An investigation of local adaptation in the model plant species Arabidopsis thaliana

Species extinction rates are causing alarm. Anthropogenic distortion of the climate system is rapidly altering the natural environment. Arabidopsis thaliana is a model species in molecular biology with widespread wild populations showing functional diversity however its ecology and evolution is poorly understood. Faced with a changing natural world, what is the adaptive potential of the model plant species Arabidopsis thaliana? This thesis focuses on the interactions of genotypes, phenotypes and environments to assess the current state of adaptation in this vagile species and to identify mechanisms for rapid adaptation to future stress, focusing on plant pathogens. Here I show that A. thaliana populations in England exhibit evidence of local adaptation and genetic structure. A large common garden experiment using genotypes gathered in natural habitats revealed functional fitness differences in genotype-by-environment interactions. Wild populations showed differential representation of RPM1 alleles suggesting non-random processes are responsible for the exhibited patterns. A further common garden experiment demonstrated ‘home site advantage’ through a correlation between fitness and home site climate, which suggests that local adaptation had occurred. Phenotypic plasticity and mechanisms for rapid adaptation could be essential for plant survival under predicted climate change. Using Xanthomonas spp. as xenopathogens, I show differing levels of pre-adaptation for pathogen response exists in wild UK populations of A. thaliana. By using a multi-generation study, I found some evidence that epigenetic modification enabled rapid adaptation to pathogen stress. Finally, I compared the metabolic expressions of phenotype among genotypes in two artificial environments. Environmental effects detected by this method are far greater than genetic ones, suggesting that metabolic plasticity can underpin environmental adaptation. Taken together, my results suggest that wild populations of A. thaliana contain a range of mechanisms for rapid adaptation to environmental change. If these capacities are general, my work offers a note of optimism about the fate of some wild plant species in the face of global climate change. Additionally, as A. thaliana is a model species in genomics, my findings may facilitate future exploitation of these traits by crop geneticists.NER

Chemical production complex optimization, pollution reduction and sustainable development

The objective of this research is to propose, develop and demonstrate chemical production complex optimization to determine the optimal configuration of chemical plants in a superstructure of possible plants. The Chemical Complex Analysis System is a new methodology that has been developed to determine the best configuration of plants in a chemical production complex based on the AIChE Total Cost Assessment (TCA) for economic, energy, environmental and sustainable costs. All new, energy-efficient, and environmentally acceptable plants using greenhouse gases that can produce potentially commercial products designed with HYSYS were integrated into the chemical complex using the System. The optimum configuration of plants was determined based on the triple bottom line that includes sales, economic, environmental and sustainable costs using the System. From eighteen new processes in the superstructure, the optimum structure had seven potentially new processes including acetic acid, graphite, formic acid, methylamines, propylene and synthesis gas production. With the additional plants in the optimal structure the triple bottom line increased from $343 to$506 million per year and energy increased from 2,150 to 5,791 TJ/year. Multicriteria optimization has been used with Monte Carlo simulation to determine the sensitivity of the optimal structure of a chemical production complex to prices, costs, and sustainable credits/cost. In essence, for each Pareto optimal solution, there is a cumulative probability distribution function that is the probability as a function of the triple bottom line. This information provides a quantitative assessment of the optimum profit versus sustainable credits/cost, and the risk (probability) that the triple bottom line will meet expectations. The capabilities of the System have been demonstrated, and this methodology could be applied to other chemical production complexes in the world for reduced emissions and energy savings. With this System, engineers will have a new capability to consider projects in depths significantly beyond current capabilities. They will be able to convert their company’s goals and capital into viable projects that meet economic, environmental and sustainable requirements

Protecting and restoring habitat to help Australia’s threatened species adapt to climate change

