Multiple axes of ecological vulnerability to climate change

Observed ecological responses to climate change are highly individualistic across species and locations, and understanding the drivers of this variability is essential for management and conservation efforts. While it is clear that differences in exposure, sensitivity, and adaptive capacity all contribute to heterogeneity in climate change vulnerability, predicting these features at macroecological scales remains a critical challenge. We explore multiple drivers of heterogeneous vulnerability across the distributions of 96 vegetation types of the ecologically diverse western US, using data on observed climate trends from 1948 to 2014 to highlight emerging patterns of change. We ask three novel questions about factors potentially shaping vulnerability across the region: (a) How does sensitivity to different climate variables vary geographically and across vegetation classes? (b) How do multivariate climate exposure patterns interact with these sensitivities to shape vulnerability patterns? (c) How different are these vulnerability patterns according to three widely implemented vulnerability paradigms—niche novelty (decline in modeled suitability), temporal novelty (standardized anomaly), and spatial novelty (inbound climate velocity)—each of which uses a distinct frame of reference to quantify climate departure? We propose that considering these three novelty paradigms in combination could help improve our understanding and prediction of heterogeneous climate change responses, and we discuss the distinct climate adaptation strategies connected with different combinations of high and low novelty across the three metrics. Our results reveal a diverse mosaic of climate change vulnerability signatures across the region's plant communities. Each of the above factors contributes strongly to this heterogeneity: climate variable sensitivity exhibits clear patterns across vegetation types, multivariate climate change data reveal highly diverse exposure signatures across locations, and the three novelty paradigms diverge widely in their climate change vulnerability predictions. Together, these results shed light on potential drivers of individualistic climate change responses and may help to inform effective management strategies.     

The role of ontogeny in wood diversity and evolution

Evolutionary developmental biology (evo-devo) explores the link between developmental patterning and phenotypic change through evolutionary time. In this review, we highlight the scientific advancements in understanding xylem evolution afforded by the evo-devo approach, opportunities for further engagement, and future research directions for the field. We review evidence that (1) heterochrony—the change in rate and timing of developmental events, (2) homeosis—the ontogenetic replacement of features, (3) heterometry—the change in quantity of a feature, (4) exaptation—the co-opting and repurposing of an ancestral feature, (5) the interplay between developmental and capacity constraints, and (6) novelty—the emergence of a novel feature, have all contributed to generating the diversity of woods. We present opportunities for future research engagement, which combine wood ontogeny within the context of robust phylogenetic hypotheses, and molecular biology.     

Thirty‐five years of spatial autocorrelation analysis in population genetics: an essay in honour of Robert Sokal (1926–2012)

We could not start this review, literally from the beginning, without expressing our sadness over the passing of Professor Robert R. Sokal. We are sure, nevertheless, that the importance of his scientific achievements will ensure he is long remembered. In this modest tribute to Professor Sokal, we highlight his contributions to the field of population genetics and spatial statistical methods. Specifically, we discuss how two papers, co‐authored with Professor N. L. Oden and published in the pages of the Biological Journal of the Linnean Society in 1978, revolutionized the field of analytical population genetics. In these papers, Sokal and Oden created an elegant framework for inferring evolutionary processes (e.g. isolation‐by‐distance, demic diffusion, selection gradients, genetic drift) from the spatial autocorrelation analysis of genetic variation patterns. We also highlight the pivotal importance of Sokal's work to the development of emerging fields (e.g. landscape and conservation genetics). We hope this virtual issue containing the papers that Professor Sokal published in BJLS, and later, related papers by other researchers, will help to remember his work and maintain his legacy of spatial analysis in genetics, ecology, and evolutionary biology. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ??, ??–??.     

