Optimizing facility location, sizing, and growth time for a cultivated resource: A case study in coral aquaculture.

Production of cultivated resources require additional planning that takes growth time into account. We formulate a mathematical programming model to determine the optimal location and sizing of growth facilities, impacted by resource survival rate as a function of its growth time. Our method informs strategic decisions regarding the number, location, and sizing of facilities, as well as operational decisions of optimal growth time for a cultivated resource in a facility to minimize total costs. We solve this facility location and sizing problem in the context of coral aquaculture for large-scale reef restoration using a two-stage algorithm and a linear mixed-integer solver. We assess growth time in a facility in terms of its impact on survival (post-deployment) considering growth quantity requirements and growth facility production constraints. We explore the sensitivity of optimal facility number, location, and sizing to changes in the geographic distribution of demand and cost parameters computationally. Results show that the relationship between growth time and survival is critical to optimizing operational decisions for grown resources. These results inform the value of data certainty to optimize the logistics of coral aquaculture production.

Coral restoration and adaptation in Australia: The first five years.

While coral reefs in Australia have historically been a showcase of conventional management informed by research, recent declines in coral cover have triggered efforts to innovate and integrate intervention and restoration actions into management frameworks. Here we outline the multi-faceted intervention approaches that have developed in Australia since 2017, from newly implemented in-water programs, research to enhance coral resilience and investigations into socio-economic perspectives on restoration goals. We describe in-water projects using coral gardening, substrate stabilisation, coral repositioning, macro-algae removal, and larval-based restoration techniques. Three areas of research focus are also presented to illustrate the breadth of Australian research on coral restoration, (1) the transdisciplinary Reef Restoration and Adaptation Program (RRAP), one of the world's largest research and development programs focused on coral reefs, (2) interventions to enhance coral performance under climate change, and (3) research into socio-cultural perspectives. Together, these projects and the recent research focus reflect an increasing urgency for action to confront the coral reef crisis, develop new and additional tools to manage coral reefs, and the consequent increase in funding opportunities and management appetite for implementation. The rapid progress in trialling and deploying coral restoration in Australia builds on decades of overseas experience, and advances in research and development are showing positive signs that coral restoration can be a valuable tool to improve resilience at local scales (i.e., high early survival rates across a variety of methods and coral species, strong community engagement with local stakeholders). RRAP is focused on creating interventions to help coral reefs at multiple scales, from micro scales (i.e., interventions targeting small areas within a specific reef site) to large scales (i.e., interventions targeting core ecosystem function and social-economic values at multiple select sites across the Great Barrier Reef) to resist, adapt to and recover from the impacts of climate change. None of these interventions aim to single-handedly restore the entirety of the Great Barrier Reef, nor do they negate the importance of urgent climate change mitigation action.

Scaling up the global reef restoration activity: Avoiding ecological imperialism and ongoing colonialism.

The health and condition of the world's reefs are in steep decline. This has triggered the development of fledgling micro-scale coral reef restoration projects along many reef coastlines. However, it is increasingly recognised that the scale and productivity of micro-scale coral gardening projects will be insufficient to meet the growing global threats to reefs. More recently, efforts to develop and implement restoration techniques for application at regional scales have been pursued by research organisations. Coral reefs are mostly located in the unindustrialised world. Yet, most of the funding, and scientific and engineering method development for larger-scale methods will likely be sourced and created in the industrialised world. Therefore, the development of the emerging at-scale global reef restoration sector will inevitably involve the transfer of methods, approaches, finances, labour and skills from the industrialised world to the unindustrialised world. This opens the door to the industrialised world negatively impacting the unindustrialised world and, in some cases, First Nations peoples. In Western scientific parlance, ecological imperialism occurs when people from industrialised nations seek to recreate environments and ecosystems in unindustrialised nations that are familiar and comfortable to them. How a coral reef 'should' look depends on one's background and perspective. While predominately Western scientific approaches provide guidance on the ecological principles for reef restoration, these methods might not be applicable in every scenario in unindustrialised nations. Imposing such views on Indigenous coastal communities without the local technical and leadership resources to scale-up restoration of their reefs can lead to unwanted consequences. The objective of this paper is to introduce this real and emerging risk into the broader reef restoration discussion.

