Professor of Plant Pathology

Center for Integrated Fungal Research
Department of Entomology and Plant Pathology
Campus Box 7244 – Partners III Building Raleigh,
NC 27695-7244

Phone: (919) 513-4866
Fax: (919) 513-0024


University of Toronto, Ph.D, 2000


Dr. Carbone’s Lab

My research interests are in evolutionary biology, molecular population genetics and genomics. Research in my laboratory is interdisciplinary and combines sampling of genetic and phenotypic variation in natural fungal populations, in silico comparative analyses of fungal genomes, and the development of integrative evolutionary analysis tools. An important aspect of our work is developing new methodologies and tools to examine the influence of mutation, recombination, gene flow, selection and demography on the evolution of fungal genomes, populations and species. Our computational goal is to effectively manage and integrate the plethora of new approaches for making inferences on population processes from DNA sequence variation, bringing together simple summary-statistics, nonparametric methods and complex parameter-rich models. We have been developing new methodologies and tools for integrating genetic and phenotypic data within an evolutionary framework. Recently we released a flexible and scalable workbench tool that manages a series of population genetic programs.

A major focus is examining the evolution of fungal secondary metabolism, specifically the sterigmatocystin (ST), O-methylsterigmatocystin (OMST) and aflatoxin (AF) biosynthetic pathway in Aspergillus. The genes for ST, OMST, and AF are clustered and these compounds are synthesized as end products by numerous ascomycetes. Although all three metabolites (ST, OMST, and AF) are potent carcinogens in animals, the biological and evolutionary significance of these bioreactive compounds in fungi is unknown. We are combining inferences from macro- and micro-evolutionary analyses to understand the conservation of these metabolites among Aspergillus species and how diversity is generated and maintained within species over long periods of time. Recent work examines genetic variation in experimental populations and in field studies using biological control strains.


PP 707 Plant-Microbe Interactions is a required course in the Plant Pathology core curriculum that is offered every Spring and is co-taught with Dr. Gary Payne. My section of the course covers the following topics: 1) introduction to population genetics concepts; 2) phylodynamics of pathogen evolution; 3) population biology and disease management; 4) inoculum source and evolutionary potential; 5) durable resistance; 6) host-pathogen coevolution; and 7) quorum-sensing systems in bacteria.

PP 715 Applied Evolutionary and Population Genetic Data Analysis is an advanced graduate course taught in the Fall of alternate years. This course introduces students to nonparametric and model-based methods for inferences on population processes (mutation, migration, drift, recombination, and selection). The goal is to provide a theoretical and conceptual overview of these methods as well as hands-on training on implementation and biological interpretation of results. Sample data sets in computer laboratories will integrate summary statistic, cladistic, coalescent, and Bayesian approaches to examine population processes in different pathosystems with specific emphasis on eukaryotic microbes, viruses and bacteria.

Selected Publications

Olarte, R. A., Horn, B. W., Dorner, J. W., Monacell, J. T., Singh, R., Stone, E. A. and I. Carbone. 2012. Effect of sexual recombination on population diversity in alfatoxin production by Aspergillus flavus and evidence for cryptic heterokaryosis. Molecular Ecology 21: 1453–1476. DOI: 10.1111/j.1365-294X.2011.05398.x.

*Paper is the topic of a News and Views Perspective article: Fisher, M. C. and D. A. Henk. 2012. Sex, drugs and recombination: the wild life of Aspergillus. Molecular Ecology 21: 1305–1306.

Abbas, H. K., Weaver, M. A., Horn, B. W., Carbone, I., Monacell, J. T. and W. T. Shier. 2011. Selection ofAspergillus flavus isolates for biological control of aflatoxins in corn. Toxin Reviews 30: 59-70.

Olson, H., Carbone, I. and M. Benson. 2011. Phylogenetic history of Phytophthora cryptogea and P. drechsleri isolates from floriculture crops in North Carolina greenhouses. Phytopathology 101:1373-1384.

Litvintseva, A. P., Carbone, I., Rossouw, J., Thakur, R., Govender, N. P., and T. G. Mitchell. 2011. Evidence that the human pathogenic fungus Cryptococcus neoformans var. grubii may have evolved in Africa. PLoS One 6(5): e19688. doi:10.1371/journal.pone.0019688.

Wu, F., Bhatnagar, D., T. Bui-Klimke, I. Carbone, R. Hellmich, G. Munkvold, P. Paul, G. Payne, E. Takle. 2011. Climate Change Impacts on Mycotoxin Risks in US Maize. World Mycotoxin Journal 4: 79-93.

Kaye, A.C., J.W. Moyer, E.J. Parks, I. Carbone, and M.A. Cubeta. 2011. Population genetic analysis of tomato spotted wilt virus on peanut in North Carolina and Virginia. Phytopathology 101:147-153.

