Density-based hierarchical clustering of pyro-sequences on a large scale--the case of fungal ITS1.

MOTIVATION: Analysis of millions of pyro-sequences is currently playing a crucial role in the advance of environmental microbiology. Taxonomy-independent, i.e. unsupervised, clustering of these sequences is essential for the definition of Operational Taxonomic Units. For this application, reproducibility and robustness should be the most sought after qualities, but have thus far largely been overlooked. RESULTS: More than 1 million hyper-variable internal transcribed spacer 1 (ITS1) sequences of fungal origin have been analyzed. The ITS1 sequences were first properly extracted from 454 reads using generalized profiles. Then, otupipe, cd-hit-454, ESPRIT-Tree and DBC454, a new algorithm presented here, were used to analyze the sequences. A numerical assay was developed to measure the reproducibility and robustness of these algorithms. DBC454 was the most robust, closely followed by ESPRIT-Tree. DBC454 features density-based hierarchical clustering, which complements the other methods by providing insights into the structure of the data. AVAILABILITY: An executable is freely available for non-commercial users at ftp://ftp.vital-it.ch/tools/dbc454. It is designed to run under MPI on a cluster of 64-bit Linux machines running Red Hat 4.x, or on a multi-core OSX system. CONTACT: dbc454@vital-it.ch or nicolas.guex@isb-sib.ch.

Artificial-Intelligence-Based Optimization of the Management of Snow Removal Assets and Resources Final Report, October 2002

Geographic information systems (GIS) and artificial intelligence (AI) techniques were used to develop an intelligent snow removal asset management system (SRAMS). The system has been evaluated through a case study examining snow removal from the roads in Black Hawk County, Iowa, for which the Iowa Department of Transportation (Iowa DOT) is responsible. The SRAMS is comprised of an expert system that contains the logical rules and expertise of the Iowa DOT’s snow removal experts in Black Hawk County, and a geographic information system to access and manage road data. The system is implemented on a mid-range PC by integrating MapObjects 2.1 (a GIS package), Visual Rule Studio 2.2 (an AI shell), and Visual Basic 6.0 (a programming tool). The system could efficiently be used to generate prioritized snowplowing routes in visual format, to optimize the allocation of assets for plowing, and to track materials (e.g., salt and sand). A test of the system reveals an improvement in snowplowing time by 1.9 percent for moderate snowfall and 9.7 percent for snowstorm conditions over the current manual system.

Mating does not influence reproductive investment, in a viviparous lizard.

Mating is crucial for females that reproduce exclusively sexually and should influence their investment into reproduction. Although reproductive adjustments in response to mate quality have been tested in a wide range of species, the effect of exposure to males and mating per se has seldom been studied. Compensatory mechanisms against the absence of mating may evolve more frequently in viviparous females, which pay higher direct costs of reproduction, due to gestation, than oviparous females. To test the existence of such mechanisms in a viviparous species, we experimentally manipulated the mating opportunity of viviparous female lizard, Lacerta (Zootoca) vivipara. We assessed the effect of mating on ovulation, postpartum body condition and parturition date, as well as on changes in locomotor performances and body temperatures during the breeding cycle. Female lizards ovulated spontaneously and mating had no influence on litter size, locomotor impairment or on selected body temperature. However, offspring production induced a more pronounced locomotor impairment and physical burden than the production of undeveloped eggs. Postpartum body condition and parturition dates were not different among females. This result suggests that gestation length is not determined by an embryonic signal. In the common lizard, viviparity is not associated with facultative ovulation and a control of litter size after ovulation, in response to the absence of mating.

Phyletic trends in uppermost Triassic (Rhaetian) Radiolaria: Two examples from Queen Charlotte Islands, British Columbia, Canada

Risella Carter and Laxtorum Blome, two genera from the diverse Rhaetian fauna of the Sandilands Formation, Queen Charlotte Islands, are used to illustrate phyletic trends in latest Triassic Radiolaria. Several distinct morphotypes constituting a lineage are recognized for each genus. These lineages are homogenous, evolved in situ, and show a continuum of variation through time. The evolution of Risella takes place entirely in the Rhaetian and all species disappear at the end of the Triassic. Earliest species of Laxtorum appear in the upper Norian and evolve rapidly in the Rhaetian. All Rhaetian species go extinct at the end of the Triassic but the genus survives marginally into the Lower Jurassic. Morphological transformations in Risella (a paronaellid) are manifest in the external/cortical shell as the shape changes from triangular to three-rayed. In Laxtorum, distal post abdominal chambers become constricted and eventually develop a terminal tube while, at the same time, an increase in size and sphericity is coupled with a reduction in the number of post abdominal chambers. Evolutionary transitions in the Risella lineage probably represent a reversion of the normal hypothesized trend for paronaellid radiolarians. In the Laxtorum lineage, comparisons with other groups and species displaying similar homeomorphies suggest the evolutionary trends are fundamental and occur repeatedly in faunas of all ages.

