A global synthesis of climate vulnerability assessments on marine fisheries: Methods,scales, and knowledge co-production

Undertaking climate vulnerability assessments (CVAs) on marine fisheries is instrumental to the identification of regions, species, and stakeholders at risk of impacts from climate change, and the development of effective and targeted responses for fisheries adaptation. In this global literature review, we addressed three important questions to characterize fisheries CVAs: (i) what are the available approaches to develop CVAs in various social–ecological contexts, (ii) are different geographic scales and regions adequately represented, and (iii) how do diverse knowledge systems contribute to current understanding of vulnerability? As part of these general research efforts, we identified and characterized an inventory of frameworks and indicators that encompass a wide range of foci on ecological and socioeconomic dimensions of climate vulnerability on fisheries. Our analysis highlighted a large gap between countries with top research inputs and the most urgent adaptation needs. More research and resources are needed in low-income tropical countries to ensure existing inequities are not exacerbated. We also identified an uneven research focus across spatial scales and cautioned a possible scale mismatch between assessment and management needs. Drawing on this information, we catalog (1) a suite of research directions that could improve the utility and applicability of CVAs, particularly the examination of barriers and enabling conditions that influence the uptake of CVA results into management responses at multiple levels, (2) the lessons that have been learned from applications in data-limited regions, particularly the use of proxy indicators and knowledge co-production to overcome the problem of data deficiency, and (3) opportunities for wider applications, for example diversifying the use of vulnerability indicators in broader monitoring and management schemes. This information is used to provide a set of recommendations that could advance meaningful CVA practices for fisheries management and promote effective translation of climate vulnerability into adaptation actions.     

Linking immune defenses and life history at the levels of the individual and the species

Immune defenses have been suggested to play an important rolein mediating life history trade-offs. Detecting and understandingsuch trade-offs, however, is complicated by the complexity ofthe immune system. The measurement of multiple immune indicesin studies of "eco-immunology" has only recently become morecommon, but has great potential for furthering an understandingof the ecological and evolutionary forces driving immunologicalvariation. Building on previous proposals, I create a frameworkintegrating immunological and life history axes that can beused to formulate predictions and interpret variation in multipletypes of immune defense at both the individual and species levelsin vertebrates. In particular, this framework predicts that"fast-living" species (those with high reproductive and lowsurvival rates) should rely more heavily on nonspecific andinflammatory immune defenses, while "slow-living" species shouldexhibit stronger specific and especially antibody-mediated immunity.At the level of individuals within species, nonspecific andinflammatory responses should be downregulated, and specificdefenses upregulated (1) in individuals experiencing the greatestdemands on their resources (for example, undertaking large reproductiveefforts); (2) in the sex investing more in a particular activity(for example, females during reproduction); and (3) during themost demanding periods of the year (for example, the breedingseason). A review of the literature reveals that incorporatingmultiple facets of the immune system into a model of the relationshipbetween immune defense and life histories brings disparate questionsand systems into a common context, and helps explain empiricalresults that are sometimes counterintuitive.     

Evolutionary and ecological functional genomics,from lab to the wild

Plant phenotypes are the result of both genetic and environmental forces that act to modulate trait expression. Over the last few years, numerous approaches in functional genomics and systems biology have led to a greater understanding of plant phenotypic variation and plant responses to the environment. These approaches, and the questions that they can address, have been loosely termed evolutionary and ecological functional genomics (EEFG), and have been providing key insights on how plants adapt and evolve. In particular, by bringing these studies from the laboratory to the field, EEFG studies allow us to gain greater knowledge of how plants function in their natural contexts.     

