A high-coverage Neandertal genome from Chagyrskaya Cave

Mafessoni, Fabrizio; Grote, Steffi; de Filippo, Cesare; Slon, Viviane; Kolobova, Kseniya A.; Viola, Bence; Markin, Sergey V.; Chintalapati, Manjusha; Peyrégne, Stéphane; Skov, Laurits; Skoglund, Pontus; Krivoshapkin, Andrey I.; Derevianko, Anatoly P.; Meyer, Matthias; Kelso, Janet; Peter, Benjamin; Prüfer, Kay; Pääbo, Svante

doi:10.1073/pnas.2004944117

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A high-coverage Neandertal genome from Chagyrskaya Cave

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Mafessoni, Fabrizio
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

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Grote, Steffi
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

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de Filippo, Cesare
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

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Slon, Viviane
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

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Chintalapati, Manjusha
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

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Peyrégne, Stéphane
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

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Skov, Laurits
Genetic Diversity through Space and Time, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

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Meyer, Matthias
Advanced DNA Sequencing Techniques, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

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Kelso, Janet
The Minerva Research Group for Bioinformatics, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

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Peter, Benjamin
Genetic Diversity through Space and Time, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

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Prüfer, Kay
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

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Pääbo, Svante
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
Neandertals and more, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

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Citation

Mafessoni, F., Grote, S., de Filippo, C., Slon, V., Kolobova, K. A., Viola, B., et al. (2020). A high-coverage Neandertal genome from Chagyrskaya Cave. Proceedings of the National Academy of Sciences, 117(26), 15132-15136. doi:10.1073/pnas.2004944117.

Cite as: https://hdl.handle.net/21.11116/0000-0006-9077-1

Abstract

We present the third high-quality genome to be determined from a Neandertal. Patterns of variation in the genome suggest that her ancestors lived in relatively isolated populations of less than 60 individuals. When we analyze this genome together with two previously sequenced Neandertal genomes, we find that genes expressed in the striatum of the brain may have changed especially much, suggesting that the striatum may have evolved unique functions in Neandertals.We sequenced the genome of a Neandertal from Chagyrskaya Cave in the Altai Mountains, Russia, to 27-fold genomic coverage. We show that this Neandertal was a female and that she was more related to Neandertals in western Eurasia [Prü}fer et al., Science 358, 655{–}658 (2017); Hajdinjak et al., Nature 555, 652{–}656 (2018)] than to Neandertals who lived earlier in Denisova Cave [Pr{ü}fer et al., Nature 505, 43{–49 (2014)], which is located about 100 km away. About 12.9% of the Chagyrskaya genome is spanned by homozygous regions that are between 2.5 and 10 centiMorgans (cM) long. This is consistent with the fact that Siberian Neandertals lived in relatively isolated populations of less than 60 individuals. In contrast, a Neandertal from Europe, a Denisovan from the Altai Mountains, and ancient modern humans seem to have lived in populations of larger sizes. The availability of three Neandertal genomes of high quality allows a view of genetic features that were unique to Neandertals and that are likely to have been at high frequency among them. We find that genes highly expressed in the striatum in the basal ganglia of the brain carry more amino-acid-changing substitutions than genes expressed elsewhere in the brain, suggesting that the striatum may have evolved unique functions in Neandertals.