Towards a collaborative, global infrastructure for biodiversity assessment

Biodiversity data are rapidly becoming available over the Internet in common formats that promote sharing and exchange. Currently, these data are somewhat problematic, primarily with regard to geographic and taxonomic accuracy, for use in ecological research, natural resources management and conservation decision-making. However, web-based georeferencing tools that utilize best practices and gazetteer databases can be employed to improve geographic data. Taxonomic data quality can be improved through web-enabled valid taxon names databases and services, as well as more efficient mechanisms to return systematic research results and taxonomic misidentification rates back to the biodiversity community. Both of these are under construction. A separate but related challenge will be developing web-based visualization and analysis tools for tracking biodiversity change. Our aim was to discuss how such tools, combined with data of enhanced quality, will help transform today's portals to raw biodiversity data into nexuses of collaborative creation and sharing of biodiversity knowledge.     

A Higher Level Classification of All Living Organisms

We present a consensus classification of life to embrace the more than 1.6 million species already provided by more than 3,000 taxonomists’ expert opinions in a unified and coherent, hierarchically ranked system known as the Catalogue of Life (CoL). The intent of this collaborative effort is to provide a hierarchical classification serving not only the needs of the CoL’s database providers but also the diverse public-domain user community, most of whom are familiar with the Linnaean conceptual system of ordering taxon relationships. This classification is neither phylogenetic nor evolutionary but instead represents a consensus view that accommodates taxonomic choices and practical compromises among diverse expert opinions, public usages, and conflicting evidence about the boundaries between taxa and the ranks of major taxa, including kingdoms. Certain key issues, some not fully resolved, are addressed in particular. Beyond its immediate use as a management tool for the CoL and ITIS (Integrated Taxonomic Information System), it is immediately valuable as a reference for taxonomic and biodiversity research, as a tool for societal communication, and as a classificatory “backbone” for biodiversity databases, museum collections, libraries, and textbooks. Such a modern comprehensive hierarchy has not previously existed at this level of specificity.     

Comparing whole‐genome shotgun sequencing and DNA metabarcoding approaches for species identification and quantification of pollen species mixtures

Molecular identification of mixed‐species pollen samples has a range of applications in various fields of research. To date, such molecular identification has primarily been carried out via amplicon sequencing, but whole‐genome shotgun (WGS) sequencing of pollen DNA has potential advantages, including (1) more genetic information per sample and (2) the potential for better quantitative matching. In this study, we tested the performance of WGS sequencing methodology and publicly available reference sequences in identifying species and quantifying their relative abundance in pollen mock communities. Using mock communities previously analyzed with DNA metabarcoding, we sequenced approximately 200Mbp for each sample using Illumina HiSeq and MiSeq. Taxonomic identifications were based on the Kraken k‐mer identification method with reference libraries constructed from full‐genome and short read archive data from the NCBI database. We found WGS to be a reliable method for taxonomic identification of pollen with near 100% identification of species in mixtures but generating higher rates of false positives (reads not identified to the correct taxon at the required taxonomic level) relative to rbcL and ITS2 amplicon sequencing. For quantification of relative species abundance, WGS data provided a stronger correlation between pollen grain proportion and sequence read proportion, but diverged more from a 1:1 relationship, likely due to the higher rate of false positives. Currently, a limitation of WGS‐based pollen identification is the lack of representation of plant diversity in publicly available genome databases. As databases improve and costs drop, we expect that eventually genomics methods will become the methods of choice for species identification and quantification of mixed‐species pollen samples.     

Taxonomic bias in occurrence information of angiosperm species in China

Taxonomic bias is a well-known shortcoming of species occurrence databases. Understanding the causes of taxonomic bias facilitates future biological surveys and addresses current knowledge gaps. Here, we investigate the main drivers of taxonomic bias in occurrence data of angiosperm species in China. We used a database including 5,936,768 records for 28,968 angiosperm species derived from herbarium specimens and literature sources. Generalized additive models(GAMs) were applied to investigate explanatory powers of 17 variables on the variation in record numbers of species. Five explanatory variables were selected for a multi-predictor GAM that explained 69% of the variation in record numbers: plant height, range size, elevational range, numbers of scientific publications and web pages. Range size was the most important predictor in the model and positively correlated with number of records. Morphological and phenological traits and social-economic factors including economic values and conservation status had weak explanatory powers on record numbers of plant species, which differs from the findings in animals, suggesting that causes of taxonomic bias in occurrence databases may vary between taxonomic groups. Our results suggest that future floristic surveys in China should more focus on range-restricted and socially or scientifically less "interesting"species.     

