This is the data set from http://dx.doi.org/10.5281/zenodo.13007. It has been converted to the genclone object as of poppr version 2.0. It contains 729 samples of the Sudden Oak Death pathogen Phytophthora ramorum genotyped over five microsatellite loci (Kamvar et. al., 2015). 513 samples were collected from forests in Curry County, OR from 2001 to mid-2014 (labeled by watershed region). The other 216 samples represents genotypes collected from Nurseries in OR and CA from Goss et. al. (2009).
genclone object with 3 hierarchical levels
called "SOURCE", "YEAR", and, "STATE". The other slot contains a
named vector of repeat lengths called "REPLEN", a matrix of xy
coordinates for the forest samples called "xy", and a palette to
color the ~SOURCE/STATE stratification called "comparePal".
Kamvar, Z. N., Larsen, M. M., Kanaskie, A. M., Hansen, E. M., & Grünwald, N. J. (2015). Spatial and temporal analysis of populations of the sudden oak death pathogen in Oregon forests. Phytopathology 105:982-989. doi: 10.1094/PHYTO-12-14-0350-FI
Zhian N. Kamvar, Meg M. Larsen, Alan M. Kanaskie, Everett M. Hansen, & Niklaus J. Grünwald. 2014. Sudden_Oak_Death_in_Oregon_Forests: Spatial and temporal population dynamics of the sudden oak death epidemic in Oregon Forests. ZENODO, doi: 10.5281/zenodo.13007
Goss, E. M., Larsen, M., Chastagner, G. A., Givens, D. R., and Grünwald, N. J. 2009. Population genetic analysis infers migration pathways of Phytophthora ramorum in US nurseries. PLoS Pathog. 5:e1000583. doi: 10.1371/journal.ppat.1000583
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