Phylogenomics-driven host test list selection for weed biological control
A concern in weed biological control research is the potential for candidate biocontrol agents to impact not only the target weed but also native or economically important flora. The degree of evolutionary relatedness between the target weed species and a non-target species is a key predictor of the...
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| Format: | Article |
| Language: | English |
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Elsevier
2024-06-01
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| Series: | Biological Control |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S104996442400094X |
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| author | Stephanie H. Chen Ben Gooden Michelle A. Rafter Gavin C. Hunter Alicia Grealy Nunzio Knerr Alexander N. Schmidt-Lebuhn |
| author_facet | Stephanie H. Chen Ben Gooden Michelle A. Rafter Gavin C. Hunter Alicia Grealy Nunzio Knerr Alexander N. Schmidt-Lebuhn |
| author_sort | Stephanie H. Chen |
| collection | DOAJ |
| description | A concern in weed biological control research is the potential for candidate biocontrol agents to impact not only the target weed but also native or economically important flora. The degree of evolutionary relatedness between the target weed species and a non-target species is a key predictor of the susceptibility of the non-target to the biocontrol agent. To manage this risk, biocontrol practitioners need to understand the phylogenetic position of the host weed relative to non-target plant species. However, comprehensively sampled phylogenetic trees are often unavailable, with incomplete information scattered across multiple publications. Further, older published phylogenies based on Sanger sequence data often lack branch resolution and support, which increases uncertainty in biocontrol decision making. Decreasing sequencing cost and technological advances have led to phylogenomic approaches being more widely used to understand evolutionary relationships between species. For example, target capture sequencing methods using bait kits such as Angiosperms353 enable cost-effective and timely phylogenomic-level analysis of flowering plant groups at different scales. Here, we introduce a workflow to embed a comprehensive understanding of evolutionary relationships into the efficient development of host test lists in weed biological control. We demonstrate the effectiveness of the workflow through a case study on the major crop weed flaxleaf fleabane (Erigeron bonariensis). Phylogenomic analysis was conducted on 280 species of the tribe Astereae (family Asteraceae) occurring in Australia and New Zealand, clarifying relationships between the target species and related clades of native and non-native Astereae. We consider the phylogenetic tree in the context of a previously proposed host test list and discuss taxonomic implications, highlighting avenues of future molecular-based work to uncover the origin of Australian fleabanes. This study provides a workflow and demonstrates the practical application of target sequence capture for phylogenomic inference to support risk analysis and decision making in classical weed biological control. |
| format | Article |
| id | doaj-art-c79add3ce7274ed18be76b816f4a6f95 |
| institution | Kabale University |
| issn | 1049-9644 |
| language | English |
| publishDate | 2024-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Biological Control |
| spelling | doaj-art-c79add3ce7274ed18be76b816f4a6f952024-11-21T06:03:12ZengElsevierBiological Control1049-96442024-06-01193105529Phylogenomics-driven host test list selection for weed biological controlStephanie H. Chen0Ben Gooden1Michelle A. Rafter2Gavin C. Hunter3Alicia Grealy4Nunzio Knerr5Alexander N. Schmidt-Lebuhn6Centre for Australian National Biodiversity Research (a joint venture between Parks Australia and CSIRO), GPO Box 1700, Canberra ACT 2601, AustraliaCSIRO Health and Biosecurity, GPO Box 1700, Canberra ACT 2601, AustraliaCSIRO Health and Biosecurity, GPO Box 2583, Brisbane QLD 4001, AustraliaCSIRO Health and Biosecurity, GPO Box 1700, Canberra ACT 2601, AustraliaCentre for Australian National Biodiversity Research (a joint venture between Parks Australia and CSIRO), GPO Box 1700, Canberra ACT 2601, AustraliaCentre for Australian National Biodiversity Research (a joint venture between Parks Australia and CSIRO), GPO Box 1700, Canberra ACT 2601, AustraliaCentre for Australian National Biodiversity Research (a joint venture between Parks Australia and CSIRO), GPO Box 1700, Canberra ACT 2601, Australia; Corresponding author.A concern in weed biological control research is the potential for candidate biocontrol agents to impact not only the target weed but also native or economically important flora. The degree of evolutionary relatedness between the target weed species and a non-target species is a key predictor of the susceptibility of the non-target to the biocontrol agent. To manage this risk, biocontrol practitioners need to understand the phylogenetic position of the host weed relative to non-target plant species. However, comprehensively sampled phylogenetic trees are often unavailable, with incomplete information scattered across multiple publications. Further, older published phylogenies based on Sanger sequence data often lack branch resolution and support, which increases uncertainty in biocontrol decision making. Decreasing sequencing cost and technological advances have led to phylogenomic approaches being more widely used to understand evolutionary relationships between species. For example, target capture sequencing methods using bait kits such as Angiosperms353 enable cost-effective and timely phylogenomic-level analysis of flowering plant groups at different scales. Here, we introduce a workflow to embed a comprehensive understanding of evolutionary relationships into the efficient development of host test lists in weed biological control. We demonstrate the effectiveness of the workflow through a case study on the major crop weed flaxleaf fleabane (Erigeron bonariensis). Phylogenomic analysis was conducted on 280 species of the tribe Astereae (family Asteraceae) occurring in Australia and New Zealand, clarifying relationships between the target species and related clades of native and non-native Astereae. We consider the phylogenetic tree in the context of a previously proposed host test list and discuss taxonomic implications, highlighting avenues of future molecular-based work to uncover the origin of Australian fleabanes. This study provides a workflow and demonstrates the practical application of target sequence capture for phylogenomic inference to support risk analysis and decision making in classical weed biological control.http://www.sciencedirect.com/science/article/pii/S104996442400094XAsteraceaeDegrees of separationFleabaneHost test listPhylogenetic distancePhylogenomics |
| spellingShingle | Stephanie H. Chen Ben Gooden Michelle A. Rafter Gavin C. Hunter Alicia Grealy Nunzio Knerr Alexander N. Schmidt-Lebuhn Phylogenomics-driven host test list selection for weed biological control Biological Control Asteraceae Degrees of separation Fleabane Host test list Phylogenetic distance Phylogenomics |
| title | Phylogenomics-driven host test list selection for weed biological control |
| title_full | Phylogenomics-driven host test list selection for weed biological control |
| title_fullStr | Phylogenomics-driven host test list selection for weed biological control |
| title_full_unstemmed | Phylogenomics-driven host test list selection for weed biological control |
| title_short | Phylogenomics-driven host test list selection for weed biological control |
| title_sort | phylogenomics driven host test list selection for weed biological control |
| topic | Asteraceae Degrees of separation Fleabane Host test list Phylogenetic distance Phylogenomics |
| url | http://www.sciencedirect.com/science/article/pii/S104996442400094X |
| work_keys_str_mv | AT stephaniehchen phylogenomicsdrivenhosttestlistselectionforweedbiologicalcontrol AT bengooden phylogenomicsdrivenhosttestlistselectionforweedbiologicalcontrol AT michellearafter phylogenomicsdrivenhosttestlistselectionforweedbiologicalcontrol AT gavinchunter phylogenomicsdrivenhosttestlistselectionforweedbiologicalcontrol AT aliciagrealy phylogenomicsdrivenhosttestlistselectionforweedbiologicalcontrol AT nunzioknerr phylogenomicsdrivenhosttestlistselectionforweedbiologicalcontrol AT alexandernschmidtlebuhn phylogenomicsdrivenhosttestlistselectionforweedbiologicalcontrol |