School of BioSciences - Research Publications
Now showing items 1-12 of 707
Occupancy and detectability modelling of vertebrates in northern Australia using multiple sampling methods
(PUBLIC LIBRARY SCIENCE, 2018-09-24)
Understanding where species occur and how difficult they are to detect during surveys is crucial for designing and evaluating monitoring programs, and has broader applications for conservation planning and management. In this study, we modelled occupancy and the effectiveness of six sampling methods at detecting vertebrates across the Top End of northern Australia. We fitted occupancy-detection models to 136 species (83 birds, 33 reptiles, 20 mammals) of 242 recorded during surveys of 333 sites in eight conservation reserves between 2011 and 2016. For modelled species, mean occupancy was highly variable: birds and reptiles ranged from 0.01-0.81 and 0.01-0.49, respectively, whereas mammal occupancy was lower, ranging from 0.02-0.30. Of the 11 environmental covariates considered as potential predictors of occupancy, topographic ruggedness, elevation, maximum temperature, and fire frequency were retained more readily in the top models. Using these models, we predicted species occupancy across the Top End of northern Australia (293,017 km2) and generated species richness maps for each species group. For mammals and reptiles, high richness was associated with rugged terrain, while bird richness was highest in coastal lowland woodlands. On average, detectability of diurnal birds was higher per day of surveys (0.33 ± 0.09) compared with nocturnal birds per night of spotlighting (0.13 ± 0.06). Detectability of reptiles was similar per day/night of pit trapping (0.30 ± 0.09) as per night of spotlighting (0.29 ± 0.11). On average, mammals were highly detectable using motion-sensor cameras for a week (0.36 ± 0.06), with exception of smaller-bodied species. One night of Elliott trapping (0.20 ± 0.06) and spotlighting (0.19 ± 0.06) was more effective at detecting mammals than cage (0.08 ± 0.03) and pit trapping (0.05 ± 0.04). Our estimates of species occupancy and detectability will help inform decisions about how best to redesign a long-running vertebrate monitoring program in the Top End of northern Australia.
Modeling biodiversity benchmarks in variable environments
Effective environmental assessment and management requires quantifiable biodiversity targets. Biodiversity benchmarks define these targets by focusing on specific biodiversity metrics, such as species richness. However, setting fixed targets can be challenging because many biodiversity metrics are highly variable, both spatially and temporally. We present a multivariate, hierarchical Bayesian method to estimate biodiversity benchmarks based on the species richness and cover of native terrestrial vegetation growth forms. This approach uses existing data to quantify the empirical distributions of species richness and cover within growth forms, and we use the upper quantiles of these distributions to estimate contemporary, "best-on-offer" biodiversity benchmarks. Importantly, we allow benchmarks to differ among vegetation types, regions, and seasons, and with changes in recent rainfall. We apply our method to data collected over 30 yr at ~35,000 floristic plots in southeastern Australia. Our estimated benchmarks were broadly consistent with existing expert-elicited benchmarks, available for a small subset of vegetation types. However, in comparison with expert-elicited benchmarks, our data-driven approach is transparent, repeatable, and updatable; accommodates important spatial and temporal variation; aligns modeled benchmarks directly with field data and the concept of best-on-offer benchmarks; and, where many benchmarks are required, is likely to be more efficient. Our approach is general and could be used broadly to estimate biodiversity targets from existing data in highly variable environments, which is especially relevant given rapid changes in global environmental conditions.
The fungal gene cluster for biosynthesis of the antibacterial agent viriditoxin.
(Springer Science and Business Media LLC, 2019)
Background: Viriditoxin is one of the 'classical' secondary metabolites produced by fungi and that has antibacterial and other activities; however, the mechanism of its biosynthesis has remained unknown. Results: Here, a gene cluster (vdt) responsible for viriditoxin synthesis was identified, via a bioinformatics analysis of the genomes of Paecilomyces variotii and Aspergillus viridinutans that both are viriditoxin producers. The function of the eight-membered gene cluster of P. variotii was characterized by targeted gene disruptions, revealing the roles of each gene in the synthesis of this molecule and establishing its biosynthetic pathway, which includes a Baeyer-Villiger monooxygenase catalyzed reaction. Additionally, a predicted catalytically-inactive hydrolase was identified as being required for the stereoselective biosynthesis of (M)-viriditoxin. The subcellular localizations of two proteins (VdtA and VdtG) were determined by fusing these proteins to green fluorescent protein, to establish that at least two intracellular structures are involved in the compartmentalization of the synthesis steps of this metabolite. Conclusions: The predicted pathway for the synthesis of viriditoxin was established by a combination of genomics, bioinformatics, gene disruption and chemical analysis processes. Hence, this work reveals the basis for the synthesis of an understudied class of fungal secondary metabolites and provides a new model species for understanding the synthesis of biaryl compounds with a chiral axis.
