Abstract
Despite the substantial role that chickens have played in human societies across the world, both the geographic and temporal origins of their domestication remain controversial. To address this issue, we analyzed 863 genomes from a worldwide sampling of chickens and representatives of all four species of wild jungle fowl and each of the five subspecies of red jungle fowl (RJF). Our study suggests that domestic chickens were initially derived from the RJF subspecies Gallus gallus spadiceus whose present-day distribution is predominantly in southwestern China, northern Thailand and Myanmar. Following their domestication, chickens were translocated across Southeast and South Asia where they interbred locally with both RJF subspecies and other jungle fowl species. In addition, our results show that the White Leghorn chicken breed possesses a mosaic of divergent ancestries inherited from other subspecies of RJF. Despite the strong episodic gene flow from geographically divergent lineages of jungle fowls, our analyses show that domestic chickens undergo genetic adaptations that underlie their unique behavioral, morphological and reproductive traits. Our study provides novel insights into the evolutionary history of domestic chickens and a valuable resource to facilitate ongoing genetic and functional investigations of the world’s most numerous domestic animal.
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Data availability
The raw sequencing data, alignment BAM files, and genotypes (VCF) have been deposited in the ChickenSD database (http://bigd.big.ac.cn/chickensd/).
Change history
20 July 2020
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Acknowledgements
We thank Andrew Lawler for his comments on the manuscript, and Wenming Zhao, Lili Dong, and Bixia Tang for their help with constructing chicken genomic variant database. This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (CAS, XDA2004010301), the National Natural Science Foundation of China (31621062 to Y.-P.Z., 31771415 and 31801054 to M.-S.W., U1902204 and 31822048 to D.-D.W., 31771405 to M.-S.P., and 31822052 to Y.J.), the Yunnan Provincial Science and Technology Department grant to Y.-P.Z. and D.-D.W., the European Research Council grant (ERC-2013-StG-337574-UNDEAD to G.L.), the Arts and Humanities Research Council (AH/L006979/1 to G.L.), the CAS-President’s International Fellowship Initiative Award (2016VBB049 to M.T., 2018VBC0016 to L.A.F.F., 2016VBA050 to A.E., and 2016VBC051 to N.Y.H.) and the West Light Foundation of CAS (Y902401081 to M.-S.W.). C.S. also thanks the support of Unit of Excellence 2019 on Biodiversity and Natural Resources Management, University of Phayao (UoE62005). The Youth Innovation Promotion Association of CAS also provided support to M.-S.W., D.-D.W. and M.-S.P. N.O.O. also thanks the CAS-TWAS President’s Fellowship Program for Doctoral Candidates. Animal Branch of the Germplasm Bank of Wild Species of CAS (the Large Research Infrastructure Funding) also supported this project. The Chinese Government contribution to CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources in Beijing (2018-GJHZ-01) is appreciated. This publication has been prepared within the framework of the UNEP/GEF project “Development and application of decision-support tools to conserve and sustainably use genetic diversity in indigenous livestock and wild relatives”, and it contributes to the CGIAR Research Program on Livestock. This work was also supported by the Animal Branch of the Germplasm Bank of Wild Species, CAS (the Large Research Infrastructure Funding). Due to the limit on the number of corresponding authors, Dr. Greger Larson cannot be listed as co-corresponding author, although his contribution deserves.
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Y.-P.Z., D.-D.W., J.-L.H., M.-S.W., M.-S.P. and Y.J. conceived the project and designed the research. M.-S.W., L.A.F.F., M.-S.P. and M.L. performed most of the analysis with contributions from S.W., N.O.O., S.-S.D., C.M., H.-M.C., Q.-K.S., Y.-H.L., L.Z., J.-F.S., X.G., Z.-Q.Z. and S.-H.F. J.-J. Z., Y.-J.W., M.-S.W., X.-Y.Y., M.-L.L, and M.-M.Y. conducted the wetlab experiments. X.-M.L., X.-Z.J., Q.-H.N. and S.J.L. contributed genome sequencing data. J.-L.H., A.E., C.S., N.Y.H., H.A., S. Suladari, M.S.A.Z., S.K., S. Sohrabi, H.K.-K., E.L., S.C., H.G.T.N.G., T.M.S., H.Z., J.-Q.J., M.-L.L., H.-M.C., C.M., S.-S.D., A.K.F.H. B., M.S.K., G.L.L.P.S, T.-T. L., O.A.M. and M.N.M.I. did sample collection and prepared the DNA samples. M.T. provided and coordinated genome sequencing of Indian samples in India. M.-S.W., L.A.F.F., G.L., A.E., M.-S.P. and J.-L.H. drafted the manuscript with inputs from all authors. G.L., L.A.F.F., J.P., B.S., J.-L.H., M.S., Y.-P.Z., D.-D.W., M.-S.W., G.Z., M.-S.P., M.T., O.H. and A.E. revised the manuscript. All authors read and approved the manuscript.
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Wang, MS., Thakur, M., Peng, MS. et al. 863 genomes reveal the origin and domestication of chicken. Cell Res 30, 693–701 (2020). https://doi.org/10.1038/s41422-020-0349-y
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DOI: https://doi.org/10.1038/s41422-020-0349-y
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