An international team of researchers has sequenced and analyzed the genome of an 80,000-year-old Neanderthal woman from Chagyrskaya Cave in the Altai Mountains, Siberia. The genome provides insights into Neanderthal population structure and history and allows the identification of genomic features unique to these human cousins.
A group of Neanderthals in a cave. Image credit: Tyler B. Tretsven.
Neanderthals and Denisovans are the closest evolutionary relatives of modern humans. Analyses of their genomes showed that they contributed genetically to present-day people outside sub-Saharan Africa.
However, the genomes of only two Neanderthals and one Denisovan have been sequenced to high quality.
One of these Neanderthal genomes was from an individual (Vindija 33) found in Vindija Cave in Croatia, whereas the other Neanderthal genome (Denisova 5 or the Altai Neanderthal) and the Denisovan genome (Denisova 3) both came from specimens discovered in Denisova Cave in the Altai Mountains.
In the new research, Dr. Fabrizio Mafessoni from the Max Planck Institute for Evolutionary Anthropology and colleagues sequenced the genome from a Neanderthal phalanx (Chagyrskaya 8) found in 2011 at Chagyrskaya Cave, which is located about 100 km away from Denisova Cave.
The researchers found that Chagyrskaya 8 lived 80,000 years ago, about 30,000 years after the Denisova 5 Neanderthal and 30,000 years before the Vindija 33 Neanderthal.
They also found that the Chagyrskaya Neanderthal was a female and that she was more closely related to Vindija 33 and other Neanderthals in western Eurasia than to Denisova 5 who lived earlier in the Altai Mountains.
“Chagyrskaya 8 is thus related to Neanderthal populations that moved east sometime between 120,000 and 80,000 years ago,” they said.
“Interestingly, the artifacts found in Chagyrskaya Cave show similarities to artifact collections in central and eastern Europe, suggesting that Neanderthal populations coming from western Eurasia to Siberia may have brought their material culture with them.”
“Some of these incoming Neanderthals encountered local Denisovan populations, as shown by Denisova 11, who had a Denisovan father and a Neanderthal mother related to the population in which Chagyrskaya 8 lived.”
From the variation in the genome, the authors estimated that Chagyrskaya 8 and other Siberian Neanderthals lived in relatively isolated populations of less than 60 individuals.
In contrast, a Neanderthal from Europe, a Denisovan from the Altai Mountains, and ancient modern humans seem to have lived in populations of larger sizes.
When the team analyzed the Chagyrskaya 8 genome together with two previously sequenced Neanderthal genomes, they found that genes expressed in a part of the brain called striatum may have changed especially much, suggesting that the striatum may have evolved unique functions in Neanderthals.
“We found that genes expressed in the striatum during adolescence showed more changes that altered the resulting amino acid when compared to other areas of the brain,” Dr. Mafessoni said.
“The results suggest that the striatum — a part of the brain which coordinates various aspects of cognition, including planning, decision-making, motivation and reward perception — may have played a unique role in Neanderthals.”
The findings were published in the Proceedings of the National Academy of Sciences.
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Fabrizio Mafessoni et al. A high-coverage Neandertal genome from Chagyrskaya Cave. PNAS, published online June 16, 2020; doi: 10.1073/pnas.2004944117