Climate Change Sentiment on Twitter: An Unsolicited Public Opinion Poll

The consequences of anthropogenic climate change are extensively debated through scientific papers, newspaper articles, and blogs. Newspaper articles may lack accuracy, while the severity of findings in scientific papers may be too opaque for the public to understand. Social media, however, is a forum where individuals of diverse backgrounds can share their thoughts and opinions. As consumption shifts from old media to new, Twitter has become a valuable resource for analyzing current events and headline news. In this research, we analyze tweets containing the word “climate” collected between September 2008 and July 2014. Through use of a previously developed sentiment measurement tool called the Hedonometer, we determine how collective sentiment varies in response to climate change news, events, and natural disasters. We find that natural disasters, climate bills, and oil-drilling can contribute to a decrease in happiness while climate rallies, a book release, and a green ideas contest can contribute to an increase in happiness. Words uncovered by our analysis suggest that responses to climate change news are predominately from climate change activists rather than climate change deniers, indicating that Twitter is a valuable resource for the spread of climate change awareness.     

Model-guided fieldwork: practical guidelines for multidisciplinary research on wildlife ecological and epidemiological dynamics

Infectious disease ecology has recently raised its public profile beyond the scientific community due to the major threats that wildlife infections pose to biological conservation, animal welfare, human health and food security. As we start unravelling the full extent of emerging infectious diseases, there is an urgent need to facilitate multidisciplinary research in this area. Even though research in ecology has always had a strong theoretical component, cultural and technical hurdles often hamper direct collaboration between theoreticians and empiricists. Building upon our collective experience of multidisciplinary research and teaching in this area, we propose practical guidelines to help with effective integration among mathematical modelling, fieldwork and laboratory work. Modelling tools can be used at all steps of a field-based research programme, from the formulation of working hypotheses to field study design and data analysis. We illustrate our model-guided fieldwork framework with two case studies we have been conducting on wildlife infectious diseases: plague transmission in prairie dogs and lyssavirus dynamics in American and African bats. These demonstrate that mechanistic models, if properly integrated in research programmes, can provide a framework for holistic approaches to complex biological systems.     

A history of scientific research at Loch Leven,Kinross, Scotland

Loch Leven is a large, shallow lake in lowland Scotland, UK. Scientific research began here almost 200 years ago. Early research characterised the biodiversity and physical characteristics of the loch, providing an important historical background for future research. In the mid-1960s, this ad hoc approach was superseded by a more structured research programme under the umbrella of the International Biological Programme. This was the beginning of the Loch Leven long-term monitoring programme. Today, the results of these studies form one of the longest and most comprehensive limnological datasets for shallow freshwater lakes in the world, comprising more than 500 physical, chemical and biological variables collected at two-weekly intervals. To celebrate the 40th anniversary of the start of the long term monitoring programme, and to highlight the scientific investigations still being conducted at Loch Leven, the NERC Centre for Ecology & Hydrology (CEH) organised a symposium entitled “Loch Leven: 40 years of scientific research” in Kinross, Scotland, UK, on 11 December 2008. This examined the role of long-term monitoring in developing our understanding of the links between pollution, climate change and ecological responses in shallow lakes. This article introduces a series of papers summarising the scientific results presented at this meeting.     

Bridging the explanatory gaps: What can we learn from a biological agency perspective?

We begin this article by delineating the explanatory gaps left by prevailing gene-focused approaches in our understanding of phenotype determination, inheritance, and the origin of novel traits. We aim not to diminish the value of these approaches but to highlight where their implementation, despite best efforts, has encountered persistent limitations. We then discuss how each of these explanatory gaps can be addressed by expanding research foci to take into account biological agency—the capacity of living systems at various levels to participate in their own development, maintenance, and function by regulating their structures and activities in response to conditions they encounter. Here we aim to define formally what agency and agents are and—just as importantly—what they are not, emphasizing that agency is an empirical property connoting neither intention nor consciousness. Lastly, we discuss how incorporating agency helps to bridge explanatory gaps left by conventional approaches, highlight scientific fields in which implicit agency approaches are already proving valuable, and assess the opportunities and challenges of more systematically incorporating biological agency into research programs.     