The impact of global climate change on genetic diversity within populations and species

Genetic diversity provides the basic substrate for evolution, yet few studies assess the impacts of global climate change (GCC) on intraspecific genetic variation. In this review, we highlight the importance of incorporating neutral and non‐neutral genetic diversity when assessing the impacts of GCC, for example, in studies that aim to predict the future distribution and fate of a species or ecological community. Specifically, we address the following questions: Why study the effects of GCC on intraspecific genetic diversity? How does GCC affect genetic diversity? How is the effect of GCC on genetic diversity currently studied? Where is potential for future research? For each of these questions, we provide a general background and highlight case studies across the animal, plant and microbial kingdoms. We further discuss how cryptic diversity can affect GCC assessments, how genetic diversity can be integrated into studies that aim to predict species' responses on GCC and how conservation efforts related to GCC can incorporate and profit from inclusion of genetic diversity assessments. We argue that studying the fate of intraspecifc genetic diversity is an indispensable and logical venture if we are to fully understand the consequences of GCC on biodiversity on all levels.     

Ecological thresholds and regime shifts: approaches to identification

There is an apparent gap between the prominence of present theoretical frameworks involving ecological thresholds and regime shifts, and the paucity of efforts to conduct simple tests and quantitative inferences on the actual appearance of such phenomena in ecological data. A wide range of statistical methods and analytical techniques are now available that render these questions tractable, some of them even dating back half a century. Yet, their application has been sparse and confined within a narrow subset of cases of ecological regime shifts. Our objective is to raise awareness on the range of techniques available, and to their principles and limitations, to promote a more operational approach to the identification of ecological thresholds and regime shifts.     

A place that answers questions: primatological field sites and the making of authentic observations

The ideals and realities of field research have shaped the development of behavioural primatology over the latter half of the twentieth century. This paper draws on interviews with primatologists as well as a survey of the scientific literature to examine the idealized notion of the field site as a natural place and the physical environment of the field as a research space. It shows that what became standard field practice emerged in the course of wide ranging debate about the techniques, personal qualities and site conditions best suited to the scientific study of the natural behaviour of apes and monkeys. Although the laboratory was a constant presence in this debate, the export of techniques from the laboratory to the field was limited, due to concerns that experimental manipulation would destroy the naturalness of the behaviour. The paper goes on to demonstrate the central significance given by primatologists to the unique social, historical and ecological circumstances of particular field sites, and to sketch some of the complexities that fieldworkers contend with in trying to realize their ideals. Primatologists seek field sites that answer their questions; but once their studies become long term, they also need to find questions that answer to ever changing conditions at those sites.     

生态整合与文明发展

探讨了快速发展中“不平衡、不协调、不可持续”问题的生态学成因,总结了社会-经济-自然复合生态系统概念提出30年来理论和方法的研究进展,阐述了生态整合的内涵、方法和将生态文明融入经济、政治、文化和社会建设的各方面和全过程的科学基础、系统方法和整合技术,指出新时期生态学的研究对象正从组分到关系、从物质到信息、从结构到功能、从学苑到社会转型;生态学的研究方法正从测量向测序、寻优向寻适的方向演化.提出社会小康、生态中和、科学大智是生态文明新时代美丽中国的新形象.     

Stable isotopes as one of nature's ecological recorders

Analyses of the natural variation in stable isotopes of components of ecological systems have provided new insights into how these systems function across paleoecological to modern timescales and across a wide range of spatial scales. Isotope abundances of the molecules in biological materials and geochemical profiles are viewed as recorders that can be used to reconstruct ecological processes or to trace ecological activities. Here, we review key short-, medium- and long-term recording capacities of stable isotopes that are currently being applied to ecological questions. The melding of advances in genetics, biochemical profiling and spatial analysis with those in isotope analyses and modeling sophistication opens the door to an exciting future in ecological research.     

Emerging model systems in eco-evo-devo: the environmentally responsive spadefoot toad

Spadefoot toads have emerged as a model system for addressing fundamental questions in ecological and evolutionary developmental biology (eco-evo-devo). Their tadpoles produce a wide range of adaptive phenotypes in direct response to diverse environmental stimuli. Such phenotypic plasticity offers an excellent opportunity to examine how an organism's ecology affects its development as well as how an organism's development influences its ecology and evolution. By characterizing and understanding the interconnectedness between an organism's environment, its development responses, and its ecological interactions in natural populations, such research promises to clarify further the role of the environment in not only selecting among diverse phenotypes, but also creating such phenotypes in the first place.     

