PhyloControl: a phylogeny visualisation platform for risk analysis in weed biological control
Facilitators: Stephanie Chen and Alexander Schmidt-Lebuhn (CSIRO, Australia)
Key question and/or issue
The workshop will focus on the process of creating host test lists for weed biological control using a new tool called PhyloControl. The tool can efficiently generate a phylogeny of a nominated target weed and its relatives using GenBank sequence data and calculate distance measures, including degrees of separation and phylogenetic (patristic) distance.
Please note that this workshop requires R (https://www.r-project.org/) and RStudio (https://posit.co/download/rstudio-desktop/) to be installed prior to the workshop.
Background information
Phylogenetic distance is a key measure used to develop species lists for host specificity tests that delimit the fundamental and realised host range of candidate weed biocontrol agents to meet the assumptions of the centrifugal phylogenetic method. Plant pathogens and insects, even those with broad host ranges, exhibit some degree of phylogenetic conservatism in their host plant associations. 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, usually visualised as a phylogenetic tree generated from genetic data, together with plant functional traits and geospatial information. Currently, the process of obtaining a host test list is not standardised, and the manual steps are time-consuming and challenging.
We introduce a user-friendly visualisation tool called PhyloControl to aid researchers in their decision-making during biocontrol risk analysis. PhyloControl integrates taxonomic data, molecular data, spatial data, and plant traits in an intuitive interface, empowering biocontrol practitioners to summarise, visualise and analyse data efficiently.
Comprehensively sampled phylogenetic trees are often unavailable, and older published phylogenies often lack branch resolution and support, which increases uncertainty. PhyloControl includes a workflow implemented through Quarto notebooks in R that allows users to download publicly available DNA sequences and perform phylogenetic analyses. Additionally, other components of the modular workflow incorporate species distribution modelling to predict the current and potential extent of target weed species. PhyloControl will streamline the development of biocontrol host tests lists to support risk analysis and decision making in classical weed biological control.
The workshop will include hands-on sections interspersed with short lectures designed to provide background on using phylogenomics and species distribution modelling in a biocontrol context, as well as showcase projects that have used PhyloControl. Attendees are expected to bring their own laptop to the workshop to run R code in RStudio. The code will be publicly available via GitHub. Attendees will be guided through PhyloControl using an example target weed at the workshop which will equip them with the knowledge to apply the tool to their own biocontrol projects in the future. The workshop will help spread awareness and encourage adoption of PhyloControl. The session will also be used to gather feedback about the tool to improve future iterations of PhyloControl.