生物多样性与稳定性机制研究进展

随着全球生物多样性的迅速丧失,生物多样性与生态系统稳定性的关系已成为人类面临的重要科学问题。许多研究表明生物多样性与稳定性存在正相互关系,但其内在机制尚不能被很好地理解并且存在争议。对生物多样性与稳定性的研究历史做简短的回顾,然后根据时间稳定性的计算方法将时间稳定性分为平均值、方差之和以及协方差之和3个统计组成部分,在此基础上对现在常见的生物多样性-稳定性机制进行分类和详细介绍。并对现在生物多样性和稳定研究的争论进行总结。建议未来生物多样性稳定性关系的研究应该建立更加综合的理论,增加实验时间,应用整合分析(meta-analysis)对已发表实验结果进行综合分析,此外,应多关注非生物量/多度的属性,控制物种属性而不是仅仅控制物种的数量。     

生物多样性研究及其问题

围绕生物多样性主要有3个理论问题需要进一步深入研究,（1）生物多样性与生态系统稳定性的关系：本世纪70年代以前,生态学家普遍认为,稳定性随生物多样性增加而提高;自70年代初一些理论生态学家向这一普遍看法提出挑战以来,在物种多样性层次出现了观点截然不同的两大阵营;（2）生物多样性和土地生产力的关系：达尔文（1872）的研究表明,生物多样性有利于土地生产力的提高,这一结论已被许多国家运用于指导农业实践;然而,本世纪70年代以来,一些生态学家向达尔文的这一观点提出了异议;（3）生物多样性与景观连通性：本世纪90年代以来,一些景观生态学家认为,景观连通性与生物多样性有正相关关系,但目前为数不多的研究还不能肯定这一结论的正确性。通过总结生物多样性的研究历史,发现,以上的急诊和结论基于27种不同的分析模型;并且这些模型中的大多数在理论上是不完善的,认为,运用理论上合理的模型、有关概念的统一正确定义和全面系统的实验对以上急诊和结论进行更进一步的论证与实证是必要的。     

A Natural View of Microbial Biodiversity within Hot Spring Cyanobacterial Mat Communities

This review summarizes a decade of research in which we have used molecular methods, in conjunction with more traditional approaches, to study hot spring cyanobacterial mats as models for understanding principles of microbial community ecology. Molecular methods reveal that the composition of these communities is grossly oversimplified by microscopic and cultivation methods. For example, none of 31 unique 16S rRNA sequences detected in the Octopus Spring mat, Yellowstone National Park, matches that of any prokaryote previously cultivated from geothermal systems; 11 are contributed by genetically diverse cyanobacteria, even though a single cyanobacterial species was suspected based on morphologic and culture analysis. By studying the basis for the incongruity between culture and molecular samplings of community composition, we are beginning to cultivate isolates whose 16S rRNA sequences are readily detected. By placing the genetic diversity detected in context with the well-defined natural environmental gradients typical of hot spring mat systems, the relationship between gene and species diversity is clarified and ecological patterns of species occurrence emerge. By combining these ecological patterns with the evolutionary patterns inherently revealed by phylogenetic analysis of gene sequence data, we find that it may be possible to understand microbial biodiversity within these systems by using principles similar to those developed by evolutionary ecologists to understand biodiversity of larger species. We hope that such an approach guides microbial ecologists to a more realistic and predictive understanding of microbial species occurrence and responsiveness in both natural and disturbed habitats.     

Assessing the functional implications of soil biodiversity in ecosystems

Soil communities are among the most species-rich components of terrestrial ecosystems. A major challenge for soil ecologists is to formulate feasible research strategies that will preserve and capitalize on the biodiversity resources of the soil. This article considers the role of soil organism diversity by concentrating on: (i) the relationship between soil biodiversity and ecosystem function; (ii) what issues need to be explored; (iii) studies carried out in the Ecotron controlled environment facility; and (iv) how stable isotope techniques can improve our understanding of the relationship between soil biodiversity and ecosystem function. It is advocated that: (i) the objective of any soil biodiversity study should always be the generation of general concepts, rather than local, system-specific observations; and (ii) any empirical study can be properly interpreted only within a quantitative ecological framework.     

