Global trade continues to increase the risk of exotic pest incursions into Australia, with shipping pathways acting as a major route for “hitchhiker” species. Australia’s biosecurity system, led by DAFF, relies on detection and surveillance measures across pre-border, border, and post-border stages to mitigate this risk. Recent advances in molecular technologies have significantly improved the sensitivity and speed of pest detection, including the use of environmental DNA (eDNA) from matrices such as dust and air. These approaches provide time-sensitive evidence for the presence of high-priority pests in complex environments such as shipping containers.
However, detection alone is not sufficient. A critical gap remains in determining the provenance of detected pests, information that is essential for identifying incursion pathways, assessing reinvasion risk, and guiding targeted response strategies. While genomic approaches such as reduced-representation sequencing (e.g. DArTseq) enable population-level resolution, their application in operational biosecurity systems remains limited. This project addresses this gap by applying genomic technologies to infer pest provenance and integrating these outputs into biosecurity decision-making frameworks.
Aim: The aim of this project is to develop and apply genomic and environmental DNA approaches to determine the geographic provenance of high-priority biosecurity pests and deliver tools to support surveillance and response decision-making.
Meet the Postdoctoral Research Fellow on this project
Dr Rachel Tulloch
Rachel is a Post Doctoral Research Fellow at the University of Canberra. Her research focuses on determining the provenance of invasive pests using genomic data. By analysing population genetic signatures, she works to reconstruct incursion pathways, distinguish between single and multiple introduction events, and assess ongoing reinvasion risk.
Using the green vegetable bug as a proof-of-concept species, she is co-designing analytical frameworks and workflows with the Department of Agriculture, Fisheries and Forestry (DAFF) to ensure outputs directly inform national surveillance, response prioritisation, and control strategies.
Her research applies population genomic and high-throughput sequencing approaches to invasive pest surveillance and expands genomic tools.
By integrating advanced sequencing technologies with robust bioinformatic pipelines, she translates complex genomic data into operational insights for policy and decision-makers. Her overarching objective is to ensure that advances in genomics deliver practical, evidence-based outcomes for Australia’s plant biosecurity system through strong partnerships with DAFF, industry, and Training Centre researchers.
Also on this project are:
Dianne Gleeson and Alejandro Trujillo-Gonzales, University of Canberra
Mike Elias, Australian Government Department for Agriculture, Fisheries and Forestry.
Approach
This project integrates genomic profiling with diagnostic standardisation to generate robust and actionable provenance information for biosecurity decision-making. Focusing on high-priority hitchhiker pest species identified in consultation with Department of Agriculture, Fisheries and Forestry, the project combines tissue-derived and environmental DNA approaches to enable both detection and geographic origin inference within operational contexts.
A central component is the development of certified reference materials (CRMs) in collaboration with National Measurement Institute to standardise calibration and validation across PCR and high-throughput sequencing workflows. These will underpin assay development and environmental testing, ensuring reproducibility and defensibility of results. Genomic approaches (e.g. DArTseq) will be used to characterise population structure and identify provenance-informative markers, which will be translated into molecular tools and tested across tissue and environmental samples (e.g. dust and air) to evaluate real-world applicability.
Key Methods and Activities
- Source specimens spanning broad geographic ranges (target: >60% of species distribution where feasible)
- Generate genome-wide datasets for target pest species (≥3 high-priority species)
- Characterise population structure and identify provenance-informative markers (target:assignment accuracy >80% at regional scale)
- Develop molecular assays for detection and provenance inference
- Develop and validate CRMs for PCR and HTS-based diagnostics
- Benchmark sensitivity, specificity, and reproducibility across workflows (target: CV <20% acrosslabs/workflows where tested)
Want to know more? Email plantbiosecurity@anu.edu.au.