Refining models of archaic admixture in Eurasia with ArchaicSeeker 2.0

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Yuan, Kai, Ni, Xumin, Liu, Chang, Pan, Yuwen, Deng, Lian, Zhang, Rui, Gao, Yang, Ge, Xueling, Liu, Jiaojiao, Ma, Xixian, Lou, Haiyi, Wu, Taoyang and Xu, Shuhua (2021) Refining models of archaic admixture in Eurasia with ArchaicSeeker 2.0. Nature Communications, 12. ISSN 2041-1723

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Abstract

We developed a method, ArchaicSeeker 2.0, to identify introgressed hominin sequences and model multiple-wave admixture. The new method enabled us to discern two waves of introgression from both Denisovan-like and Neanderthal-like hominins in present-day Eurasian populations and an ancient Siberian individual. We estimated that an early Denisovan-like introgression occurred in Eurasia around 118.8–94.0 thousand years ago (kya). In contrast, we detected only one single episode of Denisovan-like admixture in indigenous peoples eastern to the Wallace-Line. Modeling ancient admixtures suggested an early dispersal of modern humans throughout Asia before the Toba volcanic super-eruption 74 kya, predating the initial peopling of Asia as proposed by the traditional Out-of-Africa model. Survived archaic sequences are involved in various phenotypes including immune and body mass (e.g., ZNF169), cardiovascular and lung function (e.g., HHAT), UV response and carbohydrate metabolism (e.g., HYAL1/HYAL2/HYAL3), while “archaic deserts” are enriched with genes associated with skin development and keratinization.

Item Type: Article
Uncontrolled Keywords: chemistry(all),biochemistry, genetics and molecular biology(all),physics and astronomy(all) ,/dk/atira/pure/subjectarea/asjc/1600
Faculty \ School: Faculty of Science > School of Computing Sciences
UEA Research Groups: Faculty of Science > Research Groups > Computational Biology
Faculty of Science > Research Centres > Centre for Ecology, Evolution and Conservation
Faculty of Science > Research Groups > Data Science and AI
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Depositing User: LivePure Connector
Date Deposited: 09 Oct 2021 01:03
Last Modified: 18 Oct 2025 04:34
URI: https://ueaeprints.uea.ac.uk/id/eprint/81624
DOI: 10.1038/s41467-021-26503-5

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