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.     

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.     

The Ovule and 'Seed' of Araucaria Bidwilli with Discussion of the Taxonomy of the Genus II. Taxonomy

This paper deals with the taxonomic and historical backgroundof the genus Araucaria with a discussion and evaluation of charactersused as a basis for sectional division. The three existing sectionsare more clearly delimited and a new section-Sectio Bunya-isproposed for A. Bidwilli, which is removed from section Columbea.A key to the four sections is given.     

Illustrated key to the adult female <Emphasis Type="Italic">Anopheles</Emphasis> (Diptera: Culicidae) mosquitoes of Sri Lanka

The identification of adult female anopheline mosquitoes is an important aspect in malaria surveillance and control strategy throughout the world, and taxonomic keys are being regularly revised and updated as new information becomes available. However, the currently available key to the anophelines of Sri Lanka is of limited use, because they were published more than 25 years ago. This paper presents an illustrated key for the identification of 23 adult female Anopheles mosquitoes which are currently recognized as local anopheline species in Sri Lanka.     

Introducing the Internet.

The benefits to medical practitioners of using the Internet are growing rapidly as the Internet becomes easier to use and ever more biomedical resources become available on line. The Internet is the largest computer network in the world; it is also a virtual community, larger than many nation states, with its own rules of behaviour or "netiquette." There are several types of Internet connection and various ways of acquiring a connection. Once connected, you can obtain, free of charge, programs that allow easy use of the Internet''s resources and help on how to use these resources; you can access many of these resources through the hypertext references in the on line version of this series (go to http:@www.bmj.com/bmj/ to reach the electronic version). You can then explore the various methods for accessing, manipulating, or disseminating data on the Internet, such as electronic mail, telnet, file transfer protocol, and the world wide web. Results from a search of the world wide web for information on the rare condition of Recklinghausen''s neurofibromatosis illustrate the breadth of medical information available on the Internet.     

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。     

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.     

Seed Coat Microsculpturing in Brassica and Allied Genera (Subtribes Brassicinae, Raphaninae, Moricandiinae)

To obtain new information on the taxonomy of Brassica and alliedgenera, seed surfaces of 44 species (78 accessions) belongingto 11 genera of subtribes Brassicinae, Raphaninae and Moricandiinaewere examined using a scanning electron microscope. Ten typesof basic ornamentation patterns were recognized. While fourtypes were represented by only one species each, six types hadmore than one species either representing one genus (two types)or more (four types). The different species in each of the sixtypes could generally be distinguished from each other on thebasis of differences in microsculpturing features. This analysisprovides evidence for the close relationship among the variousgenera within the subtribe Brassicinae, and also the closenessof Raphanus, Enarthrocarpus and Moricandia of subtribe Raphaninaeand Moricandiinae, respectively, with the Brassicinae. Copyright2000 Annals of Botany Company Brassicinae, Moricandiinae, Raphaninae, SEM, seed coat microsculpturing, taxonomic implications     

A Linnaeus NG TM interactive key to the Lithocolletinae of North-West Europe aimed at accelerating the accumulation of reliable biodiversity data (Lepidoptera,Gracillariidae)

We present an interactive key that is available online through any web browser without the need to install any additional software, making it an easily accessible tool for the larger public. The key can be found at http://identify.naturalis.nl/lithocolletinae. The key includes all 86 North-West European Lithocolletinae, a subfamily of smaller moths (“micro-moths”) that is commonly not treated in field guides. The user can input data on several external morphological character systems in addition to distribution, host plant and even characteristics of the larval feeding traces to reach an identification. We expect that this will enable more people to contribute with reliable observation data on this group of moths and alleviate the workload of taxonomic specialists, allowing them to focus on other new keys or taxonomic work.     

Landmark superimposition for taxonomic identification

The identification of organisms is a time-consuming task even for highly specialized researchers. Many ways to accelerate the identification process have been devised – from pictorial keys to automatic, machine identification – with different degrees of success. This paper explores landmark configurations as an aid to taxonomic identification. The basic hypothesis rests on the analogy between human fingerprints and organism landmark configuration. Translated into biological terms, it asks whether individual landmark configurations can be used as diagnostic characteristics for species identification. Water mites of the genus Torrenticola were used as test organisms. The results show that identification can be made simpler through the use of landmark configurations.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 81 , 267–274.     