Parasites—the new frontier: celebrating Darwin 200

To Darwin, parasites were fascinating examples of adaptation but their significance as selective factors for a wide range of phenomena has only been studied in depth over the last few decades. This work has had its roots in behavioural/evolutionary ecology on the one hand, and in population biology/ecology on the other, thus shaping a new comprehensive field of ‘evolutionary parasitology’. Taking parasites into account has been a success story and has shed new light on several old questions such as sexual selection, the evolution of sex and recombination, changes in behaviour, adaptive life histories, and so forth. In the process, the topic of ecological immunology has emerged, which analyses immune defences in a framework of costs and benefits. Throughout, a recurrent theme is how to appropriately integrate the underlying mechanisms as evolved boundary conditions into a framework of studying the adaptive value of traits. On the conceptual side, major questions remain and await further study.     

A guide to the genomics of ecological speciation in natural animal populations

Interest in ecological speciation is growing, as evidence accumulates showing that natural selection can lead to rapid divergence between subpopulations. However, whether and how ecological divergence can lead to the buildup of reproductive isolation remains under debate. What is the relative importance of natural selection vs. neutral processes? How does adaptation generate reproductive isolation? Can ecological speciation occur despite homogenizing gene flow? These questions can be addressed using genomic approaches, and with the rapid development of genomic technology, will become more answerable in studies of wild populations than ever before. In this article, we identify open questions in ecological speciation theory and suggest useful genomic methods for addressing these questions in natural animal populations. We aim to provide a practical guide for ecologists interested in incorporating genomic methods into their research programs. An increased integration between ecological research and genomics has the potential to shed novel light on the origin of species.     

Evidence for selection at cytokine loci in a natural population of field voles (Microtus agrestis)

Individuals in natural populations are frequently exposed to a wide range of pathogens. Given the diverse profile of gene products involved in responses to different types of pathogen, this potentially results in complex pathogen-specific selection pressures acting on a broad spectrum of immune system genes in wild animals. Thus far, studies into the evolution of immune genes in natural populations have focused almost exclusively on the Major Histocompatibility Complex (MHC). However, the MHC represents only a fraction of the immune system and there is a need to broaden research in wild species to include other immune genes. Here, we examine the evidence for natural selection in a range of non-MHC genes in a natural population of field voles (Microtus agrestis). We concentrate primarily on genes encoding cytokines, signalling molecules critical in eliciting and mediating immune responses and identify signatures of natural selection acting on several of these genes. In particular, genetic diversity within Interleukin 1 beta and Interleukin 2 appears to have been maintained through balancing selection. Taken together with previous findings that polymorphism within these genes is associated with variation in resistance to multiple pathogens, this suggests that pathogen-mediated selection may be an important force driving genetic diversity at cytokine loci in voles and other natural populations. These results also suggest that, along with the MHC, preservation of genetic variation within cytokine genes should be a priority for the conservation genetics of threatened wildlife populations.     

Integrating molecular tools into freshwater ecology: developments and opportunities

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Engineering microbial systems to explore ecological and evolutionary dynamics

A major goal of biological research is to provide a mechanistic understanding of diverse biological processes. To this end, synthetic biology offers a powerful approach, whereby biological questions can be addressed in a well-defined framework. By constructing simple gene circuits, such studies have generated new insights into the design principles of gene regulatory networks. Recently, this strategy has been applied to analyze ecological and evolutionary questions, where population-level interactions are critical. Here, we highlight recent development of such systems and discuss how they were used to address problems in ecology and evolutionary biology. As illustrated by these examples, synthetic ecosystems provide a unique platform to study ecological and evolutionary phenomena that are challenging to study in their natural contexts.     