‘A river that is cutting its own bed’: the serology of syphilis between laboratory,society and the law

This paper focuses on the role of regulation in the shaping new scientific facts. Fleck chose to study the origins of a diagnostic test for a disease seen as a major public health problem, that is, a ‘scientific fact’ that had a direct and immediate influence outside the closed universe of fundamental scientific research. In 1935, when Fleck wrote his book, Genesis and development of a scientific fact, he believed that the tumultuous early history of the Wassermann reaction had come to an end, and that this reaction was successfully stabilized through the standardization of laboratory practices and thanks to the rise of a specific professional segment—the serologists. He could not have predicted that in the 15 years that followed the publication of his book, regulatory measures—barely metioned in his historical narrative—would play a key role in the destabilization of the original meaning of this reaction. The introduction of mass screening for syphilis—mainly via legislation that introduced obligatory premarital tests and promoted the testing of pregnant women—weakened in fine the link between Wassermann serology and infection by the etiological agent of syphilis, the bacterium Treponema pallidum. Fleck elected to study the Wassermann reaction because of its novelty, its complexity, and because it became the focus of a controversy regarding its origins. However, the Wassermann reaction was also one the first examples of a medical technology regulated by the state and incorporated into legal dispositions. It may therefore be seen as an exemplary case of the close intertwining of scientific investigations, their practical applications and regulatory practices.     

Origins and evolution of biological novelty

Understanding the origins and impacts of novel traits has been a perennial interest in many realms of ecology and evolutionary biology. Here, we build on previous evolutionary and philosophical treatments of this subject to encompass novelties across biological scales and eco-evolutionary perspectives. By defining novelties as new features at one biological scale that have emergent effects at other biological scales, we incorporate many forms of novelty that have previously been treated in isolation (such as novelty from genetic mutations, new developmental pathways, new morphological features, and new species). Our perspective is based on the fundamental idea that the emergence of a novelty, at any biological scale, depends on its environmental and genetic context. Through this lens, we outline a broad array of generative mechanisms underlying novelty and highlight how genomic tools are transforming our understanding of the origins of novelty. Lastly, we present several case studies to illustrate how novelties across biological scales and systems can be understood based on common mechanisms of change and their environmental and genetic contexts. Specifically, we highlight how gene duplication contributes to the evolution of new complex structures in visual systems; how genetic exchange in symbiosis alters functions of both host and symbiont, resulting in a novel organism; and how hybridisation between species can generate new species with new niches.     

Detecting and avoiding likely false‐positive findings – a practical guide

Recently there has been a growing concern that many published research findings do not hold up in attempts to replicate them. We argue that this problem may originate from a culture of ‘you can publish if you found a significant effect’. This culture creates a systematic bias against the null hypothesis which renders meta‐analyses questionable and may even lead to a situation where hypotheses become difficult to falsify. In order to pinpoint the sources of error and possible solutions, we review current scientific practices with regard to their effect on the probability of drawing a false‐positive conclusion. We explain why the proportion of published false‐positive findings is expected to increase with (i) decreasing sample size, (ii) increasing pursuit of novelty, (iii) various forms of multiple testing and researcher flexibility, and (iv) incorrect P‐values, especially due to unaccounted pseudoreplication, i.e. the non‐independence of data points (clustered data). We provide examples showing how statistical pitfalls and psychological traps lead to conclusions that are biased and unreliable, and we show how these mistakes can be avoided. Ultimately, we hope to contribute to a culture of ‘you can publish if your study is rigorous’. To this end, we highlight promising strategies towards making science more objective. Specifically, we enthusiastically encourage scientists to preregister their studies (including a priori hypotheses and complete analysis plans), to blind observers to treatment groups during data collection and analysis, and unconditionally to report all results. Also, we advocate reallocating some efforts away from seeking novelty and discovery and towards replicating important research findings of one's own and of others for the benefit of the scientific community as a whole. We believe these efforts will be aided by a shift in evaluation criteria away from the current system which values metrics of ‘impact’ almost exclusively and towards a system which explicitly values indices of scientific rigour.     

