Increasing the power of genome wide association studies in natural populations using repeated measures : evaluation and implementation

1. Genomewide association studies (GWAS) enable detailed dissections of the genetic basis for organisms' ability to adapt to a changing environment. In long-term studies of natural populations, individuals are often marked at one point in their life and then repeatedly recaptured. It is therefore essential that a method for GWAS includes the process of repeated sampling. In a GWAS, the effects of thousands of single-nucleotide polymorphisms (SNPs) need to be fitted and any model development is constrained by the computational requirements. A method is therefore required that can fit a highly hierarchical model and at the same time is computationally fast enough to be useful. 2. Our method fits fixed SNP effects in a linear mixed model that can include both random polygenic effects and permanent environmental effects. In this way, the model can correct for population structure and model repeated measures. The covariance structure of the linear mixed model is first estimated and subsequently used in a generalized least squares setting to fit the SNP effects. The method was evaluated in a simulation study based on observed genotypes from a long-term study of collared flycatchers in Sweden. 3. The method we present here was successful in estimating permanent environmental effects from simulated repeated measures data. Additionally, we found that especially for variable phenotypes having large variation between years, the repeated measurements model has a substantial increase in power compared to a model using average phenotypes as a response. 4. The method is available in the R package RepeatABEL. It increases the power in GWAS having repeated measures, especially for long-term studies of natural populations, and the R implementation is expected to facilitate modelling of longitudinal data for studies of both animal and human populations.

Motivating residents to combat invasive species on private lands: social norms and community reciprocity

Invasive species (IS) threaten biodiversity and ecosystem functioning. To achieve landscape-scale reductions in IS and the associated gains for biodiversity, IS control efforts must be expanded across private lands. Enhancing IS control across private lands requires an understanding of the factors that motivate residents to engage or prohibit residents from engaging in efforts to control IS. Drawing from the collective interest model and literature, we sought to understand how a wide range of interpersonal, intrapersonal, and contextual factors might influence resident action around combating the invasive tree albizia (Falcataria moluccana), in the Puna District of Hawaiʻi. To do so, we used a cross-sectional survey of 243 residents and elastic net regression techniques. We found that residents’ actions related to IS control were related to their perceptions of social norms and community reciprocity regarding albizia control, as well as their knowledge of effective control strategies and their risk perceptions regarding albizia. These findings suggest that, although common intervention approaches that focus on providing education or subsidies are important, they may be more effective at reducing the spread of IS if coupled with approaches that build community reciprocity and norms.

Nature-based solutions to climate change mitigation and adaptation in urban areas: perspectives on indicators, knowledge gaps, barriers, and opportunities for action

Nature-based solutions promoting green and blue urban areas have significant potential to decrease the vulnerability and enhance the resilience of cities in light of climatic change. They can thereby help to mitigate climate change-induced impacts and serve as proactive adaptation options for municipalities. We explore the various contexts in which nature-based solutions are relevant for climate mitigation and adaptation in urban areas, identify indicators for assessing the effectiveness of nature-based solutions and related knowledge gaps. In addition, we explore existing barriers and potential opportunities for increasing the scale and effectiveness of nature-based solution implementation. The results were derived from an inter- and transdisciplinary workshop with experts from research, municipalities, policy, and society. As an outcome of the workshop discussions and building on existing evidence, we highlight three main needs for future science and policy agendas when dealing with nature-based solutions: (i) produce stronger evidence on nature-based solutions for climate change adaptation and mitigation and raise awareness by increasing implementation; (ii) adapt for governance challenges in implementing nature-based solutions by using reflexive approaches, which implies bringing together new networks of society, nature-based solution ambassadors, and practitioners; (iii) consider socio-environmental justice and social cohesion when implementing nature-based solutions by using integrated governance approaches that take into account an integrative and transdisciplinary participation of diverse actors. Taking these needs into account, nature-based solutions can serve as climate mitigation and adaptation tools that produce additional cobenefits for societal well-being, thereby serving as strong investment options for sustainable urban planning.

