John Paul Cunningham

Dr. John Paul Cunningham

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Research Focus & Metrics

Academic Career Length

8Years (2019-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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30 July 2019 in GigaScience
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Journal Article
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APAlexander Piper
Alexander Piper
JBJana Batovska
Jana Batovska
NCNoel O I Cogan
Noel O I Cogan
JWJohn Weiss
John Weiss
JCJohn Paul Cunningham
John Paul Cunningham
MBMark Blacket
Mark Blacket
Trap-based surveillance strategies are widely used for monitoring of invasive insect species, aiming to detect newly arrived exotic taxa as well as track the population levels of established or endemic pests. Where these surveillance traps have low specificity and capture non-target endemic species in excess of the target pests, the need for extensive specimen sorting and identification creates a major diagnostic bottleneck. While the recent development of standardized molecular diagnostics has partly alleviated this requirement, the single specimen per reaction nature of these methods does not readily scale to the sheer number of insects trapped in surveillance programmes. Consequently, target lists are often restricted to a few high-priority pests, allowing unanticipated species to avoid detection and potentially establish populations.DNA metabarcoding has recently emerged as a method for conducting simultaneous, multi-species identification of complex mixed communities and may lend itself ideally to rapid diagnostics of bulk insect trap samples. Moreover, the high-throughput nature of recent sequencing platforms could enable the multiplexing of hundreds of diverse trap samples on a single flow cell, thereby providing the means to dramatically scale up insect surveillance in terms of both the quantity of traps that can be processed concurrently and number of pest species that can be targeted. In this review of the metabarcoding literature, we explore how DNA metabarcoding could be tailored to the detection of invasive insects in a surveillance context and highlight the unique technical and regulatory challenges that must be considered when implementing high-throughput sequencing technologies into sensitive diagnostic applications.

17 August 2020 in Agronomy
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WBWilliam Boston
William Boston
DLDiana Leemon
Diana Leemon
JCJohn Paul Cunningham
John Paul Cunningham
Carpophilus beetles are serious pests of Australian fruit and nut crops, causing significant damage through adult and larval feeding and vectoring plant diseases. Six strains of the entomopathogenic fungus Beauveria bassiana ((Balsamo) Vuillemin; Hypocreales: Cordycipitaceae), isolated from a range of hosts in Australia, together with one commercial strain, were screened for virulence to adult and larval stages of Carpophilus attacking stone fruits (C. davidsoni (Dobson)) and almonds (C. truncatus (Murray)) under laboratory conditions. The two species differed significantly in their susceptibility to the B. bassiana isolates. In the adult beetle assay, C. truncatus had a maximum Abbott’s control corrected mortality of 19% when treated with the most effective isolate, B54, compared to 52% for C.davidsoni. In larval bioassays, mortality rates for the two species were generally higher than adults: four isolates caused greater than 80% mortality in C. davidsoni; while only one isolate was considered effective against C. truncatus (causing 73% mortality), all other isolates caused less than 40% mortality. The results indicate promising potential for B. bassiana to be applied as a biopesticide as part of an integrated pest management strategy, which might take the form of a soil application against larvae or an autodissemination program using adult beetles.

25 November 2025 in Nature Ecology & Evolution
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Journal Article
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SWStuart A. West
Stuart A. West
SDSasha R. X. Dall
Sasha R. X. Dall
JCJohn Paul Cunningham
John Paul Cunningham
SASuzanne Alonzo
Suzanne Alonzo
AGAshleigh S. Griffin
Ashleigh S. Griffin
Behavioural ecology research has explained traits from foraging and cooperation to mating strategies and sex allocation. However, the size and interdisciplinary nature of this research can obscure the broader contributions that behavioural ecology has made and the major tasks for the future. We first assess the contributions of behavioural ecology to fundamental science, for both understanding nature and the scientific method. Second, we explore the application of behavioural ecology research to global challenges, from pests and pathogens to conservation and mitigating human impact. In all cases, progress has relied on a hypothesis-driven approach that combines mathematical modelling with empirical testing and the strategic choice of simplifying assumptions.

