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Genome of Ancient East Asian Individual Suggests Population Admixture, Denisovan Ties

NEW YORK – Researchers have uncovered Denisovan-origin ancestry within the genomes of early East Asian individuals. 

In 2006, miners in the Salkhit Valley in eastern Mongolia uncovered a skullcap initially dubbed Mongolanthropus that was then thought to belong to a Neanderthal or Homo erectus. However, radiocarbon dating and mitochondrial DNA analysis suggested the about 34,000-year-old skull bone came from a modern human.

Researchers from the Max Planck Institute for Evolutionary Anthropology have now sequenced the nuclear genome of the sample to find that the Salkhit individual was a female modern human who is closely related to present-day East Eurasians and Native Americans. She and another early East Asian individual who had been discovered in the Tianyuan Cave outside Beijing additionally carried alleles from Neanderthals and Densiovans, as the researchers reported Thursday in Science. But they noted that the two ancient individuals differed in the number of alleles they shared with western Eurasians, likely due to admixture with ancient Siberians in the Salkhit individual's lineage.

"This is direct evidence that modern human communities in East Asia were already quite cosmopolitan earlier than 34,000 years ago," first author Diyendo Massilani from Max Planck said in a statement. "This rare specimen shows that migration and interactions among populations across Eurasia happened frequently already some 35,000 years ago." 

He and his colleagues generated shotgun sequencing data for six DNA libraries prepared from the skullcap bone fragment. Between 0.6 percent and 5.6 percent of the DNA fragments from the libraries mapped uniquely to the human reference genome. 

However, they estimated a high level of contamination with present-day human DNA among some of the libraries. Because of this, the researchers restricted their analyses to stretches of DNA with evidence of cytosine deamination — a hallmark of ancient DNA — and lower contamination estimates.  

After confirming the Salkhit individual was a modern human, they compared the individual's genome to those of other modern humans older than 20,000 years as well as to 131 present-day populations. 

Similar to the about 40,000-year-old Tianyuan individual, the Salkhit individual is more closely related to present-day East Eurasians and Native Americans than to West Eurasians. The Tianyuan individual and the Salkhit individual are equally related to present-day East Eurasians and Native Americans, but differ in their relation to West Eurasians; West Eurasians, they found, are more closely related to the Salkhit individual.

In addition, the Salkhit individual shares as many alleles with the 31,000-year-old Yana individuals from northeastern Siberia as she does with the Tianyuan individual. However, the Yana individuals and the Tianyuan individual share fewer alleles with each other than with the Salkhit individual, suggesting there was gene flow between early East Asian and Siberian populations following the divergence of East and West Eurasians.

Further, the Tianyuan individual and the Salkhit individual share more alleles with a 35,000-year-old Belgian individual than to other Europeans — though, the Salkhit individual shares even more allele with the ancient Belgian than the Tianyuan individual, leading the researchers to suggests there was likely gene flow bringing West Euarian ancestry back into the ancestors of the Salkhit individual through a Siberian population. They estimated that the Salkhit individual derives about 75 percent of her ancestry from a Tianyuan-related population and about 25 percent from a Yana-related population.

The researchers further estimated the Salkhit individual derived about 1.7 percent of her ancestry from Neanderthals and an even smaller portion from Denisovans. Still, when the researchers analyzed the Denisovan-origin DNA in the Salkhit individual, they found it was similar to the Denisovan DNA fragments found in the Tianyuan individual, but differed from the Denisovan ancestry found among Oceanians. Scientists had previously suspected that there were at least two instances of Denisovan introgression into modern humans. 

"This supports a model of multiple independent mixture events between Denisovans and modern humans," Massilani adds.

A separate paper also appearing in Science additionally suggested that Denisovans may have been more widespread across Asia than previously thought. An international team of researchers uncovered Denisovan DNA within sediments in a cave on the Tibetan Plateau, while previous Denisovan samples have hailed from a cave in Siberia.

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