Biodiversity loss and the taxonomic bottleneck: emerging biodiversity science

Human domination of the Earth has resulted in dramatic changes to global and local patterns of biodiversity. Biodiversity is critical to human sustainability because it drives the ecosystem services that provide the core of our life-support system. As we, the human species, are the primary factor leading to the decline in biodiversity, we need detailed information about the biodiversity and species composition of specific locations in order to understand how different species contribute to ecosystem services and how humans can sustainably conserve and manage biodiversity. Taxonomy and ecology, two fundamental sciences that generate the knowledge about biodiversity, are associated with a number of limitations that prevent them from providing the information needed to fully understand the relevance of biodiversity in its entirety for human sustainability: (1) biodiversity conservation strategies that tend to be overly focused on research and policy on a global scale with little impact on local biodiversity; (2) the small knowledge base of extant global biodiversity; (3) a lack of much-needed site-specific data on the species composition of communities in human-dominated landscapes, which hinders ecosystem management and biodiversity conservation; (4) biodiversity studies with a lack of taxonomic precision; (5) a lack of taxonomic expertise and trained taxonomists; (6) a taxonomic bottleneck in biodiversity inventory and assessment; and (7) neglect of taxonomic resources and a lack of taxonomic service infrastructure for biodiversity science. These limitations are directly related to contemporary trends in research, conservation strategies, environmental stewardship, environmental education, sustainable development, and local site-specific conservation. Today’s biological knowledge is built on the known global biodiversity, which represents barely 20% of what is currently extant (commonly accepted estimate of 10 million species) on planet Earth. Much remains unexplored and unknown, particularly in hotspots regions of Africa, South Eastern Asia, and South and Central America, including many developing or underdeveloped countries, where localized biodiversity is scarcely studied or described. "Backyard biodiversity", defined as local biodiversity near human habitation, refers to the natural resources and capital for ecosystem services at the grassroots level, which urgently needs to be explored, documented, and conserved as it is the backbone of sustainable economic development in these countries. Beginning with early identification and documentation of local flora and fauna, taxonomy has documented global biodiversity and natural history based on the collection of "backyard biodiversity" specimens worldwide. However, this branch of science suffered a continuous decline in the latter half of the twentieth century, and has now reached a point of potential demise. At present there are very few professional taxonomists and trained local parataxonomists worldwide, while the need for, and demands on, taxonomic services by conservation and resource management communities are rapidly increasing. Systematic collections, the material basis of biodiversity information, have been neglected and abandoned, particularly at institutions of higher learning. Considering the rapid increase in the human population and urbanization, human sustainability requires new conceptual and practical approaches to refocusing and energizing the study of the biodiversity that is the core of natural resources for sustainable development and biotic capital for sustaining our life-support system. In this paper we aim to document and extrapolate the essence of biodiversity, discuss the state and nature of taxonomic demise, the trends of recent biodiversity studies, and suggest reasonable approaches to a biodiversity science to facilitate the expansion of global biodiversity knowledge and to create useful data on backyard biodiversity worldwide towards human sustainability.     

生物多样性国际研究态势分析

生物多样性研究是综合性和高度交叉性的跨学科研究领域,是1997年底Science周刊上预测的1998年及近期的6个重大科学热点之一。检索1986—2008年间SCIE文献数据库中关于生物多样性的研究论文(article,proceedings paper和review),利用Thomson Data Analyzer(TDA)分析工具和Aureka分析平台进行数据挖掘。分析表明,该研究涉及多个学科领域,近年来在生态学领域的论文数量增加最多,而生物多样性保护、进化生物学、生物化学与分子生物学方面的论文增长速度较快。生物多样性研究越来越重视全球变化和人类社会对生物多样性的影响,DNA技术和基因工程等先进技术在生物多样性研究和保护中的作用也更加突出。     

High-school students in university research labs? Implementing an outreach model based on the ‘science as inquiry’ approach

