School of BioSciences - Research Publications
Now showing items 1-12 of 1092
Towards meaningful monitoring: A case study of a threatened rodent
Detecting trends in species' distribution and abundance is essential for conserving threatened species, and depends upon effective monitoring programs. Despite this, monitoring programs are often designed without explicit consideration of their ability to deliver the information required by managers, such as their power to detect population changes. Here, we demonstrate the use of existing data to support the design of monitoring programs aimed at detecting declines in species occupancy. We used single–season occupancy models and baseline data to gain information on variables affecting the occupancy and detectability of the threatened brush-tailed rabbit-rat Conilurus penicillatus (Gould 1842) on the Tiwi Islands, Australia. This information was then used to estimate the survey effort required to achieve sufficient power to detect changes in occupancy of different magnitudes. We found that occupancy varied spatially, driven primarily by habitat (canopy height and cover, distance to water) and fire history across the landscape. Detectability varied strongly among seasons, and was three times higher in the late dry season (July–September), compared to the early dry (April–June). Evaluation of three monitoring scenarios showed that conducting surveys at times when detectability is highest can achieve a substantial improvement in the ability to detect declines, thus reducing the survey effort and costs. Our study highlights the need for careful consideration of survey design related to the ecology of a species, as it can lead to substantial cost savings and improved insight into species population change via monitoring.
Cross-Study Comparison Reveals Common Genomic, Network, and Functional Signatures of Desiccation Resistance in Drosophila melanogaster
(OXFORD UNIV PRESS, 2016-04-01)
Repeated attempts to map the genomic basis of complex traits often yield different outcomes because of the influence of genetic background, gene-by-environment interactions, and/or statistical limitations. However, where repeatability is low at the level of individual genes, overlap often occurs in gene ontology categories, genetic pathways, and interaction networks. Here we report on the genomic overlap for natural desiccation resistance from a Pool-genome-wide association study experiment and a selection experiment in flies collected from the same region in southeastern Australia in different years. We identified over 600 single nucleotide polymorphisms associated with desiccation resistance in flies derived from almost 1,000 wild-caught genotypes, a similar number of loci to that observed in our previous genomic study of selected lines, demonstrating the genetic complexity of this ecologically important trait. By harnessing the power of cross-study comparison, we narrowed the candidates from almost 400 genes in each study to a core set of 45 genes, enriched for stimulus, stress, and defense responses. In addition to gene-level overlap, there was higher order congruence at the network and functional levels, suggesting genetic redundancy in key stress sensing, stress response, immunity, signaling, and gene expression pathways. We also identified variants linked to different molecular aspects of desiccation physiology previously verified from functional experiments. Our approach provides insight into the genomic basis of a complex and ecologically important trait and predicts candidate genetic pathways to explore in multiple genetic backgrounds and related species within a functional framework.
Mitochondrial DNA variants help monitor the dynamics of Wolbachia invasion into host populations
(NATURE PUBLISHING GROUP, 2016-03-01)
Wolbachia is the most widespread endosymbiotic bacterium of insects and other arthropods that can rapidly invade host populations. Deliberate releases of Wolbachia into natural populations of the dengue fever mosquito, Aedes aegypti, are used as a novel biocontrol strategy for dengue suppression. Invasion of Wolbachia through the host population relies on factors such as high fidelity of the endosymbiont transmission and limited immigration of uninfected individuals, but these factors can be difficult to measure. One way of acquiring relevant information is to consider mitochondrial DNA (mtDNA) variation alongside Wolbachia in field-caught mosquitoes. Here we used diagnostic mtDNA markers to differentiate infection-associated mtDNA haplotypes from those of the uninfected mosquitoes at release sites. Unique haplotypes associated with Wolbachia were found at locations outside Australia. We also performed mathematical and qualitative analyses including modelling the expected dynamics of the Wolbachia and mtDNA variants during and after a release. Our analyses identified key features in haplotype frequency patterns to infer the presence of imperfect maternal transmission of Wolbachia, presence of immigration and possibly incomplete cytoplasmic incompatibility. We demonstrate that ongoing screening of the mtDNA variants should provide information on maternal leakage and immigration, particularly in releases outside Australia. As we demonstrate in a case study, our models to track the Wolbachia dynamics can be successfully applied to temporal studies in natural populations or Wolbachia release programs, as long as there is co-occurring mtDNA variation that differentiates infected and uninfected populations.