Substrate stabilisation and small structures in coral restoration: State of knowledge, and considerations for management and implementation.

Coral reef ecosystems are under increasing pressure from local and regional stressors and a changing climate. Current management focuses on reducing stressors to allow for natural recovery, but in many areas where coral reefs are damaged, natural recovery can be restricted, delayed or interrupted because of unstable, unconsolidated coral fragments, or rubble. Rubble fields are a natural component of coral reefs, but repeated or high-magnitude disturbances can prevent natural cementation and consolidation processes, so that coral recruits fail to survive. A suite of interventions have been used to target this issue globally, such as using mesh to stabilise rubble, removing the rubble to reveal hard substrate and deploying rocks or other hard substrates over the rubble to facilitate recruit survival. Small, modular structures can be used at multiple scales, with or without attached coral fragments, to create structural complexity and settlement surfaces. However, these can introduce foreign materials to the reef, and a limited understanding of natural recovery processes exists for the potential of this type of active intervention to successfully restore local coral reef structure. This review synthesises available knowledge about the ecological role of coral rubble, natural coral recolonisation and recovery rates and the potential benefits and risks associated with active interventions in this rapidly evolving field. Fundamental knowledge gaps include baseline levels of rubble, the structural complexity of reef habitats in space and time, natural rubble consolidation processes and the risks associated with each intervention method. Any restoration intervention needs to be underpinned by risk assessment, and the decision to repair rubble fields must arise from an understanding of when and where unconsolidated substrate and lack of structure impair natural reef recovery and ecological function. Monitoring is necessary to ascertain the success or failure of the intervention and impacts of potential risks, but there is a strong need to specify desired outcomes, the spatial and temporal context and indicators to be measured. With a focus on the Great Barrier Reef, we synthesise the techniques, successes and failures associated with rubble stabilisation and the use of small structures, review monitoring methods and indicators, and provide recommendations to ensure that we learn from past projects.

Enabling Biomimetic Place-Based Design at Scale.

Amidst the inter-related challenges of climate change, resource scarcity, and population growth, the built environment must be designed in a way that recognises its role in shaping and being shaped by complex social and ecological systems. This includes avoiding the degradation of living systems in the design and construction of buildings and infrastructure, as well as enhancing the built environment's resilience to disturbance by those systems. This paper explores the potential for biomimetic place-based design (BPD) to inform resilient and regenerative built environment outcomes by learning from local ecosystems. One recognised hurdle is the upfront resourcing required to establish the biomimetic knowledge base for each project. However, conducting BPD projects at-scale (i.e., city or region) can improve the method's value-proposition by better leveraging upfront research efforts, design concepts, and strategies. This research identifies existing barriers to the widespread adoption of BPD and presents an action framework for capability-building across industry, government, and academia to enable application at-scale. Drawing on findings from workshops in the USA and Australia, it creates a resource for colleagues looking to apply BPD in a city or region and offers next steps for research and development.

Findings of Case-Study Analysis: System-Level Biomimicry in Built-Environment Design.

Complex systems challenges like those facing 21st-century humanity, require system-level solutions that avoid siloed or unnecessarily narrow responses. System-level biomimicry aims to identify and adopt design approaches that have been developed and refined within ecosystems over 3.8 billion years of evolution. While not new, system-level biomimetic solutions have been less widely applied in urban design than the 'form' and 'process' level counterparts. This paper explores insights from a selection of system-level case studies in the built environment, using meta-analysis to investigate common challenges and priorities from these projects to support knowledge-sharing and continued development in the field. Using a grounded research approach, common themes are distilled, and findings presented regarding success and barriers to implementation and scaling. Considering the findings, and drawing on complex adaptive systems theory, the paper posits opportunities to facilitate broader implementation and mainstreaming of system-level biomimetic design approaches in the built environment.

