Quantifying responses of ecological communities to bioclimatic gradients

The biotic change along environmental gradients has been the subject of study for well over a century, forming one of the first tools to understand how environment shapes the species and ecosystems that occur. However, gradient studies have historically relied on limited observations on a single transect, limiting their inductive power. Here, I investigate how this limitation can be addressed. I present case studies to illustrate how next-generation transect studies can integrate observations from a wider range of observations of phenotypes, species and communities; together with observations from multiple taxa and gradients. Leaf carbon isotope data from bioclimatic gradients in China, South Australia and Western Australia are integrated to demonstrate a variety of species- and community-level responses to water availability, providing evidence against the previously asserted claim of a simple and universal response. Vegetation data from the same gradient is surveyed with two separate survey methodologies are co-analysed to demonstrate climate is the primary regional determinant of vegetation structure and composition in South Australia, while topographic and edaphic variables are important at a local scale. I find no evidence of ecological disjunctions that may indicate a threshold of vegetation change associated with climate shifts. Comparison of plant and ant species turnover on a spatial gradient suggested that ant communities are ca. 7.5 times more sensitive than plant assemblages to spatial change, providing evidence that future climate change may force community reorganisation and a decoupling of these two taxa, potentially disrupting important interactions and ecosystem function. Well-designed transect studies have the potential to help resolve long-standing questions around the modes of species adaptation to change, as well as improving our understanding of how climate change will shape ecosystems in to the futureThesis (Ph.D.) (Research by Publication) -- University of Adelaide, School of Biological Sciences, 201

Improving productivity in tropical lakes and reservoirs

Freshwater aquaculture, Inland fisheries

Status and management of tropical coastal fisheries in Asia

Coastal fisheries, Fishery management, Stock assessment, Conferences, Asia,

Marine fish assemblages as indicators of anthropogenic pressures:identifying sensitive metrics

Tese de doutoramento, Biologia (Biologia Marinha e Aquacultura), Universidade de Lisboa, Faculdade de Ciências, 2013Worldwide concern about the environmental threats and need for sustainable development has led to increased efforts to understand and assess anthropogenic pressure effects. However, the development of indicators for marine ecosystems is still at an early stage, due to their high spatial and temporal complexity. Based on several structural and functional traits (guild approach) and considering the effects of natural variability, the present study analysed the response of fish assemblages to several anthropogenic pressures in the Portuguese coast, by selecting fish-based metrics that best distinguish disturbed from control sites or those sensitive to gradients of pressure. In general, fish assemblages associated with both rocky reef and soft-substrate habitats were broadly affected by water pollution (sewage discharges and non-point sources of pollution), which led to changes in many metrics depending on the balance between the effluent toxicity and resources availability (e.g. trophic structure, resilience, habitat association and nursery function attributes). Conversely, fishing affected fish assemblages differentially, since in addition to the metrics related with commercial value, differences were only observed in tolerant-opportunistic and large individuals in rocky reefs, and species exhibiting vulnerable traits and dominance in soft-substrate habitats. Moreover, seasonal variability can influence the patterns of some fish-based metrics and their ability to detect pressures. The selection of the warm season after the spawning period (July-October) seems to be the more adequate to detect changes in rocky reef fish (cost-efficient). Further research is needed for soft-substrate habitats in order to select the most suitable sampling season. Finally, due to the difficulty to assess single-pressures on a wide-ranging environment, often characterized by multiple pressure contexts, an approach based on the previous selection of the expected pressure sources and applying a directional monitoring plan to analyze if the biological indicators detect changes, is strongly recommended (more cost-efficient).A preocupação global com as ameaças ambientais e a necessidade de um desenvolvimento sustentável tem levado a um crescente esforço para compreender e avaliar os efeitos das pressões antropogénicas. No entanto, o desenvolvimento de indicadores nos ecossistemas marinhos encontra-se ainda numa fase inicial, devido à sua elevada complexidade espacial e temporal. O presente estudo analisou a resposta dos peixes a várias pressões antropogénicas na costa portuguesa, através da selecção de métricas estruturais e funcionais sensíveis a gradientes de pressão, ou que melhor distinguiram as zonas perturbadas das de controlo. Em geral, as associações de peixes tanto em recifes rochosos como em substratos móveis foram amplamente afectados por águas poluídas (descargas de esgoto e poluição difusa), que levaram a alterações em várias métricas dependendo do balanço entre a toxicidade do efluente e os recursos disponíveis para os peixes. Em contrapartida, os efeitos da pesca foram mais selectivos uma vez que, para além das alterações na métricas relacionadas com o elevado interesse comercial, apenas se observaram diferenças em indivíduos de maiores dimensões e tolerantes-oportunistas nos recifes rochosos, bem como nas espécies com características mais vulneráveis e dominância de espécies nos substratos arenosos. A variabilidade sazonal pode afectar os padrões de algumas métricas e a sua capacidade de detecção de impactos. Nos recifes rochosos, a selecção da estação quente, depois da época de reprodução (Julho-Outubro), parece ser mais adequada para a detecção de alterações nos peixes, enquanto para os substratos móveis são necessários estudos para definir a melhor época de amostragem. Devido à dificuldade de analisar pressões específicas num ambiente tão amplo e sujeito a pressões múltiplas, é recomendada a aplicação de uma abordagem baseada na identificação inicial das potenciais fontes de pressão e na aplicação de um plano de monitorização direccionado para por fim verificar se os indicadores biológicos detectam alterações.Fundação para a Ciência e a Tecnologia (FCT, SFRH/BD/47034/2008

