Ecological genetics in the North Atlantic: environmental gradients and adaptation at specific loci

The North Atlantic intertidal community provides a rich set of organismal and environmental material for the study of ecological genetics. Clearly defined environmental gradients exist at multiple spatial scales: there are broad latitudinal trends in temperature, meso-scale changes in salinity along estuaries, and smaller scale gradients in desiccation and temperature spanning the intertidal range. The geology and geography of the American and European coasts provide natural replication of these gradients, allowing for population genetic analyses of parallel adaptation to environmental stress and heterogeneity. Statistical methods have been developed that provide genomic neutrality tests of population differentiation and aid in the process of candidate gene identification. In this paper, we review studies of marine organisms that illustrate associations between an environmental gradient and specific genetic markers. Such highly differentiated markers become candidate genes for adaptation to the environmental factors in question, but the functional significance of genetic variants must be comprehensively evaluated. We present a set of predictions about locus-specific selection across latitudinal, estuarine, and intertidal gradients that are likely to exist in the North Atlantic. We further present new data and analyses that support and contradict these simple selection models. Some taxa show pronounced clinal variation at certain loci against a background of mild clinal variation at many loci. These cases illustrate the procedures necessary for distinguishing selection driven by internal genomic vs. external environmental factors. We suggest that the North Atlantic intertidal community provides a model system for identifying genes that matter in ecology due to the clarity of the environmental stresses and an extensive experimental literature on ecological function. While these organisms are typically poor genetic and genomic models, advances in comparative genomics have provided access to molecular tools that can now be applied to taxa with well-defined ecologies. As many of the organisms we discuss have tight physiological limits driven by climatic factors, this synthesis of molecular population genetics with marine ecology could provide a sensitive means of assessing evolutionary responses to climate change.

Priming the Governance System for Climate Change Adaptation: The Application of a Social Ecological Inventory (SEI) to Engage Actors in Niagara, Canada

Adaptive systems of governance are increasingly gaining attention in respect to complex and uncertain social-ecological systems. Adaptive co-management is one strategy to make adaptive governance operational and holds promise with respect to community climate change adaptation as it facilitates participation and learning across scales and fosters adaptive capacity and resilience. Developing tools which hasten the realization of such approaches are growing in importance. This paper describes explores the Social Ecological Inventory (SEI) as a tool to 'prime' a regional climate change adaptation network. The SEI tool draws upon the social-ecological systems approach in which social and ecological systems are considered linked. SEIs bridge the gap between conventional stakeholder analysis and biological inventories and take place through a six phase process. A case study describes the results of applying an SEI to prime an adaptive governance network for climate change adaptation in the Niagara Region of Canada. Lessons learned from the case study are discussed and highlight how the SEI catalyzed the adaptive co-management process in the case. Future avenues for SEIs in relation to climate change adaptation emerge from this exploratory work and offer opportunities to inform research and adaptation planning.

Community-based climate change adaptation strategies for integrated prawn-fish-rice farming in Bangladesh to promote social-ecological resilience

Farming freshwater prawns with fish in rice fields is widespread in coastal regions of southwest Bangladesh because of favourable resources and ecological conditions. This article provides an overview of an ecosystem-based approach to integrated prawn-fish-rice farming in southwest Bangladesh. The practice of prawn and fish farming in rice fields is a form of integrated aquaculture-agriculture, which provides a wide range of social, economic and environmental benefits. Integrated prawn-fish-rice farming plays an important role in the economy of Bangladesh, earning foreign exchange and increasing food production. However, this unique farming system in coastal Bangladesh is particularly vulnerable to climatechange. We suggest that community-based adaptation strategies must be developed to cope with the challenges. We propose that integrated prawn-fish-rice farming could be relocated from the coastal region to less vulnerable upland areas, but caution that this will require appropriate adaptation strategies and an enabling institutional environment.

