College of Science and Engineering CSE publications Recent publications in Science and Engineering

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Recent publications in Science and Engineering

Ziegler, Alan D., Lim, H.S., Wasson, Robert J., and Williamson, Fiona C. (2021) Flood mortality in SE Asia: can palaeo‐historical information help save lives? Hydrological Processes, 35 (1). e13989.
[Excerpt] Asia is one of the world's most flood-prone regions by many metrics: high flood magnitudes, frequency, severity; the number countries affected, the area of inundation; the number of people at risk; and importantly, flood-related fatalities (AIR, 2014; Luo, Maddoks, Iceland,Ward, & Winsemius, 2015; Table 1). With respect to mortality, nearly all the countries with more than 5,000 flood-related deaths since 1985 are from Asia (11 of 13; Table 1; Figure 1). As we write this commentary, flooding associated with tropical storm Nangka has caused more than 40 deaths in Laos, Cambodia, and Vietnam(Floodlist, 2020).

Brown, Colin, Behrendt, Karl, Ping, Li, Guanghua, Qiao, Bennett, Jeff, Bao, Zhang, Addison, Jane, Kemp, David, Guodong, Han, and Jing, Zhang (2021) Refining China's grassland policies: an interdisciplinary and ex-ante analysis. The Rangeland Journal, 42 (6). pp. 435-445.
China is about to embark on a new round of grassland policies as part of its 14th Five-Year-Plan. While current grassland policies have generally been perceived positively in arresting widespread grassland degradation, concerns have arisen that the current policies may not be effective in achieving the desired reduction in livestock numbers. Furthermore there are concerns the incentive based payments that are part of these policy programs may not reflect herder opportunity costs or the marginal environmental benefits of the program with associated issues of herder satisfaction and compliance. Changes to current policy settings are being considered in response to these concerns. This paper reports on an interdisciplinary and ex-ante analysis of alternative policy settings affecting grazing and livestock management in terms of their environmental impacts, net social benefits and other impacts. The analysis finds that a bundle of instruments involving both positive and negative herder incentives is needed if desired stocking rates are to be achieved. The impact on herder incomes, both positive and negative depending on the grassland biome, along with transaction costs of implementing the policies, have the most influence on net social benefits.

Younes, Nicolas, Joyce, Karen E., and Maier, Stefan M. (2021) All models of satellite-derived phenology are wrong, but some are useful: a case study from northern Australia. International Journal of Applied Earth Observation and Geoinformation, 97 (102285).
Satellite-derived phenology (or apparent phenology) is frequently used to illustrate changes in plant phenology (i.e. true phenology) and the effects of climate forcing. However, each study uses a different method to detect phenology. Plant phenology refers to the relationship between the life cycle of plants and weather and climate events. Phenology is often studied in the field, but recently studies have transitioned towards using satellite images to monitor phenology at the plot, country, and continental scales. The problem with this approach is that there is an ever-increasing variety of earth observation satellites collecting data with different spatial, spectral, and temporal characteristics. In this paper we ask if studies that detect phenology using different sensors over the same site produce comparable results. Mangrove forests are one example where different methods have been used to examine their apparent phenology. In general, plant phenology, including mangroves, is described using few individual plants, but continental-scale descriptions of phenological events are scarce or inexistent. Few attempts have been made to describe the phenology of mangroves using satellite imagery, and each study presents a different method. We hypothesize that apparent phenology changes with: 1) areal extent; 2) site location; 3) frequency of observation; 4) spatial resolution; 5) temporal coverage; and 6) the number of cloud contaminated observations. Intuitively, one would assume that these hypotheses hold true, yet few studies have investigated this. For example, one would expect that clouds change the observed phenology of vegetation, that the number of species captured at spatial resolution will impact the apparent phenology, or that mangroves in different places display different phenologies, but how are these changes represented in the apparent phenology? We use the Enhanced Vegetation Index (EVI) to examine the changes in the start of season and peak growing season dates, as well as the shape and amplitude of the apparent phenology in each hypothesis. We use Landsat and Sentinel 2 imagery over the mangrove forests in Darwin Harbour (Northern Territory, Australia) as a case study, and found that apparent phenology does change with the sensor, site, and cloud contamination. Importantly, the apparent phenology is comparable between Landsat and Sentinel 2 sensors, but it is not comparable to phenology derived from MODIS. This is due to differences in the spatial resolution of the sensors. Cloud contamination also significantly changes the apparent phenology of vegetation. In this paper we expose the complexity of modelling phenology with remote sensing and help guide future phenology investigations.

