Are CORINE land cover classes reliable proxies of plant species assemblages? A test in Mediterranean forest landscapes

In land cover mapping, the complexity of landscapes is fitted into classes that may limit the recognition of natural variability. In this study, we tested the power of land cover classes (defined on the CORINE land cover classification scheme, a standardized legend set by EU for land cover inventory) to separate different vascular plant assemblages in forest ecosystems. In order to separately identify the role of different sources of inconsistency between land cover classes and species composition, we compared three different inventory processes, based on (i) dominant tree species as observed in the field, (ii) visual interpretation of remotely sensed images and (iii) semi-automatic supervised classification of satellite images. Our results underline that classifying forest ecosystems on the basis of their canopy species produces an over-simplification of habitat variability. Consequently, land cover maps based on non-specialized classification schemes should not be regarded as good proxies for plant biodiversity. If land cover maps are intended to describe and manage landscapes and their associated biodiversity, it is necessary to improve their capacity to represent the complexity of ecosystems.     

Ecosystem classification and inventory maps as surrogates for ground beetle assemblages in boreal forest

Aims We compare performance of ecosystem classification maps and provincial forest inventory data derived from air photography in reflecting ground beetle (Coleoptera: Carabidae) biodiversity patterns that are related to the forest canopy mosaic. Our biodiversity surrogacy model based on remotely sensed tree canopy cover is validated against field-collected ground data.Methods We used a systematic sampling grid of 198 sites, covering 84 km 2 of boreal mixedwood forest in northwestern Alberta, Canada. For every site, we determined tree basal area, characterized the ground beetle assemblage and obtained corresponding provincial forest inventory and ecosystem classification information. We used variation partitioning, ordination and misclassification matrices to compare beetle biodiversity patterns explained by alternative databases and to determine model biases originating from air photo-interpretation.Important findings Ecosystem classification data performed better than canopy cover derived from forest inventory maps in describing ground beetle biodiversity patterns. The biodiversity surrogacy models based on provincial forest inventory maps and field survey generally detected similar patterns but inaccuracies in air photo-interpretation of relative canopy cover led to differences between the two models. Compared to field survey data, air photo-interpretation tended to confuse two Picea species and two Populus species present and homogenize stand mixtures. This generated divergence in models of ecological association used to predict the relationship between ground beetle assemblages and tree canopy cover. Combination of relative canopy cover from provincial inventory with other geo-referenced land variables to produce the ecosystem classification maps improved biodiversity predictive power. The association observed between uncommon surrogates and uncommon ground beetle species emphasizes the benefits of detecting these surrogates as a part of landscape management. In order to complement conservation efforts established in protected areas, accurate, high resolution, wide ranging and spatially explicit knowledge of landscapes under management is primordial in order to apply effective biodiversity conservation strategies at the stand level as required in the extensively harvested portion of the boreal forest. In development of these strategies, an in-depth understanding of vegetation is key.     

Biodiversity of marine nematodes in Australian sandy beaches from tropical and temperate regions

The universal occurrence and abundance of nematodes provides opportunities to investigate ecological factors that may influence biodiversity. Clarke and Warwick (2001) have proposed diversity indices average taxonomic distance(AvTD), variation in taxonomic distinctness (VarTD) for computing marine nematode biodiversity based on classification trees. Faith [Biological Conservation 61 (1992) 1] had previously proposed a diversity index based on phylogenetic trees, though not applied to nematodes. Clarke and Warwick (2001) also considered an index AvPD analogous to AvTD. These indices have been applied to five very large collections of free-living nematodes from three exposed sandy beaches in Australia. Two were from a beach close to Darwin in northern Australia, two from the temperate southeast coast of Australia and one from the south of the Australian mainland. The collections extend over a considerable range of latitude, from 12°26S to 38°33S and the controversial hypothesis that latitudinal gradients per se influence the biodiversity of marine nematode assemblages is examined. AvTD did not vary among collections and its value for any collection was indistinguishable from that of random samples of the same size drawn from the total species pool. VarTD showed no variation for three of the collections, but was slightly higher than expected for the mid-latitude beach, attributed to unevenness in the classification trees. AvTD and VarTD were not greatly affected by differences in sampling intensity. PD varied directly with the number of species found but observed PD did not differ from the PD of random samples of the same number of species taken from the total species pool. Thus, the observed variation in PD is wholly accounted for by variations in species richness. The number of species found increased with decreasing latitude. It appears that species richness by itself is an adequate index of biodiversity for the free-living nematodes of these sandy beaches, and more complex indices such as AvTD, VarTD and PD are unnecessary.     

