Government of Western Australia

Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.

Classic parametric statistical significance tests, such as analysis of variance and least squares regression, are widely used by researchers in many disciplines, including psychology. For classic parametric tests to produce accurate results, the assumptions underlying them (e.g., normality and homoscedasticity) must be satisfied. These assumptions are rarely met when analyzing real data. The use of classic parametric methods with violated assumptions can result in the inaccurate computation of p values, effect sizes, and confidence intervals. This may lead to substantive errors in the interpretation of data. Many modern robust statistical methods alleviate the problems inherent in using parametric methods with violated assumptions, yet modern methods are rarely used by researchers. The authors examine why this is the case, arguing that most researchers are unaware of the serious limitations of classic methods and are unfamiliar with modern alternatives. A range of modern robust and rank-based significance tests suitable for analyzing a wide range of designs is introduced. Practical advice on conducting modern analyses using software such as SPSS, SAS, and R is provided. The authors conclude by discussing robust effect size indices.

▪ Abstract Like South Africa's Greater Cape Floristic Region, the Southwest Australian Floristic Region (SWAFR) is species rich, with a Mediterranean climate and old, weathered, nutrient-deficient landscapes. This region has 7380 native vascular plants (species/subspecies): one third described since 1970, 49% endemic, and 2500 of conservation concern. Origins are complex. Molecular phylogenies suggest multiple dispersal events into, out of, and within the SWAFR throughout the Cretaceous and Cenozoic; in many phylogenetically unrelated clades; and from many directions. Either explosive speciation or steady cladogenesis occurred among some woody sclerophyll and herbaceous families from the mid-Tertiary in response to progressive aridity. Genomic coalescence was sometimes involved. Rainforest taxa went extinct by the Pleistocene. Old lineages nevertheless persist as one endemic order (Dasypogonales) and 6–11 endemic families. Such a rich flora on old landscapes that have been exposed to European land-use practices is highly threatened. Conservation programs must minimize soil removal and use local germplasm in restoration programs.

Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.

The evaluation of feed ingredients is crucial to nutritional research and feed development for aquaculture species. In evaluating ingredients for use in aquaculture feeds, there are several important knowledge components that should be understood to enable the judicious use of a particular ingredient in feed formulation. This includes information on (1) ingredient digestibilities, (2) ingredient palatability and (3) nutrient utilization and interference. Diet design, feeding strategy, faecal collection method and method of calculation all have important implications on the determination of the digestible value of nutrients from any ingredient. There are several ways in which palatability of ingredients can be assessed, usually based on variable inclusion levels of the ingredient in question in a reference diet and feeding of those diets under an apparent satietal or self-regulating feeding regimes. However, the design of the diets, the parameters of assessment and the feeding regime can all be subject to variation depending on subtleties of the experimental design. Clearly, issues relating to feed intake are the key performance criteria in palatability assessments, and it is important that such experiments maintain sufficient stringency to allow some self-discrimination of the test feeds by the fish. The ability of fish to use nutrients from the test ingredient, or defining factors that interfere with that process, is perhaps the most complex and variable part of the ingredient evaluation process. It is crucial to discriminate effects on feed intake from effects on utilization of nutrients from ingredients (for growth and other metabolic processes). To allow an increased focus on nutrient utilization by the animals, there are several experimental strategies that can be adopted, which are based on variations in diet design and feeding regime used. Other issues such as ingredient functionality, influence on immune status and effects on organoleptic qualities are also important consideration in determining the value of ingredients in aquaculture feed formulations. A key aspect to note is the need to design all experiments with sufficient experimental capacity to detect significant effects.

The Human Phenotype Ontology (HPO)-a standardized vocabulary of phenotypic abnormalities associated with 7000+ diseases-is used by thousands of researchers, clinicians, informaticians and electronic health record systems around the world. Its detailed descriptions of clinical abnormalities and computable disease definitions have made HPO the de facto standard for deep phenotyping in the field of rare disease. The HPO's interoperability with other ontologies has enabled it to be used to improve diagnostic accuracy by incorporating model organism data. It also plays a key role in the popular Exomiser tool, which identifies potential disease-causing variants from whole-exome or whole-genome sequencing data. Since the HPO was first introduced in 2008, its users have become both more numerous and more diverse. To meet these emerging needs, the project has added new content, language translations, mappings and computational tooling, as well as integrations with external community data. The HPO continues to collaborate with clinical adopters to improve specific areas of the ontology and extend standardized disease descriptions. The newly redesigned HPO website (www.human-phenotype-ontology.org) simplifies browsing terms and exploring clinical features, diseases, and human genes.

