Scientists have identified genetic material within modern human DNA that points to the existence of two previously undiscovered ancient human relatives. These findings, published in the journal Science, suggest that early human evolution involved more interbreeding between distinct hominin groups than previously understood.
The research, led by scientists from UC Berkeley and Johns Hopkins University, utilized a new method called TRACE (TRacking Archaic Contributions via ARG Estimation) to analyze modern human genomes. This technique allows researchers to map ancient DNA segments without relying on fossil records of the extinct species themselves.
One of the newly identified ancestral lineages has been termed the 'ghost ancestor.' This group is estimated to have diverched from the modern human lineage approximately 800,000 years ago. While they did not directly interbreed with Homo sapiens until about 50,000 years ago, their genetic legacy is present in all modern humans, both within and outside of Africa. Each person alive today carries between 0.5% and 1% of their genome from this 'ghost' lineage, a proportion similar to the DNA inherited from Neanderthals.
"We were actually able to find and map genomic locations in modern humans that are from this ghost lineage and show that this ghost ancestry is in all modern humans, not only in Africans," stated co-author Yulin Zhang of UC Berkeley.
In addition to the 'ghost ancestor,' the study also detected traces of a 'super-archaic ancestor.' This lineage is believed to be 1.8 million years old and did not interbreed with Homo sapiens directly. Instead, it interbred with Denisovans, an ancient human species that lived in Eurasia between 200,000 and 32,000 years ago. The DNA from this super-archaic ancestor was then passed on to modern humans through interbreeding with Denisovans.
Denisovan DNA is already known to be present in modern human populations, particularly in Asia, where it can constitute up to 4% of some genomes. The TRACE method revealed that segments of DNA inherited from Denisovans also contained genetic material from this even older super-archaic lineage.
Arjun Biddanda, a co-author from Johns Hopkins University, commented on the interconnectedness of human evolution, noting that "human evolution was far more interconnected than we once imagined." Professor Moorjani added, "Rather than a simple branching tree, our history is increasingly emerging as a network of populations that repeatedly diverged, migrated, and mixed. Our genomes contain remnants of that history today."
The research found that many of these ancient DNA segments are located in regions of the modern genome associated with immunity and metabolic functions. Scientists suggest this is likely due to adaptation, as interbreeding introduced new genetic variations that aided survival against pathogens and changing food sources.
Previous knowledge of human interbreeding has largely been based on fossil evidence of Neanderthals and Denisovans. The TRACE method, by analyzing modern genomes alone, opens up possibilities for identifying even more ancient lineages that may be present in human DNA.