Integrating Environmental Justice and Social-Ecological Resilience for Successful Adaptation to Climate Change: Lessons from African American Communities on the Eastern Shore of the Chesapeake Bay

This research concerns the conceptual and empirical relationship between environmental justice and social-ecological resilience as it relates to climate change vulnerability and adaptation. Two primary questions guided this work. First, what is the level of resilience and adaptive capacity for social-ecological systems that are characterized by environmental injustice in the face of climate change? And second, what is the role of an environmental justice approach in developing adaptation policies that will promote social-ecological resilience? These questions were investigated in three African American communities that are particularly vulnerable to flooding from sea-level rise on the Eastern Shore of the Chesapeake Bay. Using qualitative and quantitative methods, I found that in all three communities, religious faith and the church, rootedness in the landscape, and race relations were highly salient to community experience. The degree to which these common aspects of the communities have imparted adaptive capacity has changed over time. Importantly, a given social-ecological factor does not have the same effect on vulnerability in all communities; however, in all communities political isolation decreases adaptive capacity and increases vulnerability. This political isolation is at least partly due to procedural injustice, which occurs for a number of interrelated reasons. This research further revealed that while all stakeholders (policymakers, environmentalists, and African American community members) generally agree that justice needs to be increased on the Eastern Shore, stakeholder groups disagree about what a justice approach to adaptation would look like. When brought together at a workshop, however, these stakeholders were able to identify numerous challenges and opportunities for increasing justice. Resilience was assessed by the presence of four resilience factors: living with uncertainty, nurturing diversity, combining different types of knowledge, and creating opportunities for self-organization. Overall, these communities seem to have low resilience; however, there is potential for resilience to increase. Finally, I argue that the use of resilience theory for environmental justice communities is limited by the great breadth and depth of knowledge required to evaluate the state of the social-ecological system, the complexities of simultaneously promoting resilience at both the regional and local scale, and the lack of attention to issues of justice.

National climate change adaptation research plan : freshwater biodiversity

Climate change will alter the basic physical and chemical environment underpinning all life. Species will be affected differentially by these alterations, resulting in changes to the structure and composition of present-day freshwater ecological communities, with the potential to change the ways in which these ecosystems function and the services they provide.

Storytelling beyond the anthropocene : a quest through the crises of ecocide toward new ecological paradigms

This project is a passionate and sometimes enraged thrust toward a biodiverse future. Weaving stories with deep thinking beyond the limits of the anthropocene, I am trying to recall myself in a more-than-human world. Our planet is suffering human induced ecocide which is a global crisis threatening the existence of multiple life forms. The alchemical mix of storytelling and ecological thinking could be part remedy for humanity's adaptation: a transformational mix to re-pattern the crisis into an opportunity and shift anthropocentric structures toward networks of dynamic relationships. The purpose of this project is to explore this cultural remedy. This is a quest, a search for tools that can germinate the hypothesis: storytelling in relation to ecological thinking manifests human potential in a more-than-human world. The practice-led research is guided by the philosophy and practice of Mythology, Deep ecology and Transdisciplinarity. Further navigation is sourced from Systems Thinking, Indigenous Methodologies, Biomimicry, and Quantum Physics. The journey unfolds by reawakening the Artist's function as caretaker of Mythology and pattern inciter for the collective. The resounding discovery of this adventure is Quantum Narratives: a storytelling tool for today's world, a method to connect multiple ways of knowing and diverse languages with the purpose of engaging, relating and working with living knowledge. Quantum Narratives are used to test the field study research into the Future of Water in context of Coal Seam Gas Mining in the Murray-Darling Basin and to materialise the collaborative results as the Water Stories. This thesis is a Living Script, full of imagination and complexity. Within its folds are strategies for systemic change ready to be adapted by policy and planning brokers and those who hold power for widespread remedial action.

Genetic Diversity and Adaptation of Date Palm (Phoenix dactylifera L.)

