In a new study published in the journal PLoS Genetics, researchers analyzed the genomes of two Neanderthals, a Denisovan, and two African humans; and found that 1% of the Denisovan genome was introgressed by an unknown archaic hominin ancestor; about 15% of these archaic regions were in turn introduced into modern humans and continue to exist in the genomes of humans living today.
Hubisz and others applies a new algorithm to humans, Neanderthals, and Denisovan genomes, looking for signatures of older proposed migration genres, including ancient Neanderthal humans, and unknown archaic hominins in Denisovans. Image credit: Bob Wilder, University of Buffalo.
About 50,000 years ago, a group of people migrated from Africa and intermarried with Neanderthals in Eurasia.
But that is not the only time our ancient human ancestors and their relatives exchanged DNA.
The sequence of genomes from Neanderthals and Denisovans has provided many new insights into these interracial events and into the movement of ancient human populations.
In the new study, Cornell University researchers Melissa Hubisz and Amy Williams and Adam Siepel of Cold Spring Harbor Laboratory developed a new algorithm for analyzing genomes that can identify segments of DNA that come from other species, even if that genestream happened thousands of years ago and came from an unknown source.
The scientists used the algorithm, named ARGweaver-D, to look at genomes of two Neanderthals, a Denisovan and two African humans.
They found evidence that 3% of the Neanderthal genome came from ancient humans, and estimated that the interracial occurred between 200,000 and 300,000 years ago.
Furthermore, 1% of the Denisovan Fellow probably came from an unknown and distant relative, possibly Homo erectus, and about 15% of these archaic regions are probably passed on to modern humans living today.
The findings confirm previously reported cases of gene flow between old people and their relatives, and also point to new specimens of interbreeding.
A portrait of a young Denisovan female based on a skeletal profile reconstructed from ancient DNA methylation maps. Image Credit: Maayan Harel.
“Given the number of these events, genetic exchange was likely as two groups overlapped in time and space,” the authors said.
The ARGweaver-D algorithm solves the challenging problem of identifying small remnants of gene streams that occurred hundreds of thousands of years ago, when only a handful of ancient genomes were available.
This algorithm can also be useful for studying gene flow in other species where interruptions occurred, such as in wolves and dogs.
“What I find exciting about this work is that it demonstrates what you can learn about deep human history by reconstructing together the entire evolutionary history from a collection of sequences of both modern humans and archaic hominins,” said Dr. Siepel.
“The ARGweaver-D algorithm is capable of going back in time than any other calculation method I have seen. It seems to be especially powerful for detecting ancient introgression. ”
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MJ Hubisz and others. 2020. Mapping of gene flow among ancient hominins through demographic-conscious inference of the ancestral recombination graph. PLoS Genet 16 (8): e1008895; doi: 10.1371 / journal.pgen.1008895
