School of BioSciences - Research Publications
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ItemNo Preview AvailableMetaphor-A workflow for streamlined assembly and binning of metagenomes.(Oxford University Press (OUP), 2022-12-28)Recent advances in bioinformatics and high-throughput sequencing have enabled the large-scale recovery of genomes from metagenomes. This has the potential to bring important insights as researchers can bypass cultivation and analyze genomes sourced directly from environmental samples. There are, however, technical challenges associated with this process, most notably the complexity of computational workflows required to process metagenomic data, which include dozens of bioinformatics software tools, each with their own set of customizable parameters that affect the final output of the workflow. At the core of these workflows are the processes of assembly-combining the short-input reads into longer, contiguous fragments (contigs)-and binning, clustering these contigs into individual genome bins. The limitations of assembly and binning algorithms also pose different challenges depending on the selected strategy to execute them. Both of these processes can be done for each sample separately or by pooling together multiple samples to leverage information from a combination of samples. Here we present Metaphor, a fully automated workflow for genome-resolved metagenomics (GRM). Metaphor differs from existing GRM workflows by offering flexible approaches for the assembly and binning of the input data and by combining multiple binning algorithms with a bin refinement step to achieve high-quality genome bins. Moreover, Metaphor generates reports to evaluate the performance of the workflow. We showcase the functionality of Metaphor on different synthetic datasets and the impact of available assembly and binning strategies on the final results.
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ItemThe role of mab-3 in spermatogenesis and ontogenesis of pinewood nematode, Bursaphelenchus xylophilus.(Wiley, 2021-01)BACKGROUND: Bursaphelenchus xylophilus is one of the most destructive invasive species, causing extensive economic losses worldwide. The sex ratio of female to male of B. xylophilus plays an important role in the nematode infestation. However, little is known about the processes of its sex determination. The double sex/mab-3-related family of transcription factors are highly conserved in animals, playing crucial roles in sex determination, spermatogenesis and ontogenesis. We therefore investigated its orthologue, Bxy-mab-3, in B. xylophilus. RESULTS: Bxy-mab-3 has two typical conserved DNA-binding domains. It was observed in J2 (the second-stage of juveniles), J3, J4 and male adults (specifically on the spicules), but not in eggs or female adults via mRNA in situ hybridization. RNA-Seq indicated significantly higher expression in males. RNAi showed that the body size and sperm size of male adults were markedly smaller than those of the controls. Meanwhile, almost all the RNAi-treated males failed to mate with the normal females, even 26.34% of interfered males did not produce sperm. However, RNAi of Bxy-mab-3 had no effect on the sex ratio of B. xylophilus. CONCLUSION: Bxy-mab-3 is indispensable for spermatogenesis, ontogenesis and mating behavior. It is a typical sex-determination gene with differential expression in males and females. However, knocking down Bxy-mab-3 expression could not alter the sex ratio as seen in other species. Our findings contribute towards a better understanding of the molecular events of Bxy-mab-3 in B. xylophilus, which provides promising hints for control of pine wilt disease by blocking ontogenesis and decreasing nematode fecundity.
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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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ItemQuantifying 25 years of disease-caused declines in Tasmanian devil populations: host density drives spatial pathogen spread(WILEY, 2021-05)Infectious diseases are strong drivers of wildlife population dynamics, however, empirical analyses from the early stages of pathogen emergence are rare. Tasmanian devil facial tumour disease (DFTD), discovered in 1996, provides the opportunity to study an epizootic from its inception. We use a pattern-oriented diffusion simulation to model the spatial spread of DFTD across the species' range and quantify population effects by jointly modelling multiple streams of data spanning 35 years. We estimate the wild devil population peaked at 53 000 in 1996, less than half of previous estimates. DFTD spread rapidly through high-density areas, with spread velocity slowing in areas of low host densities. By 2020, DFTD occupied >90% of the species' range, causing 82% declines in local densities and reducing the total population to 16 900. Encouragingly, our model forecasts the population decline should level-off within the next decade, supporting conservation management focused on facilitating evolution of resistance and tolerance.
