Foundations for the future: A long‐term plan for Australian ecosystem science

Australia's ecosystems are the basis of our current and future prosperity, and our national well‐being. A strong and sustainable Australian ecosystem science enterprise is vital for understanding and securing these ecosystems in the face of current and future challenges. This Plan defines the vision and key directions for a national ecosystem science capability that will enable Australia to understand and effectively manage its ecosystems for decades to come. The Plan's underlying theme is that excellent science supports a range of activities, including public engagement, that enable us to understand and maintain healthy ecosystems. Those healthy ecosystems are the cornerstone of our social and economic well‐being. The vision guiding the development of this Plan is that in 20 years' time the status of Australian ecosystems and how they change will be widely reported and understood, and the prosperity and well‐being they provide will be secure. To enable this, Australia's national ecosystem science capability will be coordinated, collaborative and connected. The Plan is based on an extensive set of collaboratively generated proposals from national town hall meetings that also form the basis for its implementation. Some directions within the Plan are for the Australian ecosystem science community itself to implement, others will involve the users of ecosystem science and the groups that fund ecosystem science. We identify six equal priority areas for action to achieve our vision: (i) delivering maximum impact for Australia: enhancing relationships between scientists and end‐users; (ii) supporting long‐term research; (iii) enabling ecosystem surveillance; (iv) making the most of data resources; (v) inspiring a generation: empowering the public with knowledge and opportunities; (vi) facilitating coordination, collaboration and leadership. This shared vision will enable us to consolidate our current successes, overcome remaining barriers and establish the foundations to ensure Australian ecosystem science delivers for the future needs of Australia.     

Ecology drives intragenomic conflict over menopause

Menopause is the transition from reproductive to non‐reproductive life well before natural death. Rather than involving a smooth, rapid change, it is normally preceded by a long period of erratic hormonal fluctuation that is accompanied by a plethora of unpleasant symptoms. Here, we (1) suggest that this turbulent period owes to conflict, between a woman's maternally inherited (MI) and paternally inherited (PI) genes, over the trade‐off between reproduction and communal care; (2) perform a theoretical analysis to show that this conflict is resolved either through silencing or fluctuating expression of one of the genes; (3) highlight which of the symptoms preceding menopause may result from antagonistic co‐evolution of MI and PI genes; (4) argue that ecological differences between ancestral human populations may explain the variability in menopause among different ethnic groups; (5) discuss how these insights may be used to inform family planning and cancer risk assessment based on a woman's ancestral background.     

A Foundation for Reliable Spatial Proteomics Data Analysis

Quantitative mass-spectrometry-based spatial proteomics involves elaborate, expensive, and time-consuming experimental procedures, and considerable effort is invested in the generation of such data. Multiple research groups have described a variety of approaches for establishing high-quality proteome-wide datasets. However, data analysis is as critical as data production for reliable and insightful biological interpretation, and no consistent and robust solutions have been offered to the community so far. Here, we introduce the requirements for rigorous spatial proteomics data analysis, as well as the statistical machine learning methodologies needed to address them, including supervised and semi-supervised machine learning, clustering, and novelty detection. We present freely available software solutions that implement innovative state-of-the-art analysis pipelines and illustrate the use of these tools through several case studies involving multiple organisms, experimental designs, mass spectrometry platforms, and quantitation techniques. We also propose sound analysis strategies for identifying dynamic changes in subcellular localization by comparing and contrasting data describing different biological conditions. We conclude by discussing future needs and developments in spatial proteomics data analysis.     

