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Item Metadata only The population status of southern hairy-nosed wombats (Lasiorhinus latifrons). I. Distribution and abundance(CSIRO Publishing, 2021) Swinbourne, M.; Taggart, D.; Ostendorf, B.There is disagreement within the community regarding whether the distribution and abundance of southern hairy-nosed wombats (Lasiorhinus latifrons) is increasing or decreasing. On one hand, farmers and graziers within areas where wombats can be found have consistently claimed that wombat numbers have increased in recent decades. Conversely, conservation groups, including the International Union for the Conservation of Nature (IUCN), claim that the wombat population is experiencing a species-wide decline, and recently upgraded its conservation status to ‘Near Threatened’. To resolve this disparity, we used a combination of field surveys and the analysis of satellite imagery to map the species-wide distribution and to estimate the overall population abundance of southern hairy-nosed wombats. We found that the wombat population has grown substantially since the last major surveys in the 1980s; however, the growth has not been uniform. While the population group in the Gawler Ranges has experienced marked population growth, there has been only relatively modest growth in the Murraylands. On the Yorke Peninsula, while the overall population numbers do not appear to have changed, some colonies have disappeared entirely. We also found a substantial population of wombats in Western Australia that had not been previously reported.Item Metadata only Stygofaunal community trends along varied rainfall conditions: Deciphering ecological niche dynamics of a shallow calcrete in Western Australia(John Wiley & Sons, 2019) Saccò, M.; Blyth, A.J.; Humphreys, W.F.; Karasiewicz, S.; Meredith, K.T.; Laini, A.; Cooper, S.J.B.; Bateman, P.W.; Grice, K.Groundwaters host highly adapted fauna, known as stygofauna, which play a key role in maintaining the functional integrity of subterranean ecosystems. Stygofaunal niche studies provide insights into the ecological dynamics shaping the delicate balance between the hydrological conditions and community diversity patterns. This work aims to unravel the ecological trends of a calcrete stygofaunal community, with special focus on niche dynamics through the Outlying Mean Index analysis (OMI) and additional calculation of Within Outlying Mean Indexes (WitOMI), under three rainfall regimes. Temperature and pH changed significantly among different rainfall conditions (P < .001), and together with salinity were the most influential drivers in shaping stygofaunal assemblages. These environmental conditions, linked with nutrient fluctuations in the groundwater, constrained changes in niche occupation for water mites, two species of beetles and juvenile amphipods (OMI analysis, P < .05). The WitOMI analysis revealed differential subniche breadths linked with taxa‐specific adaptations after different rainfall conditions. Our results indicate that stygofaunal niches are closely linked to the hydrodynamic conditions influenced by different rainfall regimes. Further long‐term investigations, incorporating broader ecological perspectives, will help to understand the impacts associated with climate change and anthropogenic pressures on one of the most threatened ecosystems in the world.Item Open Access SMRT sequencing reveals differential patterns of methylation in two O111:H- STEC isolates from a hemolytic uremic syndrome outbreak in Australia(Nature Publishing Group, 2019) Forde, B.M.; McAllister, L.J.; Paton, J.C.; Paton, A.W.; Beatson, S.A.In 1995 a severe haemolytic-uremic syndrome (HUS) outbreak in Adelaide occurred. A recent genomic analysis of Shiga toxigenic Escherichia coli (STEC) O111:H- strains 95JB1 and 95NR1 from this outbreak found that the more virulent isolate, 95NR1, harboured two additional copies of the Shiga toxin 2 (Stx2) genes encoded within prophage regions. The structure of the Stx2-converting prophages could not be fully resolved using short-read sequence data alone and it was not clear if there were other genomic differences between 95JB1 and 95NR1. In this study we have used Pacific Biosciences (PacBio) single molecule real-time (SMRT) sequencing to characterise the genome and methylome of 95JB1 and 95NR1. We completely resolved the structure of all prophages including two, tandemly inserted, Stx2-converting prophages in 95NR1 that were absent from 95JB1. Furthermore we defined all insertion sequences and found an additional IS1203 element in the chromosome of 95JB1. Our analysis of the methylome of 95NR1 and 95JB1 identified hemi-methylation of a novel motif (5'-CTGCm6AG-3') in more than 4000 sites in the 