Data and code for: Are novel and co-xenic associations common in alien fungal and fungus-like plant pathogens?

ReadMe

This repository contains the data and analysis workflow supporting the study reported in the article "Are novel and co-xenic associations common in alien fungal and fungus-like plant pathogens?", published in New Phytologist. 

Data

• Associations.xlsx
  Contains all pathogen-plant-region records, with information on the spatial scale, region and associated continent, pathogen and plant names and biogeographic status. 
• Association_types.xlsx
  Contains summarised information on pathogen–plant associations aggregated across records.  Each observation represents a unique pathogen–plant combination and includes information on association type, biogeographic status, and spatial occurrence across regions and continental groupings.
• Model_input.xlsx
  Contains the final model input dataset used for statistical analyses of pathogen–plant–region associations. Each observation represents a unique pathogen–plant–region combination with complete predictor information required for the generalised linear mixed model.
• Pathogen_masterfile.xlsx
  Contains pathogen-level attributes used in the analyses of plant–fungal associations. Each observation corresponds to a unique fungal taxon and includes taxonomic information,  range characteristics, and host range indices derived from host–pathogen associations.
• lookup_fungal_taxa_to_exclude.csv
  List of the pathogen taxa that were excluded (see Supporting Information Table S1).
• lookup_plant_status_harmonisation.csv
  List of biogeographic status combinations across the three plant-distribution sources and their harmonised classification.
• lookup_native_ranges.xlsx
  List of (sub)continental native range information for alien pathogens, derived from literature. Full references are provided in the sheet 'references'.
• regions_sf.RData
  Contains the simple feature (sf) object with the spatial data for the study regions.

Code

The repository includes a ZIP archive containing:

• rendered HTML files generated from Quarto documents, with essential code blocks included
• R scripts used for server-based analyses

Workflow:

• 0_* – data preparation
• 1_* – statistical analyses

Feedback 

Despite careful curation, errors or omissions may remain. Users are encouraged to report any issues to the corresponding author.

Article Summary

1. Rationale: Impacts of alien fungal and fungus-like plant pathogens depend on host interactions, including novel associations with native plants and co-xenic associations with alien plants that do not share the same area of origin, both largely unquantified globally.

2. Methods: Combining global distribution and association data, we characterised associations across pathogens’ introduced regions, calculated host species richness and phylogenetic divergence, and examined predictors of novel/co-xenic associations.

3. Key results: Novel/co-xenic alien pathogen–plant association records were common (53%) and dominated by widespread generalists. They were found in about one-third of alien pathogens examined, mostly within their known phylogenetic host range. However, 46% of associations remained unclassified due to limited knowledge of pathogen biogeography. Novel/co-xenic associations were more likely for pathogens with larger introduced ranges, wider phylogenetic host range, economically used hosts co-occurring in the region and host communities phylogenetically similar to the recipient regions’ plant community. They were also more likely for host plants with no economic use and restricted native ranges, and in regions with higher plant species richness.

4. Conclusion: Novel/co-xenic associations are frequent and shaped by contact opportunity, phylogenetic host range and regional community composition. Unravelling fungal and fungus-like pathogen biogeography is key to assessing their full magnitude.