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Genomic evidence of human selection on Vavilovian mimicry

Nature Ecology & Evolution volume 3, pages 1474–1482 (2019)Cite this article

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Abstract

Vavilovian mimicry is an evolutionary process by which weeds evolve to resemble domesticated crop plants and is thought to be the result of unintentional selection by humans. Unravelling its molecular mechanisms will extend our knowledge of mimicry and contribute to our understanding of the origin and evolution of agricultural weeds, an important component of crop biology. To this end, we compared mimetic and non-mimetic populations of Echinochloa crus-galli from the Yangtze River basin phenotypically and by genome resequencing, and we show that this weed in rice paddies has evolved a small tiller angle, allowing it to phenocopy cultivated rice at the seedling stage. We demonstrate that mimetic lines evolved from the non-mimetic population as recently as 1,000 yr ago and were subject to a genetic bottleneck, and that genomic regions containing 87 putative plant architecture-related genes (including LAZY1, a key gene controlling plant tiller angle) were under selection during the mimicry process. Our data provide genome-level evidence for the action of human selection on Vavilovian mimicry.

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Fig. 1: Morphology associated with Vavilovian mimicry in E. crus-galli and sampling.
Fig. 2: Phylogenetic and phenotypic differentiation of E. crus-galli in the Yangtze River basin.
Fig. 3: Genomic signatures of positive selection during the mimicry process in E. crus-galli.
Fig. 4: Haplotype diversity of 455 variations within the 87 plant architecture-related genes in NMC and MIC.
Fig. 5: LA1 was putatively under positive selection during mimicry evolution in E. crus-galli.

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Data availability

The genomic resequencing and RNA-seq data included in this study were deposited into the BIG data centre (https://bigd.big.ac.cn/) under accession number PRJCA001519.

Code availability

The custom scripts and pipelines used in this study have been deposited in Github (https://github.com/bioinplant/Vavilovian_mimicry).

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Acknowledgements

We thank H. Yamaguchi, S. Ge and G. Chen for their useful comments. This work was supported by the National Natural Science Foundation (grant number 9143511), the Zhejiang Natural Science Foundation (grant number LZ17C130001), the Jiangsu Collaborative Innovation Center for Modern Crop Production, the 111 Project (grant number B17039) and the China Agriculture Research System (grant number CARS-01-02A).

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  1. These authors contributed equally: Chu-Yu Ye, Wei Tang, Dongya Wu.

Authors and Affiliations

  1. Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China

    Chu-Yu Ye, Dongya Wu, Lei Jia, Jie Qiu, Meihong Chen, Lingfeng Mao, Feng Lin, Haiming Xu & Longjiang Fan

  2. State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China

    Wei Tang, Xiaoyue Yu & Yongliang Lu

  3. State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China

    Yonghong Wang

  4. Department of Biology, Washington University in St. Louis, St. Louis, MO, USA

    Kenneth M. Olsen

  5. Department of Biology, University of Virginia, Charlottesville, VA, USA

    Michael P. Timko

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  1. Chu-Yu Ye
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Contributions

L.F. conceived the study. D.W., C.-Y.Y., L.J., J.Q., M.C. and F.L. analysed the data. W.T., Y.L. and X.Y. performed the phenotyping. M.P.T., K.M.O., Y.W. and H.X. advised on the data analysis. M.P.T. edited the manuscript. C.-Y.Y., L.F. and D.W. wrote the manuscript. All authors read and contributed to the manuscript.

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Correspondence to Longjiang Fan.

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Ye, CY., Tang, W., Wu, D. et al. Genomic evidence of human selection on Vavilovian mimicry. Nat Ecol Evol 3, 1474–1482 (2019). https://doi.org/10.1038/s41559-019-0976-1

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