Use of indigenous ecological knowledge of the Maasai pastoralists for assessing rangeland biodiversity in Tanzania

This paper incorporates the indigenous ecological knowledge (IEK) of the Maasai pastoralists and ecological methods to assess effects of grazing and cropping on rangeland biodiversity at macro‐ and micro‐landscape scales in northern Tanzania. The joint surveys with pastoralists identified indicator plant species and their associations with micro‐landscapes and livestock grazing suitability (i.e. for cattle and small ruminant grazing), while traditional calf‐pasture reserves (alalili pl. alalilia) were evaluated for preservation of rangeland biodiversity. The macro‐landscapes comprising the cool high plateau (osupuko pl. isipuki) and montane forest highland (endim) were included in the survey. At micro‐landscape scales, the osupuko was classified into uplands (orkung'u), slopes (andamata) and dry valley bottomlands (ayarata). The micro‐landscapes were assessed in terms of herbaceous plant species and woody species richness and risks of soil erosion. Biodiversity varied at both the macro‐ and micro‐landscape scales and in accordance with the land‐use types. Greater plant species diversity and less erosion risks were found in the pastoral landscapes than in the agro‐pastoral landscapes. The calf‐grazing pastures had greater herbaceous species richness than the non‐calf pastures, which in turn had more woody species. The study concludes that the indigenous systems of landscape classification provides a valuable basis for assessing rangeland biodiversity, which ecologists should incorporate into ecological surveys of the rangelands in East Africa in the future.     

景观遗传学：概念与方法

全球变化下的物种栖息地丧失和破碎化给生物多样性保护带来了新的问题和挑战,生物多样性保护必须由单纯的物种保护上升到栖息地景观的保护。景观遗传学是定量确定栖息地景观特征对种群遗传结构影响的一门交叉学科,在生物保护及自然保护区管理方面有巨大的潜力。从生物多样性保护的角度评述了景观结构与遗传多样性的关系,介绍了景观遗传学的基本概念,研究尺度和方法,并对景观遗传学当前的研究焦点及面临的挑战做了总结。     

Integrating the statistical analysis of spatial data in ecology

In many areas of ecology there is an increasing emphasis on spatial relationships. Often ecologists are interested in new ways of analyzing data with the objective of quantifying spatial patterns, and in designing surveys and experiments in light of the recognition that there may be underlying spatial pattern in biotic responses. In doing so, ecologists have adopted a number of widely different techniques and approaches derived from different schools of thought, and from other scientific disciplines. While the adaptation of a diverse array of statistical approaches and methodologies for the analysis of spatial data has yielded considerable insight into various ecological problems, this diversity of approaches has sometimes impeded communication and retarded more rapid progress in this emergent area. Many of these different statistical methods provide similar information about spatial characteristics, but the differences among these methods make it difficult to compare the results of studies that employ contrasting approaches. The papers in this mini-series explore possible areas of agreement and synthesis between a diversity of approaches to spatial analysis in ecology.     

The Neutral—Niche Debate: A Philosophical Perspective

Ecological communities around the world are under threat while a consensus theory of community structure remains elusive. In the last decade ecologists have struggled with two seemingly opposing theories: niche-based theory that explains diversity with species’ differences and the neutral theory of biodiversity that claims that much of the diversity we observe can be explained without explicitly invoking species’ differences. Although ecologists are increasingly attempting to reconcile these two theories, there is still much resistance against the neutral theory of biodiversity. Here we argue that the dispute between the two theories is a classic example of the dichotomy between philosophical perspectives, realism and instrumentalism. Realism is associated with specific, small-scale and detailed explanations, whereas instrumentalism is linked to general, large-scale, but less precise accounts. Recognizing this will help ecologists get both niche-based and neutral theories in perspective as useful tools for understanding biodiversity patterns.     

Evaluating Tropical Biodiversity: Do We Need a More Refined Approach?

The exceptional biodiversity of tropical forests inspired the earliest ecologists such as H. W. Bates. Today we still strive to quantify and understand this diversity. Drawing on our own experience of Mamirauá reserve in Amazonas, which is located in an area that Bates explored, we argue that the emphasis of research in tropical ecosystems should shift away from species richness as an end in itself, and focus instead on other fundamental, but more tractable, questions that will increase our ecological understanding of these systems, support conservation management, and appeal to policy makers and society in general.     

Vegetation structure derived from airborne laser scanning to assess species distribution and habitat suitability: The way forward

Ecosystem structure, especially vertical vegetation structure, is one of the six essential biodiversity variable classes and is an important aspect of habitat heterogeneity, affecting species distributions and diversity by providing shelter, foraging, and nesting sites. Point clouds from airborne laser scanning (ALS) can be used to derive such detailed information on vegetation structure. However, public agencies usually only provide digital elevation models, which do not provide information on vertical vegetation structure. Calculating vertical structure variables from ALS point clouds requires extensive data processing and remote sensing skills that most ecologists do not have. However, such information on vegetation structure is extremely valuable for many analyses of habitat use and species distribution. We here propose 10 variables that should be easily accessible to researchers and stakeholders through national data portals. In addition, we argue for a consistent selection of variables and their systematic testing, which would allow for continuous improvement of such a list to keep it up-to-date with the latest evidence. This initiative is particularly needed not only to advance ecological and biodiversity research by providing valuable open datasets but also to guide potential users in the face of increasing availability of global vegetation structure products.     