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ItemDevelopment of Plasmodium-specific liver-resident memory CD8(+) T cells after heat-killed sporozoite immunization in mice(WILEY, 2021-05)Malaria remains a major cause of mortality in the world and an efficient vaccine is the best chance of reducing the disease burden. Vaccination strategies for the liver stage of disease that utilise injection of live radiation-attenuated sporozoites (RAS) confer sterile immunity, which is mediated by CD8+ memory T cells, with liver-resident memory T cells (TRM ) being particularly important. We have previously described a TCR transgenic mouse, termed PbT-I, where all CD8+ T cells recognize a specific peptide from Plasmodium. PbT-I form liver TRM cells upon RAS injection and are capable of protecting mice against challenge infection. Here, we utilize this transgenic system to examine whether nonliving sporozoites, killed by heat treatment (HKS), could trigger the development of Plasmodium-specific liver TRM cells. We found that HKS vaccination induced the formation of memory CD8+ T cells in the spleen and liver, and importantly, liver TRM cells were fewer in number than that induced by RAS. Crucially, we showed the number of TRM cells was significantly higher when HKS were combined with the glycolipid α-galactosylceramide as an adjuvant. In the future, this work could lead to development of an antimalaria vaccination strategy that does not require live sporozoites, providing greater utility.
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ItemUnbiased population heterozygosity estimates from genome-wide sequence data(WILEY, 2021-10)Abstract Heterozygosity is a metric of genetic variability frequently used to inform the management of threatened taxa. Estimating observed and expected heterozygosities from genome‐wide sequence data has become increasingly common, and these estimates are often derived directly from genotypes at single nucleotide polymorphism (SNP) markers. While many SNP markers can provide precise estimates of genetic processes, the results of ‘downstream’ analysis with these markers may depend heavily on ‘upstream’ filtering decisions. Here we explore the downstream consequences of sample size, rare allele filtering, missing data thresholds and known population structure on estimates of observed and expected heterozygosity using two reduced‐representation sequencing datasets, one from the mosquito Aedes aegypti (ddRADseq) and the other from a threatened grasshopper, Keyacris scurra (DArTseq). We show that estimates based on polymorphic markers only (i.e. SNP heterozygosity) are always biased by global sample size (N), with smaller N producing larger estimates. By contrast, results are unbiased by sample size when calculations consider monomorphic as well as polymorphic sequence information (i.e. genome‐wide or autosomal heterozygosity). SNP heterozygosity is also biased when differentiated populations are analysed together while autosomal heterozygosity remains unbiased. We also show that when nucleotide sites with missing genotypes are included, observed and expected heterozygosity estimates diverge in proportion to the amount of missing data permitted at each site. We make three recommendations for estimating genome‐wide heterozygosity: (a) autosomal heterozygosity should be reported instead of (or in addition to) SNP heterozygosity; (b) sites with any missing data should be omitted and (c) populations should be analysed in independent runs. This should facilitate comparisons within and across studies and between observed and expected measures of heterozygosity.
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ItemDefining and evaluating predictions of joint species distribution models(WILEY, 2021-03)Abstract Joint species distribution models (JSDMs) simultaneously model the distributions of multiple species, while accounting for residual co‐occurrence patterns. Despite increasing adoption of JSDMs in the literature, the question of how to define and evaluate JSDM predictions has only begun to be explored. We define four different JSDM prediction types that correspond to different aspects of species distribution and community assemblage processes. Marginal predictions are environment‐only predictions akin to predictions from single‐species models; joint predictions simultaneously predict entire community assemblages; and conditional marginal and conditional joint predictions are made at the species or assemblage level, conditional on the known occurrence state of one or more species at a site. We define five different classes of metrics that can be used to evaluate these types of predictions: threshold‐dependent, threshold‐independent, community dissimilarity, species richness and likelihood metrics. We illustrate different prediction types and evaluation metrics using a case study in which we fit a JSDM to a frog occurrence dataset collected in Melbourne, Australia. Joint species distribution models present opportunities to investigate the facets of species distribution and community assemblage processes that are not possible to explore with single‐species models. We show that there are a variety of different metrics available to evaluate JSDM predictions, and that choice of prediction type and evaluation metric should closely match the questions being investigated.