95NR1 genome. These sites were entirely unmethylated in the 95JB1 genome, and included at least 177 potential promoter regions that could contribute to regulatory differences between the strains. IS1203 mediated deactivation of a novel type IIG methyltransferase in 95JB1 is the likely cause of the observed differential patterns of methylation between 95NR1 and 95JB1. This study demonstrates the capability of PacBio SMRT sequencing to resolve complex prophage regions and reveal the genetic and epigenetic heterogeneity within a clonal population of bacteria.Item Metadata only Evolution and extinction of the giant rhinoceros Elasmotherium sibiricum sheds light on late Quaternary megafaunal extinctions(Springer Nature, 2019) Kosintsev, P.; Mitchell, K.; Devièse, T.; van der Plicht, J.; Kuitems, M.; Petrova, E.; Tikhonov, A.; Higham, T.; Comeskey, D.; Turney, C.; Cooper, A.; van Kolfschoten, T.; Stuart, A.; Lister, A.Understanding extinction events requires an unbiased record of the chronology and ecology of victims and survivors. The rhinoceros Elasmotherium sibiricum, known as the 'Siberian unicorn', was believed to have gone extinct around 200,000 years ago-well before the late Quaternary megafaunal extinction event. However, no absolute dating, genetic analysis or quantitative ecological assessment of this species has been undertaken. Here, we show, by accelerator mass spectrometry radiocarbon dating of 23 individuals, including cross-validation by compound-specific analysis, that E. sibiricum survived in Eastern Europe and Central Asia until at least 39,000 years ago, corroborating a wave of megafaunal turnover before the Last Glacial Maximum in Eurasia, in addition to the better-known late-glacial event. Stable isotope data indicate a dry steppe niche for E. sibiricum and, together with morphology, a highly specialized diet that probably contributed to its extinction. We further demonstrate, with DNA sequencing data, a very deep phylogenetic split between the subfamilies Elasmotheriinae and Rhinocerotinae that includes all the living rhinoceroses, settling a debate based on fossil evidence and confirming that the two lineages had diverged by the Eocene. As the last surviving member of the Elasmotheriinae, the demise of the 'Siberian unicorn' marked the extinction of this subfamily.Item Metadata only Adapting to change: prioritising management for the future of the Marine Scalefish Fishery(Elsevier, 2018) Nursey-Bray, M.; Magnusson, A.; Bicknell, N.; Magnusson, M.; Morison, J.; Sullivan, A.Marine scalefish fisheries face multiple challenges including management and sustainability pressures. These are going to be amplified by climate change. This paper reports on a project that used the Analytical Hierarchy Process (AHP) and semi-structured interviews to assess how marine scalefish fishers in South Australia, prioritise management objectives with a view to incorporating those views into structural industry reform to build the fishery's capacity to adapt in the face of these challenges. The project found that fishers, despite differences in geographical scale, fishing practice and species harvested, prioritised governance objectives most highly, and that economic and environmental objectives were prioritised as key and equally important; one could not exist without the other. Fishers prioritised social objectives the least as they expect these to follow from the economic and environmental objectives. Fishers also felt stocks had declined and that reform was urgently needed. Most fishers agreed that reform should include a reduction in licences. All fishers felt that recreational fishing was under-regulated and compromised commercial fishing opportunities. The project revealed that the capacity of fishers to adapt within the current operating environment is limited and that they will need government and other support to implement reform. For policy makers, this highlights that reform is culturally palatable but that it must include incentives and compensation for fishers to leave or stay in the industry.Item Open Access Detecting recent selective sweeps while controlling for mutation rate and background selection(Wiley, 2016) Huber, C.D.; DeGiorgio, M.; Hellmann, I.; Nielsen, R.A composite likelihood ratio test implemented in the program sweepfinder is a commonly used method for scanning a genome for recent selective sweeps. sweepfinder uses information on the spatial pattern (along the chromosome) of the site frequency spectrum around the selected locus. To avoid confounding effects of background selection and variation in the mutation process along the genome, the method is typically applied only to sites that are variable within species. However, the power to detect and localize