Chaitae, Apinya, Gordon, Iain J., Addison, Jane, and Marsh, Helene (2021) From protection of elephants to sustainable use of ivory in Thailand. Oryx. (In Press)
The elephant has deep cultural significance in Thailand and for the Thai people. The development of legal protection for Thai elephants reflects concerns about both human livelihoods and elephant conservation. Thus, the legal status of privately-owned domesticated, or captive Asian elephants, differs from that of wild Asian elephants, a situation that has consequences for the lawful use of ivory from domesticated animals. Prior to 2015, the lack of comprehensive measures to control the Thai ivory market enabled the laundering of illegally-sourced ivory through the country. The 2015 legal reforms of the Thai Government: 1) introduced strict controls over the possession and domestic trade of ivory from domesticated Asian elephants, and 2) aligned the protection of African elephants and their ivory with the CITES Convention. Nonetheless, the sustainability of the Thai ivory trade remains disputed, and international pressure to close the commercial trade in domestic ivory persists. This paper reviews this complex situation to inform future reforms. Consolidation of related laws would ease the enforcement tasks of officers and facilitate the compliance of stakeholders. Use of an electronic database would enhance the monitoring of ivory flow, as well as aid the implementation and enforcement of laws. This situation is a valuable example of the tensions between national and international attempts to conserve species important in wildlife trade.

Belson, Bruce, Xiang, Wei, Holdsworth, Jason, and Philippa, Bronson (2021) C++20 coroutines on microcontrollers - what we learned. IEEE Embedded Systems Letters, 13 (1). pp. 9-12.
Coroutines will be added to C++ as part of the C++20 standard. Coroutines provide native language support for asynchronous operations. This study evaluates the C++ coroutine specification from the perspective of embedded systems developers. We find that the proposed language features are generally beneficial but that memory management of the coroutine state needs to be improved. Our experiments on an ARM Cortex-M4microcontroller evaluate the time and memory costs of coroutines in comparison with alternatives, and we show that context switching with coroutines is significantly faster than with thread-based real time operating systems. Furthermore, we analysed the impact of these language features on prototypical IoT sensor software. We find that the proposed language enhancements potentially bring significant benefits to programming in C++ for embedded computers, but that the implementation imposes constraints that may prevent its widespread acceptance among the embedded development community.

Silva, Catarina N.S., Murphy, Nicholas P., Bell, James J., Green, Bridget S,, Duhamel, Guy, Cockcroft, Andrew C., Hernández, Cristián E., and Strugnell, Jan M. (2021) Global drivers of recent diversification in a marine species complex. Molecular Ecology. (In Press)
Investigating historical gene flow in species complexes can indicate how environmental and reproductive barriers shape genome divergence during speciation. The processes influencing species diversification under environmental change remain one of the central focal points of evolutionary biology, particularly for marine organisms with high dispersal potential. We investigated genome‐wide divergence, introgression patterns and inferred demographic history between species pairs of all six extant rock lobster species (Jasus spp.), which have a long larval duration of up to two years and have populated continental shelf and seamount habitats around the globe at approximately 40oS. Genetic differentiation patterns reflected geographic isolation and the environment (i.e. habitat structure). Eastern Pacific species (J. caveorum and J. frontalis) were geographically more distant and genetically more differentiated from the remaining four species. Species associated with continental shelf habitats shared a common ancestry, but are geographically distant from one another. Similarly, species associated with island/seamount habitats in the Atlantic and Indian Oceans shared a common ancestry, but are also geographically distant. Benthic temperature was the environmental variable that explained most of the genetic differentiation (FST), while controlling for the effects of geographic distance. Eastern Pacific species retained a signal of strict isolation following ancient migration, whereas species pairs from Australia and Africa, and seamounts in the Indian and Atlantic oceans, included events of introgression after secondary contact. Our results reveal important effects of habitat and demographic processes on the recent divergence of species within the genus Jasus, providing one of the first empirical studies of genome‐wide drivers of diversification that incorporates all extant species in a marine genus with long pelagic larval duration.