What happens at the gap between knowledge and practice? Spaces of encounter and misencounter between environmental scientists and local people

Researchers studying processes of global environmental change are increasingly interested in their work having impacts that go beyond academia to influence policy and management. Recent scholarship in the conservation sciences has pointed to the existence of a research-action gap and has proposed various solutions for overcoming it. However, most of these studies have been limited to the spaces of dissemination, where the science has already been done and is then to be passed over to users of the information. Much less attention has been paid to encounters that occur between scientists and nonscientists during the practice of doing scientific research, especially in situations that include everyday roles of labor and styles of communication (i.e., fieldwork). This paper builds on theories of contact that have examined encounters and relations between different groups and cultures in diverse settings. I use quantitative and qualitative evidence from Madidi National Park, Bolivia, including an analysis of past research in the protected area, as well as interviews (N = 137) and workshops and focus groups (N = 12) with local inhabitants, scientists, and park guards. The study demonstrates the significance of currently unacknowledged or undervalued components of the research-action gap, such as power, respect, and recognition, to develop a relational and reciprocal notion of impact. I explain why, within such spaces of encounter or misencounter between scientists and local people, knowledge can be exchanged or hidden away, worldviews can be expanded or further entrenched, and scientific research can be welcomed or rejected.

Setting priorities for private land conservation in fire-prone landscapes: Are fire risk reduction and biodiversity conservation competing or compatible objectives?

Although wildfire plays an important role in maintaining biodiversity in many ecosystems, fire management to protect human assets is often carried out by different agencies than those tasked for conserving biodiversity. In fact, fire risk reduction and biodiversity conservation are often viewed as competing objectives. Here we explored the role of management through private land conservation and asked whether we could identify private land acquisition strategies that fulfill the mutual objectives of biodiversity conservation and fire risk reduction, or whether the maximization of one objective comes at a detriment to the other. Using a fixed budget and number of homes slated for development, we simulated 20 years of housing growth under alternative conservation selection strategies, and then projected the mean risk of fires destroying structures and the area and configuration of important habitat types in San Diego County, California, USA. We found clear differences in both fire risk projections and biodiversity impacts based on the way conservation lands are prioritized for selection, but these differences were split between two distinct groupings. If no conservation lands were purchased, or if purchases were prioritized based on cost or likelihood of development, both the projected fire risk and biodiversity impacts were much higher than if conservation lands were purchased in areas with high fire hazard or high species richness. Thus, conserving land focused on either of the two objectives resulted in nearly equivalent mutual benefits for both. These benefits not only resulted from preventing development in sensitive areas, but they were also due to the different housing patterns and arrangements that occurred as development was displaced from those areas. Although biodiversity conflicts may still arise using other fire management strategies, this study shows that mutual objectives can be attained through land-use planning in this region. These results likely generalize to any place where high species richness overlaps with hazardous wildland vegetation.

The politics of negotiation and implementation: a reciprocal water access agreement in the Himalayan foothills, India

In this paper, we examine the on-the-ground realities of upstream-downstream negotiations and transactions over ecosystem services. We explore the engagement, negotiation, implementation, and postimplementation phases of a “reciprocal water access” (RWA) agreement between village communities and municipal water users at Palampur, Himachal Pradesh, India. We aim to highlight how external actors drove the payments for ecosystem services agenda through a series of facilitation and research engagements, which were pivotal to the RWA’s adoption, and how the agreement fared once external agents withdrew. In the postimplementation period, the RWA agreement continues to be upheld by upstream communities amidst evolving, competing land-use changes and claims. The introduction of cash payments for environmental services for forest-water relationships has given rise to multifaceted difficulties for the upstream hamlets, which has impeded the functionality of their forest management committee. Upstream communities’ formal rights and abilities to control and manage their resources are dynamic and need strengthening and assurance; these developments result in fluctuating transaction and opportunity costs not originally envisaged by the RWA agreement. The paper demonstrates the importance of an explicit understanding of the local politics of negotiation and implementation to determine the effectiveness of compensation-based mechanisms for the supply of ecosystem services.

