UHBBI Workshop Series : Phylogenetics and Evolution

Date/Time: 01 April 2011, 9:00 AM - 12:00 PM
Speaker: Shannon N. Bennett, Ph.D.
Speaker Affiliation: Department of Tropical Medicine, Medical Microbiology and Pharmacology John A. Burns School of Medicine
Venue: John A. Burns School of Medicine, Kaka’ako Campus, Medical Education Building Room 304

For more info: Mahdi Belcaid: mahdi [ at ] hawaii {dot} edu (808) 956-5175
Description: Evolution is a universal property of life and nothing in biology makes sense except in light of it. Today, our technologic capacity to acquire vast amounts of sequence data across the tree of life provides the ideal opportunity to apply phylogenetic tools to address questions about how sequences are evolving to generate everything from novel species to human disease resistance to emerging pathogens. Emerging infectious diseases represent an important area in which rapid evolution is occurring and has already had major affects, including changes in host distribution, geographic range, epidemiologic intensity, and/or virulence. Bioinformatic tools based on phylogenetics allow us to trace the evolution of pathogens throughout emergence, to identify sources of variation, random versus adaptive evolutionary mechanisms, and the gene regions involved in phenotypic change. Because the timescale of pathogen evolution, particularly viruses, is so short, transmission dynamics can be elucidated from genetic diversity changes in real time using phylodynamic tools. Here I demonstrate the application of phylogenetic and phylodynamic approaches on sequence data to identify evolutionary drivers of infectious disease emergence in pathogens such as dengue virus. We will cover multiple alignments, phylogenetic inference, tests for selection and recombination, and phylodynamics Since the workshop contains a practical component, users are encouraged to bring their own laptops and install the applications that will be used.