Marshall W. Nirenberg Collegiate Professor of Ecology and Evolutionary Biology
B. S., Fudan University, Shanghai, China, 1992
Ph. D., Pennsylvania State University, University Park, PA, 1998
Fogarty postdoctoral fellow, National Institute of Allergy and Infectious Diseases, Bethesda, MD, 1999-2001
Assistant Professor, Department of Ecology and Evolutionary Biology, University of Michigan, 2001-2005
Associate Professor, Department of Ecology and Evolutionary Biology, University of Michigan, 2005-2009
Professor, Department of Ecology and Evolutionary Biology, University of Michigan, 2009-2013
Marshall W. Nirenberg Collegiate Professor, Department of Ecology and Evolutionary Biology, University of Michigan, 2013-present.
I am most interested in the relative roles of chance and necessity in evolution. There are two major research areas in my lab.
I. Yeast as an experimental system for studying evolution.
We are using the budding yeast Saccharomyces cerevisiae and its relatives as model organisms to understand a variety of evolutionary processes, including questions about (i) mutation rate and spectrum, (ii) epistasis and fitness landscapes, (iii) gene expression evolution, (iv) expression plasticity in environmental adaptations, (v) evolutionary impacts of pleiotropy, (vi) genomic basis of adaptation, and (vii) phenotypic and fitness effects of synonymous mutations.
II. Computational evolutionary genomics.
Using evolutionary, genomic, and/or systemic approaches, we analyze publicly available data to characterize and understand pleiotropy, robustness, epistasis, gene expression noise, posttranscriptional modification, convergent evolution, positive selection, origin of new genes, and other important genetic and evolutionary phenomena. We are not limited in the study organism in this line of research, but most often analyze functional genomic data from yeasts and mammals. Projects may also involve modeling and simulation.
I also encourage students and postdoctoral fellows to develop their own projects in the general area of evolutionary genetics and genomics.
Selected Recent Publications
Shen, X., S. Song, C. Li, and J. Zhang (2022) Synonymous mutations in representative yeast genes are mostly strongly non-neutral. Nature 606:725-731.
Sun, M., and J. Zhang (2022) Preferred synonymous codons are translated more accurately: Proteomic evidence, among-species variation, and mechanistic basis. Sci. Adv. 8:eabl9812.
Liu, H., and J. Zhang (2021) The rate and molecular spectrum of mutation are selectively maintained in yeast. Nat. Commun. 12:4044.
Lyons, D.M., Z. Zou, H. Xu., and J. Zhang (2020) Idiosyncratic epistasis creates universals in mutational effects and evolutionary trajectories. Nat. Ecol. Evol. 4:1685-1693.
Chen, P., and J. Zhang (2020) Antagonistic pleiotropy conceals molecular adaptations in changing environments. Nat. Ecol. Evol. 4:461-469.
Ho, W.-C., D. Li, Q. Zhu, and J. Zhang (2020) Phenotypic plasticity as a long-term memory easing readaptations to ancestral environments. Sci. Adv. 6:eaba3388.
Zou, Z., H. Zhang, Y. Guan, and J. Zhang (2020) Deep residual neural networks resolve quartet molecular phylogenies. Mol. Biol. Evol. 37:1495-1507.
Jiang, D., and J. Zhang (2019) The preponderance of nonsynonymous A-to-I RNA editing in coleoids is nonadaptive. Nat. Commun. 10:5411.
Xu, H., J.-J. Liu, Z. Liu, Y. Li, Y.-S Jin, and J. Zhang (2019) Synchronization of stochastic expressions drives the clustering of functionally related genes. Sci. Adv. 5:eaax6525.
Xu, C. J.-K. Park, and J. Zhang (2019) Evidence that alternative transcriptional initiation is largely nonadaptive. PLOS Biol. 17:e3000197.
Wei, X. and J. Zhang (2018) The optimal mating distance resulting from heterosis and genetic incompatibility. Sci. Adv. 4:eaau5518.
Li, C., and J. Zhang (2018) Multi-environment fitness landscapes of a tRNA gene. Nat. Ecol. Evol. 2:1025-1032.
Ho, W.-C., and J. Zhang (2018) Evolutionary adaptations to new environments generally reverse plastic phenotypic changes. Nat. Commun. 9:350.
Ho, W.-C., Y. Ohya, and J. Zhang (2017) Testing the neutral hypothesis of phenotypic evolution. Proc. Natl. Acad. Sci. USA 114:12219-12224.
Li, C., Qian, W., Maclean, C. J., and J. Zhang (2016) The fitness landscape of a tRNA gene. Science 352:837-840.
EEB 410: EEB Capstone Seminars
EEB 512: Molecular and Genomic Evolution
- Molecular and genome evolution
- Center for Statistical Genetics, School of Public Health
- Bioinformatics Program, U-M Medical School
Field(s) of Study
- Evolutionary genetics and genomics
- Yuxuan Chen
- Xukang Shen
- Siliang Song
- Yun-Ju Lee
- Piaopiao Chen
- Anjali Mahilkar