Remote sensing of ecosystem services: A systematic review

Appropriate integration of remote sensing technologies into ecosystem services concepts and practices leads to potential practical benefits for the protection of biodiversity and the promotion of sustainable use of Earth's natural assets. The last decade has seen the rapid development of research efforts on the topic of ecosystem services, which has led to a significant increase in the number of scientific publications. This systematic review aims to identify, evaluate and synthesise the evidence provided in published peer reviewed studies framing their work in the context of spatially explicit remote sensing assessment and valuation of ecosystem services. Initially, a search through indexed scientific databases found 5920 papers making direct and/or indirect reference to the topic of “ecosystem services” between the years of 1960 and 2013. Among these papers, 211 make direct reference to the use of remote sensing. During the search we aimed at selecting papers that were peer-reviewed publications available through indexed bibliographic databases. For this reason, our literature search did not include books, grey literature, extended abstracts and presentations. We quantitatively present the growth of remote sensing applications in ecosystem services’ research, reviewing the literature to produce a summary of the state of available and feasible remote sensing variables used in the assessment and valuation of ecosystem services. The results provide valuable information on how remotely sensed Earth observation data are used currently to produce spatially-explicit assessments and valuation of ecosystem services. Using examples from the literature we produce a concise summary of what has been done, what can be done and what can be improved upon in the future to integrate remote sensing into ecosystem services research. The reason for doing so is to motivate discussion about methodological challenges, solutions and to encourage an uptake of remote sensing technology and data where it has potential practical applications.     

Synthetic biology and the technicity of biofuels

The principal existing real-world application of synthetic biology is biofuels. Several ‘next generation biofuel’ companies—Synthetic Genomics, Amyris and Joule Unlimited Technologies—claim to be using synthetic biology to make biofuels. The irony of this is that highly advanced science and engineering serves the very mundane and familiar realm of transport. Despite their rather prosaic nature, biofuels could offer an interesting way to highlight the novelty of synthetic biology from several angles at once. Drawing on the French philosopher of technology and biology Gilbert Simondon, we can understand biofuels as technical objects whose genesis involves processes of concretisation that negotiate between heterogeneous geographical, biological, technical, scientific and commercial realities. Simondon’s notion of technicity, the degree of concretisation of a technical object, usefully conceptualises this relationality. Viewed in terms of technicity, we might understand better how technical entities, elements, and ensembles are coming into being in the name of synthetic biology. The broader argument here is that when we seek to identify the newness of disciplines, their newness might be less epistemic and more logistic.     

Genomics in a changing arctic: critical questions await the molecular ecologist

Molecular ecology is poised to tackle a host of interesting questions in the coming years. The Arctic provides a unique and rapidly changing environment with a suite of emerging research needs that can be addressed through genetics and genomics. Here we highlight recent research on boreal and tundra ecosystems and put forth a series of questions related to plant and microbial responses to climate change that can benefit from technologies and analytical approaches contained within the molecular ecologist's toolbox. These questions include understanding (i) the mechanisms of plant acquisition and uptake of N in cold soils, (ii) how these processes are mediated by root traits, (iii) the role played by the plant microbiome in cycling C and nutrients within high‐latitude ecosystems and (iv) plant adaptation to extreme Arctic climates. We highlight how contributions can be made in these areas through studies that target model and nonmodel organisms and emphasize that the sequencing of the Populus and Salix genomes provides a valuable resource for scientific discoveries related to the plant microbiome and plant adaptation in the Arctic. Moreover, there exists an exciting role to play in model development, including incorporating genetic and evolutionary knowledge into ecosystem and Earth System Models. In this regard, the molecular ecologist provides a valuable perspective on plant genetics as a driver for community biodiversity, and how ecological and evolutionary forces govern community dynamics in a rapidly changing climate.     