Lee, Calvin K.F., Nicholson, Emily, Duncan, Clare, and Murray, Nicholas J. (2021) Estimating changes and trends in ecosystem extent with dense time-series satellite remote sensing. Conservation Biology. (In Press)
Quantifying trends in ecosystem extent is essential to understanding the status of ecosystems. Estimates of ecosystem loss are widely used to track progress toward conservation targets, monitor deforestation, and identify ecosystems undergoing rapid change. Satellite remote sensing has become an important source of information for estimating these variables. Despite regular acquisition of satellite data, many studies of change in ecosystem extent use only static snapshots, which ignores considerable amounts of data. This approach limits the ability to explicitly estimate trend uncertainty and significance. Assessing the accuracy of multiple snapshots also requires time-series reference data which is often very costly and sometimes impossible to obtain. We devised a method of estimating trends in ecosystem extent that uses all available Landsat satellite imagery. We used a dense time series of classified maps that explicitly accounted for covariates that affect extent estimates (e.g., time, cloud cover, and seasonality). We applied this approach to the Hukaung Valley Wildlife Sanctuary, Myanmar, where rapid deforestation is greatly affecting the lowland rainforest. We applied a generalized additive mixed model to estimate forest extent from more than 650 Landsat image classifications (1999-2018). Forest extent declined significantly at a rate of 0.274%/year (SE = 0.078). Forest extent declined from 91.70% (SE = 0.02) of the study area in 1999 to 86.52% (SE = 0.02) in 2018. Compared with the snapshot method, our approach improved estimated trends of ecosystem loss by allowing significance testing with confidence intervals and incorporation of nonlinear relationships. Our method can be used to identify significant trends over time, reduces the need for extensive reference data through time, and provides quantitative estimates of uncertainty.

Marc, Adrien F., Guppy, Jarrod L., Bauer, Paige, Mulvey, Peter, Jerry, Dean R., and Paris, Damien B.B.P. (2021) Validation of advanced tools to evaluate sperm function in barramundi (Lates calcarifer). Aquaculture, 531. 735802.
Barramundi (Lates calcarifer) is a tropical finfish species rapidly growing in popularity for aquaculture production. However, sperm quality tests have yet to be adapted to enable selection of highly fertile male broodstock in this species. Accordingly, in this study advanced tools were optimized to evaluate barramundi sperm function to facilitate the future study of male fertility and address some of the reproductive constraints currently observed in captive-bred broodstock. Sperm morphology data were used to calibrate and validate automated sperm counting and motility detection by computer-assisted sperm analysis (CASA; AndroVision, Minitube). Several parameters were examined to determine the optimum settings for accurate CASA sperm counting and were compared to manual haemocytometer methods including: sample dilution (1:1000, r = 0.87), minimum number of fields (n = 4, CV = 7.5%), and the effect of motile vs. immotile spermatozoa on automated counting (no effect, r = 0.99, P < .001). Assays for cell viability and DNA damage were also validated for barramundi spermatozoa using 70 °C heat-treated controls and a 5-point intact:damaged dilution curve (r = 0.98, P < .001), and DNase-treated sperm controls, respectively. Data from these optimized assessments indicated high variation between individuals for each parameter assessed and the presence of high rates of DNA and membrane damage in sperm samples tested. Further research building upon this preliminary sperm quality data, is required to identify the cause of DNA and membrane damage in barramundi spermatozoa and understand any potential relationships with paternal performance in commercial spawns.

Domingos, Jose A., Goldsbury, Julie A., Bastos Gomes, Giana, Smith, Brett G., Tomlinson, Christopher, Bade, Tim, Sander, Corey, Forrester, Justin, and Jerry, Dean R. (2021) Genotype by environment interactions of harvest growth traits for barramundi (Lates calcarifer) commercially farmed in marine vs. freshwater conditions. Aquaculture, 532. 735989.
Barramundi (Lates calcarifer), also known as Asian seabass, is a commercially important tropical aquaculture species farmed in diverse culture production systems and salinities (marine to freshwater). Despite adaptability to different culture conditions, selective breeding programs to improve growth rates in barramundi should consider the impact of genotype by environment (GxE) interactions on genetic gains. Barramundi juveniles from 144 families, originating from 24 dams and 54 sires were farmed in a seawater (SW) raceway in Bowen (QLD, Australia) and a freshwater (FW) pond environment in Townsville (QLD, Australia) - both operated under commercial culture conditions. Fish were sampled at 15 months post-hatch (mph) in the SW raceway (mean 1718 ± 309 g weight (W), 454 ± 28 mm total length (Lₜ) and 141 ± 11 mm body depth (BD) (n = 752)) and at 21 mph in the FW pond (mean 1905 ± 426 g W and 451 ± 39 mm Lt and 144 ± 15 mm BD (n = 752)). DNA parentage analyses were used to assign progeny to their respective parents, and the final dataset comprised of 1116 offspring. Moderate-low heritability estimates were found for body traits (W h² = 0.46 ± 0.10; Lt h² = 0.41 ± 0.12; BD h² = 0.49 ± 0.13; body shape H h² = 0.41 ± 0.12; and Fulton's K condition factor h² = 0.15 ± 0.07). Deformities (Def) were observed in 1.8% of fish in SW and 25.1% of fish in FW, although negligible additive genetic effects were evident (Def h² = 0.05 ± 0.04). GxE interactions were found to be moderate for harvest growth traits (W GxE rg = 0.81 ± 0.11; Lt GxE rg = 0.64 ± 0.18; BD GxE rg = 0.78 ± 0.13; H GxE rg = 0.71 ± 0.17), and high for Fulton's K condition factor (K GxE rg = 0.36 ± 0.31; P > 0.05). This study reveals the presence of weak to moderate re-ranking of genotypes for harvest growth traits in L. calcarifer farmed in marine and freshwater conditions, suggesting that GxE interactions should be taken into account in a breeding program servicing multiple environments. Incorporation of sib-information from extreme salinity environments into the selection criteria of a breeding program may therefore optimize the realization of genetic gains across distinct commercial conditions.

