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。     

华南生态秀河山

文章以作者30年来在华南植物研究所生态学研究的工作与部分成果,反映了中国科学院华南植物研究所30年来生态学科发展的趋势,并以折射广东省生态学会成立30年来生态学科之发展。文章综述认为,华南植物研究所生态科学的发展,与广东省乃至中国生态学学科发展是同步的,经历着由面上研究向定位研究的发展,定性研究向定量研究的发展,野外调查研究向野外实验生态研究的发展,以及中观研究向微观与宏观研究的发展。期间广东省的生态学工作者为学科的发展与社会的进步做出了重要的贡献。     

基于文献计量分析的区域生态安全研究热点与趋势

生态安全是生态学研究的热点议题,近年来国内外对生态安全领域相关研究力度不断增大。文章以WEB OF SCIENCE数据库和中国期刊全文数据库（CNKI）中期刊论文为数据源,从文献计量的角度,利用Excel统计论文年度发文量,通过Bibexcel得到高频词共词矩阵,导入Ucinet和Netdraw得出共现网络可视图,最后利用SPSS对关键词进行聚类分析,以探究区域生态安全研究热点和趋势。研究表明：（1）区域生态安全研究发文数量基本逐年递增,自2012年起进入快速增长阶段。（2）国内外区域生态安全的研究内容具有较大差异。国外更注重在气候变化背景下生态安全与可持续发展的关系研究;国内更加关注生态安全空间规划、生态文明建设等基本理论与生态安全实证检验。（3）共现网络可视中的关键词food safety、environment和climate change与生态安全、生态文明建设和生态保护红线一定程度上成为当前研究的热点。（4）国内外区域生态安全研究对象和研究尺度均存在较大的差异。国外主要以极端贫困国家和发展中国家为研究对象,研究尺度涉及地区、国家甚至全球;国内主要以区域为研究对象,研究尺度集中于中尺度。综上,目前区域生态安全研究的热点是区域生态安全评价及其影响因素、生态文明建设战略和可持续发展研究等,未来生态安全的研究趋势将集中于生态安全空间演变、国际与区际间安全关联和安全对策等。     

区域生态学的国际起源和研究热点

20世纪80年代以来,区域生态学迅速发展,成为生态学领域重要的分支学科。本文综述了区域生态学的国际起源、发展脉络,以及主要研究热点,对比了国内外区域生态学研究的区别以及对国内区域生态学发展的启示。分析表明,在国际上,区域生态学的研究热点主要集中在生物多样性保护、区域气候变化影响、生态系统服务、城市生态学、区域生态修复和可持续发展等方面。由于国情以及学科发展进度不同,国内外区域生态学研究在关注问题、研究思路和研究手段上存在区别。国内区域生态学受学科起步较晚、相关数据的质、量和利用率较低及对方法和模型研究尚浅的影响,未来研究要在深度利用遥感数据的基础上,加强学科理论和方法的学习,重点关注气候变化影响生态过程的机理、生态模型优化、全国生态系统服务评估与定价、区域生态安全以及区域可持续发展规划。     

国内期刊生态学文献计量特征

从文献计量学角度描述学科的发展动态,揭示学科发展规律是新学科发展进程的必要补充.论文以生态学37个分支学科的名称作为关键词,检索和统计了《维普科技期刊数据库》近15年文献.分析认为,国内期刊生态学文献符合指数增长规律,其中六个分支学科的文献所占比例较大,而生态经济、农业生态文献所占比例明显呈逐年下降趋势;文献量较小但增加迅速的学科有五个分支学科;发表文献的作者人数分布呈幂函数关系,发表10篇论文可为高产作者的分界点;发表生态学论文较多的主要机构集中于农林高校、综合性大学和中科院研究所;生态学文献在各种期刊中的分布符合布拉德福定律科学文献的分散与集中的规律.     

旅游生态学研究体系

旅游生态学是一门新兴的应用性交叉学科,学科建立的时间短,学科体系发展有待完善.从学科体系研究入手,从学科的概念、研究领域、研究内容和研究方法等方面来探讨如何构建和完善旅游生态学研究体系.提出了旅游生态系统是旅游生态学研究的核心;旅游生态系统的组成、结构、功能和管理等是旅游生态学学科研究的主要支撑,是旅游生态学的重要研究内容;旅游野外研究方法、空间分析方法、旅游生态评价和旅游生态管理等方法为学科的主要研究方法.     

