基于图论的景观图表达、分析及应用

景观结构和空间格局一直是景观生态学的核心问题,图论的应用为景观格局的分析提供了一种研究框架,基于图论的景观图逐渐被应用于生物多样性保护的连通性建模和景观规划的决策支持研究,景观图的表达、分析和应用已成为保护生物学和景观生态学研究的热点。本文首先介绍了景观图的图论基础,在Scopus数据库的基础上,检索了1993—2019年在标题、摘要和关键词中出现 “landscape graph”、“connectivity”和“network”词汇的257篇已发表的期刊论文。从年发文量、来源期刊、研究区域、研究机构、景观类型等方面分析了该领域的研究进展和发展趋势。分析发现,2017年之前,发表的期刊论文数量整体呈上升趋势,2017年之后年发文量逐年下降;主要研究力量集中在美国、西班牙、法国、加拿大和中国,发文量占到86.8%。大部分研究成果发表在“Landscape Ecology”、“Landscape and Urban Planning”和“Biological Conservation”期刊上。在研究内容上,景观图表达主要包括点的定义、边的度量和景观的模拟3方面,景观图分析研究包括分析指数、景观图划分两方面。我们重点关注了景观图在生物多样性保护、景观(生态网络)规划和管理、景观影响评价等科学与实践中的应用。基于图论的景观图通过帮助理解景观连通性变化、动物行为和栖息地保护,影响着保护科学和规划实践者。图论对保护科学和规划的影响来自于丰富的理论基础和成熟的研究方法,基于图论的景观图为景观结构和格局的生态学理解提供了跳板,并将继续成为全球研究人员和实践者的重要工具。     

Replication,Communication, and the Population Dynamics of Scientific Discovery

Many published research results are false (Ioannidis, 2005), and controversy continues over the roles of replication and publication policy in improving the reliability of research. Addressing these problems is frustrated by the lack of a formal framework that jointly represents hypothesis formation, replication, publication bias, and variation in research quality. We develop a mathematical model of scientific discovery that combines all of these elements. This model provides both a dynamic model of research as well as a formal framework for reasoning about the normative structure of science. We show that replication may serve as a ratchet that gradually separates true hypotheses from false, but the same factors that make initial findings unreliable also make replications unreliable. The most important factors in improving the reliability of research are the rate of false positives and the base rate of true hypotheses, and we offer suggestions for addressing each. Our results also bring clarity to verbal debates about the communication of research. Surprisingly, publication bias is not always an obstacle, but instead may have positive impacts—suppression of negative novel findings is often beneficial. We also find that communication of negative replications may aid true discovery even when attempts to replicate have diminished power. The model speaks constructively to ongoing debates about the design and conduct of science, focusing analysis and discussion on precise, internally consistent models, as well as highlighting the importance of population dynamics.     

Mind the gaps when using science to address conservation concerns

Conservation science and conservation action are assumed to have identical goals. However, in reality, there is a strong divide between research and practical conservation that has been mostly discussed with respect to the ‘knowing-doing gap’, i.e. the results from science are not being translated into practical management. In this commentary, we argue that there is not one but there are at least three different types of gaps impeding a positive impact of science on conservation: (1) the knowing-doing gap; (2) the thematic gap that exists between the topics addressed by conservation science and the problems faced in conservation; and (3) the disciplinary gap, i.e. the lack of communication and cooperation between different fields of science, e.g. between fundamental biodiversity research and conservation research. These different gaps have different origins and require different means to be overcome. In a survey, scientists from the field of conservation research (all contributing to this special issue on European grasslands) assessed the importance of these three gaps. They highlight that the disciplinary gap is just as relevant as the knowing-doing gap, while the importance of the thematic gap between practical conservation needs and theoretical conservation science is, in the view of the authors, of less importance. Also, the respondents identified the complexity of academic content in scientific publications as an additional cause for knowing-doing gaps. Based on our survey and various other studies analysing these gaps, we suggest two ways to overcome the gaps: if you consider yourself to be a conservation scientist make sure to address questions of relevance for conservation issues, if you are a scientist interested in fundamental issues, be open to mutual interaction and translation of scientific results with conservation scientists. The knowing-doing gap could be addressed by more readily translating the theoretical findings into practical advice. “Conservation Journals” could, for instance, require a second “Conservation Management Abstract”, which has to be published open-access, and back-to-back with the conventional abstract.     

