Study reveals two unknown extinct human populations in modern DNA

Scientists have discovered genetic evidence of two extinct human populations whose existence was previously unknown to science. The finding emerged not from fossil digs but from computational analysis of living human genomes—a methodological shift that may reshape how researchers understand our evolutionary past.

The discovery came from a team led by Priya Moorjani at UC Berkeley, with graduate student Yulin Zhang and postdoctoral researcher Arjun Biddanda as co-first authors. Their work, published in Science on July 30, 2026, analyzed genomes from 503 people worldwide using a computational tool called TRACE. The tool searches through the genetic material in modern humans for signatures of ancient lineages—patterns that reveal when distant populations interbred with our ancestors, even when no physical remains of those populations have ever been found.

The first population the researchers identified is what they call a "ghost" lineage. This group split from the human evolutionary line approximately 800,000 years ago and interbred with the ancestors of modern humans in Africa sometime more than 50,000 years ago, before the major migration of Homo sapiens out of the continent. The genetic legacy of this mixing is present in every human population studied, comprising roughly 0.5 to 1 percent of every living person's genome—a proportion comparable to the Neanderthal ancestry that scientists have known about for over a decade. Zhang emphasized that this ghost DNA is not confined to African populations; it appears in all modern humans.

The second population, termed a "super-archaic" lineage, diverged from the human line much earlier, around 1.8 million years ago. This group never interbred directly with humans. Instead, it mixed with Denisovans in Eurasia, and those Denisovans later passed traces of this ancient DNA to modern humans through subsequent interbreeding. This super-archaic ancestry is most readily detectable today in the genomes of Pacific Islander populations. Altogether, roughly 2 percent of the modern human genome now appears to derive from these two archaic populations previously unknown to science.

The research builds on more than a decade of prior work establishing that modern human DNA contains inherited material from Neanderthals and Denisovans, our closest known extinct relatives. Neanderthals, the stockier cousins of modern humans who lived in Europe and went extinct about 40,000 years ago, were once thought to have been outcompeted and eliminated by Homo sapiens due to inferior intelligence. That understanding has shifted dramatically. Neanderthals are now recognized as socially and culturally complex, technologically sophisticated, and capable of burial practices and decorative crafts. Rather than simple extinction, they appear to have been assimilated into the modern human population through interbreeding. Denisovans, who lived in Asia and died out about 30,000 years ago, similarly left their genetic mark, particularly in modern Pacific Islander populations.

The TRACE method represents a significant departure from traditional approaches to studying ancient human populations. Previous discoveries of archaic ancestry relied on comparing living human DNA against ancient DNA physically extracted from Neanderthal and Denisovan fossils—an approach impossible for populations that left no recoverable bones. The Berkeley team's tool requires neither ancient DNA nor fossils. Instead, it analyzes the tangle of family trees embedded in modern human genomes, identifying genetic patterns that signal the presence of ancient lineages. The researchers first validated TRACE by successfully rediscovering known Neanderthal and Denisovan ancestry before applying it to search for entirely new, unknown populations.

The implications extend beyond the specific findings. The fossil record remains sparse and geographically uneven, particularly in tropical Africa, where organic remains decay rapidly. Computational approaches like TRACE may prove essential for filling gaps that fossils alone may never resolve. The discovery also complicates the standard "Out of Africa" model of human dispersal, which has been the accepted framework since genetic evidence in the 1980s and 1990s settled a long-standing debate in favor of African origins. The new research shows that even before Homo sapiens migrated out of Africa around 50,000 to 70,000 years ago, the population that would eventually leave the continent had already absorbed DNA from an unrelated, unknown hominin group within Africa itself.

Scientists have urged caution in interpreting these findings. Moorjani stressed the importance of transparency, reproducibility, and open methods, noting that continued efforts to share data and software, along with careful validation across independent datasets, will help ensure discoveries are robust. Yale computational biologist Patrick Reilly, not involved in the study, echoed this caution, observing that confirmation through independent methods and future fossil evidence will be needed, as any method can produce false positives.

The broader picture emerging from two decades of fossil discoveries and genetic analysis has fundamentally altered how scientists understand human evolution. The old image of a single evolutionary ladder, with modern humans as its final rung, has given way to something far more intricate: a landscape in which multiple related human populations lived side by side for hundreds of thousands of years, repeatedly meeting, mixing, and exchanging genes across vast stretches of time and geography. Moorjani captured this shift directly: human evolution is not a branching tree but a complex web of populations connected by repeated episodes of migration and mixing. This reflects a materialist understanding of evolution as a dynamic process shaped by chance encounters, migration, and environmental pressure rather than an inevitable march toward a predetermined outcome.