基于多源遥感数据的植物物种分类与识别: 研究进展与展望

物种分类与识别是生物多样性监测的基础, 明确物种的类别及其分布是解决几乎所有生态学问题的前提。为深入了解基于多源遥感数据的植物物种分类与识别相关研究的发展现状和存在的问题, 本文对2000年以来该领域的研究进行了总结分析, 发现: 当前大多数研究集中在欧洲和北美地区的温带或北方森林以及南非的热带稀树草原; 使用最多的遥感数据是机载高光谱数据, 而激光雷达作为补充数据, 通过单木分割及提供单木的三维垂直结构信息, 显著提高了分类精度; 支持向量机和随机森林作为应用最广的非参数分类算法, 平均分类精度达80%; 随着计算机技术及机器学习领域的不断成熟, 人工神经网络在物种识别领域得以迅速发展。基于此, 本文对目前基于遥感数据的植物物种分类与识别中在分类对象复杂性、多源遥感数据整合、植物物候与纹理特征整合和分类算法技术等方面面临的挑战进行了总结, 并建议通过整合多时相监测数据、高光谱和激光雷达数据、短波红外等特定波谱信息、采用深度学习等方法来提高分类精度。     

Recontextualising biodiversity in school practice

The finding that biodiversity is a concept with different context-specific meanings has implications for its conceptual development when students are required to apply it in a diversity of contexts. An approach that may overcome these implications is that students learn to recontextualise one meaning to another. Since no empirical studies were available when this study started, it was decided to conduct a design study to develop a learning and teaching strategy for recontextualising biodiversity. In this paper, the design of such a strategy is presented. Testing of the design in two classes in upper secondary biology education showed that it is largely practisable.     

柚类种质资源研究与保护概况

结合近年来对柚类种质资源的研究工作及资料,对柚类种质资源的生物生态学特征、生产利用、起源演化、遗传相互关系及遗传多样性、分类鉴定、资源保护等方面作了简单介绍,以明确进一步研究的方向与重点.     

The interaction between land use and catchment physiognomy: understanding avifaunal patterns of the Murray–Darling Basin,Australia

Aim We assessed whether different patterns of land use within similar physiognomic catchments (= watersheds) produced discernible effects on avian assemblages and, if so, whether such effects were related to particular land‐use activities (e.g. extensive cropping). Location Murray–Darling Basin in south‐eastern Australia. Methods We used a recently (2007) published physiognomic classification of catchments based on different stream orders as our template. We used a subset of data from the second Birds Australia atlas to calculate reporting rates for each species in each subcatchment. We linked these two sets of data with proportions of major land uses within catchments to identify whether differences in proportions of land uses altered the expected avifauna for catchments of the same nominal physiognomic class. Results A significant proportion of the variation in bird reporting rates was explained by the physiognomic classification. Additional explanatory power resulted from including an interaction matrix of land‐use covariates. Livestock grazing was a major explanatory variable in classes characterized by more mountainous catchments. Cropping affected avifaunas consistently by producing a more uniform assemblage. Main conclusions The physiognomic template was an important determinant of avifaunal composition, but its interaction with land‐use variation within physiognomic classes doubled the amount of variance explained. Within a physiognomic class, if one identifies the ‘ideal’ avifaunal composition for that class one can identify land‐use mixes that are most likely to be beneficial for the avifaunas of that class and recommend directions for large‐scale management objectives vis‐à‐vis mixtures of land‐use types.     