Biomedical Data Sharing and Reuse: Attitudes and Practices of Clinical and Scientific Research Staff

Background

Significant efforts are underway within the biomedical research community to encourage sharing and reuse of research data in order to enhance research reproducibility and enable scientific discovery. While some technological challenges do exist, many of the barriers to sharing and reuse are social in nature, arising from researchers’ concerns about and attitudes toward sharing their data. In addition, clinical and basic science researchers face their own unique sets of challenges to sharing data within their communities. This study investigates these differences in experiences with and perceptions about sharing data, as well as barriers to sharing among clinical and basic science researchers.

Methods

Clinical and basic science researchers in the Intramural Research Program at the National Institutes of Health were surveyed about their attitudes toward and experiences with sharing and reusing research data. Of 190 respondents to the survey, the 135 respondents who identified themselves as clinical or basic science researchers were included in this analysis. Odds ratio and Fisher’s exact tests were the primary methods to examine potential relationships between variables. Worst-case scenario sensitivity tests were conducted when necessary.

Results and Discussion

While most respondents considered data sharing and reuse important to their work, they generally rated their expertise as low. Sharing data directly with other researchers was common, but most respondents did not have experience with uploading data to a repository. A number of significant differences exist between the attitudes and practices of clinical and basic science researchers, including their motivations for sharing, their reasons for not sharing, and the amount of work required to prepare their data.

Conclusions

Even within the scope of biomedical research, addressing the unique concerns of diverse research communities is important to encouraging researchers to share and reuse data. Efforts at promoting data sharing and reuse should be aimed at solving not only technological problems, but also addressing researchers’ concerns about sharing their data. Given the varied practices of individual researchers and research communities, standardizing data practices like data citation and repository upload could make sharing and reuse easier.     

A conceptual framework for understanding the perspectives on the causes of the science–practice gap in ecology and conservation

Applying scientific knowledge to confront societal challenges is a difficult task, an issue known as the science–practice gap. In Ecology and Conservation, scientific evidence has been seldom used directly to support decision‐making, despite calls for an increasing role of ecological science in developing solutions for a sustainable future. To date, multiple causes of the science–practice gap and diverse approaches to link science and practice in Ecology and Conservation have been proposed. To foster a transparent debate and broaden our understanding of the difficulties of using scientific knowledge, we reviewed the perceived causes of the science–practice gap, aiming to: (i) identify the perspectives of ecologists and conservation scientists on this problem, (ii) evaluate the predominance of these perspectives over time and across journals, and (iii) assess them in light of disciplines studying the role of science in decision‐making. We based our review on 1563 sentences describing causes of the science–practice gap extracted from 122 articles and on discussions with eight scientists on how to classify these sentences. The resulting process‐based framework describes three distinct perspectives on the relevant processes, knowledge and actors in the science–practice interface. The most common perspective assumes only scientific knowledge should support practice, perceiving a one‐way knowledge flow from science to practice and recognizing flaws in knowledge generation, communication, and/or use. The second assumes that both scientists and decision‐makers should contribute to support practice, perceiving a two‐way knowledge flow between science and practice through joint knowledge‐production/integration processes, which, for several reasons, are perceived to occur infrequently. The last perspective was very rare, and assumes scientists should put their results into practice, but they rarely do. Some causes (e.g. cultural differences between scientists and decision‐makers) are shared with other disciplines, while others seem specific to Ecology and Conservation (e.g. inadequate research scales). All identified causes require one of three general types of solutions, depending on whether the causal factor can (e.g. inadequate research questions) or cannot (e.g. scientific uncertainty) be changed, or if misconceptions (e.g. undervaluing abstract knowledge) should be solved. The unchanged predominance of the one‐way perspective over time may be associated with the prestige of evidence‐based conservation and suggests that debates in Ecology and Conservation lag behind trends in other disciplines towards bidirectional views ascribing larger roles to decision‐makers. In turn, the two‐way perspective seems primarily restricted to research traditions historically isolated from mainstream conservation biology. All perspectives represented superficial views of decision‐making by not accounting for limits to human rationality, complexity of decision‐making contexts, fuzzy science–practice boundaries, ambiguity brought about by science, and different types of knowledge use. However, joint knowledge‐production processes from the two‐way perspective can potentially allow for democratic decision‐making processes, explicit discussions of values and multiple types of science use. To broaden our understanding of the interface and foster productive science–practice linkages, we argue for dialogue among different research traditions within Ecology and Conservation, joint knowledge‐production processes between scientists and decision‐makers and interdisciplinarity across Ecology, Conservation and Political Science in both research and education.     

