How Global Is the Global Biodiversity Information Facility?

There is a concerted global effort to digitize biodiversity occurrence data from herbarium and museum collections that together offer an unparalleled archive of life on Earth over the past few centuries. The Global Biodiversity Information Facility provides the largest single gateway to these data. Since 2004 it has provided a single point of access to specimen data from databases of biological surveys and collections. Biologists now have rapid access to more than 120 million observations, for use in many biological analyses. We investigate the quality and coverage of data digitally available, from the perspective of a biologist seeking distribution data for spatial analysis on a global scale. We present an example of automatic verification of geographic data using distributions from the International Legume Database and Information Service to test empirically, issues of geographic coverage and accuracy. There are over 1/2 million records covering 31% of all Legume species, and 84% of these records pass geographic validation. These data are not yet a global biodiversity resource for all species, or all countries. A user will encounter many biases and gaps in these data which should be understood before data are used or analyzed. The data are notably deficient in many of the world's biodiversity hotspots. The deficiencies in data coverage can be resolved by an increased application of resources to digitize and publish data throughout these most diverse regions. But in the push to provide ever more data online, we should not forget that consistent data quality is of paramount importance if the data are to be useful in capturing a meaningful picture of life on Earth.     

The contribution of small collections to species distribution modelling: A case study from Fuireneae (Cyperaceae)

The recent and rapid digitization of biodiversity data from natural history collection (NHC) archives has enriched collections based data repositories; this data continues to inform studies of species' geographic distributions. Here we investigate the relative impact of plant data from small natural history collections (collections with < 100,000 specimens) on species distributional models in an effort to document the potential of data from small NHCs to contribute to and inform biodiversity research. We modelled suitable habitat of five test case species from Fuireneae (Cyperaceae) in the United States using specimen records available via the Global Biodiversity Information Facility and that of data ready to mobilize from two regional small herbaria. Data were partitioned into three datasets based on their source: 1) collections-based records from large NHCs accessed GBIF, 2) collections-based records from small NHCs accessed from GBIF, and 3) collections-based records from two small regional herbaria not yet mobilized to GBIF. We extracted and evaluated the ecological niche represented for each of the three datasets by applying dataset occurrences to 14 environmental factors, and we modelled habitat suitability using Maxent to compare the represented distribution of the environmental values among the datasets. Our analyses indicate that the data from small NHCs contributed unique information in both geographic and environmental space. When data from small collections were combined with data from large collections, species models of the ecological niche resulted in more refined predictions of habitat suitability, indicating that small collections can contribute unique occurrence data which enhance species distribution models by bridging geographic collection gaps and shifting modelled predictions of suitable habitat. Inclusion of specimen records from small collections in ongoing digitization efforts is essential for generating informed models of a species' niche and distribution.     

Awareness and use of biodiversity collections by fish biologists

A survey of 280 fish biologists from a diverse pool of disciplines was conducted in order to assess the use made of biodiversity collections and how collections can better collect, curate and share the data they have. From the responses, data for how fish biologists use collections, what data they find the most useful, what factors influence the decisions to use collections, how they access the data and explore why some fish biologists make the decision to not use biodiversity collections is collated and reported. The results of which could be used to formulate sustainability plans for collections administrators and staff who curate fish biodiversity collections, while also highlighting the diversity of data and uses to researchers.     

How to describe species richness patterns for bryophyte conservation?

A large amount of data for inconspicuous taxa is stored in natural history collections; however, this information is often neglected for biodiversity patterns studies. Here, we evaluate the performance of direct interpolation of museum collections data, equivalent to the traditional approach used in bryophyte conservation planning, and stacked species distribution models (S‐SDMs) to produce reliable reconstructions of species richness patterns, given that differences between these methods have been insufficiently evaluated for inconspicuous taxa. Our objective was to contrast if species distribution models produce better inferences of diversity richness than simply selecting areas with the higher species numbers. As model species, we selected Iberian species of the genus Grimmia (Bryophyta), and we used four well‐collected areas to compare and validate the following models: 1) four Maxent richness models, each generated without the data from one of the four areas, and a reference model created using all of the data and 2) four richness models obtained through direct spatial interpolation, each generated without the data from one area, and a reference model created with all of the data. The correlations between the partial and reference Maxent models were higher in all cases (0.45 to 0.99), whereas the correlations between the spatial interpolation models were negative and weak (−0.3 to −0.06). Our results demonstrate for the first time that S‐SDMs offer a useful tool for identifying detailed richness patterns for inconspicuous taxa such as bryophytes and improving incomplete distributions by assessing the potential richness of under‐surveyed areas, filling major gaps in the available data. In addition, the proposed strategy would enhance the value of the vast number of specimens housed in biological collections.     

