poppr (version 2.1.1)

Pram: Phytophthora ramorum data from OR Forests and Nurseries (OR and CA)

Description

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).

Usage

data(Pram)

format

a 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".

References

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: http://dx.doi.org/10.1094/PHYTO-12-14-0350-FI{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: http://doi.org/10.5281/zenodo.13007{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: http://dx.doi.org/10.1371/journal.ppat.1000583{10.1371/journal.ppat.1000583}

Examples

data(Pram)

# Repeat lengths (previously processed via fix_replen)
other(Pram)$REPLEN

# Color palette for source by state. Useful for minimum spanning networks
other(Pram)$comparePal