Hill, Narelle K., Woodworth, Bradley K., Phinn, Stuart R., Murray, Nicholas J., and Fuller, Richard A. (2021) Global protected‐area coverage and human pressure on tidal flats. Conservation Biology. (In Press)
Tidal flats are a globally distributed coastal ecosystem important for supporting biodiversity and ecosystem services. Local to continental‐scale studies have documented rapid loss of tidal habitat driven by human impacts, but assessments of progress in their conservation are lacking. We analysed human pressure on tidal flats, and measured their representation in protected areas using a newly developed, internally‐consistent estimate of distribution and change for the world's tidal flats. We discovered that 68% of the current extent of tidal flats is subject to moderate to very high human pressure (Human Modification Index > 0.1), but that 31% of tidal flat extent occurred within protected areas, far exceeding percent protection of the marine (6%) and terrestrial (13%) realms. Net change of tidal flat extent inside protected areas was similar to tidal flat net change outside protected areas between 1999 and 2016. Substantial shortfalls in tidal flat protection occurred across Asia, where large intertidal extents coincide with high to very high human pressure (Human Modification Index > 0.4‐1), and net tidal flat losses up to 86.4 km² (83.9 km²‐89.0 km²; 95% confidence interval) occurred inside individual protected area boundaries within the study period. Taken together, our results show substantial progress in protected area designation for tidal flats globally, but that protected area status alone does not prevent all habitat loss. Safeguarding the world's tidal flats will thus require deeper understanding of the factors that govern their dynamics and effective policy that promotes holistic coastal and catchment management strategies.

Karnaneedi, Shaymaviswanathan, Huerlimann, Roger, Johnston, Elecia B., Nugraha, Roni, Ruethers, Thimo, Taki, Aya C., Kamath, Sandip D., Wade, Nicholas M., Jerry, Dean R., and Lopata, Andreas L. (2021) Novel allergen discovery through comprehensive de novo transcriptomic analyses of five shrimp species. International Journal of Molecular Sciences, 22 (1). 32.
Shellfish allergy affects 2% of the world's population and persists for life in most patients. The diagnosis of shellfish allergy, in particular shrimp, is challenging due to the similarity of allergenic proteins from other invertebrates. Despite the clinical importance of immunological cross-reactivity among shellfish species and between allergenic invertebrates such as dust mites, the underlying molecular basis is not well understood. Here we mine the complete transcriptome of five frequently consumed shrimp species to identify and compare allergens with all known allergen sources. The transcriptomes were assembled de novo, using Trinity, from raw RNA-Seq data of the whiteleg shrimp (Litopenaeus vannamei), black tiger shrimp (Penaeus monodon), banana shrimp (Fenneropenaeus merguiensis), king shrimp (Melicertus latisulcatus), and endeavour shrimp (Metapenaeus endeavouri). BLAST searching using the two major allergen databases, WHO/IUIS Allergen Nomenclature and AllergenOnline, successfully identified all seven known crustacean allergens. The analyses revealed up to 39 unreported allergens in the different shrimp species, including heat shock protein (HSP), alpha-tubulin, chymotrypsin, cyclophilin, beta-enolase, aldolase A, and glyceraldehyde-3-phosphate dehydrogenase (G3PD). Multiple sequence alignment (Clustal Omega) demonstrated high homology with allergens from other invertebrates including mites and cockroaches. This first transcriptomic analyses of allergens in a major food source provides a valuable resource for investigating shellfish allergens, comparing invertebrate allergens and future development of improved diagnostics for food allergy.

