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 from an unknown archaic hominin ancestor; about 15% of these archaic regions were, in turn, introgressed into modern humans and continue to exist in the genomes of people alive today.
Hubisz et al applied a new algorithm to human, Neanderthal, and Denisovan genomes, looking for signatures of older proposed migration events, including ancient humans into Neanderthal, and unknown archaic hominins into Denisovans. Image credit: Bob Wilder, University at Buffalo.
Roughly 50,000 years ago, a group of humans migrated out of Africa and interbred with Neanderthals in Eurasia.
But that’s not the only time that our ancient human ancestors and their relatives swapped DNA.
The sequencing of genomes from Neanderthals and Denisovans has yielded many new insights into these interbreeding 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 came from other species, even if that gene flow occurred thousands of years ago and came from an unknown source.
The scientists used the algorithm, named ARGweaver-D, to look at genomes from two Neanderthals, a Denisovan and two African humans.
They found evidence that 3% of the Neanderthal genome came from ancient humans, and estimate that the interbreeding occurred between 200,000 and 300,000 years ago.
Furthermore, 1% of the Denisovan genome likely came from an unknown and more distant relative, possibly Homo erectus, and about 15% of these archaic regions may have been passed down to modern humans who are alive today.
The findings confirm previously reported cases of gene flow between ancient humans and their relatives, and also point to new instances of interbreeding.
A portrait of a juvenile female Denisovan 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 whenever two groups overlapped in time and space,” the authors said.
The ARGweaver-D algorithm solves the challenging problem of identifying tiny remnants of gene flow that occurred hundreds of thousands of years ago, when only a handful of ancient genomes are available.
This algorithm may also be useful for studying gene flow in other species where interbreeding occurred, such as in wolves and dogs.
“What I think is exciting about this work is that it demonstrates what you can learn about deep human history by jointly reconstructing the full evolutionary history of a collection of sequences from both modern humans and archaic hominins,” Dr. Siepel said.
“The ARGweaver-D algorithm is able to reach back further in time than any other computational method I’ve seen. It seems to be especially powerful for detecting ancient introgression.”
_____
M.J. Hubisz et al. 2020. Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph. PLoS Genet 16 (8): e1008895; doi: 10.1371/journal.pgen.1008895
