How genomics can help biodiversity conservation

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.     

试论生物多样性保护理论与实践面临的困难及现实出路

保护生物学作为一门新兴的交叉科学,已经在最近的一二十年中迅速发展成为一门独立的学科,然而,人们似乎过分沉湎于保护生物学的理论研究之中,却对这样一个事实置若罔闻;保护生物多样性的实践并未能取得预期的成效,生物多样性的危机不仅远未消除,反而越来越严峻,本文从保护生物多样性的伦理妯,保护生物学的理论,保护生物多样性的实践等多个层面上,分析了生物多样性保护面临的重重困难,着重指出,来自社会人文方面的种种不利因素,尤其是经济方面的驱动力,才是制约生物多样性保护的根源所在,并提出通过人文学科的社会经济,政策,法律等方面与自然学科的技术和理论的密切合作研究,综合地探求解决生物多样性危机的有效途径,应该成为保护生物学研究一个新的重点领域。     

One Conservation: the integrated view of biodiversity conservation

The current global situation requires urgent decision-making to reverse processes of mass extinction of thousands of species. As a way of showing the importance of joint actions in this process, we aim to present the concept of One Conservation as a new proposal for the integration of sustainability, in situ and ex situ conservation for the restoration of ecosystems. According to the United Nations, we are beginning the decade of ecosystem restoration and in association with the International Union for Conservation of Nature guidelines, we can join efforts in the conservation of the planet. The survival of many species of wild animals depends on the management of populations currently maintained in ex situ conditions (under human care). To facilitate the exchange of genetic material between in situ and ex situ populations, reproductive biotechniques have become a great tool, making it possible to restore species in their natural environments. For effective conservation to occur, there must be an integrated view of the problem as a whole, and action for solutions must take place jointly by different spheres of society. Even more, conservation must be carried out by the public sector, the private sector, the third sector, and not less importantly, the agricultural sector. Therefore, One Conservation is defined as an interconnection between ex situ and in situ conservation plans, anthropic actions in the environment, and research in different areas that encompass conservation.     

IUCN and perspectives on biodiversity conservation in a changing world

Biodiversity conservation is not a clear-cut practice and there is no blueprint solution to the question how to best halt the loss of biological diversity. Various conservation approaches are surrounded by a variety of basic assumptions about the world, nature and the human-nature relationship. These assumptions are more often implicitly hidden in practices and discourse than purposefully produced and deployed at a conscious level. The aim of our paper is to contribute to the on-going discussion on how to halt the loss of biodiversity in a dynamic global socio-ecological system. We will present an analysis of the worldview(s) and management style(s) of the oldest and largest global conservation organization: the International Union of Nature Conservation (IUCN). Popular in many conservation organisations is the strategy of integrating conservation in policy, business and society. Our discourse analysis demonstrates that although IUCN employs a strongly pluralistic practice of conservation, it is difficult to speak of a truly integrative approach yet.     

Save the planet: eliminate biodiversity

Recent work in the philosophy of biology has attempted to clarify and defend the use of the biodiversity concept in conservation science. I argue against these views, and give reasons to think that the biodiversity concept is a poor fit for the role we want it to play in conservation biology on both empirical and conceptual grounds. Against pluralists, who hold that biodiversity consists of distinct but correlated properties of natural systems, I argue that the supposed correlations between these properties are not tight enough to warrant treating and measuring them as a bundle. I additionally argue that deflationary theories of biodiversity don’t go far enough, since a large proportion of what we value in the environment falls outside bounds of what could reasonably be called “diversity”. I suggest that in current scientific practice biodiversity is generally an unnecessary placeholder for biological value of all sorts, and that we are better off eliminating it from conservation biology, or at least drastically reducing its role.     