Jackson, Micha V., Fuller, Richard A., Gan, Xiaojing, Li, Jing, Mao, Dehua, Melville, David S., Murray, Nicholas, Wang, Zongming, and Choi, Chi-Yeung (2021) Dual threat of tidal flat loss and invasive Spartina alterniflora endanger important shorebird habitat in coastal mainland China. Journal of Environmental Management, 278 (Part 2). 111549.
China's coastal wetlands are critically important to shorebirds. Substantial loss of tidal flats, shorebirds' primary foraging grounds, has occurred from land claim and other processes, and is driving population declines in multiple species. Smooth cordgrass Spartina alterniflora was intentionally introduced to the coast of China in 1979 to promote conversion of tidal flats into dry land and has since spread rapidly. The occurrence of S. alterniflora reduces the availability of foraging and roosting habitat for shorebirds, and may be particularly detrimental in places that have experienced other tidal flat loss. However, the extent to which S. alterniflora is encroaching upon important shorebird habitat throughout coastal mainland China, and its intersection with tidal flat loss, has not been quantified. Here, we i) estimate change in the spatial extent of tidal flats between 2000 and 2015 in coastal mainland China where internationally important numbers of shorebirds have been recorded; ii) map the extent of S. alterniflora coverage in 2015 at the same set of sites; and, iii) investigate where these two threats to important shorebird habitat intersect. Our analysis of remote sensing data indicated a 15% net loss in tidal flat area between 2000 and 2015 across all sites, including a net loss in tidal flat area in 39 of 53 individual sites (74%). Spartina alterniflora occurred at 28 of 53 sites (53%) in 2015, of which 22 sites (79%) also had a net loss in tidal flat area between 2000 and 2015. Combined pressures from tidal flat loss and S. alterniflora invasion were most severe in eastern coastal China. Species highly dependent on migrating through this region, which include the Critically Endangered Spoon-billed Sandpiper and Endangered Nordmann's Greenshank and Far Eastern Curlew, may be particularly impacted. Our results underscore the urgent need to arrest tidal flat declines and develop a comprehensive control program for S. alterniflora in coastal areas of mainland China that are important for shorebirds.

Infante Villamil, Sandra, Huerlimann, Roger, and Jerry, Dean R. (2021) Microbiome diversity and dysbiosis in aquaculture. Reviews in Aquaculture. (In Press)
With the continuous growth of the human population and associated need for high‐quality protein, the aquaculture sector will be required to increase significantly in productivity. This growth in productivity will be achieved through more efficient use of resources like feeds, genetic improvement and limiting the impacts of disease. One of the key links between animal productivity and disease is that of microbial diversity, with high‐throughput sequencing technologies increasing our understanding of the role microorganisms play in health, development and physiology of vertebrate and invertebrate hosts alike. Increasing our understanding of microbial–host interactions will help avoid or manage dysbiosis in aquaculture systems with the final aim of improving productivity. We review the current literature, which indicates that there is an association between productivity and microbial diversity in aquaculture systems, as changes in bacterial microbiomes are implicated in animal performance, in disease development associated with both bacterial and viral origin, and in dysbiosis triggered by environmental stressors or diet choice. Dysbiosis, whether in the form of the loss of beneficial bacteria, or the expansion of pathogens or potentially harmful microorganisms, can be used as an indicator tool for productivity monitoring purposes. Development of management strategies towards preserving the microbial balance, including maintaining or increasing diversity in the host, is critical for the health of cultured aquatic animals and will likely be critical for the expansion of aquaculture.

Thompson, Cassandra A., Hoey, Andrew S., Montanari, Stefano R., Messmer, Vanessa, Doll, Peter C., and Pratchett, Morgan S. (2021) Territoriality and condition of chevron butterflyfish (Chaetodon trifascialis) with varying coral cover on the great barrier reef, Australia. Environmental Biology of Fishes, 104. pp. 53-69.
The chevron butterflyfish, Chaetodon trifascialis, is among the most specialised coral-feeding fish, and while it is known to be very susceptible to extensive depletion of its preferred coral prey (tabular Acropora spp.), their specific responses to changing coral cover are poorly understood. The purpose of this study was to test for variation in territorial behaviour and condition of C. trifascialis relative to spatial variation in coral cover across four mid-shelf reefs on the Great Barrier Reef. Explicit consideration was also given to the territorial arrangement and interactions among sympatric individuals, with a view to better understanding the sociality of this species. Variation in overall coral cover (which ranged from 26.5-73.4% among sites) as well as cover of tabular Acropora (13.3-44.8%) had limited effect on the territoriality or body condition of C. trifascialis. Rather, individual variation in territoriality was attributable to differences in gender and size of fish. Male C. trifascialis were generally larger and also had larger territories than female counterparts. They also interacted with conspecifics (and congenerics) much more than females. Taken together, these results support previous assertions that C. trifascialis is haremic. There was, however, limited evidence of male territories encompassing the territories of >1 female. While the sociality of C. trifascialis is clearly atypical of Chaetodon butterflyfishes, more work is needed to understand their reproductive biology as well as their behavioural responses to changing coral cover.

