Filling in the GAPS: evaluating completeness and coverage of open‐access biodiversity databases in the United States

Primary biodiversity data constitute observations of particular species at given points in time and space. Open‐access electronic databases provide unprecedented access to these data, but their usefulness in characterizing species distributions and patterns in biodiversity depend on how complete species inventories are at a given survey location and how uniformly distributed survey locations are along dimensions of time, space, and environment. Our aim was to compare completeness and coverage among three open‐access databases representing ten taxonomic groups (amphibians, birds, freshwater bivalves, crayfish, freshwater fish, fungi, insects, mammals, plants, and reptiles) in the contiguous United States. We compiled occurrence records from the Global Biodiversity Information Facility (GBIF), the North American Breeding Bird Survey (BBS), and federally administered fish surveys (FFS). We aggregated occurrence records by 0.1° × 0.1° grid cells and computed three completeness metrics to classify each grid cell as well‐surveyed or not. Next, we compared frequency distributions of surveyed grid cells to background environmental conditions in a GIS and performed Kolmogorov–Smirnov tests to quantify coverage through time, along two spatial gradients, and along eight environmental gradients. The three databases contributed >13.6 million reliable occurrence records distributed among >190,000 grid cells. The percent of well‐surveyed grid cells was substantially lower for GBIF (5.2%) than for systematic surveys (BBS and FFS; 82.5%). Still, the large number of GBIF occurrence records produced at least 250 well‐surveyed grid cells for six of nine taxonomic groups. Coverages of systematic surveys were less biased across spatial and environmental dimensions but were more biased in temporal coverage compared to GBIF data. GBIF coverages also varied among taxonomic groups, consistent with commonly recognized geographic, environmental, and institutional sampling biases. This comprehensive assessment of biodiversity data across the contiguous United States provides a prioritization scheme to fill in the gaps by contributing existing occurrence records to the public domain and planning future surveys.     

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。     

Spatial and taxonomic biases in bat records: Drivers and conservation implications in a megadiverse country

Biases in data availability have serious consequences on scientific inferences that can be derived. The potential consequences of these biases could be more detrimental in the less‐studied megadiverse regions, often characterized by high biodiversity and serious risks of human threats, as conservation and management actions could be misdirected. Here, focusing on 134 bat species in Mexico, we analyze spatial and taxonomic biases and their drivers in occurrence data; and identify priority areas for further data collection which are currently under‐sampled or at future environmental risk. We collated a comprehensive database of 26,192 presence‐only bat records in Mexico to characterize taxonomic and spatial biases and relate them to species' characteristics (range size and foraging behavior). Next, we examined variables related to accessibility, species richness and security to explain the spatial patterns in occurrence records. Finally, we compared the spatial distributions of existing data and future threats to these species to highlight those regions that are likely to experience an increased level of threats but are currently under‐surveyed. We found taxonomic biases, where species with wider geographical ranges and narrow‐space foragers (species easily captured with traditional methods), had more occurrence data. There was a significant oversampling toward tropical regions, and the presence and number of records was positively associated with areas of high topographic heterogeneity, road density, urban, and protected areas, and negatively associated with areas which were predicted to have future increases in temperature and precipitation. Sampling efforts for Mexican bats appear to have focused disproportionately on easily captured species, tropical regions, areas of high species richness and security; leading to under‐sampling in areas of high future threats. These biases could substantially influence the assessment of current status of, and future anthropogenic impacts on, this diverse species group in a tropical megadiverse country.     

A journey through time: exploring temporal patterns amongst digitized plant specimens from Australia

Online access to species occurrence records has opened new windows into investigating biodiversity patterns across multiple scales. The value of these records for research depends on their spatial, temporal, and taxonomic quality. We assessed temporal patterns in records from the Australasian Virtual Herbarium, asking: (1) How temporally consistent has collecting been across Australia? (2) Which areas of Australia have the most reliable records, in terms of temporal consistency and inventory completeness? (3) Are there temporal trends in the completeness of attribute information associated with records? We undertook a multi-step filtering procedure, then estimated temporal consistency and inventory completeness for sampling units (SUs) of 50?km ×?50?km. We found temporal bias in collecting, with 80% of records collected over the period 1970–1999. South-eastern Australia, the Wet Tropics in north-east Queensland, and parts of Western Australia have received the most consistent sampling effort over time, whereas much of central Australia has had low temporal consistency. Of the SUs, 18% have relatively complete inventories with high temporal consistency in sampling. We also determined that 25% of digitized records had missing attribute information. By identifying areas with low reliability, we can limit erroneous inferences about distribution patterns and identify priority areas for future sampling.     