Mutations in tropomyosin 4 underlie a rare form of human macrothrombocytopenia
(AMER SOC CLINICAL INVESTIGATION INC, 2017-03-01)
Platelets are anuclear cells that are essential for blood clotting. They are produced by large polyploid precursor cells called megakaryocytes. Previous genome-wide association studies in nearly 70,000 individuals indicated that single nucleotide variants (SNVs) in the gene encoding the actin cytoskeletal regulator tropomyosin 4 (TPM4) exert an effect on the count and volume of platelets. Platelet number and volume are independent risk factors for heart attack and stroke. Here, we have identified 2 unrelated families in the BRIDGE Bleeding and Platelet Disorders (BPD) collection who carry a TPM4 variant that causes truncation of the TPM4 protein and segregates with macrothrombocytopenia, a disorder characterized by low platelet count. N-Ethyl-N-nitrosourea-induced (ENU-induced) missense mutations in Tpm4 or targeted inactivation of the Tpm4 locus led to gene dosage-dependent macrothrombocytopenia in mice. All other blood cell counts in Tpm4-deficient mice were normal. Insufficient TPM4 expression in human and mouse megakaryocytes resulted in a defect in the terminal stages of platelet production and had a mild effect on platelet function. Together, our findings demonstrate a nonredundant role for TPM4 in platelet biogenesis in humans and mice and reveal that truncating variants in TPM4 cause a previously undescribed dominant Mendelian platelet disorder.
A Ras GTPase associated protein is involved in the phototropic and circadian photobiology responses in fungi
(NATURE PUBLISHING GROUP, 2017-03-21)
Light is an environmental signal perceived by most eukaryotic organisms and that can have major impacts on their growth and development. The MadC protein in the fungus Phycomyces blakesleeanus (Mucoromycotina) has been postulated to form part of the photosensory input for phototropism of the fruiting body sporangiophores, but the madC gene has remained unidentified since the 1960s when madC mutants were first isolated. In this study the madC gene was identified by positional cloning. All madC mutant strains contain loss-of-function point mutations within a gene predicted to encode a GTPase activating protein (GAP) for Ras. The madC gene complements the Saccharomyces cerevisiae Ras-GAP ira1 mutant and the encoded MadC protein interacts with P. blakesleeanus Ras homologs in yeast two-hybrid assays, indicating that MadC is a regulator of Ras signaling. Deletion of the homolog in the filamentous ascomycete Neurospora crassa affects the circadian clock output, yielding a pattern of asexual conidiation similar to a ras-1 mutant that is used in circadian studies in N. crassa. Thus, MadC is unlikely to be a photosensor, yet is a fundamental link in the photoresponses from blue light perceived by the conserved White Collar complex with Ras signaling in two distantly-related filamentous fungal species.
Uncertain links in host-parasite networks: lessons for parasite transmission in a multi-host system
(The Royal Society, 2017-05-05)
For many parasites, the full set of hosts that are susceptible to infection is not known, and this could lead to a bias in estimates of transmission. We used counts of individual adult parasites from historical parasitology studies in southern Africa to map a bipartite network of the nematode parasites of herbivore hosts that occur in Botswana. Bipartite networks are used in community ecology to represent interactions across trophic levels. We used a Bayesian hierarchical model to predict the full set of host–parasite interactions from existing data on parasitic gastrointestinal nematodes of wild and domestic ungulates given assumptions about the distribution of parasite counts within hosts, while accounting for the relative uncertainty of less sampled species. We used network metrics to assess the difference between the observed and predicted networks, and to explore the connections between hosts via their shared parasites using a host–host unipartite network projected from the bipartite network. The model predicts a large number of missing links and identifies red hartebeest, giraffe and steenbok as the hosts that have the most uncertainty in parasite diversity. Further, the unipartite network reveals clusters of herbivores that have a high degree of parasite sharing, and these clusters correspond closely with phylogenetic distance rather than with the wild/domestic boundary. These results provide a basis for predicting the risk of cross-species transmission of nematode parasites in areas where livestock and wildlife share grazing land. This article is part of the themed issue ‘Opening the black box: re-examining the ecology and evolution of parasite transmission’.
