Histogram-based DNA analysis for the visualization of chromosome, genome and species information

We describe a novel approach to explore DNA nucleotide sequence data, aiming to produce high-level categorical and structural information about the underlying chromosomes, genomes and species. The article starts by analyzing chromosomal data through histograms using fixed length DNA sequences. After creating the DNA-related histograms, a correlation between pairs of histograms is computed, producing a global correlation matrix. These data are then used as input to several data processing methods for information extraction and tabular/graphical output generation. A set of 18 species is processed and the extensive results reveal that the proposed method is able to generate significant and diversified outputs, in good accordance with current scientific knowledge in domains such as genomics and phylogenetics.

A trophic analysis of target species of macrobenthos in a subtropical coast community: a taxa relationship essay

Studies on the feeding habits of aquatic organisms are a requirement for the management and sustainable use of marine ecosystems. The aim of the present research was to analyze the habits and trophic similarities of decapods, starfish and fish in order to propose trophic relationships between taxa, using Hennigian methods of phylogenetic systematics. This new grouping hypothesis, based on shared and exclusive food items and food types, corresponds to the broad taxonomic groups used in the analysis. Our results indicate that algae, Mollusca, Polychaeta, Crustacea, Echinodermata and Actinopterygii are the most exploited common resources among the species studied. Starfish were differentiated from other organisms for being stenophagic, and were grouped for feeding on bivalve mollusks. A larger group of fish and crustaceans shares algae and mainly crustaceans as food items. A third group united all eight species of Actinopterygii. This largest subgroup of fish is typically carnivorous, feeding on Anthozoa and a great quantity of Crustacea. Synodus foetens has a special position among fishes, due to its unique feeding on nematodes. A Euclidean distance dendrogram obtained in a previous publication grouped S. foetens with starfish. That result was based on a few non-exclusive shared similarities in feeding modes, as well as on shared absences of items, which are not an adequate grouping factor. Starfish are stenophagic, eating bivalves almost exclusively. Synodus foetens and Isopisthus parvipinnis have restricted food items, and are thus intermediary in relation to starfish, decapods, and other fish, which are euryphagous. The trophic cladogram displays details of food items, whether or not shared by all species. The resulting trophic analysis is consistent with known historical relationships.

Light-distortion analysis as a possible indicator of visual quality after refractive lens exchange with diffractive multifocal intraocular lenses

METHODS: Refractive lens exchange was performed with implantation of an AT Lisa 839M (trifocal) or 909MP (bifocal toric) IOL, the latter if corneal astigmatism was more than 0.75 diopter (D). The postoperative visual and refractive outcomes were evaluated. A prototype light-distortion analyzer was used to quantify the postoperative light-distortion indices. A control group of eyes in which a Tecnis ZCB00 1-piece monofocal IOL was implanted had the same examinations. RESULTS: A trifocal or bifocal toric IOL was implanted in 66 eyes. The control IOL was implanted in 18 eyes. All 3 groups obtained a significant improvement in uncorrected distance visual acuity (UDVA) (P < .001) and corrected distance visual acuity (CDVA) (P Z .001). The mean uncorrected near visual acuity (UNVA) was 0.123 logMAR with the trifocal IOL and 0.130 logMAR with the bifocal toric IOL. The residual refractive cylinder was less than 1.00 D in 86.7% of cases with the toric IOL. The mean light-distortion index was significantly higher in the multifocal IOL groups than in the monofocal group (P < .001), although no correlation was found between the light-distortion index and CDVA. CONCLUSIONS: The multifocal IOLs provided excellent UDVA and functional UNVA despite increased light-distortion indices. The light-distortion analyzer reliably quantified a subjective component of vision distinct from visual acuity; it may become a useful adjunct in the evaluation of visual quality obtained with multifocal IOLs.

Comparative leaf morphological analysis of 20 species of Chrysobalanaceae

Morphological studies focusing on vegetative traits are useful in identifying species when fertile material is not available. The aim of this study was to assess the application of comparative leaf morphology to identify species of the Chrysobalanaceae family. The morphological observations were made with a stereomicroscope. We used the diaphanization technique for viewing venation details. It is shown the descriptions of the leaf morphology, illustrations and an identification key for 20 species from genera Couepia, Licania and Parinari (Chrysobalanaceae) occurring in the Adolpho Ducke Forest Reserve, Manaus, AM, Brazil. The key was constructed using the DELTA (DEscription Language for TAxonomy) software. Leaf traits such as the presence of intersecondary venation and the type of insertion of secondary veins were recorded for each species. These morphological leaf traits are reliable for identifying species of Chrysobalanaceae

Comparative analysis of tidepool fish species composition on tropical coastal rocky reefs at State of Ceará, Brazil

