Key facts
- Evidence suggests humans interbred with a third archaic lineage, dubbed a "ghost lineage," before migrating out of Africa.
- This ghost lineage contributed between 0.5% and 1.1% of modern human genomes.
- The DNA from this lineage appears to have arrived before modern humans left Africa, indicated by its presence in African populations and shorter segments compared to Neanderthal/Denisovan DNA.
- The last common ancestor of this ghost lineage and modern humans is estimated to be over 800,000 years ago.
- A "super archaic" lineage, possibly Homo erectus, also contributed a small amount of DNA to certain modern human populations, particularly in Oceania.
While interbreeding with Neanderthals and Denisovans is well-established, new genomic analysis has revealed evidence of a third, previously unidentified archaic lineage that contributed to the modern human genome. Researchers developed a tool called TRACE, which analyzes ancestral recombination graphs to identify DNA segments that appear "old" in terms of common ancestry but have undergone less recombination than expected. This suggests they have been in the modern human lineage for a long time.
Using TRACE on modern human genomes, scientists found segments of DNA, accounting for approximately 0.5% to 1.1% of the genome, that do not match Neanderthal or Denisovan DNA. This "ghost lineage" DNA is present in all modern human populations, indicating the interbreeding occurred before the out-of-Africa migration. African populations show more diversity from this lineage, with some segments unique to them.
The analysis estimates that the last common ancestor of this ghost lineage and modern humans existed over 800,000 years ago. The segments are, on average, shorter than those from Neanderthals and Denisovans, suggesting they have been integrated into the human genome for a longer period, consistent with their arrival before the exodus from Africa.
Furthermore, the research identified a "super archaic" lineage, potentially Homo erectus, which branched off nearly 1.8 million years ago. This lineage contributed a very small fraction, about 0.3%, of the Denisovan DNA found in some modern populations, particularly in Oceania. The significance of these archaic sequences, including their potential adaptive roles, is still under investigation, but they are less common near genes involved in metabolism and immune function.