Functional dissection of a gene expression oscillator in C. elegans

Gene expression oscillations control diverse biological processes. One such example of gene expression oscillations, are those found for thousands of genes during C. elegans larval development. However, it remains unclear whether and how gene expression oscillations regulate development processes in C. elegans. In this work, I aimed to study the molecular architecture and the system properties of the C. elegans oscillator to provide insight into potential developmental functions and reveal features that are unique, as well as those that are shared among oscillators. Here, performing temporally highly resolved mRNA-sequencing across all larval stages (L1-L4) of C. elegans development, we identified 3,739 genes, whose transcripts revealed high-amplitude oscillations (>2-fold from peak to trough), peaking once every larval stage with stable amplitudes, but variable periods. Oscillations appeared tightly coupled to the molts, but were absent from freshly hatched larvae, developmentally arrested dauer larvae and adults. Quantitative characterization of transitions between oscillatory and stable states of the oscillator showed that the stable states are similar to a particular phase of the oscillator, which coincided with molt exit. Given that these transitions are sensitive to food, we postulate that feeding might impact the state of the oscillator. These features appear rather unique, and hence a better understanding may help to reveal general principles of gene expression oscillators. Our RNAPII ChIP-seq revealed rhythmic occupancy of RNAPII at the promoters of oscillating genes, suggesting that mRNA transcript oscillations arise from rhythmic transcription. Given that oscillations are coupled to the repetitive molts and that the molecular mechanisms that regulate molting are unknown, we aimed to find transcription factors important for molting and oscillations. Hence, we screened 92 transcription factors that oscillate on the mRNA level for their role in molting and identified grh-1, myrf1, blmp-1, bed-3, nhr-23, nhr-25 and ztf-6. We showed that oscillatory activity of GRH-1 is required for timely completion of the molt, to prevent cuticle rupturing, and for oscillatory expression of structural components of the cuticle and ‘ECM regulators’, among others, including grh-1 itself. Hence, we propose GRH-1 as a putative component of the (sub-)oscillator that regulates molting. We showed that loss of BLMP-1 increased the duration of molts, affected cuticle integrity, and changed the oscillatory dynamics of a subset of genes in diverse ways. We postulate that BLMP-1 acts as factor that couples gene expression oscillations, and potentially sub-oscillators or repetitive developmental processes. In conclusion, this work provides insight into the function of the oscillator, and its system properties. Moreover, we identified relevant factors, which we propose as a starting point to unravel the molecular wiring of the C. elegans oscillator and its functional relevance