Classification of key ecological attributes and stresses of biodiversity for ecosystem-based conservation assessments and management

A whole systems thinking approach to conservation has spawned new approaches in adaptive management planning that require a crucial understanding of what is essential for the functionality of ecosystems and the biodiversity they embrace. In this context, the key ecological attributes (KEA) have been introduced as aspects of a conservation target's biology or ecology that, if missing or altered, would lead to the loss of that target over time. Ecological stresses describe the impaired status of KEAs. Whilst for threats, the drivers of stresses, a systematic classification has been suggested and adopted by IUCN, all existing proposals for stresses and KEAs are preliminary. In order to fill the gap and provide conservation analysts and practitioners with a standard terminology supporting adaptive management planning we suggest a first hierarchical framework and comprehensive classification of key ecological attributes and corresponding stresses to biodiversity. Analyzing 22 vulnerability assessments in 13 countries, spread across 5 continents, as well as an extensive literature review, we identified 144 specific KEAs and stresses. These are differentiated and classified according to three hierarchical levels, 11 KEA and stress classes and 42 general KEAs and stresses. Our classification may help with describing and understanding both the natural functionality and also impaired functioning of biodiversity targets, as well as assist with the development of appropriate conservation strategies. The classification of key ecological attributes is presented as a list but it is important to recognize that the diverse array of KEAs and stresses are systemically interrelated across scales.     

Integrating approaches leads to more effective conservation of biodiversity

Recent debates have discussed whether a species-approach or an ecosystem-approach is better for protecting biodiversity. Rather than perpetuate this debate, we argue that critical new scientific and conservation insights arise from combining and integrating approaches along a continuum. We present a suite of case studies and other examples, which highlight the value and synergies derived from an integrated approach for developing management-relevant understanding aimed at protecting biodiversity. Attempts to conserve biodiversity should therefore be multi-faceted in approach and thinking. They also should be long-term as well as driven by well-developed questions focused on closing key knowledge gaps.     

Impacts of traditional land uses on biodiversity outside conservation areas: effects on dung beetle communities of Vaalbos National Park

Grazing is one of the key processes in terrestrial ecosystems and this can be provided by both indigenous and domestic ungulates. However, a question remains whether or not traditional forms of land use such as the grazing of domestic animals support the maintenance of biodiversity. If it does not, then the second question becomes to what extent does grazing of domestic animals alter the systems and processes that support biodiversity? This study demonstrates that in attempting to answer this question, small organisms like dung beetles are ideal indicators that can be used to express significant differences between conserved (indigenous) and non‐conserved (domestic) land. As a general trend, studies that investigated these differences displayed differences through analysis of the diversity indices. This method has in most cases demonstrated a lack of contrast between conserved and non‐conserved land. In the existence of such uncertainty this study has demonstrated that in such cases, where the analysis of biodiversity indices fail to demonstrate significant differences a closer examination of actual species such as guilds and functional groups could confirm significant differences between conserved and non‐conserved land. These apparently conflicting findings reflect the need to consider the actual elements of biodiversity (e.g. species) when assessing conservation issues rather than just the statistical measures of biodiversity.     

利用基于自然的解决方案促进生物多样性保护

生物多样性丧失是当今人类面临的重要危机之一,在以“爱知目标”为代表的生物多样性保护目标均未实现的背景下,如何推进变革性转型以遏制和扭转生物多样性丧失趋势成为当务之急。基于自然的解决方案(NbS)因其坚持整体性、系统性、多样性、稳定性、可持续性、权衡性和包容性等原则,成为应对全球危机的重要途径。该文通过分析机理和功能层面生物多样性和NbS的关系,阐明了NbS利用恢复生态系统的复杂性和营养级来指引生物多样性保护的路径,提出了利用NbS促进生物多样性保护的双重内涵,一是以提升生态系统多样性、稳定性、持续性为目标,二是利用自然生态过程。在建立NbS和生物多样性关联认知的基础上,该文进一步梳理了NbS的概念内涵与生物多样性保护目标的一致性,以及NbS在生态空间、农业空间、城镇空间对生物多样性保护的相关方法,归纳了NbS促进生物多样性的国内外实践案例,讨论了NbS协同促进生物多样性保护、应对气候变化和可持续发展的多重效益,展望了NbS纳入生物多样性保护战略规划的愿景,以期为促进《昆明-蒙特利尔全球生物多样性框架》等框架履约、推进NbS在生物多样性保护主流化提供参考。     

Biocomplexity and conservation of biodiversity hotspots: three case studies from the Americas

The perspective of 'biocomplexity' in the form of 'coupled natural and human systems' represents a resource for the future conservation of biodiversity hotspots in three direct ways: (i) modelling the impact on biodiversity of private land-use decisions and public land-use policies, (ii) indicating how the biocultural history of a biodiversity hotspot may be a resource for its future conservation, and (iii) identifying and deploying the nodes of both the material and psycho-spiritual connectivity between human and natural systems in service to conservation goals. Three biocomplexity case studies of areas notable for their biodiversity, selected for their variability along a latitudinal climate gradient and a human-impact gradient, are developed: the Big Thicket in southeast Texas, the Upper Botanamo River Basin in eastern Venezuela, and the Cape Horn Archipelago at the austral tip of Chile. More deeply, the biocomplexity perspective reveals alternative ways of understanding biodiversity itself, because it directs attention to the human concepts through which biodiversity is perceived and understood. The very meaning of biodiversity is contestable and varies according to the cognitive lenses through which it is perceived.     

