Our ancestors interbred with at least two ancient human lineages in addition to Neanderthals and Denisovans, and now an improved method has given us a much better idea of which bits of our DNA came from them. In fact, it shows that nearly the entire genome of one of these “ghost ancestors” is preserved in small bits spread among all living humans.
In any person alive today, between 0.5 and 1 per cent of their DNA comes from this ghost ancestor, says at the University of California, Berkeley. But different people have different bits of DNA from them and, crucially, they are spread fairly evenly around the genome.
“We find that almost all regions of the genome have ghost ancestry,” says team member , also at Berkeley.
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This means that, if all the bits could be put together, it might be possible to assemble almost an entire genome of this ghost ancestor, though the team hasn’t attempted this.
Earlier research revealed that Homo sapiens interbred with Neanderthals and Denisovans within the past 50,000 years. These studies have relied on the ancient DNA sequences from fossils.
While other work has also identifed ghost ancestry from human genomes, this team’s new approach is much more powerful, says Moorjani. It is based on constructing a “family tree” for parts of the genome, which has only recently become computationally possible. The researchers showed this approach works by identifying Neanderthal and Denisovan DNA from modern human genomes alone.
“I believe it is the next frontier of research in human genetics, because it allows us to even learn about our ancestors for whom we don’t have any fossil [DNA] evidence,” says Moorjani.
Only a small part of the Neanderthal and Denisovan genomes remain collectively preserved within us. “Long segments of the genome are devoid of, or have very low fractions of, Neanderthal or Denisovan ancestry,” says team member at Johns Hopkins University in Maryland. “Yet we were able to find high-ish fractions of this ghost ancestry in these regions.”
The researchers think this is because the populations of Neanderthals and Denisovans were very small, and therefore were more likely to have detrimental mutations. “Most likely there was selection against Neanderthal or Denisovan ancestry in these regions,” says Moorjani.
But much more of the DNA deriving from one ghost ancestor appears to have been selected for, or it was at least neutral in evolutionary terms. This is probably because the population of this ghost ancestor was much larger, she says.
The team’s work suggests that the ghost ancestor split away from the main lineages leading to modern humans around 800,000 years ago. Then, some time later, the two lineages came back together and interbred.
“Because all modern humans carry signatures of the ghost ancestry, it’s most likely that the gene flow occurred in Africa, and that this population existed in Africa,” says Moorjani. Based on all these factors, this ghost ancestor could be a species known from fossils, such as Homo heidelbergensis, the researchers speculate.
The second ghost ancestor identified by their approach is much older. It split from the main lineage leading to modern humans around 1.8 million years ago. At some point later on, Denisovans in Eurasia interbred with this “super-archaic” ancestor.
“Modern humans have also inherited these super-archaic segments through the Denisovan gene flow, and now we can find blocks of this super-archaic ancestry,” says Moorjani.
This is important and innovative work, says at the Natural History Museum in London.
He agrees that the more recent ghost ancestor could have been Homo heidelbergensis – fossil evidence shows this species was present in Africa as recently as 300,000 years ago. The most likely candidate for the super-archaic ghost lineage has to be Homo erectus, he says.
“These results are exciting,” says Stringer. “They provide indirect ways of reconstructing parts of the genomes of more primitive species like Homo erectus and Homo heidelbergensis.”
Science