Effective marine management requires comprehensive data on the status of marine biodiversity. However, efficient methods that can document biodiversity in our oceans are currently lacking. Environmental DNA (eDNA) sourced from seawater offers a new avenue for investigating the biota in marine ecosystems. Here, we investigated the potential of eDNA to inform on the breadth of biodiversity present in a tropical marine environment. Directly sequencing eDNA from seawater using a shotgun approach resulted in only 0.34% of 22.3 million reads assigning to eukaryotes, highlighting the inefficiency of this method for assessing eukaryotic diversity. In contrast, using 'tree of life' (ToL) metabarcoding and 20-fold fewer sequencing reads, we could detect 287 families across the major divisions of eukaryotes. Our data also show that the best performing 'universal' PCR assay recovered only 44% of the eukaryotes identified across all assays, highlighting the need for multiple metabarcoding assays to catalogue biodiversity. Lastly, focusing on the fish genus Lethrinus, we recovered intra- and inter-specific haplotypes from seawater samples, illustrating that eDNA can be used to explore diversity beyond taxon identifications. Given the sensitivity and low cost of eDNA metabarcoding we advocate this approach be rapidly integrated into biomonitoring programs.

Phoma stem canker (blackleg), caused by Leptosphaeria maculans , is an important disease on oilseed rape (canola, rapeseed, Brassica napus , Brassica juncea , Brassica rapa ) causing seedling death, lodging or early senescence in Australia, Canada and Europe, but not in China. The two forms of L. maculans (A group and B group) that occur on oilseed rape are now considered to be separate species. The epidemiology and severity of phoma stem canker differs between continents due to differences in the pathogen population structure, oilseed rape species and cultivars grown, climate and agricultural practices. Epidemics are most severe in Australia, where only the A group occurs, and can be damaging in Canada and western Europe, where both A and B groups occur, although their proportions vary within regions and throughout the year. Epidemics are slight in China, where the A group has not been found. Dry climates (Australia, western Canada) lengthen the persistence of infected debris and may synchronize the release of airborne ascospores (after rain) with seedling emergence. L. maculans spreads from cotyledon and leaf infections down petioles to reach the stem, with infections on cotyledons and leaves early in the season producing the most damaging stem cankers at the stem base (crown). Development of both crown cankers and phoma stem lesions higher up stems is most rapid in regions with high temperatures from flowering to harvest, such as Australia and Canada. Breeding for resistance (genetic, disease escape or tolerance), stubble management, crop rotation and fungicide seed treatments are important strategies for control of phoma stem canker in all areas. Fungicide spray treatments are justified only in regions such as western Europe where high yields are obtained, and accurate forecasts of epidemic severity are needed to optimize their use.

Abstract Many methods have been developed in the last 70 years to predict the natural mortality rate, M, of a stock based on empirical evidence from comparative life history studies. These indirect or empirical methods are used in most stock assessments to (i) obtain estimates of M in the absence of direct information, (ii) check on the reasonableness of a direct estimate of M, (iii) examine the range of plausible M estimates for the stock under consideration, and (iv) define prior distributions for Bayesian analyses. The two most cited empirical methods have appeared in the literature over 2500 times to date. Despite the importance of these methods, there is no consensus in the literature on how well these methods work in terms of prediction error or how their performance may be ranked. We evaluate estimators based on various combinations of maximum age (tmax), growth parameters, and water temperature by seeing how well they reproduce >200 independent, direct estimates of M. We use tenfold cross-validation to estimate the prediction error of the estimators and to rank their performance. With updated and carefully reviewed data, we conclude that a tmax-based estimator performs the best among all estimators evaluated. The tmax-based estimators in turn perform better than the Alverson–Carney method based on tmax and the von Bertalanffy K coefficient, Pauly’s method based on growth parameters and water temperature and methods based just on K. It is possible to combine two independent methods by computing a weighted mean but the improvement over the tmax-based methods is slight. Based on cross-validation prediction error, model residual patterns, model parsimony, and biological considerations, we recommend the use of a tmax-based estimator (M=4.899tmax−0.916, prediction error = 0.32) when possible and a growth-based method (M=4.118K0.73L∞−0.33 , prediction error = 0.6, length in cm) otherwise.