In this study we designed, implemented, and evaluated an outreach programme for high-school biology students rooted in the ‘science as inquiry’ approach. Accordingly, students learn about science from experts in the field, as well as through in-class exposure to the history and philosophy of science. Our sample consisted of 11th graders (n?=?497), ages 16–17, attending advanced biology classes. Our goal was to determine whether this programme had a significant effect on students’ understanding of the ‘nature of science’ (NOS) and on their attitudes towards science. Using a controlled pre-post research design, we asked participants to complete a Likert-like questionnaire. Also, we conducted post-programme semi-structured interviews with 35 of the participants. Results show that completion of the programme significantly enhanced participants’ NOS understanding and improved their attitudes towards science. Participants expressed a deep level of NOS understanding and explicitly stated that the field visits to experts’ labs had changed their attitude towards science. We believe that our outreach programme can be adapted for teaching other sciences and for societies worldwide, as long as there is access to university laboratories and researchers willing to interact with young citizens and potential future scientists.     

Biodiversity amongst microorganisms and its relevance

Concluding remarks from the joint IUBS/IUMS workshop on Biodiversity amongst microorganisms and its relevance held in Amsterdam on 7–8 September 1991. An international microbial ecology programme can be justified in its own right now that appropriate investigative tools have been developed. Microorganisms influence global change, and indicate global health and environmental quality. At the same time, an inventory of the world's microbial species and their properties is required, together with associated culture collections and genomes. Sampling methods need to be standardized, both for species and functions. Extreme environments are a particularly rich source of microbial genomes, and endangered habitats should be sampled as a matter of priority. Cataloguing and conserving the world's microbial biodiversity is justifiable and scientifically important.     

生物多样性信息学研究进展

生物多样性信息学是一门蓬勃发展的新学科。它将现代的信息技术带入生物多样性及其相关学科的研究领域。它在生物多样性基础数据的数字化、模型工具和各种工具软件的开发、数据整合, 以及全球、地区和国家尺度生物多样性信息网络等多个方面的发展, 向我们展示了未来在全球范围内自由、免费共享生物多样性数据和信息, 以及人们行动起来共同关注、调查与监测野外生物多样性的前景。目前, 已有大量数字化的物种编目、标本馆标本、多媒体影像、研究文献等生物多样性基础信息可以通过互联网检索和利用。其中, 最值得关注的是一些成功的国际性研究项目, 如物种2000、全球生物多样性信息网络、生命条形码以及网络生命大百科全书。这些项目的成功不仅体现在对大量基础信息和数据的发布, 而且它们通过与生物多样性信息标准TDWG(Biodiversity Information Standards: TDWG)的合作, 推动了达尔文核心标准(Darwin Core)等一些重要的生物多样性信息标准的应用, 以及地区和国家性生物多样性信息节点的建立, 这些都为将来全球范围生物多样性信息的共享和数据交换奠定了重要基础。在数字化信息的基础上, 研究人员也开发了一些在特定研究领域应用的数据挖掘和模型工具, 例如基于数字化标本的地理分布预测工具MAXENT, 分类学专家知识管理的LifeDesk。公民科学理念的发展则向我们展示了公众和科学爱好者广泛参与以互联网为基础的生物多样性信息学研究活动。因此, 生物多样性信息学的发展前景广阔, 它将为我们实现全球保护战略目标, 应对生物多样性危机, 解决全球气候变化条件下生物多样性资源管理和利用建立坚实的信息基础。     

Ecology and urban planning

Urban areas harbour diverse nature ranging from semi-natural habitats to wastelands, parks and other highly human-influenced biotopes with their associated species assemblages. Maintenance of this urban biodiversity for the residents and for its intrinsic value in the face of increasing population and expanding cities requires that ecological knowledge should be better integrated into urban planning. To achieve this goal understanding of ecological patterns and processes in urban ecosystems is needed. The first step in the necessary urban ecological research is to find out what kind of nature exists in cities. Second, knowledge about ecological processes important in urban nature is required. Although ecological processes in cities are the same as in rural areas, some of them, such as invasion by alien species, are more prevalent in urban than in rural conditions. Third, based on ecological knowledge, management schemes maintaining the diversity of urban nature should be designed. These procedures should also include protection of urban nature, e.g. in urban national parks. Finally, as ecology alone cannot provide the complex information about human influence on urban ecosystems, interdisciplinary research involving natural and social sciences is imperative for a holistic approach to integrating ecology into the process of urban planning.     