selective sweeps can be greatly improved if invariable sites are also included in the analysis. In the spirit of a Hudson–Kreitman–Aguadé test, we suggest adding fixed differences relative to an out‐group to account for variation in mutation rate, thereby facilitating more robust and powerful analyses. We also develop a method for including background selection, modelled as a local reduction in the effective population size. Using simulations, we show that these advances lead to a gain in power while maintaining robustness to mutation rate variation. Furthermore, the new method also provides more precise localization of the causative mutation than methods using the spatial pattern of segregating sites alone.Item Metadata only Cytological analysis of ginseng carpel development(Springer, 2017) Silva, J.; Kim, Y.; Xiao, D.; Sukweenadhi, J.; Hu, T.; Kwon, W.; Hu, J.; Yang, D.; Zhang, D.Panax ginseng Meyer, commonly known as ginseng, is considered one of the most important herbs with pharmaceutical values due to the presence of ginsenosides and is cultivated for its highly valued root for medicinal purposes. Recently, it has been recognized that ginseng fruit contains high contents of triterpene such as ginsenoside Re as pharmaceutical compounds. However, it is unclear how carpel, the female reproductive tissue of flowers, is formed during the three-year-old growth before fruit is formed in ginseng plants. Here, we report P. ginseng carpel development at the cytological level, starting from the initial stage of ovule development to seed development. The carpel of P. ginseng is composed of two free stigmas, two free styles, and one epigynous bilocular ovary containing one ovule in each locule. Based on our cytological study, we propose that the female reproductive development in P. ginseng can be classified into seven stages: early phase of ovule development, megasporogenesis, megagametogenesis, pre-fertilization, fertilization, post-fertilization, and seed development. We also describe the correlation of the female and male gametophyte development and compare morphological differences in carpel development between ginseng and other higher plants. One unique feature for ginseng seed development is that it takes 40 days for the embryo to develop to the early torpedo stage and that the embryo is small relative to the seed size, which could be a feature of taxonomic importance. This study will provide an integral tool for the study of the reproductive development and breeding of P. ginseng.Item Metadata only Eradicating abundant invasive prey could cause unexpected and varied biodiversity outcomes: The importance of multispecies interactions(Wiley, 2018) Lurgi, M.; Ritchie, E.; Fordham, D.; Frair, J.1. Abundant and widely distributed invasive prey can negatively affect co-occurring native species by competing for food and/or shelter, removing vegetation cover and reducing habitat complexity (changing predation risk), and by sustaining elevated abundances of invasive mesopredators. However, information regarding the community and trophic consequences of controlling invasive prey and their temporal dynamics remain poorly understood. 2. We used multispecies ecological network models to simulate the consequences of changing European rabbit Oryctolagus cuniculus abundance in an arid mammalian community. We quantified how changes in the dominant prey (rabbits) affected multiple trophic levels, examining changes in predator–prey interactions through time and how they affected native prey persistence. 3. Our results suggest that removal of rabbits can benefit native biodiversity immediately at removal rates between 30% and 40%. However, beyond these levels, densities of small native mammals will decline in the short term. The processes underpinning these declines are: (a) increased competition for resources (vegetation) with kangaroos Macropus spp., whose numbers increase due to their release from competition with rabbits and (b) increased predation (prey switching) by feral cats Felis catus. Both effects are mediated by dingoes Canis dingo, a native apex predator. 4. Importantly, native mammal abundance recovers after a time delay, which is prolonged when high rates of rabbit control are applied. This is likely due to a reduction in hyperpredation by invasive feral cats and red foxes Vulpes vulpes following rabbit removal. 5. Continued eradication of rabbits in arid Australia will benefit native species due to a decrease in apparent competition for resources and by alleviating hyperpredation from invasive mesopredators. Furthermore, ecosystem-level conservation benefits of reducing invasive prey abundance are as important as direct control of invasive mesopredators. 