BACKGROUND: In February 2016, a new fungal disease was spotted in wheat fields across eight districts in Bangladesh. The epidemic spread to an estimated 15,000 hectares, about 16 % of the cultivated wheat area in Bangladesh, with yield losses reaching up to 100 %. Within weeks of the onset of the epidemic, we performed transcriptome sequencing of symptomatic leaf samples collected directly from Bangladeshi fields. RESULTS: Reinoculation of seedlings with strains isolated from infected wheat grains showed wheat blast symptoms on leaves of wheat but not rice. Our phylogenomic and population genomic analyses revealed that the wheat blast outbreak in Bangladesh was most likely caused by a wheat-infecting South American lineage of the blast fungus Magnaporthe oryzae. CONCLUSION: Our findings suggest that genomic surveillance can be rapidly applied to monitor plant disease outbreaks and provide valuable information regarding the identity and origin of the infectious agent.

BACKGROUND: Wetlands are species-rich habitats performing valuable ecosystem services such as flood protection, water quality enhancement, food chain support and carbon sequestration. Worldwide, wetlands have been drained to convert them into agricultural land or industrial and urban areas. A realistic estimate is that 50 % of the world's wetlands have been lost. SCOPE: This paper reviews the relationship between wetlands and agriculture with the aim to identify the successes and failures of agricultural use in different types of wetlands, with reference to short-term and long-term benefits and issues of sustainability. It also addresses a number of recent developments which will lead to pressure to reclaim and destroy natural wetlands, i.e. the continuous need for higher production to feed an increasing world population and the increasing cultivation of energy crops. Finally, attention is paid to the development of more flood-tolerant crop cultivars. CONCLUSIONS: Agriculture has been carried out in several types of (former) wetlands for millennia, with crop fields on river floodplain soils and rice fields as major examples. However, intensive agricultural use of drained/reclaimed peatlands has been shown to lead to major problems because of the oxidation and subsidence of the peat soil. This does not only lead to severe carbon dioxide emissions, but also results in low-lying land which needs to be protected against flooding. Developments in South-East Asia, where vast areas of tropical peatlands are being converted into oil palm plantations, are of great concern in this respect. Although more flood-tolerant cultivars of commercial crop species are being developed, these are certainly not suitable for cultivation in wetlands with prolonged flooding periods, but rather will survive relatively short periods of waterlogging in normally improved agricultural soils. From a sustainability perspective, reclamation of peatlands for agriculture should be strongly discouraged. The opportunities for agriculture in naturally functioning floodplains should be further investigated. The development and use of crop cultivars with an even stronger flood tolerance could form part of the sustainable use of such floodplain systems. Extensive use of wetlands without drastic reclamation measures and without fertilizer and pesticides might result in combinations of food production with other wetland services, with biodiversity remaining more or less intact. There is a need for research by agronomists and environmental scientists to optimize such solutions.

Abstract Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods 1,2 . A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome 3,4 . Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins 5–7 . However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes 8 . This 15-fold increase in genus-level sampling relative to comparable nuclear studies 9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.

Summary The effect of different durations of waterlogging and subsequent drainage is described for 3‐wk‐old wheat ( Triticum aestivum ) plants. In a pot experiment, plants were subjected to waterlogging to the soil surface for 0, 3, 7, 14, 21 or 28 d, and then drained to allow recovery for up to 25 d. During waterlogging, the seminal root system stopped growing. Adventitious roots grew to a maximum length of c . 150 mm. Leaf nitrogen concentration was severely decreased by waterlogging. When waterlogged pots were drained, seminal root mass did not recover to control values, even when waterlogging lasted only 3 or 7 d, due to death of existing apices and no initiation of new lateral roots. By contrast, adventitious roots resumed elongation after drainage. By the end of the experiment, shoot mass remained two‐ to threefold lower in plants from all waterlogged treatments compared with continuously drained controls, due to lower tiller numbers and shorter final leaf lengths in previously waterlogged plants. The results demonstrate that even short periods (as little as 3 d) of waterlogging have considerable long‐term effects on the growth of young wheat plants.

