Research output: Contribution to journal › Article › peer-review
Exome Sequencing Provides Evidence of Polygenic Adaptation to a Fat-Rich Animal Diet in Indigenous Siberian Populations. / Hsieh, Ping Hsun; Hallmark, Brian; Watkins, Joseph et al.
In: Molecular Biology and Evolution, Vol. 34, No. 11, 01.11.2017, p. 2913-2926.Research output: Contribution to journal › Article › peer-review
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TY - JOUR
T1 - Exome Sequencing Provides Evidence of Polygenic Adaptation to a Fat-Rich Animal Diet in Indigenous Siberian Populations
AU - Hsieh, Ping Hsun
AU - Hallmark, Brian
AU - Watkins, Joseph
AU - Karafet, Tatiana M.
AU - Osipova, Ludmila P.
AU - Gutenkunst, Ryan N.
AU - Hammer, Michael F.
N1 - © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
PY - 2017/11/1
Y1 - 2017/11/1
N2 - Siberia 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 ∼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.
AB - Siberia 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 ∼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.
KW - adaptation
KW - diet
KW - extreme climates
KW - polygenic selection
KW - Siberia
KW - Extreme climates
KW - Diet
KW - Polygenic selection
KW - Adaptation
KW - DNA, Mitochondrial/genetics
KW - Humans
KW - Phylogeny
KW - Genetic Variation/genetics
KW - Gene Flow/genetics
KW - Asian Continental Ancestry Group/genetics
KW - Dietary Fats
KW - Exome/genetics
KW - Acclimatization/genetics
KW - Adaptation, Biological/genetics
KW - Demography/methods
KW - Multifactorial Inheritance/genetics
KW - Gene Frequency/genetics
KW - Whole Exome Sequencing/methods
KW - Biological Evolution
KW - Ethnic Groups/genetics
KW - Alleles
KW - Genetics, Population/methods
KW - DEMOGRAPHIC INFERENCE
KW - MUTATION-RATE
KW - HIGH-ALTITUDE
KW - ACID-METABOLISM
KW - HUMAN-EVOLUTION
KW - HUNTER-GATHERER
KW - GENOME SEQUENCE
KW - GENETIC-VARIATION
KW - NATURAL-SELECTION
KW - HISTORY
UR - http://www.scopus.com/inward/record.url?scp=85044162688&partnerID=8YFLogxK
U2 - 10.1093/molbev/msx226
DO - 10.1093/molbev/msx226
M3 - Article
C2 - 28962010
AN - SCOPUS:85044162688
VL - 34
SP - 2913
EP - 2926
JO - Molecular Biology and Evolution
JF - Molecular Biology and Evolution
SN - 0737-4038
IS - 11
ER -
ID: 12179215