Tribute to Tinbergen: Public Engagement in Ethology

Public engagement in research, called citizen science, has led to advances in a range of fields like astronomy, ornithology, and public health. While volunteers have been making and sharing observations according to protocols set by researchers in numerous disciplines, citizen science practices are less common in the field of animal behavior. We consider how citizen science might be used to address animal behavior questions at Tinbergen's four levels of analysis. We briefly review resources and methods for addressing technical issues surrounding volunteer participation—such as data quality—so that citizen science can make long‐standing contributions to the field of animal behavior.     

Tapping into non-English-language science for the conservation of global biodiversity

The widely held assumption that any important scientific information would be available in English underlies the underuse of non-English-language science across disciplines. However, non-English-language science is expected to bring unique and valuable scientific information, especially in disciplines where the evidence is patchy, and for emergent issues where synthesising available evidence is an urgent challenge. Yet such contribution of non-English-language science to scientific communities and the application of science is rarely quantified. Here, we show that non-English-language studies provide crucial evidence for informing global biodiversity conservation. By screening 419,679 peer-reviewed papers in 16 languages, we identified 1,234 non-English-language studies providing evidence on the effectiveness of biodiversity conservation interventions, compared to 4,412 English-language studies identified with the same criteria. Relevant non-English-language studies are being published at an increasing rate in 6 out of the 12 languages where there were a sufficient number of relevant studies. Incorporating non-English-language studies can expand the geographical coverage (i.e., the number of 2° × 2° grid cells with relevant studies) of English-language evidence by 12% to 25%, especially in biodiverse regions, and taxonomic coverage (i.e., the number of species covered by the relevant studies) by 5% to 32%, although they do tend to be based on less robust study designs. Our results show that synthesising non-English-language studies is key to overcoming the widespread lack of local, context-dependent evidence and facilitating evidence-based conservation globally. We urge wider disciplines to rigorously reassess the untapped potential of non-English-language science in informing decisions to address other global challenges.Please see the Supporting information files for Alternative Language Abstracts.

A survey of 419,680 peer-reviewed papers in 16 languages reveals that non-English-language studies can expand geographical (by 12-25%) and taxonomic (by 5-32%) coverage of English-language evidence on the effectiveness of biodiversity conservation interventions, especially in biodiverse regions.     

A horizon scan of global conservation issues for 2012

Our aim in conducting annual horizon scans is to identify issues that, although currently receiving little attention, may be of increasing importance to the conservation of biological diversity in the future. The 15 issues presented here were identified by a diverse team of 22 experts in horizon scanning, and conservation science and its application. Methods for identifying and refining issues were the same as in two previous annual scans and are widely transferable to other disciplines. The issues highlight potential changes in climate, technology and human behaviour. Examples include warming of the deep sea, increased cultivation of perennial grains, burning of Arctic tundra, and the development of nuclear batteries and hydrokinetic in-stream turbines.     

科技考古研究范式之思考

范式自20世纪60年代创立以来,已普遍使用于多个科学研究领域,并于七八十年代引入至考古学。目前,国内外学界对考古学的研究范式有不少讨论,但对科技考古的研究范式的认知仍属空白。本文在简要介绍科学研究范式和考古学研究范式的基础上,首次提出了科技考古研究的3种范式,即科技范式、考古范式、科技考古融合范式,详细阐述了3种研究范式的理论、方法、实践等。此外,本文还指出：科技范式是推动科技考古研究发展的“发动机”,考古范式是掌控科技考古研究方向的“方向盘”,而科技考古融合范式则是协调科技考古各研究领域的“中控台”,真正让科技与考古融为一体。最后,笔者还对在科技考古研究范式下如何构建研究人员的知识体系提出了一些看法。     

The Use and Abuse of Transcranial Magnetic Stimulation to Modulate Corticospinal Excitability in Humans