Database records as a surrogate for sampling effort provide higher species richness estimations

The compilation of all the available taxonomic and distributional information on the species present in a territory frequently generates a biased picture of the distribution of biodiversity due to the uneven distribution of the sampling effort performed. Thus, quality protocol assessments such as those proposed by Hortal et al. (Conservation Biology 21:853–863, 2007) must be done before using this kind of information for basic and applied purposes. The discrimination of localities that can be considered relatively well-surveyed from those not surveyed enough is a key first step in this protocol and can be attained by the previous definition of a sampling effort surrogate and the calculation of survey completeness using different estimators. Recently it has been suggested that records from exhaustive databases can be used as a sampling-effort surrogate to recognize probable well-surveyed localities. In this paper, we use an Iberian dung beetle database to identify the 50 × 50 km UTM cells that appear to be reliably inventoried, using both data derived from standardized sampling protocols and database records as a surrogate for sampling effort. Observed and predicted species richness values in the shared cells defined as well-surveyed by both methods suggest that the use of database records provides higher species richness values, which are proportionally greater in the richest localities by the inclusion of rare species.     

A web-based GIS tool for exploring the world's biodiversity: The Global Biodiversity Information Facility Mapping and Analysis Portal Application (GBIF-MAPA)

Legacy biodiversity data from natural history and survey collections are rapidly becoming available in a common format over the Internet. Over 110 million records are already being served from the Global Biodiversity Information Facility (GBIF). However, our ability to use this information effectively for ecological research, management and conservation lags behind. A solution is a web-based Geographic Information System for enabling visualization and analysis of this rapidly expanding data resource. In this paper we detail a case study system, GBIF Mapping and Analysis Portal Application (MAPA), developed for deployment at distributed database portals. Building such a system requires overcoming a series of technical and research challenges. These challenges include: assuring fast speed of access to the vast amounts of data available through these distributed biodiversity databases; developing open standards based access to suitable environmental data layers for analyzing biodiversity distribution; building suitably flexible and intuitive map interfaces for refining the scope and criteria of an analysis; and building appropriate web-services based analysis tools that are of primary importance to the ecological community and make manifest the value of online biodiversity GBIF data. After discussing how we overcome these challenges, we provide case studies showing two examples of the use of GBIF-MAPA analysis tools.     

Patterns,biases and prospects in the distribution and diversity of Neotropical snakes

Motivation

We generated a novel database of Neotropical snakes (one of the world's richest herpetofauna) combining the most comprehensive, manually compiled distribution dataset with publicly available data. We assess, for the first time, the diversity patterns for all Neotropical snakes as well as sampling density and sampling biases.

Main types of variables contained

We compiled three databases of species occurrences: a dataset downloaded from the Global Biodiversity Information Facility (GBIF), a verified dataset built through taxonomic work and specialized literature, and a combined dataset comprising a cleaned version of the GBIF dataset merged with the verified dataset.

Spatial location and grain

Neotropics, Behrmann projection equivalent to 1° × 1°.

Time period

Specimens housed in museums during the last 150 years.

Major taxa studied

Squamata: Serpentes.

Software format

Geographical information system (GIS).

Results

The combined dataset provides the most comprehensive distribution database for Neotropical snakes to date. It contains 147,515 records for 886 species across 12 families, representing 74% of all species of snakes, spanning 27 countries in the Americas. Species richness and phylogenetic diversity show overall similar patterns. Amazonia is the least sampled Neotropical region, whereas most well‐sampled sites are located near large universities and scientific collections. We provide a list and updated maps of geographical distribution of all snake species surveyed.