Nest building, sexual selection and parental investment

Avian nest building has traditionally been viewed as resulting in natural selection advantages, but it is also been associated with courtship and pair formation. We hypothesize that nest-building activity could be used as a sexually selected display, allowing each sex to obtain reliable information on the condition of the other. In this paper, we test the ‘good parent’ process in a scenario where nest size is a sexually selected trait. Thus, individuals with more extreme displays (larger nests) might obtain benefits in terms of either parental investment or differential parental investment by the partner. We predicted that: (1) species in which both sexes contribute to nest building have larger nests than those in which the nest is built only by one sex, because both sexes are using the nest-building process as a signal of their quality; (2) species in which both sexes work together in the nest-building process invest more in reproduction, because each can assess the other more reliably than in species where only one sex participates in nest building; and (3) in light of the two preceding predictions, nest size should be positively related to investment in parental care. A comparative analysis of 76 passerine species confirmed that nest size, relative to the species' body size, is larger when both sexes build the nest and that species with a larger nest relative to their body size invest more in reproduction. This revised version was published online in July 2006 with corrections to the Cover Date.     

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.     

An improved statistical methodology to estimate and analyze impedances and transfer functions

Curran-Everett, Douglas, Yiming Zhang, M. Douglas Jones,Jr., and Richard H. Jones. An improved statistical methodology toestimate and analyze impedances and transfer functions. J. Appl.Physiol. 83: 2146-2157, 1997.Estimating the mathematical relationship between pulsatile time series (e.g., pressure and flow) isan effective technique for studying dynamic systems. Thefrequency-domain relationship between time series, often calculated asan impedance (pressure/flow), is known more generally as a frequency-response or transfer function (output/input). Current statistical methods for transfer function analysis 1) assumeerroneously that repeated observations on a subject are independent,2) have limited statistical value and power, or 3) arerestricted to use in single subjects rather than in an entire sample.This paper develops a regression model for transfer function analysisthat corrects each of these deficiencies. Spectral densities of the input and output time series and the cross-spectral density between them are first estimated from discrete Fourier transforms and then usedto obtain regression estimates of the transfer function. Statisticalcomparisons of the transfer function estimates use a test statisticthat is distributed as ². Confidence intervals foramplitude and phase can also be calculated. By correctly modelingrepeated observations on each subject, this improved statisticalapproach to transfer function estimation and analysis permits thesimultaneous analysis of data from all subjects in a sample, improvesthe power of the transfer function model, and has broad relevance tothe study of dynamic physiological systems.

     

The effect of age on encounters between male crab spiders

In males that compete aggressively for females, size and agemay determine which males obtain access to these females. Inthe present study, we use the crab spider, Misumena vatia, aspecies with males that do not grow after becoming sexuallymature adults, to test the hypothesis that age affects the successof males competing for access to females. M. vatia is an excellentspecies to test this hypothesis because it is possible to disentangleage from size, characters that typically vary together in thespecies usually tested. We staged encounters between similar-sizedolder and younger adult male M. vatia in the presence of a femaleto determine the role of age in male access to females. Encountersbetween the males occurred during 63.3% of these pairings. Youngermales won significantly more (70.2%) of the encounters thandid older ones, but did not initiate significantly more encountersthan did older ones (62.5%). Although older males won only 29.8%of these encounters, they initiated significantly more (76.5%)of them than predicted by chance. This design also allowed usto test Parker's hypothesis that older individuals should exhibita higher level of aggression than younger ones. However, attacksby younger males were most likely to include extensive bodilycontact, whereas attacks by older males involved significantlyless contact. These results counter the frequent assertion thatolder individuals usually prevail over younger ones in contestsfor access to females, and that older males are more likelyto engage in highly overt aggression than are younger ones.Aging may decrease reproductive opportunities and success ratesof male M. vatia, affecting as many as nearly one-fourth oftheir encounters.     

