HICLAS: a taxonomic database system for displaying and comparing biological classification and phylogenetic trees.
MOTIVATION: Numerous database management systems have been developed for processing various taxonomic data bases on biological classification or phylogenetic information. In this paper, we present an integrated system to deal with interacting classifications and phylogenies concerning particular taxonomic groups. RESULTS: An information-theoretic view (taxon view) has been applied to capture taxonomic concepts as taxonomic data entities. A data model which is suitable for supporting semantically interacting dynamic views of hierarchic classifications and a query method for interacting classifications have been developed. The concept of taxonomic view and the data model can also be expanded to carry phylogenetic information in phylogenetic trees. We have designed a prototype taxonomic database system called HICLAS (HIerarchical CLAssification System) based on the concept of taxon view, and the data models and query methods have been designed and implemented. This system can be effectively used in the taxonomic revisionary process, especially when databases are being constructed by specialists in particular groups, and the system can be used to compare classifications and phylogenetic trees. AVAILABILITY: Freely available at the WWW URL: http://aims.cps.msu.edu/hiclas/ CONTACT: [email protected]; [email protected] (+info)
Genomic fingerprinting and development of a dendrogram for Brucella spp. isolated from seals, porpoises, and dolphins.
Genomic DNA from reference strains and biovars of the genus Brucella was analyzed using pulsed-field gel electrophoresis (PFGE). Fingerprints were compared to estimate genetic relatedness among the strains and to obtain information on evolutionary relationships. Electrophoresis of DNA digested with the restriction endonuclease XbaI produced fragment profiles for the reference type strains that distinguished these strains to the level of species. Included in this study were strains isolated from marine mammals. The PFGE profiles from these strains were compared with those obtained from the reference strains and biovars. Isolates from dolphins had similar profiles that were distinct from profiles of Brucella isolates from seals and porpoises. Distance matrix analyses were used to produce a dendrogram. Biovars of B. abortus were clustered together in the dendrogram; similar clusters were shown for biovars of B. melitensis and for biovars of B. suis. Brucella ovis, B. canis, and B. neotomae differed from each other and from B. abortus, B. melitensis, and B. suis. The relationship between B. abortus strain RB51 and other Brucella biovars was compared because this strain has replaced B. abortus strain 19 for use as a live vaccine in cattle and possibly in bison and elk. These results support the current taxonomy of Brucella species and the designation of an additional genomic group(s) of Brucella. The PFGE analysis in conjunction with distance matrix analysis was a useful tool for calculating genetic relatedness among the Brucella species. (+info)
Numerical taxonomy of some yellow-pigmented bacteria isolated from plants.
Phenetic data on over 60 heterotrophic, Gram-negative, yellow chromogenic bacteria from plant material were collected and analysed using numerical taxonomic methods. Marker strains representing 42 taxa were included in the analyses. At similarity levels of 80% or above, eight distinct clusters were obtained, the first four of which included yellow chromogens. Custer I contained isolates from green healthy leaves of Agrostis tenuis, Festuca rubra, Holcus lanata, Lolium perenne and Poa pratensis, and clusters 2 and 3 consisted of isolates from Holcus lanata seeds and leaves of P. pratensis respectively. Cluster 4 contained seven subgroups and was equated with the family Enterobacteriaceae. Erwinia herbicola strains from a variety of sources formed a homogeneous subgroup, readily distinguishable from authentic strains of E. amylovora, E. carotovora, other representative erwiniae, and from all other enterobacteria studied. These data emphasize the heterogeneous nature of yellow-pigmented bacteria from plants, and support the inclusion of E. herbicola and other Erwinia species in the Enterobacteriaceae. (+info)
Evidence on the origin of cassava: phylogeography of Manihot esculenta.
Cassava (Manihot esculenta subsp. esculenta) is a staple crop with great economic importance worldwide, yet its evolutionary and geographical origins have remained unresolved and controversial. We have investigated this crop's domestication in a phylogeographic study based on the single-copy nuclear gene glyceraldehyde 3-phosphate dehydrogenase (G3pdh). The G3pdh locus provides high levels of noncoding sequence variation in cassava and its wild relatives, with 28 haplotypes identified among 212 individuals (424 alleles) examined. These data represent one of the first uses of a single-copy nuclear gene in a plant phylogeographic study and yield several important insights into cassava's evolutionary origin: (i) cassava was likely domesticated from wild M. esculenta populations along the southern border of the Amazon basin; (ii) the crop does not seem to be derived from several progenitor species, as previously proposed; and (iii) cassava does not share haplotypes with Manihot pruinosa, a closely related, potentially hybridizing species. These findings provide the clearest picture to date on cassava's origin. When considered in a genealogical context, relationships among the G3pdh haplotypes are incongruent with taxonomic boundaries, both within M. esculenta and at the interspecific level; this incongruence is probably a result of lineage sorting among these recently diverged taxa. Although phylogeographic studies in animals have provided many new evolutionary insights, application of phylogeography in plants has been hampered by difficulty in obtaining phylogenetically informative intraspecific variation. This study demonstrates that single-copy nuclear genes can provide a useful source of informative variation in plants. (+info)
Zebrafish in context: uses of a laboratory model in comparative studies.
With the recent interest in the reintegration of evolutionary and developmental biology has come a growing need for understanding the phylogenetic relations and degree of generality of the model organisms upon which we rely so heavily. In vertebrate biology the zebrafish Danio rerio has become a paradigmatic system for studies at levels of organization from molecular to interspecific. Studies of model systems in development are often techniques-driven rather than questions-based; however, informative hypotheses for developmental research can be derived from phylogenetic distributions of characters. With some understanding of how general the characters of interest are, a thoughtful comparison of the requirements of the questions with the lists of available embryos, reagents, and protocols can guide choices of new vertebrate models. We describe here the phylogenetic placement of zebrafish within the vertebrate world and discuss how generally observations on zebrafish can be taken to apply. We outline a practical protocol for investigating development in a comparative context, illustrated with an example from an ongoing study of teleost tail fin evolution. The principles and procedures presented here apply equally well to any comparative study with an interest in evolution, at any level of phylogeny from intraspecific studies to comparisons across phyla. (+info)
Proposal for a standardized temporal scheme of biological classification for extant species.
With respect to conveying useful comparative information, current biological classifications are seriously flawed because they fail to (i) standardize criteria for taxonomic ranking and (ii) equilibrate assignments of taxonomic rank across disparate kinds of organisms. In principle, these problems could be rectified by adopting a universal taxonomic yardstick based on absolute dates of the nodes in evolutionary trees. By using procedures of temporal banding described herein, a simple philosophy of biological classification is proposed that would retain a manageable number of categorical ranks yet apply them in standardized fashion to time-dated phylogenies. The phylogenetic knowledge required for a time-standardized nomenclature arguably may emerge in the foreseeable future from vast increases in multilocus DNA sequence information (coupled with continued attention to phylogeny estimation from traditional systematic data). By someday encapsulating time-dated phylogenies in a familiar yet modified hierarchical ranking scheme, a temporal-banding approach would improve the comparative information content of biological classifications. (+info)
The classification of smile patterns.
Although "smile therapy" is still in its infancy, society has already placed a great demand on dentists to evaluate and treat smiles. The smile classification scheme and vocabulary presented in this article will aid in discussions between patient and dentist regarding esthetic treatment. (+info)
An ontology for bioinformatics applications.
MOTIVATION: An ontology of biological terminology provides a model of biological concepts that can be used to form a semantic framework for many data storage, retrieval and analysis tasks. Such a semantic framework could be used to underpin a range of important bioinformatics tasks, such as the querying of heterogeneous bioinformatics sources or the systematic annotation of experimental results. RESULTS: This paper provides an overview of an ontology [the Transparent Access to Multiple Biological Information Sources (TAMBIS) ontology or TaO] that describes a wide range of bioinformatics concepts. The present paper describes the mechanisms used for delivering the ontology and discusses the ontology's design and organization, which are crucial for maintaining the coherence of a large collection of concepts and their relationships. AVAILABILITY: The TAMBIS system, which uses a subset of the TaO described here, is accessible over the Web via http://img.cs.man.ac.uk/tambis (although in the first instance, we will use a password mechanism to limit the load on our server). The complete model is also available on the Web at the above URL. (+info)