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J Bioinform Comput Biol. 2018 Apr;16(2):1840011. doi: 10.1142/S0219720018400115.

Neanderthal and Denisovan ancestry in Papuans: A functional study.

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* St. Petersburg State University, Institute of Translational Biomedicine, St. Petersburg, Russia.
† Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute for Science and Technology, Moscow, Russia.
‡ Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.
§ Faculty of Computer Science, National Research University - Higher School of Economics, Moscow, Russia.
¶ Department of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia.


Sequencing of complete nuclear genomes of Neanderthal and Denisovan stimulated studies about their relationship with modern humans demonstrating, in particular, that DNA alleles from both Neanderthal and Denisovan genomes are present in genomes of modern humans. The Papuan genome is a unique object because it contains both Neanderthal and Denisovan alleles. Here, we have shown that the Papuan genomes contain different gene functional groups inherited from each of the ancient people. The Papuan genomes demonstrate a relative prevalence of Neanderthal alleles in genes responsible for the regulation of transcription and neurogenesis. The enrichment of specific functional groups with Denisovan alleles is less pronounced; these groups are responsible for bone and tissue remodeling. This analysis shows that introgression of alleles from Neanderthals and Denisovans to Papuans occurred independently and retention of these alleles may carry specific adaptive advantages.


D-statistic; Denisovan; GSEA; Neanderthal; Papuan; Yoruba; neurogenesis; transcription factor


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