Marine biological collections in the 21st century

From the time of Linnaeus forward, it has been appreciated that collections, not least marine biological collections, are fundamental to the understanding of the biodiversity of life on earth, especially when they contain type specimens which define individual species. Historical collections are particularly rich in types and also represent a model of the biodiversity of marine life at the time of the collection, often centuries ago. The taxonomic and systematic importance of collections is well appreciated, as is the significance of time series of data in this period of anthropogenic environmental change. The application of new techniques increases the value of collected material even further, for example, molecular biology techniques allowing the recognition of new (often cryptic) taxa and their distributions, and stable isotope analyses releasing information on past and present ontogenies, geographical distributions and diets. Moreover the new era of information technology with associated digitization enables the release of the information stored in the collections to the scientists of the world.     

Regionalization of the avifauna of the Baja California Peninsula, Mexico: a parsimony analysis of endemicity and distributional modelling approach

Aim To analyse the distributional patterns of the Baja California Peninsula's resident avifauna, and to generate a regionalization based on a method that uses a parsimony analysis (parsimony analysis of endemicity, PAE) of point data and modelled potential distributions. Location The Baja California Peninsula, Mexico. Methods A data base was constructed containing records of 113 species of resident terrestrial birds present in the Baja California Peninsula. Records and localities were obtained from the literature and from specimens housed in scientific collections world‐wide. Raw data points and potential distribution maps obtained using the software Genetic Algorithms for Rule‐set Prediction (GARP), were analysed with PAE. Results The data base consisted of 4164 unique records (only one combination of species/locality) belonging to 113 terrestrial resident bird species, in a total of 809 localities. From the point distribution matrix, the analysis generated 500 equally parsimonious trees, from which a strict consensus cladogram with 967 steps was obtained. The cladogram shows a basal polytomy and some geographical correspondence of a few resolved groups obtained in the analysis. These results do not allow the recognition of areas defined by avifaunistic associations. From the potential distribution matrix, the analysis generated 501 equally parsimonious trees, and a strict consensus cladogram of 516 steps was obtained. The cladogram shows a higher resolution because of the number of resolved groups with better geographical correspondence and therefore regions are well‐defined. Main conclusions The correspondence of some groupings of species suggest their validity as areas with biogeographical (historical and/or ecological) meaning. This regionalization in the Baja California avifauna seems to be consistent with previous regionalizations for other groups. Hence, PAE is a useful tool for area categorization if reliable point records and prediction tools are available. Our results suggest that the geographical definition is much better using potential data generated by GARP, particularly when they are contrasted with the results from point data. Thus, this is an excellent alternative for developing biogeographical studies, as well as for improving the use of data from scientific collections and other sources of biodiversity information.     

Biological collections and ecological/environmental research: a review,some observations and a look to the future