CONTEXT: In cross-sectional studies, serum TSH concentrations increase with age. This has not been examined longitudinally, and it is uncertain whether the TSH increase reflects healthy aging or occult thyroid failure. METHODS: We measured serum TSH, free T(4), thyroid peroxidase, and thyroglobulin antibodies in 1100 participants in the 1981 and 1994 Busselton Health Surveys and derived a reference group of 908 individuals without thyroid disease or thyroid antibodies. We examined changes in thyroid function longitudinally and, in 781 participants, explored associations with the CAPZB polymorphism rs10917469. RESULTS: At 13 yr follow-up, mean serum TSH increased from 1.49 to 1.81 mU/liter, a change in mean TSH (ΔTSH) of 0.32 mU/liter [95% confidence interval (CI) 0.27, 0.38, P < 0.001], whereas mean free T(4) concentration was unchanged (16.6 vs. 16.6 pmol/liter, P = 0.7). The TSH increase was most marked in the elderly, such that gender-adjusted ΔTSH increased by 0.08 mU/liter (95% CI 0.04, 0.11) for each decade of baseline age. People with higher baseline TSH values had proportionally smaller increases in TSH, with each additional 1.0 mU/liter of baseline TSH associated with a 0.13 mU/liter decrease (age and gender adjusted) in ΔTSH (95% CI 0.09, 0.16). The ΔTSH did not differ significantly by CAPZB genotype. CONCLUSIONS: Aging is associated with increased serum TSH concentrations, with no change in free T(4) concentrations. The largest TSH increase is in people with the lowest TSH at baseline. This suggests that the TSH increase arises from age-related alteration in the TSH set point or reduced TSH bioactivity rather than occult thyroid disease.

study area was trawled, and 86% was not trawled. Trawling activity was aggregated; the most intensively trawled areas accounting for 90% of activity comprised 77% of footprint on average. Regional swept area ratio (SAR; ratio of total swept area trawled annually to total area of region, a metric of trawling intensity) and footprint area were related, providing an approach to estimate regional trawling footprints when high-resolution spatial data are unavailable. If SAR was ≤0.1, as in 8 of 24 regions, there was >95% probability that >90% of seabed was not trawled. If SAR was 7.9, equal to the highest SAR recorded, there was >95% probability that >70% of seabed was trawled. Footprints were smaller and SAR was ≤0.25 in regions where fishing rates consistently met international sustainability benchmarks for fish stocks, implying collateral environmental benefits from sustainable fishing.

A comparison of Mycobacterium tuberculosis complex isolates from seals (pinnipeds) in Australia, Argentina, Uruguay, Great Britain and New Zealand was undertaken to determine their relationships to each other and their taxonomic position within the complex. Isolates from 30 cases of tuberculosis in six species of pinniped and seven related isolates were compared to representative and standard strains of the M. tuberculosis complex. The seal isolates could be distinguished from other members of the M. tuberculosis complex, including the recently defined 'Mycobacterium canettii' and 'Mycobacterium caprae', on the basis of host preference and phenotypic and genetic tests. Pinnipeds appear to be the natural host for this 'seal bacillus', although the organism is also pathogenic in guinea pigs, rabbits, humans, Brazilian tapir (Tapirus terrestris) and, possibly, cattle. Infection caused by the seal bacillus is predominantly associated with granulomatous lesions in the peripheral lymph nodes, lungs, pleura, spleen and peritoneum. Cases of disseminated disease have been found. As with other members of the M. tuberculosis complex, aerosols are the most likely route of transmission. The name Mycobacterium pinnipedii sp. nov. is proposed for this novel member of the M. tuberculosis complex (the type strain is 6482(T)=ATCC BAA-688(T)=NCTC 13288(T)).

Conventional farming practices can lead to soil degradation and a decline in productivity. Regenerative agriculture (RA) is purported by advocates as a solution to these issues that focuses on soil health and carbon sequestration. The fundamental principles of RA are to keep the soil covered, minimise soil disturbance, preserve living roots in the soil year round, increase species diversity, integrate livestock, and limit or eliminate the use of synthetic compounds (such as herbicides and fertilisers). The overall objectives are to rejuvenate the soil and land and provide environmental, economic, and social benefits to the wider community. Despite the purported benefits of RA, a vast majority of growers are reluctant to adopt these practices due to a lack of empirical evidence on the claimed benefits and profitability. We examined the reported benefits and mechanisms associated with RA against available scientific data. The literature suggests that agricultural practices such as minimum tillage, residue retention, and cover cropping can improve soil carbon, crop yield, and soil health in certain climatic zones and soil types. Excessive use of synthetic chemicals can lead to biodiversity loss and ecosystem degradation. Combining livestock with cropping and agroforestry in the same landscape can increase soil carbon and provide several co-benefits. However, the benefits of RA practices can vary among different agroecosystems and may not necessarily be applicable across multiple agroecological regions. Our recommendation is to implement rigorous long-term farming system trials to compare conventional and RA practices in order to build knowledge on the benefits and mechanisms associated with RA on regional scales. This will provide growers and policy-makers with an evidence base from which to make informed decisions about adopting RA practices to realise their social and economic benefits and achieve resilience against climate change.