An integrated framework to identify wildlife populations under threat from climate change

Climate change is a major threat to global biodiversity that will produce a range of new selection pressures. Understanding species responses to climate change requires an interdisciplinary perspective, combining ecological, molecular and environmental approaches. We propose an applied integrated framework to identify populations under threat from climate change based on their extent of exposure, inherent sensitivity due to adaptive and neutral genetic variation and range shift potential. We consider intraspecific vulnerability and population‐level responses, an important but often neglected conservation research priority. We demonstrate how this framework can be applied to vertebrates with limited dispersal abilities using empirical data for the bat Plecotus austriacus. We use ecological niche modelling and environmental dissimilarity analysis to locate areas at high risk of exposure to future changes. Combining outlier tests with genotype–environment association analysis, we identify potential climate‐adaptive SNPs in our genomic data set and differences in the frequency of adaptive and neutral variation between populations. We assess landscape connectivity and show that changing environmental suitability may limit the future movement of individuals, thus affecting both the ability of populations to shift their distribution to climatically suitable areas and the probability of evolutionary rescue through the spread of adaptive genetic variation among populations. Therefore, a better understanding of movement ecology and landscape connectivity is needed for predicting population persistence under climate change. Our study highlights the importance of incorporating genomic data to determine sensitivity, adaptive potential and range shift potential, instead of relying solely on exposure to guide species vulnerability assessments and conservation planning.     

The major histocompatibility complex and autism spectrum disorder

Autism spectrum disorder (ASD) is a complex disorder that appears to be caused by interactions between genetic changes and environmental insults during early development. A wide range of factors have been linked to the onset of ASD, but recently both genetic associations and environmental factors point to a central role for immune-related genes and immune responses to environmental stimuli. Specifically, many of the proteins encoded by the major histocompatibility complex (MHC) play a vital role in the formation, refinement, maintenance, and plasticity of the brain. Manipulations of levels of MHC molecules have illustrated how disrupted MHC signaling can significantly alter brain connectivity and function. Thus, an emerging hypothesis in our field is that disruptions in MHC expression in the developing brain caused by mutations and/or immune dysregulation may contribute to the altered brain connectivity and function characteristic of ASD. This review provides an overview of the structure and function of the three classes of MHC molecules in the immune system, healthy brain, and their possible involvement in ASD. ? 2012 Wiley Periodicals, Inc. Develop Neurobiol, 2012.     

Molecular ecology of fungal entomopathogens: molecular genetic tools and their applications in population and fate studies

The power of molecular genetic techniques to address ecological research questions has opened a distinct interdisciplinary research area collectively referred to as molecular ecology. Molecular ecology combines aspects of diverse research fields like population and evolutionary genetics, as well as biodiversity, conservation biology, behavioural ecology, or species-habitat interactions. Molecular techniques detect specific DNA sequence characteristics that are used as genetic markers to discriminate individuals or taxonomic groups, for instance in analyses of population and community structures, for elucidation of phylogenetic relationships, or for the characterization and monitoring of specific strains in the environment. Here, we summarize the PCR-based molecular techniques used in molecular ecological research on fungal entomopathogens and discuss novel techniques that may have relevance to the studies of entomopathogenic fungi in the future. We discuss the flow chart of the molecular ecology approaches and we highlight some of the critical steps involved. There are still many unresolved questions in the understanding of the ecology of fungal entomopathogens. These include population characteristics and relations of genotypes and habitats as well as host-pathogen interactions. Molecular tools can provide substantial support for ecological research and offer insight into this far inaccessible systems. Application of molecular ecology approaches will stimulate and accelerate new research in the field of entomophathogen ecology.     

Preface: Recent advances in Crustacean Genomics

Aquatic plants fulfil a wide range of ecological roles, and make a substantial contribution to the structure, function and service provision of aquatic ecosystems. Given their well-documented importance in aquatic ecosystems, research into aquatic plants continues to blossom. The 14th International Symposium on Aquatic Plants, held in Edinburgh in September 2015, brought together 120 delegates from 28 countries and six continents. This special issue of Hydrobiologia includes a select number of papers on aspects of aquatic plants, covering a wide range of species, systems and issues. In this paper, we present an overview of current trends and future directions in aquatic plant research in the early twenty first century. Our understanding of aquatic plant biology, the range of scientific issues being addressed and the range of techniques available to researchers have all arguably never been greater; however, substantial challenges exist to the conservation and management of both aquatic plants and the ecosystems in which they are found. The range of countries and continents represented by conference delegates and authors of papers in the special issue illustrates the global relevance of aquatic plant research in the early twenty first century but also the many challenges that this burgeoning scientific discipline must address.