Housed worldwide, mostly in museums and herbaria, is a vast collection of biological specimens developed over centuries. These biological collections, and associated taxonomic and systematic research, have received considerable long‐term public support. The work remaining in systematics has been expanding as the estimated total number of species of organisms on Earth has risen over recent decades, as have estimated numbers of undescribed species. Despite this increasing task, support for taxonomic and systematic research, and biological collections upon which such research is based, has declined over the last 30‐40 years, while other areas of biological research have grown considerably, especially those that focus on environmental issues. Reflecting increases in research that deals with ecological questions (e.g. what determines species distribution and abundance) or environmental issues (e.g. toxic pollution), the level of research attempting to use biological collections in museums or herbaria in an ecological/environmental context has risen dramatically during about the last 20 years. The perceived relevance of biological collections, and hence the support they receive, should be enhanced if this trend continues and they are used prominently regarding such environmental issues as anthropogenic loss of biodiversity and associated ecosystem function, global climate change, and decay of the epidemiological environment. It is unclear, however, how best to use biological collections in the context of such ecological/environmental issues or how best to manage collections to facilitate such use. We demonstrate considerable and increasingly realized potential for research based on biological collections to contribute to ecological/environmental understanding. However, because biological collections were not originally intended for use regarding such issues and have inherent biases and limitations, they are proving more useful in some contexts than in others. Biological collections have, for example, been particularly useful as sources of information regarding variation in attributes of individuals (e.g. morphology, chemical composition) in relation to environmental variables, and provided important information in relation to species' distributions, but less useful in the contexts of habitat associations and population sizes. Changes to policies, strategies and procedures associated with biological collections could mitigate these biases and limitations, and hence make such collections more useful in the context of ecological/environmental issues. Haphazard and opportunistic collecting could be replaced with strategies for adding to existing collections that prioritize projects that use biological collections and include, besides taxonomy and systematics, a focus on significant environmental/ecological issues. Other potential changes include increased recording of the nature and extent of collecting effort and information associated with each specimen such as nearby habitat and other individuals observed but not collected. Such changes have begun to occur within some institutions. Institutions that house biological collections should, we think, pursue a mission of ‘understanding the life of the planet to inform its stewardship’ ( Krishtalka & Humphrey, 2000 ), as such a mission would facilitate increased use of biological collections in an ecological/environmental context and hence lead to increased appreciation, encouragement and support from the public for these collections, their associated research, and the institutions that house them.     

The data void in modeling current and future distributions of tropical species

Conserving biodiversity in the face of climate change requires a predictive ecology of species distributions. Nowhere is this need more acute than in the tropics, which harbor the majority of Earth's species and face rapid and large climate and land‐use changes. However, the study of species distributions and their responses to climate change in high diversity tropical regions is potentially crippled by a lack of basic data. We analyzed a database representing more than 800 000 unique geo‐referenced natural history collections to determine what fraction of tropical plant species has sufficient numbers of available collections for use in the habitat or niche models commonly used to predict species responses to climate change. We found that more than nine out of 10 species from the three principle tropical realms are so poorly collected (n < 20 records) that they are essentially invisible to modern modeling and conservation tools. In order to predict the impact of climate change on tropical species, efforts must be made to increase the amount of data available from tropical countries through a combination of collecting new specimens and digitizing existing records.     

Gradients in the distribution of riverine benthos

SUMMARY. 1. Numerous hypotheses regarding the controls on species distributions in streams depend on longitudinal analyses of collections of stream organisms. Techniques for the detection of trends and for the detection of station groupings among biological collections have been widely reported, but rarely compared with each other. We have conducted an analysis of ten or eleven samples from each of thirteen stations along a stream abiotic gradient, and have compared several techniques.
2. An analysis of longitudinal distribution must first assess the existence of a gradient in biotic composition. Random skewers on species proportions were the most sensitive in demonstrating such a gradient. Q and M statistics were most useful in further describing the trend due to their additive properties; i.e. the importance of one or more stations in dictating the trend may be determined. Cluster analysis, as well as percent faunal similarity, was most efficient at isolating station groupings. Techniques such as faunal replacement and species loss calculations are generally more useful in testing hypotheses about controls on species distributions, and should be employed where potential causal factors may be isolated.     

Spatial conservation priorities are highly sensitive to choice of biodiversity surrogates and species distribution model type

