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Ancient East Asian Genomes Indicate Genetic Continuity in Region

NEW YORK (GenomeWeb) – An analysis of two ancient genomes from East Asia indicates a level of genetic continuity between hunter-gatherers and modern populations in the region.

An international team of researchers sequenced DNA recovered from two 8,000-year-old human skeletons buried near the border of Russia and Korea. As the group reported today in Science Advances, a comparison of those sequences to modern populations in the region found that the Neolithic genomes were highly similar to those of the traditional Ulchi fishermen who live in the region, as well as to modern Koreans and Japanese.

"Genetically speaking, the populations across northern East Asia have changed very little for around eight millennia," senior author Andrea Manica from the University of Cambridge said in a statement. "Once we accounted for some local intermingling, the Ulchi and the ancient hunter-gatherers appeared to be almost the same population from a genetic point of view, even though there are thousands of years between them."

This is in contrast to what occurred in Europe, Manica and his colleagues noted. There, waves of migration led to the replacement of early hunter-gatherer populations.

The researchers sequenced five early Neolithic samples from the Devil's Gate cave to low coverage before focusing on the two samples, both female, with the highest coverage. These samples dated back some 7,700 years to a time when the people living there were hunter-fisher-gatherers.

They assigned the mitochondrial genome of one sample to haplogroup D4, which is found among present-day East Asian populations. The mitochondrial genome of the other sample could only be resolved to the M branch, of which D4 is a member.

Despite the low — 0.005X and 0.001X — coverage of the samples, the researchers could tease out some likely phenotypes from SNPs they identified. For the higher coverage sample, they noted that she likely had brown eyes and thick, straight hair. She was also likely lactose intolerant and unlikely to have the alcohol flush response.

Manica and his colleagues compared both Devil's Gate genomes to those from modern-day Eurasians as well as to published ancient genomes. Using both principal components analysis and the unsupervised clustering ADMIXTURE approach, the Devil's Gate genomes fell within the cluster of modern people living near that site. Outgroup f3 statistics likewise showed that modern populations in the region exhibited the greatest affinity with the ancient samples. That affinity declined with increasing geographical distance, they noted.

In particular, the Ulchi — who live near Devil's Gate — were the most closely related. They were followed by the Oroqen and Hezhen, who, like the Ulchi, are Tungusic speakers from the Amur Basin. Modern Koreans and Japanese were also related.

To the researchers, this indicated that there has been genetic continuity, and perhaps phenotypic continuity, in this region. They modeled the Ulchi as a mixture of Devil's Gate and modern populations using admixture f3 statistics to find that the Ulchi were best represented by Devil's Gate alone. However, analysis using D statistics noted that the Ulchi had some affinity with other modern populations, suggesting that the continuity wasn't absolute, though still quite high. The Ulchi, the researchers said, are likely the descendants of the Devil's Gate or a closely related population.

This contrasts with the waves of migration that occurred in Europe, they noted. There, hunter-gatherers were replaced by farmers from the Levant, who were followed by horse-riders from Central Asia. Each influx of migrants there appeared to be driven by technological advances.

These findings instead indicate that the hunter-gatherers in this region of East Asia added additional food-producing practices to their original lifestyle.

"Our work suggests that these groups form a strong genetic lineage descending directly from the early Neolithic hunter-gatherers who inhabited the same region thousands of years previously," lead author Veronika Siska, also from Cambridge, said in a statement.