Scientists at UC Berkeley have identified genetic evidence of two previously unknown human lineages that interbred with modern humans at different points in evolutionary history. The discovery, published July 30 in the journal Science, adds to the growing understanding that human evolution involved repeated encounters and genetic mixing among multiple related populations rather than a simple branching pattern.
The first unknown lineage, referred to as a ghost ancestor, interbred with Homo sapiens in Africa more than 50,000 years ago, before the major human migration out of Africa. This ghost lineage separated from the ancestors of modern humans approximately 800,000 years ago, a timeframe that overlaps with Middle Pleistocene Homo groups documented in Africa. Genetic material from this population comprises roughly 1 percent of the modern human genome—a proportion comparable to Neanderthal ancestry—and appears in both African and non-African populations today.
The second unknown population, designated a super-archaic ancestor, descended from a lineage dating back approximately 1.8 million years. This ancient hominin appears to have interbred with Denisovans in Eurasia more than 200,000 years ago. Denisovans subsequently mixed with Homo sapiens, allowing a small portion of this extremely ancient DNA to enter modern human genomes indirectly.
The research team developed a novel analytical technique called TRACE (TRacking Archaic Contributions via ARG Estimation) to make these discoveries. Rather than relying on fossil DNA, which is scarce for most extinct hominins, TRACE examines hundreds of present-day human genomes and reconstructs ancestral relationships among DNA segments across many generations. The method successfully identified previously known Neanderthal and Denisovan ancestry while also revealing genetic contributions from the two unknown lineages.
Analysis of the archaic DNA segments revealed that many cluster in genomic regions associated with immune function and metabolism, suggesting that interbreeding may have provided evolutionary advantages as human populations adapted to new environments, pathogens, and food sources. Researchers anticipate that improved global genome databases and additional Denisovan sequences will enable the identification of other previously unknown ancient human lineages.
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