of how much recombination has taken place. So the researchers developed a software tool they call TRACE to look for these sequences. The modern human genome has areas, called “deserts,” that lack Neanderthal and Denisovan DNA entirely. That has led to the suggestion that the human genome can’t tolerate dramatically different variants in these areas. But the ghost lineage DNA shows up in both Neanderthal and Denisovan deserts. So there seems to be something actively problematic with the DNA from those lineages in these regions. Something else suggested by other data is that the Denisovan population had also undergone a separate episode of interbreeding, this with a far older lineage. This “super archaic” lineage appears to have split from modern humans far earlier, suggesting it came from Homo erectus or another human ancestor. Because some populations—primarily in Southeast Asia and Oceania—have relatively high levels of Denisovan DNA, it’s possible that some of this superarchaic DNA found its way into our genomes. The team went looking for it, searching for DNA that looked considerably older than the three known lineages. There’s not much—only about 0.3 percent of the Denisovan DNA in genomes from Oceania can be traced back to the superarchaic lineage. So although a tiny fraction of the genomes in some modern humans comes from this introgression, it’s definitely out there. And it apparently comes from a lineage that branched off from ours nearly 1.8 million years ago. The work doesn’t really get into the significance of these archaic sequences. They’re less common in the neighborhood of genes, but some genes nearby are often involved in metabolism and immune function. It’s not clear whether these ancient variants are adaptive in any way, though. It’s also impossible to say much about the ghost lineage beyond the fact that our ancestors encountered it in Africa. Still, we now have samples of a fair amount of its DNA. And there’s always a chance that ancient DNA or archeology could ultimately tell us a bit more about what these ghosts might have been. Science, 2026. DOI: 10.1126/science.aef8874 (About DOIs).