The value of coarse species range maps to inform local biodiversity conservation in a global context

Range maps of thousands of species, compiled and made freely available by the International Union for Conservation of Nature, are being increasingly applied to support spatial conservation planning. However, their coarse nature makes them prone to commission and omission errors, and they lack information on the variations in abundance within species’ distributions, calling into question their value to inform decisions at the fine scales at which conservation often takes place. Here, we tested if species ranges can reliably be used to estimate the responsibility of sites for the global conservation of species. We defined ‘specific responsibility’ as the fraction of a species’ population within a given site, considering it useful for prioritising species within sites; and defined ‘overall responsibility’ as the sum of specific responsibility across species within a site, assuming it informative of priorities among sites. Taking advantage of an exceptionally detailed dataset on the distribution and abundance of bird species at a near‐continental scale – a level of information rarely available to local decision‐makers – we created a benchmark against which we tested estimates of responsibility derived from range maps. We investigated approaches for improving these estimates by complementing range maps with plausibly available local data. We found that despite their coarse nature, range maps provided good estimates of sites’ overall responsibility, but relatively poor estimates of specific responsibility. Estimates were improved by combining range maps with local species lists or local abundance data, easily available through local surveys on the sites of interest, or simulated expert knowledge. Our results suggest that combining range maps with local data is a promising route for improving the effectiveness of local conservation decisions at contributing to reducing global biodiversity losses. This is all the more urgent in hyper‐diverse poorly‐known regions where conservation‐relevant decisions must proceed despite a paucity of biodiversity data.     

Accommodating dynamic oceanographic processes and pelagic biodiversity in marine conservation planning

Pelagic ecosystems support a significant and vital component of the ocean's productivity and biodiversity. They are also heavily exploited and, as a result, are the focus of numerous spatial planning initiatives. Over the past decade, there has been increasing enthusiasm for protected areas as a tool for pelagic conservation, however, few have been implemented. Here we demonstrate an approach to plan protected areas that address the physical and biological dynamics typical of the pelagic realm. Specifically, we provide an example of an approach to planning protected areas that integrates pelagic and benthic conservation in the southern Benguela and Agulhas Bank ecosystems off South Africa. Our aim was to represent species of importance to fisheries and species of conservation concern within protected areas. In addition to representation, we ensured that protected areas were designed to consider pelagic dynamics, characterized from time-series data on key oceanographic processes, together with data on the abundance of small pelagic fishes. We found that, to have the highest likelihood of reaching conservation targets, protected area selection should be based on time-specific data rather than data averaged across time. More generally, we argue that innovative methods are needed to conserve ephemeral and dynamic pelagic biodiversity.     

Changing conservation strategies in Europe: a framework integrating ecosystem services and dynamics

Protecting species and their habitats through the designation and management of protected areas is central to present biodiversity conservation efforts in Europe. Recent awareness of the importance of ecosystem dynamics in changing environments and of human needs for the sustainable provision of ecosystem services expose potential weaknesses in current European conservation management strategies and policy. Here we examine these issues in the light of information gained from reviews, workshops, interviews and discussions undertaken within the RUBICODE project. We present a new conceptual framework that joins conventional biodiversity conservation with new requirements. The framework links cultural and aesthetic values applied in a static environment to the demands of dynamic ecosystems and societal needs within social–ecological systems in a changing Europe. We employ this framework to propose innovative ways in which ecosystem service provision may be used to add value to traditional conservation approaches by supporting and complementing present European biodiversity conservation strategy and policy while remaining within the guidelines of the Convention on Biological Diversity.     

