PhyloControl: A phylogeny visualisation platform for risk analysis in weed biological control
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...
Saved in:
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2025-10-01
|
| Series: | Biological Control |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1049964425001690 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849771758098317312 |
|---|---|
| author | Stephanie H. Chen Lauren Stevens Ben Gooden Michelle A. Rafter Nunzio Knerr Peter H. Thrall Louise Ord Alexander N. Schmidt-Lebuhn |
| author_facet | Stephanie H. Chen Lauren Stevens Ben Gooden Michelle A. Rafter Nunzio Knerr Peter H. Thrall Louise Ord Alexander N. Schmidt-Lebuhn |
| author_sort | Stephanie H. Chen |
| collection | DOAJ |
| description | 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 to native and economically important plant species. Host test lists need to be developed from an understanding of evolutionary relationships, usually visualised as a phylogenetic tree, 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, open-source visualisation tool called PhyloControl to aid researchers in biocontrol risk analysis. 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. 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 perform phylogenetic analyses on GenBank DNA sequences. The modular workflow also incorporates 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. |
| format | Article |
| id | doaj-art-82a99345bc274a4fa945287c5c8016f0 |
| institution | DOAJ |
| issn | 1049-9644 |
| language | English |
| publishDate | 2025-10-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Biological Control |
| spelling | doaj-art-82a99345bc274a4fa945287c5c8016f02025-08-20T03:02:30ZengElsevierBiological Control1049-96442025-10-0120910585910.1016/j.biocontrol.2025.105859PhyloControl: A phylogeny visualisation platform for risk analysis in weed biological controlStephanie H. Chen0Lauren Stevens1Ben Gooden2Michelle A. Rafter3Nunzio Knerr4Peter H. Thrall5Louise Ord6Alexander N. Schmidt-Lebuhn7CSIRO, Centre for Australian National Biodiversity Research (A Joint Venture Between Parks Australia and CSIRO), GPO Box 1700, Canberra ACT 2601, AustraliaCSIRO Information Management and Technology, Clayton, VIC 3168, AustraliaCSIRO Health and Biosecurity, GPO Box 1700, Canberra ACT 2601, AustraliaCSIRO Health and Biosecurity, GPO Box 2583, Brisbane QLD 4001, AustraliaCSIRO, Centre for Australian National Biodiversity Research (A Joint Venture Between Parks Australia and CSIRO), GPO Box 1700, Canberra ACT 2601, AustraliaCSIRO National Collections & Marine Infrastructure, GPO Box 1700, Canberra ACT 2601, AustraliaCSIRO Information Management and Technology, Eveleigh NSW 2015, AustraliaCSIRO, Centre for Australian National Biodiversity Research (A Joint Venture Between Parks Australia and CSIRO), GPO Box 1700, Canberra ACT 2601, Australia; Corresponding author.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 to native and economically important plant species. Host test lists need to be developed from an understanding of evolutionary relationships, usually visualised as a phylogenetic tree, 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, open-source visualisation tool called PhyloControl to aid researchers in biocontrol risk analysis. 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. 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 perform phylogenetic analyses on GenBank DNA sequences. The modular workflow also incorporates 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.http://www.sciencedirect.com/science/article/pii/S1049964425001690Biological controlPhylogeneticsSpecies distribution modellingWeeds |
| spellingShingle | Stephanie H. Chen Lauren Stevens Ben Gooden Michelle A. Rafter Nunzio Knerr Peter H. Thrall Louise Ord Alexander N. Schmidt-Lebuhn PhyloControl: A phylogeny visualisation platform for risk analysis in weed biological control Biological Control Biological control Phylogenetics Species distribution modelling Weeds |
| title | PhyloControl: A phylogeny visualisation platform for risk analysis in weed biological control |
| title_full | PhyloControl: A phylogeny visualisation platform for risk analysis in weed biological control |
| title_fullStr | PhyloControl: A phylogeny visualisation platform for risk analysis in weed biological control |
| title_full_unstemmed | PhyloControl: A phylogeny visualisation platform for risk analysis in weed biological control |
| title_short | PhyloControl: A phylogeny visualisation platform for risk analysis in weed biological control |
| title_sort | phylocontrol a phylogeny visualisation platform for risk analysis in weed biological control |
| topic | Biological control Phylogenetics Species distribution modelling Weeds |
| url | http://www.sciencedirect.com/science/article/pii/S1049964425001690 |
| work_keys_str_mv | AT stephaniehchen phylocontrolaphylogenyvisualisationplatformforriskanalysisinweedbiologicalcontrol AT laurenstevens phylocontrolaphylogenyvisualisationplatformforriskanalysisinweedbiologicalcontrol AT bengooden phylocontrolaphylogenyvisualisationplatformforriskanalysisinweedbiologicalcontrol AT michellearafter phylocontrolaphylogenyvisualisationplatformforriskanalysisinweedbiologicalcontrol AT nunzioknerr phylocontrolaphylogenyvisualisationplatformforriskanalysisinweedbiologicalcontrol AT peterhthrall phylocontrolaphylogenyvisualisationplatformforriskanalysisinweedbiologicalcontrol AT louiseord phylocontrolaphylogenyvisualisationplatformforriskanalysisinweedbiologicalcontrol AT alexandernschmidtlebuhn phylocontrolaphylogenyvisualisationplatformforriskanalysisinweedbiologicalcontrol |