Pressure to conserve biodiversity with limited resources has led to increasing use of species distribution models (SDMs) for spatial conservation prioritization. Published spatial prioritization exercises often focus on well‐studied groups, with data compiled from on‐line databases of ad‐hoc collections. Conservation plans generally aim to protect all components of biodiversity, and it is implied that the species used in prioritization act as surrogates. Here, we assess the sensitivity of spatial priorities to model and surrogate choice using a case study from a fragmented agricultural area of south eastern Australia that is poorly represented in the national reserve system. We model the distributions of 30 species of bird, microbat and bee using two types of SDM; generalised linear models based on systematic surveys that yield presence and absence observations, and MaxEnt models based on biodiversity database records. Eight prioritization scenarios were tested using Zonation software, and were based on either the presence–background or presence–absence SDMs and combinations of surrogacy among the three taxa. We found low correlations between SDMs generated for the same species using different modelling frameworks (μ = 0.18, n = 26). Area under the receiver operating characteristic curve (AUC) estimates generated by MaxEnt were optimistic; on average 1.36 times higher than when tested against the systematic survey data. Conservation priorities were sensitive to the choice of surrogate and type of data used to fit SDMs, and though bats and birds formed moderately good surrogates for each other, there was less compelling evidence of surrogacy for bees. Because valid surrogacy is unlikely with most existing data sets, investment in high quality data for less‐surveyed groups prior to planning should still be a priority. If this is not possible, then it is advisable to analyse the sensitivity of conservation plans to the assumed surrogacy and quality of data available.     

利用最大熵模型和规则集遗传算法模型预测孑遗植物裸果木的潜在地理分布及格局

利用野外调查的16个居群分布点和7个环境因子图层, 选择最大熵模型(MAXENT)和规则集遗传算法模型(GARP), 在地理和环境空间上模拟了第三纪孑遗植物裸果木(Gymnocarpos przewalskii)在中国西北地区的潜在分布。结果表明: (1)裸果木的潜在适生区全部集中在西北荒漠区, 其中最佳适生区主要集中在3个区域, 一是河西走廊中部和玉门以西、宁夏北部及内蒙古乌拉特后旗; 二是塔里木盆地西北缘; 三是柴达木盆地西北缘两片极小的高度适生区。裸果木的生态位被确定在一个较广的干旱环境空间: 适生区极端最高气温基本上在29.2-36.8 ℃之间, 极端最低气温在-18.3至-13.4 ℃之间; 年平均降水量40-200 mm; 潜在蒸发率在3-15之间。(2) MAXENT和GARP模型都较好地预测了裸果木的潜在分布, 但GARP产生了相对较大、较连续的潜在分布区, 部分过预测了破碎化生境; 而MAXENT预测到的潜在分布区, 在不同区域具有不同的环境适生性指数, 而且成功地排除了不合理的破碎化分布, 从而更直观地展示了裸果木的潜在分布格局和生态位要求。     

Will climate change promote future invasions?

Biological invasion is increasingly recognized as one of the greatest threats to biodiversity. Using ensemble forecasts from species distribution models to project future suitable areas of the 100 of the world's worst invasive species defined by the International Union for the Conservation of Nature, we show that both climate and land use changes will likely cause drastic species range shifts. Looking at potential spatial aggregation of invasive species, we identify three future hotspots of invasion in Europe, northeastern North America, and Oceania. We also emphasize that some regions could lose a significant number of invasive alien species, creating opportunities for ecosystem restoration. From the list of 100, scenarios of potential range distributions show a consistent shrinking for invasive amphibians and birds, while for aquatic and terrestrial invertebrates distributions are projected to substantially increase in most cases. Given the harmful impacts these invasive species currently have on ecosystems, these species will likely dramatically influence the future of biodiversity.     

Quantifying regional biodiversity in the tropics: A case study of freshwater fish in Trinidad and Tobago

Extinction rates are predicted to accelerate during the Anthropocene. Quantifying and mitigating these extinctions demands robust data on distributions of species and the diversity of taxa in regional biotas. However, many assemblages, particularly those in the tropics, are poorly characterized. Targeted surveys and historical museum collections are increasingly being used to meet the urgent need for accurate information, but the extent to which these contrasting data sources support meaningful inferences about biodiversity change in regional assemblages remains unclear. Here, we seek to elucidate uncertainty surrounding regional biodiversity estimates by evaluating the performance of these alternative methods in estimating the species richness and assemblage composition of the freshwater fish of Trinidad & Tobago. We compared estimates of regional species richness derived from two freshwater fish datasets: a targeted two year survey of Trinidad & Tobago rivers and historical museum collection records submitted to The University of the West Indies Zoology Museum. Richness was estimated using rarefaction and extrapolation, and assemblage composition was benchmarked against a recent literature review. Both datasets provided similar estimates of regional freshwater fish species richness (50 and 46 species, respectively), with a large overlap (85%) in species identities. Regional species richness estimates based on survey and museum data are thus comparable, and consistent in the species they include. Our results suggest that museum collection data are a viable option for setting reliable baselines in many tropical systems, thereby widening options for meaningful monitoring and evaluation of temporal trends. Abstract in Spanish is available with online material.     