Chemical defenses in Sacoglossan Opisthobranchs: Taxonomic trends and evolutionary implications

Sacoglossan sea slugs (Mollusca: Opisthobranchia) are one of the few groups of specialist herbivores in the marine environment. Sacoglossans feed suctorially on the cell sap of macroalgae, from which they 'steal' chloroplasts (kleptoplasty) and deterrent substances (kleptochemistry), retaining intracellularly both host plastids and chemicals. The ingested chloroplasts continue to photosynthesize for periods ranging from a few hours or days up to 3 months in some species. Shelled, more primitive sacoglossans feed only on the siphonalean green algal genus Caulerpa, and they do not have functional kleptoplasty. The diet of sacoglossans has radiated out from this ancestral food. Among the shell-less Plakobranchidae (=Elysiidae), the more primitive species feed on other siphonales (families Derbesiaceae, Caulerpaceae, Bryopsidaceae and Codiaceae) and fix carbon, while the more 'advanced' species within the Plakobranchidae and Limapontioidae have a more broad dietary range. Most of these 'advanced' species are unable to fix carbon because the chloroplasts of their food algae are mechanically disrupted during ingestion. Mesoherbivores are likely to be eaten if they live on palatable seaweeds, their cryptic coloration and form not always keeping them safe from predators. Sacoglossans prefer to live on and eat chemically defended seaweeds, and they use ingested algal chemicals as deterrents of potential predators. The most ancestral shelled sacoglossans (Oxynoidae) and some Plakobranchidae such as Elysia translucens, Thuridilla hopei and Bosellia mimetica have developed a diet-derived chemical defense mechanism. Oxynoids and Thuridilla hopei are able to biomodify the algal metabolites. However, the Plakobranchidae Elysia timida and E. viridis, together with Limapontioidea species, are characterized by their ability to de novo synthesize polypropionate metabolites. A whole analysis of kleptoplasty and chemical defenses in sacoglossans may offer a better understanding of the ecology and evolution of these specialized opisthobranchs. In this paper we summarize some of the latest findings, related mainly to Mediterranean species, and offer a plausible evolutionary scenario based on the biological and chemical trends we can distinguish in them.

Climate and vegetation history of western Portugal inferred from Albian near-shore deposits (Gale Formation, Lusitanian Basin)

The late Early Cretaceous greenhouse climate has been studied intensively based on proxy data derived essentially from open marine archives. In contrast, information on continental climatic conditions and on the accompanying response of vegetation is relatively scarce, most notably owing to the stratigraphic uncertainties associated with many Lower Cretaceous terrestrial deposits. Here, we present a palynological record from Albian near-shore deposits of the Lusitanian Basin of W Portugal, which have been independently dated using Sr-isotope signals derived from low-Mg oyster shell calcite. Sr-87/Sr-86 values fluctuate between 0.707373 +/- 0.00002 and 0.707456 +/- 0.00003; absolute values and the overall stratigraphic trend match well with the global open marine seawater signature during Albian times. Based on the new Sr-isotope data, existing biostratigraphic assignments of the succession are corroborated and partly revised. Spore-pollen data provide information on the vegetation community structure and are flanked by sedimentological and clay mineralogical data used to infer the overall climatic conditions prevailing on the adjacent continent. Variations in the distribution of climate-sensitive pollen and spores indicate distinct changes in moisture availability across the studied succession with a pronounced increase in hygrophilous spores in late Early Albian times. Comparison with time-equivalent palynofloras from the Algarve Basin of southern Portugal shows pronounced differences in the xerophyte/hygrophyte ratio, interpreted to reflect the effect of a broad arid climate belt covering southern and southeastern Iberia during Early Albian times.

A generalization of Cope's rule

For numerous shelly invertebrates, Cope's rule is shown in this paper to merely describe the particular case where volume increase is strictly coupled with diameter or length. Allometries, which are frequently observed in the evolution of the shells' geometry, mean that their size, volume and surface can vary independently. The consequences of this can be summarized as follows : 1) volume increase not coupled with an increase of diameter or length of the organisms generates increasing involution and/or lateral width in the shell of cephalopods, foraminifera and radiolarians; 2) an increase of the biomineralizing surface, not coupled with volume increase, generates increasing apparent complexity in the sutures and growth lines in ammonites, and an increase in the complexity and number of chambers in foraminifera.