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ItemModelling the joint effects of body size and microclimate on heat budgets and foraging opportunities of ectotherms(WILEY, 2021-03)Abstract Body size affects the body temperature of an ectotherm by altering both heating rates and the microclimate experienced. These joint effects are rarely considered in the analyses of climatic constraints on ectotherms but nonetheless influence body temperatures and thus activity periods and foraging opportunities. Here we develop and test transient heat‐budget models that use height‐specific microclimatic forcing to compute the dynamics of size‐dependent body temperatures of ectotherms in sun and in shade. We incorporate a model of behavioural thermoregulation and use it to compute potential body temperatures and then to map these to ecologically relevant indices, including foraging opportunities and thermal constraints. To illustrate potential applications, we combine a microclimate model driven by a global climate database with the transient behavioural algorithm developed for lizards to explore how body size (10 and 1,000 g) and size‐specific microclimate (at natural heights of 1 and 7.5 cm, respectively) interactively influence body temperatures and ecological indices at a warm, arid location in Australia in both spring and summer. To explore microclimatic effects, we contrast temperatures and indices for animals positioned at their natural versus reciprocal heights above the ground. Our simulations show that the behavioural and ecological consequences of size can be strongly biased when joint effects of body size and size‐imposed microclimate are ignored. For example, the two body sizes did not differ in total foraging time when compared at their natural heights, but did differ if compared at the same height, the direction of this difference reversing with the height at which they were compared. We show how computed foraging times can be translated to potential foraging radii from a central place (burrow or shade‐providing bush), thereby illustrating how body size can be physiologically translated into habitat connectivity as a function of different shade configurations, for example, as modified by fire regimes or shrub dieback. All functions are now integrated into the biophysical modelling r package NicheMapR and as a Shiny app, which should provide new insights and avenues for investigation into functional interactions between body size and habitat structure for ectotherms.
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ItemEfficient effort allocation in line-transect distance sampling of high-density species: When to walk further, measure less-often and gain precision(WILEY, 2021-06)Abstract Line‐transect distance sampling is widely used to estimate population densities using distances of observed targets from transect lines to model detectability. When the target taxa are high density, the frequent measuring of distances may make the method seem impractical. We present a method that improves the efficiency of distance sampling when the target species occurs at high density. Only a proportion of targets are measured to model the detection function, and the time saved on the survey is then used to cover a longer total length of transect and accrue a larger ‘count only’ sample. This approach can improve the precision of the population density estimate when the cost of measuring the distance to a detected target is more than half the cost of walking to the next target. We find the optimal proportion of distances to measure that minimises the variance of the density estimate for a fixed survey budget. We quantify how much this optimised strategy increases the precision of the density estimate compared with conventional line‐transect distance sampling. We then use simulated distance sampling data to test our expressions, and illustrate circumstances under which the optimised approach would be beneficial using distance sampling data on high‐density plants. The simulations indicate that the optimised method delivers benefits in precision, but the magnitude of the benefit is lower than predicted from our expressions, which are based on an asymptotic approximation of the variance. We apply an adjustment to the predicted benefit equation to account for this difference, and show that, in all three plant case studies, the optimised approach could improve the precision gained from a distance sampling survey between 20% and 50%. This new approach could broaden the ecological contexts in which distance sampling is applied, to include estimation of densities of abundant taxa where plots are conventionally used. The method may have interesting applications for other survey types, including multispecies surveys or those using cues or signs that occur at high density.