Renewal ecology: conservation for the Anthropocene

The global scale and rapidity of environmental change is challenging ecologists to reimagine their theoretical principles and management practices. Increasingly, historical ecological conditions are inadequate targets for restoration ecology, geographically circumscribed nature reserves are incapable of protecting all biodiversity, and the precautionary principle applied to management interventions no longer ensures avoidance of ecological harm. In addition, human responses to global environmental changes, such as migration, building of protective infrastructures, and land use change, are having their own negative environmental impacts. We use examples from wildlands, urban, and degraded environments, as well as marine and freshwater ecosystems, to show that human adaptation responses to rapid ecological change can be explicitly designed to benefit biodiversity. This approach, which we call “renewal ecology,” is based on acceptance that environmental change will have transformative effects on coupled human and natural systems and recognizes the need to harmonize biodiversity with human infrastructure, for the benefit of both.     

Through the Jungle of Biological Diversity

Biological diversity would apparently seem the most intuitive and easily studied of all the ecological concepts. However, in practice biodiversity has suffered from great number of definitions that vary with the specific needs of the different researchers, thus making it extremely confusing as an ecological concept. In this paper, I shortly review the concept of biodiversity showing that there exists a substantial ambiguity among ecologists as far as biodiversity conceptualization and evaluation is concerned. I conclude that, due to this major disagreement on its very nature, biodiversity may be defined simply as a set of multivariate summary statistics for quantifying different characteristics of community structure.     

Old and new challenges in using species diversity for assessing biodiversity

Although the maintenance of diversity of living systems is critical for ecosystem functioning, the accelerating pace of global change is threatening its preservation. Standardized methods for biodiversity assessment and monitoring are needed. Species diversity is one of the most widely adopted metrics for assessing patterns and processes of biodiversity, at both ecological and biogeographic scales. However, those perspectives differ because of the types of data that can be feasibly collected, resulting in differences in the questions that can be addressed. Despite a theoretical consensus on diversity metrics, standardized methods for its measurement are lacking, especially at the scales needed to monitor biodiversity for conservation and management purposes. We review the conceptual framework for species diversity, examine common metrics, and explore their use for biodiversity conservation and management. Key differences in diversity measures at ecological and biogeographic scales are the completeness of species lists and the ability to include information on species abundances. We analyse the major pitfalls and problems with quantitative measurement of species diversity, look at the use of weighting measures by phylogenetic distance, discuss potential solutions and propose a research agenda to solve the major existing problems.     

The composite insect trap: an innovative combination trap for biologically diverse sampling

Documentation of insect diversity is an important component of the study of biodiversity, community dynamics, and global change. Accurate identification of insects usually requires catching individuals for close inspection. However, because insects are so diverse, most trapping methods are specifically tailored to a particular taxonomic group. For scientists interested in the broadest possible spectrum of insect taxa, whether for long term monitoring of an ecosystem or for a species inventory, the use of several different trapping methods is usually necessary. We describe a novel composite method for capturing a diverse spectrum of insect taxa. The Composite Insect Trap incorporates elements from four different existing trapping methods: the cone trap, malaise trap, pan trap, and flight intercept trap. It is affordable, resistant, easy to assemble and disassemble, and collects a wide variety of insect taxa. Here we describe the design, construction, and effectiveness of the Composite Insect Trap tested during a study of insect diversity. The trap catches a broad array of insects and can eliminate the need to use multiple trap types in biodiversity studies. We propose that the Composite Insect Trap is a useful addition to the trapping methods currently available to ecologists and will be extremely effective for monitoring community level dynamics, biodiversity assessment, and conservation and restoration work. In addition, the Composite Insect Trap will be of use to other insect specialists, such as taxonomists, that are interested in describing the insect taxa in a given area.     

Assessing macroinvertebrate biodiversity in freshwater ecosystems: advances and challenges in DNA-based approaches

Assessing the biodiversity of macroinvertebrate fauna in freshwater ecosystems is an essential component of both basic ecological inquiry and applied ecological assessments. Aspects of taxonomic diversity and composition in freshwater communities are widely used to quantify water quality and measure the efficacy of remediation and restoration efforts. The accuracy and precision of biodiversity assessments based on standard morphological identifications are often limited by taxonomic resolution and sample size. Morphologically based identifications are laborious and costly, significantly constraining the sample sizes that can be processed. We suggest that the development of an assay platform based on DNA signatures will increase the precision and ease of quantifying biodiversity in freshwater ecosystems. Advances in this area will be particularly relevant for benthic and planktonic invertebrates, which are often monitored by regulatory agencies. Adopting a genetic assessment platform will alleviate some of the current limitations to biodiversity assessment strategies. We discuss the benefits and challenges associated with DNA-based assessments and the methods that are currently available. As recent advances in microarray and next-generation sequencing technologies will facilitate a transition to DNA-based assessment approaches, future research efforts should focus on methods for data collection, assay platform development, establishing linkages between DNA signatures and well-resolved taxonomies, and bioinformatics.     

