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Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation

Abstract

The panda lineage dates back to the late Miocene1 and ultimately leads to only one extant species, the giant panda (Ailuropoda melanoleuca). Although global climate change and anthropogenic disturbances are recognized to shape animal population demography2,3 their contribution to panda population dynamics remains largely unknown. We sequenced the whole genomes of 34 pandas at an average 4.7-fold coverage and used this data set together with the previously deep-sequenced panda genome4 to reconstruct a continuous demographic history of pandas from their origin to the present. We identify two population expansions, two bottlenecks and two divergences. Evidence indicated that, whereas global changes in climate were the primary drivers of population fluctuation for millions of years, human activities likely underlie recent population divergence and serious decline. We identified three distinct panda populations that show genetic adaptation to their environments. However, in all three populations, anthropogenic activities have negatively affected pandas for 3,000 years.

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Figure 1: Current geographic populations of the giant panda and inferred genetic populations.
Figure 2: Demographic history of the giant panda reconstructed from the reference and population resequencing genomes.
Figure 3: Annotation of genes containing selected SNPs on the basis of the KEGG database.

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Acknowledgements

This study was supported by grants from the National Natural Science Foundation of China (31230011), the Knowledge Innovation Program of the Chinese Academy of Sciences (KSCX2-EW-Z-4) and the State Forestry Administration of China. We thank the Chongqing Zoo, the Fuzhou Research Center of the Giant Panda, the Shanghai Zoo, the Shanghai Wildlife Park and the Zhengzhou Zoo for assistance during sample collection. We acknowledge T. Meng for generation of the panda distribution map, R.N. Gutenkunst for suggestions on analysis with ∂a∂i, H. Li for suggestions on PSMC simulations and L. Goodman, J. Elser, M. Holyoak, S. Kumar and R.R. Swaisgood for comments and revisions of this manuscript. We also thank G. Tian, M. Jian, H. Jiang, M. Zhao, Q. Zhang, B. Wang, Y. Huang, G. Wang, C. Lin and F. Xi for laboratory assistance and B. Li for assistance on polar bear data analysis.

Author information

Authors and Affiliations

Authors

Contributions

F.W. designed the research and interpreted data. Jun Wang led the genome sequencing and supervised the analysis. P.Z., S. Zhang, L.Z., H.Z., Z.Z., X.J. and J.Z. prepared the samples. S. Zhao, P.Z., X. Zhan, Y.H., Jian Wang and H.Y. performed research. S. Zhao, Q.W., S.D., X. Zhan, P.Z., X.G., W.H., W.F., D.L., X. Zhang and Q.C. analyzed the data. X. Zhan, F.W., P.Z., S. Zhao, Q.W. and S.D. wrote and revised the manuscript.

Corresponding authors

Correspondence to Jun Wang or Fuwen Wei.

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Supplementary Figures 1–9, Supplementary Tables 1–14 and Supplementary Note (PDF 7812 kb)

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Zhao, S., Zheng, P., Dong, S. et al. Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation. Nat Genet 45, 67–71 (2013). https://doi.org/10.1038/ng.2494

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