Summary for policy makers Australia’s biodiversity is threatened by climate change, but we currently know little about the scale of the threat or how to deploy on ground conservation actions to protect biodiversity against the changes expected. In this project we predict the impacts of climate change for threatened species and delineate the best options for climate adaptation for all these species collectively via protecting and restoring their habitat.For 504 of Australia’s currently threatened species we predict their distributional responses to climate change, under three climate change scenarios of increasing severity: early mitigation, delayed mitigation and business-as-usual. We then simulate the optimal placement of new protected areas and where necessary, restoration of critical habitat for those species most affected by a changing climate, taking into account variation in the costs and benefits of taking action in different places.We measured the benefits of protecting and restoring habitat by considering the long-term availability and quality of habitat for threatened species as climate changes. We undertook a state-of-the-art multi-action optimisation that accounts for spatial and temporal habitat connectivity under climate change. The scale of the prioritisation analysis implemented here is unprecedented in the conservation literature, and is only possible because of recent advances in software sophistication and parallel computer processing power.We discovered that:• Fifty-nine of the 355 threatened plant species and 11 of the 149 threatened animals considered could completely lose their climatically suitable range by 2085 under the most pessimistic (business as usual) climate change scenario, while four plant species face almost certain extinction due to complete loss of suitable range even under the most optimistic mitigation scenario tested.• Climate is predicted to become unsuitable across more than half of their geographic distribution for 310 (61%) of the modelled species under the business-as-usual scenario and for 80 (16%) species under the early mitigation scenario.• For an available budget of $3 billion, protecting an additional 877,415 km2 of intact habitat, and restoring 1,190 km2 of degraded habitat immediately was identified by our analysis as the optimal set of actions to help the 504 threatened species adapt to climate change assuming early mitigation. Under a more pessimistic business-as-usual climate change scenario, 837,914 km2 of protection is required, along with 77 km2 of restoration. In all cases, appropriate threat management within the protected areas is required.• Within the$3 billion budget, optimal allocation of protection focuses on forests and woodland areas of eastern Australia, Northern Territory, the Great Western Woodlands of Western Australia, and southern South Australia. Restoration effort is required mostly in south-eastern Australia.• We tested a range of conservation budgets from $500 million to$8 billion, and found that the spatial pattern of priority does not change dramatically, and that conservation gains do not level off within that range, i.e. that each dollar invested up to at least 8 billion generates additional benefits for threatened species under climate change.Our analysis deals only with threatened species, i.e. those currently most vulnerable to threats including climate change, and while this doesn’t represent all Australian native animals and plants and how they may all be best provided for, these species have great immediate significance for national biodiversity policy.In summary, the 504 threatened species considered in this study require an increase of between 838,077 km2 and 878,590 km2 in areas protected against loss or degradation either through legislation to protect habitat, designation of protected areas, or negotiations of long-lasting voluntary conservation covenants.Please cite this report as: Maggini, R, Kujala, H, Taylor, MFJ, Lee, JR, Possingham, HP, Wintle, BA, Fuller, RA 2013 Protecting and restoring habitat to help Australia’s threatened species adapt to climate change, National Climate Change Adaptation Research Facility,  Gold Coast, pp. 59.Australia’s biodiversity is threatened by climate change, but we currently know little about the scale of the threat or how to deploy on ground conservation actions to protect biodiversity against the changes expected. In this project we predict the impacts of climate change for threatened species and delineate the best options for climate adaptation for all these species collectively via protecting and restoring their habitat.For 504 of Australia’s currently threatened species we predict their distributional responses to climate change, under three climate change scenarios of increasing severity: early mitigation, delayed mitigation and business-as-usual. We then simulate the optimal placement of new protected areas and where necessary, restoration of critical habitat for those species most affected by a changing climate, taking into account variation in the costs and benefits of taking action in different places.We measured the benefits of protecting and restoring habitat by considering the long-term availability and quality of habitat for threatened species as climate changes. We undertook a state-of-the-art multi-action optimisation that accounts for spatial and temporal habitat connectivity under climate change. The scale of the prioritisation analysis implemented here is unprecedented in the conservation literature, and is only possible because of recent advances in software sophistication and parallel computer processing power.We discovered that: Fifty-nine of the 355 threatened plant species and 11 of the 149 threatened animals considered could completely lose their climatically suitable range by 2085 under the most pessimistic (business as usual) climate change scenario, while four plant species face almost certain extinction due to complete loss of suitable range even under the most optimistic mitigation scenario tested.Climate is predicted to become unsuitable across more than half of their geographic distribution for 310 (61%) of the modelled species under the business-as-usual scenario and for 80 (16%) species under the early mitigation scenario.For an available budget of 3 billion, protecting an additional 877,415 km2 of intact habitat, and restoring 1,190 km2 of degraded habitat immediately was identified by our analysis as the optimal set of actions to help the 504 threatened species adapt to climate change assuming early mitigation. Under a more pessimistic business-as-usual climate change scenario, 837,914 km2 of protection is required, along with 77 km2 of restoration. In all cases, appropriate threat management within the protected areas is required.Within the $3 billion budget, optimal allocation of protection focuses on forests and woodland areas of eastern Australia, Northern Territory, the Great Western Woodlands of Western Australia, and southern South Australia. Restoration effort is required mostly in south-eastern Australia.We tested a range of conservation budgets from$500 million to $8 billion, and found that the spatial pattern of priority does not change dramatically, and that conservation gains do not level off within that range, i.e. that each dollar invested up to at least$8 billion generates additional benefits for threatened species under climate change. Our analysis deals only with threatened species, i.e. those currently most vulnerable to threats including climate change, and while this doesn’t represent all Australian native animals and plants and how they may all be best provided for, these species have great immediate significance for national biodiversity policy.In summary, the 504 threatened species considered in this study require an increase of between 838,077 km2 and 878,590 km2 in areas protected against loss or degradation either through legislation to protect habitat, designation of protected areas, or negotiations of long-lasting voluntary conservation covenants.Please cite this report as: Maggini, R, Kujala, H, Taylor, MFJ, Lee, JR, Possingham, HP, Wintle, BA, Fuller, RA 2013 Protecting and restoring habitat to help Australia’s threatened species adapt to climate change, National Climate Change Adaptation Research Facility,  Gold Coast, pp. 59.&nbsp