Biogeography and ecology: two views of one world

Both biogeography and ecology seek to understand the processes that determine patterns in nature, but do so at different spatial and temporal scales. The two disciplines were not always so different, and are recently converging again at regional spatial scales and broad temporal scales. In order to avoid confusion and to hasten progress at the converging margins of each discipline, the following papers were presented at a symposium in the International Biogeography Society''s 2011 meeting, and are now published in this issue of the Philosophical Transactions of the Royal Society B. In a novel approach, groups of authors were paired to represent biogeographic and ecological perspectives on each of four topics: niche, comparative ecology and macroecology, community assembly, and diversity. Collectively, this compilation identifies points of agreement and disagreement between the two views on these central topics, and points to future research directions that may build on agreements and reconcile differences. We conclude this compilation with an overview on the integration of biogeography and ecology.     

Theoretical models for branch formation in plants

Various branch architectures are observed in living organisms including plants. Branch formation has traditionally been an area of interest in the field of developmental biology, and theoretical approaches are now commonly used to understand the complex mechanisms involved. In this review article, we provide an overview of theoretical approaches including mathematical models and computer simulations for studying plant branch formation. These approaches cover a wide range of topics. In particular, we focus on the importance of positional information in branch formation, which has been especially revealed by theoretical research in plants including computations of developmental processes.

     

Report on the 12th symposium on invertebrate neurobiology held 31 August–4 September 2011 at the Balaton Limnological Research Institute of the Hungarian Academy of Sciences, Tihany, Hungary

In August 2011, the 12th international symposium of ISIN was held by Lake Balaton in Tihany, Hungary. This convivial and stimulating meeting provided a forum for discussion of a range of invertebrate organisms in neuroscience research. Here the main topics covered at the meeting are reviewed.     

Using Moment Equations to Understand Stochastically Driven Spatial Pattern Formation in Ecological Systems

Spatial patterns in biological populations and the effect of spatial patterns on ecological interactions are central topics in mathematical ecology. Various approaches to modeling have been developed to enable us to understand spatial patterns ranging from plant distributions to plankton aggregation. We present a new approach to modeling spatial interactions by deriving approximations for the time evolution of the moments (mean and spatial covariance) of ensembles of distributions of organisms; the analysis is made possible by “moment closure,” neglecting higher-order spatial structure in the population. We use the growth and competition of plants in an explicitly spatial environment as a starting point for exploring the properties of second-order moment equations and comparing them to realizations of spatial stochastic models. We find that for a wide range of effective neighborhood sizes (each plant interacting with several to dozens of neighbors), the mean-covariance model provides a useful and analytically tractable approximation to the stochastic spatial model, and combines useful features of stochastic models and traditional reaction-diffusion-like models.     

栖息地破碎化与鸟类生存

栖息地破碎化给野生动物带来的不良后果是全球生态学家和保护生物学家共同关心的问题.自从提出栖息地破碎化是导致生物多样性丧失的关键因素之一的论点后,近20年来,栖息地破碎化研究一直是生态学和保护生物学最活跃的前沿研究领域之一.栖息地破碎化是一动态过程,可在多尺度上发生并蕴涵着复杂的空间模式变化.栖息地破碎化对鸟类的生态学效应主要体现在面积效应、隔离效应和边缘效应等.这些效应影响着鸟类的分布、基因交流、种群动态、扩散行为、种间关系和生活史特征等,最终影响着鸟类的生存.介绍和总结了栖息地破碎化过程、研究的理论依据及栖息地破碎化对鸟类生存产生的诸多影响.     

拟南芥中MATE基因家族的研究进展

多药和有毒化合物排出家族（Multidrug and Toxic Compound Extrusion, MATE）是一个新的次级转运蛋白家族,此类转运蛋白对氨基葡糖、阳离子染料、多种抗生素和药物有转运作用。拟南芥中的MATE基因家族是一个多基因家族,大概由56个成员构成,本文综述了拟南芥中MATE家族基因的研究进展,包括3个方面：第一是拟南芥中MATE家族成员的构成及主要特征;第二描述了转运蛋白的主要功能;第三分析了其功能多样的大致原因。此外,还展望了此家族研究的一些前景。     

Rethinking complexity: modelling spatiotemporal dynamics in ecology

In the past few years, part of theoretical ecology has focused on the spatiotemporal dynamics generated by simple ecological models. To a large extent, the results obtained have changed our view of complexity. Specifically, simple rules are able to produce complex spatiotemporal patterns. Consequently, some of the complexity underlying nature does not necessarily have complex causes. The emerging framework has far-reaching implications in ecology and evolution. This is improving our understanding of topics such as the problem of scales, the response to habitat fragmentation, the relationship between chaos and extinction, and how high diversity levels are supported in nature.     

