School of BioSciences - Research Publications

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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, 2022-06-28)
    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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    Population bottlenecks constrain host microbiome diversity and genetic variation impeding fitness.
    Ørsted, M ; Yashiro, E ; Hoffmann, AA ; Kristensen, TN ; Dyer, KA (Public Library of Science (PLoS), 2022-05)
    It is becoming increasingly clear that microbial symbionts influence key aspects of their host's fitness, and vice versa. This may fundamentally change our thinking about how microbes and hosts interact in influencing fitness and adaptation to changing environments. Here we explore how reductions in population size commonly experienced by threatened species influence microbiome diversity. Consequences of such reductions are normally interpreted in terms of a loss of genetic variation, increased inbreeding and associated inbreeding depression. However, fitness effects of population bottlenecks might also be mediated through microbiome diversity, such as through loss of functionally important microbes. Here we utilise 50 Drosophila melanogaster lines with different histories of population bottlenecks to explore these questions. The lines were phenotyped for egg-to-adult viability and their genomes sequenced to estimate genetic variation. The bacterial 16S rRNA gene was amplified in these lines to investigate microbial diversity. We found that 1) host population bottlenecks constrained microbiome richness and diversity, 2) core microbiomes of hosts with low genetic variation were constituted from subsets of microbiomes found in flies with higher genetic variation, 3) both microbiome diversity and host genetic variation contributed to host population fitness, 4) connectivity and robustness of bacterial networks was low in the inbred lines regardless of host genetic variation, 5) reduced microbial diversity was associated with weaker evolutionary responses of hosts in stressful environments, and 6) these effects were unrelated to Wolbachia density. These findings suggest that population bottlenecks reduce hologenomic variation (combined host and microbial genetic variation). Thus, while the current biodiversity crisis focuses on population sizes and genetic variation of eukaryotes, an additional focal point should be the microbial diversity carried by the eukaryotes, which in turn may influence host fitness and adaptability with consequences for the persistence of populations.
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    Conservation genetics as a management tool: The five best-supported paradigms to assist the management of threatened species
    Willi, Y ; Kristensen, TN ; Sgro, CM ; Weeks, AR ; orsted, M ; Hoffmann, AA (NATL ACAD SCIENCES, 2022-01-04)
    About 50 y ago, Crow and Kimura [An Introduction to Population Genetics Theory (1970)] and Ohta and Kimura [Genet. Res. 22, 201-204 (1973)] laid the foundations of conservation genetics by predicting the relationship between population size and genetic marker diversity. This work sparked an enormous research effort investigating the importance of population dynamics, in particular small population size, for population mean performance, population viability, and evolutionary potential. In light of a recent perspective [J. C. Teixeira, C. D. Huber, Proc. Natl. Acad. Sci. U.S.A. 118, 10 (2021)] that challenges some fundamental assumptions in conservation genetics, it is timely to summarize what the field has achieved, what robust patterns have emerged, and worthwhile future research directions. We consider theory and methodological breakthroughs that have helped management, and we outline some fundamental and applied challenges for conservation genetics.
