"Phylogenetic community structure shapes plant-pathogen networks" - Code and Supporting Material for Reproducibility

This repository holds code and supporting material for reproducing the figures and analyses described in the associated manuscript. The contents are divided into three zip files, each of which holds a folder. plant_pathogen_matrices.zip - This folder holds presence-absence count tables of all pathogen OTUs for each plant species. There is a separate matrix for each of the three focal habitats. sequence_processing_code.zip - This folder holds the workflow used to generate analysis-ready Phyloseq objects from the raw fastq files and associated metadata. It includes generating ASVs with DADA2, assigning taxonomy based on the UNITE database, clustering OTUs based on fungal phylogeny, designating putative plant pathogens, and quality-filtering the dataset. figures_and_statistics_code.zip - This folder holds the workflow used to produce all the figures and analyses shown in the manuscript. It includes the Phyloseq object produced by the sequence_processing_code.zip workflow, which contains the count tables, OTU taxonomy, OTU phylogenies, and DNA sequence information for all associated analyses. figure_sourcedata.zip - This folder contains the underlying data used for plotting each of the main figures and a readme file describing the contents of each dataset.