Beyond Neanderthals and Denisovans, a "ghost lineage" from Africa contributed DNA to modern humans before our ancestors left the continent. Scientists, largely from a Berkeley-based group, utilized advanced analytical techniques and developed a software tool called TRACE to identify this previously unknown ancestry.

TRACE analyzes ancestral recombination graphs, which reconstruct the history of DNA segments. It identifies sequences that appear "old" in terms of common ancestry but "young" in terms of recombination, a signature of introgression from a separate lineage. The tool successfully identified known Neanderthal and Denisovan DNA and, in African populations, revealed a significant amount of DNA from this ghost lineage, estimated to be 0.5 to 1.1 percent of current human genomes.

This ghost lineage shared a common ancestor with modern humans over 800,000 years ago, predating the split with Neanderthals and Denisovans. The DNA segments are shorter than those from Neanderthals and Denisovans, suggesting they have been in the modern human genome longer, consistent with interbreeding occurring before the exodus from Africa. The research also found evidence of a "super archaic" lineage contributing a small fraction of DNA, possibly from Homo erectus, to some modern human genomes.