21 March 2023 in Insects
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Journal Article
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DJDuncan Douglas Jaroslow
Duncan Douglas Jaroslow
JCJohn Paul Cunningham
John Paul Cunningham
DSDavid I. Smith
David I. Smith
MSMartin J. Steinbauer
Martin J. Steinbauer
Invasive insects pose an increasing risk to global agriculture, environmental stability, and public health. Giant pine scale (GPS), Marchalina hellenica Gennadius (Hemiptera: Marchalinidae), is a phloem feeding scale insect endemic to the Eastern Mediterranean Basin, where it primarily feeds on Pinus halepensis and other Pinaceae. In 2014, GPS was detected in the southeast of Melbourne, Victoria, Australia, infesting the novel host Pinus radiata. An eradication program was unsuccessful, and with this insect now established within the state, containment and management efforts are underway to stop its spread; however, there remains a need to understand the insect’s phenology and behaviour in Australia to better inform control efforts. We documented the annual life cycle and seasonal fluctuations in activity of GPS in Australia over a 32 month period at two contrasting field sites. Onset and duration of life stages were comparable to seasons in Mediterranean conspecifics, although the results imply the timing of GPS life stage progression is broadening or accelerating. GPS density was higher in Australia compared to Mediterranean reports, possibly due to the absence of key natural predators, such as the silver fly, Neoleucopis kartliana Tanasijtshuk (Diptera, Chamaemyiidae). Insect density and honeydew production in the Australian GPS population studied varied among locations and between generations. Although insect activity was well explained by climate, conditions recorded inside infested bark fissures often provided the weakest explanation of GPS activity. Our findings suggest that GPS activity is strongly influenced by climate, and this may in part be related to changes in host quality. An improved understanding of how our changing climate is influencing the phenology of phloem feeding insects such as GPS will help with predictions as to where these insects are likely to flourish and assist with management programs for pest species.

17 March 2021 in bioRxiv
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APAlexander Piper
Alexander Piper
NCNoel OI I. Cogan
Noel OI I. Cogan
JCJohn Paul Cunningham
John Paul Cunningham
MBMark Blacket
Mark Blacket
Appropriate design and selection of PCR primers plays a critical role in determining the sensitivity and specificity of a metabarcoding assay. Despite several studies applying metabarcoding to insect pest surveillance, the diagnostic performance of the short “mini-barcodes” required by high-throughput sequencing platforms has not been established across the broader taxonomic diversity of invasive insects. We address this by computationally evaluating the diagnostic sensitivity and predicted amplification bias for 68 published and novel cytochrome c oxidase subunit 1 (COI) primers on a curated database of 110,676 insect species, including 2,625 registered on global invasive species lists. We find that mini-barcodes between 125-257 bp can provide comparable resolution to the full-length barcode for both invasive insect pests and the broader Insecta, conditional upon the subregion of COI targeted and the genetic similarity threshold used to identify species. Taxa that could not be identified by any barcode lengths were phylogenetically clustered within ‘problem groups’, many arising through taxonomic inconsistencies rather than insufficient diagnostic information within the barcode itself. Substantial variation in predicted PCR bias was seen across published primers, with those including 4-5 degenerate nucleotide bases showing almost no mismatch to major insect orders. While not completely universal, a single COI mini-barcode can successfully differentiate the majority of pest and non-pest insects from their congenerics, even at the small amplicon size imposed by 2 × 150 bp sequencing. We provide a ranked summary of high-performing primers and discuss the bioinformatic steps required to curate reliable reference databases for metabarcoding studies.

19 October 2023 in Australian Journal of Grape and Wine Research
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Journal Article
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CCC. W. Clarke
C. W. Clarke
JHJ. Henneken
J. Henneken
BCB. M. Carmody
B. M. Carmody
JCJohn Paul Cunningham
John Paul Cunningham
Background and Aims. Grapevine phylloxera, Daktulosphaira vitifoliae (Fitch), feeds on roots and leaves of Vitis spp. Susceptibility to phylloxera differs among rootstocks, such that Vitis spp. grafted onto resistant rootstocks can safeguard vineyards from phylloxera-induced damage in the long term. Diverse phylloxera genetic strains, however, vary in their ability to survive on different rootstocks. The 5C Teleki rootstock (V. berlandieri×V. riparia) is widely planted worldwide, but its resistance to phylloxera has not been characterised against the genetically diverse phylloxera strains present in Australia. Methods and Results. 5C Teleki roots and Vitis vinifera L. (positive control), either excised in Petri dishes or planted as whole plants in pots, were inoculated with eggs of six phylloxera strains (G1, G4, G19, G20, G30, and G38). On excised roots, G19, G20, G30, and G38 phylloxera survived to reproductive adults. The G1 and G4 phylloxera did not survive past the first instar stage. In potted vines, G4, G19, G20, G30, and G38 phylloxera strains induced nodosities on roots, but adults were only found on roots inoculated with G19 and G20 phylloxera strains. Conclusions. Results showed that 5C Teleki is resistant to the G1 phylloxera and susceptible to G19 strains. Performance of G4, G20, G30, and G38 differs depending on the assay used. 5C Teleki is likely tolerant of these strains. Significance of the study: the 5C Teleki rootstock is resistant to the G1 phylloxera strain but likely tolerant of others present in Australia. This implies that the rootstock can still host a population of phylloxera, and strict farm-gate hygiene should be employed to stop spread among vineyards and regions.