phylocontrol-geninput

A phylogeny and spatial data visualisation interface for risk analysis and decision support in weed biological control.

Introduction

PhyloControl is a user-friendly visualisation tool to aid biocontrol researchers in their decision-making during risk analysis. Thorough host-specificity testing is crucial to minimise the risk of off-target damage by biocontrol agents to native and economically important plant species. To facilitate this, host test lists need to be developed from an understanding of evolutionary relationships. The process of obtaining a host test list is currently not standardised, and the manual steps may be time-consuming and challenging, introducing risks if taxonomic associations with the target weeds are uncertain or if the taxonomy of potential non-target species is poorly resolved. PhyloControl integrates taxonomic data, molecular data, spatial data, and plant traits in an intuitive interactive interface, empowering biocontrol practitioners to summarise, visualise, and analyse data efficiently.

This repository, phylocontrol-geninput, contains the four Quarto notebooks to generate inputs for the R Shiny visualisation application. The application is available from the phylocontrol-viz repository and contains the source code for the {phylocontrol.viz} package.

Install and run

To run these Quarto notebooks, clone this repository to your local computer and open the .qmd files using RStudio to edit and run them. Each notebook is self-contained and can be run independently. This allows users to skip steps if you already have input data from other sources.

Key outputs from each notebook

1_Species_list.qmd

A csv file containing a list of scientific names of the target weed and related species e.g. Erigeron_species_list.csv

2_Occurrences.qmd

A csv file of point occurrence data containing the key columns ‘species’, ‘decimalLatitude’, ‘decimalLongitude’, and ‘country’ e.g. Erigeron_occurrences.csv

3_Species_distribution_modelling.qmd

A sdm/ folder containing folders maxent_results/ and/or climatch_results/. There is another directory indicating the climate layers used e.g. chelsa2.1_bio/ which then contains a folder for each species run. Key outputs for visualisation are the grid files e.g. maxent_predict.grd and climatch_predict.grd and in the case of MaxEnt, the maxent_thresholds.csv file.

4_Sequences_and_phylogenomics.qmd

A phylogenetic tree in Newick format e.g. Erigeron.tre. It should be outgroup rooted.

It is recommended to copy the output files needed for the PhyloControl visualisation application into a separate directory set up specifically for the visualisation app which contains a folder for each study group e.g. App_data/Erigeron/.

You can also optionally add a text file containing the default target weed as well as a csv file containing traits to visualise with heatmaps. For an example of this directory structure, have a look at the App_data folder in the supplementary data for the manuscript.

Demo server

Try out the demo version of the visualisation application.

Code of Conduct

Please note that this project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Citing PhyloControl

The PhyloControl paper is currently in review. For now, please cite the pre-print on bioRxiv.

Stephanie H. Chen, Lauren Stevens, Ben Gooden, Michelle A. Rafter, Nunzio Knerr, Peter H. Thrall, Louise Ord, Alexander N. Schmidt-Lebuhn (2025). PhyloControl: a phylogeny visualisation platform for risk analysis in weed biological control. bioRxiv. DOI: 10.1101/2025.06.11.658203