Life History Effects Linked to an Advantage for wAu Wolbachia in Drosophila
Wolbachia endosymbiont infections can persist and spread in insect populations without causing apparent effects on reproduction of their insect hosts, but the mechanisms involved are largely unknown. Here, we test for fitness effects of the wAu infection of Drosophila simulans by comparing multiple infected and uninfected polymorphic isofemale lines derived from nature. We show a fitness advantage (higher offspring number) for lines with the wAu Wolbachia infection when breeding on grapes, but only where there was Talaromyces and Penicillium fungal mycelial growth. When breeding on laboratory medium, the wAu infection extended the development time and resulted in larger females with higher fecundity, life history traits, which may increase fitness. A chemical associated with the fungi (ochratoxin A) did not specifically alter the fitness of wAu-infected larvae, which developed slower and emerged with a greater weight regardless of toxin levels. These findings suggest that the fitness benefits of Wolbachia in natural populations may reflect life history changes that are advantageous under particular circumstances, such as when breeding occurs in rotting fruit covered by abundant mycelial growth.
Phenotypic Responses to a Lifestyle Intervention Do Not Account for Inter-Individual Variability in Glucose Tolerance for Individuals at High Risk of Type 2 Diabetes
(FRONTIERS MEDIA SA, 2019-03-26)
Background: Lifestyle interventions have been shown to delay or prevent the onset of type 2 diabetes among high risk adults. A better understanding of the variability in physiological responses would support the matching of individuals with the best type of intervention in future prevention programmes, in order to optimize risk reduction. The purpose of this study was to determine if phenotypic characteristics at baseline or following a 12 weeks lifestyle intervention could explain the inter-individual variability in change in glucose tolerance in individuals with high risk for type 2 diabetes. Methods: In total, 285 subjects with normal glucose tolerance (NGT, FINDRISC score > 12), impaired fasting glucose (IFG) and impaired glucose tolerance (IGT) were recruited for a 12 weeks lifestyle intervention. Glucose tolerance, insulin sensitivity, anthropometric characteristics and aerobic fitness were measured. Variability of responses was examined by grouping participants by baseline glycemic status, by cluster analysis based on the change in glucose tolerance and by Principal Component Analysis (PCA). Results: In agreement with other studies, the mean response to the 12 weeks intervention was positive for the majority of parameters. Overall, 89% improved BMI, 80% waist circumference, and 81% body fat while only 64% improved fasting plasma glucose and 60% 2 h glucose. The impact of the intervention by glycaemic group did not show any phenotypic differences in response between NGT, IFG, and IGT. A hierarchical cluster analysis of change in glucose tolerance identified four sub-groups of "responders" (high and moderate) and "non-responders" (no response or deteriorated) but there were few differences in baseline clincal and physiological parameters or in response to the intervention to explain the overall variance. A further PCA analysis of 19 clinical and physiological univariables could explain less than half (48%) of total variability. Conclusion: We found that phenotypic characteristics from standard clinical and physiological parameters were not sufficient to account for the inter-individual variability in glucose tolerance following a 12 weeks lifestyle intervention in inidivuals at high risk for type 2 diabetes. Further work is required to identify biomarkers that complement phenotypic traits and better predict the response to glucose tolerance.
Insecticide resistance status of Aedes aegypti and Aedes albopictus mosquitoes in Papua New Guinea
BACKGROUND: Aedes aegypti and Ae. albopictus are important vectors of infectious diseases, especially those caused by arboviruses such as dengue, chikungunya and Zika. Aedes aegypti is very well adapted to urban environments, whereas Ae. albopictus inhabits more rural settings. Pyrethroid resistance is widespread in these vectors, but limited data exist from the Southwest Pacific Region, especially from Melanesia. While Aedes vector ecology is well documented in Australia, where incursion of Ae. albopictus and pyrethroid resistance have so far been prevented, almost nothing is known about Aedes populations in neighbouring Papua New Guinea (PNG). With pyrethroid resistance documented in parts of Indonesia but not in Australia, it is important to determine the distribution of susceptible and resistant Aedes populations in this region. METHODS: The present study was aimed at assessing Aedes populations for insecticide resistance in Madang and Port Moresby, located on the north and south coasts of PNG, respectively. Mosquitoes were collected using ovitraps and reared in an insectary. Standard WHO bioassays using insecticide-treated filter papers were conducted on a total of 253 Ae. aegypti and 768 Ae. albopictus adult mosquitoes. Subsets of samples from both species (55 Ae. aegypti and 48 Ae. albopictus) were screened for knockdown resistance mutations in the voltage-sensitive sodium channel (Vssc) gene, the target site of pyrethroid insecticides. RESULTS: High levels of resistance against pyrethroids were identified in Ae. aegypti from Madang and Port Moresby. Aedes albopictus exhibited susceptibility to pyrethroids, but moderate levels of resistance to DDT. Mutations associated with pyrethroid resistance were detected in all Ae. aegypti samples screened. Some genotypes found in the present study had been observed previously in Indonesia. No Vssc mutations associated with pyrethroid resistance were found in the Ae. albopictus samples. CONCLUSIONS: To our knowledge, this is the first report of pyrethroid resistance in Ae. aegypti mosquitoes in PNG. Interestingly, usage of insecticides in PNG is low, apart from long-lasting insecticidal nets distributed for malaria control. Further investigations on how these resistant Ae. aegypti mosquito populations arose in PNG and how they are being sustained are warranted.
