Holloway and McClamma Professor of Experimental Pathology, Department of Pathology, Immunology and Laboratory Medicine, Emerging Pathogen Institute, University of Florida, College of Medicine
The last 25 years have witnessed an unprecedented development of molecular evolution, phylogenetic and population genetic methods. On one hand, the advent of PCR technologies has allowed for the generation and rapid accumulation of nucleotide sequence data from many organisms including several eukaryotic species, bacteria, viruses and eventually the full human genome. On the other hand, the increase in computational speed of computer clusters, as well as desktop and laptop computers, has allowed for the implementation of sophisticated algorithms that would not have been computationally feasible just two decades ago.
The discovery of fast-evolving viruses, such as HIV and HCV, poses special challenges to evolutionary theory. The understanding of both inter- and intra-host evolution of these viruses is crucial and has broad applications ranging from molecular epidemiology to drugresistance, pathogenesis and forensics. Molecular evolution of pathogenic viruses includes experimental work to isolate and sequence viral strains from different hosts or from the same host over time, DNA and RNA sequencing techniques, as well as the development and application of phylogenetic and population genetic methods to gain insights on the interplay between viral evolutionary patterns, origin and spread of epidemic outbreaks and pathogenesis.
More recently, our lab has also been investigating the molecular evolution and phylogeography of pathogenic bacteria such as MRSA and V. Cholera. Phylogenomics and phylogeography of bacteria is a new exciting field of research, based on the analysis of genome-wide SNPs, using state-of-the art phylogenetic methods and the Bayesian coalescent framework. Full genome bacterial sequences are obtained with the Illumina technology and analyzed with in-house pipelines implemented in the Galaxy software platform.