Understanding investment in biodiversity conservation in Mexico

Documenting financial resources in biodiversity conservation is a key aspect worldwide in order to set priorities and use effectively the limited resources available. In Mexico, a megadiverse country, studies on financial resources invested in biodiversity conservation are scarce and do not address funding for conservation comprehensively. Using recent data from several sources and applying criteria based on the national priorities for conservation, we compiled, systematized and analyzed data at a national scale on financing sources, financial resources and conservation organizations and their projects. The information obtained is presented in various ways and part of it (case study) is already an information system that can be continuously up-dated. Some of the results show the following: a steady diversification of mechanisms and methods for raising funds for conservation; an increase in governmental budgets; the acknowledgment by the private sector of the importance of biodiversity conservation; a greater technical capacity in people and organizations working in conservation; a greater accessibility of financial resources to support and maintain conservation projects; yet a short term vision in conservation projects; among other. Although the results obtained through this study are a first approach, they can now be used as a baseline to continue gathering and analyzing information on conservation financing in Mexico.     

Broken barriers: human-induced changes to gene flow and introgression in animals: an examination of the ways in which humans increase genetic exchange among populations and species and the consequences for biodiversity

We identify two processes by which humans increase genetic exchange among groups of individuals: by affecting the distribution of groups and dispersal patterns across a landscape, and by affecting interbreeding among sympatric or parapatric groups. Each of these processes might then have two different effects on biodiversity: changes in the number of taxa through merging or splitting of groups, and the extinction/extirpation of taxa through effects on fitness. We review the various ways in which humans are affecting genetic exchange, and highlight the difficulties in predicting the impacts on biodiversity. Gene flow and hybridization are crucially important evolutionary forces influencing biodiversity. Humans alter natural patterns of genetic exchange in myriad ways, and these anthropogenic effects are likely to influence the genetic integrity of populations and species. We argue that taking a gene-centric view towards conservation will help resolve issues pertaining to conservation and management. Editor's suggested further reading in BioEssays A systemic view of biodiversity and its conservation: Processes, interrelationships, and human culture Abstract.     

Operationalizing biodiversity for conservation planning

Biodiversity has acquired such a general meaning that people now find it difficult to pin down a precise sense for planning and policy-making aimed at biodiversity conservation. Because biodiversity is rooted in place, the task of conserving biodiversity should target places for conservation action; and because all places contain biodiversity, but not all places can be targeted for action, places have to be prioritized. What is needed for this is a measure of the extent to which biodiversity varies from place to place. We do not need a precise measure of biodiversity to prioritize places. Relative estimates of similarity or difference can be derived using partial measures, or what have come to be called biodiversity surrogates. Biodiversity surrogates are supposed to stand in for general biodiversity in planning applications. We distinguish between true surrogates, those that might truly stand in for general biodiversity, and estimator surrogates, which have true surrogates as their target variable. For example, species richness has traditionally been the estimator surrogate for the true surrogate, species diversity. But species richness does not capture the differences in composition between places; the essence of biodiversity. Another measure, called complementarity, explicitly captures the differences between places as we iterate the process of place prioritization, starting with an initial place. The relative concept of biodiversity built into the definition of complementarity has the level of precision needed to undertake conservation planning.     

Parasites in biodiversity conservation: friend or foe?

Parasites stabilise food webs and facilitate species coexistence but can also lead to population- or species-level extinctions. So, in biodiversity conservation, are parasites friends or foes? This question is misleading: it implies that parasites are not part of biodiversity. Greater integration of parasites into global biodiversity and ecosystem conservation efforts is required.     

集成生态系统服务与生物多样性的系统保护规划

生物多样性和生态系统服务的保护与可持续管理是当今世界面临的重大挑战之一,但如何判识与优化集成生态系统服务与生物多样性保护对象的保护优先区网络,相关研究还很有限。针对“三江并流”区,选取珍稀濒危与特有动植物物种和自然植被类型作为生物多样性保护对象,以调节服务(碳存储、固碳和土壤保持)、文化服务(自然游憩)和供给服务(水源供给)为生态系统服务保护对象。应用系统保护规划方法,首先判识出单一生物多样性和生态系统服务保护优先区;然后,分析这些保护优先区间的相关关系,并选择与生物多样性正相关的生态系统服务类型,判识集成生态系统服务与生物多样性的保护优先区;最后,评估了集成生态系统服务与生物多样性保护优先区在六类已建保护地中的保护状况。结果表明：(1)“三江并流”区多情景规划得到的生物多样性与生态系统服务保护优先区之间均呈正相关关系;(2)与分别针对生态系统服务和生物多样性的规划情景相比,集成生态系统服务与生物多样性保护优先区能够同时对两类保护对象提供最高的保护覆盖率;(3)集成生态系统服务和生物多样性保护优先区占研究区总面积的48.9%,其已建保护地覆盖率为32.5%,说明现有保护地体系仍存在保护...     