Abstract An Integrated Risk Assessment for Climate Change (IRACC) is developed and applied to assess the vulnerability of sharks and rays on Australia's Great Barrier Reef (GBR) to climate change. The IRACC merges a traditional climate change vulnerability framework with approaches from fisheries ecological risk assessments. This semi‐quantitative assessment accommodates uncertainty and can be applied at different spatial and temporal scales to identify exposure factors, at‐risk species and their key biological and ecological attributes, critical habitats a`nd ecological processes, and major knowledge gaps. Consequently, the IRACC can provide a foundation upon which to develop climate change response strategies. Here, we describe the assessment process, demonstrate its application to GBR shark and ray species, and explore the issues affecting their vulnerability to climate change. The assessment indicates that for the GBR, freshwater/estuarine and reef associated sharks and rays are most vulnerable to climate change, and that vulnerability is driven by case‐specific interactions of multiple factors and species attributes. Changes in temperature, freshwater input and ocean circulation will have the most widespread effects on these species. Although relatively few GBR sharks and rays were assessed as highly vulnerable, their vulnerability increases when synergies with other factors are considered. This is especially true for freshwater/estuarine and coastal/inshore sharks and rays. Reducing the impacts of climate change on the GBR's sharks and rays requires a range of approaches including mitigating climate change and addressing habitat degradation and sustainability issues. Species‐specific conservation actions may be required for higher risk species (e.g. the freshwater whipray, porcupine ray, speartooth shark and sawfishes) including reducing mortality, preserving coastal catchments and estuarine habitats, and addressing fisheries sustainability. The assessment identified many knowledge gaps concerning GBR habitats and processes, and highlights the need for improved understanding of the biology and ecology of the sharks and rays of the GBR.

Abstract Monitoring communities of fish is important for the management and sustainability of fisheries and marine ecosystems. Baited remote underwater video systems (BRUVs) are among the most effective nondestructive techniques for sampling bony fishes and elasmobranchs (sharks, rays, and skates). However, BRUVs sample visually conspicuous biota; hence, some taxa are undersampled or not recorded at all. We compared the diversity of fishes characterized using BRUVs with diversity detected via environmental DNA (eDNA) metabarcoding. We sampled seawater and captured BRUVs imagery at 48 locales that included reef and seagrass beds inside and outside a marine reserve (Jurien Bay in Western Australia). Eighty‐two fish genera from 13 orders were detected, and the community of fishes described using eDNA and BRUVs combined yielded &gt;30% more generic richness than when either method was used alone. Rather than detecting a homogenous genetic signature, the eDNA assemblages mirrored the BRUVs’ spatial explicitness; differentiation of taxa between seagrass and reef was clear despite the relatively small geographical scale of the study site (∼35 km 2 ). Taxa that were not sampled by one approach, due to limitations and biases intrinsic to the method, were often detected with the other. Therefore, using BRUVs and eDNA in concert provides a more holistic view of vertebrate marine communities across habitats. Both methods are noninvasive, which enhances their potential for widespread implementation in the surveillance of marine ecosystems.

The International Rare Diseases Research Consortium (IRDiRC) was founded in 2011 with the conviction that rare diseases research had reached a critical juncture. Proof of principle existed that rare diseases could be diagnosed, new treatments successfully developed and approved, and improvements in quality and quantity of life achieved. Government research funders, companies, scientists, and patient advocacy groups had all demonstrated their commitment and effectiveness in contributing to progress in rare diseases research. However, the work was largely atomized, with each organization, each country, and the champions of each disease pursuing independent, often duplicative solutions. The scale of the "rare disease problem"-thousands of rare diseases, the vast preponderance of them with no approved treatment, and decades-long diagnostic odysseys for many patients-led to the realization that the time had arrived for global cooperation and collaboration among the many stakeholders active in rare diseases research, to capitalize on these proofs of principle, and maximize the output of rare diseases research efforts around the world. IRDiRC's initial aims were to aid in the achievement of two overarching objectives: to contribute to the development of 200 new therapies and the means to diagnose most rare diseases by the year 2020. 1 For more detailed information on the history, governance, and nascent stages of the Consortium, please refer to the accompanying piece on the first 6 years of IRDiRC.