High variability in patterns of population decline: the importance of local processes in species extinctions

A fundamental goal of conservation science is to improve conservation practice. Understanding species extinction patterns has been a central approach towards this objective. However, uncertainty remains about the extent to which species-level patterns reliably indicate population phenomena at the scale of local sites, where conservation ultimately takes place. Here, we explore the importance of both species- and site-specific components of variation in local population declines following habitat disturbance, and test a suite of hypotheses about their intrinsic and extrinsic drivers. To achieve these goals, we analyse an unusually detailed global dataset for species responses to habitat disturbance, namely primates in timber extraction systems, using cross-classified generalized linear mixed models. We show that while there are consistent differences in the severity of local population decline between species, an equal amount of variation also occurs between sites. The tests of our hypotheses further indicate that a combination of biological traits at the species level, and environmental factors at the site level, can help to explain these patterns. Specifically, primate populations show a more marked decline when the species is characterized by slow reproduction, high ecological requirements, low ecological flexibility and small body size; and when the local environment has had less time for recovery following disturbance. Our results demonstrate that individual species show a highly heterogeneous, yet explicable, pattern of decline. The increased recognition and elucidation of local-scale processes in species declines will improve our ability to conserve biodiversity in the future.     

Mesozoic marine tetrapod diversity: mass extinctions and temporal heterogeneity in geological megabiases affecting vertebrates

The fossil record is our only direct means for evaluating shifts in biodiversity through Earth''s history. However, analyses of fossil marine invertebrates have demonstrated that geological megabiases profoundly influence fossil preservation and discovery, obscuring true diversity signals. Comparable studies of vertebrate palaeodiversity patterns remain in their infancy. A new species-level dataset of Mesozoic marine tetrapod occurrences was compared with a proxy for temporal variation in the volume and facies diversity of fossiliferous rock (number of marine fossiliferous formations: FMF). A strong correlation between taxic diversity and FMF is present during the Cretaceous. Weak or no correlation of Jurassic data suggests a qualitatively different sampling regime resulting from five apparent peaks in Triassic–Jurassic diversity. These correspond to a small number of European formations that have been the subject of intensive collecting, and represent ‘Lagerstätten effects’. Consideration of sampling biases allows re-evaluation of proposed mass extinction events. Marine tetrapod diversity declined during the Carnian or Norian. However, the proposed end-Triassic extinction event cannot be recognized with confidence. Some evidence supports an extinction event near the Jurassic/Cretaceous boundary, but the proposed end-Cenomanian extinction is probably an artefact of poor sampling. Marine tetrapod diversity underwent a long-term decline prior to the Cretaceous–Palaeogene extinction.     

运用聚类分析与Google Maps于大量物种出现记录之研究

物种出现记录包含博物馆动物标本、植物标本、生态调查与物种观察等资料。在台湾生物多样性信息机构(Taiwan Biodiversity Information Facility,TaiBIF)物种出现记录整合平台中,已整合台湾26个数据集,包含超过150万笔物种出现记录,其中约有85%的数据具有地理信息。我们利用数据库中所汇整的鲤科数据,包括11个数据集、超过8,800笔出现记录数据,利用网格式、切割式与密度式3种聚类分析算法分别绘制出不同的空间可视化结果,藉此解决大量物种出现记录于Google Maps上呈现效能与可视化不佳之问题。同时我们也探讨了3种聚类分析法之结果与鲤科的专家意见范围地图(expertopinion range maps)比对的差异。期望透过本研究可快速且有效地呈现物种分布资料,进而帮助研究者挖掘出大量数据所隐含的知识,并为生态保育提供重要参考。     

Managing biodiversity data within the context of climate change: towards best practice

Decision makers, planners and researchers have identified the need to assess the effects of climate change on biodiversity, resulting in extensive research across a number of fields. The availability of comprehensive, accurate and relevant data is central to undertaking effective research. However, the quality and availability of biodiversity information is substantially determined by current and historical data collection strategies. If researchers and planners are to make effective use of existing and future investments in biodiversity information, a strategic approach should be taken in identifying and implementing best practice information management. This paper discusses ways to improve institutional support for information management and increase the availability of quality information. The paper reviews the most common areas of climate change and biodiversity research, and identifies best practices in information management, focusing on data used within biodiversity and climate change analyses.     

