Selected Recent Publications



  • S. Xu, Z. He, Z. Zhang, Z. Guo, W. Guo, H. Lyu, J. Li, M. Yang, Z. Du, Y. Huang, R. Zhou, C. Zhong, D. E. Boufford, M. Lerdau, C-I Wu., N. C. Duke, The International Mangrove Consortium, S. Shi*. 2017. The origin, diversification and adaptation of a major mangrove clade (Rhizophoreae) revealed by whole genome sequencing. National Science Review. DOWNLOAD

  • M. Yang, Z. He, S. Shi*, C-I. Wu.*. 2017. Can genomic data alone tell us whether speciation happened with gene flow? Molecular Ecology. DOWNLOAD

  • M. Yang, Z. He, Y. Huang, L. Lu, Y. Yan, L. Hong, H. Shen, Y. Liu, Q. Guo, L. Jiang, Y. Zhang, A. Greenberg, R. Zhou, X. Ge, C-I. Wu.*, S. Shi*. 2017. The emergence of the hyperinvasive vine, Mikania micrantha (Asteraceae), via admixture and founder events inferred from population transcriptomics. Molecular Ecology. DOWNLOAD

  • S. Xu, Z. He, Z. Guo, Z. Zhang, J. G. Wyckoff, A. Greenberg, C-I. Wu.*, S. Shi*. 2017. Genome-wide convergence during evolution of mangroves from woody plants. Molecular Biology and Evolution. DOWNLOAD

  • Y. Yang, J. Li, S. Yang, X. Li, L. Fang, C. Zhong, N. C. Duke, R. Zhou*, S. Shi*. 2017. Effects of Pleistocene sea-level fluctuations on mangrove population dynamics: a lesson from Sonneratia alba. BMC Evolutionary Biology. DOWNLOAD


  • Z. Guo, Y. Huang, Y. Chen, N. C. Duke, C. Zhong, S. Shi*. 2016. Genetic discontinuities in a dominant mangrove Rhizophora apiculata (Rhizophoraceae) in the Indo-Malesian region. Journal of Biogeography. DOWNLOAD

  • Z. Zhang, Z. He, S. Xu, X. Li, W. Guo, Y. Yang, C. Zhong, R. Zhou*, S. Shi*. 2016. Transcriptome analyses provide insights into the phylogeny and adaptive evolution of the mangrove fern genus Acrostichum. Scientific Reports. DOWNLOAD

  • Y. Yang, N. C. Duke, F. Peng, J. Li, S. Yang, C. Zhong, R. Zhou*, S. Shi*. 2016. Ancient Geographical Barriers Drive Differentiation among Sonneratia caseolaris Populations and Recent Divergence from S. lanceolata. Frontiers in Plant Science. DOWNLOAD

  • X. Li, N. C. Duke, Y. Yang, L. Huang, Y. Zhu, Z. Zhang, R. Zhou, C. Zhong, Y. Huang* , S. Shi*. 2016. Re-Evaluation of Phylogenetic Relationships among Species of the Mangrove Genus Avicennia from Indo-West Pacific Based on Multilocus Analyses. PloS One. DOWNLOAD

  • J. Li, Y. Yang, Q. Chen, L. Fang, Z. He, W. Guo, S. Qiao, Z. Wang, M. Guo, C. Zhong, R. Zhou*, S. Shi*. 2016. Pronounced genetic differentiation and recent secondary contact in the mangrove tree Lumnitzera racemosa revealed by population genomic analyses. Scientific Reports. DOWNLOAD


  • Y. Yang, S. Yang, J. Li, Y. Deng, Z. Zhang, S. Xu, W. Guo, C. Zhong, R. Zhou*, S. Shi*. 2015. Transcriptome analysis of the Holly mangrove Acanthus ilicifolius and its terrestrial relative, Acanthus leucostachyus, provides insights into adaptation to intertidal zones. BMC Genomics. DOWNLOAD


  • Y. Yang, S. Yang, L. Fang, J. Li, C. Zhong, R. Zhou*, S. Shi*. 2014. Phylogenetic position of Sonneratia griffithii based on sequences of the nuclear ribosomal internal transcribed spacer and 13 nuclear genes. Journal of Systematic and Evolution. DOWNLOAD


  • Z. He, X. Li, S. Ling, Y. Fu, E. Hungate, S. Shi*, C-I. Wu.*. 2013. Estimating DNA polymorphism from next generation sequencing data with high error rate by dual sequencing applications. BMC Genomics. DOWNLOAD