Acquiring sufficient information on the genetic variation, genetic differentiation, and the ecological and genetic relationships among individuals and populations are essential for establishing guidelines on conservation and utilization of the genetic resources of a species, and more particularly when biotic and abiotic stresses are considered. The aim of this study was to assess the extent and pattern of genetic variation in date palm (Phoenix dacttylifera L) cultivars; the genetic diversity and structure in its populations occurring over geographical ranges; the variation in economically and botanically important traits of it and the variation in its drought adaptive traits, in conservation and utilization context. In this study, the genetic diversity and relationships among selected cultivars from Sudan and Morocco were assessed using microsatellite markers. Microsatellite markers were also used to investigate the genetic diversity within and among populations collected from different geographic locations in Sudan. In a separate investigation, fruits of cultivars selected from Sudan, involved morphological and chemical characterization, and morphological and DNA polymorphism of the mother trees were also investigated. Morphological and photosynthetic adjustments to water stress were studied in the five most important date palm cultivars in Sudan, namely, Gondaila, Barakawi, Bitamoda, Khateeb and Laggai; and the mechanism enhancing photosynthetic gas exchange in date palm under water stress was also investigated. Results showed a significant (p < 0.001, t-test) differentiation between Sudan and Morocco groups of cultivars. However, the major feature of all tested cultivars was the complete lack of clustering and the absence of cultivars representing specific clones. The results indicated high genetic as well as compositional and morphological diversity among cultivars; while, compositional and morphological traits were found to be characteristic features that strongly differentiate cultivars as well as phenotypes. High genetic diversity was observed also in different populations. Slight but significant (p < 0.01, AMOVA) divergence was observed for soft and dry types; however, the genetic divergence among populations was relatively weak. The results showed a complex genetic relationships between some of the tested populations especially when isolation by distance was considered. The results of the study also revealed that date palm cultivars and phenotypes possess specific direct or interaction effects due to water availability on a range of morphological and physiological traits. Soft and dry phenotypes responded differently to different levels of water stress, while the dry phenotype was more sensitive and conservative. The results indicated that date palm has high fixation capacity to photosynthetic CO2 supply with interaction effect to water availability, which can be considered as advantageous when coping with stresses that may arise with climate change. In conclusion, although a large amount of diversity exists among date palm germplasm, the findings in this study show that the role of biological nature of the tree, isolation by distance and environmental effects on structuring date palm genome was highly influenced by human impacts. Identity of date palm cultivars as developed and manipulated by date palm growers, in the absence of scientific breeding programmes, may continue to mainly depend on tree morphology and fruit characters. The pattern of genetic differentiation may cover specific morphological and physiological traits that contribute to adaptive mechanisms in each phenotype. These traits can be considered for further studies related to drought adaptation in date palm.

A participatory systems approach to understanding climate adaptation needs

Emerging literature on climate adaptation suggests the need for effective ways of engaging or activating communities and supporting community roles, coupled with whole-of-system approaches to understanding climate change and adaptation needs. We have developed and evaluated a participatory approach to elicit community and stakeholder understanding of climate change adaptation needs, and connect diverse community members and local office bearers towards potential action. The approach was trialed in a series of connected social-ecological systems along a transect from a rural area to the coast and islands of ecologically sensitive Moreton Bay in Queensland, Australia. We conducted ‘climate roundtables’ in each of three areas along the transect, then a fourth roundtable reviewed and extended the results to the region as a whole. Influence diagrams produced through the process show how each climate variable forecast to affect this region (heat, storm, flood, sea-level rise, fire, drought) affects the natural environment, infrastructure, economic and social behaviour patterns, and psychosocial responses, and how sets of people, species and ecosystems are affected, and act, differentially. The participatory process proved effective as a way of building local empathy, a local knowledge base and empowering participants to join towards future climate adaptation action. Key principles are highlighted to assist in adapting the process for use elsewhere.