Beyond Paradise—Meeting the Challenges in Tropical Biology in the 21st Century

Tropical ecosystems support a diversity of species and ecological processes that are unparalleled anywhere else on Earth. Despite their tremendous social and scientific importance, tropical ecosystems are rapidly disappearing. To usher tropical ecosystems and the human communities dependent upon them through the environmental transformations of the 21st century, tropical biologists must provide critical knowledge in three areas: 1) the structure and function of tropical ecosystems; 2) the nature and magnitude of anthropogenic effects on tropical ecosystems; and 3) the socio‐economic drivers of these anthropogenic effects. To develop effective strategies for conservation, restoration, and sustainable management of tropical ecosystems, scientific perspectives must be integrated with social necessities. A new set of principles built on a framework for pursuing relevant tropical biological research will facilitate interdisciplinary approaches, integrate biological knowledge with the social sciences, and link science with policy. We propose four broad recommendations for immediate action in tropical biology and conservation that are fundamental to all biological and social disciplines in the tropics: 1) assemble and disseminate information on life's diversity in the tropics; 2) enhance tropical field stations and build a worldwide network to link them with tropical field biologists at their field sites; 3) bring the field of tropical biology to the tropics by strengthening institutions in tropical countries through novel partnerships between tropical and temperate zone institutions and scientists; and 4) create concrete mechanisms to increase interactions between tropical biologists, social scientists, and policy makers.     

A pervasive denigration of natural history misconstrues how biodiversity inventories and taxonomy underpin scientific knowledge

Embracing comparative biology, natural history encompasses those sciences that discover, decipher and classify unique (idiographic) details of landscapes, and extinct and extant biodiversity. Intrinsic to these multifarious roles in expanding and consolidating research and knowledge, natural history endows keystone support to the veracity of law-like (nomothetic) generalizations in science. What science knows about the natural world is governed by an inherent function of idiographic discovery; characteristic of natural history, this relationship is exemplified wherever an idiographic discovery overturns established wisdom. This nature of natural history explicates why inventories are of such epistemological importance. Unfortunately, a Denigration of Natural History weakens contemporary science from within. It expresses in the prevalent, pervasive failure to appreciate this pivotal role of idiographic research: a widespread disrespect for how natural history undergirds scientific knowledge. Symptoms of this Denigration of Natural History present in negative impacts on scientific research and knowledge. One symptom is the failure to appreciate and support the inventory and monitoring of biodiversity. Another resides in failures of scientiometrics to quantify how taxonomic publications sustain and improve knowledge. Their relevance in contemporary science characteristically persists and grows; so the temporal eminence of these idiographic publications extends over decades. This is because they propagate a succession of derived scientific statements, findings and/or conclusions - inherently shorter-lived, nomothetic publications. Widespread neglect of natural science collections is equally pernicious, allied with disregard for epistemological functions of specimens, whose preservation maintains the veracity of knowledge. Last, but not least, the decline in taxonomic expertise weakens research capacity; there are insufficient skills to study organismal diversity in all of its intricacies. Beyond weakening research capacities and outputs across comparative biology, this Denigration of Natural History impacts on the integrity of knowledge itself, undermining progress and pedagogy throughout science. Unprecedented advances in knowledge are set to follow on consummate inventories of biodiversity, including the protists. These opportunities challenge us to survey biodiversity representatively—detailing the natural history of species. Research strategies cannot continue to ignore arguments for such an unprecedented investment in idiographic natural history. Idiographic shortcuts to general (nomothetic) insights simply do not exist. The biodiversity sciences face a stark choice. No matter how charismatic its portrayed species, an incomplete ‘Brochure of Life’ cannot match the scientific integrity of the ‘Encyclopedia of Life’.     