The magnitude and direction of reported physiological effects induced using transcranial magnetic stimulation (TMS) to modulate human motor cortical excitability have proven difficult to replicate routinely. We conducted an online survey on the prevalence and possible causes of these reproducibility issues. A total of 153 researchers were identified via their publications and invited to complete an anonymous internet-based survey that asked about their experience trying to reproduce published findings for various TMS protocols. The prevalence of questionable research practices known to contribute to low reproducibility was also determined. We received 47 completed surveys from researchers with an average of 16.4 published papers (95% CI 10.8–22.0) that used TMS to modulate motor cortical excitability. Respondents also had a mean of 4.0 (2.5–5.7) relevant completed studies that would never be published. Across a range of TMS protocols, 45–60% of respondents found similar results to those in the original publications; the other respondents were able to reproduce the original effects only sometimes or not at all. Only 20% of respondents used formal power calculations to determine study sample sizes. Others relied on previously published studies (25%), personal experience (24%) or flexible post-hoc criteria (41%). Approximately 44% of respondents knew researchers who engaged in questionable research practices (range 32–70%), yet only 18% admitted to engaging in them (range 6–38%). These practices included screening subjects to find those that respond in a desired way to a TMS protocol, selectively reporting results and rejecting data based on a gut feeling. In a sample of 56 published papers that were inspected, not a single questionable research practice was reported. Our survey revealed that approximately 50% of researchers are unable to reproduce published TMS effects. Researchers need to start increasing study sample size and eliminating—or at least reporting—questionable research practices in order to make the outcomes of TMS research reproducible.     

两种自然保护区设计方法——数学建模和计算机模拟

传统的自然保护区设计方法是打分法和Gap分析法,这两种方法简单易行但可靠性不高;地理信息系统(GIS)在保护区设计领域的应用也为人熟悉.关注近年来快速发展而国内使用不多的两种方法——数学建模和计算机模拟.数学建模主要用来从一组备选地块中选择一部分组成自然保护区,包括线性和非线性模型,用启发式算法或最优化算法求解.启发式算法具有速度快、灵活等优点,但解通常不是最优的,不能保证稀缺资源的最优化利用.最优化算法运算效率低,变量较多比如数百时就可能遇到计算困难,但解是最优的.预计两种算法都将继续发展.计算机模拟主要用于保护区评价、功能区划分、预测特定环境比如空间特征和气候变化对物种的影响等,多用启发式算法,与其它软件结合把结果以图画显示出来.两种方法特别是计算机模拟均要求保护区设计者有较强的专业知识.讨论了两种方法面临的问题和新的研究方向,至少包括:1)基础数据依然需要完善;2)一些新的因素比如动态性和不确定性如何在模型中考虑并与其它因素结合;3)气候变化预景下模拟参数如何评估和调整;4)如何协调保护与发展的关系;5)方法的实际应用需要研究者与决策者之间建立交流机制;6)多领域专家和相关利益方应有机会参与保护区设计.     

The importance of timing and number of surveys in fungal biodiversity research

Practical conservation of biological diversity is dependent on reliable knowledge about what kind, how much, and where the diversity is. To obtain such knowledge three questions, why, what, and how, must be answered before commencing any biodiversity survey. While the questions why and what are often value decisions and thus determined outside the realm of scientific research, the question about how the surveys are conducted lies in the heart of science. Here, we report an intensive repeated survey of wood-inhabiting fungi with the aim of determining the optimal timing and number of the surveys for reliable estimation of the diversity of this species group. The research focusing on the ecology of wood-inhabiting fungi has been increasing but little is known about the reliability of the methods. The variation in the estimates of diversity among surveys was high and the results varied between studied species groups. The site-scale detectability for species belonging to different groups varied from 10 to 95% depending on the survey month and the species group. We conclude that because detectability of many fungi turned out to be poor even when surveys were conducted at an optimal time, the common practice of using a single fruit body survey to estimate fungal diversity of any given area is not enough. We suggest that multiple surveys at an optimal time should be a norm in fungal diversity studies. Improper methodology results in unreliable outcomes that have potential to hamper our goal of conserving the biological diversity.     