Horn, B. W., Moore, G. G. and I. Carbone. 2011. Sexual reproduction in aflatoxin-producing Aspergillus nomius. Mycologia 103: 174–183. DOI: 10.3852/10-115.

Moore, G. G., Singh, R., Horn, B. W., and I. Carbone. 2009. Recombination and lineage-specific gene loss in the aflatoxin gene cluster of Aspergillus flavus. Molecular Ecology 18: 4870-4887.

Parks, R., Carbone, I., Murphy, P and C. Cowger. 2009. Population genetic analysis of an eastern U.S. wheat powdery mildew population reveals geographic subdivision and recent common ancestry with U.K. and Israeli populations. Phytopathology 99: 840-849.

Lourenço Jr., V., Moya, A., González-Candelas, F., Carbone, I., Maffia, L. A. and E. S. G. Mizubuti. 2009.Molecular diversity and evolutionary processes of Alternaria solani in Brazil inferred using genealogical and coalescent approaches. Phytopathology 99: 765-774.

Horn, B. W., Moore, G. G. and I. Carbone. 2009. Sexual reproduction in Aspergillus flavus. Mycologia 101: 423-429.

Goss, E. M., Carbone, I., and N. J. Grünwald. 2009. Ancient isolation and independent evolution of the three clonal lineages of the exotic sudden oak death pathogen Phytophthora ramorum. Molecular Ecology18: 1161-1174.

Horn, B. W., Ramirez-Prado, J. H. and I. Carbone. 2009. The sexual state of Aspergillus parasiticus. Mycologia 101: 275-280.

Horn, B. W., Ramirez-Prado, J. H. and I. Carbone. 2009. Sexual reproduction and recombination in the aflatoxin-producing fungus Aspergillus parasiticus. Fungal Genetics and Biology 46: 169-175. (cover page)(recommended by Faculty of 1000 Biology)

Ramirez-Prado, J. H., Moore, G. G., Horn, B. W. and I. Carbone. 2008. Characterization and population analysis of the mating-type genes in Aspergillus flavus and Aspergillus parasiticus. Fungal Genetics and Biology 45: 1292-1299.

Brown DE, Powell A. J., Carbone I. and R. A Dean. 2008. GT-Miner: a graph-theoretic data miner, viewer and model processor. Bioinformation 3(5): 235-237.

Charlton, N. D., Carbone, I., Tavantzis, S. M., and M. A. Cubeta. 2008. Phylogenetic relatedness of the M2 double-stranded RNA in Rhizoctonia fungi. Mycologia 100: 555-564.

Parks, R., Carbone, I. Murphy, J. P., Marshall, D. S. and C. Cowger. 2008. Virulence structure of the Eastern U.S. wheat powdery mildew population. Plant Disease 92: 1074-1082.

Powell, A. J. Conant, G. C., Brown, D. E. Carbone, I. and R. A. Dean. 2008. Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens. BMC Genomics 9: 147.

Clark, C. M. and I. Carbone. 2008. Chloroplast DNA phylogeography in long lived Huon Pine(Lagarostrobos franklinii), a Tasmanian rainforest conifer. Canadian Journal of Forest Research 38: 1576-1589.

Carbone, I., Jakobek, J. L., Ramirez-Prado, J. H. and B. W. Horn. 2007. Recombination, balancing selection and adaptive evolution in the aflatoxin gene cluster of Aspergillus parasiticus. Molecular Ecology 16: 4401-4417. (recommended by Faculty of 1000 Biology)

Carbone, I., Ramirez-Prado, J. H., Jakobek, J. L., and B. W. Horn. 2007. Gene duplication, modularity and adaptation in the evolution of the aflatoxin gene cluster. BMC Evolutionary Biology 7:111.

Moser, J. M., Carbone, I., Arasu, P. and G. Gibson. 2007. Impact of population structure on genetic diversity of a potential vaccine target in the canine hookworm (Ancyclostoma caninum). Journal of Parasitology 93: 796-805.

Deng, J., Carbone, I. and R. A Dean. 2007. The evolutionary history of cytochrome P450 genes in four filamentous ascomycetes. BMC Evolutionary Biology 7: 30.

Gómez-Alpizar, L., I. Carbone, and J. B. Ristaino. 2007. An Andean origin of Phytophthora infestansinferred from nuclear and mitochondrial gene genealogies. Proc Nat. Acad. Sci. 104: 3306-3311.

Malvárez, G, Carbone, I., Grünwald N. J., Subbarao, K. V., Schafer, M. and L. M. Kohn. 2007. New populations of Sclerotinia sclerotiorum from lettuce in California and peas and lentils in Washington. Phytopathology 97: 512-525.