Modelling the known and unknown plant biodiversity of the Amazon Basin

Aims The overall aim of this study is to provide the data needed for Amazonian conservation and the sustainable management of the region. To this end I model the hypothetical distribution of plant species richness across the Amazon Basin, the distribution of the proportion of this species richness that can be accounted for by described species, and hence the distribution of the biodiversity which remains unknown. Location Amazonia, Neotropics. Methods Species richness across the Amazon Basin is estimated by comparing the occurrences of 1584 species of Magnoliophyta whose taxonomy and geographical distributions are relatively well known. These data are used to collate checklists for squares of 1° latitude by 1° longitude. Comparison of the checklists allows estimation of the relative expected diversity in the vicinity of each degree square. Summing the distributions of the hypothetical real ranges gives the proportion of the biodiversity that can be accounted for by described species. Subtraction of the second distribution from the first gives a distribution of the contribution to the overall biodiversity that the model predicts, potentially, results from as yet undescribed species. Results Collections documented in recent botanical monographs show an extremely biased distribution with the best knowledge being found in a very few relatively well‐collected areas. At the degree square level, this model predicts that gamma biodiversity in the Amazon Basin is uniformly high across most of the basin. The model predicts that four large areas of the basin are particularly poorly known, and that they should contain large numbers of uncollected species. Main conclusions The model presented here highlights the difficulties of quantifying Amazonian plant diversity and its distribution. The low density of collections, and especially their extremely clumped distribution, undermines confidence in theories that seek to explain the apparent distribution of biodiversity. The model's prediction is substantially different from published predictions of the distribution of alpha diversity. Testing of this model in the areas identified as lacunae would require collecting programmes designed to collect fertile material of rare species. If the model's predictions are approximately accurate, the plant biodiversity of the Amazon Basin is considerably underestimated.     

基于物种的大尺度生物多样性热点研究方法

生物多样性热点是建立保护区、制定保护决策的依据,是生物保护研究的热点问题之一。基于物种的研究方法是大尺度陆地生物多样性热点的主要研究方法,但数据的缺乏限制了直接根据物种丰富度确定热点的方法,因此研究中经常采用其他方法间接的反映物种情况,介绍了4种主要的基于物种的替代方法:指示种、高级分类单元、环境模型和景观异质性,详细阐述了各种方法存在的利弊,并从数据的可获取性、操作的便捷性和对物种特征的反映3个方面对各种方法进行了评价。任何单一的方法都无法准确反映出生物多样性热点的真实分布。合适的研究方法是权衡研究目的、时间和资金的结果,建议选择优势互补的多种方法。     

Cryptic polychaete diversity: a review

This review summarises the current knowledge on cryptic species of polychaetes, one of the most dominant taxa in marine communities, and gives a brief overview of the different methods that has been used for their disclosure. Cryptic species constitute an important part of biodiversity and they are common among all kinds of polychaetes, with different life history traits, and may have sympatric as well as allopatric distributions. It is emphasised that cryptic species must not be neglected for a variety of reasons, and even though the magnitude of cryptic species is largely unknown the available data on polychaetes clearly demonstrate that morphology alone seriously underestimate the number of species. It is suggested that future research should focus on appropriately designed case‐studies using combined approaches, as well as on large‐scale whole sample analyses using next‐generation sequencing in order to be able to answer the many questions that still remains.     