Female ornamentation and the fecundity trade-off in a sex-role reversed pipefish
Sexual ornaments found only in females are a rare occurrence in nature. One explanation for this is that female ornaments are costly to produce and maintain and, therefore, females must trade-off resources related to reproduction to promote ornament expression. Here, we investigate whether a trade-off exists between female ornamentation and fecundity in the sex-role reversed, wide-bodied pipefish, Stigmatopora nigra. We measured two components of the disk-shaped, ventral-striped female ornament, body width, and stripe thickness. After controlling for the influence of body size, we found no evidence of a cost of belly width or stripe thickness on female fecundity. Rather, females that have larger ornaments have higher fecundity and thus accurately advertise their reproductive value to males without incurring a cost to fecundity. We also investigated the relationship between female body size and egg size and found that larger females suffer a slight decrease in egg size and fecundity, although this decrease was independent of female ornamentation. More broadly, considered in light of similar findings in other taxa, lack of an apparent fecundity cost of ornamentation in female pipefish underscores the need to revisit theoretical assumptions concerning the evolution of female ornamentation.
NLRP1 restricts butyrate producing commensals to exacerbate inflammatory bowel disease
(NATURE PUBLISHING GROUP, 2018-09-13)
Anti-microbial signaling pathways are normally triggered by innate immune receptors when detecting pathogenic microbes to provide protective immunity. Here we show that the inflammasome sensor Nlrp1 aggravates DSS-induced experimental mouse colitis by limiting beneficial, butyrate-producing Clostridiales in the gut. The colitis-protective effects of Nlrp1 deficiency are thus reversed by vancomycin treatment, but recapitulated with butyrate supplementation in wild-type mice. Moreover, an activating mutation in Nlrp1a increases IL-18 and IFNγ production, and decreases colonic butyrate to exacerbate colitis. We also show that, in patients with ulcerative colitis, increased NLRP1 in inflamed regions of the colon is associated with increased IFN-γ. In this context, NLRP1, IL-18 or IFN-γ expression negatively correlates with the abundance of Clostridiales in human rectal mucosal biopsies. Our data identify the NLRP1 inflammasome to be a key negative regulator of protective, butyrate-producing commensals, which therefore promotes inflammatory bowel disease.
Reflection of near-infrared light confers thermal protection in birds
(NATURE PUBLISHING GROUP, 2018-09-06)
Biologists have focused their attention on the optical functions of light reflected at ultraviolet and human-visible wavelengths. However, most radiant energy in sunlight occurs in 'unseen' near-infrared (NIR) wavelengths. The capacity to reflect solar radiation at NIR wavelengths may enable animals to control heat gain and remain within their critical thermal limits. Here, using a continent-wide phylogenetic analysis of Australian birds, we show that species occupying hot, arid environments reflect more radiant energy in NIR wavelengths than species in thermally benign environments, even when controlling for variation in visible colour. Biophysical models confirm that smaller species gain a greater advantage from high NIR reflectivity in hot, arid environments, reducing water loss from compensatory evaporative cooling by up to 2% body mass per hour. These results highlight the importance of NIR reflectivity for thermal protection, which may become increasingly critical as the frequency of extreme climatic events increases.
An IMD-like pathway mediates both endosymbiont control and host immunity in the cereal weevil Sitophilus spp.
