School of BioSciences - Research Publications
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ItemFungicides have transgenerational effects on Rhopalosiphum padi but not their endosymbionts(JOHN WILEY & SONS LTD, 2022-11)
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ItemA working guide to spatial mechanistic modelling in Julia(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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ItemGenome-wide SNPs of vegetable leafminer, Liriomyza sativae: Insights into the recent Australian invasion(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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ItemWarmer temperatures reduce chemical tolerance in the redlegged earth mite (Halotydeus destructor), an invasive winter-active pest(JOHN WILEY & SONS LTD, 2022-07)
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ItemThe mitogenome of Halotydeus destructor (Tucker) and its relationships with other trombidiform mites as inferred from nucleotide sequences and gene arrangements(WILEY, 2021-10)The redlegged earth mite, Halotydeus destructor (Tucker, 1925: Trombidiformes, Eupodoidea, Penthaleidae), is an invasive mite species. In Australia, this mite has become a pest of winter pastures and grain crops. We report the complete mitogenome for H. destructor, the first to represent the family Penthaleidae, superfamily Eupodoidea. The mitogenome of H. destructor is 14,691 bp in size, and has a GC content of 27.87%, 13 protein-coding genes, two rRNA genes, and 22 tRNA genes. We explored evolutionary relationships of H. destructor with other members of the Trombidiformes using phylogenetic analyses of nucleotide sequences and the order of protein-coding and rRNA genes. We found strong, consistent support for the superfamily Tydeoidea being the sister taxon to the superfamily Eupodoidea based on nucleotide sequences and gene arrangements. Moreover, the gene arrangements of Eupodoidea and Tydeoidea are not only identical to each other but also identical to that of the hypothesized arthropod ancestor, showing a high level of conservatism in the mitogenomic structure of these mite superfamilies. Our study illustrates the utility of gene arrangements for providing complementary information to nucleotide sequences with respect to inferring the evolutionary relationships of species within the order Trombidiformes. The mitogenome of H. destructor provides a valuable resource for further population genetic studies of this important agricultural pest. Given the co-occurrence of closely related, morphologically similar Penthaleidae mites with H. destructor in the field, a complete mitogenome provides new opportunities to develop metabarcoding tools to study mite diversity in agro-ecosystems. Moreover, the H. destructor mitogenome fills an important taxonomic gap that will facilitate further study of trombidiform mite evolution.
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ItemHigh Incidence of Related Wolbachia across Unrelated Leaf-Mining Diptera(MDPI, 2021-09)The maternally inherited endosymbiont, Wolbachia pipientis, plays an important role in the ecology and evolution of many of its hosts by affecting host reproduction and fitness. Here, we investigated 13 dipteran leaf-mining species to characterize Wolbachia infections and the potential for this endosymbiont in biocontrol. Wolbachia infections were present in 12 species, including 10 species where the Wolbachia infection was at or near fixation. A comparison of Wolbachia relatedness based on the wsp/MLST gene set showed that unrelated leaf-mining species often shared similar Wolbachia, suggesting common horizontal transfer. We established a colony of Liriomyza brassicae and found adult Wolbachia density was stable; although Wolbachia density differed between the sexes, with females having a 20-fold higher density than males. Wolbachia density increased during L. brassicae development, with higher densities in pupae than larvae. We removed Wolbachia using tetracycline and performed reciprocal crosses between Wolbachia-infected and uninfected individuals. Cured females crossed with infected males failed to produce offspring, indicating that Wolbachia induced complete cytoplasmic incompatibility in L. brassicae. The results highlight the potential of Wolbachia to suppress Liriomyza pests based on approaches such as the incompatible insect technique, where infected males are released into populations lacking Wolbachia or with a different incompatible infection.
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ItemGlobal patterns in genomic diversity underpinning the evolution of insecticide resistance in the aphid crop pest Myzus persicae.(Springer Science and Business Media LLC, 2021-07-07)The aphid Myzus persicae is a destructive agricultural pest that displays an exceptional ability to develop resistance to both natural and synthetic insecticides. To investigate the evolution of resistance in this species we generated a chromosome-scale genome assembly and living panel of >110 fully sequenced globally sampled clonal lines. Our analyses reveal a remarkable diversity of resistance mutations segregating in global populations of M. persicae. We show that the emergence and spread of these mechanisms is influenced by host-plant associations, uncovering the widespread co-option of a host-plant adaptation that also offers resistance against synthetic insecticides. We identify both the repeated evolution of independent resistance mutations at the same locus, and multiple instances of the evolution of novel resistance mechanisms against key insecticides. Our findings provide fundamental insights into the genomic responses of global insect populations to strong selective forces, and hold practical relevance for the control of pests and parasites.