Freshwater biodiversity: importance, threats, status and conservation challenges

Freshwater biodiversity is the over‐riding conservation priority during the International Decade for Action ‐‘Water for Life’ ‐ 2005 to 2015. Fresh water makes up only 0.01% of the World's water and approximately 0.8 % of the Earth's surface, yet this tiny fraction of global water supports at least 100 000 species out of approximately 1.8 million ‐ almost 6% of all described species. Inland waters and freshwater biodiversity constitute a valuable natural resource, in economic, cultural, aesthetic, scientific and educational terms. Their conservation and management are critical to the interests of all humans, nations and governments. Yet this precious heritage is in crisis. Fresh waters are experiencing declines in biodiversity far greater than those in the most affected terrestrial ecosystems, and if trends in human demands for water remain unaltered and species losses continue at current rates, the opportunity to conserve much of the remaining biodiversity in fresh water will vanish before the ‘Water for Life’ decade ends in 2015. Why is this so, and what is being done about it? This article explores the special features of freshwater habitats and the biodiversity they support that makes them especially vulnerable to human activities. We document threats to global freshwater biodiversity under five headings: overexploitation; water pollution; flow modification; destruction or degradation of habitat; and invasion by exotic species. Their combined and interacting influences have resulted in population declines and range reduction of freshwater biodiversity worldwide. Conservation of biodiversity is complicated by the landscape position of rivers and wetlands as ‘receivers’ of land‐use effluents, and the problems posed by endemism and thus non‐substitutability. In addition, in many parts of the world, fresh water is subject to severe competition among multiple human stakeholders. Protection of freshwater biodiversity is perhaps the ultimate conservation challenge because it is influenced by the upstream drainage network, the surrounding land, the riparian zone, and ‐ in the case of migrating aquatic fauna ‐ downstream reaches. Such prerequisites are hardly ever met. Immediate action is needed where opportunities exist to set aside intact lake and river ecosystems within large protected areas. For most of the global land surface, trade‐offs between conservation of freshwater biodiversity and human use of ecosystem goods and services are necessary. We advocate continuing attempts to check species loss but, in many situations, urge adoption of a compromise position of management for biodiversity conservation, ecosystem functioning and resilience, and human livelihoods in order to provide a viable long‐term basis for freshwater conservation. Recognition of this need will require adoption of a new paradigm for biodiversity protection and freshwater ecosystem management ‐ one that has been appropriately termed ‘reconciliation ecology’.     

Effectiveness of Protected Areas for biodiversity conservation: Mammal occupancy patterns in the Iguaçu National Park,Brazil

Protected areas – widely recognized as the main strategy for biodiversity conservation – have greatly expanded, covering ∼15% of the Earth; however, we still lack detailed information on biodiversity to evaluate their effectiveness. This is particularly urgent for biodiversity hotspots where protected areas are islands within human modified landscapes. We focus on mammals of the Iguaçu National Park – one of the most important parks in the Atlantic Forest hotspot – to evaluate the effectiveness of protected areas in conserving biodiversity. We monitored 300 km² with 37 cameras traps during five years to assess if (1) species occupancy declined over time, and (2) if species occupancy/detectability are spatially associated with illegal hunting, proximity to tourism infrastructure and distance from the edge, estimating the proportion of the park where these negative effects are detected. Many species that are rare in most Atlantic Forest remnants presented high occupancy within the park, and no decline in occupancy was observed over time. However, the distribution of 11 species was spatially associated primarily with the distance from the edge and proximity to tourism infrastructure, resulting in a decline, across half of the park area, from 13 to 23% in occupancy and from 19 to 35% in detectability (values averaged among species). These negative effects should be even stronger on smaller protected areas, which are the majority in highly altered hotspots. Re-establishing and properly managing buffer zones and restricting tourism to localized areas are essential to ensure the effectiveness of protected areas for biodiversity conservation.