Looking to the past to understand the future of tropical conservation: The importance of collecting basic data

Tropical biodiversity is under threat from a wide variety of anthropogenic stressors. Understanding the effect of major stressors—most notably land use change, over‐harvesting, emergence of novel pathogens, and climate change—is a major goal of tropical biology. However, to do so requires baseline data with which to compare present‐day patterns. Unfortunately, the tropics suffer from a lack of basic historical data; the few studies which have published such data have proven invaluable. In 1989, Fauth et al. described their studies of reptile and amphibian diversity and population demographics across tropical elevational gradients in Costa Rica. Since then, Fauth et al.'s basic ecological data have been widely used to document shifting patterns of species composition and abundance. Here, 30 years later, we argue that (a) collecting foundational ecological data remains incredibly important, especially in the tropics, and especially in those taxa which are generally understudied (e.g., reptiles and amphibians), (b) despite being one of the original goals of the 1989 study, the mechanisms driving biogeographical patterns of diversity remain unclear (both in the tropics and globally), and (c) that revisiting sites of historic biodiversity surveys—particularly those along gradients of environmental change—is incredibly important to our understanding of how tropical diversity is currently, and will continue to be, affected by activities in the Anthropocene. In its simplest terms, there has never been a time where the collection of basic data in the tropics has ever been more important.     

淡水鱼类功能多样性及其研究方法

目前,群落功能多样性备受生态学界关注,被认为是能解决生态问题的一种重要途径。我国对于群落功能多样性主要集中在植物群落和微生物群落,而在鱼类群落方面的研究几乎是空白。我国鱼类资源正面临着严重威胁,包括水坝建设导致的鱼类通道受阻、水库形成造成鱼类产卵场功能消失、过度捕捞、水质恶化和富营养化加重、外来种入侵等因素,导致渔业资源急剧衰退,水生生态系统功能下降。以淡水鱼类群落为例,对鱼类功能多样性的数据获取及处理分析与评价、测定指标及计算方法与研究难点等进行综述,以期为鱼类资源保护提供新的理论依据和切入点。     

In search of a functional flora—towards a greater integration of ecology and taxonomy

Large-scale biodiversity informatics projects will not properly address the needs of one important potential user group. Ecologists do not have ready access to datasets which allow them to assign plant species to functional types. We believe that information technology has developed sufficiently to allow taxonomists and ecologists to work together to address this need and develop specimen databases to combine taxonomic data with ecological and ecophysiological information so that this information will be assigned to the correct taxon in the future. Digital images provide a rapid and economical method of vouchering specimen data, reducing the need to store physical vouchers in herbaria.     

模拟植物多样性的大尺度分布：从气候和生产力推知的一种可能性（英文）

 鉴于全球植被/生物群区在现状气候条件下已经被很好地模拟并在未来气候变化情景下得到很好的预测,人们有必要和急需模拟大尺度（区域、洲际至全球）植物多样性的分布格局。陆地生物圈模型的发展（从生物地理模型和生物地球化学模型到动态和耦合的植被模型）,气候-生物多样性相互关系和生产力-生物多样性相互关系研究成果的增多,以及基于现有生物多样性调查的全球生物多样性理论和经验制图的进步,加大了模拟大尺度植物多样性格局的可能性。本文的目的是：综述当前气候-生物多样性相互关系和生产力-生物多样性相互关系的主要研究成果以及大尺度     

Bayesian data analysis in population ecology: motivations,methods, and benefits

During the 20th century ecologists largely relied on the frequentist system of inference for the analysis of their data. However, in the past few decades ecologists have become increasingly interested in the use of Bayesian methods of data analysis. In this article I provide guidance to ecologists who would like to decide whether Bayesian methods can be used to improve their conclusions and predictions. I begin by providing a concise summary of Bayesian methods of analysis, including a comparison of differences between Bayesian and frequentist approaches to inference when using hierarchical models. Next I provide a list of problems where Bayesian methods of analysis may arguably be preferred over frequentist methods. These problems are usually encountered in analyses based on hierarchical models of data. I describe the essentials required for applying modern methods of Bayesian computation, and I use real-world examples to illustrate these methods. I conclude by summarizing what I perceive to be the main strengths and weaknesses of using Bayesian methods to solve ecological inference problems.