Main conclusions

The biodiversity metrics of Neotropical snakes reflect patterns previously documented for other vertebrates, suggesting that similar factors may determine the diversity of both ectothermic and endothermic animals. We suggest conservation strategies for high‐diversity areas and sampling efforts be directed towards Amazonia and poorly known species.     

Global and national trends,gaps, and opportunities in documenting and monitoring species distributions

Conserving and managing biodiversity in the face of ongoing global change requires sufficient evidence to assess status and trends of species distributions. Here, we propose novel indicators of biodiversity data coverage and sampling effectiveness and analyze national trajectories in closing spatiotemporal knowledge gaps for terrestrial vertebrates (1950 to 2019). Despite a rapid rise in data coverage, particularly in the last 2 decades, strong geographic and taxonomic biases persist. For some taxa and regions, a tremendous growth in records failed to directly translate into newfound knowledge due to a sharp decline in sampling effectiveness. However, we found that a nation’s coverage was stronger for species for which it holds greater stewardship. As countries under the post-2020 Global Biodiversity Framework renew their commitments to an improved, rigorous biodiversity knowledge base, our findings highlight opportunities for international collaboration to close critical information gaps.

Conserving and managing biodiversity in the face of ongoing global change requires sufficient evidence to assess status and trends of species distributions. This study analyzes national trajectories in closing spatiotemporal knowledge gaps for terrestrial vertebrates (1950-2019) based on novel indicators of data coverage and sampling effectiveness.     

Skeletal completeness of the non‐avian theropod dinosaur fossil record

Non‐avian theropods were a highly successful clade of bipedal, predominantly carnivorous, dinosaurs. Their diversity and macroevolutionary patterns have been the subject of many studies. Changes in fossil specimen completeness through time and space can bias our understanding of macroevolution. Here, we quantify the completeness of 455 non‐avian theropod species using the skeletal completeness metric (SCM), which calculates the proportion of a complete skeleton preserved for a specimen. Temporal patterns of theropod skeletal completeness show peaks in the Carnian, Oxfordian–Kimmeridgian and Barremian–Aptian, and lows in the Berriasian and Hauterivian. Lagerstätten primarily drive the peaks in completeness and observed taxonomic diversity in the Oxfordian–Kimmeridgian and the Barremian–Aptian. Theropods have a significantly lower distribution of completeness scores than contemporary sauropodomorph dinosaurs but change in completeness through time for the two groups shows a significant correlation when conservation Lagerstätten are excluded, possibly indicating that both records are primarily driven by geology and sampling availability. Our results reveal relatively weak temporal sampling biases acting on the theropod record but relatively strong spatial and environmental biases. Asia has a significantly more complete record than any other continent, the mid northern latitudes have the highest abundance of finds, and most complete theropod skeletons come from lacustrine and aeolian environments. We suggest that these patterns result from historical research focus, modern climate dynamics, and depositional transportation energy plus association with conservation Lagerstätten, respectively. Furthermore, we find possible ecological biases acting on different theropod subgroups, but body size does not influence theropod completeness on a global scale.     

crabs—A software program to generate curated reference databases for metabarcoding sequencing data

The measurement of biodiversity is an integral aspect of life science research. With the establishment of second- and third-generation sequencing technologies, an increasing amount of metabarcoding data is being generated as we seek to describe the extent and patterns of biodiversity in multiple contexts. The reliability and accuracy of taxonomically assigning metabarcoding sequencing data have been shown to be critically influenced by the quality and completeness of reference databases. Custom, curated, eukaryotic reference databases, however, are scarce, as are the software programs for generating them. Here, we present crabs (Creating Reference databases for Amplicon-Based Sequencing), a software package to create custom reference databases for metabarcoding studies. crabs includes tools to download sequences from multiple online repositories (i.e., NCBI, BOLD, EMBL, MitoFish), retrieve amplicon regions through in silico PCR analysis and pairwise global alignments, curate the database through multiple filtering parameters (e.g., dereplication, sequence length, sequence quality, unresolved taxonomy, inclusion/exclusion filter), export the reference database in multiple formats for immediate use in taxonomy assignment software, and investigate the reference database through implemented visualizations for diversity, primer efficiency, reference sequence length, database completeness and taxonomic resolution. crabs is a versatile tool for generating curated reference databases of user-specified genetic markers to aid taxonomy assignment from metabarcoding sequencing data. crabs can be installed via docker and is available for download as a conda package and via GitHub ( https://github.com/gjeunen/reference_database_creator ).     