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    Temperatures that sterilize males better match global species distributions than lethal temperatures
    Parratt, SR ; Walsh, BS ; Metelmann, S ; White, N ; Manser, A ; Bretman, AJ ; Hoffmann, AA ; Snook, RR ; Price, TAR (NATURE RESEARCH, 2021-05-24)
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    A phylogeny for the Drosophila montium species group: A model clade for comparative analyses
    Conner, WR ; Delaney, EK ; Bronski, MJ ; Ginsberg, PS ; Wheeler, TB ; Richardson, KM ; Peckenpaugh, B ; Kim, KJ ; Watada, M ; Hoffmann, AA ; Eisen, MB ; Kopp, A ; Cooper, BS ; Turelli, M (ACADEMIC PRESS INC ELSEVIER SCIENCE, 2021-03-05)
    The Drosophila montium species group is a clade of 94 named species, closely related to the model species D. melanogaster. The montium species group is distributed over a broad geographic range throughout Asia, Africa, and Australasia. Species of this group possess a wide range of morphologies, mating behaviors, and endosymbiont associations, making this clade useful for comparative analyses. We use genomic data from 42 available species to estimate the phylogeny and relative divergence times within the montium species group, and its relative divergence time from D. melanogaster. To assess the robustness of our phylogenetic inferences, we use 3 non-overlapping sets of 20 single-copy coding sequences and analyze all 60 genes with both Bayesian and maximum likelihood methods. Our analyses support monophyly of the group. Apart from the uncertain placement of a single species, D. baimaii, our analyses also support the monophyly of all seven subgroups proposed within the montium group. Our phylograms and relative chronograms provide a highly resolved species tree, with discordance restricted to estimates of relatively short branches deep in the tree. In contrast, age estimates for the montium crown group, relative to its divergence from D. melanogaster, depend critically on prior assumptions concerning variation in rates of molecular evolution across branches, and hence have not been reliably determined. We discuss methodological issues that limit phylogenetic resolution - even when complete genome sequences are available - as well as the utility of the current phylogeny for understanding the evolutionary and biogeographic history of this clade.
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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, 2022-04-29)
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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, 2022-04-22)
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    A wMel Wolbachia variant in Aedes aegypti from field-collected Drosophila melanogaster with increased phenotypic stability under heat stress.
    Gu, X ; Ross, PA ; Rodriguez-Andres, J ; Robinson, KL ; Yang, Q ; Lau, M-J ; Hoffmann, AA (Wiley, 2022-04)
    Mosquito-borne diseases remain a major cause of morbidity and mortality. Population replacement strategies involving the wMel strain of Wolbachia are being used widely to control mosquito-borne diseases. However, these strategies may be influenced by temperature because wMel is vulnerable to heat. wMel infections in Drosophila melanogaster are genetically diverse, but few transinfections of wMel variants have been generated in Aedes aegypti. Here, we successfully transferred a wMel variant (termed wMelM) originating from a field-collected D. melanogaster into Ae. aegypti. The new wMelM variant (clade I) is genetically distinct from the original wMel transinfection (clade III), and there are no genomic differences between wMelM in its original and transinfected host. We compared wMelM with wMel in its effects on host fitness, temperature tolerance, Wolbachia density, vector competence, cytoplasmic incompatibility and maternal transmission under heat stress in a controlled background. wMelM showed a higher heat tolerance than wMel, likely due to higher overall densities within the mosquito. Both wMel variants had minimal host fitness costs, complete cytoplasmic incompatibility and maternal transmission, and dengue virus blocking under laboratory conditions. Our results highlight phenotypic differences between Wolbachia variants and wMelM shows potential as an alternative strain in areas with strong seasonal temperature fluctuations.
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    Chromosome Comparisons of Australian Scaptodrosophila Species
    Stocker, AJ ; Schiffer, M ; Gorab, E ; Hoffmann, A (MDPI, 2022-04-01)
    The Scaptodrosophila represent a diverse group of Diptera closely related to Drosophila. Although they have radiated extensively in Australia, they have been the focus of few studies. Here, we characterized the karyotypes of 12 Scaptodrosophila species from several species groups and showed that they have undergone similar types of karyotypic change to those seen in Drosophila. This includes heterochromatin amplification involved in length changes of the sex and 'dot' chromosomes as well as the autosomes, particularly in the coracina group of species. Numerous weak points along the arms of the polytene chromosomes suggest the presence of internal repetitive sequence DNA, but these regions did not C-band in mitotic chromosomes, and their analysis will depend on DNA sequencing. The nucleolar organizing regions (NORs) are at the same chromosome positions in Scaptodrosophila as in Drosophila, and the various mechanisms responsible for changing arm configurations also appear to be the same. These chromosomal studies provide a complementary resource to other investigations of this group, with several species currently being sequenced.