Genetic and physiological analysis of Rht8 in bread wheat: an alternative source of semi-dwarfism with a reduced sensitivity to brassinosteroids

Over the next decade, wheat grain production must increase to meet the demand of a fast growing human population. One strategy to meet this challenge is to raise wheat productivity by optimizing plant stature. The Reduced height 8 (Rht8) semi-dwarfing gene is one of the few, together with the Green Revolution genes, to reduce stature of wheat (Triticum aestivum L.), and improve lodging resistance, without compromising grain yield. Rht8 is widely used in dry environments such as Mediterranean countries where it increases plant adaptability. With recent climate change, its use could become increasingly important even in more northern latitudes. In the present study, the characterization of Rht8 was furthered. Morphological analyses show that the semi-dwarf phenotype of Rht8 lines is due to shorter internodal segments along the wheat culm, achieved through reduced cell elongation. Physiological experiments show that the reduced cell elongation is not due to defective gibberellin biosynthesis or signalling, but possibly to a reduced sensitivity to brassinosteroids. Using a fine-resolution mapping approach and screening 3104 F(2) individuals of a newly developed mapping population, the Rht8 genetic interval was reduced from 20.5 cM to 1.29 cM. Comparative genomics with model genomes confined the Rht8 syntenic intervals to 3.3 Mb of the short arm of rice chromosome 4, and to 2 Mb of Brachypodium distachyon chromosome 5. The very high resolution potential of the plant material generated is crucial for the eventual cloning of Rht8.     

Intact memory for irrelevant information impairs perception in amnesia

Memory and perception have long been considered separate cognitive processes, and amnesia resulting from medial temporal lobe (MTL) damage is thought to reflect damage to a dedicated memory system. Recent work has questioned these views, suggesting that amnesia can result from impoverished perceptual representations in the MTL, causing an increased susceptibility to interference. Using a perceptual matching task for which fMRI implicated a specific MTL structure, the perirhinal cortex, we show that amnesics with MTL damage including the perirhinal cortex, but not those with damage limited to the hippocampus, were vulnerable to object-based perceptual interference. Importantly, when we controlled such interference, their performance recovered to normal levels. These findings challenge prevailing conceptions of amnesia, suggesting that effects of damage to specific MTL regions are better understood not in terms of damage to a dedicated declarative memory system, but in terms of impoverished representations of the stimuli those regions maintain.     

Evidence of host-associated populations of Cryptosporidium parvum in Italy

Recent studies have revealed extensive genetic variation among isolates of Cryptosporidium parvum, an Apicomplexan parasite that causes gastroenteritis in both humans and animals worldwide. The parasite's population structure is influenced by the intensity of transmission, the host-parasite interaction, and husbandry practices. As a result, C. parvum populations can be panmictic, clonal, or even epidemic on both a local scale and a larger geographical scale. To extend the study of C. parvum populations to an unexplored region, 173 isolates of C. parvum collected in Italy from humans and livestock (calf, sheep, and goat) over a 10-year period were genotyped using a multilocus scheme based on 7 mini- and microsatellite loci. In agreement with other studies, extensive polymorphism was observed, with 102 distinct multilocus genotypes (MLGs) identified among 173 isolates. The presence of linkage disequilibrium, the confinement of MLGs to individual farms, and the relationship of many MLGs inferred using network analysis (eBURST) suggest a predominantly clonal population structure, but there is also evidence that part of the diversity can be explained by genetic exchange. MLGs from goats were found to differ from bovine and sheep MLGs, supporting the existence of C. parvum subpopulations. Finally, MLGs from isolates collected between 1997 and 1999 were also identified as a distinct subgroup in principal-component analysis and eBURST analysis, suggesting a continuous introduction of novel genotypes in the parasite population.     

A carbohydrate-rich diet increases social immunity in ants

Increased potential for disease transmission among nest-mates means living in groups has inherent costs. This increased potential is predicted to select for disease resistance mechanisms that are enhanced by cooperative exchanges among group members, a phenomenon known as social immunity. One potential mediator of social immunity is diet nutritional balance because traits underlying immunity can require different nutritional mixtures. Here, we show how dietary protein–carbohydrate balance affects social immunity in ants. When challenged with a parasitic fungus Metarhizium anisopliae, workers reared on a high-carbohydrate diet survived approximately 2.8× longer in worker groups than in solitary conditions, whereas workers reared on an isocaloric, high-protein diet survived only approximately 1.3× longer in worker groups versus solitary conditions. Nutrition had little effect on social grooming, a potential mechanism for social immunity. However, experimentally blocking metapleural glands, which secrete antibiotics, completely eliminated effects of social grouping and nutrition on immunity, suggesting a causal role for secretion exchange. A carbohydrate-rich diet also reduced worker mortality rates when whole colonies were challenged with Metarhizium. These results provide a novel mechanism by which carbohydrate exploitation could contribute to the ecological dominance of ants and other social groups.     

