A set of keys for biochemical identification of environmental Vibrio species

A set of biochemical keys which provide fast and presumptive identification for Vibrio spp. is presented. They have been specially designed for environmental isolates, and can be used for strains that are Gram-negative, give a positive oxidase test, grow on TCBS medium and are facultative anaerobes. The keys are constituted by 28 tests and a maximum of 10 tests are needed for the most complicated identification. They have been designed for routine purposes, especially for studies with a high number of isolates. Some tests are included in enzyme-activity based kits that could be used with these keys through certain results, principally for environmental isolates, should be confirmed by standard methods.     

交互式检索表提升分类学研究与应用效率:以兰科植物为例

与传统的连续检索表相比,基于计算机等数字终端的多通道交互式检索表具有很多优势,如易于携带、实时更新、界面直观、使用方便、用户广泛、产生新数据集且便于研究以及能够推动分类学知识的普及等。本文以兰科植物为例介绍了交互式检索表的特点、程序建立和应用。兰科植物是生物多样性保育的旗舰类群,具有很强的观赏和药用价值,但中国兰科植物种类繁多,分类困难。我们在自主研发交互式检索表软件MagIden的基础上,以《中国植物志》和Flora of China的描述为依据,制作了中国兰科植物交互式电子检索表,为分类学研究者和爱好者提供了一个新的、鉴定中国兰科植物的中英文双语工具;同时,交互式检索表生成的MVSP和Bayes形态特征数据集可用于聚类分析和分支分类学研究。交互式检索表在数据积累、更新和分析利用等方面具有独特的优势,是提高传统植物分类学研究与应用效率的重要工具。     

Improvement and update of a set of keys for biochemical identification of Vibrio species

M. ALSINA AND A.R. BLANCH. 1994. Two biochemical keys for fast and presumptive identification of certain Vibrio species are presented. They constitute a new improved version of a set of keys previously described, which were specially designed for environmental and clinical isolates. They may be used for Gram-negative, oxidase-positive, facultative anaerobes that grow on TCBS agar. The revised set of biochemical keys consists of 29 tests and a maximum of 10 tests is still sufficient for the most complicated identification. The new keys maintain the same criteria and characteristics of the original set of keys.     

Some ideas for activities involving the construction of computer-based identification keys

Conserving global biodiversity depends on public awareness, hence the vital role of education and the recent thinking that biodiversity conservation should form part of a new and general scientific literacy taught in schools. A crucial aspect of biodiversity conservation is species identification. Taxonomy in general, and identification keys in particular, are often seen as boring and outdated. Indeed, curricula focused on contemporary areas of biology tend to give a low priority to taxonomy or ignore it completely. However, concern for diminishing global biodiversity has provoked a renewed interest in both traditional and more innovative identification methods, including computer-aided taxonomy.

Some ideas for applying information and communication technology (ICT) to constructing identification keysare discussed. The use of linked web pages is proposed as the most easily used and readily accessible method for Year 8 pupils (ages 12 – 13). It is suggested that there is more educational value in pupils then testing and evaluating each other's keys rather than simply using them and that to facilitate this, web-based keys can easily be exchanged via a network.

It is concluded that this approach promotes a wide range of transferable ICT skills, but applies them in the context of a current problem facing real biologists, so illustrating how computer technology is assisting biodiversity research.     

Taxonomic identification of Amazonian tree crowns from aerial photography

Question: To what extent can aerial photography be used for taxonomic identification of Amazonian tree crowns? Objective: To investigate whether a combination of dichotomous keys and a web‐based interface is a suitable approach to identify tree crowns. Location: The fieldwork was conducted at Tiputini Biodiversity Station located in the Amazon, eastern Ecuador. Methods: High‐resolution imagery was taken from an airplane flying at a low altitude (600 m) above the ground. Imagery of the observable upper layer of the tree crowns was used for the analysis. Dichotomous identification keys for different types of crowns were produced and tested. The identification keys were designed to be web‐based interactive, using Google Earth as the main online platform. The taxa analysed were Iriartea, Astrocaryum, Inga, Parkia, Cecropia, Pourouma, Guarea, Otoba, Lauraceae and Pouteria. Results: This paper demonstrates that a combination of photo‐imagery, dichotomous keys and a web‐based interface can be useful for the taxonomic identification of Amazonian trees based on their crown characteristics. The keys tested with an overall identification accuracy of over 50% for five of the ten taxa with three of them showing accuracy greater than 70% (Iriartea, Astrocaryum and Cecropia). Conclusions: The application of dichotomous keys and a web‐based interface provides a new methodological approach for taxonomic identification of various Amazonian tree crowns. Overall, the study showed that crowns with a medium‐rough texture are less reliably identified than crowns with smoother or well‐defined surfaces.     

