A new computational approach that can detect ancient hominin ancestry in modern humans without requiring archaic reference genomes reveals a more complex picture of human evolution than previously imagined. Leveraging this approach, researchers report that an unidentified "ghost" population contributed DNA to the ancestors of all modern humans before they dispersed out of Africa. To date, sequencing of Neanderthal and Denisovan genomes has shown that interbreeding between modern humans and archaic hominins shaped present-day genomes. It's suspected that modern humans also interbred with other, as-yet-unidentified archaic human groups, often called "ghost" populations. Moreover, evidence from living populations and Denisovan genomes points to even older "super-archaic" lineages that split from the human family tree nearly one million years ago or more. However, the scarcity of archaic DNA samples, particularly from older or geographically diverse populations, and the dependence of existing methods on reference genomes have limited the ability to reconstruct the full history of archaic introgression.
Here, Yulin Zhang and colleagues developed a new computational method called TRACE that reconstructs ancestral recombination graphs (ARGs) – detailed maps of how genomes have evolved through recombination and shared ancestry – to detect the genetic signatures of ancient interbreeding. Unlike previous approaches, TRACE requires neither an archaic reference genome nor data from an unadmixed outgroup population, allowing scientists to identify previously unknown archaic contributions using only the genomes of living people. The authors validated the approach in simulations and applied it to high-coverage genomes from global human populations, including the 1000 Genomes dataset. TRACE successfully recovered known Neanderthal and Denisovan ancestry while uncovering previously unknown episodes of interbreeding with archaic human groups. The findings suggest that an unidentified "ghost" population contributed DNA to the ancestors of all modern humans before they dispersed out of Africa, rather than only to specific African populations as previously proposed. Surprisingly, this ghost ancestry is also found in genomic regions thought to reject Neanderthal and Denisovan DNA, suggesting those regions may have specifically selected against those lineages rather than against all archaic ancestry. TRACE also found evidence that Oceanians inherited traces of an even more ancient "super-archaic" human lineage indirectly through Denisovans, revealing that the genetic legacy of modern humans was shaped by multiple waves of interbreeding with now-extinct human groups.
For reporters interested in research integrity topics, study co-author Priya Moorjani said, "The increasing scale and complexity of genomic datasets make transparency, reproducibility, and open methods more important than ever. Continued efforts to share data, software, and benchmarking frameworks, together with careful validation across independent datasets, will help ensure that new discoveries are both robust and reproducible."