Influence of Seeding Ratio,Planting Date,and Termination Date on Rye-Hairy Vetch Cover Crop Mixture Performance under Organic Management

Cover crop benefits include nitrogen accumulation and retention, weed suppression, organic matter maintenance, and reduced erosion. Organic farmers need region-specific information on winter cover crop performance to effectively integrate cover crops into their crop rotations. Our research objective was to compare cover crop seeding mixtures, planting dates, and termination dates on performance of rye (Secale cereale L.) and hairy vetch (Vicia villosa Roth) monocultures and mixtures in the maritime Pacific Northwest USA. The study included four seed mixtures (100% hairy vetch, 25% rye-75% hairy vetch, 50% rye-50% hairy vetch, and 100% rye by seed weight), two planting dates, and two termination dates, using a split-split plot design with four replications over six years. Measurements included winter ground cover; stand composition; cover crop biomass, N concentration, and N uptake; and June soil NO₃ ^--N. Rye planted in mid-September and terminated in late April averaged 5.1 Mg ha^-1 biomass, whereas mixtures averaged 4.1 Mg ha^-1 and hairy vetch 2.3 Mg ha^-1. Delaying planting by 2.5 weeks reduced average winter ground cover by 65%, biomass by 50%, and cover crop N accumulation by 40%. Similar reductions in biomass and N accumulation occurred for late March termination, compared with late April termination. Mixtures had less annual biomass variability than rye. Mixtures accumulated 103 kg ha^-1 N and had mean C:N ratio <17:1 when planted in mid-September and terminated in late April. June soil NO₃ ^--N (0 to 30 cm depth) averaged 62 kg ha^-1 for rye, 97 kg ha^-1 for the mixtures, and 119 kg ha^-1 for hairy vetch. Weeds comprised less of the mixtures biomass (20% weeds by weight at termination) compared with the monocultures (29%). Cover crop mixtures provided a balance between biomass accumulation and N concentration, more consistent biomass over the six-year study, and were more effective at reducing winter weeds compared with monocultures.     

Priority threat management of invasive animals to protect biodiversity under climate change

Climate change is a major threat to global biodiversity, and its impacts can act synergistically to heighten the severity of other threats. Most research on projecting species range shifts under climate change has not been translated to informing priority management strategies on the ground. We develop a prioritization framework to assess strategies for managing threats to biodiversity under climate change and apply it to the management of invasive animal species across one‐sixth of the Australian continent, the Lake Eyre Basin. We collected information from key stakeholders and experts on the impacts of invasive animals on 148 of the region's most threatened species and 11 potential strategies. Assisted by models of current distributions of threatened species and their projected distributions, experts estimated the cost, feasibility, and potential benefits of each strategy for improving the persistence of threatened species with and without climate change. We discover that the relative cost‐effectiveness of invasive animal control strategies is robust to climate change, with the management of feral pigs being the highest priority for conserving threatened species overall. Complementary sets of strategies to protect as many threatened species as possible under limited budgets change when climate change is considered, with additional strategies required to avoid impending extinctions from the region. Overall, we find that the ranking of strategies by cost‐effectiveness was relatively unaffected by including climate change into decision‐making, even though the benefits of the strategies were lower. Future climate conditions and impacts on range shifts become most important to consider when designing comprehensive management plans for the control of invasive animals under limited budgets to maximize the number of threatened species that can be protected.