Marshalling existing biodiversity data to evaluate biodiversity status and trends in planning exercises

A thorough understanding of biodiversity status and trends through time is necessary for decision-making at regional, national, and subnational levels. Information readily available in databases allows for development of scenarios of species distribution in relation to habitat changes. Existing species occurrence data are biased towards some taxonomic groups (especially vertebrates), and are more complete for Europe and North America than for the rest of the world. We outline a procedure for development of such biodiversity scenarios using available data on species distribution derived from primary biodiversity data and habitat conditions, and analytical software, which allows estimation of species’ distributions, and forecasting of likely effects of various agents of change on the distribution and status of the same species. Such approaches can translate into improved knowledge for countries regarding the 2010 Biodiversity Target of reducing significantly the rate of biodiversity loss—indeed, using methodologies such as those illustrated herein, many countries should be capable of analyzing trends of change for at least part of their biodiversity. Sources of errors that are present in primary biodiversity data and that can affect projections are discussed.     

Sampling bias and the use of ecological niche modeling in conservation planning: a field evaluation in a biodiversity hotspot

Ecological niche modeling (ENM) has become an important tool in conservation biology. Despite its recent success, several basic issues related to algorithm performance are still being debated. We assess the ability of two of the most popular algorithms, GARP and Maxent, to predict distributions when sampling is geographically biased. We use an extensive data set collected in the Brazilian Cerrado, a biodiversity hotspot in South America. We found that both algorithms give richness predictions that are very similar to other traditionally used richness estimators. Also, both algorithms correctly predicted the presence of most species collected during fieldwork, and failed to predict species collected only in very few cases (usually species with very few known localities, i.e., <5). We also found that Maxent tends to be more sensitive to sampling bias than GARP. However, Maxent performs better when sampling is poor (e.g., low number of data points). Our results indicates that ENM, even when provided with limited and geographically biased localities, is a very useful technique to estimate richness and composition of unsampled areas. We conclude that data generated by ENM maximize the utility of existing biodiversity data, providing a very useful first evaluation. However, for reliable conservation decisions ENM data must be followed by well-designed field inventories, especially for the detection of restricted range, rare species.     

Historical Museology Meets Tropical Biodiversity Conservation

The great scientific importance of historical collections is a well-established fact. On the contrary, their value as vehicles to promote public awareness and effective conservation projects in some of the most valuable biodiversity hotspots in the tropics appear to have been greatly overlooked by Natural History Museums and similar institutions. Utilising the vertebrate collections of Italian institutions as a case study, the great potential of these medium-sized museums to popularising and promoting biodiversity in some of the most valuable regions of the world, utilising the history of their collections and of the men which collected and studied them, is emphasised.     

Applying climatically associated species pools to the modelling of compositional change in tropical montane forests

Aim Predictive species distribution modelling is a useful tool for extracting the maximum amount of information from biological collections and floristic inventories. However, in many tropical regions records are only available from a small number of sites. This can limit the application of predictive modelling, particularly in the case of rare and endangered species. We aim to address this problem by developing a methodology for defining and mapping species pools associated with climatic variables in order to investigate potential species turnover and regional species loss under climate change scenarios combined with anthropogenic disturbance. Location The study covered an area of 6800 km² in the highlands of Chiapas, southern Mexico. Methods We derived climatically associated species pools from floristic inventory data using multivariate analysis combined with spatially explicit discriminant analysis. We then produced predictive maps of the distribution of tree species pools using data derived from 451 inventory plots. After validating the predictive power of potential distributions against an independent historical data set consisting of 3105 botanical collections, we investigated potential changes in the distribution of tree species resulting from forest disturbance and climate change. Results Two species pools, associated with moist and cool climatic conditions, were identified as being particularly threatened by both climate change and ongoing anthropogenic disturbance. A change in climate consistent with low‐emission scenarios of general circulation models was shown to be sufficient to cause major changes in equilibrium forest composition within 50 years. The same species pools were also found to be suffering the fastest current rates of deforestation and internal forest disturbance. Disturbance and deforestation, in combination with climate change, threaten the regional distributions of five tree species listed as endangered by the IUCN. These include the endemic species Magnolia sharpii Miranda and Wimmeria montana Lundell. Eleven vulnerable species and 34 species requiring late successional conditions for their regeneration could also be threatened. Main conclusions Climatically associated species pools can be derived from floristic inventory data available for tropical regions using methods based on multivariate analysis even when data limitations prevent effective application of individual species modelling. Potential consequences of climate change and anthropogenic disturbance on the species diversity of montane tropical forests in our study region are clearly demonstrated by the method.