Systematic data in biodiversity studies: use it or lose it

Systematic data in the form of collections data are useful in biodiversity studies in many ways, most importantly because they serve as the only direct evidence of species distributions. However, collecting bias has been demonstrated for most areas of the world and has led some to propose methods that circumvent the need for collections data. New methods that model collections data in combination with abiotic data and predict potential total species distribution are examined using 25,111 records representing 5,123 species of plants and animals from Guyana; some methods use the reduced number of 320 species. These modeled species distributions are evaluated and potential high-priority biodiversity sites are selected based on the concept of irreplaceability, a measure of uniqueness. The major impediments to using collections data are the lack of data that are available in a useful format and the reluctance of most systematists to become involved in biodiversity and conservation research.     

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.     

Research in the garden: Averting the collections crisis

Botanic gardens and arboreta are a vibrant part of the natural history collections community, serving society in areas such as education, recreation, and research. Unfortunately, at the present time dwindling support and advocacy for collections-based reissued search has placed these institutions in the midst of a collections crisis. In this review, I assess the historical importance of living plant collections in supporting research, examine why their research potential is currently unmet, and provide a series of rationales in support of collections-based research. To avert this crisis several things must occur, the most basic of which is stronger advocacy for living collections and the research derived from them. Traditional views of collections management need to be evaluated under new light and the pool of researchers expanded. Formal, on-site programs are not required for collections to be used for research, as off-site scientists can make great contributions. Toward this end, collaborative links between the garden and research communities ought to be enhanced through the pivotal role played by curators and collections managers. Investment in data-management systems are also required to increase collection value and improve the ability to disseminate information to researchers who require it. If provided the necessary leadership and support, living plant collections have great potential to meet future scientific needs.     

Mass digitization of scientific collections: New opportunities to transform the use of biological specimens and underwrite biodiversity science

New information technologies have enabled the scientific collections community and its stakeholders to adapt, adopt, and leverage novel approaches for a nearly 300 years old scientific discipline. Now, few can credibly question the transformational impact of technology on efforts to digitize scientific collections, as IT now reaches into almost every nook and cranny of society. Five to ten years ago this was not the case. Digitization is an activity that museums and academic institutions increasingly recognize, though many still do not embrace, as a means to boost the impact of collections to research and society through improved access. The acquisition and use of scientific collections is a global endeavor, and digitization enhances their value by improved access to core biodiversity information, increases use, relevance and potential downstream value, for example, in the management of natural resources, policy development, food security, and planetary and human health. This paper examines new opportunities to design and implement infrastructure that will support not just mass digitization efforts, but also a broad range of research on biological diversity and physical sciences in order to make scientific collections increasingly relevant to societal needs and interest.     

Towards a virtual reality for plant-associated fungi in the United States and Canada

At present knowledge of fungal biodiversity in North America is scattered in diverse sources ranging from well-reviewed, comprehensive databases to unedited databases of reports from the literature, information on file cards, and uncomputerized reference collections. Resources available electronically were used to determine their relative importance in evaluating the plant-associated fungi known from the United States and to a lesser extent Canada. The results demonstrate that the literature provides the greatest information but that reference collections in the US National Fungus Collections contribute between 22–31% additional data. Little overlap exists between fungi isolated as endophytes and those reported in the literature or as reference collections. Eighty to 100% of the plant-associated fungi reported from Canada are accounted for in comprehensive resources for the United States. A comprehensive database of plant-associated fungi in Canada, the United States, and eventually Mexico would serve as a valuable resource for those making plant quarantine decisions.     

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.     

论植物园的活植物收集

对植物园活植物收集评价、引种中的取样方法和迁地保护种群大小等问题进行了论述.对活植物收集的评价包括科学性和代表性,最具有科学意义的是经过调查从野外收集的有完整记录的材料,其次是从植物园等机构 引种的有记录的材料,再次是从各地引种的基本上无记录的材料.根据收集物的代表性可分为具有保护意义的收集和保护性收集.取样技术主要针对保护性收集而言,要求收集样本能涵盖该物种95%以上、频率大于5%的等位基因.活植物收集种群的大小应从科学性和现实性二方面来考虑,对植物园里大量的具有保护意义的收集,其种群大小为乔木10～20株,灌木40～50株,草本100～200株;对于保护性收集则至少为乔木50～100株,灌木200株或更多,草本300～500株以上.另外,对当前植物园活植物收集圃建设的一些重要问题也进行了探讨.     

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.     

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.     