FunRich: An open access standalone functional enrichment and interaction network analysis tool

As high‐throughput techniques including proteomics become more accessible to individual laboratories, there is an urgent need for a user‐friendly bioinformatics analysis system. Here, we describe FunRich, an open access, standalone functional enrichment and network analysis tool. FunRich is designed to be used by biologists with minimal or no support from computational and database experts. Using FunRich, users can perform functional enrichment analysis on background databases that are integrated from heterogeneous genomic and proteomic resources (>1.5 million annotations). Besides default human specific FunRich database, users can download data from the UniProt database, which currently supports 20 different taxonomies against which enrichment analysis can be performed. Moreover, the users can build their own custom databases and perform the enrichment analysis irrespective of organism. In addition to proteomics datasets, the custom database allows for the tool to be used for genomics, lipidomics and metabolomics datasets. Thus, FunRich allows for complete database customization and thereby permits for the tool to be exploited as a skeleton for enrichment analysis irrespective of the data type or organism used. FunRich ( http://www.funrich.org ) is user‐friendly and provides graphical representation (Venn, pie charts, bar graphs, column, heatmap and doughnuts) of the data with customizable font, scale and color (publication quality).     

全球外来入侵生物与植物有害生物数据库的比较评价

[目的]为了明确全球生物安全与植物保护领域内数据库建设进展和我国数据库的建设成效,对全球重要的外来入侵生物与植物有害生物数据库进行分类介绍和比较评价研究.[方法]根据数据库收录物种的地理范围、类群及数据库特色功能,对数据库进行分类.对重要数据库的主要功能进行简要介绍,设立多指标评价体系将我国数据库与国际优质数据库进行比...     

GBD-Explorer: Extending open source java GIS for exploring ecoregion-based biodiversity data

Biodiversity and ecosystem data are both geo-referenced and “species-referenced”. Ecoregion classification systems are relevant to basic ecological research and have been increasingly used for making policy and management decisions. There are practical needs to integrate taxonomic data with ecoregion data in a GIS to visualize and explore species distribution conveniently. In this study, we represent the species distributed in an ecoregion as a taxonomic tree and extend the classic GIS data model to incorporate operations on taxonomic trees. A prototype called GBD-Explorer was developed on top of the open source JUMP GIS. We use the World Wildlife Fund (WWF) terrestrial ecoregion and WildFinder species databases as an example to demonstrate the rich capabilities implemented in the prototype.     

Effect of non-native species on taxonomic and functional diversity of fish communities in different river types

Recent researches suggest that functional diversity represents the response of communities to environmental alterations better than taxonomic diversity. However, there is scarce information about how the functional diversity of freshwater fishes is affected by habitat type and the dominance of non-native species. To address this question, we analysed a large database containing 15 morpho-functional traits of 61 fish species from the Pannon Biogeographic region (Hungary). Based on a fish faunistic list and relative abundance of taxa, we quantified the taxonomic and functional diversity of riverine communities for?>?700 sites of six habitat types. We asked how non-native fishes affected the taxonomic and functional diversity in different river types and at the local scale (i.e. at the site level), and how the diversity measures of native fauna elements changes along the invasion gradient. Our results showed that both functional and taxonomic richness increases with habitat complexity, from small headwater streams to large rivers. Therefore taxonomic diversity served as a good proxy for functional diversity along the environmental gradient of river types. Non-natives showed considerable functional diversity relative to their species number in each habitat type. Diversity values of native fauna elements initially increased, and then showed a major decrease along the invasion gradient. River type-specific evaluations highlighted the importance of considering the proliferation of invasive species based on both taxonomic and functional diversity indices. We argue that type-specific action plans are needed in conservation management to preserve the taxonomic and functional diversity of native fishes in Hungary, but also elsewhere.

     

Mixed messages from multiple information sources on invasive species: a case of too much of a good thing?

Aim The increasing number and availability of online databases of alien species beg a question of their comparability given most do not adopt standard criteria in the definition of species status or taxonomic treatment and vary in their comprehensiveness. In this study, we compare the consistency of two major European databases for the regions they have in common. We assess whether they use consistent terminology to classify species status, provide similar taxonomic classification and coverage, deliver comparable estimates of alien richness per country and identify comparable correlates of alien richness. Location Northern Europe. Methods Data on the total number of alien species as well as the number of established alien species were extracted from the online databases DAISIE and NOBANIS for 13 European countries and classified into comparable taxonomic groups. Analyses across countries examined trends in alien species richness, correlations among taxonomic groups and the explanatory power of population density, country area and per capita GDP on alien species richness. Results Alien species richness, intertaxon correlations and the significance of individual drivers of invasion were all strongly database dependent. Differences were more marked for total numbers of aliens than established aliens. Over all taxonomic groups, DAISIE had lower species richness and fewer significant intertaxon correlations but presented a greater number of significant explanatory models of alien species richness. Trends in species richness were not generally correlated between the two databases with human population density being a more important driver in DAISIE while country area had greater explanatory power in NOBANIS. Main conclusions Considerable caution should be applied when collating data from different databases because often their underlying structure and content may differ markedly. For Europe, the analysis indicates that having two contrasting databases is not an ideal basis for implementing invasive species policy and moves should be made soon to establish a central pan‐European database.     