Silva, Catarina N. S., Young, Emma F., Murphy, Nicholas P., Bell, James J., Green, Bridget S., Morley, Simon A., Duhamel, Guy, Cockcroft, Andrew C., and Strugnell, Jan M. (2021) Climatic change drives dynamic source–sink relationships in marine species with high dispersal potential. Ecology and Evolution. (In Press)
While there is now strong evidence that many factors can shape dispersal, the mechanisms influencing connectivity patterns are species‐specific and remain largely unknown for many species with a high dispersal potential. The rock lobsters Jasus tristani and Jasus paulensis have a long pelagic larval duration (up to 20 months) and inhabit seamounts and islands in the southern Atlantic and Indian Oceans, respectively. We used a multidisciplinary approach to assess the genetic relationships between J. tristani and J. paulensis, investigate historic and contemporary gene flow, and inform fisheries management. Using 17,256 neutral single nucleotide polymorphisms we found low but significant genetic differentiation. We show that patterns of connectivity changed over time in accordance with climatic fluctuations. Historic migration estimates showed stronger connectivity from the Indian to the Atlantic Ocean (influenced by the Agulhas Leakage). In contrast, the individual‐based model coupled with contemporary migration estimates inferred from genetic data showed stronger inter‐ocean connectivity in the opposite direction from the Atlantic to the Indian Ocean driven by the Subtropical Front. We suggest that the J. tristani and J. paulensis historical distribution might have extended further north (when water temperatures were lower) resulting in larval dispersal between the ocean basis being more influenced by the Agulhas Leakage than the Subtropical Front. As water temperatures in the region increase in accordance with anthropogenic climate change, a southern shift in the distribution range of J. tristani and J. paulensis could further reduce larval transport from the Indian to the Atlantic Ocean, adding complexity to fisheries management.

Law, Lisa, Azzali, Simona, and Conejos, Sheila (2021) Planning for the temporary: temporary urbanism and public space in a time of COVID-19. Town Planning Review, 92 (1). pp. 65-74.
It is a cliché to say we live in strange times: COVID-19 has focused our attention on schedules of lockdowns and long-term economic effects, and has even slowed down our experience of time due to increased cognitive loads. But as planners or urban designers it is our urban places that have also become strange: COVID-19 is altering our use of, and behaviour in, public space – from physical and social distancing to staying at home or even leaving the city altogether. We are concerned with how long we will tolerate state encroachments in public space, especially new techniques of surveillance and control, but we also see local governments opening up streets to give more public spaces back to pedestrians. In this Viewpoint we explore these paradoxes of public space in a time of COVID-19, from its temporary disappearance to the potential for temporary changes to underpin lasting strategies for liveable, economically viable and resilient public space. Although some link temporary urbanism to neo-liberal urban development and austerity policies (Stevens et al., 2019), we ponder how the COVID-19 moment critiques the status quo by providing new openings for shifting temporary urbanism into the mainstream planning toolkit. Does COVID-19 present an opportunity to make temporariness more deliberate and programmatic,thereby catalysing long-term change?