<Emphasis Type="Italic">In Vitro</Emphasis> Preservation of Spanish Biodiversity

Spanish territories contain many of the hot spots of plant biodiversity among European countries. Most of the Spanish territory is found in the Mediterranean basin and in the Canary Islands, a region of great floral singularity and diversity (Macaronesian bioregion). Therefore, an important effort must be made to contribute to its conservation. Several strategies can be considered, but seed conservation under standard conditions is the most resource-efficient method. However, the application of this methodology is not always possible for recalcitrant seeds or species for which vegetative propagation is necessary or convenient under some circumstances. Micropropagation is one of the measures suggested for preserving endangered species. During the 1990s, several in vitro culture protocols for Spanish endemics were established. The main purpose of this strategy was to obtain a considerable number of individuals to reduce the loss of natural populations. Likewise, diverse slow growth protocols were developed for this material. However, these efforts usually did not lead to the establishment of in vitro collections. The advantages and disadvantages of the in vitro conservation strategy will be reviewed for some cases. The establishment of the in vitro protocols together with the development of cryopreservation techniques created the ideal conditions to generate cryogenic collections. In this paper, we review the knowledge and experience accumulated during the last decades in micropropagation, slow growth, and cryopreservation for Spanish plant wild species. Their application in the development ex situ collections and their contribution toward an integrated system to conserve threatened species will be discussed.     

Plant biodiversity and ethnobotany of Borana pastoralists in Southern Oromia, Ethiopia

A survey of plant biodiversity and ethnobotanical studies was conducted in southern Ethiopia using an integrated approach of botanical collections, group discussions, interviews and questionnaires. Species richness, growth forms and uses of native wild plants are described. Borana pastoralists distinguished and named 86% of the plant species identified. A total of 327 plant species distributed among 197 genera and 69 families are documented: 40% are trees/shrubs, 30% forbs (non-woody plants other than grasses and sedges), 16% grasses, 10% climbers, 2% sedges and 2% succulents. Based on richness of species and usefulness, the most important families are Poaceae, Fabaceae, Lamiaceae and Asteraceae. Two hundred forty-eight species (76%) are used by Borana pastoralists, out of which 42% have multiple uses. Indigenous knowledge of pastoralists on use and management of their plant resources is a valuable source of information for conservation and sustainable utilization of the plant biodiversity and, hence, conservation based on indigenous knowledge is recommended.     

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.     

DNA banking for plant breeding,biotechnology and biodiversity evaluation

The manipulation of DNA is routine practice in botanical research and has made a huge impact on plant breeding, biotechnology and biodiversity evaluation. DNA is easy to extract from most plant tissues and can be stored for long periods in DNA banks. Curation methods are well developed for other botanical resources such as herbaria, seed banks and botanic gardens, but procedures for the establishment and maintenance of DNA banks have not been well documented. This paper reviews the curation of DNA banks for the characterisation and utilisation of biodiversity and provides guidelines for DNA bank management. It surveys existing DNA banks and outlines their operation. It includes a review of plant DNA collection, preservation, isolation, storage, database management and exchange procedures. We stress that DNA banks require full integration with existing collections such as botanic gardens, herbaria and seed banks, and information retrieval systems that link such facilities, bioinformatic resources and other DNA banks. They also require efficient and well-regulated sample exchange procedures. Only with appropriate curation will maximum utilisation of DNA collections be achieved.     

Variation in "biodiversity value" of peatmoss species in Sphagnum section Acutifolia (Sphagnaceae)

Species are the most common currency by which biodiversity is measured, but species are not equivalent in "biodiversity value" because of differences in phylogenetic history and current population processes. Morphologically defined species in Sphagnum section Acutifolia (Bryophyta) were compared with regard to how phylogenetically distinct each is from its sister species and how much nucleotide variation each encompasses. Comparisons were based on sequence variation at seven nuclear and chloroplast loci. Assignment of collections to morphospecies accounted for about 57-75% of the overall nucleotide variation at the seven loci, but morphospecies differed greatly in how much nucleotide diversity they encompass. In addition, morphospecies varied widely in their genetic distinctiveness, estimated as the length of the stem branch from the most recent common ancestor and numbers of differentially fixed and shared polymorphic nucleotides among taxa. Levels of molecular diversity within morphospecies were not correlated with their degree of isolation. Factors that affected the biodiversity value of species include age, mode of origin, demographic history, and reproductive biology.     