Prevalences of Pospiviroid Contamination in Large Seed Lots of Tomato and Capsicum, and Related Seed Testing Considerations.

Analyses of pospiviroids in commercial seed lots of tomato and capsicum, determined by testing of 12,000 to 40,000 seeds per lot, have enabled the development of empirically-derived distribution curves for the observed prevalences of viroids in those commodities. Those distribution curves can be considered in conjunction with statistically-based estimates of detection that would be achieved using other sample sizes. Statistical calculations using binomial distributions show that sample sizes of 3000 and 9400 seeds allow detection of viroid prevalences as low as 0.1% and 0.032%, respectively, with 95% confidence. Applying those calculations to observed viroid prevalences in contaminated tomato seed lots, it is estimated that the use of sample sizes of 3000 and 9400 seeds would detect 15% and 42%, respectively, of the contaminated seed lots identified using the larger sample sizes of approximately 20,000 seeds reported in this study. It is concluded that the higher costs associated with testing of larger sample sizes represent a worthwhile investment in agricultural biosecurity.

Viroid-infected Tomato and Capsicum Seed Shipments to Australia.

Pospiviroid species are transmitted through capsicum and tomato seeds. Trade in these seeds represents a route for the viroids to invade new regions, but the magnitude of this hazard has not been adequately investigated. Since 2012, tomato seed lots sent to Australia have been tested for pospiviroids before they are released from border quarantine, and capsicum seed lots have been similarly tested in quarantine since 2013. Altogether, more than 2000 seed lots have been tested. Pospiviroids were detected in more than 10% of the seed lots in the first years of mandatory testing, but the proportion of lots that were infected declined in subsequent years to less than 5%. Six pospiviroid species were detected: Citrus exocortis viroid, Columnea latent viroid, Pepper chat fruit viroid, Potato spindle tuber viroid, Tomato chlorotic dwarf viroid and Tomato apical stunt viroid. They were detected in seed lots exported from 18 countries from every production region. In many seed lots, the detectable fraction (prevalence) of infected seeds was estimated to be very small, as low as 6 × 10-5 (~1 in 16,000; CI 5 × 10-6 to 2.5 × 10-4) for some lots. These findings raise questions about seed production practices, and the study indicates the geographic distributions of these pathogens are uncertain, and there is a continuing threat of invasion.

A Risk Assessment Framework for the Socioeconomic Impacts of Electricity Transmission Infrastructure Failure Due to Space Weather: An Application to the United Kingdom.

Space weather phenomena have been studied in detail in the peer-reviewed scientific literature. However, there has arguably been scant analysis of the potential socioeconomic impacts of space weather, despite a growing gray literature from different national studies, of varying degrees of methodological rigor. In this analysis, we therefore provide a general framework for assessing the potential socioeconomic impacts of critical infrastructure failure resulting from geomagnetic disturbances, applying it to the British high-voltage electricity transmission network. Socioeconomic analysis of this threat has hitherto failed to address the general geophysical risk, asset vulnerability, and the network structure of critical infrastructure systems. We overcome this by using a three-part method that includes (i) estimating the probability of intense magnetospheric substorms, (ii) exploring the vulnerability of electricity transmission assets to geomagnetically induced currents, and (iii) testing the socioeconomic impacts under different levels of space weather forecasting. This has required a multidisciplinary approach, providing a step toward the standardization of space weather risk assessment. We find that for a Carrington-sized 1-in-100-year event with no space weather forecasting capability, the gross domestic product loss to the United Kingdom could be as high as £15.9 billion, with this figure dropping to £2.9 billion based on current forecasting capability. However, with existing satellites nearing the end of their life, current forecasting capability will decrease in coming years. Therefore, if no further investment takes place, critical infrastructure will become more vulnerable to space weather. Additional investment could provide enhanced forecasting, reducing the economic loss for a Carrington-sized 1-in-100-year event to £0.9 billion.

