Comparison of Similarity Coefficients used for Cluster Analysis with Amplified Fragment Length Polymorphism Markers in the Silkworm, Bombyx mori

Establishing accurate genetic similarity and dissimilarity between individuals is an essential and decisive point for clustering and analyzing inter and intra population diversity because different similarity and dissimilarity indices may yield contradictory outcomes. We assessed the variations caused by three commonly used similarity coefficients including Jaccard, Sorensen-Dice and Simple matching in the clustering and ordination of seven Iranian native silkworm, Bombyx mori L. (Lepidoptera: Bombycidae), strains analyzed by amplified fragment length polymorphism markers. Comparisons among the similarity coefficients were made using the Spearman correlation analysis, dendrogram evaluation (visual inspection and consensus fork index - CIC), projection efficiency in a two-dimensional space, and groups formed by the Tocher optimization procedure. The results demonstrated that for almost all methodologies, the Jaccard and Sorensen-Dice coefficients revealed extremely close results, because both of them exclude negative co-occurrences. Due to the fact that there is no guarantee that the DNA regions with negative cooccurrences between two strains are indeed identical, the use of coefficients such as Jaccard and Sorensen-Dice that do not include negative co-occurrences was imperative for closely related organisms

Morphometry of the Cranial Base in Subjects with Class III Malocclusion

The significance of the cranial base in the development of Class III malocclusion remains uncertain. The purpose of this study was to determine whether the form of the cranial base differs between prepubertal Class I and Class III subjects. Lateral cephalographs of 73 children of European-American descent aged between 5 and 11 years with Class III malocclusion were compared with those of their counterparts with a normal, Class I molar occlusion. The cephalographs were traced, checked, and subdivided into seven age- and sex-matched groups. Average geometries, scaled to an equivalent size, were generated based on 13 craniofacial landmarks by means of Procrustes analysis, and these configurations were statistically tested for equivalence. Bivariate and multivariate analyses utilizing 5 linear and angular measurements were undertaken to corroborate the Procrustes analysis. Graphical analysis, utilizing thin-plate spline and finite element methods, was performed for localization of differences in cranial base morphology. Results indicated that cranial base morphology differed statistically for all age-wise comparisons. Graphical analysis revealed that the greatest differences in morphology occurred in the posterior cranial base region, which generally consisted of horizontal compression, vertical expansion, and size contraction. The sphenoidal region displayed expansion, while the anterior regions showed shearing and local increases in size. It is concluded that the shape of the cranial base differs in subjects with Class III malocclusion compared with the normal Class I configuration, due in part to deficient orthocephalization, or failure of the cranial base to flatten during development.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/67377/2/10.1177_00220345970760021101.pd

Leaf Morphology, Taxonomy and Geometric Morphometrics: A Simplified Protocol for Beginners

Taxonomy relies greatly on morphology to discriminate groups. Computerized geometric morphometric methods for quantitative shape analysis measure, test and visualize differences in form in a highly effective, reproducible, accurate and statistically powerful way. Plant leaves are commonly used in taxonomic analyses and are particularly suitable to landmark based geometric morphometrics. However, botanists do not yet seem to have taken advantage of this set of methods in their studies as much as zoologists have done. Using free software and an example dataset from two geographical populations of sessile oak leaves, we describe in detailed but simple terms how to: a) compute size and shape variables using Procrustes methods; b) test measurement error and the main levels of variation (population and trees) using a hierachical design; c) estimate the accuracy of group discrimination; d) repeat this estimate after controlling for the effect of size differences on shape (i.e., allometry). Measurement error was completely negligible; individual variation in leaf morphology was large and differences between trees were generally bigger than within trees; differences between the two geographic populations were small in both size and shape; despite a weak allometric trend, controlling for the effect of size on shape slighly increased discrimination accuracy. Procrustes based methods for the analysis of landmarks were highly efficient in measuring the hierarchical structure of differences in leaves and in revealing very small-scale variation. In taxonomy and many other fields of botany and biology, the application of geometric morphometrics contributes to increase scientific rigour in the description of important aspects of the phenotypic dimension of biodiversity. Easy to follow but detailed step by step example studies can promote a more extensive use of these numerical methods, as they provide an introduction to the discipline which, for many biologists, is less intimidating than the often inaccessible specialistic literature