污染生态化学:现状与展望

随着生态学和环境化学的发展和交叉,形成了一门新的学科－污染生态化学。目前,它的主要研究内容包括化学污染物的迁移转化及其微观生态化学过程、化学污染的生态效应与毒理及生态风险评价、全球变化的生态化学、生态系统中化学污染物的分析与监测和污染控制生态化学等５个方面。在知识创新的科学目标指导下,污染生态化学今后的工作必须加强从理论上进行突破,在对基础研究进行深入的同时,应该特别注意开展一些应用研究,从而实现     

The emergence of ecological engineering as a discipline

Pioneering efforts in ecological engineering (a precedent setting engineering and applied science discipline in which the self-engineering capabilities of ecosystems are managed for the benefit of the environment and humankind) research and practice have proven to be tremendous strides toward establishing a new engineering discipline with a science base in ecology. Case studies, demonstrations and applications pertaining to restoration, rehabilitation, conservation, sustainability, reconstruction, remediation and reclamation of ecosystems using ecological engineering techniques are numerous. This has brought the field to the current level where many scientists and engineers adequately support the concept of, and need for, ecological engineering, and generally agree that ecological engineering has been sufficiently defined. There is also general agreement that full emergence as an engineering discipline remains a difficult task. Certain general characteristics of existing engineering disciplines can guide the emergence of ecological engineering and thus are a vital context covered in this paper. From the context of engineering practice, three concepts are evident including: (1) establishment of formal foundations for ecological engineering research and development; (2) development of core ecological engineering sciences and curricula; and (3) certification in ecological design. These elements are important components of a formal approach to develop ecological engineering as a principled, quantitative, recognized, practical, novel, and formal engineering discipline that coalesces past and future research and practice into cohesive underpinnings.     

Quantitatively Evaluating Restoration Experiments: Research Design, Statistical Analysis, and Data Management Considerations

Conceptual and logistical challenges associated with the design and analysis of ecological restoration experiments are often viewed as being insurmountable, thereby limiting the potential value of restoration experiments as tests of ecological theory. Such research constraints are, however, not unique within the environmental sciences. Numerous natural and anthropogenic disturbances represent unplanned, uncontrollable events that cannot be replicated or studied using traditional experimental approaches and statistical analyses. A broad mix of appropriate research approaches (e.g., long-term studies, large-scale comparative studies, space-for-time substitution, modeling, and focused experimentation) and analytical tools (e.g., observational, spatial, and temporal statistics) are available and required to advance restoration ecology as a scientific discipline. In this article, research design and analytical options are described and assessed in relation to their applicability to restoration ecology. Significant research benefits may be derived from explicitly defining conceptual models and presuppositions, developing multiple working hypotheses, and developing and archiving high-quality data and metadata. Flexibility in research approaches and statistical analyses, high-quality databases, and new sampling approaches that support research at broader spatial and temporal scales are critical for enhancing ecological understanding and supporting further development of restoration ecology as a scientific discipline.     

Clustering more than two million biomedical publications: comparing the accuracies of nine text-based similarity approaches

Background

We investigate the accuracy of different similarity approaches for clustering over two million biomedical documents. Clustering large sets of text documents is important for a variety of information needs and applications such as collection management and navigation, summary and analysis. The few comparisons of clustering results from different similarity approaches have focused on small literature sets and have given conflicting results. Our study was designed to seek a robust answer to the question of which similarity approach would generate the most coherent clusters of a biomedical literature set of over two million documents.

Methodology

We used a corpus of 2.15 million recent (2004-2008) records from MEDLINE, and generated nine different document-document similarity matrices from information extracted from their bibliographic records, including titles, abstracts and subject headings. The nine approaches were comprised of five different analytical techniques with two data sources. The five analytical techniques are cosine similarity using term frequency-inverse document frequency vectors (tf-idf cosine), latent semantic analysis (LSA), topic modeling, and two Poisson-based language models – BM25 and PMRA (PubMed Related Articles). The two data sources were a) MeSH subject headings, and b) words from titles and abstracts. Each similarity matrix was filtered to keep the top-n highest similarities per document and then clustered using a combination of graph layout and average-link clustering. Cluster results from the nine similarity approaches were compared using (1) within-cluster textual coherence based on the Jensen-Shannon divergence, and (2) two concentration measures based on grant-to-article linkages indexed in MEDLINE.