6. Synthesis and applications. Multispecies ecological network models provide wildlife managers with tools to better understand and predict the complex effects of species removal and control on both intact and modified ecosystems. Our results show that management of the Australian arid zone can benefit from controlling invasive prey as well as invasive predators. However, invasive species control can cause unexpected outcomes on native biodiversity. This extends to other systems where dominant prey may play fundamental roles in ecosystem structure and function.Item Metadata only Another emerging mosquito-borne disease? Endemic Ross River virus transmission in the absence of marsupial reservoirs(Oxford University Press, 2018) Flies, E.; Lau, C.; Carver, S.; Weinstein, P.Ross River virus (RRV) is endemic to Australia and Papua New Guinea, with marsupials (especially macropods) as the primary reservoir hosts. Its geographic range was thought to be limited by the distribution of reservoir hosts, but recent evidence suggests that the virus can circulate endemically in the Pacific Islands, where marsupials are absent. RRV therefore has the potential for wider emergence because mammalian diversity in the Pacific Islands is limited and the possible species that have been sustaining endemic transmission are panglobal in distribution. Furthermore, RRV is a vector generalist and can be transmitted by numerous mosquito species, including Culex and the globally invasive Aedes aegypti and Ae. albopictus. We review the evidence for RRV expanding its host and geographic range from prehistoric times to the present and for it to potentially pose a threat as another emerging arbovirus with significant implications for human health far beyond its currently known endemic range.Item Open Access Climate change could drive marine food web collapse through altered trophic flows and cyanobacterial proliferation(Public Library of Science (PLoS), 2018) Ullah, H.; Nagelkerken, I.; Goldenberg, S.; Fordham, D.; Loreau, M.Global warming and ocean acidification are forecast to exert significant impacts on marine ecosystems worldwide. However, most of these projections are based on ecological proxies or experiments on single species or simplified food webs. How energy fluxes are likely to change in marine food webs in response to future climates remains unclear, hampering forecasts of ecosystem functioning. Using a sophisticated mesocosm experiment, we model energy flows through a species-rich multilevel food web, with live habitats, natural abiotic variability, and the potential for intra- and intergenerational adaptation. We show experimentally that the combined stress of acidification and warming reduced energy flows from the first trophic level (primary producers and detritus) to the second (herbivores), and from the second to the third trophic level (carnivores). Warming in isolation also reduced the energy flow from herbivores to carnivores, the efficiency of energy transfer from primary producers and detritus to herbivores and detritivores, and the living biomass of detritivores, herbivores, and carnivores. Whilst warming and acidification jointly boosted primary producer biomass through an expansion of cyanobacteria, this biomass was converted to detritus rather than to biomass at higher trophic levels-i.e., production was constrained to the base of the food web. In contrast, ocean acidification affected the food web positively by enhancing trophic flow from detritus and primary producers to herbivores, and by increasing the biomass of carnivores. Our results show how future climate change can potentially weaken marine food webs through reduced energy flow to higher trophic levels and a shift towards a more detritus-based system, leading to food web simplification and altered producer-consumer dynamics, both of which have important implications for the structuring of benthic communities.Item Open Access Biogeochemical cycling of silver in acidic, weathering environments(MDPI, 2017) Shuster, J.; Reith, F.; Izawa, M.; Flemming, R.; Banerjee, N.; Southam, G.Under acidic, weathering conditions, silver (Ag) is considered to be highly mobile and can be dispersed within near-surface environments. In this study, a range of regolith materials were sampled from three abandoned open pit mines located in the Iberian Pyrite Belt, Spain. Samples were analyzed for Ag mineralogy, content, and distribution using micro-analytical techniques and high-resolution electron microscopy. While Ag concentrations were variable within these materials, elevated Ag concentrations occurred in gossans. The detection of Ag within younger regolith materials, i.e., terrace iron formations and mine soils, indicated that Ag cycling was a continuous process. Microbial