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Neanderthal, Ancient Human Genomes Provide Insights on Human Traits, Social Structures

NEW YORK (GenomeWeb) – Several new studies are offering a clearer look at the genetics of ancient humans and Neanderthals, along with Neanderthal contributions to non-disease features and behaviors in present-day human populations with a history of archaic hominin admixture.

For a study appearing online today in the American Journal of Human Genetics, Max Planck Institute for Evolutionary Anthropology researchers Janet Kelso and Michael Dannemann delved into non-disease phenotypes found in modern humans that can be traced back to sequences inherited from Neanderthals.

Using array-based genotyping profiles, physical trait descriptions, and self-reported diet and behavioral information for 112,000 UK Biobank pilot study participants, the researchers characterized Neanderthal sequences that seem to have been under positive selection in human genomes in the time since modern human-Neanderthal mixing and mingling outside of Africa.

Archaic alleles turned up in regions associations with everything from height to sleep patterns, mood, and smoking status, the duo found. Introgressed Neanderthal alleles were particularly prevalent in parts of the genome influencing skin tone and hair color, the authors reported, though they noted that "archaic and non-archaic variants contribute equally to skin and hair phenotypes."

Further, the Neanderthal variants that persist in present-day human genomes were associated with both light and dark hair colors and skin tones in the study, hinting that Neanderthals "might have differed in their hair and skin tones, much as people now do," Danneman said in a statement.

Another study, published today in Science, explored the links between Neanderthals sequences and human disease. Max Planck Institute for Evolutionary Anthropology researcher Svante Pääbo led an international team that sequenced and started analyzing the genome of a 50,000-year-old female Neanderthal from the Vindija Cave in Croatia. Using a dozen DNA samples from a Vindija Neanderthal bone fragment, the researchers produced a genome sequence covering the 1.8 billion bases of the Neanderthal genome at an average depth of 30-fold coverage. They then compared the sequence to a high-coverage genome sequence for the Altai Neanderthal from southern Siberia that was published online in Nature in late 2013.

Past studies have pointed to Neanderthal-inherited sequences in parts of the human genome related to immunity and diseases such as depression and heart disease. Others have considered the role that these sequences may play in environmental adaptations, including a 2016 study in Current Biology reporting ties between archaic hominin species and both immunity and skin pigmentation. Researchers estimate that, on average, Neanderthal alleles have frequencies of up to 2 percent in non-African genomes.

By comparing the high-coverage Vindija and Altai Neanderthal genomes, the Max Planck team picked up roughly 1.3 variants for every 10,000 bases of genome sequence. Both Neanderthal genomes were marked by relatively low rates of heterozygosity, pointing to small populations. But the Altai Neanderthal showed long stretches of homozygosity that seemed to stem from inbreeding that was absent in the Vindija Neanderthal.

The researchers estimated that some 10 to 20 percent of the Neanderthal genome is present in current human genomes in one way or another. In the non-African populations outside of Oceania, some 1.8 percent to 2.6 percent of human genome sequences stem from Neanderthal ancestors, on average, though they noted that the proportion of Neanderthal ancestry was slightly higher in East Asian populations than in populations from western Eurasia.

It may now be possible to find even more Neanderthal variants contributing to human features and conditions, the researchers reported, since the newly sequenced Neanderthal from Croatia appeared to share slightly closer genetic ties to the Neanderthal population that passed DNA down to humans.

For a more modern human-focused Science study, Eske Willerslev and his colleagues from the University of Copenhagen, the University of Cambridge, and elsewhere sequenced four individuals from an Upper Paleolithic hunter-gatherer population that lived in what is now Russia. They sequenced the genome from the 34,000-year-old Sunghir archeological site to average depths ranging from 1.11- to 10.75-fold apiece.

Despite the small population size estimated for the hunter-gatherer population, the team did not see signs of excess relatedness between the forager individuals, consistent with early adoption of social structures that discourage inbreeding in this hunter-gatherer group.

"Although the number of ancient genomes available remains small," the authors wrote, "the differences in inbreeding levels, and thus group organization, between the [Upper Paleolithic foragers] and Neanderthals are intriguing."

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