LitDB - Keeping Track of Research Papers From Your Institute Made Simple

Background

In science peer-reviewed publications serve as an important indicator of scientific excellence and productivity. Therefore, every scientist and institution must carefully maintain and update records of their scientific publications. However, in most institutions and universities articles are often managed in a redundant file-based and non-central way. Whereas excellent reference management software packages such as Zotero, Endnote or Mendeley exist to manage bibliographies and references when writing scientific articles, we are not aware of any open source database solution keeping track of publication records from large scientific groups, entire institutions and/or universities.

Results

We here describe LitDB, a novel open source literature database solution for easy maintenance of publication lists assigned to various topics. In the last 2 years more than 50 users have been using LitDB at our research institute. The LitDB system is accessed via a web browser. Publications can be uploaded through direct exports from reference manager libraries or by entering PubMed IDs. Single users or user groups can track their citation counts, h-index and impact factor statistics and gain insights into the publication records of other users. It offers various visualization functions like coauthor networks and provides ways to organize publications from dedicated projects and user groups. The latter is in particular beneficial to manage publication lists of large research groups and research initiatives through a “crowd-sourcing” effort.

Conclusions

Keeping track of papers authored and published by a research group, institute or university is an important and non-trivial task. By using a centralized web-based platform for publication management such as LitDB the compilation of project- and group-related publication lists becomes easily manageable and it is less likely that papers are forgotten along the way.

     

A closer look at novel climates: new methods and insights at continental to landscape scales

Novel climates – emerging conditions with no analog in the observational record – are an open problem in ecological modeling. Detecting extrapolation into novel conditions is a critical step in evaluating bioclimatic projections of how species and ecosystems will respond to climate change. However, biologically informed novelty detection methods remain elusive for many modeling algorithms. To assist with bioclimatic model design and evaluation, we present a first‐approximation assessment of general novelty based on a simple and consistent characterization of climate. We build on the seminal global analysis of Williams et al. (2007 PNAS, 104, 5738) by assessing of end‐of‐21st‐century novelty for North America at high spatial resolution and by refining their standardized Euclidean distance into an intuitive Mahalanobian metric called sigma dissimilarity. Like this previous study, we found extensive novelty in end‐of‐21st‐century projections for the warm southern margin of the continent as well as the western Arctic. In addition, we detected localized novelty in lower topographic positions at all latitudes: By the end of the 21st century, novel climates are projected to emerge at low elevations in 80% and 99% of ecoregions in the RCP4.5 and RCP8.5 emissions scenarios, respectively. Novel climates are limited to 7% of the continent's area in RCP4.5, but are much more extensive in RCP8.5 (40% of area). These three risk factors for novel climates – regional susceptibility, topographic position, and the magnitude of projected climate change – represent a priori evaluation criteria for the credibility of bioclimatic projections. Our findings indicate that novel climates can emerge in any landscape. Interpreting climatic novelty in the context of nonlinear biological responses to climate is an important challenge for future research.     

Incorporating climate change adaptation into marine protected area planning

Climate change is increasingly impacting marine protected areas (MPAs) and MPA networks, yet adaptation strategies are rarely incorporated into MPA design and management plans according to the primary scientific literature. Here we review the state of knowledge for adapting existing and future MPAs to climate change and synthesize case studies (n = 27) of how marine conservation planning can respond to shifting environmental conditions. First, we derive a generalized conservation planning framework based on five published frameworks that incorporate climate change adaptation to inform MPA design. We then summarize examples from the scientific literature to assess how conservation goals were defined, vulnerability assessments performed and adaptation strategies incorporated into the design and management of existing or new MPAs. Our analysis revealed that 82% of real‐world examples of climate change adaptation in MPA planning derive from tropical reefs, highlighting the need for research in other ecosystems and habitat types. We found contrasting recommendations for adaptation strategies at the planning stage, either focusing only on climate refugia, or aiming for representative protection of areas encompassing the full range of expected climate change impacts. Recommendations for MPA management were more unified and focused on adaptative management approaches. Lastly, we evaluate common barriers to adopting climate change adaptation strategies based on reviewing studies which conducted interviews with MPA managers and other conservation practitioners. This highlights a lack of scientific studies evaluating different adaptation strategies and shortcomings in current governance structures as two major barriers, and we discuss how these could be overcome. Our review provides a comprehensive synthesis of planning frameworks, case studies, adaptation strategies and management actions which can inform a more coordinated global effort to adapt existing and future MPA networks to continued climate change.     