microfossils were observed within crevices of gossan and their presence highlights the preservation of mineralized cells and the potential for biogeochemical processes contributing to metal mobility in the rock record. An acidophilic, iron-oxidizing microbial consortium was enriched from terrace iron formations. When the microbial consortium was exposed to dissolved Ag, more than 90% of Ag precipitated out of solution as argentojarosite. In terms of biogeochemical Ag cycling, this demonstrates that Ag re-precipitation processes may occur rapidly in comparison to Ag dissolution processes. The kinetics of Ag mobility was estimated for each type of regolith material. Gossans represented 0.6–146.7 years of biogeochemical Ag cycling while terrace iron formation and mine soils represented 1.9–42.7 years and 0.7–1.6 years of Ag biogeochemical cycling, respectively. Biogeochemical processes were interpreted from the chemical and structural characterization of regolith material and demonstrated that Ag can be highly dispersed throughout an acidic, weathering environment.Item Metadata only Leaf fossils of Proteaceae subfamily Persoonioideae, tribe Persoonieae: tracing the past of an important Australasian sclerophyll lineage(CSIRO Publishing, 2017) Carpenter, R.; Tarran, M.; Hill, R.Fossils from the Eocene of South Australia and Western Australia and the Oligo–Miocene of Victoria represent the first known Australian leaf fossils of subfamily Persoonioideae, tribe Persoonieae. Persoonieaephyllum blackburnii sp. nov. is described from Middle Eocene Nelly Creek sediments near Lake Eyre, South Australia. Persoonieae are an important clade for understanding vegetation transitions in Australasia. The Nelly Creek leaf fossils are small (∼6 mm wide) and belong to an assemblage that has some characteristics of open vegetation, which is also inferred for the Oligo–Miocene of the Latrobe Valley, Victoria. In contrast, the Western Australian Late Eocene Persoonieae occur with diverse Lauraceae and other elements now typical of closed rainforests, and may, therefore, have been derived from communities that are unlike those in which most Persoonieae now occur. All fossil Persoonieae leaves so far known are hypostomatic (or virtually so), a state of stomatal distribution now only found in species of reasonably mesic habitats in New Zealand, New Caledonia and eastern Australian eucalypt forests. The ancestral state of stomatal distribution in Persoonieae leaves is unclear, but evidence suggests ancient associations of amphistomaty with open habitats, evolutionary loss of adaxial stomata in more closed vegetation, and the evolution of pronounced xerophylly within south-western Australian heathlands.Item Metadata only The dual benefit of arbuscular mycorrhizal fungi under soil zinc deficiency and toxicity: linking plant physiology and gene expression(Kluwer Academic Publishers, 2017) Watts-Williams, S.; Cavagnaro, T.; Tyerman, S.Background and aims: Colonisation of roots by arbuscular mycorrhizal fungi (AMF) can increase plant biomass and nutrition under soil zinc (Zn) deficiency and toxicity conditions, but the genes and transporters involved in these processes are unknown. The aim here was to determine whether there is a ZIP (Zrt-, Irt-like protein) transporter gene that is differentially-regulated by mycorrhizal colonisation that may be involved in mycorrhizal Zn uptake. Methods: We grew Medicago truncatula plants at soil Zn concentrations ranging from deficient to toxic, with and without inoculation of the AMF Rhizophagus irregularis, and measured plant dry weight, shoot nutrient concentrations and the expression of phosphate, aquaporin and ZIP genes in the roots. Results: At low and high soil Zn concentrations, there were positive biomass responses to AMF colonisation. Furthermore, at low soil Zn concentrations, MtZIP6 was highly up-regulated in the mycorrhizal plants. With increasing soil Zn concentration, expression of the AMF-induced phosphate transporter gene MtPT4 increased, and mycorrhizal colonisation was maintained. Conclusions: We have identified two different mechanisms by which AMF colonisation can increase plant biomass under low and high Zn stress: first, up-regulation of MtZIP6 at low soil Zn to supplement Zn uptake from the rhizosphere; and second, persistence of mycorrhizal colonisation and expression of MtPT4, which at high Zn could promote increased plant biomass and reduced tissue Zn concentration.Item Open Access Mycorrhizal fungi enhance plant nutrient acquisition and modulate nitrogen loss with variable water regimes(Blackwell Publishing, 2018) Bowles, T.; Jackson, L.; Cavagnaro, T.Climate change will alter both the amount and pattern of precipitation and soil water availability, which