Childrens' Understanding of the Classification of Living Organisms

This study investigated the effectiveness of three different instructional materials for learning how to identify fish at the species level in a blended classroom and out-of-classroom scenario. A sample of 195 first-year students of biology or geoecology at the University of Tuebingen participated in a course on identification of European freshwater fish species at a public aquarium. Prior to studying the species in the aquarium's fish tanks, students prepared themselves in a classroom nearby with one of three different learning materials: (1) preserved specimens and paper-based dichotomous identification keys; (2) digital videos; or (3) digital videos with preserved specimens and paper-based dichotomous identification keys. Students' acquisition of knowledge and their motivation were measured twice, once after preparing in the classroom and once after visiting the aquarium. Results showed that students who had prepared themselves with digital videos identified significantly more species correctly but were less motivated than those students who had learnt only with preserved specimens and dichotomous identification keys. When both instructional methods were combined students performed well in the post-tests and were motivated to learn, suggesting that the combination of both instructional approaches encourages motivation without any outcome losses.     

Bryophytes for Beginners: The usability of a printed dichotomous key versus a multi-access computer-based key for bryophyte identification

Bryophytes are a rewarding study group in field biology and the UK bryophyte flora has international importance to biodiversity conservation. We designed an identification key to common woodland moss species and compared the usability of two formats, web-based multi-access and printed dichotomous key, with undergraduate students. The rate of correct species identification and identification speed both showed an advantage for the printed dichotomous key. Our findings suggest that, even in the digital age, printed keys remain valuable in biological education and that quality of key design is more important than presentation medium. We discuss the relative advantages of multi-access and dichotomous keys and how to approach bryophyte identification with beginners.     

A review of numerical methods in bacterial identification

Part A of this review describes the particular computer-assisted identification service operated by the NCTC. In Part B, the use of probability matrices is examined, discussing various methods of calculating likelihoods and the problems that arise when calculating these from probability matrices. Part C describes the alternative numerical methods of constructing identification keys and the supplementary methods of selecting best sets of characters to aid identification. Finally, in Part D, the prospects and limitations of numerical methods in bacterial identification are assessed, first with regard to methodology used and then in terms of performance and practical limitations.     

烟粉虱寄生蜂辅助鉴定系统的研究

介绍了一种基于Web的烟粉虱[Bemisia tabaci(Gennadius)]寄生蜂辅助鉴定系统。该系统属于多路径存取检索方式,不仅提供各特征及其性状的文字描述,同时还提供各个特征对剩余物种的鉴别效力排名,以及各性状的相关图片,供用户参考。     

Vegetative Identification of Tropical Woody Plants: State of the Art and Annotated Bibliography1

This annotated bibliography is provided in order to assess the achievements and gaps in the literature on vegetative identification of woody plants in the tropics. The bibliography includes 258 references divided into general references (48), pantropical and multi‐continental keys (4), Africa (46), Asia (53), Australia and New Guinea (21), and the Neotropics (86). Vegetative keys are not easy shortcuts to the identification of woody tropical plants to species. Identification of sterile material requires as much, if not more, training as that required for using keys that emphasize floral and fruit characters. Nevertheless, the literature surveyed in this bibliography may be helpful to biologists seeking references for the geographic region in which they work, models for the construction of vegetative keys and field guides, and/or the types of characters that should be observed in the field.     

A study of a hierarchical structure of proteins and ligand binding sites of receptors using the triangular spatial relationship-based structure comparison method and development of a size-filtering feature designed for comparing different sizes of protein structures

The presence of receptors and the specific binding of the ligands determine nearly all cellular responses. Binding of a ligand to its receptor causes conformational changes of the receptor that triggers the subsequent signaling cascade. Therefore, systematically studying structures of receptors will provide insight into their functions. We have developed the triangular spatial relationship (TSR)-based method where all possible triangles are constructed with C_α atoms of a protein as vertices. Every triangle is represented by an integer denoted as a “key” computed through the TSR algorithm. A structure is thereby represented by a vector of integers. In this study, we have first defined substructures using different types of keys. Second, using different types of keys represents a new way to interpret structure hierarchical relations and differences between structures and sequences. Third, we demonstrate the effects of sequence similarity as well as sample size on the structure-based classifications. Fourth, we show identification of structure motifs, and the motifs containing multiple triangles connected by either an edge or a vertex are mapped to the ligand binding sites of the receptors. The structure motifs are valuable resources for the researchers in the field of signal transduction. Next, we propose amino-acid scoring matrices that capture “evolutionary closeness” information based on BLOSUM62 matrix, and present the development of a new visualization method where keys are organized according to evolutionary closeness and shown in a 2D image. This new visualization opens a window for developing tools with the aim of identification of specific and common substructures by scanning pixels and neighboring pixels. Finally, we report a new algorithm called as size filtering that is designed to improve structure comparison of large proteins with small proteins. Collectively, we provide an in-depth interpretation of structure relations through the detailed analyses of different types of keys and their associated key occurrence frequencies, geometries, and labels. In summary, we consider this study as a new computational platform where keys are served as a bridge to connect sequence and structure as well as structure and function for a deep understanding of sequence, structure, and function relationships of the protein family.     