Conclusions

PubMed''s own related article approach (PMRA) generated the most coherent and most concentrated cluster solution of the nine text-based similarity approaches tested, followed closely by the BM25 approach using titles and abstracts. Approaches using only MeSH subject headings were not competitive with those based on titles and abstracts.     

Toward a more expansive conception of ecological science

There are two competing conceptions of the nature and domain of ecological science in the popular and academic literature, an orthodox conception and a more expansive conception. The orthodox conception conceives ecology as a natural biological science distinct from the human social sciences. The more expansive conception views ecology as a science whose domain properly spans both the natural and social sciences. On the more expansive conception, non-traditional ecological disciplines such as ecological psychology, ecological anthropology and ecological economics may legitimately be regarded as sub-disciplines of ecology, and the practitioners of such disciplines as ecologists. The orthodox-expansionist issue is significant both for the practice of ecology and for the self-identity of the philosophy of ecology. I argue in favour of the expansionist conception of ecology on general conceptual grounds, and by developing the case for one particular non-traditional ecological discipline, ecological psychology.     

景观生态学三维格局研究进展

非生物与生物的密切交互造就了多种多样的三维景观格局,景观生态学作为研究格局和生态学过程的学科,其在三维空间的探索随着激光雷达等三维数据提取技术的完善取得了快速进步.三维数据的引入使得研究更贴近真实地表景观,研究结果与相关生态学指标具有更明显的同向趋势.这改善了传统研究缺乏生态学意义的问题.但由于研究背景不同,研究方法和研究结论仍缺乏普适性.另一方面,研究结果对尺度变化的敏感度也因三维数据量的扩大而增加,如何选择并处理适宜尺度的数据使结论更加科学,是未来需要注意并探讨的问题.未来,随着数据获取更加便捷,研究将向长时间多尺度多源数据集成化发展,除动态监测及预测外,结合景观规划设计的可持续规划和生态恢复应用也是重要的研究方向之一.     

pyResearchInsights—An open‐source Python package for scientific text analysis

1. With an increasing number of scientific articles published each year, there is a need to synthesize and obtain insights across ever‐growing volumes of literature. Here, we present pyResearchInsights, a novel open‐source automated content analysis package that can be used to analyze scientific abstracts within a natural language processing framework.
2. The package collects abstracts from scientific repositories, identifies topics of research discussed in these abstracts, and presents interactive concept maps to visualize these research topics. To showcase the utilities of this package, we present two examples, specific to the field of ecology and conservation biology.
3. First, we demonstrate the end‐to‐end functionality of the package by presenting topics of research discussed in 1,131 abstracts pertaining to birds of the Tropical Andes. Our results suggest that a large proportion of avian research in this biodiversity hotspot pertains to species distributions, climate change, and plant ecology.
4. Second, we retrieved and analyzed 22,561 abstracts across eight journals in the field of conservation biology to identify twelve global topics of conservation research. Our analysis shows that conservation policy and landscape ecology are focal topics of research. We further examined how these conservation‐associated research topics varied across five biodiversity hotspots.
5. Lastly, we compared the utilities of this package with existing tools that carry out automated content analysis, and we show that our open‐source package has wider functionality and provides end‐to‐end utilities that seldom exist across other tools.

     

应用生态学的现状与发展

应用生态学可定义为研究协调人类与生物、资源、环境之间关系以达到和谐目的的科学。生态学已成为包含上百个分支的庞大学科, 当前的弱点和存在问题主要是:缺乏科学的严格性、实验技能和应用技术薄弱以及生态学在迅速扩展过程中正失去自身的学科边界。数学和计算机技术在生态学研究和实践中的应用, 生态实验、宏观生态学研究和生态工程技术的研究和发展可能是未来应用生态学研究最活跃的领域。     

A method of inferring the relationship between Biomedical entities through correlation analysis on text

Background

One of the most important processes in a machine learning-based natural language processing is to represent words. The one-hot representation that has been commonly used has a large size of vector and assumes that the features that make up the vector are independent of each other. On the other hand, it is known that word embedding has a great effect in estimating the similarity between words because it expresses the meaning of the word well. In this study, we try to clarify the correlation between various terms in the biomedical texts based on the excellent ability of estimating similarity between words shown by word embedding. Therefore, we used word embedding to find new biomarkers and microorganisms related to a specific diseases.

