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Algorithm Points to Complex Hominin Mixing History

NEW YORK – The Denisovan genome contains "super-archaic" sequences from an unknown hominin, while the Neanderthal genome contains sequences stemming from human introgression deep in hominin history, according to a new analysis by investigators at Cornell University and the Cold Spring Harbor Laboratory.

In a statement, Adam Siepel, a quantitative biology researcher at CSHL, suggested that the study "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."

For a paper published in PLOS Genetics on Thursday, Siepel and his colleagues searched for signs of past introgression in hominins using genome sequences from humans, Neanderthals, and Denisovans utilizing an updated version of an ancestral recombination graph (ARG)-based Bayesian algorithm known as ARGweaver-D.

Along with signs of human introgression in the Neanderthal genome, which appeared to go back some 200,000 to 300,000 years, the team's results pointed to sequences from an unknown ancient archaic hominin that left DNA peppered across around 1 percent of the Denisovan genome.

Based on these and other findings, Siepel called ARGweaver-D "especially powerful for detecting ancient introgression."

The algorithm, an extension of ARGweaver, makes it possible to explore relationships across the genome for related groups or sub-species using ancestral recombination graph patterns, the team explained, bringing in specific demographic data ranging from population splits or size shifts to migration events.

"This Bayesian algorithm probabilistically samples ancestral recombination graphs (ARGs) that specify not only tree topologies and branch lengths along the genome, but also indicate migrant lineages," the authors wrote, noting that these ARGs "can therefore be parsed to produce probabilities of introgression along the genome."

After using ARGweaver-D to find Neanderthal introgression into the human genome in simulated datasets, the researchers applied similar predictions to pick up archaic hominin introgression in genome sequences for individuals from French Basque and Papuan populations that were missing in individuals from Khomani San and Mandenka populations in Africa.

From there, the team turned its attention to the more distant mixing events in the hominin family tree, analyzing whole-genome sequence data for two present-day African individuals profiled through the Simons Genome Diversity Panel (SGDP), along with the Altai Neanderthal genome, a Vindija Neanderthal genome, and a genome sequence generated for a Denisovan individual.

That analysis unearthed human introgression over roughly 3 percent of the genome in both the Altai and the Vindija Neanderthals, while such introgression was predicted at just 0.37 percent of Denisovan genome sites, within the range of false-positive estimates. But a so-called "super-archaic hominin" did seem to have a more pronounced history of introgression in the Denisovan, leaving sequences at around 1 percent of sites in the Denisovan genome.

Some 15 percent of those sequences also seemed to land in the genomes of modern human populations that mixed with Denisovans, the researchers reported, prompting speculation around the potential identity of the unknown super-archaic hominin.

"While these fractions are too small to draw strong conclusions, it is plausible that if Homo erectus mixed with the Denisovans, they may have also mixed with Neanderthals, perhaps in the Middle East; or perhaps DNA passed from Homo erectus to Neanderthal through the Denisovans," the authors suggested. "Altogether, given the number of gene flow events now documented among ancient hominins, it may be reasonable to assume that genetic exchange was likely whenever two groups overlapped in time and space."

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