Site-Directed Mutagenesis of IRX9, IRX9L and IRX14 Proteins Involved in Xylan Biosynthesis: Glycosyltransferase Activity Is Not Required for IRX9 Function in Arabidopsis
(PUBLIC LIBRARY SCIENCE, 2014-08-13)
Xylans constitute the main non-cellulosic polysaccharide in the secondary cell walls of plants. Several genes predicted to encode glycosyltransferases are required for the synthesis of the xylan backbone even though it is a homopolymer consisting entirely of β-1,4-linked xylose residues. The putative glycosyltransferases IRX9, IRX14, and IRX10 (or the paralogs IRX9L, IRX14L, and IRX10L) are required for xylan backbone synthesis in Arabidopsis. To investigate the function of IRX9, IRX9L, and IRX14, we identified amino acid residues known to be essential for catalytic function in homologous mammalian proteins and generated modified cDNA clones encoding proteins where these residues would be mutated. The mutated gene constructs were used to transform wild-type Arabidopsis plants and the irx9 and irx14 mutants, which are deficient in xylan synthesis. The ability of the mutated proteins to complement the mutants was investigated by measuring growth, determining cell wall composition, and microscopic analysis of stem cross-sections of the transgenic plants. The six different mutated versions of IRX9 and IRX9-L were all able to complement the irx9 mutant phenotype, indicating that residues known to be essential for glycosyltransferases function in homologous proteins are not essential for the biological function of IRX9/IRX9L. Two out of three mutated IRX14 complemented the irx14 mutant, including a mutant in the predicted catalytic amino acid. A IRX14 protein mutated in the substrate-binding DxD motif did not complement the irx14 mutant. Thus, substrate binding is important for IRX14 function but catalytic activity may not be essential for the function of the protein. The data indicate that IRX9/IRX9L have an essential structural function, most likely by interacting with the IRX10/IRX10L proteins, but do not have an essential catalytic function. Most likely IRX14 also has primarily a structural role, but it cannot be excluded that the protein has an important enzymatic activity.
Conservation of the patchily distributed and declining purple-crowned fairy-wren (Malurus coronatus coronatus) across a vast landscape: the need for a collaborative landscape-scale approach.
(Public Library of Science (PLoS), 2013)
Conservation of species that are patchily distributed must consider processes that influence both the occurrence of individuals within patches, and the persistence of populations across multiple habitat patches within the landscape. Here we present a rare regional assessment of the population size and distribution of a patchily distributed, threatened species, the purple-crowned fairy-wren (Malurus coronatus coronatus), across a vast landscape. We used data from aerial vegetation mapping of waterways, with on-ground bird surveys to predict the occurrence of suitable habitat for M. c. coronatus across 14 catchments in the Kimberley region of Western Australia. Suitable habitat was extremely limited (305 km of riparian vegetation) and fragmented (342 patches) along the 2700 km of waterway surveyed within catchments where the species occurs. Populations were predicted to be large on the Fitzroy, Durack and Drysdale catchments, and small on the Isdell and northern Pentecost catchments, and a total population of 2834 to 4878 individuals could be supported. The sub-populations spanned numerous patches of habitat across multiple properties of varying tenure. Therefore, a landscape-scale approach to conservation management, across multiple tenures, is critical to safe-guard connectivity within populations. The greatest benefit may be achieved by a combination of broad-scale actions to reduce the impact of ubiquitous threatening processes, and fine-scale targeted effort in areas where populations are most vulnerable. Controlling access of stock to waterways and management of fire are most important to conserve suitable habitat. Such a landscape-scale approach to conservation may be of benefit to other patchily distributed species.