Resident perceptions of natural resources between cities and across scales in the Pacific Northwest

As the global population becomes increasingly urban, research is needed to explore how local culture, land use, and policy will influence urban natural resource management. We used a broad-scale comparative approach and survey of residents within the Portland (Oregon)-Vancouver (Washington) metropolitan areas, USA, two states with similar geographical and ecological characteristics, but different approaches to land-use planning, to explore resident perceptions about natural resources at three scales of analysis: property level (“at or near my house”), neighborhood (“within a 20-minute walk from my house”), and metro level (“across the metro area”). At the metro-level scale, nonmetric multidimensional scaling revealed that the two cities were quite similar. However, affinity for particular landscape characteristics existed within each city with the greatest difference generally at the property-level scale. Portland respondents expressed affinity for large mature trees, tree-lined streets, public transportation, and proximity to stores and services. Vancouver respondents expressed affinity for plentiful accessible parking. We suggest three explanations that likely are not mutually exclusive. First, respondents are segmented based on preferences for particular amenities, such as convenience versus commuter needs. Second, historical land-use and tax policy legacies may influence individual decisions. Third, more environmentally attuned worldviews may influence an individual’s desire to produce environmentally friendly outcomes. Our findings highlight the importance of acknowledging variations in residents’ affinities for landscape characteristics across different scales and locations because these differences may influence future land-use policies about urban natural resources.

Global environmental change: local perceptions, understandings, and explanations

Global environmental change (GEC) is an increasingly discussed phenomenon in the scientific literature as evidence of its presence and impacts continues to grow. Yet, while the documentation of GEC is becoming more readily available, local perceptions of GEC— particularly in small-scale societies—and preferences about how to deal with it, are still largely overlooked. Local knowledge and perceptions of GEC are important in that agents make decisions (including on natural resource management) based on individual perceptions. We carried out a systematic literature review that aims to provide an exhaustive state-of-the-art of the degree to and manner in which the study of local perceptions of change are being addressed in GEC research. We reviewed 126 articles found in peer-reviewed journals (between 1998 and 2014) that address local perceptions of GEC. We used three particular lenses of analysis that are known to influence local perceptions, namely (i) cognition, (ii) culture and knowledge, and (iii) possibilities for adaptation.We present our findings on the geographical distribution of the current research, the most common changes reported, perceived drivers and impacts of change, and local explanations and evaluations of change and impacts. Overall, we found the studies to be geographically biased, lacking methodological reporting, mostly theory based with little primary data, and lacking of indepth analysis of the psychological and ontological influences in perception and implications for adaptation. We provide recommendations for future GEC research and propose the development of a “meta-language” around adaptation, perception, and mediation to encourage a greater appreciation and understanding of the diversity around these phenomena across multiple scales, and improved codesign and facilitation of locally relevant adaptation and mitigation strategies.

Trust, confidence, and equity affect the legitimacy of natural resource governance

Social-ecological systems are often highly complex, making effective governance a considerable challenge. In large, heterogeneous systems, hierarchical institutional regimes may be efficient, but effective management outcomes are dependent on stakeholder support. This support is shaped by perceptions of legitimacy, which risks being undermined where resource users are not engaged in decision-making. Although legitimacy is demonstrably critical for effective governance, less is known about the factors contributing to stakeholders’ perceptions of legitimacy or how these perceptions are socially differentiated. We quantitatively assessed stakeholder perceptions of legitimacy (indicated by support for rules) and their contributory factors among 307 commercial fishers and tourism operators in Australia’s Great Barrier Reef Marine Park. Legitimacy was most strongly associated with trust in information from governing bodies, followed by confidence in institutional performance and the equity of management outcomes. Legitimacy differed both within and among resource user groups, which emphasizes the heterogeneous nature of commonly defined stakeholder groups. Overall, tourism operators perceived higher legitimacy than did commercial fishers, which was associated with higher trust in information from management agencies. For fishers, higher levels of trust were associated with: (1) engagement in fisheries that had high subsector cohesion and positive previous experiences of interactions with governing bodies; (2) location in areas with greater proximity to sources of knowledge, resources, and decision-making; and (3) engagement in a Reef Guardian program. These findings highlight the necessity of strategies and processes to build trust among all user groups in large social-ecological systems such as the Great Barrier Reef Marine Park. Furthermore, the social differentiation of perceptions that were observed within user groups underscores the importance of targeted strategies to engage groups that may not be heard through traditional governance channels.