Cross-disciplinary approaches for better research: The case of birds and bats

Across a wide range of disciplines, mounting evidence points to solutions for addressing the global biodiversity and climate crisis through sustainable land use development. Managing ecosystem services offers promising potential of combining environmental, economic, and social interests in this process. Achieving sustainability, however, requires collaboration across disciplines, or in short “cross-disciplinary” approaches. Multi-, inter- and transdisciplinary approaches are often used as synonyms, although they are defined by different levels of integrating results and perspectives. We highlight challenges and opportunities related to these cross-disciplinary approaches by using research on bird- and bat-mediated ecosystem services as a case - with a focus on sustainable agricultural development. Examples from transdisciplinary collaborations show how more integrative and inclusive approaches promote the implementation of basic and applied ecological research into land use practices. Realizing this opportunity requires strong partnerships between science, practice and policy, as well as integration of diverse skills and perspectives. If appropriately funded and guided, this effort is rewarded by improved data quality, more targeted concepts, as well as improvement implementation and impact of sustainability research and practice. We outline a stepwise approach for developing these processes and highlight case studies from bird and bat research to inspire cross-disciplinary approaches within and beyond ecology.     

Translational Research and Youth Development

Borrowing the term “translational research” (TR) from medicine, along with some of the ideas and practices that define it, holds promise as a way of linking research more closely to the practice of youth development. However, doing so entails substantial adaptation. TR is more than a new name for applied research. It comprehends the sequence of very different kinds of research that connect new knowledge with practice and ultimately with enhanced youth development. Research syntheses and evidence-based programs and practices are central to TR, which draws on a variety of research methods and traditions, including epidemiology, “basic” research, evaluation, and implementation science. Syntheses are needed in all these areas along with communication among researchers representing them as well as with practitioners. The flow of information is bi-directional; research is informed by practice and practitioners conduct research.     

Mapping Public Engagement with Research in a UK University

Notwithstanding that ‘public engagement’ is conceptualised differently internationally and in different academic disciplines, higher education institutions largely accept the importance of public engagement with research. However, there is limited evidence on how researchers conceptualise engagement, their views on what constitutes engagement and the communities they would (or would not) like to engage with. This paper presents the results of a survey of researchers in the Open University that sought to gather data to fill these gaps. This research was part of an action research project designed to embed engagement in the routine practices of researchers at all levels. The findings indicate that researchers have a relatively narrow view of public engagement with research and the communities with which they interact. It also identified that very few strategically evaluate their public engagement activities. We conclude by discussing some of the interventions we have introduced with the aim of broadening and deepening future researcher engagement.     

Body-size distributions and size-spectra: universal indicators of ecological status?

The sizes of individual organisms, rather than their taxonomy, are used to inform management and conservation in some aquatic ecosystems. The European Science Foundation Research Network, SIZEMIC, facilitates integration of such approaches with the more taxonomic approaches used in terrestrial ecology. During its 4-year tenure, the Network is bringing together researchers from disciplines including theorists, empiricists, government employees, and practitioners, via a series of meetings, working groups and research visits. The research conducted suggests that organismal size, with a generous helping of taxonomy, provides the most probable route to universal indicators of ecological status.     

The more things changed,the more they stayed the same: Trends in conservation focus 2010–2019

The conservation literature provides an important resource for conservation practice and reflects key areas of current research interest, but not necessarily those of highest priority, in the field of conservation science. In one of the most comprehensive studies of its kind, this paper evaluates 4388 articles from three leading conservation journals with different impact factors (Biological Conservation, Conservation Letters, and Oryx) for the period 2010–2019. The analysis shows that previously identified trends still hold true in many instances, including a continuing taxonomic bias towards vertebrates and particularly in favour of mammals. Geographical biases also persist, favouring Europe and North America with respect to where research is undertaken, who writes about it, and how it is funded, although publication of research conducted in Africa is increasing. It is difficult to evaluate changes in author gender outside the decade studied as this topic has not been widely considered in previous studies, but parity in authorship has not yet been achieved in any of the journals examined. To overcome the biases identified, researchers, editors, and funding organisations collectively still need to do more to redirect conservation efforts where they are most urgently needed and encourage more women and more researchers from lower income countries to participate in research by helping to remove the barriers that currently limit them.     

对青藏高原野生动物保护生物学研究的思考

青藏高原是我国重要的生态屏障区,动物资源丰富,物种独特,是开展野生动物保护生物学研究的天然实验室。尽管青藏高原野生动物保护研究已取得重要成就,但随着科学技术的发展与进步,未来可以在以下3个方面进一步加强。一是坚持高原野生动物种群及栖息地的长期监测;二是利用多学科交叉及宏微观结合的技术与方法开展整合生物学研究;三是进一步加强高原野生动物保护生物学研究青年科技人才的培养。