Poblete, Jaime A., Dirks, Paul H.G.M., Chang, Zhaoshan, Huizenga, Jan Marten, Griessmann, Martin, and Hall, Chris (2021) The Watershed tungsten deposit, Northeast Queensland, Australia: Permian metamorphic tungsten mineralization overprinting Carboniferous magmatic tungsten. Economic Geology. (In Press)
The Watershed tungsten deposit (49.2 Mt avg 0.14% WO3) lies within the Mossman orogen, which comprises deformed Silurian-Ordovician metasedimentary rocks of the Hodgkinson Formation intruded by Carboniferous-Permian granites of the Kennedy Igneous Association. The Hodgkinson Formation in the Watershed area comprises skarn-altered conglomerate, psammite, and slate units that record four deformation events evolving from ductile, isoclinal, colinear folding with transposition (D1–D3) to brittle ductile shear zones (D4). Multiple felsic to intermediate dikes cut across the metasedimentary rocks at Watershed including: (1) Carboniferous, monzonite dikes (zircon U/Pb age of 350 ± 7 Ma) emplaced during D1–2; and (2) Permian granite plutons and dikes (zircon U/Pb ages of 291 ± 6, 277 ± 6, and 274 ± 6 Ma) and diorite (zircon U/Pb age of 281 ± 5 Ma) emplaced during D4. Tungsten mineralization is largely restricted to skarn-altered conglomerate, which preserves a peak metamorphic mineralogy formed during ductile deformation and comprises garnet (Grt40–87 Alm0–35Sps1–25Adr0–16), actinolite, quartz, clinopyroxene (Di36–59Hd39–61Jhn1–5), and titanite. A first mineralization event corresponds to the crystallization of disseminated scheelite in monzonite dikes (pre-D3) and adjacent units, with scheelite grains aligned in the S1–2 fabric and affected by D3 folding. This event enriched the Hodgkinson Formation in tungsten. The bulk of the scheelite mineralization formed during a second event and is concentrated in multistaged, shear-related, quartz-oligoclase-bearing veins and vein halos (muscovite 40Ar-39Ar weighted average age of 276 ± 6 Ma), which were emplaced during D4. The multistage veins developed preferentially in competent, skarn-altered conglomerate units and formed synchronous with four retrograde alteration stages. The retrograde skarn minerals include clinozoisite after garnet, quartz, plagioclase, scheelite, and phlogopite with minor sodium-rich amphibole, which formed during retrograde stages 1 and 2, accompanied by later muscovite, calcite, and chlorite formed during retrograde stage 3. Retrograde stage 4 was a late-tectonic, noneconomic sulfide stage. The principal controls on scheelite mineralization at Watershed were the following: (1) early monzonite dikes enriched in scheelite; (2) D4 shear zones that acted as fluid conduits transporting tungsten from source areas to traps; (3) skarn-altered conglomerate lenses that provide a competent host to facilitate vein formation and a source for calcium to form scheelite; and (4) an extensional depositional environment characterized by vein formation and normal faulting, which provide trapping structures for tungsten-bearing fluids, with decompression being a likely control on scheelite deposition. The coexistence of scheelite with oligoclase in monzonite dikes and veins suggests that tungsten was transported as NaHWO4⁠. Exploration in the area should target Carboniferous monzonite, associated with later syn-D4 shear zones cutting skarn-altered conglomerate.

Spence, Joshua S., Sanislav, Ioan V., and Dirks, Paul H.G.M. (2021) 1750–1710 Ma deformation along the eastern margin of the North Australia Craton. Precambrian Research, 353. 106019.
In this contribution, we present field-based evidence that in the Mary Kathleen Domain from the Eastern Fold Belt of the Mount Isa Inlier the 1790–1750 Ma metasediments of the Leichhardt Superbasin were sheared and folded between 1750 and 1710 Ma. The Mary Kathleen Domain consists of a series of anastomosing high and low strain domains intruded syn- to late-tectonically by a series of 1740–1710 Ma felsic and mafic plutons and dykes. The timing relationships in the high strain domains are unclear due to mylonitisation and transposition but in the lower strain domains are well-preserved. The earliest deformation, D1, consists of a series of low angle truncation surfaces and shear zones that are folded around large scale N-S trending upright folds during D2. The D2 folds were refolded during D3 along NW to EW trending fold axes. An undeformed granitic pluton from the Mt Godkin area dated at ~1710 Ma that crosscuts the D2-D3 folds and the youngest detrital zircon population of ~1750 Ma constrains the timing of D1-D3 deformation between 1750 and 1710 Ma. Later, N-S (D4) and N-E (D5) trending brittle-ductile shears are interpreted to indicate a late Isan Orogeny overprint. The occurrence of contemporaneous folding in the Western Fold Belt suggests that between 1750 and 1710 Ma the eastern margin of the North Australia Craton was experiencing a significant deformation event that can be correlated with similarly aged deformation events from other parts of the North Australia Craton, from South Australia Craton and from East Antarctica. Following the assembly of most of the Nuna Supercontinent by 1.8 Ga, we postulate that the 1750–1710 Ma deformation and plutonism observed in Mount Isa Inlier is part of a series of worldwide orogenic events that contributed to the final configuration of the Nuna Supercontinent.