  • R. Zhang, T. Liu, W. Wu., Y. Li, L. Chao, L. Huang, Y. Huang, S. Shi, R. Zhou*. 2013. Molecular evidence for natural hybridization in the mangrove fern genus Acrostichum. BMC Plant Biology. DOWNLOAD


  • S. Liang, L. Fang, R. Zhou, T. Tang, S. Deng, S. Dong, Y. Huang, C. Zhong, S. Shi*. 2012. Transcriptional Homeostasis of a Mangrove Species, Ceriops tagal, in Saline Environments, as Revealed by Microarray Analysis. PloS One. DOWNLOAD


  • R. Zhou, S. Ling, W. Zhao, N. Osada, S. Chen, M. Zhang, Z. He, H. Bao, C. Zhong, B. Zhang, X. Lu, D. Turissini, N. C. Duke, J. Lu*, S. Shi*, C-I. Wu*. 2011. Population Genetics in Nonmodel Organisms: II. Natural Selection in Marginal Habitats Revealed by Deep Sequencing on Dual Platforms. Molecular Biology and Evolution. DOWNLOAD

  • Z. He, W. Zhai, H. Wen, T. Tang, Y. Wang, X. Lu, A. J. Greenberg, R. R. Hudson, C-I. Wu*, S. Shi*. 2011. Two Evolutionary Histories in the Genome of Rice: the Roles of Domestication Genes. PloS Genetics. DOWNLOAD


  • K. Chen, Y. Zhang, T. Tang, S. Shi*. 2010. Cis-regulatory change and expression divergence between duplicate genes formed by genome duplication of Arabidopsis thaliana. Chinese Science Bulletin. DOWNLOAD


  • H. Bao, H. Guo, J. Wang, R. Zhou, X. Lu, S. Shi*. 2009. MapView: visualization of short reads alignment on a desktop computer. Bioinformatics. DOWNLOAD

  • H. Bao, Y. Xiong, H. Guo, R. Zhou, X. Lu, Z. Yang, Y. Zhong, S. Shi*. 2009. MapNext: a software tool for spliced and unspliced alignments and SNP detection of short sequence reads. BMC Genomics. DOWNLOAD


  • Y. Yu, T. Tang, Q. Qian, Y. Wang, M. Yan, D. Zeng, B. Han, C-I. Wu*, S. Shi*, J. Li*. 2008. Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication. Plant Cell. DOWNLOAD

  • R. Zhou, X. Gong, D. Boufford, C-I. Wu, S. Shi*. 2008. Testing a hypothesis of unidirectional hybridization in plants: Observations on Sonneratia, Bruguiera and Ligularia . BMC Evolutionary Biology. DOWNLOAD


  • R. Zhou, K. Zeng, W. Wu, X. Chen, Z. Yang, S. Shi*, C-I. Wu*. 2007. Population Genetics of Speciation in Nonmodel Organisms: I. Ancestral Polymorphism in Mangroves. Molecular Biology and Evolution. DOWNLOAD

  • K. Zeng*, S. Shi, C-I. Wu. 2007. Compound Tests for the Detection of Hitchhiking Under Positive Selection. Molecular Biology and Evolution. DOWNLOAD

  • K. Zeng*, S. Mano, S. Shi, C-I. Wu. 2007. Comparisons of Site- and Haplotype-Frequency Methods for Detecting Positive Selection. Molecular Biology and Evolution. DOWNLOAD


  • J. Lu, T. Tang, H. Tang, J. Huang, S. Shi*, C-I. Wu*. 2006. The accumulation of deleterious mutations in the rice genomes: A hypothesis on the cost of domestication. Trends in Genetics. DOWNLOAD

  • K. Zeng*, Y. Fu, S. Shi, C-I. Wu. 2006. Statistical Tests for Detecting Positive Selection by Utilizing High-Frequency Variants. Genetics. DOWNLOAD

  • T. Tang, J. Lu, J. Huang, J. He, S. R. McCouch, Y. Shen, Z. Ka, M. D. Purugganan, S. Shi*, C-I. Wu*. 2006. Genomic Variation in Rice: Genesis of Highly Polymorphic Linkage Blocks during Domestication. PloS Genetics. DOWNLOAD


  • C-I. Wu, S. Shi, Y. Zhang. 2004. A case for conservation. Nature. DOWNLOAD

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