will directly affect plant growth and nutrient acquisition, and potentially, ecosystem functions like nutrient cycling and losses as well. Given their role in facilitating plant nutrient acquisition and water stress resistance, arbuscular mycorrhizal (AM) fungi may modulate the effects of changing water availability on plants and ecosystem functions. The well-characterized mycorrhizal tomato (Solanum lycopersicum L.) genotype 76R (referred to as MYC+) and the mutant mycorrhiza-defective tomato genotype rmc were grown in microcosms in a glasshouse experiment manipulating both the pattern and amount of water supply in unsterilized field soil. Following 4 weeks of differing water regimes, we tested how AM fungi affected plant productivity and nutrient acquisition, short-term interception of a 15NH4+ pulse, and inorganic nitrogen (N) leaching from microcosms. AM fungi enhanced plant nutrient acquisition with both lower and more variable water availability, for instance increasing plant P uptake more with a pulsed water supply compared to a regular supply and increasing shoot N concentration more when lower water amounts were applied. Although uptake of the short-term 15NH4+ pulse was higher in rmc plants, possibly due to higher N demand, AM fungi subtly modulated NO3- leaching, decreasing losses by 54% at low and high water levels in the regular water regime, with small absolute amounts of NO3- leached (<1 kg N/ha). Since this study shows that AM fungi will likely be an important moderator of plant and ecosystem responses to adverse effects of more variable precipitation, management strategies that bolster AM fungal communities may in turn create systems that are more resilient to these changes.Item Restricted Understanding and encouraging greater nature engagement in Australia: results from a national survey(Taylor & Francis, 2015) Zuo, A.; Wheeler, S.; Edwards, J.Interaction with nature has a range of significant health, ecological and economic benefits and a number of governments are implementing policies to increase humans’ engagement with nature. Using a large nationally representative survey sample in Australia, this study provides a detailed comment on the feasibility of such a policy, as well as contributing to an understanding of the characteristics of individuals who engaged in one or more of five dimensions of nature interaction, namely: nature engagement; conservation participation; nature advocacy; environmentally friendly purchasing and future engagement with nature conservation. The results indicate that age, income, education, marital status and household structure are all important influences on various types of nature engagement. It is suggested that increasing opportunities for young people to interact with nature is important, as well as supporting older people's involvement in conservation, plus focusing on the need to target and direct various policies.Item Metadata only Evaluation of fungicides for the management of Botryosphaeria canker of grapevines(American Phytopathological Society, 2012) Pitt, W.; Sosnowski, M.; Huang, R.; Qiu, Y.; Steel, C.; Savocchia, S.The family Botryosphaeriaceae comprises a number of species that are associated with the dieback disease of grapevine (Vitis vinifera), referred to as Botryosphaeria canker. To date, there are few effective agents available for the management of this disease. In this study, fungicides were evaluated for controlling the disease using a combination of in vitro tests and field trials. Twenty fungicides registered for use on other diseases in Australian viticulture were tested in vitro for their effect on mycelial growth of four species within the Botryosphaeriaceae. The concentrations of fungicide at which 50% of mycelial growth is inhibited (EC50 values) were significantly affected both by fungicide and isolate (P < 0.001). Differences in sensitivities of the four species to the fungicides were negligible (0.41 to 0.59 mg/liter). The most effective fungicides were fludioxonil, carbendazim, fluazinam, tebuconazole, flusilazole, penconazole, procymidone, iprodione, myclobutanil, and pyraclostrobin, for which EC50 values were <1.0 mg/liter. These fungicides were evaluated under field conditions, in addition to the pruning wound protectants Bacseal Super, Garrison, and ATCS tree wound dressing, as well as the biological control agent Vinevax. In field trials, carbendazim (Bavistin), fluazinam (Shirlan), tebuconazole (Folicur), Garrison, and ATCS tree wound dressing applied to freshly cut pruning wounds were the most effective and reduced infection by Diplodia seriata and D. mutila by 41 to 65%. These results suggest that the occurrence of Botryosphaeria canker on grapevines may be reduced via treatment of