Coastal Fisheries of South America and the Caribbean

The importance of fisheries for coastal communities and livelihoods in South America-Latin America; and the Caribbean (LAC) is well documented. This is particularly the case for 'coastal fisheries', including subsistence, traditional (artisanal) and advanced artisanal (or semi-industrial) varieties. There are, however, major gaps in knowledge about these fisheries, and major challenges in their assessment and management. Therein lies the key theme of this document, which seeks to contribute to a better understanding of coastal fisheries in the LAC region, as well as to generate discussion about ways to move towards sustainable fisheries. The document includes three main components. First, an introductory chapter provides an overview of general trends in the fisheries of the LAC countries, as well as some of the key challenges they are facing in terms of sustainability. Second, a set of twelve chapters each reporting on the coastal fisheries of one country in South America-Latin America; and the North America (Caribbean); collectively covering fisheries of each main subregion: the Caribbean islands (North America (Caribbean)-North America (Caribbean)-Barbados; Cuba, Dominican Republic, Grenada, Puerto Rico, Trinidad and Tobago), North and Central America (North America (Central America)-Costa Rica; Mexico) and South America (Argentina, South America (Northeastern)-Brazil; South America (Northwestern)-South America (Northwestern)-Colombia; Uruguay). All these country-specific chapters follow an integrated approach, to the extent possible, covering aspects ranging from the biological to the socio-economic. Third, the final component of the document contains a synthesis of information from the countries examined, an analysis of the main issues and challenges faced by the various fisheries, an outline of policy directions to improve fisheries management systems in the LAC region, identification of routes toward more integrated approaches for coastal fisheries management, and recommendations for 'ways forward' in dealing with fishery assessment and governance issues in the region

Interactive real-time musical systems

PhDThis thesis focuses on the development of automatic accompaniment systems. We investigate previous systems and look at a range of approaches that have been attempted for the problem of beat tracking. Most beat trackers are intended for the purposes of music information retrieval where a `black box' approach is tested on a wide variety of music genres. We highlight some of the diffculties facing offline beat trackers and design a new approach for the problem of real-time drum tracking, developing a system, B-Keeper, which makes reasonable assumptions on the nature of the signal and is provided with useful prior knowledge. Having developed the system with offline studio recordings, we look to test the system with human players. Existing offline evaluation methods seem less suitable for a performance system, since we also wish to evaluate the interaction between musician and machine. Although statistical data may reveal quantifiable measurements of the system's predictions and behaviour, we also want to test how well it functions within the context of a live performance. To do so, we devise an evaluation strategy to contrast a machine-controlled accompaniment with one controlled by a human. We also present recent work on a real-time multiple pitch tracking, which is then extended to provide automatic accompaniment for harmonic instruments such as guitar. By aligning salient notes in the output from a dual pitch tracking process, we make changes to the tempo of the accompaniment in order to align it with a live stream. By demonstrating the system's ability to align offline tracks, we can show that under restricted initial conditions, the algorithm works well as an alignment tool

Myth or reality? – Assessing the suitability of biodegradable plastics within a circular bioeconomy framework

The proposition of a circular bioeconomy framework was introduced as a means of moving from a fossil-based to bio-based economy. With an emphasis on resource efficiency and waste valorisation, it has supported the development of biodegradable bioplastics (BBPs), notably in food packaging applications. Designed to be treated alongside organic waste, BBPs open new streams for plastic waste management within the food-energy-waste nexus, but their suitability in the current social, policy and sustainability landscape remains to be determined. Taking a systems-thinking approach, this thesis explores the compatibility of (certified) BBP packaging under a circular bioeconomy framework, focusing on a co-mingled food and BBP waste stream for anaerobic co-digestion. It uncovers major technical, policy and social challenges and urges for caution when deploying these novel plastic packaging materials on the consumer market. Chapter 1 provides a brief introduction to BBPs and their framing in the wider context of plastic sustainability and organic waste management, followed by aims and objectives in Chapter 2. Chapter 3 provides a comprehensive literature review, depicting the importance and ubiquity of plastics, their environmental impact and the role BBPs could play in a circular bioeconomy framework from a systems-thinking perspective. Chapter 4 details the anaerobic co-digestion treatment of different BBPs with food waste and the impact of BBPs on biogas and methane yields and on microbial communities. The need for consistent experimental design of co-digestion trials is also discussed. Guided by these results, Chapter 5 presents the outcomes of a stakeholder study on attitudes towards BBPs in the current waste management infrastructure and policy landscape to explore how BBPs are perceived and managed on-the-ground in the United Kingdom. Chapters 6 & 7 build on a major finding from the stakeholder study, which outlined the importance of consumers in enabling circularity in the system. Chapter 6 covers a systems framework developed to identify and structure systemic factors that influence how consumers interact with BBP packaging, with a focus on disposal routes. The framework is then applied in practice, based on a survey conducted at two academic institutions, and the role of contextual setting is explored through a comparative case study presented in Chapter 7. Chapter 8 extends the debate on the suitability of BBPs further upstream in the value chain and consumption system and addresses the functional properties of BBP packaging in the context of a shelf-life study, anchoring BBPs in the food system they are embedded within. Chapter 9 summarises key findings and suggests future research related to this thesis. The Appendix contains supplementary figures and data for Chapters 4-8.Open Acces