Artificial neural networks for species identification by taxonomists

This paper is a study of the value of applying artificial neural networks (ANNs), specifically a multilayer perceptron (MLP), to identification of higher plants using morphological characters collected by conventional means. A practical methodology is thus demonstrated to enable botanical or zoological taxonomists to use ANNs as advisory tools for identification purposes. A comparison is made between the ability of the neural network and that of traditional methods for plant identification by means of a case study in the flowering plant genus Lithops N.E. Brown (Aizoaceae). In particular, a comparison is made with taxonomic keys generated by means of the DELTA system. The ANN is found to perform better than the DELTA key generator, for conditions where the available data is limited, and species relatively difficult to distinguish.     

Education and taxonomy: the role of the Field Studies Council and AIDGAP

The taxonomic disciplines, classification and identification, are fundamental to most biological sciences. Yet, taxonomic teaching and research have declined to a level where adequate support for the other sciences can no longer be sustained. New teaching initiatives are needed, combined with the provision of suitable resource materials and identification guides. Bodies such as the Field Studies Council and the Linnean Society have a tradition of publishing identification keys, but the experience of the AIDGAP project, first started in 1976, shows that considerable thought must be given to content and presentation. Testing prior to publication is vital.     

The potential for computer-aided identification in biodiversity research

Species identification lies at the heart of most ecological studies, but it is recognized as a difficult and often frustrating task. Taxonomists have sought to overcome the difficulties of species identification by developing a range of tools and techniques that have increasingly involved the use of computers. We describe recent developments in computer-aided species identification, which have been in four main areas; multi-access keys; hypertext keys; expert systems; and neural networks. We also suggest which technique might be appropriate for a particular taxonomic group.     

Identification Keys,the “Natural Method,” and the Development of Plant Identification Manuals

The origins of field guides and other plant identification manuals have been poorly understood until now because little attention has been paid to 18th century botanical identification guides. Identification manuals came to have the format we continue to use today when botanical instructors in post-Revolutionary France combined identification keys (step-wise analyses focusing on distinctions between plants) with the “natural method” (clustering of similar plants, allowing for identification by gestalt) and alphabetical indexes. Botanical works featuring multiple but linked techniques to enable plant identification became very popular in France by the first decade of the 19th century. British botanists, however, continued to use Linnaeus’s sexual system almost exclusively for another two decades. Their reluctance to use other methods or systems of classification can be attributed to a culture suspicious of innovation, anti-French sentiment and the association of all things Linnaean with English national pride, fostered in particular by the President of the Linnean Society of London, Sir James Edward Smith. The British aversion to using multiple plant identification technologies in one text also helps explain why it took so long for English botanists to adopt the natural method, even after several Englishmen had tried to introduce it to their country. Historians of ornithology emphasize that the popularity of ornithological guides in the 19th and 20th centuries stems from their illustrations, illustrations made possible by printing technologies that improved illustration quality and reduced costs. Though illustrations are the most obvious features of late 19th century and 20th century guides, the organizational principles that make them functional as identification devices come from techniques developed in botanical works in the 18th century.     

Finding the maximum a posteriori probability (MAP) in a Bayesian taxonomic key is NP-hard

As an alternative to dichotomous keys, tabular keys are used for taxonomic identification. With the use of computers, keys based on the Bayes formula can also be made available more widely. For the development of a key, the maximum a posterior probability (MAP) for a taxon is important because it allows to evaluate the quality of a key. If it is low, the taxon is hard to distinguish from other taxa. In this paper, we show that finding MAP in a Bayesian key is NP-hard. Estimates for MAP or other measures have to be used for the estimation of the quality of a Bayesian key.     

Optimized DNA extraction methods for encysted embryos of the endangered fairy shrimp, Branchinecta sandiegonensis

The San Diego fairy shrimp Branchinecta sandiegonensis is a federally endangered species endemic to vernal pools in southern California, USA. Filling events in these habitats are highly variable, with some pools failing to hold water long enough for reproduction over many successive years. Studies of this species are thus hindered by the relatively rare appearance of aquatically active life history phases. Because diapausing cysts are abundant and present at all times, they provide an underutilized opportunity for both species identification and genetic studies. However, methods for extracting DNA from cysts are technically challenging because of their structure and size. Here we present a protocol for extracting DNA from B. sandiegonensis cysts in sufficient quantities for “DNA Barcoding”, microsatellite analysis and other genotyping and sequencing applications. The technique will aid in population genetic studies and species identification (since taxonomic keys only distinguish among adults), and will be applicable to other crustaceans with similar diapausing cysts.     

Keys to the genera of social wasps of South-East Asia (Hymenoptera: Vespidae)

Illustrated identification keys are provided for higher taxa and all genera of social wasps found in South‐East Asia.