School of BioSciences - Research Publications

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    Fungicides have transgenerational effects on Rhopalosiphum padi but not their endosymbionts
    Chirgwin, E ; Yang, Q ; Umina, PA ; Gill, A ; Soleimannejad, S ; Gu, X ; Ross, P ; Hoffmann, AA (JOHN WILEY & SONS LTD, 2022-11)
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    A working guide to spatial mechanistic modelling in Julia
    Schouten, R ; Baudrot, V ; Umina, P ; Maino, J (Wiley Open Access, 2022-05)
    Models that can predict the dynamics of larger scale ecological processes are increasingly important in a rapidly changing world. The Julia language gives a unique opportunity to produce new, generic tools to develop spatial mechanistic models, and to simultaneously increase their performance, resolution and predictive power. Here, we describe two new Julia software packages, DynamicGrids.jl and Dispersal.jl, that facilitate the development of spatial mechanistic models that are concise, extensible and performant, with several key attributes. First, they allow arbitrary spatially and temporally heterogeneous inputs (e.g. regional climatic data to drive population dynamics). Second, they apply rules to discrete spatial grids, including: (a) single grid cells (e.g. population growth, Allee effects, land‐use change), (b) neighborhoods (e.g. local dispersal); and (c) arbitrary locations (e.g. long‐distance wind dispersal, human‐mediated dispersal). Finally, they allow interactions between multiple grids (e.g. predator–prey models, management/environmental feedbacks). Through in‐line examples, we explore how these properties can be used to develop simple and complex grid‐based mechanistic models that run on both CPUs and GPUs. We demonstrate models of population growth, wind and self‐directed dispersal and host–parasitoid dynamics. We also demonstrate the ease by which custom rules can be combined with rules provided by packages, and the potential for use in other fields and interdisciplinary research. These Julia packages provide concise, extensible and performant tools for a wide range of grid‐based spatial models in ecology and beyond. More broadly, they highlight new opportunities for ecological modelling using the Julia language, with its combination of clear syntax, extensibility from its solution to the expression problem and its performance on CPUs and GPUs.
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    Is what you see what you get? The relationship between field observed and laboratory observed aphid parasitism rates in canola fields
    Ward, SE ; Umina, PA ; Parry, H ; Balfour-Cunningham, A ; Cheng, X ; Heddle, T ; Holloway, JC ; Langley, C ; Severtson, D ; Van Helden, M ; Hoffmann, AA (JOHN WILEY & SONS LTD, 2022-08)
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    Spirotetramat resistance in Myzus persicae (Sulzer) (Hemiptera: Aphididae) and its association with the presence of the A2666V mutation
    Umina, PA ; Bass, C ; van Rooyen, A ; Chirgwin, E ; Arthur, AL ; Pym, A ; Mackisack, J ; Mathews, A ; Kirkland, L (JOHN WILEY & SONS LTD, 2022-11)
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    Genome-wide SNPs of vegetable leafminer, Liriomyza sativae: Insights into the recent Australian invasion
    Xu, X ; Schmidt, TL ; Liang, J ; Ridland, PM ; Chung, J ; Yang, Q ; Jasper, ME ; Umina, PA ; Liu, W ; Hoffmann, AA (WILEY, 2022-07)
    Liriomyza sativae, the vegetable leafminer, is an important agricultural pest originally from the Americas, which has now colonized all continents except Antarctica. In 2015, L. sativae arrived on the Australian mainland and established on the Cape York Peninsula in the northeast of the country near the Torres Strait, which provides a possible pathway for pests to enter Australia and evade biosecurity efforts. Here, we assessed genetic variation in L. sativae based on genome-wide single nucleotide polymorphisms (SNPs) generated by double digest restriction-site-associated DNA sequencing (ddRAD-seq), aiming to uncover the potential origin(s) of this pest in Australia and contribute to reconstructing its global invasion history. Our fineRADstructure results and principal component analysis suggest Australian mainland populations were genetically close to populations from the Torres Strait, whereas populations from Asia, Africa, and Papua New Guinea (PNG) were more distantly related. Hawaiian populations were genetically distinct from all other populations of L. sativae included in our study. Admixture analyses further revealed that L. sativae from the Torres Strait may have genetic variation originating from multiple sources including Indonesia and PNG, and which has now spread to the Australian mainland. The L. sativae lineages from Asia and Africa appear closely related. Isolation-by-distance (IBD) was found at a broad global scale, but not within small regions, suggesting that human-mediated factors likely contribute to the local spread of this pest. Overall, our findings suggest that an exotic Liriomyza pest invaded Australia through the Indo-Papuan conduit, highlighting the importance of biosecurity programs aimed at restricting the movement of pests and diseases through this corridor.
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    Australian Bryobia mites (Trombidiformes: Tetranychidae) form a complex of cryptic taxa with unique climatic niches and insecticide responses
    Umina, PA ; Weeks, AR ; Maino, JL ; Hoffmann, AA ; Song, SV ; Thia, J ; Severtson, D ; Cheng, X ; van Rooyen, A ; Arthur, AA (JOHN WILEY & SONS LTD, 2022-07)
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    Warmer temperatures reduce chemical tolerance in the redlegged earth mite (Halotydeus destructor), an invasive winter-active pest
    Thia, JA ; Cheng, X ; Maino, J ; Umina, PA ; Hoffmann, AA (JOHN WILEY & SONS LTD, 2022-07)
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    Climate contributes to the evolution of pesticide resistance
    Maino, JL ; Umina, PA ; Hoffmann, AA (WILEY, 2018-02)
    Abstract Aim The evolution of pesticide resistance through space and time is of great economic significance to modern agricultural production systems, and consequently, is often well documented. It can thus be used to dissect the evolutionary and ecological processes that underpin large‐scale evolutionary responses. There are now nearly 600 documented cases of pesticide resistance in arthropod pests. Although the evolution of resistance is often attributed to the persistent use of chemicals for pest suppression, the rate of development of resistance should also depend on other factors, including climatic conditions that influence population size and generation time. Here, we test whether climatic variables are linked to evolution of resistance by examining the spatial pattern of pyrethroid resistance in an important agricultural pest. Location Southern, agricultural regions of Australia. Time period 2007–2015. Major taxa studied The redlegged earth mite, Halotydeus destructor. Methods We quantified patterns of chemical usage based on paddock histories and collated long‐term climatic data. These data were then compared against presence–absence data on resistance using a boosted regression‐tree approach, applied here for the first time to the spatial categorization of pesticide resistance. Results Although chemical usage was a key driver of resistance, our analysis revealed climate‐based signals in the spatial distribution of resistance, linked to regional variation in aridity, temperature seasonality and precipitation patterns. Climatic regions supporting increased voltinism were positively correlated with resistance, in line with expectations that increased voltinism should accelerate evolutionary responses to selection pressures. Main conclusions Our findings suggest that the prediction of rapid evolutionary processes at continental scales, such as pesticide resistance, will be improved through methods that incorporate climate and ecology, in addition to more immediate selection pressures, such as chemical usage. Boosted regression trees present a powerful tool in the management of resistance issues that has hitherto not been used.
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    Discovery of metabolic resistance to neonicotinoids in green peach aphids (Myzus persicae) in Australia
    de Little, SC ; Edwards, O ; van Rooyen, AR ; Weeks, A ; Umina, PA (WILEY, 2017-08)