#### ReadMe File for Humphrey et al., 2014. Molecular Ecology #### PART 1: ReadMe for PTH_Data/ ## for all files: 'NA' = not available (missing data) ## FILE(S): master.199.txt master.199.txt master.199.txt leaf.master.199.txt leaf.master.160.txt leaf.master.125.txt leaf.master.4.txt These data files contain information on each bacterial sample observed or isolated as part of this study. The script data.source.final.r manipulates the data from these files to compile a total bacterial count per leaf, as well as breaks down this total into the contribution from several specific bacterial OTUs. See script comments for additional details. # Column headers and description for each header: # These header definitions pertain to all of the aforementioned files. morphotype.id identifier for each morphotype that the isolate groups within leaf.id unique identifier for each leaf collected as part of this survey type bacterial "type" observed within each plated leaf homogenate isolate.id identifier for each bacterial isolate (leaf.id + type = bacteria isolate id) otu.inferred This column (binary; 0/1) indicates whether the OTU for this sample was statistically inferred using a Bayesian approach (see Methods of manuscript for details) CFU.1 The raw counts of bacteria of this type within the first replicate spot on the King's B petri dish CFU.2 The raw counts of bacteria of this type within the second replicate spot on the King's B petri dish dilution The dilution factor of the 40-ul spot on the King's B plate (see Methods for details) CFU The calculated CFU for this type in the leaf (accounting for dilution factor of spot and fraction of leaf homogenate plated) otu.03 The unique ID of the OTU to which this sample was assigned RDP.03 The name of the OTU named by Ribosomal Database Project after a randomly selected sequence from each 97% 16S rRNA cluster (see Methods) height Height in cm of the stem from which the samples leaf was derived n.leaves The number of leaves on the stem from which the samples leaf was derived n.mines The number of leaf mines from Scapyomyza nigrita leaf miners on the leaves along the stem from which the samples leaf was derived n.mined.leaves The number of leaf mines from Scapyomyza nigrita leaf miners on the leaves along the stem from which the samples leaf was derived is.mined Whether or not (binary; 0/1) the sampled leaf itself had a S. nigrita leaf mine on it leaf.num The leaf position (counting from the most basal leaf on the stem) of the sampled leaf beetle Whether or not (binary; 0/1) the sampled leaf itself had Phaedon sp. beetle damage on it n.mts The number of bacterial types observed within the indicated leaf sample n.otus.03 The number of 97% 16S rRNA OTUs observed within the indicated leaf sample tot.cfu The bacterial CFU summed across all types within the sampled leaf log.tot.cfu log10 of the previous column avg.cfu average CFU per type per leaf log.avg.cfu log10 of the previous column leaf.area Area of the sampled leaf (cm-2) area.yellow.not.mined Area of leaf not mined (cm-2) area.mined Area of leaf mined (cm-2) area.beetle.not.mined Area of leaf not beetle damaged (cm-2) percent.mined Proportion of leaf area mined (cm-2) percent.yellow Proportion of leaf area chlorotic (cm-2) percent.beetle Proportion of leaf area damaged by beetles (cm-2) percent.dmg Total proportion damaged (mined+beetle+chlorosis; cm-2) total.dmg Total area damaged (mined+beetle+chlorosis; cm-2) ## FILE: geodist_new.txt Pairwise distance in meters between plots from which leaves were sampled. This is an input file for Mantel test. See PTH_Scripts/R/2013-12-CommunityAnalyses.r for details. ## FILE: field.hormone.exp.master.txt Data from field experiment using hormone treatments in plots of bittercress (see Methods). # Column headers and their descriptions: tx Treatment (mock vs. tx) - two levels plot.type The plot "condition" which describes the plot type that was further divided in to mock vs. tx sub.plot Quadrants of the sub-plot from which plant data were recorded (see Methods for details and Figure S1 for exp. design) stem.num The arbitrary stem i.d. for the plants from which data were recorded height Stem height in cm n.leaves The number of leaves on the stem n.stips The number of stipples (feeding punctures) created by S. nigrita adult females n.stip.leaves The number of leaves with stippled on them n.mines The number of mines totalled across all leaves on the stem n.mined.leaves The number of leaves with mines along the stem ## FILE: dmg1.txt Input file for perMANOVA of Unifrac distances vs. leaf damage; contains