Idealized, Inaccurate but Successful: A Pragmatic Approach to Evaluating Models in Theoretical Ecology

Ecologists attempt to understand the diversity of life with mathematical models. Often, mathematical models contain simplifying idealizations designed to cope with the blooming, buzzing confusion of the natural world. This strategy frequently issues in models whose predictions are inaccurate. Critics of theoretical ecology argue that only predictively accurate models are successful and contribute to the applied work of conservation biologists. Hence, they think that much of the mathematical work of ecologists is poor science. Against this view, I argue that model building is successful even when models are predictively inaccurate for at least three reasons: models allow scientists to explore the possible behaviors of ecological systems; models give scientists simplified means by which they can investigate more complex systems by determining how the more complex system deviates from the simpler model; and models give scientists conceptual frameworks through which they can conduct experiments and fieldwork. Critics often mistake the purposes of model building, and once we recognize this, we can see their complaints are unjustified. Even though models in ecology are not always accurate in their assumptions and predictions, they still contribute to successful science.     

基于模型的景观格局与生态过程研究

景观格局与生态过程关系的研究是景观生态学的主要特色和理论核心之一。模型可以充分利用实验和观测数据并综合不同时间和空间尺度上的信息提炼规律或揭示内在机制,模拟景观格局与生态过程的动态与相互关系,成为景观生态学研究的有力工具。结合研究实例,总结了基于模型的景观格局研究、生态过程研究和格局-过程关系研究的发展现状和薄弱环节,同时探讨了通过构建耦合模型研究格局-过程相互关系的途径。总结了景观模型研究亟待发展的领域与发展趋势。     

Assignment methods: matching biological questions with appropriate techniques

Assignment methods, which use genetic information to ascertain population membership of individuals or groups of individuals, have been used in recent years to study a wide range of evolutionary and ecological processes. In applied studies, the first step of articulating the biological question(s) to be addressed should be followed by selection of the method(s) best suited for the analysis. However, this first step often receives less attention than it should, and the recent proliferation of assignment methods has made the selection step challenging. Here, we review assignment methods and discuss how to match the appropriate methods with the underlying biological questions for several common problems in ecology and conservation (assessing population structure; measuring dispersal and hybridization; and forensics and mixture analysis). We also identify several topics for future research that should ensure that this field remains dynamic and productive.     

What Do We Study in Evolutionary Ethnobiology? Defining the Theoretical Basis for a Research Program

Many scientific fields investigate the relationship between humans and nature from different perspectives and with a wide range of questions. These fields include, for example, human ecology, human behavioral ecology, and evolutionary psychology, and they are linked through the fact that they all adopt ecological and/or evolutionary hypotheses to understand this phenomenon. In this paper, we define for the first time the field of evolutionary ethnobiology, which seeks to understand these relationships in a broad perspective, considering an interdisciplinary program that integrates the advances, tools, and insights from different scientific fields. This theoretical and methodological integration is necessary for the formation of theoretical bases in ethnobiology and in other areas that investigate the relationship between humans and nature.     

生态学中的尺度及尺度转换方法

尺度作为生态学的重要范式,已经引起了广泛重视,但对尺度问题的研究还不够成熟.尺度具有多维性特点,即功能尺度、空间尺度、时间尺度等,但生态学研究的重点是空间和时间尺度.并且时空尺度还具有复杂性、变异性特征.尺度研究的根本目的在于通过适宜的空间和时间尺度来揭示和把握复杂的生态学规律.为此,科学有效的尺度选择和尺度转换方法不可或缺.常见的尺度转换方法有图示法、回归分析、变异函数、自相关分析、谱分析、分形和小波变换,同时遥感和地理信息系统技术在尺度研究中也发挥着重要作用.结合实例对上述方法进行了分析和论述,认为各种方法都有其内在的优势和不足,新方法的引入和应用对于尺度转换方法体系的充实和完善非常重要.有关尺度的研究将进一步加强,研究的重点是尺度变异性、不同尺度间的相互作用机制以及尺度转换方法等.     

Repair or regenerate—how can we tip the balance?

The fourth EMBO conference on ‘The Molecular and Cellular Basis of Regeneration and Repair’, held in September 2012, brought together researchers from both the regeneration and wound‐healing fields. The meeting spanned a wide range of research topics from basic science to clinical application, and a veritable melting pot of model organisms and approaches resulted in an excellent fourth conference in this series.     

整体大于部分之和: 生态自组织斑图及其涌现属性

近30年来, 自组织理论已经发展成为解释生态系统呈现规则空间格局的有效理论。伴随着生态系统自发有序空间格局的生成, 自组织过程产生一系列的涌现属性, 这些特征对生态系统功能至关重要。在此, 我们将介绍这一正蓬勃发展的研究领域的主要理论进展。首先, 叙述了自组织这一概念的发展历程与定义, 详细阐述了自组织理论的两个经典理论框架: 图灵原理与相分离原理。然后, 根据几个典型的生态自组织研究案例, 描述了图灵原理与相分离原理在不同生态系统中的具体数学模型表达形式。接着, 分别阐述了图灵原理的涌现属性对生态系统功能以及相分离原理的涌现属性对细胞功能的作用。最后, 从多尺度自组织斑图、瞬态斑图和生物个体行为自组织3个方面对未来生态自组织理论发展方向进行了探讨。自组织研究在生态学与生物学研究中方兴未艾, 希望更多的学者在未来关注与参与该领域的发展。     

Environmental marginality and geographic range limits: a case study with Arabidopsis lyrata ssp. lyrata