A new institution devoted to insect science: The Florida Museum of Natural History,McGuire Center for Lepidoptera and Biodiversity

Abstract The Florida Museum of Natural History's McGuire Center for Lepidoptera and Biodiversity, on the University of Florida campus in Gainesville, Florida, has become one of the world's largest institutions for research on butterflies and moths, and an important research facility for insect science. The facility was constructed by combining the staff and merging the Lepidoptera holdings from the Allyn Museum of Entomology, the Florida State Collection of Arthropods and other University of Florida collections, and now includes over ten million specimens from all over the world, rivaling some of the largest Lepidoptera research collections globally. The facility includes a team of domestic and international researchers studying many areas of lepidopterology, including behavior, biodiversity, biogeography, ecology, genomics, physiology, systematics and taxonomy. In this paper, we introduce the McGuire Center, its staff, and the many research activities for researchers across entomological disciplines.     

Colombia,an unknown genetic diversity in the era of Big Data

Background

Latin America harbors some of the most biodiverse countries in the world, including Colombia. Despite the increasing use of cutting-edge technologies in genomics and bioinformatics in several biological science fields around the world, the region has fallen behind in the inclusion of these approaches in biodiversity studies. In this study, we used data mining methods to search in four main public databases of genetic sequences such as: NCBI Nucleotide and BioProject, Pathosystems Resource Integration Center, and Barcode of Life Data Systems databases. We aimed to determine how much of the Colombian biodiversity is contained in genetic data stored in these public databases and how much of this information has been generated by national institutions. Additionally, we compared this data for Colombia with other countries of high biodiversity in Latin America, such as Brazil, Argentina, Costa Rica, Mexico, and Peru.

Results

In Nucleotide, we found that 66.84% of total records for Colombia have been published at the national level, and this data represents less than 5% of the total number of species reported for the country. In BioProject, 70.46% of records were generated by national institutions and the great majority of them is represented by microorganisms. In BOLD Systems, 26% of records have been submitted by national institutions, representing 258 species for Colombia. This number of species reported for Colombia span approximately 0.46% of the total biodiversity reported for the country (56,343 species). Finally, in PATRIC database, 13.25% of the reported sequences were contributed by national institutions. Colombia has a better biodiversity representation in public databases in comparison to other Latin American countries, like Costa Rica and Peru. Mexico and Argentina have the highest representation of species at the national level, despite Brazil and Colombia, which actually hold the first and second places in biodiversity worldwide.

Conclusions

Our findings show gaps in the representation of the Colombian biodiversity at the molecular and genetic levels in widely consulted public databases. National funding for high-throughput molecular research, NGS technologies costs, and access to genetic resources are limiting factors. This fact should be taken as an opportunity to foster the development of collaborative projects between research groups in the Latin American region to study the vast biodiversity of these countries using ‘omics’ technologies.

     

How to infer population trends in sparse data: examples with opportunistic sighting records for great white sharks

Aim Biodiversity is declining at accelerating rates. Understanding past and ongoing changes to biodiversity is paramount in prioritizing conservation action and restoring functional ecosystems. Yet long‐term, systematic data on the distribution and abundance of species are sparse. For many organisms, specimen collections and anecdotal accounts of chance sightings or captures constitute the only source of information. Such data have the potential to provide valuable insights on long‐term ecosystem changes, but are often neglected because they are difficult to analyse quantitatively. Here we review available methods and introduce a new approach. Location Historic data on sightings and captures of great white sharks in the eastern Adriatic and off eastern Canada serve to illustrate the utility of both the existing methods and the new approach. Method Unlike existing methods, the new approach focuses on estimating population trends rather than verifying extinction and explicitly addresses uncertainty over observation effort via two tiers of sensitivity analysis. It fits a series of generalized linear models that provide multiple estimates of declines under alternate scenarios regarding the appropriate reference period and observer trends. Programming code to implement the approach in freely available software is provided as supplementary material. Results Example analyses of great white shark sightings suggest that local populations of this species have suffered dramatic declines, both in the eastern Adriatic and along Canada’s eastern coast. Although not yet extinct, this top predator may therefore no longer be able to fulfil its former ecological role. Main conclusions Careful quantitative analyses of imperfect historical data can provide valuable insights into past ecological changes. Such insights are crucial to improved management and restoration of individual species and their ecosystems. We therefore hope that our review of available methods will facilitate quantitative evaluations of species for which analysis was previously impeded by a lack of systematically collected data.     

Artenvielfalt in Zoologischen Gärten

Some thoughts about biodiversity in zoo animals were given. The reduction of species is a development of the last decades: More and more zoos minimized their collections as part of a new “zoo-philosophy” not realizing that people come into the zoos to see animals!