Effects of environmental variation on ecological and evolutionary dynamics

Environmental variation is a fact of life for all the species on earth: for any population of any particular species, the local environmental conditions are liable to vary in both time and space. In today's world, anthropogenic activity is causing habitat loss and fragmentation for many species, which may profoundly alter the characteristics of environmental variation in remaining habitat. Previous research indicates that, as habitat is lost, the spatial configuration of remaining habitat will increasingly affect the dynamics by which populations are governed. Through the use of mathematical models, this thesis asks how environmental variation interacts with species properties to influence population dynamics, local adaptation, and dispersal evolution. More specifically, we couple continuous-time continuous-space stochastic population dynamic models to landscape models. We manipulate environmental variation via parameters such as mean patch size, patch density, and patch longevity. Among other findings, we show that a mixture of high and low quality habitat is commonly better for a population than uniformly mediocre habitat. This conclusion is justified by purely ecological arguments, yet the positive effects of landscape heterogeneity may be enhanced further by local adaptation, and by the evolution of short-ranged dispersal. The predicted evolutionary responses to environmental variation are complex, however, since they involve numerous conflicting factors. We discuss why the species that have high levels of local adaptation within their ranges may not be the same species that benefit from local adaptation during range expansion. We show how habitat loss can lead to either increased or decreased selection for dispersal depending on the type of habitat and the manner in which it is lost. To study the models, we develop a recent analytical method, Perturbation expansion, to enable the incorporation of environmental variation. Within this context, we use two methods to address evolutionary dynamics: Adaptive dynamics, which assumes mutations occur infrequently so that the ecological and evolutionary timescales can be separated, and via Genotype distributions, which assume mutations are more frequent. The two approaches generally lead to similar predictions yet, exceptionally, we show how the evolutionary response of dispersal behaviour to habitat turnover may qualitatively depend on the mutation rate.

The Emerging Phenotype: Ecological Genetics of Color, Form and Sex in the Common Frog

One of the main aims of evolutionary biology is to explain why organisms vary phenotypically as they do. Proximately, this variation arises from genetic differences and from environmental influences, the latter of which is referred to as phenotypic plasticity. Phenotypic plasticity is thus a central concept in evolutionary biology, and understanding its relative importance in causing the phenotypic variation and differentiation is important, for instance in anticipating the consequences of human induced environmental changes. The aim of this thesis was to study geographic variation and local adaptation, as well as sex ratios and environmental sex reversal, in the common frog (Rana temporaria). These themes cover three different aspects of phenotypic plasticity, which emerges as the central concept for the thesis. The first two chapters address geographic variation and local adaptation in two potentially thermally adaptive traits, namely the degree of melanism and the relative leg length. The results show that although there is an increasing latitudinal trend in the degree of melanism in wild populations across Scandinavian Peninsula, this cline has no direct genetic basis and is thus environmentally induced. The second chapter demonstrates that although there is no linear, latitudinally ordered phenotypic trend in relative leg length that would be expected under Allen s rule an ecogeographical rule linking extremity length to climatic conditions there seems to be such a trend at the genetic level, hidden under environmental effects. The first two chapters thus view phenotypic plasticity through its ecological role and evolution, and demonstrate that it can both give rise to phenotypic variation and hide evolutionary patterns in studies that focus solely on phenotypes. The last three chapters relate to phenotypic plasticity through its ecological and evolutionary role in sex determination, and consequent effects on population sex ratio, genetic recombination and the evolution of sex chromosomes. The results show that while sex ratios are strongly female biased and there is evidence of environmental sex reversals, these reversals are unlikely to have caused the sex ratio skew, at least directly. The results demonstrate that environmental sex reversal can have an effect on the evolution of sex chromosomes, as the recombination patterns between them seem to be controlled by phenotypic, rather than genetic, sex. This potentially allows Y chromosomes to recombine, lending support for the recent hypothesis suggesting that sex-reversal may play an important role on the rejuvenation of Y chromosomes.

Substrate Selectivity and Molecular Adaptation in the Outer Membrane Proteases of Yersinia pestis and Salmonella enterica

