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A selection pressure landscape for 870 human polygenic traits

Nature Human Behaviour volume 5, pages 1731–1743 (2021)Cite this article

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Abstract

Characterizing the natural selection of complex traits is important for understanding human evolution and both biological and pathological mechanisms. We leveraged genome-wide summary statistics for 870 polygenic traits and attempted to quantify signals of selection on traits of different forms in European ancestry across four periods in human history and evolution. We found that 88% of these traits underwent polygenic change in the past 2,000–3,000 years. Recent selection was associated with ancient selection signals in the same trait. Traits related to pigmentation, body measurement and nutritional intake exhibited strong selection signals across different time scales. Our findings are limited by our use of exclusively European data and the use of genome-wide association study data, which identify associations between genetic variants and phenotypes that may not be causal. In sum, we provide an overview of signals of selection on human polygenic traits and their characteristics across human evolution, based on a European subset of human genetic diversity. These findings could serve as a foundation for further populational and medical genetic studies.

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Fig. 1
Fig. 2: Selection pressure in the present day and in recent history.
Fig. 3: Selection pressure in recent history.
Fig. 4: Selection pressure during the pan-Neolithic period.
Fig. 5: Selection pressure analysis for humans since speciation.
Fig. 6: Relation among selection pressures at different time scales.
Fig. 7: Population-average polygenic risk score trajectory for 765 traits.
Fig. 8: Genomic architectures impacted selection pressure.

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Data availability

All GWAS summary statistics analysed in the current study could be downloaded from the public domain. All data generated in the current study could be obtained from the Supplementary Information.

Code availability

Scripts used for this study is available at https://github.com/WeiCSong/selection.

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Acknowledgements

The study was supported by National Natural Science Foundation of China (no. 81971292, G.N.L.), the Natural Science Foundation of Shanghai (no. 21ZR1428600, G.N.L.), the Program for Professor of Special Appointment (Eastern Scholar) at Shanghai Institutions of Higher Learning (grant no. 1610000043, G.N.L.) and the Interdisciplinary Program of Shanghai Jiao Tong University (no. YG2019QNA59, G.N.L.). The authors thank all researchers and consortia that share their GWAS summary statistics with the scientific community. W.S. thanks J. Song for his inspiration on this study.

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Author notes

  1. These authors contributed equally: Weichen Song, Yueqi Shi

Authors and Affiliations

  1. Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China

    Weichen Song, Weidi Wang, Weihao Pan, Wei Qian, Shunying Yu, Min Zhao & Guan Ning Lin

  2. Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China

    Weichen Song, Weidi Wang, Shunying Yu, Min Zhao & Guan Ning Lin

  3. Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China

    Yueqi Shi

  4. Department of Stomatology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China

    Yueqi Shi

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Contributions

G.N.L. designed and supervised the study. Y.S. collected and preprocessed the data. W.S. analysed the data and drafted the manuscript. W.P., W.Q. and W.W. assisted with the methodology. Y.S., S.Y. and M.Z. interpreted the data. All authors read, revised and approved the manuscript.

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Correspondence to Guan Ning Lin.

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The authors declare no competing interests.

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Peer review information Nature Human Behaviour thanks Eugenio Lopez-Cortegano and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Song, W., Shi, Y., Wang, W. et al. A selection pressure landscape for 870 human polygenic traits. Nat Hum Behav 5, 1731–1743 (2021). https://doi.org/10.1038/s41562-021-01231-4

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