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My research goals are interdisciplinary and combine sampling of genetic and phenotypic variation in natural fungal populations and the development of evolutionary analysis tools. Our tools and methodologies are phylogenetically based and combine cladistic, coalescent, and Bayesian approaches to examine the complex underlying microevolutionary processes - mutation, recombination, gene flow and demography - which have shaped contemporary fungal populations. Our approaches complement and build on existing macroevolutionary methods to enhance our understanding of the dynamic processes leading to population divergence and speciation. Our goal is to provide statistical inferences of population processes which has important applications in phylogeography - in retracing the natural history of indigenous populations or species, conservation biology - in identifying the origin of invading individuals and estimating the effective population sizes of founding populations, and epidemiology - in identifying appropriate genotypes for targeted breeding programs and optimally adapted genotypes for reintroduction strategies and biocontrol. The main computational goals of our research are to 1) develop methodologies for integrating results from the coalescent in phylogenetic network reconstruction, 2) develop a robust evolutionary framework for network inference in the presence of recombination, 3) develop new network-based approaches for integrating biological data and testing for significant associations among multiple molecular and phenotypic data sets, and 4) develop computer software programs implementing new network inference algorithms and test these algorithms for accuracy and power using empirical and simulated data sets. The automation will facilitate the analysis of larger, more complex molecular genetic and phenotypic data sets, in a holistic fashion. Our overall goal is to further launch evolutionary methods in population genetics and accelerate the exploration of rapidly expanding genomic databases.
For additional information on Dr. Carbone's research:
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