Palma, Ana C., Goosem, Miriam, Fensham, Roderick J., Goosem, Steve, Preece, Noel D., Stevenson, Pablo R., and Laurance, Susan G.W. (2021) Dispersal and recruitment limitations in secondary forests. Journal of Vegetation Science. e12975. (In Press)
Aims: Secondary forests are expanding rapidly in tropical regions and could play an important role in conserving native biodiversity and stabilising global climate. The recovery rate of plant communities in secondary forests varies considerably due to mechanisms associated with seed dispersal and recruitment dynamics. We explored these mechanisms along a chronosequence of tropical secondary forests in an agricultural landscape that was extensively cleared. Location: We explored these mechanisms along a chronosequence of secondary forests in tropical Australia. Methods: We used selected plant traits to characterise plant species and compared community composition between demographic stages (i.e. soil seedbank, understorey and overstorey) and forest age categories. We collected soil samples to assess seedbank composition and used quadrants and transects to assess understorey and overstorey plant community composition at each site. Results: For all demographic stages, we found that young (4-12 years) and intermediate-aged forests (16-20 years) were dominated by early successional, small-seeded species and traits associated with disturbed forests. In old secondary forest (23-34 years) some traits associated with late successional stages were present (e.g. large seeds, trees). However, the traits and species composition of mature forests remained distinct from all secondary forests. Across the chronosequence, forest age and demographic stage were significant factors in discriminating species and trait composition between forest sites. We found clear plant community similarities within demographic stages, despite the forest age differences. This suggests stronger limitations to dispersal and recruitment between demographic stages than between forest ages. Conclusions: Our results show that secondary forests in this region assemble slowly with dispersal and recruitment limitations constraining their recovery. Although a successional transition in species and plant traits composition along the chronosequence is clear, similarities to mature forests remain low. The slow recovery of late successional and large-seeded species in these secondary forests suggests that active restoration of such species may be necessary if we want to enhance the capacity of these forests to conserve native biodiversity.

Zhao, Xu, Fu, Lebing, Wei, Junhao, Huizenga, Jan, Liu, Yan, Chen, Jiajie, and Wang, Dianzhong (2021) Generation and structural modification of the giant Kengdenongshe VMS-type Au-Ag-Pb-Zn polymetallic deposit in the East Kunlun Orogen, East Tethys: constraints from geology, fluid inclusions, noble gas and stable isotopes. Ore Geology Reviews, 131. 104041.
The Kengdenongshe giant Au-Ag-Pb-Zn polymetallic deposit is located in the East Kunlun Orogen (EKO). It contains about 42.2 t of Au, 608.6 t of Ag and 1.05 Mt of Pb and Zn with an average grade of Au 2.31 g/t, Ag 19.29 g/t and Pb + Zn 3.49 wt% (Pb: 1.23 wt%, Zn: 2.26 wt%). The NWW-trending ore bodies are predominantly hosted in Late Permian to Triassic rhyolitic tuff, which formed during Late Permian back-arc extension to Triassic arc-continental collision. The ore bodies are subdivided into Pb-Zn rich ore bodies on the top with high grades of Pb and Zn and low grades of Au and Ag, and Au-Ag rich ore bodies below with high grades of Au and Ag and low grades of Pb and Zn. The Pb-Zn rich ore bodies occur as vein, stockwork, and in breccia, and comprise quartz, pyrite, galena, sphalerite, and small amounts of chalcopyrite. The Au-Ag rich ore bodies consist of auriferous barite-sulfide-oxide veins and contain barite, pyrite (early strawberry and oolitic pyrite and later eu- to subhedral pyrite), galena, sphalerite, chalcopyrite, tetrahedrite and covellite. Gold is present as electrum, kustelite and native gold and silver is present as polybasite, pearceite, kongsbergite, and as minor native silver in microfractures in sulfides. The hydrothermal alteration minerals include, from bottom to top, quartz + barite + calcite around the Au-Ag rich orebodies, quartz + chlorite + epidote around the Pb-Zn rich orebodies, and quartz + K-feldspar within the tuff. Fluid inclusions from both the Pb-Zn rich and the Au-Ag rich orebodies consist of two phases (V–L-type) fluid inclusions of which the vapor phase has a size of 10–40 vol%. Fluid inclusions microthermometry reveal homogenization temperatures of fluid inclusions in Pb-Zn rich and Au-Ag rich ore bodies of 128–230 °C and 110–320 °C, with corresponding salinities of 0.7–9.9 and 0.2–18.3 wt% NaCl equivalent, respectively. H-O-S-Pb stable isotope and He-Ar noble gas isotope data indicate a mixed magmatic water-seawater source for both the Pb-Zn and Au-Ag rich ore bodies, and an additional meteoric water component for the Au-Ag rich ore bodies. The Pb-Zn and Au-Ag rich ore bodies share the same sulfur and lead sources, i.e. sulfur is derived from crustal magma and seawater/marine sulfate, and the lead originated from a mixed magmatic-ancient crustal sedimentary source. Collectively, the regional geology, mineralogy, alteration, and geochemistry indicate that the Kengdenongshe Au-Ag-Pb-Zn polymetallic deposit can be characterized as a VMS-type (volcanic-associated massive sulfide) deposit. Formation of the ore-hosting rhyolite tuff and mineralization are associated with Late Permian to Triassic marine volcanic exhalation. Middle to Late Triassic basin closure and arc-continent collision modified the deposit and resulted in the location inversion of the Pb-Zn and Au-Ag rich orebodies.

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