Researchers at the University of California, Berkeley, have developed a computational method that can identify DNA inherited from extinct human populations even when no sequenced genome from those groups is available.
The method, called TRACE, analyzes genealogical patterns across present-day human genomes. When researchers applied it to worldwide genomic datasets, they found evidence of two previously uncharacterized archaic human lineages that contributed DNA to modern populations. The findings were published in Science.
Reconstructing ancestry without ancient DNA
Scientists have previously identified Neanderthal and Denisovan contributions to the modern human genome by comparing present-day sequences with DNA recovered from ancient remains. However, the scarcity of well-preserved ancient DNA has limited researchers’ ability to study other extinct populations.
TRACE—short for TRacking Archaic Contributions via ARG Estimation—addresses that limitation by working with contemporary genomes alone. The method uses ancestral recombination graphs, which reconstruct how sections of DNA from different individuals relate to one another through shared ancestry and recombination events.
“Genealogies preserve a record of our evolutionary past,” said Priya Moorjani, an associate professor of molecular and cell biology at UC Berkeley and a senior author of the study.
Archaic DNA can appear in these reconstructed genealogies as unusually old branches contained within relatively long genomic segments. TRACE combines those signals to distinguish DNA introduced through interbreeding from genetic variation that populations inherited from a more distant common ancestor. The researchers tested the method through simulations under multiple demographic scenarios before applying it to human genome data.
Detecting two unknown lineages
The researchers applied TRACE to whole-genome sequences from the 1000 Genomes Project and individuals from Oceanian populations. The method first recovered known regions of Neanderthal and Denisovan ancestry, supporting its ability to detect previously documented interbreeding events.
TRACE also identified DNA from an unknown lineage that diverged from modern humans around the period when Neanderthals and Denisovans separated from the modern human lineage. The researchers estimated that this group interbred with modern human ancestors in Africa before the most recent migration out of Africa. People in both African and non-African populations carry approximately 0.5 to one percent ancestry from this lineage.
A second signal appeared within Denisovan-derived regions in Oceanian genomes. The researchers attributed it to a much older, or “super-archaic,” lineage that interbred with Denisovans, which later passed some of that DNA to modern humans.
The method does not establish the identities of either ancestral population. The estimated timelines overlap with hominin groups that lived during those periods, but genomic or protein evidence would be needed to make a more direct connection.
Expanding the reach of genomic analysis
Because TRACE does not require an ancient reference genome or a population assumed to lack archaic ancestry, it could help researchers investigate evolutionary histories that remain inaccessible through conventional ancient-DNA comparisons.
The study also highlights the importance of population diversity in genomic databases. Broader sampling could give researchers enough information to detect weaker signals from additional ancestral groups and distinguish ancestry patterns that appear only in particular populations.
The team has made the TRACE software and analysis pipeline available for other researchers. Although the study focused on humans, the same approach could be adapted to investigate interbreeding and evolutionary relationships in other species using existing genome collections.
This article was created with the assistance of Generative AI and has undergone editorial review before publishing.