Rymovirus: a cautionary tale.

A recent proposal that the genus Rymovirus be assimilated into the genus Potyvirus is examined, discussed, and rejected. It illustrates the danger of using 'sequence identity' as a proxy for phylogenetic relatedness to distinguish closely related but distinct groups of viruses.

The phylogenetics of the global population of potato virus Y and its necrogenic recombinants.

Potato virus Y (PVY) is a major pathogen of potatoes and other solanaceous crops worldwide. It is most closely related to potyviruses first or only found in the Americas, and it almost certainly originated in the Andes, where its hosts were domesticated. We have inferred the phylogeny of the published genomic sequences of 240 PVY isolates collected since 1938 worldwide, but not the Andes. All fall into five groupings, which mostly, but not exclusively, correspond with groupings already devised using biological and taxonomic data. Only 42 percent of the sequences are not recombinant, and all these fall into one or other of three phylogroups; the previously named C (common), O (ordinary), and N (necrotic) groups. There are also two other distinct groups of isolates all of which are recombinant; the R-1 isolates have N (5' terminal minor) and O (major) parents, and the R-2 isolates have R-1 (major) and N (3' terminal minor) parents. Many isolates also have additional minor intra- and inter-group recombinant genomic regions. The complex interrelationships between the genomes were resolved by progressively identifying and removing recombinants using partitioned sequences of synonymous codons. Least squared dating and BEAST analyses of two datasets of gene sequences from non-recombinant heterochronously-sampled isolates (seventy-three non-recombinant major ORFs and 166 partial ORFs) found the 95% confidence intervals of the TMRCA estimates overlap around 1,000 CE (Common Era; AD). We attempted to identify the most accurate datings by comparing the estimated phylogenetic dates with historical events in the worldwide adoption of potato and other PVY hosts as crops, but found that more evidence from gene sequences of non-potato isolates, especially from South America, was required.

Essential requirements for catchment sediments to have ongoing impacts to water clarity in the great barrier reef.

Increasing concerns over decreasing water quality and the state of coral reefs and seagrass meadows along the inshore and mid-shelf regions of the Great Barrier Reef has led to a large-scale government catchment sediment and nutrient reduction program. However the mechanistic understanding of how fine sediments washed out of catchments and transported within flood plumes leads to ongoing increases in turbidity at locations far downstream from estuaries long after flood plumes have dissipated is poorly understood. Essential criteria which need to be met in order for catchment-derived sediments to play a major role in nearshore water quality are proposed. Preliminary estimates of these essential criteria suggest that it is dynamically possible for fine sediments washed out of catchments during floods to be preferentially re-mobilised at downstream locations following the dissipation of flood plumes. However the longer-term influence of catchment-derived material on water quality is dependent upon the rate of degradation of floc particles that fall out of flood plumes and the rate of background deposition; neither of which are well quantified.

Environmental perverse incentives in coastal monitoring.

It can be argued that the intensity of monitoring of coastal marine environments lags behind the equivalent terrestrial environments. This results in a paucity of long-term time series of key environmental parameters such as turbidity. This lack of management information of the sources and sinks, and causes and impacts of stressors to the coastal marine environment, along with a lack of co-ordination of information collection is compromising the ability of environmental impact assessments of major coastal developments to discriminate between local and remote anthropogenic impacts, and natural or background processes. In particular, the quasi outsourcing of the collection of coastal information can lead to a perverse incentive whereby in many cases nobody is actively or consistently monitoring the coastal marine environment effectively. This is particularly the case with regards to the collection of long-term and whole-of-system scale data. This lack of effective monitoring can act to incentivise poor environmental performance.

