logo   Predicting plant host susceptibility to novel pests


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phyloSuscept is an application designed to predict which plant species are most likely to be susceptible to a particular plant pest, based on the known host range of that pest. It requires that user input a a comma-delimited (.csv) file with plant species that are known hosts of the pest. The user then has two options to select plant species of concern to evaluate:

(1) Custom: user can input a second list of plant species to evaluate for likely susceptibility (a comma-delimited (.csv) file).
(2) APHIS List: user can choose a pre-set list of 116 important crops (NASS), 447 trees (FIAS), and 806 US Federally Endangered plant taxa (FESA) -- view list

phyloSuscept creates a phylogenetic tree of the combined lists of plant taxa and calculates the evolutionary distances between each pair of plants. These distances are then used to calculated the probability that the pest will be able to attack each host of concern, based on results from:

Gilbert, G.S., R. Magarey, K. Suiter, and C.O. Webb. 2012. Evolutionary tools for phytosanitary risk analysis: phylogenetic signal as a predictor of host range of plant pests and pathogens. Evolutionary Applications 5: 869-878 doi:10.1111/j.1752-4571.2012.00265.x.

Probabilities are calculated separately for fungi, bacteria, oomycetes, insects, mites, nematodes, viruses, and plant parasites. User receives phylogenetic trees, distance matrices, and indices of the probability that each species of concern is likely to be attacked by a pest with that known host range. Please see user guide for detailed information.

phyloSuscept is a statistical tool still in development: use at your own risk.
For comments or more information, please contact Gregory Gilbert at ggilbert@ucsc.edu.

1. First, create a comma-delimited file with the scientific names of the plant species that are known hosts for your pest (download knownhosts.csv as an example by right-clicking and saving).

2. If you plan to use the custom version, create a separate file of plant species of concern (download localspecies.csv as an example by right-clicking and saving).

3. Click the Browse buttons to navigate to and select your file of known hosts.

4. Click on the Custom or APHIS button for Species of Concern, as desired. If choosing Custom, click the Browse button to select your file of species of concern.

5. Click the Upload and Execute button. Click where indicated to download the output results as a zip folder.

Upload Known & Concerned Species Files

Known species list:

Concerned species list: