The Nature of Folk-Botanical Life Forms

Original work by Brent Berlin, Eugene Hunn, Cecil Brown, and other ethnoscientists has produced significant findings pertaining to claims of universality for folk-biological ranks, in general, and folk-botanical life forms, in particular. These findings implicitly call into question conventional wisdom in the history of biology, which tends to consider life forms as the outworn vestiges of scholastic tradition or as merely socially practical ways of carving up the living world. Unfortunately, however, ethnobiologists continue to rely on faulty analytical schema for assessing the nature of life forms which philosophers and historians of biology have developed in their ignorance of the popular conceptual foundations of folk taxonomy. The error is compounded by the adoption into ethnosystematics of the most empiricistically reductionist, and logically confused, interpretation of such schema that derives from the neo-Adansonian, or pheneticist, school of modern system-atics. This interpretation confounds (1) meaning and reference, (2) the semantics of cognitively distinct object domains, and (3) the conceptual differences between common sense and science. These points are challenged, and it is concluded that life forms, though anthropocentrically biased, are no more "artificial" or "special-purpose" than higher-order scientific taxa. Finally, the problem of so-called "unaffiliated" and "ambiguous" generics is addressed and a new analysis offered.     

Concepts of rational taxonomy

The problems are discussed related to development of concepts of rational taxonomy and rational classifications (taxonomic systems) in biology. Rational taxonomy is based on the assumption that the key characteristic of rationality is deductive inference of certain partial judgments about reality under study from other judgments taken as more general and a priory true. Respectively, two forms of rationality are discriminated--ontological and epistemological ones. The former implies inference of classifications properties from general (essential) properties of the reality being investigated. The latter implies inference of the partial rules of judgments about classifications from more general (formal) rules. The following principal concepts of ontologically rational biological taxonomy are considered: "crystallographic" approach, inference of the orderliness of organismal diversity from general laws of Nature, inference of the above orderliness from the orderliness of ontogenetic development programs, based on the concept of natural kind and Cassirer's series theory, based on the systemic concept, based on the idea of periodic systems. Various concepts of ontologically rational taxonomy can be generalized by an idea of the causal taxonomy, according to which any biologically sound classification is founded on a contentwise model of biological diversity that includes explicit indication of general causes responsible for that diversity. It is asserted that each category of general causation and respective background model may serve as a basis for a particular ontologically rational taxonomy as a distinctive research program. Concepts of epistemologically rational taxonomy and classifications (taxonomic systems) can be interpreted in terms of application of certain epistemological criteria of substantiation of scientific status of taxonomy in general and of taxonomic systems in particular. These concepts include: consideration of taxonomy consistency from the standpoint of inductive and hypothetico-deductive argumentation schemes and such fundamental criteria of classifications naturalness as their prognostic capabilities; foundation of a theory of "general taxonomy" as a "general logic", including elements of the axiomatic method. The latter concept constitutes a core of the program of general classiology; it is inconsistent due to absence of anything like "general logic". It is asserted that elaboration of a theory of taxonomy as a biological discipline based on the formal principles of epistemological rationality is not feasible. Instead, it is to be elaborated as ontologically rational one based on biologically sound metatheories about biological diversity causes.     

Charles Darwin's views of classification in theory and practice

It has long been argued that Charles Darwin was the founder of the school of "evolutionary taxonomy" of the Modern Synthesis and, accordingly, that he recognized genealogy and similarity as dual, synergistic criteria for classification. This view is based on three questionable interpretations: first, of isolated passages in the 13th chapter of the Origin of Species; second, of one phrase in a letter that Darwin wrote about the work of an author he had partly misunderstood; and third, of his taxonomic practice in the barnacle monographs, which only implicitly embody his philosophy of classification, if at all. These works, seen in fuller context and with the perspective of extensive correspondence, are consistent with the view that Darwin advocated only genealogy as the basis of classification, and that similarity was merely a tool for discovering evolutionary relationships. Darwin was neither a Mayrian taxonomist nor a cladist, and he did not approach systematic issues in the same terms that we do in the late 20th century.     

UniRef: comprehensive and non-redundant UniProt reference clusters

MOTIVATION: Redundant protein sequences in biological databases hinder sequence similarity searches and make interpretation of search results difficult. Clustering of protein sequence space based on sequence similarity helps organize all sequences into manageable datasets and reduces sampling bias and overrepresentation of sequences. RESULTS: The UniRef (UniProt Reference Clusters) provide clustered sets of sequences from the UniProt Knowledgebase (UniProtKB) and selected UniProt Archive records to obtain complete coverage of sequence space at several resolutions while hiding redundant sequences. Currently covering >4 million source sequences, the UniRef100 database combines identical sequences and subfragments from any source organism into a single UniRef entry. UniRef90 and UniRef50 are built by clustering UniRef100 sequences at the 90 or 50% sequence identity levels. UniRef100, UniRef90 and UniRef50 yield a database size reduction of approximately 10, 40 and 70%, respectively, from the source sequence set. The reduced redundancy increases the speed of similarity searches and improves detection of distant relationships. UniRef entries contain summary cluster and membership information, including the sequence of a representative protein, member count and common taxonomy of the cluster, the accession numbers of all the merged entries and links to rich functional annotation in UniProtKB to facilitate biological discovery. UniRef has already been applied to broad research areas ranging from genome annotation to proteomics data analysis. AVAILABILITY: UniRef is updated biweekly and is available for online search and retrieval at http://www.uniprot.org, as well as for download at ftp://ftp.uniprot.org/pub/databases/uniprot/uniref. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

Three numerical approaches to the classification of Chinese species of genus Abelia

In the last 10—20 years there has bee n increasing awareness of the problem concerning the aims and practices of taxonomy. In particular, there has been growing interest in the development of numerical methods in biological taxonomy as an aid to making systematics a quantitative science, a step which comes in time to almost every scientific discipline. Numerical taxonomy is the evaluation by numerical methods of the affinity or similarity between taxonomic units and the employment of these affinities in erecting a hierarchic order of taxa. The present rapid development of these ideas is presumably a result of the development of computer techniques. Numerical taxonomic approach has been applied to the studies of entomology and microbiology in China to some extent since 1975. But so far it hasn’t been commonly used in botany. The present report is a preliminary study on 9 spp. of the genus Abelia. A set of binary data with 54 characters is used for computing association coefficient; and a set of quantitative data with 47 characters for distance coefficient and correlation coefficient. For the mathematical models were chosen the non-metric simple matching association coefficient, the geometrical distance of Riemannian space and correlation coefficient. Computational procedures are stepwise presented in detail and computer programmes are written in the background of Algol-60 language. Cluster analysis is compared with simple linkage, average linkage and multi-correlation. The results of DC and CC for 9 spp. of Abelia agree closely with the traditional taxonomy, because the data we collected mainly come from morphological characters. It would seem that the results of quantita tive data are more appropriate for seed plants. It is, therefore, postulated that our programes are complementary and very useful to a wide range of classification entities, such as microbes, animals and plants in present situation in China. In conclusion, a comparison between the conventional taxonomy and numerical taxonomy has been made, and a brief discussion of three problems, i.e. the monothetic versus polythetic, divisive versus agglomerative, weighting versus unweighting.     

Determination of the degree of similarity of cholera and NAG vibrios

The numeric taxonomy taking into account 80 signs has demonstrated the similarity of NAG and cholera vibrios, the average similarity coefficient exceeding 80 %. Among NAG vibrios, 53 % of the strains have been found to deviate from the central strain of V. cholerae mainly with regard to their utilization of the sources of carbon. The use of the citrate sign for the study of the biological properties of NAG vibrios is proposed.     

MODELING BRAIN EVOLUTION FROM BEHAVIOR: A PERMUTATIONAL REGRESSION APPROACH

This paper has two complementary purposes: first, to present a method to perform multiple regression on distance matrices, with permutation testing appropriate for path-length matrices representing evolutionary trees, and then, to apply this method to study the joint evolution of brain, behavior and other characteristics in marsupials. To understand the computation method, consider that the dependent matrix is unfolded as a vector y; similarly, consider X to be a table containing the independent matrices, also unfolded as vectors. A multiple regression is computed to express y as a function of X. The parameters of this regression (R² and partial regression coefficients) are tested by permutations, as follows. When the dependent matrix variable y represents a simple distance or similarity matrix, permutations are performed in the same manner as the Mantel permutational test. When it is an ultrametric matrix representing a dendrogram, we use the double-permutation method (Lapointe and Legendre 1990, 1991). When it is a path-length matrix representing an additive tree (cladogram), we use the triple-permutation method (Lapointe and Legendre 1992). The independent matrix variables in X are kept fixed with respect to one another during the permutations. Selection of predictors can be accomplished by forward selection, backward elimination, or a stepwise procedure. A phylogenetic tree, derived from marsupial brain morphology data (28 species), is compared to trees depicting the evolution of diet, sociability, locomotion, and habitat in these animals, as well as their taxonomy and geographical relationships. A model is derived in which brain evolution can be predicted from taxonomy, diet, sociability and locomotion (R² = 0.75). A new tree, derived from the “predicted” data, shows a lot of similarity to the brain evolution tree. The meaning of the taxonomy, diet, sociability, and locomotion predictors are discussed and conclusions are drawn about the evolution of brain and behavior in marsupials.     

Actual state of gammaridean amphipoda taxonomy and catalogue of species from Chile

The taxonomy of gammaridean amphipods is poorly known in Chile. The lack of literature has discouraged investigation of this group, which has been overlooked for years. This has led to the exclusion of amphipods from biological and ecological studies done in our country. I present here a preliminary report on the actual state of the group with reference mainly to its taxonomy, ecological studies and a species catalogue. I have only included species from continental Chile north of 56 °S, Juan Fernandez Archipelago and Isla de Pascua. Species from Chilean Subantarctic and Antarctic waters are excluded, because they are well covered by other authors. There are 168 known for Chile, 36 of them undescribed or with their status not clear. This report is based on a revision of the species recorded for Chile, analysis of samples from the Chilean coast and the work of ecologists who are using the group as material for study.     

Fuzzy measures on the Gene Ontology for gene product similarity

One of the most important objects in bioinformatics is a gene product (protein or RNA). For many gene products, functional information is summarized in a set of Gene Ontology (GO) annotations. For these genes, it is reasonable to include similarity measures based on the terms found in the GO or other taxonomy. In this paper, we introduce several novel measures for computing the similarity of two gene products annotated with GO terms. The fuzzy measure similarity (FMS) has the advantage that it takes into consideration the context of both complete sets of annotation terms when computing the similarity between two gene products. When the two gene products are not annotated by common taxonomy terms, we propose a method that avoids a zero similarity result. To account for the variations in the annotation reliability, we propose a similarity measure based on the Choquet integral. These similarity measures provide extra tools for the biologist in search of functional information for gene products. The initial testing on a group of 194 sequences representing three proteins families shows a higher correlation of the FMS and Choquet similarities to the BLAST sequence similarities than the traditional similarity measures such as pairwise average or pairwise maximum.     

Taxonomie, écologie et lutte biologique

Summary It is impossible to study modern taxonomy without taking into consideration the population genetic and ecology. Thé Linnean concept of monotypic species should be replaced by the biometric study of the frequency of the variability of the biological characters (particularly morphological) used in taxonomy. The study of populations offers a larger scientific interest than the one of isolated types. It gives the possibility of caracterizing the evolution stability of the species. So, Taxonomy can help considerably in biological control. By revealing large variability species, it gives a criterion of their adjusting plasticity. But, by definition, the biological control is based on the adjusting capacity of the entomophagous insects either to a new host or to a new environment. Information given by the taxonomist on the species stability has consequently a great value in the choice and use of the Entomophagous insects. — Ecologists using biological control, expect from the taxonomist to lie more than a label, which implies the use of biometric analysis methods in Entomophagous taxonomy.      

Components of morphological variation in Baikalian endemial cyclopid Acanthocyclops signifer complex from different localities

Use of traditional methods for morphological studies only permits the analysis of a small part of the information embodied in morphological structures. Besides comparing populations using the mean values of characters which allows one to estimate their morphological similarity, analysis of variation among individuals within a population can be informative. Variation among individuals consists of factorial and stochastic components. The factorial component is an upper estimate of genetic heterogeneity and thus permits one to evaluate the population's adaptability. The stochastic component (estimated by fluctuating asymmetry, i.e. random deviations from perfect bilateral symmetry), being a measure of developmental stability, is an indicator of a population's fitness. Assessment of measurement error is necessary for assessment of the true value of the stochastic component and for selection of the most informative characters. Such analysis allows one to extract additional information from morphological data in comparison with methods traditionally used on copepods. This approach was applied to an analysis of morphological variation in the study of the Baikalian endemic cyclopoid Acanthocyclops signifer (Mazepova) from three different isolated localities. Characters typically used in studies of taxonomy of this group are considered here. Measurement error was rather high (more than 50% of the stochastic component), which can be explained by technical difficulties of measuring the characters. All populations differ in the mean values of the characters. This shows the taxonomic heterogeneity of this group and reveals the necessity of its taxonomic revision. Populations also differ in the level of stochastic and factorial components of the total variance. The data are interpreted from the point of view of taxonomy and the possible evolution of the group.     

Managing biological control services through multi‐trophic trait interactions: review and guidelines for implementation at local and landscape scales

Ecological studies are increasingly moving towards trait‐based approaches, as the evidence mounts that functions, as opposed to taxonomy, drive ecosystem service delivery. Among ecosystem services, biological control has been somewhat overlooked in functional ecological studies. This is surprising given that, over recent decades, much of biological control research has been focused on identifying the multiple characteristics (traits) of species that influence trophic interactions. These traits are especially well developed for interactions between arthropods and flowers – important for biological control, as floral resources can provide natural enemies with nutritional supplements, which can dramatically increase biological control efficiency. Traits that underpin the biological control potential of a community and that drive the response of arthropods to environmental filters, from local to landscape‐level conditions, are also emerging from recent empirical studies. We present an overview of the traits that have been identified to (i) drive trophic interactions, especially between plants and biological control agents through determining access to floral resources and enhancing longevity and fecundity of natural enemies, (ii) affect the biological control services provided by arthropods, and (iii) limit the response of arthropods to environmental filters, ranging from local management practices to landscape‐level simplification. We use this review as a platform to outline opportunities and guidelines for future trait‐based studies focused on the enhancement of biological control services.     

A genetic approach to species criteria in the amoeba genus Naegleria using allozyme electrophoresis

The present study employs allozyme electrophoresis to characterize and inter-relate 61 isolates of Naegleria. Diploidy was confirmed, with heterozygotes observed at 29 of the 33 loci established and in all but two isolates. With a single exception, isolates clustered at two levels of similarity, either below 21% or above 52%. It is argued that such a major discontinuity provides a sound biological basis for a species concept in Naegleria. On this basis the present species-level taxonomy does not reflect the genetic diversity of the genus. The study recognized 18 genetic groups of species rank. The subspecies N. australiensis italica deserves specific rank; additional thermophilic species not closely related to N. fowleri and N. lovaniensis are recognized; and N. gruberi as currently conceived is a complex of 10 species, at least five of which are represented in the formal culture collections. Most species are genetically too different for relationships to be elucidated by allozyme electrophoresis, supporting the view that some of the times of divergence within the genus are extremely ancient.     

Variation in pathogenicity of isolates of Cercospora spp. attacking Heliotropium spp.

The pathogenicity of a set of 13 Cercospora samples collected in France, Turkey and Australia from four Heliotropium species has been evaluated with a detached leaf technique. All of five Euro-Asian Heliotropium species tested were susceptible to all Cercospora species isolates. However, variation in the degree of partial resistance to different isolates was observed and showed some similarity for isolates from the same region of origin. Further studies are required to clarify the taxonomy of Cercospora blight strains, but the consequences of the noted differences in pathogenicity are discussed in relation to the biological control ofH. europaeum L. in Australia.     

FBIS: A regional DNA barcode archival & analysis system for Indian fishes

DNA barcode is a new tool for taxon recognition and classification of biological organisms based on sequence of a fragment of mitochondrial gene, cytochrome c oxidase I (COI). In view of the growing importance of the fish DNA barcoding for species identification, molecular taxonomy and fish diversity conservation, we developed a Fish Barcode Information System (FBIS) for Indian fishes, which will serve as a regional DNA barcode archival and analysis system. The database presently contains 2334 sequence records of COI gene for 472 aquatic species belonging to 39 orders and 136 families, collected from available published data sources. Additionally, it contains information on phenotype, distribution and IUCN Red List status of fishes. The web version of FBIS was designed using MySQL, Perl and PHP under Linux operating platform to (a) store and manage the acquisition (b) analyze and explore DNA barcode records (c) identify species and estimate genetic divergence. FBIS has also been integrated with appropriate tools for retrieving and viewing information about the database statistics and taxonomy. It is expected that FBIS would be useful as a potent information system in fish molecular taxonomy, phylogeny and genomics. AVAILABILITY: The database is available for free at http://mail.nbfgr.res.in/fbis/     

Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches

The practice of classifying organisms into hierarchical groups originated with Aristotle and was codified into nearly immutable biological law by Linnaeus. The heart of taxonomy is the biological species, which forms the foundation for higher levels of classification. Whereas species have long been established among sexual eukaryotes, achieving a meaningful species concept for prokaryotes has been an onerous task and has proven exceedingly difficult for describing viruses and bacteriophages. Moreover, the assembly of viral "species" into higher-order taxonomic groupings has been even more tenuous, since these groupings were based initially on limited numbers of morphological features and more recently on overall genomic similarities. The wealth of nucleotide sequence information that catalyzed a revolution in the taxonomy of free-living organisms necessitates a reevaluation of the concept of viral species, genera, families, and higher levels of classification. Just as microbiologists discarded dubious morphological traits in favor of more accurate molecular yardsticks of evolutionary change, virologists can gain new insight into viral evolution through the rigorous analyses afforded by the molecular phylogenetics of viral genes. For bacteriophages, such dissections of genomic sequences reveal fundamental flaws in the Linnaean paradigm that necessitate a new view of viral evolution, classification, and taxonomy.     

基于Web的中国昆虫科级鉴别分类系统InsectID的设计与开发

详细介绍了国内首个昆虫科级鉴别分类网络系统InsectID(见http://insectx.3322.org)的设计思路、各组成部分的结构与功能,讨论了开发过程中分类检索表的转化与再现、系统分类树与特征解释机制的实现等关键问题。该系统具有分类单元全面、信息可靠、鉴定简单、扩充性强、更新便捷等诸多优点,是昆虫分类研究与教学的有力工具,也适用于其他生物分类系统的构建。     

A fast word search algorithm for the representation of sequence similarity in genomic DNA.

Representation of sequence similarity by dot matrix plots is a method widely used for comparing biological sequences. The user is presented with an overall view of similarity between two sequences. Computation of this plot has been reconsidered here. An improvement is proposed through the preprocessing of the data into an automation recognizing the word structure of a sequence. The main advantage of this approach is to systematically eliminate the repetitions during word comparison. Simple heuristics are also considered to greatly speed up pattern matching. As a result, large sequences are handled very efficiently. This is illustrated by a comparison of large genomic DNA. The algorithm has been implemented in an interactive application on a microcomputer.