Increase of biodiversity in homogeneous Scots pine stands by an ecologically diversified management

Three important parameters of biodiversity in first generation Scots pine (Pinus sylvestris) forests on sandy soils have been evaluated: herbal layer diversity, natural regeneration and stand structure. The study took place in the Belgian Campine region, where the original oak–birch forest, degraded to heathlands in the course of time, were finally replaced by monocultures of Scots pine. These first generation pine forests are characterized by a low biodiversity. In maturing stands of this type, however, a spontaneous increase of biodiversity is noticed. Herbal species richness is very limited in all age classes. Different natural regeneration patterns are found. Referring to stand structure, the lengthening of the rotation favours the ingrowth of several hardwood species. As a consequence, the homogenous Scots pine stands are gradually and spontaneously transformed into heterogeneous mixed stands, featuring a noticeable increase in biodiversity. Selected human interventions may further increase biodiversity. The fundamental management principles are discussed: avoidance of major disturbances, lengthening of the rotation period, use of native tree species and natural regeneration, protection of microbiotopes and permanent monitoring.     

中国生物多样性保护优先区域生物多样性调查和评估方法

我国高度重视生物多样性保护,而开展本底调查是生物多样性保护的基础。但以往研究对苔藓、生物多样性相关传统知识等关注不够,而且调查大部分集中在生物多样性丰富区域。随着我国社会经济的快速发展,全国土地利用格局和生态环境发生了巨大变化,已有的部分调查成果数据与实际情况不符,难以满足我国生物多样性保护管理需求,因此亟待组织开展全国生物多样性调查与评估工作。在整理历史和现有生物多样性调查技术的基础上,推荐采用网格法开展全国生物多样性调查,按照10 km×10 km分辨率,将全国划分为97109个调查网格;制定了陆生高等植物、植被、陆生哺乳动物、鸟类、两栖类和爬行类、昆虫、大型真菌、内陆鱼类、内陆浮游生物、内陆大型底栖无脊椎动物、内陆周丛藻类以及生物多样性相关传统知识12个类群县域生物多样性调查评估技术规定;建立了全国统一、动态更新、信息共享的生物多样性数据库和信息化管理平台。从调查内容规范、评估指标体系和技术要求等方面探讨了陆域生态系统与物种调查、重点河流水生生物调查、重点物种调查、生物多样性相关传统知识调查技术方法,并构建生物多样性综合评估指标体系,规范了生物多样性保护优先区域生物多样性调查和评估。技术方法在横断山南、武陵山、太行山、西双版纳等生物多样性保护优先区域得到应用,同时北京、江苏、浙江和湖北等省份和祁连山、武夷山等区域也采用该技术体系开展调查,网格法得到逐步推广,并获得大量的生物多样性基础数据,为我国生物多样性保护和可持续利用、生物多样性公约履约等提供了基础数据。     

稻田节肢动物群落营养层及优势功能集团的组成与多样性动态

该项研究通过系统调查,把稻田节肢动物群落按营养和取食关系划分为三个营养层(基位物种,中位物种,顶位物种)和不同的功能集团,在物种、功能集团和营养层三个组织层次水平上探讨了稻田节肢动物群落的结构和多样性,较全面地考察了整个群落中物种和功能集团在时间上的结构动态、功能关系和数量消长规律。结果表明：功能集团多样性与种多样性的变化趋势较一致,在群落研究中似乎可以用对功能集团的研究代替对种的研究,从而简化物种间复杂的网络关系,认为这是研究群落物种间功能关系的途径之一。营养层多样性在时间序列过程中波动性较小,所以可用于群落相似性和稳定性的分析。研究分析了中性昆虫对害虫调控的意义,认为对于天敌作用的评价应以整个群落为基础,全面考虑天敌、害虫、以及中性昆虫的数量、丰盛度、空间时间生态位等信息。     

基于栖息地的城市湿地公园生物多样性特征与指标研究

城市湿地公园具有与湿地类似的生态功能和典型特征,对城市地区的生物多样性保护具有重要意义。本文对不同地区的城市湿地公园进行研究,包括不同气候类型、使用年份和面积大小等不同方面,并对野生动物栖息地特别是鸟类栖息地进行了数据统计和分类分析。通过文献研究、数据统计和比较分析,探索城市湿地公园生物多样性保护指标体系的基本组成及其相关性。本文写作目的是建立适当的城市湿地公园栖息地评估标准,支持生态中国建设。     