Overfishing, uncertainty, and ocean governance: Lord Perry's question revisited

“Why does overfishing persist in the face of regulation?” The author argues that over fishing,a fundamental cause of the crisis facing our oceans, is the result of the failure of our fishing management agencies (ultimately our politicians and communities) to embrace a small suite of powerful tools (more correctly strategic approaches) which have been developed to account for uncertainty. Broad success in managing fisheries to achieve sustainability goals will only come if these tools are enthusiastically applied. This will not happen until organisational cultures within fishery management agencies undergo a major shift leading to an asset-based biodiversity conservation, rather than resource exploitation, to be placed at the centre of ocean governance.This thesis examines these issues in the context of case studies covering regional, national and provincial (State) fishery management agencies. With the exception of the case study of a regional fishery (the southern ocean krill fishery) all case studies are drawn from Australian experiences. The central recommendation of the thesis is that fishery management agencies, worldwide, should be replaced by biodiversity asset management agencies

Once and Future Gulf of Mexico Ecosystem: Restoration Recommendations of an Expert Working Group

The Deepwater Horizon (DWH) well blowout released more petroleum hydrocarbons into the marine environment than any previous U.S. oil spill (4.9 million barrels), fouling marine life, damaging deep sea and shoreline habitats and causing closures of economically valuable fisheries in the Gulf of Mexico. A suite of pollutants—liquid and gaseous petroleum compounds plus chemical dispersants—poured into ecosystems that had already been stressed by overfishing, development and global climate change. Beyond the direct effects that were captured in dramatic photographs of oiled birds in the media, it is likely that there are subtle, delayed, indirect and potentially synergistic impacts of these widely dispersed, highly bioavailable and toxic hydrocarbons and chemical dispersants on marine life from pelicans to salt marsh grasses and to deep-sea animals. As tragic as the DWH blowout was, it has stimulated public interest in protecting this economically, socially and environmentally critical region. The 2010 Mabus Report, commissioned by President Barack Obama and written by the secretary of the Navy, provides a blueprint for restoring the Gulf that is bold, visionary and strategic. It is clear that we need not only to repair the damage left behind by the oil but also to go well beyond that to restore the anthropogenically stressed and declining Gulf ecosystems to prosperity-sustaining levels of historic productivity. For this report, we assembled a team of leading scientists with expertise in coastal and marine ecosystems and with experience in their restoration to identify strategies and specific actions that will revitalize and sustain the Gulf coastal economy. Because the DWH spill intervened in ecosystems that are intimately interconnected and already under stress, and will remain stressed from global climate change, we argue that restoration of the Gulf must go beyond the traditional "in-place, in-kind" restoration approach that targets specific damaged habitats or species. A sustainable restoration of the Gulf of Mexico after DWH must: 1. Recognize that ecosystem resilience has been compromised by multiple human interventions predating the DWH spill; 2. Acknowledge that significant future environmental change is inevitable and must be factored into restoration plans and actions for them to be durable; 3. Treat the Gulf as a complex and interconnected network of ecosystems from shoreline to deep sea; and 4. Recognize that human and ecosystem productivity in the Gulf are interdependent, and that human needs from and effects on the Gulf must be integral to restoration planning. With these principles in mind, the authors provide the scientific basis for a sustainable restoration program along three themes: 1. Assess and repair damage from DWH and other stresses on the Gulf; 2. Protect existing habitats and populations; and 3. Integrate sustainable human use with ecological processes in the Gulf of Mexico. Under these themes, 15 historically informed, adaptive, ecosystem-based restoration actions are presented to recover Gulf resources and rebuild the resilience of its ecosystem. The vision that guides our recommendations fundamentally imbeds the restoration actions within the context of the changing environment so as to achieve resilience of resources, human communities and the economy into the indefinite future