SHI Suhua
SHI Suhua, Ph.D.
School of Life Sciences
State Key Laboratory of Biocontrol

Office: He Dan Qing Hall 302 l Phone: +86 20 8411 3677 l Fax: +86 20 3402 2356 l Email: l
Subject: Adaptive evolution, evolutionary and ecological genomics, speciation, population genetics, phylogeography, molecular phylogeny

Research Interests
Biological adaptation, or the seemingly perfect fit between living organisms and their environments, is a most fascinating phenomenon in nature. This wonderment was the puzzle that motivated Charles Darwin. The research in our group focuses on the adaptive evolution and population history of species living in special and marginal environments. Our aim is to understand the mechanisms and the processes by which the population genetic and genomic patterns are produced in such challenging environments. By using modern technology and methods of genomics, molecular biology, and bioinformatics, we collect and assess large-scale data and hope to understand the adaptive evolution and speciation in three groups of plants:
1) mangroves--- the woody plants growing in the vicissitude of the intertidal zones in the tropics and subtropics; they are singularly exposed to the changes in the sea level.
2) invasive species--- these are species that flourish when moved from one environment to another. Instead of withering, they prosper, causing mayhem in the land of invasion. Mikania micrantha, originated in the Americas, is the worst case of invasion in southern China.
3) rice --- this is the best example of domestication, a special form of selection.

Winners of National Science Funds for Outstanding Young Scholars, Ministry of Science and Technology. 1999.
The Outstanding Young Scholar Award by Qiu Shi Science and Technologies Foundation. (Hong Kong) 2001.
1st Prize of Ministry Nature and Science Awards, Ministry of Education, China. 2002, 2008 (twice)
2nd Prize of National Nature and Science Awards, National Office for Science and Technology Awards, 2011.

Recent Publications
1. Wu C.-I., S. Shi, Y. Zhang. 2004. A case for conservation. Nature 428: 213-214.
2. Lu J., 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: 126-131.
3. Zeng K., S. Shi, Y-X Fu, C-I Wu. 2006. Statistical Tests for Detecting Positive Selection by Utilizing High-Frequency Variants. Genetics 174: 1431-1439.
4. Tang T., J. Lu, J. Huang, J. He, S. R. McCouch,Y. Shen, Z. Kai,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.
5. Zeng K., Shi S., Wu C-I. 2007. Compound tests for the detection of hitchhiking under positive selection. Molecular Biology and Evolution 24: 1898-1908.
6. Zeng K., S. Mano, S. Shi, C-I, Wu, 2007, Comparisons of Site- and Haplotype-frequency Methods for Detecting Positive Selection. Molecular Biology and Evolution 24: 1562-1574.
7. Zhou R., 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: 2746-2754.
8. Lu J., Y. Shen, Q. Wu, S. Kumar, B. He, S. Shi, R. W. Carthew, S. Wang, C-I Wu. 2008. The birth and death of microRNA genes in Drosophila. Nature Genetics 40:351-355.
9. Zhou R., X. Gong, D. Boufford, C-I Wu, S. Shi*, 2008.Testing hypothesis of unidirectional hybridization in plants: observations on Sonneratia, Bruguiera and Ligularia. BMC Evolutionary Biology 8:149.
10. Yu Y., Tang T., Qian Q., Wang Y., Yan M., Zeng D., Han B., Wu C-I, Shi S*., Li J*.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: 2946-2959.
11. Bao H., H. Guo, J. Wang, R. Zhou, X. Lu, S. Shi*, 2009. MapView: visualization of short reads alignment on a desktopcomputer. Bioinformatics25:1554-1555.
12. Bao H., Y. Xiong, H. Guo, R. Zhou, X. Lu and S. Shi*, 2009. MapNext: A software tool for spliced and unspliced alignments and SNP detection of short sequence reads. BMC Genomics 10(Suppl 3):S13.
13. Tang, T.,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. PNAS107(29): 12935-12940.
14. Zhou R., S. Ling, W. Zhao, Naoki Osada, S. Chen, M. Zhang, Z. He, H. Bao, C. Zhong, B. Zhang, X. Lu, David Turissini, Norman C. Duke, J. Lu, S. Shi*, C-I Wu*. 2011. Population genetics in non-model organisms: II. Natural selection in marginal habitats revealed by deep sequencing on dual platforms. Molecular Biology and Evolution 28(10):2833-2842.
15. He Z, Zhai W, Wen H, Tang T, Wang Y, S. Shi*, C-I Wu*. 2011. Two Evolutionary Histories in the Genome of Rice: the Roles of Domestication Genes. PLoS Genet 7(6): e1002100.
16. Shen, Y., Y. Lv, W. Liu, M. Wen, T. Tang, R. Zhang, E. Hungate, S. Shi*, CI. Wu*, 2011. Testing hypotheses on the rate of molecular evolution in relation to gene expression using microRNAs. PNAS108(38): 15942-15947.