Ecological risk assessment, prediction, and assessing risk predictions.

Ecological risk assessment embodied in an adaptive management framework is becoming the global standard approach for formally assessing and managing the ecological risks of technology and development. Ensuring the continual improvement of ecological risk assessment approaches is partly achieved through the dissemination of not only the types of risk assessment approaches used, but also their efficacy. While there is an increasing body of literature describing the results of general comparisons between alternate risk assessment methods and models, there is a paucity of literature that post hoc assesses the performance of specific predictions based on an assessment of risk and the effectiveness of the particular model used to predict the risk. This is especially the case where risk assessments have been used to grant consent or approval for the construction of major infrastructure projects. While postconstruction environmental monitoring is increasingly commonplace, it is not common for a postconstruction assessment of the accuracy and performance of the ecological risk assessment and underpinning model to be undertaken. Without this "assessment of the assessment," it is difficult for other practitioners to gain insight into the performance of the approach and models used and therefore, as argued here, this limits the rate of improvement of risk assessment approaches.

Evolutionary dynamics of the N1 neuraminidases of the main lineages of influenza A viruses.

Influenza A virus infects a wide range of hosts including birds, humans, pigs, horses, and other mammals. Because hosts differ in immune system structure and demography, it is therefore expected that host populations leave different imprints on the viral genome. In this study, we investigated the evolutionary trajectory of the main lineages of N1 type neuraminidase (NA) gene sequences of influenza A viruses by estimating their evolutionary rates and the selection pressures exerted upon them. We also estimated the time of emergence of these lineages. The Eurasian (avian-like) and North American (classical) swine lineages, the human (seasonal) and avian H5N1 lineages, and a long persisting avian lineage were studied and compared. Nucleotide substitution rates ranged from 1.9x10(-3) to 4.3x10(-3) substitutions per site per year, with the H5N1 lineage estimated to have the greatest rate. The evolutionary rates of the H1N1 human lineage appeared to be slightly greater after it re-emerged in 1977 than before it disappeared in the 1950s. Comparing across the lineages, substitution rates appeared to correlate with the number of positively selected sites and with the degree of asymmetry of the phylogenetic trees. Some lineages had strongly asymmetric trees, implying repeated genotype replacement and narrow genetic diversity. Positively selected sites were identified in all lineages, with the H5N1 lineage having the largest number. A great number of isolates of the H5N1 lineage were sequenced in a short time period and the phylogeny of the lineage was more symmetric. We speculate that the rate and selection estimations made for this lineage could have been influenced by sampling and may not represent the long-term trends.

Ecosystem-based fisheries management requires a change to the selective fishing philosophy.

Globally, many fish species are overexploited, and many stocks have collapsed. This crisis, along with increasing concerns over flow-on effects on ecosystems, has caused a reevaluation of traditional fisheries management practices, and a new ecosystem-based fisheries management (EBFM) paradigm has emerged. As part of this approach, selective fishing is widely encouraged in the belief that nonselective fishing has many adverse impacts. In particular, incidental bycatch is seen as wasteful and a negative feature of fishing, and methods to reduce bycatch are implemented in many fisheries. However, recent advances in fishery science and ecology suggest that a selective approach may also result in undesirable impacts both to fisheries and marine ecosystems. Selective fishing applies one or more of the "6-S" selections: species, stock, size, sex, season, and space. However, selective fishing alters biodiversity, which in turn changes ecosystem functioning and may affect fisheries production, hindering rather than helping achieve the goals of EBFM. We argue here that a "balanced exploitation" approach might alleviate many of the ecological effects of fishing by avoiding intensive removal of particular components of the ecosystem, while still supporting sustainable fisheries. This concept may require reducing exploitation rates on certain target species or groups to protect vulnerable components of the ecosystem. Benefits to society could be maintained or even increased because a greater proportion of the entire suite of harvested species is used.