Alarming evidence of widespread mite extinctions in the shadows of plant,insect and vertebrate extinctions

This paper, which addresses the issue of the extinction of mite species at the global scale for the first time, highlights mite diversity, assesses the evidence for an extinction process, discusses contributing factors and estimates losses. The ~1 250 000 mite species occupy an enormous variety of terrestrial and freshwater ecosystems from the equator to the polar regions and to high altitudes. Some groups provide essential ecosystem services, including the incorporation of organic matter into the soil. The maintenance of mite diversity is inextricably linked to the continuance of floristic diversity, habitat complexity and insect diversity. The majority of mite species are assumed to be in the tropical rainforests, of which >50% has been destroyed or severely degraded. Most biodiversity hotspots are in tropical forests; endemic phytoseiid mite species are at least 17 times more concentrated in the hotspots than outside. Habitat destruction and degradation continue on an enormous scale, with increasing human population growth and resource consumption the overarching drivers of extinction. Moreover, climate change is likely to be worsening the effects of the other drivers at an increasing rate. The small body of direct evidence and a considerable body of indirect evidence strongly suggest the continuing, widespread extinction of mite species. Based on estimates of overall biodiversity loss, ~15% of mite species were likely to have become extinct by 2000, with losses currently expected to increase by between 0.6% and 6.0% by 2060. More detailed information on both spatial differences in mite assemblages and anthropogenic threats worldwide is crucial because they underpin the total number of species and their vulnerability to extinction, respectively. The rapid expansion of the protected area estate to capture the maximum possible area of ecosystem heterogeneity, especially in the biodiversity hotspots, is essential, as is best practice management of these areas.     

Deficiency in African plant distribution data – missing pieces of the puzzle

Biodiversity is spatially unevenly distributed and so is the information on its spatial patterns. This uneven distribution of information on species occurrences is an important impediment to the conservation of biodiversity. Based on 185 427 collection records of 5873 plant species in sub-Saharan Africa, we analyse the availability of distribution data suitable for the GIS-based mapping of plant diversity patterns at a one-degree resolution. Using the bioclimatic model GARP, distribution ranges for each species were modelled. In order to identify data-deficient areas, the documented and modelled diversity patterns were compared. Only for a few, well-known centres of plant diversity are there comparatively many data collection records available. For several of the areas with very few collection records, such as the Guinean montane forests, the north-western Congolian lowland forests, and the southern Albertine Rift montane forests, the model predicts a species richness much higher than currently documented. In many of the data deficient areas, difficult conditions for scientific research appear to have limited collection activities for decades. Only strategic field collections can fill these gaps. Another cause of data deficiency is that data collected and digitized do not match the quality requirements for GIS-based work at the super-regional scale. In particular, regional databases documenting partial ranges of species are rarely connected. One challenge for the Global Strategy for Plant Conservation is therefore to establish international collaborative structures and technical standards that will allow analysis of biogeographical patterns across political boundaries.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 150 , 355–368.     

The risks of using molecular biodiversity data for incidental detection of species of concern

Incidental detection of species of concern (e.g., invasive species, pathogens, threatened and endangered species) during biodiversity assessments based on high‐throughput DNA sequencing holds significant risks in the absence of rigorous, fit‐for‐purpose data quality and reporting standards. Molecular biodiversity data are predominantly collected for ecological studies and thus are generated to common quality assurance standards. However, the detection of certain species of concern in these data would likely elicit interest from end users working in biosecurity or other surveillance contexts (e.g., pathogen detection in health‐related fields), for which more stringent quality control standards are essential to ensure that data are suitable for informing decision‐making and can withstand legal or political challenges. We suggest here that data quality and reporting criteria are urgently needed to enable clear identification of those studies that may be appropriately applied to surveillance contexts. In the interim, more pointed disclaimers on uncertainties associated with the detection and identification of species of concern may be warranted in published studies. This is not only to ensure the utility of molecular biodiversity data for consumers, but also to protect data generators from uncritical and potentially ill‐advised application of their science in decision‐making.     

