Ecology and Evolutionary Genetics of Fungi The overall objective in our research is to understand how fungi evolve. We examine both the patterns of fungal evolution as well as the mechanisms responsible for the observed patterns of evolution. We study fungal populations from the environment, human hosts, clinics, and the laboratory to address a variety of issues such as the rates and effects of spontaneous mutations; the persistence and spread of mutations in natural environments and human populations; and the origins of novel traits, genotypes and species. Our research uses microbiological, molecular, ecological and quantitative genetic tools. Our current research includes the following topics: 1. Population genetics of fungi, including wild mushrooms and human and animal fungal pathogens 2. Fungal mitochondrial DNA variation and inheritance 3. Development of biomarkers for efficient identification of human fungal pathogens. 4. Genetic analyses of quantitative traits in human fungal pathogens.
Ecology & Evolution; Microbiology & Plant Biology
- Singh, R. S., Xu, J., Kulathinal, R (Editors). (In progress) Evolution in the fast lane: rapid evolution of genes and genetic systems. Oxford University Press.
- Xu, J. and Wu, Q. (In progress) Essentials of Life Science. 2nd Edition. 3. Xu, J. (Editor). 2010. Microbial Population Genetics. Horizon Bioscience. UK 2.Xu, J. and Wu, Q. 2006. Essentials of Life Science. 1st Edition. Higher Education Press (Beijing) and Thomson Scientific (Toronto).
- 1. Xu, J. (Editor). 2005. Evolutionary Genetics of Fungi. Horizon Scientific Press. UK. Contributions to books: 22. Xu, J. 2012. Rapid evolution in experimental populations of all major life forms. In Rapidly Evolving Genes and Genetic Systems (eds. Singh, R. S., Xu, J., Kulathinal, R). Oxford University Press. Pp. 40-52. 21.
- Idnurm, A and J. Xu. (In press). Experimental and natural evolution in theCryptococcus neoformans and Cryptococcus gattii species complex. In Evolution of Virulence in Eukaryotic Microbes (eds. David Sibley, Barbara Howlett, Joseph Heitman), Wiley/Blackwell Press 20. Litvintseva, A.P., J. Xu, and T. G. Mitchell. (2011) Population Structure and Ecology of Cryptococcus. In Cryptococcus and Cryptococcosis. (Editors J. Heitman, J. Kwon-Chung, J. Perfect, A. Casadevall). ASM Press. 19. Xu, J.,W. Manosuthi, U. Banerjee, L-P Zhu, J.H. Chen, S. Kohno, K. Izumikawa, Y.H. Chen, S. Sungkanuparph, T. S. Harrison, M. Fisher. (2011) Cryptococcosis in Asia.. In Cryptococcus and Cryptococcosis. (Editors J. Heitman, J. Kwon-Chung, J. Perfect, A. Casadevall). ASM Press. 18. Xu, J.(2011) Microbial ecology in the age of metagenomics. In Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches(Editor Frans J. de Bruijn). Wiley/Blackwell (To be published in 2011) 17. Luo, Y.Q., K. Lin, and J. Xu. (2010) Comparative Microbial Genomics: Analytical Tools, Population Genetic Patterns and Evolutionary Implications. Chapter 2. In Microbial Population Genetics. (Editor J. Xu), Horizon Scientific Press. 16. Eardly, B.D. and J. Xu. (2010) Population Genetics of the Symbiotic Nitrogen-fixing Bacteria Rhizobia. Chapter 5. In Microbial Population Genetics. (Editor J. Xu), Horizon Scientific Press. 15. Xu, J. (2010) Population Genetics in the Age of Metagenomics: Impact on Investigations of Viral, Bacterial, Archaeal and Eukaryotic Microbial Communities Chapter 12. In Microbial Population Genetics. (Editor J. Xu), Horizon Scientific Press. 14. Xu, J. (2009)Metagenomics and ecosystems biology: conceptual frameworks, tools, and methods. In Metagenomics: Theory, Methods and Applications (Editor Diana Marco), Caister Academic Press. 13. Xu, J. (2009) Reproduction and sex in microorganisms. Encyclopedia of Life Supporting Systems. UN-UNESCO. 12.Xu, J. (2008) Using 1-2 individual organisms to address population genetic questions. In Genetic Inheritance Patterns. Nova Publishers. 11. Xu, J. (2007)Origin, evolution and extinction of asexual fungi: experimental tests using Cryptococcus neoformans. Pp. 461-476. In Sex in Fungi. American Society for Microbiology Press. 10. Xu, J., M. Cheng, Q. Tan, and Y. Pan. (2005) Molecular population genetics of basidiomycete fungi. In Evolutionary Genetics of Fungi (J. Xu editor). Horizon Scientific Press, England. Pp. 189-220. 9. Xu, J. (2005) Fundamentals of fungal molecular population genetic analyses. In Evolutionary Genetics of Fungi (J. Xu editor). Horizon Scientific Press, England. Pp. 87-116. 8. Yan, Z. and J. Xu (2005) Fungal mitochondrial inheritance and evolution. In Evolutionary Genetics of Fungi (J. Xu editor). Horizon Scientific Press, England. Pp. 221-252. 