pruning wounds with selected fungicides as soon as possible after pruning.Item Metadata only The extent of forest in dryland biomes(American Association for the Advancement of Science, 2017) Bastin, J.; Berrahmouni, N.; Grainger, A.; Maniatis, D.; Mollicone, D.; Moore, R.; Patriarca, C.; Picard, N.; Sparrow, B.; Abraham, E.; Aloui, K.; Atesoglu, A.; Attorre, F.; Bassüllü, Ç.; Bey, A.; Garzuglia, M.; García-Montero, L.; Groot, N.; Guerin, G.; Laestadius, L.; et al.Dryland biomes cover two-fifths of Earth's land surface, but their forest area is poorly known. Here, we report an estimate of global forest extent in dryland biomes, based on analyzing more than 210,000 0.5-hectare sample plots through a photo-interpretation approach using large databases of satellite imagery at (i) very high spatial resolution and (ii) very high temporal resolution, which are available through the Google Earth platform. We show that in 2015, 1327 million hectares of drylands had more than 10% tree-cover, and 1079 million hectares comprised forest. Our estimate is 40 to 47% higher than previous estimates, corresponding to 467 million hectares of forest that have never been reported before. This increases current estimates of global forest cover by at least 9%.Item Open Access Interactions between FLORAL ORGAN NUMBER₄ and floral homeotic genes in regulating rice flower development(Oxford University Press, 2017) Xu, W.; Tao, J.; Chen, M.; Dreni, L.; Luo, Z.; Hu, Y.; Liang, W.; Zhang, D.The floral meristem (FM) is self-maintaining at the early stages of flower development, but it is terminated when a fixed number of floral organs are produced. The FLORAL ORGAN NUMBER4 (FON4; also known as FON2) gene, an ortholog of Arabidopsis CLAVATA3 (CLV3), is required for regulating FM size and determinacy in rice. However, its interactions with floral homeotic genes remain unknown. Here, we report the genetic interactions between FON4 and floral homeotic genes OsMADS15 (an A-class gene), OsMADS16 (also called SUPERWOMAN1, SPW1, a B-class gene), OsMADS3 and OsMADS58 (C-class genes), OsMADS13 (a D-class gene), and OsMADS1 (an E-class gene) during flower development. We observed an additive phenotype in the fon4 double mutant with the OsMADS15 mutant allele dep (degenerative palea). The effect on the organ number of whorl 2 was enhanced in fon4 spw1. Double mutant combinations of fon4 with osmads3, osmads58, osmads13, and osmads1 displayed enhanced defects in FM determinacy and identity, respectively, indicating that FON4 and these genes synergistically control FM activity. In addition, the expression patterns of all the genes besides OsMADS13 had no obvious change in the fon4 mutant. This work reveals how the meristem maintenance gene FON4 genetically interacts with C, D, and E floral homeotic genes in specifying FM activity in monocot rice.Item Open Access Comparison of SNP and CAPS markers application in genetic research in wheat and barley(BioMed Central, 2016) Shavrukov, Y.Background: Barley and bread wheat show large differences in frequencies of Single Nucleotide Polymorphism (SNP) as determined from genome-wide studies. These frequencies have been estimated as 2.4-3 times higher in the entire barley genome than within each diploid genomes of wheat (A, B or D). However, barley SNPs within individual genes occur significantly more frequently than quoted. Differences between wheat and barley are based on the origin and evolutionary history of the species. Bread wheat contains rarer SNPs due to the double genetic ‘bottle-neck’ created by natural hybridisation and spontaneous polyploidisation. Furthermore, wheat has the lowest level of useful SNP-derived markers while barley is estimated to have the highest level of polymorphism. Results: Different strategies are required for the development of suitable molecular markers in these cereal species. For example, SNP markers based on high-throughput technology (Infinium or KASP) are very effective and useful in both barley and bread wheat. In contrast, Cleaved Amplified Polymorphic Sequences (CAPS) are more widely and successfully employed in small-scale experiments with highly polymorphic genetic regions containing multiple SNPs in barley, but not in wheat. However, preliminary ‘in silico’ search databases for assessing the potential value of SNPs have yet to be developed. Conclusions: This mini-review summarises results supporting the development of different strategies for the application of effective SNP and CAPS markers in wheat and barley.Item Metadata only A hybrid approach to monthly streamflow forecasting: integrating hydrological model outputs into a Bayesian artificial neural network(Elsevier, 2016) Humphrey, G.; Gibbs, M.; Dandy, G.; Maier, H.Abstract not available