Reference datasets of tufAle and UPA markers to identify algae in metabarcoding surveys
(ELSEVIER SCIENCE BV, 2017-04-01)
The data presented here are related to the research article "Multi-marker metabarcoding of coral skeletons reveals a rich microbiome and diverse evolutionary origins of endolithic algae" (Marcelino and Verbruggen, 2016) . Here we provide reference datasets of the elongation factor Tu (tufA) and the Universal Plastid Amplicon (UPA) markers in a format that is ready-to-use in the QIIME pipeline (Caporaso et al., 2010) . In addition to sequences previously available in GenBank, we included newly discovered endolithic algae lineages using both amplicon sequencing (Marcelino and Verbruggen, 2016)  and chloroplast genome data (Marcelino et al., 2016; Verbruggen et al., in press) , . We also provide a script to convert GenBank flatfiles into reference datasets that can be used with other markers. The tufA and UPA reference datasets are made publicly available here to facilitate biodiversity assessments of microalgal communities.
Towards the PCR-based identification of Palaearctic Culicoides biting midges (Diptera: Ceratopogonidae): results from an international ring trial targeting four species of the subgenus Avaritia
BACKGROUND: Biting midges of the genus Culicoides (Diptera: Ceratopogonidae) are biological vectors of internationally important arboviruses. To understand the role of Culicoides in the transmission of these viruses, it is essential to correctly identify the species involved. Within the western Palaearctic region, the main suspected vector species, C. obsoletus, C. scoticus, C. dewulfi and C. chiopterus, have similar wing patterns, which makes it difficult to separate and identify them correctly. METHODS: In this study, designed as an inter-laboratory ring trial with twelve partners from Europe and North Africa, we assess four PCR-based assays which are used routinely to differentiate the four species of Culicoides listed above. The assays based on mitochondrial or ribosomal DNA or microarray hybridisation were tested using aliquots of Culicoides DNA (extracted using commercial kits), crude lysates of ground specimens and whole Culicoides (265 individuals), and non-Culicoides Ceratopogonidae (13 individuals) collected from across Europe. RESULTS: A total of 800 molecular assays were implemented. The in-house assays functioned effectively, although specificity and sensitivity varied according to the molecular marker and DNA extraction method used. The Obsoletus group specificity was overall high (95-99%) while the sensitivity varied greatly (59.6-100%). DNA extraction methods impacted the sensitivity of the assays as well as the type of sample used as template for the DNA extraction. CONCLUSIONS: The results are discussed in terms of current use of species diagnostic assays and the future development of molecular tools for the rapid differentiation of cryptic Culicoides species.
Predicting the risk of avian influenza A H7N9 infection in live-poultry markets across Asia
(NATURE PUBLISHING GROUP, 2014-06-01)
Two epidemic waves of an avian influenza A (H7N9) virus have so far affected China. Most human cases have been attributable to poultry exposure at live-poultry markets, where most positive isolates were sampled. The potential geographic extent of potential re-emerging epidemics is unknown, as are the factors associated with it. Using newly assembled data sets of the locations of 8,943 live-poultry markets in China and maps of environmental correlates, we develop a statistical model that accurately predicts the risk of H7N9 market infection across Asia. Local density of live-poultry markets is the most important predictor of H7N9 infection risk in markets, underscoring their key role in the spatial epidemiology of H7N9, alongside other poultry, land cover and anthropogenic predictor variables. Identification of areas in Asia with high suitability for H7N9 infection enhances our capacity to target biosurveillance and control, helping to restrict the spread of this important disease.
Mapping the zoonotic niche of Ebola virus disease in Africa
(ELIFE SCIENCES PUBLICATIONS LTD, 2014-09-08)
Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976-2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.