The Poincaré Polynomial of a Linear Code

We introduce the Poincaré polynomial of a linear q-ary code and its relation to the corresponding weight enumerator. The question of whether the Poincaré polynomial is a complete invariant is answered affirmatively for q = 2, 3 and negatively for q ≥ 4. Finally we determine this polynomial for MDS codes and, by means of a recursive formula, for binary Reed-Muller codes

The power of perturbation theory

We study quantum mechanical systems with a discrete spectrum. We show that the asymptotic series associated to certain paths of steepest-descent (Lefschetz thimbles) are Borel resummable to the full result. Using a geometrical approach based on the PicardLefschetz theory we characterize the conditions under which perturbative expansions lead to exact results. Even when such conditions are not met, we explain how to define a different perturbative expansion that reproduces the full answer without the need of transseries, i.e. non-perturbative effects, such as real (or complex) instantons. Applications to several quantum mechanical systems are presented

Kinetics of maternal immunity against rabies in fox cubs (Vulpes vulpes)

BACKGROUND: In previous experiments, it was demonstrated that maternal antibodies (maAb) against rabies in foxes (Vulpes vulpes) were transferred from the vixen to her offspring. However, data was lacking from cubs during the first three weeks post partum. Therefore, this complementary study was initiated. METHODS: Blood samples (n = 281) were collected from 64 cubs (3 to 43 days old) whelped by 19 rabies-immune captive-bred vixens. Sera was collected up to six times from each cub. The samples were analysed by a fluorescence focus inhibition technique (RFFIT), and antibody titres (nAb) were expressed in IU/ml. The obtained data was pooled with previous data sets. Subsequently, a total of 499 serum samples from 249 cubs whelped by 54 rabies-immune vixens were fitted to a non-linear regression model. RESULTS: The disappearance rate of maAb was independent of the vixens' nAb-titre. The maAb-titre of the cubs decreased exponentially with age and the half-life of the maAb was estimated to be 9.34 days. However, maAb of offspring whelped by vixens with high nAb-titres can be detected for longer by RFFIT than that of offspring whelped by vixens with relatively low nAb-titres. At a mean critical age of about 23 days post partum, maAb could no longer be distinguished from unspecific reactions in RFFIT depending on the amount of maAb transferred by the mother. CONCLUSIONS: The amount of maAb cubs receive is directly proportional to the titre of the vixen and decreases exponentially with age below detectable levels in seroneutralisation tests at a relatively early age

Isolation-by-Distance and Outbreeding Depression Are Sufficient to Drive Parapatric Speciation in the Absence of Environmental Influences

A commonly held view in evolutionary biology is that speciation (the emergence of genetically distinct and reproductively incompatible subpopulations) is driven by external environmental constraints, such as localized barriers to dispersal or habitat-based variation in selection pressures. We have developed a spatially explicit model of a biological population to study the emergence of spatial and temporal patterns of genetic diversity in the absence of predetermined subpopulation boundaries. We propose a 2-D cellular automata model showing that an initially homogeneous population might spontaneously subdivide into reproductively incompatible species through sheer isolation-by-distance when the viability of offspring decreases as the genomes of parental gametes become increasingly different. This simple implementation of the Dobzhansky-Muller model provides the basis for assessing the process and completion of speciation, which is deemed to occur when there is complete postzygotic isolation between two subpopulations. The model shows an inherent tendency toward spatial self-organization, as has been the case with other spatially explicit models of evolution. A well-mixed version of the model exhibits a relatively stable and unimodal distribution of genetic differences as has been shown with previous models. A much more interesting pattern of temporal waves, however, emerges when the dispersal of individuals is limited to short distances. Each wave represents a subset of comparisons between members of emergent subpopulations diverging from one another, and a subset of these divergences proceeds to the point of speciation. The long-term persistence of diverging subpopulations is the essence of speciation in biological populations, so the rhythmic diversity waves that we have observed suggest an inherent disposition for a population experiencing isolation-by-distance to generate new species