Macrophenology: insights into the broad-scale patterns,drivers, and consequences of phenology

Plant phenology research has surged in recent decades, in part due to interest in phenological sensitivity to climate change and the vital role phenology plays in ecology. Many local-scale studies have generated important findings regarding the physiology, responses, and risks associated with shifts in plant phenology. By comparison, our understanding of regional- and global-scale phenology has been largely limited to remote sensing of green-up without the ability to differentiate among plant species. However, a new generation of analytical tools and data sources—including enhanced remote sensing products, digitized herbarium specimen data, and public participation in science—now permits investigating patterns and drivers of phenology across extensive taxonomic, temporal, and spatial scales, in an emerging field that we call macrophenology. Recent studies have highlighted how phenology affects dynamics at broad scales, including species interactions and ranges, carbon fluxes, and climate. At the cusp of this developing field of study, we review the theoretical and practical advances in four primary areas of plant macrophenology: (1) global patterns and shifts in plant phenology, (2) within-species changes in phenology as they mediate species' range limits and invasions at the regional scale, (3) broad-scale variation in phenology among species leading to ecological mismatches, and (4) interactions between phenology and global ecosystem processes. To stimulate future research, we describe opportunities for macrophenology to address grand challenges in each of these research areas, as well as recently available data sources that enhance and enable macrophenology research.     

Two-Sided Edge Effect Studies and the Restoration of Endangered Ecosystems

Edge effect is the modification of ecological patterns and processes that occur around the edge of two adjacent ecosystems. Depending on their aim, edge effect studies have adopted one of the following methodological approaches: (1) the one‐sided approach—which studies ecological patterns and processes from an edge to the interior of just one of the habitats and (2) the two‐sided approach—which studies ecological patterns and processes across the whole gradient from the interior of one habitat to the interior of the other habitat, passing through the edge zone. A database containing information on 317 published papers revealed that both methodological approaches were equally used until the end of the 1980s. During the 1990s, the question of how organisms respond to habitat destruction and fragmentation led to an abrupt increase in the number of one‐sided studies. Recently, however, two‐sided studies have become more frequent. In this review, we put forth theoretical arguments of why the two‐sided edge effect approach can produce a broader understanding of the ecological processes associated with edges. We highlight that two‐sided edge effect studies must become more experimental and predictive, focusing on the factors controlling edge dynamics. Finally, we point out that two‐sided edge effect studies have the potential to create a positive research agenda for the restoration and expansion of endangered ecosystems.     

Long-Distance Interdisciplinarity Leads to Higher Scientific Impact

Scholarly collaborations across disparate scientific disciplines are challenging. Collaborators are likely to have their offices in another building, attend different conferences, and publish in other venues; they might speak a different scientific language and value an alien scientific culture. This paper presents a detailed analysis of success and failure of interdisciplinary papers—as manifested in the citations they receive. For 9.2 million interdisciplinary research papers published between 2000 and 2012 we show that the majority (69.9%) of co-cited interdisciplinary pairs are “win-win” relationships, i.e., papers that cite them have higher citation impact and there are as few as 3.3% “lose-lose” relationships. Papers citing references from subdisciplines positioned far apart (in the conceptual space of the UCSD map of science) attract the highest relative citation counts. The findings support the assumption that interdisciplinary research is more successful and leads to results greater than the sum of its disciplinary parts.