从文献计量角度分析中国生物多样性研究现状

以汤森路透科技集团的WEB OF KNOWLEDGE信息平台提供的Science Citation Index Expanded数据库为数据源,检索到从1997年至2009年期间国际生物多样性研究论文文献219773篇,其中11182篇来自于中国学者。利用NoteExpress软件,对这13a间生物多样性研究论文发表的国家分布、年度分布、研究机构、引用情况、期刊分布和学科分类等做的分析与比较表明:1)全球生物多样性研究的论文数量一直呈增长趋势,中国13年间每年发文量占当年全球生物多样性论文总量的百分率逐年增加;2)从论文总被引频次、篇均引用次数和h-index三项论文影响力特征参数分析,中国与国际其他国家相比有一定差距;3)从学科分类来看,与国际相比,中国在生物多样性保护领域、进化生物学和海洋与淡水生物学领域研究略显不足,昆虫学和真菌学研究领域活跃。     

Macroecology and consilience

Consilience means that all fields of human knowledge should be internally consistent. Within the broad span of the ecological and evolutionary sciences, there are many fields that seem only remotely related conceptually. Macroecology has emerged as a research programme that focuses on statistical patterns of ecological and biogeographically relevant traits among different species within a taxon. The concepts needed to understand these patterns require the interface of disciplines as different as systematics, ecosystem ecology, palaeontology and community ecology. By building conceptual links among a wide range of disciplines, macroecology is contributing, and will continue to contribute, to the growing realization that all of biology is indeed consilient.     

生物多样性研究的几个国际热点

ＤＩＶＥＲＳＩＴＡＳ是国际上生物多样性研究的主要项目,到１９９５年时,这项目发展到一个新的阶段．研究内容由过去４个方面发展到目前代表ＤＩＶＥＲＳＹＦＡＳ核心的５个主要项目组成部分及４个交叉项目组成部分。系统学作为生物学的一门分支学科,它的重要任务之一就是要研究生命的多样性．为了世界性地提高对系统学研究重要性的认识,加强系统学基础设施和人才资源,国际上制定了２０００年系统学议程项目。此外,本文还介绍了ＩＵＢＳ组织的物种２０００项目。     

Step back from the forest and step up to the Bonn Challenge: how a broad ecological perspective can promote successful landscape restoration

We currently face both an extinction and a biome crisis embedded in a changing climate. Many biodiverse ecosystems are being lost at far higher rates than they are being protected or ecologically restored. At the same time, natural climate solutions offer opportunities to restore biodiversity while mitigating climate change. The Bonn Challenge is a U.N. programme to restore biodiversity and mitigate climate change through restoration of the world's degraded landscapes. It provides an unprecedented chance for ecological restoration to become a linchpin tool for addressing many environmental issues. Unfortunately, the Forest and Landscape Restoration programme that underpins the Bonn Challenge, as its name suggests, remains focused on trees and forests, despite rising evidence that many non‐forest ecosystems also offer strong restoration potential for biodiversity and climate mitigation. We see a need for restoration to step back to be more inclusive of different ecosystem types and to step up to provide integrated scientific knowledge to inform large‐scale restoration. Stepping back and up will require assessments of where to restore what species, with recognition that in many landscapes multiple habitat types should be restored. In the process, trade‐offs in the delivery of different ecosystem services (e.g. carbon, biodiversity, water, albedo, livestock forage) should be clearly addressed. We recommend that biodiversity safeguards be included in policy and implemented in practice, to avoid undermining the biophysical relationships that provide ecosystem resilience to climate change. For ecological restoration to contribute to international policy goals will require integrated large‐scale science that works across biome boundaries.     