OBSERVATIONS ON SHELL MORPHOLOGY, ENZYMES AND RANDOM AMPLIFIED POLYMORPHIC DNA (RAPD) IN BULINUS AFRICANUS GROUP SNAILS (GASTROPODA: PLANORBIDAE) IN ZANZIBAR

The taxonomic status of Bulinus globosus and B. nasutus as separatespecies remains unclear, espécially in areas of EastAfrica where their distribution overlaps. In order to throwfurther light on this question, a study was carried out on snailscollected from the islands Unguja and Pemba, collectively knownas Zanzibar, which lie in the Indian Ocean close to mainlandAfrica. In total, 169 snails from 22 sample sites were characterisedby three methods: morphometric analysis of 15 shell measurements,enzyme analysis involving three enzyme systems and analysiswith random amplified polymorphic DNA (RAPD). Enzyme analysesindicated that both B. nasutus and B. globosus were presenton each island and their distribution was allopatric. Shellvariation was considerable but did not clearly differentiatethese taxa. Similarly, RAPD analysis indicated substantial geneticvariation with in and between samples; more often than not,no two RAPD profiles were identical within the sample. On Pemba,B. globosus is more widely dispersed than B. nasutus which isconfined to the eastern coast of the central region. On Unguja,B. globosus is found in more northern areas than B. nasutus. (Received 15 August 1996; accepted 31 January 1997)     

Molecular Markers in the Identification of Some Early Flowering Curcuma L. (Zingiberaceae) Species

In this paper, isozymes have been used for the first time astools to aid identification of someCurcuma L. species that arestill taxonomically confused. These markers were employed toconfirm the taxonomic identification and to distinguish thetaxa analysed; the results were used to describe the relationshipwithin the early-flowering group. Twenty-one isozymes were initiallytested; out of these, eight isozymes showed reliable polymorphismto distinguish between the taxa analysed. Patterns from isozymedata were analysed using cluster analysis and UPGMA to producea dendrogram depicting the degree of relationship among thespecies. Copyright 1999 Annals of Botany Company Curcuma, Zingiberaceae, isozymes, species identification.     

Isozyme and RAPD Analysis of the Genetic Diversity Within and BetweenVigna luteolaandV. marina

Nineteen accessions ofVigna luteola,five ofV. marinassp.oblonga,and two ofV. marinassp.marinawere analysed using variation ofisozymes and RAPD markers to obtain better insight into geneticrelationships within and between these taxonomic entities. Thirteenputative isozyme loci were scored, seven of which were polymorphic.Both species showed very low genetic diversity indices and mostof the variation was detected among populations. Pairwise Nei'sgenetic distances based on allozyme frequencies were also verylow and the accessions ofV. marinassp.marinawere the least relatedto the others. RAPD analysis was more discriminating and 66bands out of a total of 85 were polymorphic. Based on the presenceor absence of bands, Jaccard's similarity index was calculated.Similarity ranged from 0.476 to 0.98. Matrices derived fromboth isozyme and RAPD data were used to construct UPGMA dendrograms.In the tree obtained from Nei's genetic distance, based on allozymefrequencies, accessions belonging toV. marinassp.oblongaweremixed withV. luteolaaccessions; on the other hand, the twoV.marinassp.marinaclustered separately, with oneV. luteola.Thedendrogram derived from RAPD data showed three main groups correspondingto the three taxa analysed. Moreover, according to these data,V.marinassp.oblongais more closely related toV. luteolathan toV.marinassp.marina.Copyright 1997 Annals of Botany Company Vigna luteola(Jacq.) Benth.; Vigna marina(Burm.) Merrill; isozymes; RAPDs; genetic relationships; genetic variation     

A Taxonomic Study of Two Closely Related Species : Terminalia ivorensis A. C hev. and T. glaucescens Planch. ex Benth. in Nigeria

The distribution of Terminalia ivorensis and T. glaucescensin Nigeria was studied and detailed morphological studies madeduring extensive field trips. Greater attention and repeatedvisits were made to zones where the two plant were observedto be growing together normally. There were indications of intermediateplants in transition areas between forest and savanna. Comparativefruit and seeding developmental studies showed differences infruit shape and mode of germination. Some aspects of floralbiology were investigated. Cultivated plants subjected to savannaconditions were readily identified. Reliability of some featuresused in identification such as habitat, stressed in keys ofpresent floras, and the possible relationships between the twoclosely related plants are discussed while investigation continuesalong anatomical and cytological lines. Terminalia spp., taxonomy, distribution morphology     

Identification of Entomopathogenic Nematodes in the Steinernematidae and Heterorhabditidae (Nemata: Rhabditida)

This paper contains taxonomic keys for the identification of species of the genera Steinernema and Heterorhabditis. Morphometrics of certain life stages are presented in data tables so that the morphometrics of species identified using the keys can be checked in the tables. Additionally, SEM photographs and diagnoses of the families and genera of Steinernematidae and Heterorhabditidae are presented.