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.     

Assessing the Primary Data Hosted by the Spanish Node of the Global Biodiversity Information Facility (GBIF)

In order to effectively understand and cope with the current ‘biodiversity crisis’, having large-enough sets of qualified data is necessary. Information facilitators such as the Global Biodiversity Information Facility (GBIF) are ensuring increasing availability of primary biodiversity records by linking data collections spread over several institutions that have agreed to publish their data in a common access schema. We have assessed the primary records that one such publisher, the Spanish node of GBIF (GBIF.ES), hosts on behalf of a number of institutions, considered to be a highly representative sample of the total mass of available data for a country in order to know the quantity and quality of the information made available. Our results may provide an indication of the overall fitness-for-use in these data. We have found a number of patterns in the availability and accrual of data that seem to arise naturally from the digitization processes. Knowing these patterns and features may help deciding when and how these data can be used. Broadly, the error level seems low. The available data may be of capital importance for the development of biodiversity research, both locally and globally. However, wide swaths of records lack data elements such as georeferencing or taxonomical levels. Although the remaining information is ample and fit for many uses, improving the completeness of the records would likely increase the usability span for these data.     

基于在线数据库的鳞翅目刺蛾科昆虫物种多样性及其全球分布格局

鳞翅目刺蛾科昆虫在全球范围内广泛分布, 是重要经济林、行道林的主要害虫。本研究通过对在线数据库中刺蛾科昆虫分布数据进行整理分析, 阐明其在全球范围内的物种多样性及分布格局, 并初步探讨造成其物种分布不均的原因, 从而为物种多样性保护及害虫防治提供科学依据。通过检索生物条形码数据库(Barcode of Life Data System V4, BOLD V4)和全球生物多样性信息数据库(Global Biodiversity Information Facility, GBIF)中记录的标本信息, 并结合部分地区鳞翅目昆虫名录及野外采集样本数据, 对刺蛾科昆虫的分布信息进行汇总分析并绘制分布图。统计得到具有明确地理坐标的刺蛾科昆虫分布信息61,947条, 共187属637种。结果表明, 在世界动物地理区系尺度上, 东洋区刺蛾科昆虫物种多样性最高, 共72属, 古北区31属, 澳新区及新热带区均为27属, 非洲热带区22属, 新北区19属。在国家尺度上, 中国存在刺蛾科昆虫123种, 越南116种, 其次为哥斯达黎加(75种)和澳大利亚(69种)。中低纬度地区具有较高的刺蛾科昆虫物种多样性和丰富度, 这有可能与该地区的气候历史条件及丰富的寄主植物资源有关。     

Spatial turnover in the global avifauna

Despite its wide implications for many ecological issues, the global pattern of spatial turnover in the occurrence of species has been little studied, unlike the global pattern of species richness. Here, using a database on the breeding distributions of birds, we present the first global maps of variation in spatial turnover for an entire taxonomic class, a pattern that has to date remained largely a matter of conjecture, based on theoretical expectations and extrapolation of inconsistent patterns from different biogeographic realms. We use these maps to test four predictions from niche theory as to the form that this variation should take, namely that turnover should increase with species richness, towards lower latitudes, and with the steepness of environmental gradients and that variation in turnover is determined principally by rare (restricted) species. Contrary to prediction, we show that turnover is high both in areas of extremely low and high species richness, does not increase strongly towards the tropics, and is related both to average environmental conditions and spatial variation in those conditions. These results are closely associated with a further important and novel finding, namely that global patterns of spatial turnover are driven principally by widespread species rather than the restricted ones. This complements recent demonstrations that spatial patterns of species richness are also driven principally by widespread species, and thus provides an important contribution towards a unified model of how terrestrial biodiversity varies both within and between the Earth's major land masses.     

