Selected Recent Publications



  • Z. He, X. Feng, Q. Chen, L. Li, S. Li, K. Han, Z. Guo, J. Wang, M. Liu, C. Shi, S. Xu, S. Shao, X. Liu, X. Mao, W. Xie, X. Wang, R. Zhang, G. Li, W. Wu, Z. Zheng, C. Zhong, N. Duke, D. Boufford, G. Fan, C-I. Wu, R. Ricklefs, S. Shi*. 2022. Evolution of coastal forests based on a full set of mangrove genomes. Nature Ecology & Evolution, doi: 10.1038/s41559-022-01744-9. LINK

  • R. Zhang, Z. Guo*, L. Fang, C. Zhong, N. Duke, S. Shi*. 2022. Population subdivision promoted by a sea-level-change-driven bottleneck: a glimpse from the evolutionary history of the mangrove plant Aegiceras corniculatum. Molecular Ecology, 31(3): 780-797. LINK


  • Qipian Chen, H. Yang, X. Feng, Qingjian Chen, S. Shi*, C-I. Wu*, Z. He*. 2021. Two decades of suspect evidence for adaptive molecular evolution — negative selection confounding positive selection signals. National Science Review, doi: 10.1093/nsr/nwab217. LINK

  • S. Xu, Z. Guo, X. Feng, S. Shao, Y. Yang, J. Li, C. Zhong, Z. He*, S. Shi*. 2021. Where whole-genome duplication is most beneficial: adaptation of mangroves to a wide salinity range between land and sea. Molecular Ecology, doi: 10.1111/mec.16320. LINK

  • X. Mao, W. Xie, X. Li, S. Shi*, Z. Guo*. 2021. Establishing community-wide DNA barcode references for conserving mangrove forests in China. BMC Plant Biology, 21: 571. DOWNLOAD

  • X. Feng, G. Li, S. Xu, W. Wu, Q. Chen, S. Shao, M. Liu, N. Wang, C. Zhong, Z. He*, S. Shi. 2021. Genomic insights into molecular adaptation to intertidal environments in the mangrove Aegiceras corniculatum. New Phytologist, 231(6): 2346-2358. LINK


  • Z. Wang, Z. Guo*, C. Zhong, H. Lyu, X. Li, N. Duke, S. Shi*. 2020. Genomic variation patterns of subspecies defined by phenotypic criteria: analyses of the mangrove species complex, Avicennia marina. Journal of Systematics and Evolution, doi: 10.1111/jse.12709. DOWNLOAD

  • S. Xu, J. Wang, Z. Guo, Z. He*, S. Shi*. 2020. Genomic convergence in the adaptation to extreme environments. Plant Communications, 1: 100117. DOWNLOAD

  • Z. He, S. Xu, S. Shi*. 2020. Adaptive convergence at the genomic level — prevalent, uncommon or very rare? National Science Review, 7(6): 947-951. DOWNLOAD

  • Z. He, S. Xu, Z. Zhang, W. Guo, H. Lyu, C. Zhong, D. Boufford, N. Duke, The International Mangrove Consortium, S. Shi*. 2020. Convergent adaptation of the genomes of woody plants at the land-sea interface. National Science Review, 7(6): 978-993. DOWNLOAD

  • X. Feng, S. Xu, J. Li, Y. Yang, Q. Chen, H. Lyu, C. Zhong, Z. He*, S. Shi*. 2020. Molecular adaptation to salinity fluctuation in tropical intertidal environments of a mangrove tree Sonneratia alba. BMC Plant Biology, 20:178. DOWNLOAD

  • X. Wang, Z. He, S. Shi*, C-I. Wu*. 2020. Genes and speciation: is it time to abandon the biological species concept? National Science Review, 7(8): 1387-1397. DOWNLOAD

  • W. Xie, C. Zhong, X. Li, Z. Guo*, S. Shi. 2020. Hybridization with natives augments the threats of introduced species in Sonneratia mangroves. Aquatic Botany, 160: 103166. DOWNLOAD


  • Z. He, X. Li, M. Yang, X. Wang, C. Zhong, N. C. Duke, C-I. Wu*, S. Shi*. 2019. Speciation with gene flow via cycles of isolation and migration: Insights from multiple mangrove taxa. National Science Review, 6(2): 275-288. DOWNLOAD


  • L. Liu, Z. Guo, C. Zhong, S. Shi*. 2018. DNA barcoding reveals insect diversity in the mangrove ecosystems of the Hainan Island, China. Genome, 61(11): 797-806. DOWNLOAD

  • Z. Liu, G. Chen, T. Zhu, Z. Zeng, Z. Lyu, J. Wang, K. Messenger, A. Greenberg, Z. Guo, Z. Yang, S. Shi*, Y. Wang*. 2018. Prevalence of cryptic species in morphologically uniform taxa – Fast speciation and evolutionary radiation in Asian frogs. Molecular Phylogenetics and Evolution, 127: 723-731. DOWNLOAD

