Some of the “ghosts” in human DNA are real remnants of extinct hominin populations whose bones have never been found. Researchers at the University of Berkeley and Johns Hopkins used a computer program called Tracing Archaic Contributions with ARG Estimation (TRACE) to search modern human genomes for unusually ancient DNA. Their analysis identified genetic material from two unidentified lineages that together account for about 2% of the modern human genome.
DNA inherited from extinct relatives
Modern humans interbred with at least two extinct relatives, Neanderthals and Denisovans. Most people outside Africa carry approximately 1% to 2% Neanderthal DNA. Their DNA began mixing with ours more than 50,000 years ago, and the process continued for about 7,000 years before the Neanderthals became extinct. People in Asia and Oceania also carry between 0.1% and 5% Denisovan DNA.
Scientists reconstructed this ancestry by comparing living human genomes with DNA recovered from fossil hominins. However, researchers have read the complete DNA sequences of only six of these individuals: four Neanderthals and two Denisovans, all from Eurasia. Other hominin groups, including Homo heidelbergensis in Africa and Homo erectus, also coexisted with our ancestors.
Scientists have not been able to test directly whether modern humans carry DNA from these groups. Ancient DNA degrades rapidly outside permanently frozen environments, making it extremely unlikely that researchers could read the genome of someone who lived in a warm climate a million years ago.
This lack of ancient DNA creates a major challenge for reconstructing human evolution. If another group interbred with our ancestors and later disappeared, researchers might have no fossils or genomes with which to identify it. In such cases, the only surviving evidence could be the DNA that group left in the genomes of its descendants. Scientists refer to these populations as ghost lineages.
Searching modern genomes for ghost lineages
The researchers used the structure of human DNA to look for these hidden ancestors. Human DNA is organized into 23 chromosomes, and each short segment along a chromosome has its own history of inheritance. Because chromosomes are reshuffled through recombination in every generation, adjacent segments may have followed very different ancestral paths.
As a result, a single chromosome contains thousands of separate family trees arranged side by side. Geneticists can combine these trees into an ancestral recombination graph, or ARG.
ARGs can also provide information about when different parts of the genome were inherited. Tracing a DNA segment backward eventually leads to the ancestor who originally carried that sequence. For most human DNA, that ancestor lived relatively recently. DNA inherited from an extinct relative, however, can lead much farther back because the lineage separated from ours hundreds of thousands of years ago.
To search for such unusually old branches, the team developed TRACE. The researchers first tested the program on a simulated genome to determine whether it could identify regions that appeared ancient. They then analyzed 503 human genomes from the public 1000 Genomes Project, representing five populations: British, Han Chinese, Telugu from India, Yoruba from Nigeria and Luhya from Kenya.
Earlier researchers had identified ancient DNA by matching modern sequences with genomes recovered from ancient remains. TRACE detected the same known archaic interval, even without relying on a fossil genome, suggesting that the method could also identify relatives for whom no fossils or directly sequenced DNA exist.
Two unidentified ancestral populations
The researchers identified genome segments that appear to come from a ghost hominin group that split from the lineage leading to modern humans about 830,000 years ago. This was approximately the same period when the Neanderthal and Denisovan lineages separated.
All five populations in the study carried between 0.5% and 1.1% DNA from this lineage. The finding suggests that the group interbred with modern humans in Africa before some modern human populations migrated to Eurasia.
The analysis also revealed a second, much older lineage in genomes from Oceania, a region where Denisovan DNA is most common. This population split from the human lineage about 1.8 million years ago. Its DNA was consistently found within Denisovan inheritance, suggesting that the older group interbred with Denisovans, who later interbred with the ancestors of modern humans and passed on some of that ancient DNA.
The researchers concluded that the two ghost lineages together make up about 2% of the modern human genome. The result highlights how often human ancestry involved the separation and later mixing of populations.
The identities of both groups remain uncertain. The first split from our lineage around the same time as Homo heidelbergensis, while the second is old enough to have been related to Homo erectus. These populations remain anonymous until further evidence reveals who they were, but the DNA they left behind is tangible evidence that they existed.
Source: sciworthy.com