Integrating needs of the local community to conserve forest biodiversity in the state of Kelantan

Kelantan State, claimed to be one of the poorest states in Malaysia, has forest lands, nature reserves and other protected natural areas which are under increasing threat from a variety of human activities. At the same time, the State government lacks financial resources and skilled manpower to manage the protected forest lands adequately. The present strategies to manage protected forest areas are inadequate to overcome these constraints. Alternative strategies are needed to conserve Kelantan's forest biodiversity. Furthermore, conservation efforts will not be effective without the active cooperation and participation of people living in and near the forest areas. To achieve this, it is essential that the people share the benefits and responsibilities of forest resource management with the state government.A proposal to involve the local people in an integrated action plan is discussed in this paper. It aims to find options of protecting forest land encroachment in the State with an ultimate goal of increasing the capacity of the poor to carry out activities on a sustained basis. It is hoped that the proposed project will help the State government to improve economic status as well as environmental awareness and reduced dependence on forest lands.Much of the forest lands in Kelantan are threatened by encroachment from the people who live around the forest areas. This encroachment is not only the result of poverty and shortage of land, but is also due to the unclear forest boundaries. People also do not understand the significance of forest biodiversity. It is important therefore that the local people are encouraged not to encroach into the forest areas. There has to be support from the top in order to sustain integration efforts. Both the State and the central government agencies must be a part of the planning and implementation process. The challenge becomes one of integrating the needs of the local people with development priorities of the government. In practical terms, this paper hopes to arrive at a workable methodology rather than be a purely scientific exercise which can serve as a model to the other states experiencing similar problems.Presented at the Asean Seminar on Management and Conservation of Biodiversity, 29 November–1 December 1993, Kuala Lumpur.     

In search of the best correlates for local organismal biodiversity in cultivated areas

Based on a transect consisting of 19 identical trap stations in cultivated areas and seminatural habitats, the correlation of species numbers of higher taxonomic groups with total species numbers of flowering plants and arthropods per trap site was calculated. A total of 191214 invertebrate specimens and 2221 species of plants and animals were analysed. Considering the value of the correlation coefficient R2 as well as the effort for sorting and identification, a top twenty list of indicator groups favours Heteroptera, flowering plants, Symphyta and aculeate Hymenoptera as the best choice for biodiversity evaluation. In general, flight traps rated better than pitfall traps. In most taxonomic groups, diversity indices such as the Shannon and the Simpson index were only weakly correlated with local species diversity.     

BioTIME: A database of biodiversity time series for the Anthropocene

Motivation

The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community‐led open‐source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene.

Main types of variables included

The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record.

Spatial location and grain

BioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km² (158 cm²) to 100 km² (1,000,000,000,000 cm²).

Time period and grain

BioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.

Major taxa and level of measurement

BioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.

Software format

.csv and .SQL.

     

occAssess: An R package for assessing potential biases in species occurrence data

Species occurrence records from a variety of sources are increasingly aggregated into heterogeneous databases and made available to ecologists for immediate analytical use. However, these data are typically biased, i.e. they are not a probability sample of the target population of interest, meaning that the information they provide may not be an accurate reflection of reality. It is therefore crucial that species occurrence data are properly scrutinised before they are used for research. In this article, we introduce occAssess, an R package that enables straightforward screening of species occurrence data for potential biases. The package contains a number of discrete functions, each of which returns a measure of the potential for bias in one or more of the taxonomic, temporal, spatial, and environmental dimensions. Users can opt to provide a set of time periods into which the data will be split; in this case separate outputs will be provided for each period, making the package particularly useful for assessing the suitability of a dataset for estimating temporal trends in species'' distributions. The outputs are provided visually (as ggplot2 objects) and do not include a formal recommendation as to whether data are of sufficient quality for any given inferential use. Instead, they should be used as ancillary information and viewed in the context of the question that is being asked, and the methods that are being used to answer it. We demonstrate the utility of occAssess by applying it to data on two key pollinator taxa in South America: leaf‐nosed bats (Phyllostomidae) and hoverflies (Syrphidae). In this worked example, we briefly assess the degree to which various aspects of data coverage appear to have changed over time. We then discuss additional applications of the package, highlight its limitations, and point to future development opportunities.     

