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The history and evolution of the Denisovan-EPAS1 haplotype in Tibetans

View ORCID ProfileXinjun Zhang, View ORCID ProfileKelsey Witt, View ORCID ProfileAmy Ko, View ORCID ProfileKai Yuan, Shuhua Xu, View ORCID ProfileRasmus Nielsen, View ORCID ProfileEmilia Huerta-Sanchez
doi: https://doi.org/10.1101/2020.10.01.323113
Xinjun Zhang
1Department of Ecology and Evolutionary Biology, University of California Los Angeles
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Kelsey Witt
2Department of Ecology and Evolutionary Biology, Brown University
3Center for Computational Molecular Biology, Brown University
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Amy Ko
4Department of Integrative Biology, University of California Berkeley
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Kai Yuan
5Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
6School of Life Science and Technology, Shanghai Technology University, Shanghai, China
7Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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Shuhua Xu
5Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
6School of Life Science and Technology, Shanghai Technology University, Shanghai, China
7Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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Rasmus Nielsen
4Department of Integrative Biology, University of California Berkeley
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Emilia Huerta-Sanchez
2Department of Ecology and Evolutionary Biology, Brown University
3Center for Computational Molecular Biology, Brown University
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  • For correspondence: emilia_huerta-sanchez@brown.edu
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Abstract

Recent studies suggest that admixture with archaic hominins played an important role in facilitating biological adaptations to new environments. For example, interbreeding with Denisovans facilitated the adaptation to high altitude environments on the Tibetan Plateau. Specifically, the EPAS1 gene, a transcription factor that regulates the response to hypoxia, exhibits strong signatures of both positive selection and introgression from Denisovans in Tibetan individuals. Interestingly, despite being geographically closer to the Denisova cave, East Asian populations do not harbor as much Denisovan ancestry as populations from Melanesia. Recently, two studies have suggested two independent waves of Denisovan admixture into East Asians, one of which is shared with South Asians and Oceanians. Here we leverage data from EPAS1 in 78 Tibetan individuals to interrogate which of these two introgression events introduced the EPAS1 beneficial sequence into the ancestral population of Tibetans, and we use the distribution of introgressed segment lengths at this locus to infer the timing of the introgression and selection event. We find that the introgression event unique to East Asians most likely introduced the beneficial haplotype into the ancestral population of Tibetans around 43,000 (15,700–60,000) years ago, and selection started 12,000 (1,925-50,000) years ago. Our estimates suggest that one of the most convincing examples of adaptive introgression is in fact selection acting on standing archaic variation.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 02, 2020.
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The history and evolution of the Denisovan-EPAS1 haplotype in Tibetans
Xinjun Zhang, Kelsey Witt, Amy Ko, Kai Yuan, Shuhua Xu, Rasmus Nielsen, Emilia Huerta-Sanchez
bioRxiv 2020.10.01.323113; doi: https://doi.org/10.1101/2020.10.01.323113
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The history and evolution of the Denisovan-EPAS1 haplotype in Tibetans
Xinjun Zhang, Kelsey Witt, Amy Ko, Kai Yuan, Shuhua Xu, Rasmus Nielsen, Emilia Huerta-Sanchez
bioRxiv 2020.10.01.323113; doi: https://doi.org/10.1101/2020.10.01.323113

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