Effects of climate change on biodiversity: a review and identification of key research issues

Current knowledge of effects of climate change on biodiversity is briefly reviewed, and results are presented of a survey of biological research groups in the Netherlands, aimed at identifying key research issues in this field. In many areas of the world, biodiversity is being reduced by humankind through changes in land cover and use, pollution, invasions of exotic species and possibly climate change. Assessing the impact of climate change on biodiversity is difficult, because changes occur slowly and effects of climate change interact with other stress factors already imposed on the environment. Research issues identified by Dutch scientists can be grouped into: (i) spatial and temporal distributions of taxa; (ii) migration and dispersal potentials of taxa; (iii) genetic diversity and viability of (meta) populations of species; (iv) physiological tolerance of species; (v) disturbance of functional interactions between species; and (vi) ecosystem processes. Additional research should be done on direct effects of greenhouse gases, and on interactions between effects of climate change and habitat fragmentation. There are still many gaps in our knowledge of effects of climate change on biodiversity. An interdisciplinary research programme could possibly focus only on one or few of the identified research issues, and should generate input data for predictive models based on climate change scenarios.     

What do Israeli high school students understand about biodiversity? An evaluation of the high school biology programme, ‘Nature in a World of Change’

One of the most serious problems facing our planet is the biodiversity crisis. As a solution to this problem, both scientists and educators have emphasised the need for educating people about how to conserve the Earth’s biodiversity. As a small contribution to this effort, we have designed a learning unit about biodiversity, Nature in a world of change, which has recently been implemented with 74 12th-grade Israeli high-school biology students. This unit consists of two components: an introductory module and a collection of three articles adapted from the primary scientific literature. This paper focuses on an in-depth examination with 25 students participating in the programme’s implementation. The evaluation process includes a self-assessment of prior basic ecological knowledge and a post-test focusing on concepts and issues central to the understanding of biodiversity, such as niche and Simpson’s Index. Analysis of perturbations in a food web (by an invasive species) was a special focus of the assessments, reflecting similar concerns prevalent among the scientific community. The results of this evaluation revealed that students with a solid ecological background could successfully deal with the newly acquired concepts presented in the module and the articles.     

谈中国植物科学基础研究与农业发展

该文讨论了加强植物科学基础研究的必要性及其对我国农业发展的重要影响。为了更好地为中国的农业发展服务,进一步加强植物科学基础研究非常重要。为了促进植物科学的发展,我国既要积极参与国际竞争,又要重视知识创新、技术发展以及技术平台建设等多个方面,还要重视传统学科如植物分类学等的发展。过去10年间,我们见证了中国科学家在植物科学领域取得的重要成就,随着越来越多的高水平人才回国,建议国家增加投入支持我国的植物科学基础研究。     

遗传多样性的分子检测

生物多样性的保护和可持续利用是维持全球经济稳定和发展的重要因素,也是保持我们赖以生存环境的重要内容。为了实现这一目的,必须尽快建立一套对生物多样性认识和检测的有效方法,逐步认清全球生物多样性的基本状况。本文论述了生物多样性特别是物种间和物种内多样性的几种主要检测方法,着重介绍分子标记的最新进展及比较基因组学的兴起在生物多样性研究中的广泛应用。     

Identifying spatial components of ecological and evolutionary processes for regional conservation planning in the Cape Floristic Region, South Africa

Abstract. Conservation seeks ultimately to protect and maintain biodiversity indefinitely. Most biodiversity features targeted in past conservation planning have been largely aspects of ecological and biogeographical pattern rather than process. However, the persistence of biodiversity can only be ensured through consideration of the ecological and evolutionary processes that underpin biodiversity, as well as its present spatial pattern. This paper identifies spatial surrogates of ecological and evolutionary processes for regional conservation planning in one of the world's biodiversity hotspots, the Cape Floristic Region. We identified six types of spatial components (namely edaphic interfaces, upland–lowland interfaces, sand movement corridors, riverine corridors, upland–lowland gradients and macroclimatic gradients) as surrogates for key processes such as ecological and geographical diversification, and species migration. Spatial components were identified in a GIS using published data and expert knowledge. Options for achieving targets for process components have been seriously compromised by habitat transformation. Between 30 and 75% of the original extent of the spatial components currently remain functional. Options for achieving upland–lowland and macroclimatic gradients are very limited in the lowlands where most of the habitat has been transformed by agriculture. We recommend that future studies place their research on ecological and evolutionary processes in a spatially explicit framework. Areas maintaining adaptive diversification (e.g. environmental gradients, ecotones) or containing historically isolated populations should be identified and protected. The spatial dimensions of eco-logical processes such as drought and fire refugia also need to be determined and such insights incorporated in conservation planning. Finally, connectivity within these areas should be ensured to maintain species migration and gene flow.     