This study compared tidepool fish assemblages within and among habitats at Iparana and Pecém beaches, State of Ceará, Northeast Brazil, using visual census techniques. A total of 8,914 fishes, representing 25 families and 43 species were recorded. The most abundant taxon was Sparisoma spp, followed by Haemulon parra (Desmarest, 1823), Acanthurus chirurgus (Bloch, 1787) and Abudefduf saxatilis (Linnaeus, 1758). Haemulidae was the most abundant family in number of individuals, followed by Scaridae, Acanthuridae and Pomacentridae. Within- and between- site differences in species assemblages probably reflected environmental discontinuities and more localized features, such as pool isolation episodes, or environmental complexity, both acting isolated or interactively. The locality of Iparana was probably subjected to a greater fishing pressure and tourism than Pecém, a potential cause for the observed lowest fish abundance and biodiversity. We conclude that tidepool ichthyofauna may be quite variable between and within reef sites. Thus, observations taken from or damages caused on one area may not be generalized to or mitigated by the protection of adjacent sites.

Comparative dietary analysis of Eurycheilichthys pantherinus and Pareiorhaphis hystrix: two Loricariidae species (Ostariophysi, Siluriformes) from Campos Sulinos biome, southern Brazil

This work was carried out in Marco river, São José dos Ausentes municipality, state of Rio Grande do Sul, southern Brazil. This region is located within the Campos Sulinos biome, an area of great biological importance due to its high diversity and endemism of fish. The feeding habits and food overlap between Eurycheilichthys pantherinus (Reis & Schaefer, 1992) (n=108) and Pareiorhaphis hystrix Pereira & Reis, 2002 (n=60) are described. Monthly samples were obtained between September 2000 and July 2001 with dipnets using the kick sampling technique. Stomach contents were analyzed based on frequency of occurrence, volumetric frequency and index of alimentary importance. The level of dietary specialization and food overlap were determined by the Levins measure and the Morisita index, respectively. Eurycheilichthys pantherinus fed mainly on immature aquatic insects, such as Dipterans and Ephemeropterans, and was classified as insectivore. Pareiorhaphis hystrix fed mainly on detritus associated with small amounts of aquatic insects, and was classified as detritivore. Species are clearly segregated by the use of food resources in Marco River. Their diets did not overlap and the differences observed in their feeding habits probably contribute for their coexistence.

Empirical testing of genuine savings as an indicator of weak sustainability: a three-country analysis of long run trends

Genuine Savings has emerged as a widely-used indicator of sustainable development. In this paper, we use long-term data stretching back to 1870 to undertake empirical tests of the relationship between Genuine Savings (GS) and future well-being for three countries: Britain, the USA and Germany. Our tests are based on an underlying theoretical relationship between GS and changes in the present value of future consumption. Based on both single country and panel results, we find evidence supporting the existence of a cointegrating (long run equilibrium) relationship between GS and future well-being, and fail to reject the basic theoretical result on the relationship between these two macroeconomic variables. This provides some support for the GS measure of weak sustainability. We also show the effects of modelling shocks, such as World War Two and the Great Depression.

Molecular karyotype analysis and mapping of housekeeping genes to chromosomes of selected species complexes of Leishmania

The molecular karyotypes for 20 reference strais of species complexes of Leishmania were determined by contour-clamped homogeneous eletric field (CHEF) electrosphoresis. Determination of number/position of chromosome-sized bands and chromosomal DNA locations of house-keeping genes were the two criteria used for differentiating and classifying the Leishmania species. We have established two gel running conditions of optimal separation of chromosomes, wich resolved DNA molecules as large as 2,500 kilobase pairs (kb). Chromosomes were polymorphic in number (22-30) and size (200-2,500 kb) of bands among members of five complexes of Leishmania. Although each stock had a distinct karyotype, in general the differences found between strains and/or species within each complex were not clear enough for parasite identification. However, each group showed a specific number of size-concordant DNA molecules, wich allowed distinction among the Leishmania complex parasites. Clear differences between the Old and New world groups of parasites or among some New World Leishmania species were also apparent in relation to the chromosome locations of beta-tubulin genes. Based on these results as well as data from other published studies the potencial of using DNA karyotype for identifying and classifying leishmanial field isolates is discussed.

Multilocus sequence analysis reveals the genetic diversity of European fruit tree phytoplasmas and supports the existence of inter-species recombination

The genetic diversity of three temperate fruit tree phytoplasmas ‘Candidatus Phytoplasma prunorum’, ‘Ca. P. mali’ and ‘Ca. P. pyri’ has been established by multilocus sequence analysis. Among the four genetic loci used, the genes imp and aceF distinguished 30 and 24 genotypes, respectively, and showed the highest variability. Percentage of substitution for imp ranged from 50 to 68% according to species. Percentage of substitution varied between 9 and 12% for aceF, whereas it was between 5 and 6% for pnp and secY. In the case of ‘Ca P. prunorum’ the three most prevalent aceF genotypes were detected in both plants and insect vectors, confirming that the prevalent isolates are propagated by insects. The four isolates known to be hypo-virulent had the same aceF sequence, indicating a possible monophyletic origin. Haplotype network reconstructed by eBURST revealed that among the 34 haplotypes of ‘Ca. P. prunorum’, the four hypo-virulent isolates also grouped together in the same clade. Genotyping of some Spanish and Azerbaijanese ‘Ca. P. pyri’ isolates showed that they shared some alleles with ‘Ca. P. prunorum’, supporting for the first time to our knowledge, the existence of inter-species recombination between these two species.