Many insects developing on nutritionally unbalanced diets have evolved symbiotic associations with vertically transmitted intracellular bacteria (endosymbionts) that provide them with metabolic components, thereby improving the host's abilities to thrive on such poor ecological niches. While host-endosymbiont coevolutionary constraints are known to entail massive genomic changes in the microbial partner, host's genomic evolution remains elusive, particularly with regard to the immune system. In the cereal weevil Sitophilus spp., which houses Sodalis pierantonius, endosymbionts are secluded in specialized host cells, the bacteriocytes that group together as an organ, the bacteriome. We previously reported that at standard conditions, the bacteriome highly expresses the coleoptericin A (colA) antimicrobial peptide (AMP), which was shown to prevent endosymbiont escape from the bacteriocytes. However, following the insect systemic infection by pathogens, the bacteriome upregulates a cocktail of AMP encoding genes, including colA. The regulations that allow these contrasted immune responses remain unknown. In this short report, we provide evidence that an IMD-like pathway is conserved in two sibling species of cereal weevils, Sitophilus oryzae and Sitophilus zeamais. RNA interference (RNAi) experiments showed that imd and relish genes are essential for (i) colA expression in the bacteriome under standard conditions, (ii) AMP up-regulation in the bacteriome following a systemic immune challenge, and (iii) AMP systemic induction following an immune challenge. Histological analyses also showed that relish inhibition by RNAi resulted in endosymbiont escape from the bacteriome, strengthening the involvement of an IMD-like pathway in endosymbiont control. We conclude that Sitophilus' IMD-like pathway mediates both the bacteriome immune program involved in endosymbiont seclusion within the bacteriocytes and the systemic and local immune responses to exogenous challenges. This work provides a striking example of how a conserved immune pathway, initially described as essential in pathogen clearance, also functions in the control of mutualistic associations.
A New Subclade of Leptosphaeria biglobosa Identified from Brassica rapa
Blackleg (Phoma stem canker) of crucifers is a globally important disease caused by the ascomycete species complex comprising of Leptosphaeria maculans and Leptosphaeria biglobosa. Six blackleg isolates recovered from Brassica rapa cv. Mizspoona in the Willamette Valley of Oregon were characterized as L. biglobosa based on standard pathogenicity tests and molecular phylogenetic analysis. These isolates were compared to 88 characterized L. biglobosa isolates from western Canada, 22 isolates from Australia, and 6 L. maculans isolates from Idaho, USA using maximum parsimony and distance analysis of phylogenetic trees generated from the ITS rDNA (internal transcribed spacer rDNA) sequence, and the actin and β-tubulin gene sequences. The L. biglobosa isolates derived from B. rapa collected in Oregon formed a separate subclade based on concatenated gene sequences or a single gene sequence, regardless of the analyses. Pathogenicity tests showed that these isolates failed to infect either resistant or susceptible B. napus cultivars, but caused severe symptoms on three B. rapa cultivars (Accession number: UM1113, UM1112, and UM1161), a B. oleracea var. capitata (cabbage) cultivar (Copenhagen Market), and two B. juncea cultivars (CBM, a common brown Mustard, and Forge). These findings demonstrated that the L. biglobosa isolates derived from a B. rapa crop in Oregon were genetically distinct from existing species of L. biglobosa, and constitute a new subclade, herein proposed as L. biglobosa 'americensis'.
Verbal probabilities: <it>Very likely</it> to be <it>somewhat</it> more confusing than numbers
(PUBLIC LIBRARY SCIENCE, 2019-04-17)
People interpret verbal expressions of probabilities (e.g. 'very likely') in different ways, yet words are commonly preferred to numbers when communicating uncertainty. Simply providing numerical translations alongside reports or text containing verbal probabilities should encourage consistency, but these guidelines are often ignored. In an online experiment with 924 participants, we compared four different formats for presenting verbal probabilities with the numerical guidelines used in the US Intelligence Community Directive (ICD) 203 to see whether any could improve the correspondence between the intended meaning and participants' interpretation ('in-context'). This extends previous work in the domain of climate science. The four experimental conditions we tested were: 1. numerical guidelines bracketed in text, e.g. X is very unlikely (05-20%), 2. click to see the full guidelines table in a new window, 3. numerical guidelines appear in a mouse over tool tip, and 4. no guidelines provided (control). Results indicate that correspondence with the ICD 203 standard is substantially improved only when numerical guidelines are bracketed in text. For this condition, average correspondence was 66%, compared with 32% in the control. We also elicited 'context-free' numerical judgements from participants for each of the seven verbal probability expressions contained in ICD 203 (i.e., we asked participants what range of numbers they, personally, would assign to those expressions), and constructed 'evidence-based lexicons' based on two methods from similar research, 'membership functions' and 'peak values', that reflect our large sample's intuitive translations of the terms. Better aligning the intended and assumed meaning of fuzzy words like 'unlikely' can reduce communication problems between the reporter and receiver of probabilistic information. In turn, this can improve decision making under uncertainty.