生物多样性信息学:一个正在兴起的新方向及其关键技术

生物多样性科学和生物信息学是生命科学中两个极为重要也是十分活跃的交叉学科,生物多样性信息学则是目前正在兴起的一个新方向,基发展必将进一步深化信息技术在生物多样性研究中的应用。本文简要介绍了国内外该领域的主要目标与进展,讨论了有关的关键技术（如数据库间的互操作与数字图书馆）,并列出了两个原型系统（Ｓｐｅｃｉｅｓ２０００和ＧＢＩＦ）和其他相关系统的网址。     

The contribution of scientific information to the conservation and management of freshwater biodiversity in tropical Asia

Tropical Asia (i.e. the Oriental biogeographic region) is the most densely populated and degraded region on Earth with the highest deforestation rates in the tropics. Flow regulation is a significant threat to riverine biodiversity in the region, and its impacts are combined with overharvesting, pollution and other sources of habitat degradation. In addition to these immediate threats, the potential impacts of exotic species and climate change are difficult to predict. Uncertainty about impact effects arises also from the fact that knowledge of the rich freshwater biodiversity of tropical Asia is incomplete, and up-to-date national or regional inventories are lacking. In part, this reflects taxonomic constraints, and a limited representation of Asian science in the international limnological and conservation literature. A survey of recent (1992–2001) international journals dealing with freshwater ecology and limnology in general, on one hand, and conservation biology on the other, reveal that the representation of scientists based in tropical Asia was extremely low. Scientists from tropical Asia authored fewer than 2% of more than 4500 papers dealing with freshwater biology; 57% of them were published in Hydrobiologia. Less than 0.1% of freshwater biology papers dealt with the conservation of biodiversity in tropical Asian fresh waters. The representation of Asian freshwater science in the conservation biology literature was also poor; 0.6% of 1880 papers surveyed. Such limited dissemination of information reflects a variety of constraints (e.g. manpower, funding, language, and entrenched attitudes), arising from sources both within and outside the region. Even the data that are published are not effectively deployed toward conservation ends. Awareness of some of the more egregious examples of overharvesting (e.g. of river turtles) in the region has increased, but strategies for the protection of riverine biodiversity remain underdeveloped. Where legislation to protect water resources has been put in place, it has been directed towards enhancing human use of water – not biodiversity conservation – and enforcement is weak. Exceptionally, the Chinese government has produced national `Red Data Books' for endangered freshwater vertebrates, and legislation aimed at protecting species at risk, particularly from overharvesting, are in place. Huge obstacles remain, especially in the management of rivers crossing international boundaries. The Mekong River Commission (MRC) provides an example of a model for an international drainage basin that has made significant progress in establishing appropriate structures and mechanisms for sustainable development in a challenging political landscape. Not all of the Mekong riparian states participate in the MRC, and this will be essential for sustainable management. However, even within national borders, local interests can override drainage-basin perspectives. In many places in Asia, preservation of near-pristine freshwater environments is not a realistic option. Sustaining human livelihoods is an over-riding concern, and recognition of this fact must be built in to biodiversity conservation efforts. This has special implications for the management of exotic species, as the example of fish introductions to the Sepik River in Papua New Guinea shows. Notwithstanding the various factors that constrain publication by scientists in tropical Asia, we must recognise that poor dissemination research results will have consequences for the long-term preservation of the habitats and biodiversity that we study. A change in research strategy that establishes priorities, recognises the inevitability of trade-offs, and includes greater emphasis on engagement and partnerships – as in the MRC – is mandated.