Analysis of parity between protein-based electrophoretic methods for the characterization of oral Candida species

Electrophoretic studies of multilocus-enzymes (MLEE) and whole-cell protein (SDS-PAGE) were carried out in order to evaluate the parity between different methods for the characterization of five Candida species commonly isolated from oral cavity of humans by numerical taxonomy methods. The obtained data revealed that sodium dodecyl sulfate polyacrylamide gel electrophoresis is more efficient in grouping strains in their respective species while MLEE has much limited resolution in organizing all strains in their respective species-specific clusters. MLEE technique must be regarded for surveys in which just one species of Candida is involved.

Molecular analysis of an odorant-binding protein gene in two sympatric species of Lutzomyia longipalpis s.l.

Lutzomyia longipalpis s.l. is the main vector of American visceral leishmaniasis (AVL) and occurs as a species complex. DNA samples from two Brazilian sympatric species that differ in pheromone and courtship song production were used to analyse molecular polymorphisms in an odorant-binding protein ( obp29 ) gene. OBPs are proteins related to olfaction and are involved in activities fundamental to survival, such as foraging, mating and choice of oviposition site. In this study, the marker obp29 was found to be highly polymorphic in Lu. longipalpis s.l. , with no fixed differences observed between the two species. A pairwise fixation index test indicated a moderate level of genetic differentiation between the samples analysed.

Statistical Analysis of Eco-Toxicologic Data of Mammals from a Polluted Area

Several eco-toxicological studies have shown that insectivorous mammals, due to theirfeeding habits, easily accumulate high amounts of pollutants in relation to other mammal species. To assess the bio-accumulation levels of toxic metals and their in°uenceon essential metals, we quantified the concentration of 19 elements (Ca, K, Fe, B, P,S, Na, Al, Zn, Ba, Rb, Sr, Cu, Mn, Hg, Cd, Mo, Cr and Pb) in bones of 105 greaterwhite-toothed shrews (Crocidura russula) from a polluted (Ebro Delta) and a control(Medas Islands) area. Since chemical contents of a bio-indicator are mainly compositional data, conventional statistical analyses currently used in eco-toxicology can givemisleading results. Therefore, to improve the interpretation of the data obtained, weused statistical techniques for compositional data analysis to define groups of metalsand to evaluate the relationships between them, from an inter-population viewpoint.Hypothesis testing on the adequate balance-coordinates allow us to confirm intuitionbased hypothesis and some previous results. The main statistical goal was to test equalmeans of balance-coordinates for the two defined populations. After checking normality,one-way ANOVA or Mann-Whitney tests were carried out for the inter-group balances

Morphometric shape analysis using learning vector quantization neural networks - an example distinguishing two microtine vole species

Closely related species may be very difficult to distinguish morphologically, yet sometimes morphology is the only reasonable possibility for taxonomic classification. Here we present learning-vector-quantization artificial neural networks as a powerful tool to classify specimens on the basis of geometric morphometric shape measurements. As an example, we trained a neural network to distinguish between field and root voles from Procrustes transformed landmark coordinates on the dorsal side of the skull, which is so similar in these two species that the human eye cannot make this distinction. Properly trained neural networks misclassified only 3% of specimens. Therefore, we conclude that the capacity of learning vector quantization neural networks to analyse spatial coordinates is a powerful tool among the range of pattern recognition procedures that is available to employ the information content of geometric morphometrics.

Track analysis of the Mexican species of Cerambycidae (Insecta, Coleoptera)

A track analysis of 221 species belonging to 68 genera of Mexican Cerambycidae was undertaken in order to identify their main distributional patterns. Based on the comparison of the individual tracks, fifteen generalized tracks were obtained: six are placed in the Neotropical region, seven are shared by the Neotropical region and the Mexican Transition Zone, one is situated in the Mexican Transition Zone, and one is shared by the Nearctic region and the Mexican Transition Zone. Eight nodes were found in the intersection of these generalized tracks, five of them located in the Neotropical region and three in the Mexican Transition Zone. Distributional patterns of Mexican Cerambycidae show two basic patterns: one mostly Neotropical, in the Mesoamerican dominion (Mexican Pacific Coast and Mexican Gulf biogeographic provinces) and another in the Mexican Transition Zone (Transmexican Volcanic Belt and Balsas Basin biogeographic provinces).