Session 2: Next generation national fruit fly diagnostics and handbook

SESSION 2: MORE ACCURATE AND TIMELY DIAGNOSTICS
TO BETTER INFORM BIOSECURITY DECISIONS
Next generation national fruit fly
diagnostics and handbook
Mark Schutze

biosecurity built on science
Next generation national fruit fly
diagnostics and handbook
Mark Schutze
Lecturer, QUT
Plant Biosecurity Cooperative Research Centre

 Tephritidae: a diverse family
- Over 5,000 species
- Pests in multiple genera, especially:
 Anastrepha
 Ceratitis
 Rhagoletis
What is the research addressing?

 Tephritidae: a diverse family
- Over 5,000 species
- Pests in multiple genera, especially:
 Anastrepha
 Ceratitis
 Rhagoletis
- Bactrocera
 Over 500 species
 Asia/Pacific centre of diversity

 Taxonomy and diagnostics ok for many, but not all
- Problematic pest species groups & complexes, e.g.
 Bactrocera dorsalis – Oriental fruit fly complex
 Bactrocera musae – Banana fruit fly complex
 Bactrocera frauenfeldi – Mango fruit fly complex
 Zeugodacus tau

 Taxonomy and diagnostics ok for many, but not all
- Some species are extremely variable
- Thoracic and abdominal colour patterns
 Often used as diagnostic characters

 Molecular markers (e.g., COI barcode)
- Work for some but not others – especially species complexes
- Unknown for many pest and closely related species
- Need to develop new Bactrocera- specific diagnostics

 Existing resources
- Primary literature

 Existing resources
- Primary literature
- Specific diagnostic resources

 Complexes relatively poorly represented
- Especially B. dorsalis, Z. tau
- Ongoing uncertainty about what’s what
- New species being added all the time
- Taxonomic revisions (incl. elevation of Zeugodacus)

 Intraspecific variation not fully covered
- E.g., B. correcta: “scutum black with dark red-
brown along lateral and posterior margins”

 APPROACH: Systematic research
- Include fresh Bactrocera and Zeugodacus from areas of high diversity (incl. Aus.)
- Key pest species and complexes; maximise intraspecific variation
- Molecular information from genomic approaches
 Hybrid enrichment and transcriptomics
 Phylogenetics and marker discovery
- Link directly to morphological variability
What are we doing about it?

 APPROACH: Systematic research
- Include fresh Bactrocera and Zeugodacus from areas of high diversity (incl. Aus.)
- Key pest species and complexes; maximise intraspecific variation
- Molecular information from genomic approaches
 Hybrid enrichment and transcriptomics
 Phylogenetics and marker discovery
- Link directly to morphological variability
 OBJECTIVE: Develop robust phylogenetics to lend confidence to
species relationships and identify taxon-specific molecular diagnostics

 >14,000 specimens, >100 species from Malaysia, Philippines, PNG,
Solomon Is., Fiji, Thailand, Australia (Qld)
Results so far

 >14,000 specimens, >100 species from Malaysia, Philippines, PNG,
Solomon Is., Fiji, Thailand, Australia (Qld)
 Transcriptomics:
- Five new transcriptomes for Bactrocera; one for Zeugodacus
- 1646 single copy loci present across all reference samples
- Refined to 1041 useable, of which 547 present in all tephritids, a further 69 best candidates for
diagnostics testing
- Five had avg % divergence greater than COI
- One, POP4, most promising as a ‘Bactrocera-specific barcode’
Results so far

Preliminary RAxML
POP4

biosecurity built on scienceZeugodacus
B. dorsalis complex
B. tryoni complex
B. frauenfeldi complex

B. frauenfeldi complex

 Anchored hybrid enrichment
- 47 samples shipped to Dr Bryan Lessard
- Representing a range of specimens: closely related species and intra-specific variation
- Underway, results due back imminently
 Potential for hundreds of diagnostic loci to evaluate, screen, validate
 Honours student evaluating other markers, ITS1, across a broad range of
species to evaluate utility
Results so far

 Linking with all-new diagnostic image bank of key taxa and close
relatives; one-to-one/DNA-morphology
Results so far

 Bactrocera tryoni
complex
- B. tryoni
- B. neohumeralis
- B. aquilonis -?
- B. melas - ?
A special case: The Qfly complex
?
?

 Bactrocera tryoni complex
- Linking with molecular research at Lincoln Univ – Karen Armstrong’s lab
- Include in our broader molecular work
- Mating compatibility studies

 Mating tests complete between two populations of B. aquilonis
- Kununurra vs Broome
- Random mating!
 Kununurra selected
- Cross with B. tryoni
- IAEA-Seibersdorf
- Early 2017
Results so far

 Diagnosticians: the people who need to identify flies!
- Reduce, ideally remove, ambiguity
- Pest from non-pest
- Exotic from native
 State and Federal agencies
- Departments of Agriculture
- Quarantine workers
 Horticultural industry
 Broader tephritid scientific community, here and abroad
Beneficiaries

 Research
- manuscripts – applied and pure (some in prep)
- taxonomic revisions
 New diagnostic tools: tailor-made molecular markers (e.g., POP4…)
The end-products

 Research
- manuscripts – applied and pure
- taxonomic revisions
 New diagnostic tools – tailor-made molecular markers (e.g., POP4)
 Version 3 of the Australian Handbook for the Identification of Fruit Flies
- Fully revised and updated format
 Fully revised ‘hard copy’ – new images, heavily pictorial
 Extended online resources – species pages, groundwork for online Lucid key
The end-products

 Plant Health Australia take a lead role to:
- Coordinate validation and endorsement of new diagnostic resources
- Facilitation of training workshops towards end of project
- Custodians of the Handbook
Delivery of end-products

 Physical handbook
- Useful for the front-line diagnostician
 Online resources
- More complex identifications, including those requiring molecular work
- Species profile pages
 Distribution
 Biology
 Pest status, quarantine concern, etc…
Use of research

 Dr. Craig Hull, Commonwealth Fruit Fly Coordinator, Plant Health Policy,
Department of Agriculture and Water Resources
“Fruit flies are the number-one pest of concern for international trade of horticultural
commodities.
Diagnostics are a critical component of the plant biosecurity system, and we rely on
having access to the most up to date high quality research that our international
trading partners can have confidence in.
This project will help keep Australia at the forefront of fruit fly diagnostics and
provide information that will support our international market access as well as help
safeguard us from exotic fruit fly species.”
End user advocate perspective

 Complete hybrid enrichment, digitisation, and marker development
 Validate newly developed molecular markers
 Complete mating tests for B. tryoni vs B. aquilonis
 Complete a Lucid key, at least of all key target taxa
 Start work on V. 3 of Handbook
 ‘Future proof’ to perpetuate beyond life of project
The future…

 For more information, please email
m.schutze@qut.edu.au

Session 2: Next generation national fruit fly diagnostics and handbook

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Session 2: Next generation national fruit fly diagnostics and handbook