Exome Sequencing Provides Evidence of Polygenic Adaptation to a Fat-Rich Animal Diet in Indigenous Siberian Populations
Karafet, Tatiana M.
Osipova, Ludmila P.
Gutenkunst, Ryan N.
Hammer, Michael F.
AffiliationUniv Arizona, Dept Ecol & Evolutionary Biol
Univ Arizona, Interdisciplinary Program Stat
Univ Arizona, Dept Math
Univ Arizona, ARL Div Biotechnol
Univ Arizona, Dept Mol & Cellular Biol
MetadataShow full item record
PublisherOXFORD UNIV PRESS
CitationPingHsun Hsieh, Brian Hallmark, Joseph Watkins, Tatiana M. Karafet, Ludmila P. Osipova, Ryan N. Gutenkunst, Michael F. Hammer; Exome Sequencing Provides Evidence of Polygenic Adaptation to a Fat-Rich Animal Diet in Indigenous Siberian Populations, Molecular Biology and Evolution, Volume 34, Issue 11, 1 November 2017, Pages 2913–2926, https://doi.org/10.1093/molbev/msx226
JournalMOLECULAR BIOLOGY AND EVOLUTION
Rights© The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved.
Collection InformationThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at email@example.com.
AbstractSiberia is one of the coldest environments on Earth and has great seasonal temperature variation. Long-term settlement in northern Siberia undoubtedly required biological adaptation to severe cold stress, dramatic variation in photoperiod, and limited food resources. In addition, recent archeological studies show that humans first occupied Siberia at least 45,000 years ago; yet our understanding of the demographic history of modern indigenous Siberians remains incomplete. In this study, we use whole-exome sequencing data from the Nganasans and Yakuts to infer the evolutionary history of these two indigenous Siberian populations. Recognizing the complexity of the adaptive process, we designed a model-based test to systematically search for signatures of polygenic selection. Our approach accounts for stochasticity in the demographic process and the hitchhiking effect of classic selective sweeps, as well as potential biases resulting from recombination rate and mutation rate heterogeneity. Our demographic inference shows that the Nganasans and Yakuts diverged similar to 12,000-13,000 years ago from East-Asian ancestors in a process involving continuous gene flow. Our polygenic selection scan identifies seven candidate gene sets with Siberian-specific signals. Three of these gene sets are related to diet, especially to fat metabolism, consistent with the hypothesis of adaptation to a fat-rich animal diet. Additional testing rejects the effect of hitchhiking and favors a model in which selection yields small allele frequency changes at multiple unlinked genes.
Note12 month embargo; published online: 12 September 2017
VersionFinal accepted manuscript
SponsorsNational Science Foundation [PLR-1203874, DEB-1146074]; State Research Project [0324-2016-0002]
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- Issue date: 2017 Jan
- Modes of Rapid Polygenic Adaptation.
- Authors: Jain K, Stephan W
- Issue date: 2017 Dec 1
- Genomic Evidence of Local Adaptation to Climate and Diet in Indigenous Siberians.
- Authors: Hallmark B, Karafet TM, Hsieh P, Osipova LP, Watkins JC, Hammer MF
- Issue date: 2018 Nov 14
- A Working Model of the Deep Relationships of Diverse Modern Human Genetic Lineages Outside of Africa.
- Authors: Lipson M, Reich D
- Issue date: 2017 Apr 1
- [Characteristic of the Genetic Variability of Four Polymorphic Variants (rs2069705, rs17880053, rs11126176, and rs804271) in Representative Samples of Indigenous and Alien Populations of Siberia].
- Authors: Kucher AN, Babushkina NP, Kulish EV, Makeeva OA, Bragina EY, Goncharova IA, Eremina ER, Puzyrev VP
- Issue date: 2015 Aug