Some of the “ghosts” in human DNA are not mythical at all. Researchers have found evidence that modern humans inherited genetic material from extinct hominin populations whose bones—and whose complete genomes—have never been identified. A new analysis of modern human genomes suggests that two such ghost lineages together account for about 2 percent 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 percent Neanderthal DNA. Neanderthal DNA began mixing with the DNA of our ancestors more than 50,000 years ago, in an episode that lasted about 7,000 years before the Neanderthals became extinct.
People in Asia and Oceania also carry between 0.1 and 5 percent Denisovan DNA. Scientists reconstructed this ancestry by comparing living human genomes with DNA recovered from fossil hominins.
However, researchers have so far decoded the complete genomes of only six ancient individuals: four Neanderthals and two Denisovans, all from Eurasia. Other hominin groups, including Homo heidelbergensis in Africa and Homo erectus, also lived during periods when they could have encountered the ancestors of modern humans. Yet scientists have not been able to test directly whether these groups contributed DNA to people living today.
Ancient DNA degrades rapidly outside permanently frozen environments. As a result, the chances of recovering readable DNA from someone who lived in a warm climate a million years ago are almost zero.
Finding “ghost” lineages in modern genomes
The absence of ancient DNA makes human evolution difficult to reconstruct. If an extinct population interbred with our ancestors and then disappeared, researchers might have no fossil or genome from that population. Its only surviving trace could be the DNA it left in modern humans—a so-called ghost lineage.
Scientists at the University of Berkeley and Johns Hopkins recently used modern human genomes to search for these hidden lineages. Human DNA is organized into 23 long strands called chromosomes. Each short segment along a chromosome has its own history, inherited through a particular chain of ancestors.
Because chromosomes are recombined in every generation, adjacent segments can follow different ancestral paths. A single chromosome therefore contains thousands of separate family trees arranged along its length. Geneticists combine these histories into an ancestral recombination graph, or ARG.
ARGs can help estimate when different parts of the genome acquired their current forms. Tracing a DNA segment backward eventually leads to an ancestor who originally carried that segment. For most human DNA, this ancestor lived relatively recently. DNA inherited from extinct relatives follows branches that reach much farther back because those lineages split from our own hundreds of thousands of years ago.
The researchers developed a computer program called Tracing Archaic Contributions with ARG Estimation, or TRACE. The program scans ARGs for branches that extend unexpectedly far into the past, which could indicate DNA inherited from an archaic or otherwise extinct population.
Evidence for two unknown populations
First, the researchers tested TRACE on a simulated genome to determine whether it could identify regions that appeared unusually ancient. They then analyzed 503 human genomes from the publicly available 1000 Genomes Project. The genomes represented five populations: British, Han Chinese, Telugu from India, Yoruba from Nigeria, and Luhya from Kenya.
Earlier researchers identified ancient DNA by comparing modern genomes with the genomes of ancient individuals. TRACE detected the same fossil-free interval, suggesting that it may also identify genetic contributions from relatives for whom no fossil or sequenced genome has been found.
The analysis identified genome segments that appear to come from a ghost hominin population that split from the lineage leading to modern humans about 830,000 years ago. This was approximately when the Neanderthal and Denisovan lineages separated. All five populations in the study carried between 0.5 and 1.1 percent DNA from this group, suggesting that the interbreeding occurred in Africa before modern human populations migrated into Eurasia.
The researchers also found evidence of a second and much older lineage in genomes from Oceania, where Denisovan DNA is most common. This population split from the modern human lineage about 1.8 million years ago. Its DNA was consistently found within Denisovan ancestry, suggesting that the older population interbred with Denisovans. The Denisovans may then have passed that inherited DNA to the ancestors of modern humans.
An incomplete human family tree
The researchers concluded that the two ghost lineages account for about 2 percent of the modern human genome. The finding suggests that human evolution involved repeated episodes of separation and interbreeding rather than a simple, branching family tree.
The identities of both populations remain uncertain. The first split from our lineage around the same time as Homo heidelbergensis, while the second is old enough to be associated with Homo erectus. Until researchers uncover fossils or other direct evidence, these populations will remain anonymous—but the genetic traces they left behind are real.
Source: sciworthy.com