Addressing surprise and uncertain futures in marine science, marine governance, and society

On an increasingly populated planet, with decreasing biodiversity and limited new opportunities to tap unexploited natural resources, there is a clear need to adjust aspects of marine management and governance. Although sectarian management has succeeded in addressing and managing some important threats to marine ecosystems, unintended consequences are often associated with overlooking nonlinear interactions and cumulative impacts that increase the risk of surprises in social-ecological systems. In this paper, we begin to untangle science-governance-society (SGS) interdependencies in marine systems by considering how to recognize the risk of surprise in social and ecological dynamics. Equally important is drawing attention to our state of preparedness, adaptation, and timeliness of response in ecosystem governance and society, which involve fostering transformations away from rigid and nonintegrated structures of governance. More inclusive decision-making processes, deeper understanding of complexity, and colearning across SGS can help to build constructive solutions that are likely to benefit multiple stakeholders and build capacity to understand and respond to change.

Changes in biodiversity and trade-offs among ecosystem services, stakeholders, and components of well-being: the contribution of the International Long-Term Ecological Research network (ILTER) to Programme on Ecosystem Change and Society (PECS)

The International Long-Term Ecological Research (ILTER) network comprises > 600 scientific groups conducting site-based research within 40 countries. Its mission includes improving the understanding of global ecosystems and informs solutions to current and future environmental problems at the global scales. The ILTER network covers a wide range of social-ecological conditions and is aligned with the Programme on Ecosystem Change and Society (PECS) goals and approach. Our aim is to examine and develop the conceptual basis for proposed collaboration between ILTER and PECS. We describe how a coordinated effort of several contrasting LTER site-based research groups contributes to the understanding of how policies and technologies drive either toward or away from the sustainable delivery of ecosystem services. This effort is based on three tenets: transdisciplinary research; cross-scale interactions and subsequent dynamics; and an ecological stewardship orientation. The overarching goal is to design management practices taking into account trade-offs between using and conserving ecosystems toward more sustainable solutions. To that end, we propose a conceptual approach linking ecosystem integrity, ecosystem services, and stakeholder well-being, and as a way to analyze trade-offs among ecosystem services inherent in diverse management options. We also outline our methodological approach that includes: (i) monitoring and synthesis activities following spatial and temporal trends and changes on each site and by documenting cross-scale interactions; (ii) developing analytical tools for integration; (iii) promoting trans-site comparison; and (iv) developing conceptual tools to design adequate policies and management interventions to deal with trade-offs. Finally, we highlight the heterogeneity in the social-ecological setting encountered in a subset of 15 ILTER sites. These study cases are diverse enough to provide a broad cross-section of contrasting ecosystems with different policy and management drivers of ecosystem conversion; distinct trends of biodiversity change; different stakeholders’ preferences for ecosystem services; and diverse components of well-being issues.

Farmers’ knowledge and use of soil fauna in agriculture: a worldwide review

General knowledge of the small, invisible, or hidden organisms that make soil one of the most biodiverse habitats on Earth is thought to be scarce, despite their importance in food systems and agricultural production. We provide the first worldwide review of high-quality research that reports on farmers’ knowledge of soil organisms in agriculture. The depth of farmers’ knowledge varied; some farming communities held detailed local taxonomies and observations of soil biota, or used soil biological activity as indicators of soil fertility, while others were largely unaware of soil fauna. Elicitation of soil biota knowledge was often incidental to the main research goal in many of the reviewed studies. Farmers are rarely deliberately or deeply consulted by researchers on their existing knowledge of soil biota, soil ecology, or soil ecological processes. Deeper understanding of how farmers use and value soil life can lead to more effective development of collaborative extension programs, policies, and management initiatives directed at maintaining healthy, living soils.