Use of Geographic Information Systems to monitor and predict non-native aquatic plant dispersal through north-eastern North America

North America has a growing problem with invasive aquatic plants. At every level of the aquatic food web, long-standing checks and balances have become dramatically eroded by the introduction of non-native species. The northeastern United States contains thousands of diverse freshwater habitats, highly heterogeneous in geology and locale, where nuisance aquatic plant growth results in decreased lake water quality, interference with recreational access, degraded flood control structures, and impacts to their aesthetic quality. Early infestation and spread of exotic species is often poorly documented at local and state levels. Consequently, successful management of these species depends on continuous monitoring and definitive identification by both public officials and waterside homeowners. With new mapping capabilities employing software such as Geographic Information Systems (GIS) coupled with the growing computerization of taxonomic records and online availability of regional herbarium records, we have been able to illustrate the␣temporal and geographic spread of these species, thus enabling aquatic ecologists and managers to make predictions of future infestations. In this paper we evaluate these techniques focusing on three of the most pervasive of exotic aquatic plant species in New York State: Myriophyllum spicatum, Trapa natans and Potamogeton crispus.     

中国菌物名录数据库在大型真菌红色名录编制中的作用

长期以来, 分类学的研究成果主要以平面的方式发表在各种纸质文献资料中。近年来, 随着计算机和人工智能等新兴技术的发展和应用, 平面资料信息的数字化成为一种趋势, 世界各国都非常重视本国生物资源信息的收集汇总, 构建了多种数据库, 为科学研究、政府决策、资源保护、合理利用和科学传播提供了重要的信息基础。本研究探索并建立从菌物学平面资料信息构建数据库的流程和方法, 并在中国菌物名录数据库和Index Fungorum所收集数据的基础上进行数据挖掘和分析。通过软件操作和程序设计, 在数据库中提取相关信息, 辅助完成了《中国生物多样性红色名录——大型真菌卷》的编制工作, 同时梳理和规范了菌物拉丁和汉语学名, 为菌物分类研究和资源评估与保护提供基础。     

海洋生物多样性信息资源

海洋生物多样性甚高, 但却饱受人为的破坏及干扰。目前全球最大的含点位数据的在线开放性数据库是海洋生物地理信息系统(OBIS), 共约12万种3,700万笔资料; 另一个较大的数据库世界海洋生物物种登录(WoRMS)已收集全球22万种海洋生物之物种分类信息。除此之外, 以海洋生物为主的单一类群的数据库只有鱼库(FishBase)、藻库(AlgaeBase)及世界六放珊瑚(Hexacorallians of the World)3个。跨类群及跨陆海域的全球性物种数据库则甚多, 如网络生命大百科(EOL)、全球生物物种名录(CoL)、整合分类信息系统(ITIS)、维基物种(Wikispecies)、ETI生物信息(ETI Bioinformatics)、生命条形码(BOL)、基因库(GenBank)、生物多样性历史文献图书馆(BHL)、海洋生物库(SeaLifeBase); 海洋物种鉴定入口网(Marine Species Identification Portal)、FAO渔业及水产养殖概要(FAO Fisheries and Aquaculture Fact Sheets)等可查询以分类或物种解说为主的数据库。全球生物多样性信息网络(GBIF)、发现生命(Discover Life)、水生物图库(AquaMaps)等则是以生态分布数据为主, 且可作地理分布图并提供下载功能, 甚至于可以改变水温、盐度等环境因子的参数值, 利用既定的模式作参数改变后之物种分布预测。谷歌地球(Google Earth)及国家地理(National Geographic)网站中的海洋子网页, 以及珊瑚礁库(ReefBase)等官方机构或非政府组织之网站, 则大多以海洋保育的教育倡导为主, 所提供的信息及素材可谓包罗万象, 令人目不暇给。更令用户感到方便的是上述许多网站或数据库彼此间均已可交互链接及查询。另外, 属于搜索引擎的谷歌图片(Google Images)与谷歌学术(Google Scholar)透过海洋生物数据库所提供的直接链接, 在充实物种生态图片与学术论文上亦发挥极大帮助, 让用户获得丰富多样的信息。为了保育之目的, 生物多样性数据库除了整合与公开分享外, 还应鼓励并推荐大家来使用。本文乃举Rainer Froese在巴黎演讲之内容为例, 介绍如何使用海洋生物多样性之数据来预测气候变迁对鱼类分布的影响。最后就中国大陆与台湾目前海洋生物多样性数据库的现况、两岸的合作及如何与国际接轨作介绍。     

