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Team Characterizing DNA from Ancient Human with Recent Neanderthal Ancestry

COLD SPRING HARBOR, NY (GenomeWeb) – An international team has discovered recent Neanderthal ancestry in an ancient jaw sample from a modern human who lived in present-day Romania roughly 37,000 to 42,000 years ago, attendees heard at the Biology of Genomes meeting.

The finding clashes with the notion that most mixing between modern humans and Neanderthals occurred in the Middle East shortly after humans migrated out of Africa, explained Qiaomei Fu, a researcher affiliated with the Max Planck Institute for Evolutionary Anthropology, the Chinese Academy of Sciences, and Harvard Medical School. Fu presented the work during a session on evolutionary and non-human genomics here today.

Instead, genetic patterns in the ancient human hint at the potential of admixture between modern humans and Neanderthals in Europe that may have persisted until not long before Neanderthals disappeared from the continent some 40,000 years ago.

Past studies have uncovered gene flow from Neanderthals into all tested modern human populations outside of Africa, with non-African individuals carrying between 1 percent and 4 percent Neanderthal sequences in their genomes, on average. The details of this modern human-Neanderthal mixing remain somewhat murky, though it's believed that the archaic and modern human groups first encountered each other not long after humans migrated out of Africa.

To flesh out the details of these interactions, researchers are tapping into fossils samples found outside of Africa after this time, between about 100,000 years ago and 30,000 years ago, Fu noted.

In this case, she and her colleagues focused on DNA from a mandible found at the Pestera cu Oase site in Romania, which contained relatively low levels of endogenous DNA, pronounced DNA degradation, and a large proportion of microbial contaminants that interfered with attempts to directly shotgun sequence the ancient human.

To get around such complications, the team turned to in-solution capture, isolating ancient DNA from more than 2 million sites in the genome.

Though the individual — known as Oase 1 — was clearly human, Fu explained, the resulting sequences indicated that some 5 to 11 percent of his genome originated from Neanderthals.

To look at this in more detail, the researchers used another capture step to scrutinize more than 78,000 sites in the genome that typically differ between modern humans and Neanderthals.

From those variants, the team detected long stretches of Neanderthal DNA that had not been interrupted by admixture, suggesting the individual's Neanderthal ancestry was more recent than that of any modern human tested previously.

In particular, Fu said, roughly half of the Oase 1 individual's chromosome 12 sequence coincided with Neanderthals rather than modern humans. Based on the SNP patterns detected in the sample, the researchers estimated that the individual had a Neanderthal ancestor within the past four to six generations, pointing to later-than-anticipated admixture between Neanderthals and the modern human population to which Oase 1 belonged.

Meanwhile, comparisons between genetic variants in Oase 1 and those in present-day populations or previously sequenced ancient samples suggested that the ancient individual from Romania belonged to a population that was becoming somewhat European.

But while this group resembled both European and Asian populations, Fu noted, it appears to have been far removed from agricultural populations in Europe and does not appear to have contributed much genetically to present-day human populations.

The team is continuing to tease apart patterns from genetic profiles in the sample, including genotyping analyses of the Oase 1 individual's Y chromosome, she said.