Methods

In this study, we try to analyze the correlation between diseases-markers and diseases-microorganisms. First, we need to construct a corpus that seems to be related to them. To do this, we extract the titles and abstracts from the biomedical texts on the PubMed site. Second, we express diseases, markers, and microorganisms’ terms in word embedding using Canonical Correlation Analysis (CCA). CCA is a statistical based methodology that has a very good performance on vector dimension reduction. Finally, we tried to estimate the relationship between diseases-markers pairs and diseases-microorganisms pairs by measuring their similarity.

Results

In the experiment, we tried to confirm the correlation derived through word embedding using Google Scholar search results. Of the top 20 highly correlated disease-marker pairs, about 85% of the pairs have actually undergone a lot of research as a result of Google Scholars search. Conversely, for 85% of the 20 pairs with the lowest correlation, we could not actually find any other study to determine the relationship between the disease and the marker. This trend was similar for disease-microbe pairs.

Conclusions

The correlation between diseases and markers and diseases and microorganisms calculated through word embedding reflects actual research trends. If the word-embedding correlation is high, but there are not many published actual studies, additional research can be proposed for the pair.

     

基于文献计量分析的中国乡村生态学研究综述

我国已全面建成了小康社会,新发展阶段对乡村生态环境保护治理提出更高要求,乡村生态振兴既要提升生态环境质量,又要促进农民农村共同富裕的实现。在时代发展需求中,乡村生态学的研究成果不断丰富,概念内涵不断扩展,有必要对过去20年中国乡村生态学研究进行梳理和总结,为美丽乡村建设、自然资源保护、乡村可持续发展提供理论依据。对中国乡村生态学研究进行文献计量和可视化分析,通过绘制可视化知识图谱,梳理了20年以来中国乡村生态学研究的发展脉络,提出人类感知与社会需求的层级递进是推动乡村生态学研究发展的一个主要驱动力;针对乡村生态热点,提出4个方面的研究趋势,即乡村生态环境精细化治理与预警、乡村建设中的生态环境政策和制度、乡村景观规划与乡村生态文化建设和农村生产生活消费绿色化发展与可持续性;最后,围绕需求层级理论和乡村生态系统服务,构建了乡村生态学学科边界框架,强调在多学科交叉的基础上,针对乡村生态研究的多层次多尺度的特征,重点开展乡村生态系统中社会、经济、生态多要素对乡村生态系统的综合作用及其之间相互影响关系的研究。     

对我国分子生态学研究近期发展战略的一些思考

分子生态学是多学科交叉的整合性研究领域, 是运用进化生物学理论解决宏观生物学问题的科学。经过半个多世纪的发展, 本学科已日趋成熟, 它不仅已经广泛渗透到宏观生物学的众多学科领域, 而且已经成为连接和融合很多不同学科的桥梁, 是目前最具活力的研究领域之一。其研究的范畴, 从最基础的理论和方法技术, 到格局和模式的发现和描述, 到对过程和机制的深入探讨, 再到付诸于实践的行动和规划指导等各个层次。分子生态学的兴起给宏观生物学带来了若干飞跃性的变化, 使宏观生物学由传统的以观察、测量和推理为主的描述性研究转变为以从生物和种群的遗传构成的变化和历史演化背景上检验、证明科学假设及揭示机制和规律为主的机制性/解释性研究, 因而使得对具有普遍意义的科学规律、生态和进化过程及机制的探索成为可能。分子生态学已经进入组学研究时代, 这使得阐明复杂生态过程、生物地理过程和适应性演化过程的机制性研究由原来难以企及的梦想变成完全可以实现的探求; 它也带来了全新的挑战, 其中最有深远影响的将是对分子生态学研究至关重要的进化生物学基础理论方面的突破, 例如遗传变异理论、种群分化理论、表观遗传因素的作用, 乃至进化生物学的基本知识构架等等。这些方面的进展必将使宏观生物学迎来一场空前的革命, 并对生态学的所有分支学科产生重大影响, 甚至催生诸如生态表观组学这样的新分支学科。对于中国科学家来说, 分子生态学组学时代的开启, 更是一个千载难逢的机遇, 为提出和建立生命科学的新方法、新假说、新思想和新理论提供了莫大的探索空间——此前我们对宏观生物学方法、理论和思想的发展贡献很小。然而, 限制组学时代重大突破的关键因素是理论、概念、理念、实验方法或分析方法方面的创新和突破, 这正是我国分子生态学研究最薄弱的环节。我国教育部门应尽快调整生命科学本科生培养的理念和方法, 以培养具备突出创新潜力的年轻一代后备人才; 同时, 科研项目资助部门和研究人员不仅应清醒地认识本学科领域的发展态势, 更要及时调整思路, 树立新的项目管理理念和治学 理念。     