The challenges of integrating biodiversity and ecosystem services monitoring and evaluation at a landscape-scale wetland restoration project in the UK

There is an increasing emphasis on the restoration of ecosystem services as well as of biodiversity, especially where restoration projects are planned at a landscape scale. This increase in the diversity of restoration aims has a number of conceptual and practical implications for the way that restoration projects are monitored and evaluated. Landscape-scale projects require monitoring of not only ecosystem services and biodiversity but also of ecosystem processes since these can underpin both. Using the experiences gained at a landscape-scale wetland restoration project in the UK, we discuss a number of issues that need to be considered, including the choice of metrics for monitoring ecosystem services and the difficulties of assessing the interactions between ecosystem processes, biodiversity, and ecosystem services. Particular challenges that we identify, using two pilot data sets, include the decoupling of monetary metrics used for monitoring ecosystem services from biophysical change on the ground and the wide range of factors external to a project that influence the monitoring results. We highlight the fact that the wide range of metrics necessary to evaluate the ecosystem service, ecosystem process, and biodiversity outcomes of landscape-scale projects presents a number of practical challenges, including the need for high levels of varied expertise, high costs, incommensurate monitoring outputs, and the need for careful management of monitoring results, especially where they may be used in making decisions about the relative importance of project aims.

Integrated science and art education for creative climate change communication

An interdisciplinary field trip to a remote marine lab joined graduate students from fine arts and natural resource science departments to think creatively about the topic of climate change and science communication. We followed a learning cycle framework to allow the students to explore marine ecosystems and participate in scientific lectures, group discussions, and an artist-led project making abstract collages representing climate change processes. Students subsequently worked in small groups to develop environmental communication material for public visitors. We assessed the learning activity and the communication product using pre- and post-field trip participant surveys, focus group discussions, and critiques by art and communication experts of the products. Significant changes in knowledge about climate change occurred in program participants. Incorporating artists and the arts into this activity helped engage multiple senses and emphasized social interaction, as well as providing support to participants to think creatively. The production of art helped to encourage peer learning and normalize the different views among participants in communicating about climate change impacts. Students created effective communication products based on external reviews. Disciplinary differences in cultures, language, and standards challenged participating faculty, yet unanticipated outcomes such as potentially transformative learning and improved teacher evaluations resulted.

The “social” aspect of social-ecological systems: a critique of analytical frameworks and findings from a multisite study of coastal sustainability

We evaluate whether society can adequately be conceptualized as a component of social-ecological systems, given social theory and the current outputs of systems-based research. A mounting critique from the social sciences posits that resilience theory has undertheorized social entities with the concept of social-ecological systems. We trace the way that use of the term has evolved, relating to social science theory. Scientometic and network analysis provide a wide range of empirical data about the origin, growth, and use of this term in academic literature. A content analysis of papers in Ecology and Society demonstrates a marked emphasis in research on institutions, economic incentives, land use, population, social networks, and social learning. These findings are supported by a review of systems science in 18 coastal assessments. This reveals that a systems-based conceptualization tends to limit the kinds of social science research favoring quantitative couplings of social and ecological components and downplaying interpretive traditions of social research. However, the concept of social-ecological systems remains relevant because of the central insights concerning the dynamic coupling between humans and the environment, and its salient critique about the need for multidisciplinary approaches to solve real world problems, drawing on heuristic devices. The findings of this study should lead to more circumspection about whether a systems approach warrants such claims to comprehensiveness. Further methodological advances are required for interdisciplinarity. Yet there is evidence that systems approaches remain highly productive and useful for considering certain social components such as land use and hybrid ecological networks. We clarify advantages and restrictions of utilizing such a concept, and propose a reformulation that supports engagement with wider traditions of research in the social sciences.