Proteolysis is important in bacterial pathogenesis and colonization of animal and plant hosts. In this work I have investigated the functions of the bacterial outer membrane proteases, omptins, of Yersinia pestis and Salmonella enterica. Y. pestis is a zoonotic pathogen that causes plague and has evolved from gastroenteritis-causing Yersinia pseudotuberculosis about 13 000 years ago. S. enterica causes gastroenteritis and typhoid fever in humans. Omptins are transmembrane β-barrels with ten antiparallel β-strands and five surface-exposed loops. The loops are important in substrate recognition, and variation in the loop sequences leads to different substrate selectivities between omptins, which makes omptins an ideal platform to investigate functional adaptation and to alter their polypeptide substrate preferences. The omptins Pla of Y. pestis and PgtE of S. enterica are 75% identical in their amino acid sequences. Pla is a multifunctional protein with proteolytic and non-proteolytic functions, and it increases bacterial penetration and proliferation in the host. Functions of PgtE increase migration of S. enterica in vivo and bacterial survival in mouse macrophages, thus enhancing bacterial spread within the host. Mammalian plasminogen/fibrinolytic system maintains the balance between coagulation and fibrinolysis and participates in several cellular processes, e.g., cell migration and degradation of extracellular matrix proteins. This system consists of activation cascades, which are strictly controlled by several regulators, such as plasminogen activator inhibitor 1 (PAI-1), α2-antiplasmin (α2AP), and thrombin-activatable fibrinolysis inhibitor (TAFI). This work reveals novel interactions of the omptins of Y. pestis and S. enterica with the regulators of the plasminogen/fibrinolytic system: Pla and PgtE inactivate PAI-1 by cleavage at the reactive site peptide bond, and degrade TAFI, preventing its activation to TAFIa. Structure-function relationship studies with Pla showed that threonine 259 of Pla is crucial in plasminogen activation, as it prevents degradation of the plasmin catalytic domain by the omptin and thus maintains plasmin stability. In this work I constructed chimeric proteins between Pla and Epo of Erwinia pyrifoliae that share 78% sequence identity to find out which amino acids and regions in Pla are important for its functions. Epo is neither a plasminogen activator nor an invasin, but it degrades α2AP and PAI-1. Cumulative substitutions towards Pla sequence turned Epo into a Pla-like protein. In addition to threonine 259, loops 3 and 5 are critical in plasminogen activation by Pla. Turning Epo into an invasin required substitution of 31 residues located at the extracellular side of the Epo protein above the lipid bilayer, and also of the β1-strand in the N-terminal transmembrane region of the protein. These studies give an example of how omptins adapt to novel functions that advantage their host bacteria in different ecological niches.

Forest governance and climate change adaptation : Case studies of four African countries

Africa is threatened by climate change. The adaptive capacity of local communities continues to be weakened by ineffective and inefficient livelihood strategies and inappropriate development interventions. One of the greatest challenges for climate change adaptation in Africa is related to the governance of natural resources used by vulnerable poor groups as assets for adaptation. Practical and good governance activities for adaptation in Africa is urgently and much needed to support adaptation actions, interventions and planning. The adaptation role of forests has not been as prominent in the international discourse and actions as their mitigation role. This study therefore focused on the forest as one of the natural resources used for adaptation. The general objective of this research was to assess the extent to which cases of current forest governance practices in four African countries Burkina Faso, The Democratic Republic of Congo (DRC), Ghana and Sudan are supportive to the adaptation of vulnerable societies and ecosystems to impacts of climate change. Qualitative and quantitative analyses from surveys, expert consultations and group discussions were used in analysing the case studies. The entire research was guided by three conceptual sets of thinking forest governance, climate change vulnerability and ecosystem services. Data for the research were collected from selected ongoing forestry activities and programmes. The study mainly dealt with forest management policies and practices that can improve the adaptation of forest ecosystems (Study I) and the adaptive capacity through the management of forest resources by vulnerable farmers (Studies II, III, IV and V). It was found that adaptation is not part of current forest policies, but, instead, policies contain elements of risk management practices, which are also relevant to the adaptation of forest ecosystems. These practices include, among others, the management of forest fires, forest genetic resources, non-timber resources and silvicultural practices. Better livelihood opportunities emerged as the priority for the farmers. These vulnerable farmers had different forms of forest management. They have a wide range of experience and practical knowledge relevant to ensure and achieve livelihood improvement alongside sustainable management and good governance of natural resources. The contributions of traded non-timber forest products to climate change adaptation appear limited for local communities, based on their distribution among the stakeholders in the market chain. Plantation (agro)forestry, if well implemented and managed by communities, has a high potential in reducing socio-ecological vulnerability by increasing the food production and restocking degraded forest lands. Integration of legal arrangements with continuous monitoring, evaluation and improvement may drive this activity to support short, medium and long term expectations related to adaptation processes. The study concludes that effective forest governance initiatives led by vulnerable poor groups represent one practical way to improve the adaptive capacities of socio-ecological systems against the impacts of climate change in Africa.