Ecological plant epigenetics: Evidence from model and non‐model species,and the way forward

Growing evidence shows that epigenetic mechanisms contribute to complex traits, with implications across many fields of biology. In plant ecology, recent studies have attempted to merge ecological experiments with epigenetic analyses to elucidate the contribution of epigenetics to plant phenotypes, stress responses, adaptation to habitat, and range distributions. While there has been some progress in revealing the role of epigenetics in ecological processes, studies with non‐model species have so far been limited to describing broad patterns based on anonymous markers of DNA methylation. In contrast, studies with model species have benefited from powerful genomic resources, which contribute to a more mechanistic understanding but have limited ecological realism. Understanding the significance of epigenetics for plant ecology requires increased transfer of knowledge and methods from model species research to genomes of evolutionarily divergent species, and examination of responses to complex natural environments at a more mechanistic level. This requires transforming genomics tools specifically for studying non‐model species, which is challenging given the large and often polyploid genomes of plants. Collaboration among molecular geneticists, ecologists and bioinformaticians promises to enhance our understanding of the mutual links between genome function and ecological processes.     

Trends in biological control: public interest,international networking and research direction

We investigated trends in biological control to both capture its evolution and explore future opportunities. We examined recent changes in public interest, international networking and peer-reviewed research. A Google Trends analysis revealed that the popularity of biological control is decreasing in terms of search hits on the internet. This trend is potentially worrying for the biological control community, given that public interest tends to drive political decisions regarding regulatory processes and governmental funding of research. To examine patterns of international collaboration, we established the list of authors who published their work in the three main biological control journals from the early 1990s to 2016. International co-authorship has intensified and the biological control sector is increasingly characterized by multilateral collaboration. We surveyed papers published in BioControl and Biological Control over the last 25 years to identify research trends with respect to target pests, commodities, biological control agents and biological control approaches. Finally, we report that articles on biological control are published in the broad-based scientific journals Science and Nature on a regular basis. This reflects contributions that biological control research makes to scientific discussions in general. Our analyses revealed a thriving scientific discipline with several major research trends in arthropod, plant pathogen and weed biological control.     

A bibliometric analysis of research trends in bat echolocation studies between 1970 and 2021

Bats are among the few mammals that have acquired a sophisticated echolocation ability, attracting considerable attention for their uniqueness. Over the past 50 years, numerous research projects have been designed to study bat echolocation. The overall trend is complex and the dynamics of those publications are difficult to capture. In this study, we conducted quantitative bibliometric analyses of academic articles to identify global research trends in bat echolocation. Data were retrieved from the Web of Science, with 2914 articles sampled in our dataset from 1970 to 2021. We analyzed the global research trends in terms of annual publications, active journals, authors, institutions, and countries. We identified growth trends in the past 50 years, to which the United States was found to be the largest contributor. The University of Bristol, the University of Munich, and the Smithsonian Institute were the representative institutions of publication records. Meanwhile, Acta Chiropterologica, Journal of Experimental Biology, and Journal of the Acoustical Society of America were the top three active platforms for bat echolocation research. Co-occurrence analysis of keywords identified five clusters that correspond to five major research topics in bat echolocation: “habitat use and conservation,” “evolution,” “physiology and nervous system,” “communication and social call,” and “hunting and predation.” The overlay visualization indicated that studies on the evolution of bat echolocation had become the latest research trend, which we summarized and reviewed. Lastly, based on the results obtained, we discussed the importance of future directions for integrative multi-omics studies to uncover the mechanisms and evolution of bat echolocation.