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Researchers Sequence Genome of Individual With Neanderthal Mother, Denisovan Father

NEW YORK (GenomeWeb) – Researchers have sequenced the genome of an ancient individual who had a Neanderthal mother and a Denisovan father.

Neanderthals and Denisovans diverged from each other about 390,000 years ago, though there has been evidence of admixture between the two ancient hominin groups after that split, just as there is evidence of admixture between Neanderthals and non-African modern humans, and between Denisovans and non-African modern humans after their lineages diverged

The Max Planck Institute for Evolutionary Anthropology's Svante Pääbo and his colleagues sequenced the genome of an individual from whom they recovered a fragment of a long bone in Denisova Cave in Siberia. Over the years, both Neanderthals and Denisovans lived in the vicinity of the cave. But this individual, they reported today in Nature, was a first-generation Neanderthal-Denisovan offspring.

"We knew from previous studies that Neanderthals and Denisovans must have occasionally had children together," co-first author and Max Planck researcher Viviane Slon said in a statement. "But I never thought we would be so lucky as to find an actual offspring of the two groups."

This bone fragment, dubbed Denisova 11, was excavated and found to be more than 50,000 years old. It was determined by collagen peptide mass fingerprinting to be of hominin origin and its mitochondrial DNA was found to be of Neanderthal origin. Analysis of the bone indicated the individual it belonged to was at least 13 years old at death.

After six DNA extractions to make 10 DNA libraries, the researchers sequenced the Denisova 11 genome to a mean 2.6-fold coverage on the Illumina MiSeq or HiSeq 2500 platforms. Based on the coverage of the X chromosome as compared to the autosomes, they concluded Denisova 11 was female. Using three different methods, the researchers estimated that contaminating present-day human DNA made up 1.7 percent of their data at most.

When they compared the Denisova 11 genome to Neanderthal and Denisovan genomes, the researchers found that 38.6 percent of fragments from Denisova 11 carried Neanderthal alleles and that 42.3 percent of fragments carried Denisovan ones. This suggests that both ancient hominin groups contributed to Denisova 11's ancestry about equally.

A few scenarios could have resulted in such a mix, the researchers said. Denisova 11 could have belonged to a population with mixed Neanderthal and Denisovan ancestry or she could have had one parent from each ancient hominin group. But based on analyses of heterozygosity and the distribution of Neanderthal- or Denisovan-like alleles within the Denisova 11 genome, the researchers found that the inherited allele pattern in Denisova 11 best matched what would be expected in a first-generation Neanderthal-Denisovan offspring.

Denisova 11 shares derived alleles seen in the Altai Neanderthal genome 12.4 percent of the time, while she shares those in the Vindija 33.19 Neanderthal genome 19.6 percent of the time. This suggested to the researchers that her mother came from a Neanderthal population that was more closely related to Vindija 33.19 than the Altai Neanderthal, even though Vindija 33.19 lived some 20,000 years later in a different part of Europe.

The researchers also reported that Denisova 11's Denisovan father had had a Neanderthal ancestor about 300 generations to 600 generations before his time. However, this paternal Neanderthal ancestry came from a different group than the one that supplied Denisova 11's maternal Neanderthal ancestry.

All in all, this suggested to the researchers that mixing among archaic and modern hominin groups was likely common when and where the populations overlapped.

"It is striking that we find this Neanderthal/Denisovan child among the handful of ancient individuals whose genomes have been sequenced," Pääbo added in a statement. "Neanderthals and Denisovans may not have had many opportunities to meet. But when they did, they must have mated frequently — much more so than we previously thought."