Poster: Epidemiology: Population Biology Genetics
Tools for analysis of clonal population genetic data in R
Z. KAMVAR (1), J. Brooks (2), N. Grünwald (3) (1) Oregon State University, U.S.A.; (2) Oregon State University, U.S.A.; (3) USDA-ARS, U.S.A.
Knowledge of the population dynamics and evolution of plant pathogens allows inferences on evolutionary processes involved in their adaptation to hosts, pesticides, and other environmental pressures. These microbial pathogens often require different tools for analysis due to the fact that they can be clonal or partially clonal. With the advent of high-throughput sequencing technologies, obtaining genome-wide data has become easier and cheaper than ever before with techniques such as genotyping-by-sequencing. In 2013, we created the widely used R package poppr for analysis of clonal populations. In 2015, we published several additional extensions to poppr for use with genomic data including the ability to define clones based on a genetic distance threshold, minimum spanning networks with reticulation, and sliding window analysis of the index of association. We present here an overview of poppr as it pertains to traditional and high-throughput population genetic data with select applications.