DOI: 10.5061/dryad.hqbzkh1ps
title: Microsatellite allele length of Phytophthora ramorum in San Mateo County California

description: We implement a population genetics approach to clarify the role that
 temporal and environmental variability, spatially distinct locations, and
 different hosts may have in the epidemiology of plant disease and the
 microevolution of its causative pathogen. In California and Southern
 Oregon (USA), the introduction of the invasive pathogen Phytophthora
 ramorum, causal agent of the widespread disease Sudden Oak Death (SOD),
 has resulted in extensive mortality of various oaks (Quercus sp.) and of
 tanoak (Notholithocarpus densiflorus). Although the disease can infect
 over a hundred hosts, California bay laurel (Umbellularia californica) is
 the most competent transmissive host but is not lethally affected by the
 disease. Using population genetics data, we identify the relationship
 among P. ramorum populations in bay laurels, oaks and tanoaks to clarify
 the contribution of each host on the epidemiology of SOD and the
 microevolution of its causal agent and to explore differences in
 population structure across sites and years. We conclude that bay laurel
 is the  primary source for infections of both tanoak and oak, and
 that tanoak contributes minimally to oak infection but can infect bay
 laurel, creating a secondary pathogen amplification process. Overall,
 pathogen diversity is associated with rainfall and presence of bay
 laurels, which sustain the largest populations of the pathogen.
 Additionally, we clarify that while bay laurels are a common source of
 inoculum, oaks and tanoaks act as sinks that maintain host-specific
 pathogen genotypes not observed in bay laurel populations. Finally, we
 conclude that different sites support a dominance of different pathogen
 genotypes. Some genotypes were widespread, while others were limited to a
 subset of the plots. Sites with higher bay laurel densities sustained a
 higher genotypic diversity of the pathogen. This work provides novel
 insight into the ecology and evolutionary trajectories of SOD epidemics in
 natural ecosystems.
description: Six sets of primers were used on the extracted <em>P.
 ramorum</em> DNA to amplify the following ten microsatellite loci
 known to be variable in the NA1 lineage; Ms18 and Ms64 (Ivors et al.
 2006), Ms39a, Ms39b, Ms43b, Ms43b, Ms45 (Prospero et al. 2007) and
 MsILVO145a, MsILVO145b, MsILVO145c (Vercauteren et al. 2010). PCR
 reactions were carried out as described by Eyre et al. (2013) and the
 thermal cycling program for each primer was set by following the varying
 protocols outlined in Ivors et al. 2006, Prospero et al. 2007, Mascheretti
 et al. 2008, and Vercauteren et al. 2010. Fragment analysis was performed
 with a 3730 ABI Sequencer using a LIZ 500 size standard (Applied
 Biosystems, Foster City, California). Fragment sizes were scored using
 Peakscanner V1.0 (ABI Biosystems) and were then converted to the
 appropriate number of microsatellite motif repeats for analysis. Each
 isolate was assigned a multilocus genotype (MLG) isolate using the Poppr
 package in R version 3.4.0 (R Core Team, 2017) for genetic analysis of
 populations with clonal reproduction (Kamvar et al. 2014).
  
description: # Microsatellite allele length of Phytophthora ramorum in San Mateo County
 California The table
 contains allele lengths at several loci without flanking regions ##
 Description of the data and file structure The first column identifies the
 Multi Locus Genotype (MLG) number, each MLG has a unique allele
 combination The second column indicates how many isolates of the pathogen
 belong to each MLG All other columns: each column identifies a different
 locus. Alleles at each locus for each MLG are identified by a number
 (length of microsatellite nucleotide sequence). All loci are 2n, and
 alleles are separated by a forward slash.