生物多样性科学前沿

由国际生物科学联盟（ＩＵＢＳ）在１９９１年首先提出,至今已由其它５个重要国际组织或项目（ＳＣＯＰＥ、ＵＮＥＳＣＯ,ＩＣＳＵ,ＩＧＢＰ－ＧＣＴＥ及ＩＵＭＳ）共同主持的ＤＩＶＥＲＳＩＴＡＳ是迄今生物多样性科学研究唯一的国际性项目。１９９６年７月,科学指导委员会草拟了本阶段新的操作计划,并于同年８月在ＩＵＢＳ执行委员会上讨论。操作计划详述了１０个组成方面的内容,其中５个为核心组成部分,其它５个为特别目标     

Links between global taxonomic diversity,ecological diversity and the expansion of vertebrates on land

Tetrapod biodiversity today is great; over the past 400 Myr since vertebrates moved onto land, global tetrapod diversity has risen exponentially, punctuated by losses during major extinctions. There are links between the total global diversity of tetrapods and the diversity of their ecological roles, yet no one fully understands the interplay of these two aspects of biodiversity and a numerical analysis of this relationship has not so far been undertaken. Here we show that the global taxonomic and ecological diversity of tetrapods are closely linked. Throughout geological time, patterns of global diversity of tetrapod families show 97 per cent correlation with ecological modes. Global taxonomic and ecological diversity of this group correlates closely with the dominant classes of tetrapods (amphibians in the Palaeozoic, reptiles in the Mesozoic, birds and mammals in the Cenozoic). These groups have driven ecological diversity by expansion and contraction of occupied ecospace, rather than by direct competition within existing ecospace and each group has used ecospace at a greater rate than their predecessors.     

中国生物物种编目进展与展望

发现并描述地球上的生物物种, 建立可靠的生物分类系统, 编制权威且具有时效性的生物物种名录, 实现生物物种多样性信息的数字化和共享, 对于生物多样性科学研究、资源管理、科学决策和社会经济发展都有重要意义。在全球和区域层面, 生物物种编目工作越来越被重视, 也取得了一些可喜的进展。为反映中国生物物种编目工作近些年取得的成绩, 本文联合各相关类群的专家, 分别总结了脊椎动物、昆虫和其他无脊椎动物、植物、菌物等主要类群的物种编目进展情况, 并就将来如何更好地促进生物编目工作的开展提出了展望。现有数据显示, 中国已记录哺乳动物698种, 鸟类1,450种, 爬行类586种, 两栖类611种, 淡水鱼类1,591种, 高等植物38,493种(其中维管植物35,379种), 菌物约27,900种, 但尚无全面的包括所有昆虫和无脊椎动物的物种名录。近10年, 中国新增维管植物5个新科、86个新属、2,090个新种、374个新记录; 新增菌物新物种4,679个, 隶属于36纲140目438科1,372属。     

Overlooked pitfalls in multi-class machine learning classification in radiation oncology and how to avoid them

In radiation oncology, Machine Learning classification publications are typically related to two outcome classes, e.g. the presence or absence of distant metastasis. However, multi-class classification problems also have great clinical relevance, e.g., predicting the grade of a treatment complication following lung irradiation. This work comprised two studies aimed at making work in this domain less prone to statistical blindsides.In multi-class classification, AUC is not defined, whereas correlation coefficients are. It may seem like solely quoting the correlation coefficient value (in lieu of the AUC value) is a suitable choice. In the first study, we illustrated using Monte Carlo (MC) models why this choice is misleading. We also considered the special case where the multiple classes are not ordinal, but nominal, and explained why Pearson or Spearman correlation coefficients are not only providing incomplete information but are actually meaningless.The second study concerned surrogate biomarkers for a clinical endpoint, which have purported benefits including potential for early assessment, being inexpensive, and being non-invasive. Using a MC experiment, we showed how conclusions derived from surrogate markers can be misleading. The simulated endpoint was radiation toxicity (scale of 0–5). The surrogate marker was the true toxicity grade plus a noise term. Five patient cohorts were simulated, including one control. Two of the cohorts were designed to have a statistically significant difference in toxicity. Under 1000 repeated experiments using the biomarker, these two cohorts were often found to be statistically indistinguishable, with the fraction of such occurrences rising with the level of noise.     

Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics

Next-generation sequencing (NGS) technologies have enabled the application of broad-scale sequencing in microbial biodiversity and metagenome studies. Biodiversity is usually targeted by classifying 16S ribosomal RNA genes, while metagenomic approaches target metabolic genes. However, both approaches remain isolated, as long as the taxonomic and functional information cannot be interrelated. Techniques like self-organizing maps (SOMs) have been applied to cluster metagenomes into taxon-specific bins in order to link biodiversity with functions, but have not been applied to broad-scale NGS-based metagenomics yet. Here, we provide a novel implementation, demonstrate its potential and practicability, and provide a web-based service for public usage. Evaluation with published data sets mimicking varyingly complex habitats resulted into classification specificities and sensitivities of close to 100% to above 90% from phylum to genus level for assemblies exceeding 8 kb for low and medium complexity data. When applied to five real-world metagenomes of medium complexity from direct pyrosequencing of marine subsurface waters, classifications of assemblies above 2.5 kb were in good agreement with fluorescence in situ hybridizations, indicating that biodiversity was mostly retained within the metagenomes, and confirming high classification specificities. This was validated by two protein-based classifications (PBCs) methods. SOMs were able to retrieve the relevant taxa down to the genus level, while surpassing PBCs in resolution. In order to make the approach accessible to a broad audience, we implemented a feature-rich web-based SOM application named TaxSOM, which is freely available at http://www.megx.net/toolbox/taxsom. TaxSOM can classify reads or assemblies exceeding 2.5 kb with high accuracy and thus assists in linking biodiversity and functions in metagenome studies, which is a precondition to study microbial ecology in a holistic fashion.     

Threshold Concepts and Their Use in Rangeland Management and Restoration: The Good, the Bad, and the Insidious

Ecological thresholds describe abrupt changes in ecological properties in time or space. In rangeland management, thresholds reflect changes in vegetation and soils that are expensive or impossible to reverse. The threshold concept has catalyzed important advances in rangeland management thinking, but it has also introduced two classes of drawbacks. First, the ambiguity of the term "threshold" and the desire for simplicity in its application has led to an overemphasis on classification thresholds, such as vegetation cover values. Uncritical use of classification thresholds may lead to the abandonment of management efforts in land areas that would otherwise benefit from intervention. Second, it is possible that the invocation of thresholds and irreversible degradation may eventually result in the wholesale conversion of land areas that would have been recoverable or served important societal functions, such as biodiversity maintenance, that are not reflected in threshold definitions. I conclude with a recommendation to clarify the nature of thresholds by defining the relationships among pattern, process, and degradation and distinguishing preventive thresholds from restoration thresholds. We must also broaden the attributes used to define states and thresholds.     

Stability of butterfly assemblages in relation to the level of numerical resolution and altitude

Quick studies on biodiversity are frequently used in conservation assessments. Conclusions from these studies would be consistent if assemblages under consideration are stable over time. The stability of butterfly assemblages in the Picos de Europa in northern Spain was examined at several levels of numerical resolution. The survey was carried out in 1993 and 1995, which allowed at least one complete turnover of all individuals in each locality. Butterfly assemblages were usually stable at the levels of number of species and total number of individuals, species presence and absence, and abundance rankings. But, absolute abundances of individual species changed from 1993 to 1995 out of synchrony with one another. Regional distributions and altitudinal ranges of species were also stable. Assemblages were similar in both study years, judging by similar site ordinations by reciprocal averaging. Overall, these results are in accordance with most studies where stability has been examined at several numerical levels; they also suggest that abundances of individual species do not vary enough to disrupt overall assemblage abundance rankings. Butterfly assemblages at sites at higher altitude tended to be more unstable in terms of abundance rankings and absolute abundances. This agrees with ecological theory predicting less stable assemblages in physically harsh environments. We concluded that monitoring for a relatively short time period can give a clear picture of both local and regional butterfly biodiversity and species composition.