New technique pinpoints human DNA inherited from ‘ghost’ ancestors

A new study by UC Berkeley researchers has identified genetic traces of two previously unknown human ancestors in the modern human genome, alongside known contributions from Neanderthals and Denisovans. Using a technique called TRACE, the team analyzed hundreds of modern human genomes to pinpoint regions inherited from these ‘ghost’ ancestors, establishing a timeline for when interbreeding occurred. The findings suggest that modern humans interbred with multiple hominin groups over millions of years, challenging the traditional view of human evolution as a simple branching tree.

The first unknown ancestor, referred to as a ghost lineage, interbred with modern humans in Africa before 50,000 years ago, contributing around 1% of the genome to all modern humans. This lineage diverged from the human family tree around 800,000 years ago, similar to the split between Neanderthals and Denisovans. The second ancestor, a super-archaic lineage, interbred with Denisovans in Eurasia more than 200,000 years ago, with some of its DNA later passed to modern humans.

The researchers used TRACE to reconstruct genealogical relationships across modern human genomes, identifying regions with unusually ancient ancestry. While some of these regions matched Neanderthal or Denisovan DNA, others did not, revealing contributions from the two new lineages. The ghost ancestry was found in all modern humans, while the super-archaic ancestry was detected in populations with Denisovan DNA, such as those in Oceania.

The study highlights the pervasive nature of interbreeding among early human populations, with archaic DNA segments often linked to immunity and metabolic functions. The researchers suggest that these genetic exchanges provided raw material for natural selection, aiding adaptation to new environments. The findings open new avenues for exploring human evolution, with potential to uncover additional lineages as genome databases expand.