Understanding the factors that govern the distribution of species is a central goal of evolutionary ecology. It is commonly assumed that geographic range limits reflect ecological niche limits and that species experience increasingly marginal conditions towards the edge of their ranges. Using spatial data and ecological niche models we tested these hypotheses in Arabidopsis lyrata. Specifically, we asked whether range limits coincide with predicted niche limits in this system and whether the suitability of sites declines towards the edge of the species’ range in North America. We further explored patterns of environmental change towards the edge of the range and asked whether genome‐wide patterns of genetic diversity decline with increasing peripherality and environmental marginality. Our results suggest that latitudinal range limits coincide with niche limits. Populations experienced increasingly marginal environments towards these limits – though patterns of environmental change were more complex than most theoretical models for range limits assume. Genomic diversity declined towards the edge of the species’ range and with increasing distance from the estimated centre of the species’ niche in environmental space, but not with the suitability of sites based on niche model predictions. Thus while latitudinal range limits in this system are broadly associated with niche limits, the link between environmental conditions and genetic diversity (and thus the adaptive potential of populations) is less clear.     

2009年第五届“现代生态学讲座”国际会议综述

"现代生态学讲座"系列会议是由国内外华人生态学家联合发起、为加强现代生态学的新理论、新观点、新方法和热点问题的交流与合作的国际会议.总结了2009年6月27～29日在兰州大学举行的第五届现代生态学讲座国际会议的全部二十五场报告,围绕"宏观生态学和可持续发展科学"的会议主题,分别从森林生态学、草地生态学、全球变化生态学、根际和土壤生态学、分子和行为生态学以及农业生态学等角度进行了分类总结.全部报告可归纳为"生态系统服务功能的物质基础"和"生态系统服务的生态学机制"两个大的基础理论问题,而解决问题的途径必须在人类-自然耦合生态系统的大框架下进行探索.对该会议的进一步改善提出了一些建议.     

景观格局与生态过程的耦合研究:传承与创新

景观格局与生态过程的耦合关系是景观生态学研究的核心主题,耦合研究的范围和程度需要进一步系统梳理。从景观格局与生态过程耦合的内涵、方法等方面,系统总结了当前两者研究的特点以及存在问题。进一步从格局-过程耦合基本理论传承与提升、研究方法现代化和多元化、研究尺度多样化、研究对象的扩展与集成、自然-人文-社会视角的耦合、格局-过程耦合的管理和调控等六个方面展望了未来学科发展方向。最后,提出了未来创新目标,如提高景观格局量化的准确性和针对性、辨明景观格局影响的尺度性、增强生态过程模拟的时效性等。     

中国园林生态学发展综述

运用文献计量等方法对已有科研成果进行统计分析,结果表明:中国近50年园林生态学科领域科研发展经过了起步探索(1962-1981)、缓慢发展(1982-2001)、快速发展(2002-2011)3个时期,园林生态学作为生态学一个新的分支学科,于20世纪90年代末初见端倪,作为一门新兴独立的应用生态学分支学科于21世纪初已基本形成.中国园林生态学领域的研究包括园林生态系统中生物与环境相互作用关系问题、人与环境相互作用关系问题以及园林生态系统与其他生态系统之间相互作用关系问题.当代园林生态研究主要有生态效益研究、生物与环境研究、人的需求与行为研究、生态规划与生态管理研究4个方面,目前园林生态学研究主要侧重生物与环境研究和生态效益研究,两方面的研究成果占总体研究成果的76.3％.不同研究方面也有各自的侧重点,如生物与环境研究侧重对植物的研究,生态效益研究侧重净化环境、水土保持和防灾减灾,生态规划与生态管理研究则侧重生态规划与设计.对四个研究方面的论文主题词检索和高频主题关键词的分布进行统计,结果显示,研究的热点有多样性、群落、水土保持、防灾避险、净化环境、生态规划与设计等.对CNKI中4个研究方面成果中获基金资助项目论文进行统计(不排重),总体成果中基金项目论文所占比重为10.8％,国家和地方基金是园林生态学科研基金资助的主要来源,基金论文比例之和达到85.4％,且国家和地方基金资助论文较多的是“生态与环境研究”和“生态效益研究”,合计占基金论文79.1％.SCI-E中收录的文献基金论文率为47.1％,是CNKI数据库收录的文献基金论文率的4.3倍,且国际基金是基金论文的主要资助来源之一,说明中国园林生态学领域部分科研成果得到国际学界关注.基于CNKI相关主题词统计,“园林生态学”的研究成果只有“景观生态学”的1％,“城市生态学”的8.3％,“园林生态学”学科系统理论研究在相关生态学科研究中所占比重很低,其理论和方法研究还较薄弱.今后在进一步完善学科理论体系、持续开展生态效益和园林植物研究的同时,为更好地研究和解决人-自然复合生态系统问题,提供更多的科学理论支撑,还需拓展交叉生态心理学或环境心理学等其他相关理论,更多地关注人与环境互相作用关系以及生态规划与生态管理等方面的研究,既使环境更好地满足人的行为需求,也使人认识到改变一些行为能更好地保护环境.