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Archaic Introgression Patterns Point to Three Denisovan Lineages

NEW YORK (GenomeWeb) – Two distinct Denisovan lineages interbred with the ancestors of present-day populations in Papua New Guinea, according to new research, which suggests South Asia may have been the heart of the archaic hominin's historical region.

"People used to think that Denisovans lived on the Asian mainland and far to the north," senior and corresponding author Murray Cox, a statistics and bioinformatics researcher at Massey University, said in a statement. "Our work instead shows that the center of archaic diversity was not in Europe or the frozen north, but instead in tropical Asia."

In a paper published online today in Cell, an international team led by investigators in Singapore and New Zealand scrutinized genome sequences for 161 participants in the Indonesian Genome Diversity Project, representing more than a dozen island populations in Island Southeast Asia and Papua New Guinea. With these data — together with more than 300 human genomes from other parts of the world and the Altai Denisovan genome that was sequenced by an international team in 2010 — they focused in on modern genome sequences stemming from Denisovan introgression.

The team then compared the Denisovan haplotype blocks that are introgressed in populations from these regions with those in the Denisovan reference genome, identifying three Denisovan lineages that appear to have split from one another between at least 250,000 years ago and more than 350,000 years ago.

In particular, the researchers reported that present-day Papuans carry ancestral DNA from at least two distinct Denisovan lineages that diverged roughly 363,000 years ago, including a lineage that left traces of introgressed DNA exclusively in Oceania. Remnants of a third Denisovan lineage, which branched off around 283,000 years ago and includes the Altai Denisovan, persist in some modern East Asians.

"The genetic diversity within the Denisovan clade is consistent with their deep divergence and separation into at least three geographically disparate branches, with one contributing an introgression signal in Oceania and to a lesser extent across Asia, another apparently restricted to New Guinea and nearby islands, and a third in East Asia and Siberia," Cox and his co-authors wrote.

Just as Denisovan and Neanderthal DNA has been used to retrace ancient human migrations, these new results again demonstrate the archaic hominin insights that can be gleaned from contemporary human genomes. In a 2018 study in Cell, a team from the University of Washington and Princeton University proposed at least two Denisovan populations, based on introgression profiles in genome sequences from more than 5,600 individuals in Eurasia and Oceania.

"The emerging picture suggests that far from moving into sparsely inhabited country, modern humans experienced repeated and persistent interactions as they expanded out of Africa into this highly structured archaic landscape across Eurasia," the authors concluded. "This genetic contact yielded a rich legacy, including hundreds of gene variants that continue to contribute to the adaptive success of anatomically modern humans today."