Imputing missing data in plant traits: A guide to improve gap-filling

Aim

Globally distributed plant trait data are increasingly used to understand relationships between biodiversity and ecosystem processes. However, global trait databases are sparse because they are compiled from many, mostly small databases. This sparsity in both trait space completeness and geographical distribution limits the potential for both multivariate and global analyses. Thus, ‘gap-filling’ approaches are often used to impute missing trait data. Recent methods, like Bayesian hierarchical probabilistic matrix factorization (BHPMF), can impute large and sparse data sets using side information. We investigate whether BHPMF imputation leads to biases in trait space and identify aspects influencing bias to provide guidance for its usage.

Innovation

We use a fully observed trait data set from which entries are randomly removed, along with extensive but sparse additional data. We use BHPMF for imputation and evaluate bias by: (1) accuracy (residuals, RMSE, trait means), (2) correlations (bi- and multivariate) and (3) taxonomic and functional clustering (valuewise, uni- and multivariate). BHPMF preserves general patterns of trait distributions but induces taxonomic clustering. Data set–external trait data had little effect on induced taxonomic clustering and stabilized trait–trait correlations.

Main Conclusions

Our study extends the criteria for the evaluation of gap-filling beyond RMSE, providing insight into statistical data structure and allowing better informed use of imputed trait data, with improved practice for imputation. We expect our findings to be valuable beyond applications in plant ecology, for any study using hierarchical side information for imputation.     

A new comprehensive database of alien plant species in Chile based on herbarium records

There is an urgent need for comprehensive national databases on alien plant species, especially in developing countries. Despite the fact that plant invasions are considered a major threat to biodiversity, they have been poorly studied or not considered a conservation priority in South America. We aim to assess alien plant distribution in Chile, using the first comprehensive public alien plant database, and discuss the implications of using herbarium records to develop national databases of alien plants. We used herbarium records to assemble a comprehensive national database of alien plants. We calculated the number of alien and native species and specimens recorded in each 10 × 10 km cell. We evaluated sampling efforts and tested for relationships between alien and native species collections, as well as other spatial patterns along the latitudinal gradient. Alien and native species richness was positively correlated. Alien plants were mostly collected in central Chile, with few species collected in both the extreme north and south. However, native plants were strongly collected in central Chile, as well as in both extremes of the country. Alien and native plants followed the same pattern of accumulation along the latitudinal gradient, with native plants being relatively more collected than alien plants. Herbarium records provide valuable baseline information to evaluate plant species distribution. However, there are important gaps in this database, (e.g. variable sampling effort for alien and native plants, incomplete information on life-history traits). Given scientists and land managers increasing demand for baseline information and the high cost of collecting such data in developing countries, herbarium records should be used more frequently for research and management of plant invasions.     

Nature’s untold stories: an overview on the availability and type of on-line data on long-term biodiversity monitoring

Long-term field-based monitoring is time and resource demanding. Consequently, there are few robust biodiversity databases that contain both a baseline and repeat measurements. On-line repositories represent a potential goldmine of conservation-relevant data, and are increasingly incentivized by funding agencies. However, there remains scarce information on their distribution and availability, limiting the possibility to exploit them to their full potential. Here we comprehensively searched and assessed open-access datasets where biodiversity has been monitored in the same site for at least 4 years, and where species and site locations were clearly reported. We located data on 75,669 field sites (9436 of which are in biodiversity hotspots), for a total of 28,723,226 records, monitoring a total of 15,046 different taxa. We found strong geographic and taxonomic biases. Monitoring sites were predominantly located in the Palearctic and Nearctic biogeographic realms and in the forest biome. Where fauna was monitored, the focus was mostly on amphibians and birds. Supporting open-access policies and developing strategies to fill the identified gaps will be crucial for improving our understanding of global biodiversity trends. Our results suggest, however, that we are on the right trajectory, with a vast storehouse of readily available (and often high quality) yet largely under-analysed biodiversity data now available online from a range of sources. We argue that such data can provide the required biodiversity baselines for national- or local-scale studies.