presence/absence of damage on leaves from which Pseudomonas spp. isolates were derived. ## FILE: unweighted_unifrac_dm.txt Unweighted and non-normalized Unifrac distances among leaf samples with respect to Pseudomonas spp. diversity (based on CFU counts). This file was used as input file for perMANOVA analysis of Unifrac distance vs. herbivory See PTH_Scripts/R/2013-12-PseudomonasAnalyses.r for details. ## FILE: weighted_normalized_unifrac_dm.txt Weighted and normalized Unifrac distances among leaf samples with respect to Pseudomonas spp. diversity (based on CFU counts). This file was used as input file for perMANOVA analysis of Unifrac distance vs. herbivory See PTH_Scripts/R/2013-12-PseudomonasAnalyses.r for details. #### PART 2: ReadMe for PTH_Scripts/ ##FILE: Mathematica/BayesianIsolateAssignment.nb This file contains the Mathematica code to calculate the prior probability that no off-diagonal observations were made in our sample of 160 isolates. Off-diagonal observations mean that either (1) the morphotype of an isolate matches other morphotypes present within more than one OTU, or (2) ##FILE: R/data.source.final.r This R script file contains the required code to generate the final data frames used for the analyses described in the community analyses and Pseudomonas analyses files (below). See comments in script for details. The entire script is executable in total and will not output much, but instead stores all of the downstream data frames as objects. ##FILE: R/2013-12-CommunityAnalyses.r This R script file contains all of the code for the community analyses in the manuscript, details of which are in the code comments. Each code block can be run in R as a whole, and many of the results outputs are already generated for export using functions such as write.table(). If not, the particular model results (e.g.) can be reconstructed just by summarizing the results of the various objects that have been produced by the code. ##FILE: R/2013-12-PseudomonasAnalyses.r This R script file contains all code required to perform analyses of Pseudomonas diversity. Each code block pertains to a separate analysis, as above, and the results are stored as model objects. ##FILE: R/g.test.r This R script is required source code for running the G-test that appears as the second code block in 2013-12-PseudomonasAnalyses.r. There is no need to manually load the functions in this script, as they are already called from within 2013-12-PseudomonasAnalyses.r. ##FILE: R/2013-12-FieldHormoneExperiment.r This R script file contains GLMM scripts for the SA/JA/Mock bittercress field experiment (see Methods; results displayed in Figure 2). #### PART 3: ReadMe for PTH_SequenceData/ ##FILES: 16S/ 16S.1.aln.final.fasta 16S.1.aln.final.phylip Multiple sequence alignments from which the phylogenetic tree depicted in Figure S2 was produced using RAxML. ##FILE: 16S/raxml1.csh This file contains the shell script that was used to execute the RAxML run that produced the following tree results: RAxML_bestTree.run2 RAxML_bipartitions.run2 RAxML_bipartitionsBranchLabels.run2 RAxML_bootstrap.run2 RAxML_info.run2 ##FILE: 16S/RAxML_bipartitions.run2 This Newick file contains the tree depicted in Figure S2. ##FILES: Pseudomonas_MLST/ PTH2013_FinalMLSTAlignment.fasta PTH2013_FinalMLSTAlignment.phylip Multiple sequence alignments from which the Pseudomonas phylogenetic tree depicted in was produced using RAxML. This tree topology forms the basis for designating isolates as either Pseudomonas syringae group or P. fluorescens group. Notably, 34E and 8B are sister to all known major Pseudomonas groups and were thus not included in the G-test reported in the manuscript. ##FILE: Pseudomonas_MLST/raxml2.csh This file contains the shell script that was used to execute the RAxML run that produced the following tree results: RAxML_bestTree.mlstPseudomonas RAxML_bipartitions.mlstPseudomonas RAxML_bipartitionsBranchLabels.mlstPseudomonas RAxML_bootstrap.mlstPseudomonas RAxML_info.mlstPseudomonas These tree files were generated from a separate run from that depicted in Figure 6A and differs only in the bootstrap support for internal nodes, which stems from difficulties placing the taxa 34E and 8B. The major nodes representing the P. syringae and P. fluorescens groups are reconstructed to a similar degree of confidence. Re-running the tree after pruning 34E and 8B should produce a tree with high bootstrap support for most internal nodes. P. stutzeri sequence was used as an outgroup, and the P. putida lineage was collapsed for clarity in the tree depicted in Figure 6A.