  • Y. Yang, W. Guo, X. Shen, J. Li, S. Yang, S. Chen, Z. He, R. Zhou*, S. Shi*. 2018. Identification and characterization of evolutionarily conserved alternative splicing events in a mangrove genus Sonneratia. Scientific Reports, 8(1): 4425. DOWNLOAD

  • Z. Guo, X. Li, Z. He, Y. Yang, W. Wang, C. Zhong, A. Greenberg, C-I. Wu, N. C. Duke, S. Shi*. 2018. Extremely low genetic diversity across mangrove taxa reflects past sea level changes and hints at poor future responses. Global Change Biology, 24(4): 1741-1748. DOWNLOAD

  • H. Lyu, Z. He, C-I. Wu, S. Shi*. 2018. Convergent adaptive evolution in marginal environments: unloading transposable elements as a common strategy among mangrove genomes. New Phytologist, 217(1): 428-438. DOWNLOAD


  • 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, 4(5): 721-734. 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, 26(11): 2845-2849. 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, 26(13): 3405-3423. 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, 34(4): 1008-1015. 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, 17(1): 22. 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, 43(9): 1856-1868. 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, 6: 35634. 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, 7: 1618. 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, 11(10): e0164453. 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, 6: 29486. 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, 16(1): 605. DOWNLOAD

  • Y. Chen, Y. Hou, Z. Guo, W. Wang, C. Zhong, R. Zhou*, S. Shi*. 2015. Applications of Multiple Nuclear Genes to the Molecular Phylogeny, Population Genetics and Hybrid Identification in the Mangrove Genus Rhizophora. PloS One, 10(12): e0145058. DOWNLOAD

  • Z. He, Z. Zhang, W. Guo, Y. Zhang, R. Zhou, S. Shi*. 2015. De Novo Assembly of Coding Sequences of the Mangrove Palm (Nypa fruticans) Using RNA-Seq and Discovery of Whole-Genome Duplications in the Ancestor of Palms. PloS One, 10(12): e0145385. 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, 53(1): 47-52. DOWNLOAD

Before 2014

  • 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, 14(1): 535. 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, 13(1): 74. 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, 7(5): e36499. 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, 28(10): 2833-2842. 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, 7(6): e1002100. DOWNLOAD

  • Y. Shen, Y. Lv, L. Huang, W. Liu, M. Wen, T. Tang, R. Zhang, E. Hungate, S. Shi*, C-I. Wu*. 2011. Testing hypotheses on the rate of molecular evolution in relation to gene expression using microRNAs. PNAS, 201110098. 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, 55(22): 2359-2365. DOWNLOAD

  • T. Tang, S. Kumar, Y. Shen, J. Lu, M-L. Wu, S. Shi, W-H. Li, C-I. Wu. 2010. Adverse interactions between micro-RNAs and target genes from different species. PNAS, 107(29): 12935-12940. 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, 25(12): 1554-1555. 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, 10(3): S13. 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, 20(11): 2946-2959. 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, 8(1): 149. DOWNLOAD

  • J. Lu, Y. Shen, Q. Wu, S. Kumar, B. He, S. Shi, R. W. Carthew, S. M. Wang, C-I. Wu. 2008. The birth and death of microRNA genes in Drosophila. Nature Genetics, 40(3): 351. 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, 24(12): 2746-2754. DOWNLOAD

  • K. Zeng*, S. Shi, C-I. Wu. 2007. Compound Tests for the Detection of Hitchhiking Under Positive Selection. Molecular Biology and Evolution, 24(8): 1898-1908. 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, 24(7): 1562-1574. 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, 22(3): 126-131. DOWNLOAD

  • K. Zeng*, Y. Fu, S. Shi, C-I. Wu. 2006. Statistical Tests for Detecting Positive Selection by Utilizing High-Frequency Variants. Genetics, 174(3): 1431-1439. 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, 2(11): e199. DOWNLOAD

  • S. Shi*, Y. Huang, K. Zeng, F. Tan, H. He, J. Huang, Y. Fu*. 2005. Molecular phylogenetic analysis of mangroves: independent evolutionary origins of vivipary and salt secretion. Molecular Phylogenetics and Evolution, 34(1): 159-166. DOWNLOAD

  • R. Zhou, S. Shi*, C-I. Wu. 2005. Molecular criteria for determining new hybrid species—An application to the Sonneratia hybrids. Molecular Phylogenetics and Evolution, 35(3): 595-601. DOWNLOAD

  • C-I. Wu, S. Shi, Y. Zhang. 2004. A case for conservation. Nature, 428(6979): 213. DOWNLOAD

  • Y. Zhong, Q. Zhao, S. Shi, Y. Huang, M. Hasegawa. 2002. Detecting evolutionary rate heterogeneity among mangroves and their close terrestrial relatives. Ecology Letters, 5(3): 427-432. DOWNLOAD

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