A research team has used new genomic analysis techniques to identify traces of an unknown ancestral lineage that interbred with humans before they migrated out of Africa.

Researchers based at UC Berkeley have identified evidence of a previously unknown human ancestral lineage, referred to as a "ghost lineage," within modern human genomes. By analyzing genomic data, the team found that this group interbred with modern humans before the population expanded out of Africa. The findings suggest this lineage shares a common ancestor with modern humans dating back over 800,000 years.

Using TRACE to analyze ancestry

The research team developed a software tool called TRACE to identify sequences in the human genome that originated from separate lineages. The tool works by identifying segments that appear old in terms of common ancestry but young in terms of recombination frequency. When tested against known Neanderthal and Denisovan DNA, the tool demonstrated an accuracy rate of over 90 percent with a false discovery rate of less than 0.25 percent.

Characteristics of the ghost lineage

The ghost lineage DNA comprises approximately 0.5 to 1.1 percent of current human genomes and is present in all modern human populations. While the segments are present in regions where Neanderthal and Denisovan DNA are absent, researchers noted that these sequences are less common near genes, though some nearby genes are associated with immune function and metabolism. The study also identified a separate, "super archaic" lineage that contributed about 0.3 percent of the Denisovan DNA found in populations from Oceania, which may have branched off from human ancestors nearly 1.8 million years ago.