整合空间信息在生物多样性丧失等研究中的重要性

无数证据表明,地球可能正经历着有史以来的第六次物种大灭绝。在这一背景下,研究生物多样性丧失机制及其对生态系统功能的影响具有重要意义。从先前的相关研究中,已逐渐清晰地认识到造成多样性丧失的几大机制,并对这些机制发生的空间尺度有了一定了解。然而,空间本身对多样性丧失研究的影响仍被该领域的很多研究所忽视。因为生物多样性丧失过程发生在不同空间尺度中,所造成的多样性丧失格局也具有不同的空间尺度特征。忽略空间信息很可能会对多样性丧失等相关研究造成很大干扰,甚至得出错误的结论,其结果也很难正确地运用于不同空间尺度的多样性保护当中。整合空间信息已成为当前生物多样性丧失研究,乃至整个生态学研究的前沿和热点之一。为促进这一趋势在国内的发展,将结合多样性丧失的估计与监测、几大多样性丧失机制(全球环境变化与生境片段化、生物入侵等)来阐述空间信息对当前及今后多样性丧失机制研究的重要性,并用实例展示未充分考虑空间信息而可能造成的后果。最后探讨我国当前科技条件下进行整合空间信息的生物多样性丧失等研究的可行性。     

外来种对生物多样性的影响及其控制

外来种是那些借助自身力量或其它外界力量传播到其未曾分布过的地域 ,并且能进行繁殖传播的生物。外来种入侵已成为一种引人关注的现象。外来种通过竞争、捕食、牧食、改变生境和传播疾病等方式对本地生物产生威胁 ,影响本地生物多样性。外来种入侵成了生物多样性丧失的两个主要影响之一 (另一影响是生境的破坏 )。因此 ,探寻阻止或减少外来种入侵的方法很有必要。目前 ,人们运用机械法、化学法和生物控制法来控制外来种。在外来种入侵的初始阶段或外来种数量不多时 ,运用机械法较好。化学法有带来新环境污染的危险。生物控制法是应用天敌来防治或消灭有害生物。在外来种的控制上 ,生物控制法有一些成功的案例 ,但它并不是万能的。有些生物控制剂可能对非目标种产生影响 ,这要求在释放前对生物控制剂作更严格的检测。     

Bias in freshwater biodiversity sampling: the case of Iberian water beetles

Extensive distributional data bases are key tools in ecological research, and good-quality data are required to provide reliable conservation strategies and an understanding of biodiversity patterns and processes. Although the evaluation of data bases requires the incorporation of estimates of sampling effort and bias, no studies have focused on these aspects for freshwater biodiversity data. We used here a comprehensive data base of water beetles from the Iberian Peninsula and the Balearic Islands, and examine whether these data provide an unbiased, reliable picture of their diversity and distribution in the study area. Based on theoretical estimates using the Clench function on the accumulated number of records as a surrogate of sampling effort, about a quarter of the Iberian and Balearic 50 × 50 km Universal Transverse Mercator grid cells can be considered well prospected, with more than 70% of the theoretical species richness actually recorded. These well-surveyed cells are not evenly distributed across biogeographical and physicoclimatic subregions, reflecting some geographical bias in the distribution of sampling effort. Our results suggest that recording was skewed by relatively simple variables affecting collector activity, such as the perceived 'attractiveness' of mountainous landscapes and protected areas with recently described species, and accessibility of sampling sites (distance from main research centres). We emphasize the importance of these evaluation exercises, which are useful to locate areas needed of further sampling as well as to identify potential biases in the distribution of current biodiversity patterns.     

