Oral Technical Session: Ecology and Epidemiology

103-O

Application of the R package poppr for analysis of population genetic data.
Z. N. KAMVAR (1), J. F. Tabima (1), N. J. Grünwald (2)
(1) Oregon State University, Corvallis, OR, U.S.A.; (2) USDA-ARS, Corvallis, OR, U.S.A.

Plant pathogen populations are often clonal or partially clonal, making analysis difficult. Many analysis methods assume panmixia and cannot be used for clonal or partially clonal populations. We thus created the R package poppr for conducting analysis of these populations commonly observed in plant pathology. Poppr provides a set of tools for repeatable analysis using hierarchically sampled populations. Clone censoring data is readily implemented for any level of a population hierarchy. To test for clonal reproduction we included analysis of linkage disequilibrium using the index of association combined with significance tests based on permutation. Several genetic distances, such as Nei's, Roger's and Bruvo's distance for microsatellites, are also implemented with the ability to produce dendrograms with bootstrap support or minimum spanning networks. With other packages in R, poppr further allows analyses of populations including richness, diversity, and evenness among multilocus genotypes. Poppr can analyze dominant and co-dominant marker data resulting from AFLP, SSR, SNP or similar kinds of data. We have made use of the functions in poppr for visualization of multilocus genotypes at http://phytophthora-id.org and have applied this package for analyses of Phytophthora plurivora populations. We continue to develop poppr and are currently working on tools for analysis of dense single nucleotide polymorphism data resulting from genotyping-by-sequencing.