Scientists have uncovered new evidence that modern humans inherited DNA from two previously unknown ancient human relatives, revealing another surprising chapter in our evolutionary history.
The discovery was made using a new genetic analysis method that can identify traces of long-extinct human groups even when no ancient DNA from them has ever been found.
The research, led by scientists at the University of California, Berkeley, was published in Science.
For years, researchers have known that modern humans interbred with Neanderthals and Denisovans after leaving Africa around 50,000 years ago.
Those encounters left small amounts of their DNA in people living today.
However, scientists also suspected that other unknown human relatives had contributed to our genetic makeup, but proving this was difficult because no fossil DNA from these mysterious groups was available.
To solve this problem, the Berkeley team developed a new method called TRACE. Instead of relying on ancient fossils, TRACE studies the complete genomes of living people from around the world.
By comparing hundreds of modern human genomes, the system reconstructs family relationships stretching back hundreds of thousands or even millions of years, allowing researchers to identify pieces of DNA that came from unknown ancestors.
Using this approach, the team discovered evidence of two previously hidden human lineages.
The first, which the researchers call a “ghost” ancestor, mixed with modern humans in Africa more than 50,000 years ago, before our species spread across Europe and Asia. This ancient population split from the ancestors of modern humans around 800,000 years ago, roughly the same time that Neanderthals and Denisovans separated from our evolutionary line.
The researchers found that this ghost ancestry is not limited to African populations. Instead, it appears in people around the world because the interbreeding happened before the major migration out of Africa. Today, each person carries about 0.5% to 1% of their DNA from this unknown group, similar to the amount of Neanderthal DNA found in many modern humans.
The second newly identified lineage is even older. Known as the “super-archaic” ancestor, this human relative lived around 1.8 million years ago. Rather than mixing directly with modern humans, this ancient group first interbred with Denisovans somewhere in Eurasia. Later, when Denisovans and modern humans had children together, a small amount of this extremely ancient DNA was passed into our own species.
Although scientists cannot yet identify exactly which human species these two groups belonged to, the estimated dates provide important clues.
The ghost ancestor may have been related to Middle Pleistocene human populations that lived in Africa about 800,000 years ago, while the super-archaic lineage may have been connected to Homo erectus, one of the earliest human species to spread beyond Africa nearly two million years ago.
The study also showed that these ancient DNA segments are spread throughout the human genome rather than being confined to a few isolated regions. Some of them appear in genes involved in the immune system and metabolism, suggesting they may have helped early humans adapt to new diseases, environments and food sources.
The findings paint a far more complex picture of human evolution than scientists once imagined. Instead of a simple family tree with separate branches, human history now looks more like a network, with different human groups repeatedly meeting, migrating and having children together over hundreds of thousands of years.
Researchers believe this is only the beginning. As more people from different parts of the world contribute their genetic information to research and additional ancient fossils are studied, scientists expect to uncover even more hidden branches of the human family tree.
The new TRACE method may also prove useful beyond human evolution. Researchers say it could help reveal unknown chapters in the evolutionary history of many other species, offering a powerful new way to explore life’s distant past without needing ancient DNA preserved in fossils.