DNA宏条形码技术在海洋浮游动物多样性和生态学研究中的应用

浮游动物是海洋生态系统的关键类群,其覆盖门类广泛,多样性高。传统形态鉴定技术需要检测人员具备专业的形态鉴定知识,且费时费力。宏条形码技术无需分离生物个体,而是提取拖网采集到的浮游动物混合样本的总DNA,或者水体中的环境DNA （eDNA）,依托高通量测序平台测序,能够实现对大规模样本快速、准确、经济的分析,在海洋浮游动物生态学研究中得到越来越广泛的应用。分析了DNA宏条形码技术常用的核糖体和线粒体分子标记,在浮游动物多样性和数量研究中的可靠性和不足,并给出在海洋浮游动物群落监测,食物关系分析及生物入侵早期预警等研究中的应用。未来,开发多基因片段组合条形码,发展完备的参考数据库及实现准确的量化研究是DNA宏条形码技术发展的重要方向。     

Temporal and sociocultural effects of human colonisation on native biodiversity: filtering and rates of adaptation

Modern human societies have negatively impacted native species richness and their adaptive capacity on every continent, in clearly contrasting ways. We propose a general model to explain how the sequence, duration and type of colonising society alter native species richness patterns through changes in evolutionary pressures. These changes cause different ‘filtering effects' on native species, while simultaneously altering the capacity of surviving species to adapt to further anthropogenic pressures. This framework may better explain the observed native species extinction rates and extirpation legacies following human colonisation events, as well as better predict future patterns of human impact on biodiversity.     

Identifiability and estimation of causal effects in randomized trials with noncompliance and completely nonignorable missing data

Summary .  In this article, we first study parameter identifiability in randomized clinical trials with noncompliance and missing outcomes. We show that under certain conditions the parameters of interest are identifiable even under different types of completely nonignorable missing data: that is, the missing mechanism depends on the outcome. We then derive their maximum likelihood and moment estimators and evaluate their finite-sample properties in simulation studies in terms of bias, efficiency, and robustness. Our sensitivity analysis shows that the assumed nonignorable missing-data model has an important impact on the estimated complier average causal effect (CACE) parameter. Our new method provides some new and useful alternative nonignorable missing-data models over the existing latent ignorable model, which guarantees parameter identifiability, for estimating the CACE in a randomized clinical trial with noncompliance and missing data.     

基于优势种的生物多样性保护价值空间异质性研究——以长白山生态功能区为例

生物多样性保护是生态系统的主导功能之一,对生物多样性空间异质性的研究有助于准确认识区域的保护价值及重要性,但目前可借鉴的生物多样性价值空间异质性评价方法和经验偏少。以长白山生态功能区核心区为研究区域,基于生物多样性丰富区域优势物种的分布及其环境因子,通过Maxent评估生物多样性保护价值,将研究区域分为生物多样性保护高价值区、中价值区和一般价值区,并开展景观分析与评估。研究结果表明:研究区域内生物多样性保护高价值区域占总面积的42.9%、主要分布于长白山保护区内,保护区内的高价值斑块也较保护区外完整、面积大;研究区域内生物多样性高价值斑块的平均面积和最大斑块面积远高于中价值区和一般价值区,其斑块景观较完整、破碎化水平相对较低,是研究区域生物多样性保护价值和生态系统稳定性的重要基础。植被是对研究区域生物多样性影响最大的环境因子,其次是土层厚度和海拔。从生态系统完整性和过程连续性保护的需要,保护区南部缓冲区可考虑调整为核心区,保护区外还有较大面积的生物多样性高价值和中价值区域也应纳入保护区进行保护;长白山西坡是生物多样性高价值斑块最破碎的区域,应在未来的保护工作中予以特别关注。本研究表明关联优势种空间分布及环境因子是认识生物多样性价值及空间异质性的有效手段,本研究方法可为生态红线划定和国家公园设计提供参考。