7. Xu, J. (2004) Gene Genealogical analyses of human fungal pathogens. Pp.299-318. “Pathogenic Fungi: Structural Biology and Taxonomy" (editors Gioconda San-Blas, Richard Calderone), Horizon Scientific Press. 6. Tey, R., S. Han, Z. Yan, X. Li, K. Lazzazera, S. Sun, and J. Xu. (2003) Genotypic and phenotypic diversities of human pathogenic yeasts. Research Advances in Microbiology. Global Research Network. 3: 67-85. 5. Xu, J. (2003) Molecular population genetics of the commercial mushroom Agaricus bisporus. Research Advances in Microbiology. Global Research Network. 3:35-50 4. Mitchell, T. G. and J. Xu. (2003) Molecular methods to identify pathogenic fungi. Pp.677-702. Pathogenic Fungi in Humans and Animals (2nd Edition). Editor D. H. Howard. Marcel Dekker, New York. 3. Xu, J. and Mitchell, T. G. 2003. Population genetic analyses of medically important fungi. Pp. 703-722. Pathogenic Fungi in Humans and Animals (2nd Edition). Editor D. H. Howard. Marcel Dekker, New York. 2. Xu, J. and Mitchell, T. G. 2002. Population genetic analyses of Candida. Pp.55-64. Chapter 4. in "Candida and Candidiasis"(3rd edition). Editor R. Calderone, P. Magee, N. Gow, P. Fidel, D. Sanglard, S. Filler, D. Coleman and B. Merz. American Society for Microbiology Press. Washington, D. C. 1. Xu, J. and Mitchell, T. G. 2002. Strain variation and clonality in species of Candidaand Cryptococcus neoformans. Pp. 739-750. Chapter 33. in Fungal Pathogenesis: Principles and Clinical Applications. Editor Richard Calderone and R. L. Cihlar. Marcel Dekker, Inc., New York, N.Y. Articles in Peer-Reviewed Journals (*Corresponding author, underlined: students and trainees in my lab) 88. Zhang, Y., Yu, Z.-F., Xu, J., and Zhang, K.Q*. Divergence and dispersal of the nematode-trapping fungus Arthrobotrys oligospora from China. Environmental Microbiology Report (In press). 87. Maganti, H*., D. Bartfai, J. Xu. Ecological structuring of yeasts associated with trees around Hamilton, Ontario, Canada. FEMS Yeast Research (In press) 86. Ge S-H., J. Xie, J. Xu; J. Li; D-M Li, L-L Zong; Y-C Zheng, F-Y Bai*. Prevalence of specific and phylogenetically closely related genotypes in the population of Candida albicans associated with genital candidiasis in China. Fungal Genetics and Biology (In press) 85. Ma, H-C., J-R. Wu, X. Zeng, D. Zhang, Z. Xiong, and J. Xu*. Diversity and stress-tolerance of symbiotic nitrogen-fixing bacteria from legumes in the Dry-Hot Valleys of southwest China. African Journal of Microbiology Research (In press). 84. Yang, J., L. Wang, X. Ji, Y. Feng, X. Li, C. Zou, J. Xu, Y. Ren, Q. Mi, J. Wu, S. Liu, Y. Liu, X. Huang, H. Wang, X. Niu, J. Li, L. Liang, Y. Luo, K. Ji, W. Zhou, Z. Yu, G. Li, Y. Liu, L. Li, M. Qiao, L. Feng, and K. Zhang*. 2011. Genomic and proteomic analyses of the fungus Arthrobotrys oligospora provide insights into nematode-trap formation. PLoS Pathogen 7(9): e1002179. doi:10.1371/journal.ppat.1002179 83. Chowdhary A, S.S. Hiremath, S. Sun, T. Kowshiki, H.S. Randhawa, and J. Xu*. 2011. Genetic differentiation, recombination and clonal expansion in environmental populations of Cryptococcus gattii in India. Environmental Microbiology 13(7):1875-88. doi: 10.1111/j.1462-2920.2011.02510.x 82. Chowdhary, A.*, H. S. Randhawa, G. Sundar, S. Kathuria, A. Prakash, Z. U. Khan,S. SUN & J. Xu. 2011. In vitro antifungal susceptibility profiles and genotypes of 308 clinical and environmental isolates of Cryptococcus neoformans var. grubii and Cryptococcus gattii serotype B from north-western India. Journal of Medical Microbiology 60:961-967. 81. Rajkumar S.S., R.J. Rudd, J.C. Okoniewski, J. Xu, S. Chaturvedi, and V. Chaturvedi*. 2011. Dispersal of a single, clonal genotype of Geomyces destructansamong New York bats with geomycosis (White Nose Syndrome). Emerging Infectious Diseases http://www.cdc.gov/EID/content/17/7/1273.htm; DOI: 10.3201/eid1707.102056 80. Maganti H, D. Yamamura, and J. Xu*. 2011. Prevalent nosocomial clusters among causative agents for candidemia in Hamilton, Canada. Medical MycologyDOI:10.3109/13693786.2010.547880 79. Cao. CW, Liang L*, Wang WJ, Luo H, Huang SB, Liu DH, Xu J, Henk DA, Fisher MC. 2011. Common reservoirs for Penicillium marneffei infection in humans and rodents, China. Emerging Infectious Diseases 17:209-214. 78. Randhawa, H. S.*, T. Kowshik, A. Chowdhary, K. Preeti Sinha, Z. U. Khan, J. Xu. 2011. Seasonal variations in prevalence of Cryptococcus neoformans var. grubiiandCryptococcus gattii in decayed wood inside trunk hollows of diverse tree species in north- western India: a retrospective study. Medical Mycology49:320-323
- Qiao M, Zhang Y, Li SF, Baral H.-O., Weber E., Su HY, Xu J, Zhang KQ, Yu ZF. 2011. Orbilia blumenaviensis and its Arthrobotrys anamorph.Mycological Progress. On line: DOI: 10.1007/s11557-011-0744-3.