Ghost lineage in Africa contributed 1.5 billion bases to human DNA

A previously unknown archaic human lineage contributed DNA to modern humans, according to a study published on July 31, 2026. Researchers at the University of California, Berkeley, identified genetic segments from a "ghost lineage" that interbred with ancestors of all present-day populations before the out-of-Africa expansion.

The discovery affects all modern humans, as the ghost lineage DNA appears in every population tested. African populations carry more diverse and distinct segments, while non-African groups show about 100 genomic regions entirely devoid of this archaic ancestry. The findings come from analysis of roughly 500 modern human genomes.

The work matters because it reveals a third major interbreeding event in human history, beyond those with Neanderthals and Denisovans. The ghost lineage split from modern humans over 800,000 years ago, roughly the same time as the Neanderthal-Denisovan ancestor diverged. Its DNA makes up 0.5 to 1.1 percent of current genomes, covering nearly 1.5 billion bases.

The Berkeley team developed a software tool called TRACE to detect introgressed sequences by looking for DNA that appears both old in common ancestry and young in recombination history. TRACE first successfully identified known Neanderthal and Denisovan segments with over 90 percent accuracy and a false discovery rate below 0.25 percent. When applied to African genomes, it found only 0.1 percent Neanderthal or Denisovan ancestry, consistent with its low error rate.

The ghost lineage segments are shorter on average than Neanderthal and Denisovan ones, indicating they entered the modern human genome earlier. Interestingly, this archaic DNA appears in genomic "deserts" where Neanderthal and Denisovan DNA is absent, suggesting something specifically problematic about those lineages in those regions. The study also detected a tiny fraction of even older DNA—about 0.3 percent of Denisovan sequences in Oceanian genomes—from a "superarchaic" lineage that branched off nearly 1.8 million years ago.

The researchers note that the ghost lineage DNA is less common near genes, but nearby genes are often involved in metabolism and immune function. It remains unclear whether these ancient variants are adaptive. The team hopes that future ancient DNA or archaeological discoveries might reveal more about this mysterious population.