Invasive species in China — an overview

China is a vast country with rich biodiversity, which makes China especially vulnerable to invasive species. It has a long history of introduction of non-native species, especially those with perceived beneficial impacts. Its rapid economic development, including an explosive growth in international trade and transportation, has increased the potential for new introductions. Currently, alien species are widespread in the country, occur in many ecosystems, represent most major taxonomic groups, and are introduced unintentionally as well as intentionally for cultivation. The paper lists various cases of invasive species which have caused significant threats or damages to local natural or artificial ecosystems, and indicates that two example industries (fresh water fisheries and lawn grasses) have brought or tend to bring in many invasive species and hence have caused or will cause changes and loss of biodiversity in local ecosystems. Based on these studies, it is suggested that China combat the problem through enhancing awareness, development of a database on invasive species, strengthening international co-operation, preparing case studies and introducing the necessary legislation, regulations and monitoring.     

Taxonomic and Distributional Databases of Fishes in Taiwan

The fishes of Taiwan comprise total 2450 species in 250 families, about 1/10 of the world's fishes. Curatorial and distributional data of Taiwanese fish have been integrated into a database that can be accessed interactively on the Internet at http://fishdb.sinica.edu.tw. The database includes the following items: basic information and specimen photo of each species, distributional database, bibliographic database, curatorial database, inquiring system for Chinese fish names of the world fishes, and new version of erratum of Fishes of Taiwan. The above regional database of Taiwanese fishes provides hyperlinks to fish data for each species in the global fish data, FishBase, of ICLARM (http://www.fishbase.org). Through the collaboration with FishBase and other global networks for taxonomic purposes, like Species 2000, BioNet, or GBIF (Global Biodiversity Information Facilities), users in the world can also obtain updated data provided by Taiwan. We hope our experience with database establishment can be used as a model to help other countries to develop their own regional fish databases or even to build up databases of other groups of organisms. There should be one good approach for all people in the world for sharing complete and updated biodiversity information via the Internet.     

外来物种入侵大数据采集方法的建立与应用

为准确、快速地获取入侵生物野外调查数据, 我们基于全球卫星导航系统、地理信息系统、移动互联网等现代信息技术提出了外来物种入侵大数据采集方法, 设计并研发了数据表单可自定义的野外调查工具软件——云采集。该系统以Android手机为数据采集终端, 采用C#和Java语言设计开发, 运用卫星导航定位技术实现野外调查发生位置的快速采集, 通过定义9种调查指标的数据类型及指标(列值)默认值、图像拍摄、语音录入、排序等4个辅助属性, 建立调查指标与手机客户端数据录入界面的关联, 实现用户界面可定制的数据录入模式。该系统在国家重点研发项目、福建省科技重大专项及福建省红火蚁(Solenopsis invicta)疫情普查等项目的调查任务中予以应用。实践检验表明: 该系统实现了野外调查数据的离线采集、数据同步、数据查询与输出管理, 将移动智能终端采集取代传统的纸笔记录, 简化了野外调查的流程, 提高了入侵生物野外调查的数据质量, 为外来生物入侵野外调查大数据采集提供了信息化支持。     

The alien flora of Europe: a taxonomic and biogeographic review

Abstract. A geographic and taxonomic overview of the non-indigenous plant species of Europe, based on the ‘Flora Europaea’ is given. The flora of Europe includes 1568 species which have either expanded their ranges within Europe under human influence (naturalized European species) or are of non-European origin (exotic species). The latter group consists of 580 species (37%) which form a diverse group in terms of their taxonomic composition and geographic origin. The exotics are represented by 113 families, of which the Compositae, Rosaceae and Gramineae are most important. The ratio of species to families is low. Most exotic species in Europe originate from the Americas and Asia. Countries of southern Europe have a higher relative number of exotics in their non-native flora than northern ones. The species-range size distribution differs between naturalized European and exotic species; the latter are on average more widespread than the naturalized.