Genetic Correlations in Mutation Processes

We study the role of phylogenetic trees on correlations in mutation processes. Generally, correlations decay exponentially with the generation number. We find that two distinct regimes of behavior exist. For mutation rates smaller than a critical rate, the underlying tree morphology is almost irrelevant, while mutation rates higher than this critical rate lead to strong tree-dependent correlations. We show analytically that identical critical behavior underlies all multiple point correlations. This behavior generally characterizes branching processes undergoing mutation.Comment: revtex, 8 pages, 2 fig

Optical characterization of marine phytoplankton assemblages within surface waters of the western Arctic Ocean

An extensive data set of measurements within the Chukchi and Beaufort Seas is used to characterize the optical properties of seawater associated with different phytoplankton communities. Hierarchical cluster analysis of diagnostic pigment concentrations partitioned stations into four distinct surface phytoplankton communities based on taxonomic composition and average cell size. Concurrent optical measurements of spectral absorption and backscattering coefficients and remote-sensing reflectance were used to characterize the magnitudes and spectral shapes of seawater optical properties associated with each phytoplankton assemblage. The results demonstrate measurable differences among communities in the average spectral shapes of the phytoplankton absorption coefficient. Similar or smaller differences were also observed in the spectral shapes of nonphytoplankton absorption coefficients and the particulate backscattering coefficient. Phytoplankton on average, however, contributed only 25% or less to the total absorption coefficient of seawater. Our analyses indicate that the interplay between the magnitudes and relative contributions of all optically significant constituents generally dampens any influence of varying phytoplankton absorption spectral shapes on the total absorption coefficient, yet there is still a marked discrimination observed in the spectral shape of the ratio of the total backscattering to total absorption coefficient and remote-sensing reflectance among the phytoplankton assemblages. These spectral variations arise mainly from differences in the bio-optical environment in which specific communities were found, as opposed to differences in the spectral shapes of phytoplankton optical properties per se. These results suggest potential approaches for the development of algorithms to assess phytoplankton community composition from measurements of seawater optical properties in western Arctic waters

Force-induced desorption of a linear polymer chain adsorbed on an attractive surface

We consider a model of self-avoiding walk on a lattice with on-site repulsion and an attraction for every vertex of the walk visited on the surface to study force-induced desorption of a linear polymer chain adsorbed on an attractive surface and use the exact enumeration technique for analyzing how the critical force for desorption $f_c(T)$ depends on the temperature. The curve $f_c(T)$ gives the boundary separating the adsorbed phase from the desorbed phase. Our results show that in two dimensions where surface is a line the force $f_c(T)$ increases monotonically as temperature is lowered and becomes almost constant at very low temperatures. In case of three-dimensions we, however, find re-entrance, i. e. $f_c(T)$ goes through a maximum as temperature is lowered. The behaviour of the polymer chain at different values of temperature and force is examined by calculating the probability distribution of the height from the surface of the vertex at which external force is applied.Comment: Preprint 15 pages with 8figures and two tables. The file table-2d.ps and table-3d.ps lists C_N(Ns,h) for given N with all possible Ns and h in two and three dimension

CT and MR imaging features of a case of calcifying epithelial odontogenic tumor.

Calcifying epithelial odontogenic tumor is a rare lesion. We report the imaging features of a calcifying epithelial odonto genic tumor. The imaging including conventional radiograph, CT and MR imaging revealed a well-defined lesion in the alveolar bone of the left maxilla, which contained an impacted tooth and some small radiopacities. CT and MR imaging demonstrated a contrast enhancement mainly at the central portion of the lesion

On the accuracy of language trees

Historical linguistics aims at inferring the most likely language phylogenetic tree starting from information concerning the evolutionary relatedness of languages. The available information are typically lists of homologous (lexical, phonological, syntactic) features or characters for many different languages. From this perspective the reconstruction of language trees is an example of inverse problems: starting from present, incomplete and often noisy, information, one aims at inferring the most likely past evolutionary history. A fundamental issue in inverse problems is the evaluation of the inference made. A standard way of dealing with this question is to generate data with artificial models in order to have full access to the evolutionary process one is going to infer. This procedure presents an intrinsic limitation: when dealing with real data sets, one typically does not know which model of evolution is the most suitable for them. A possible way out is to compare algorithmic inference with expert classifications. This is the point of view we take here by conducting a thorough survey of the accuracy of reconstruction methods as compared with the Ethnologue expert classifications. We focus in particular on state-of-the-art distance-based methods for phylogeny reconstruction using worldwide linguistic databases. In order to assess the accuracy of the inferred trees we introduce and characterize two generalizations of standard definitions of distances between trees. Based on these scores we quantify the relative performances of the distance-based algorithms considered. Further we quantify how the completeness and the coverage of the available databases affect the accuracy of the reconstruction. Finally we draw some conclusions about where the accuracy of the reconstructions in historical linguistics stands and about the leading directions to improve it.Comment: 36 pages, 14 figure

The anisotropy of granular materials

The effect of the anisotropy on the elastoplastic response of two dimensional packed samples of polygons is investigated here, using molecular dynamics simulation. We show a correlation between fabric coefficients, characterizing the anisotropy of the granular skeleton, and the anisotropy of the elastic response. We also study the anisotropy induced by shearing on the subnetwork of the sliding contacts. This anisotropy provides an explanation to some features of the plastic deformation of granular media.Comment: Submitted to PR

Fast computation of distance estimators

BACKGROUND: Some distance methods are among the most commonly used methods for reconstructing phylogenetic trees from sequence data. The input to a distance method is a distance matrix, containing estimated pairwise distances between all pairs of taxa. Distance methods themselves are often fast, e.g., the famous and popular Neighbor Joining (NJ) algorithm reconstructs a phylogeny of n taxa in time O(n(3)). Unfortunately, the fastest practical algorithms known for Computing the distance matrix, from n sequences of length l, takes time proportional to l·n(2). Since the sequence length typically is much larger than the number of taxa, the distance estimation is the bottleneck in phylogeny reconstruction. This bottleneck is especially apparent in reconstruction of large phylogenies or in applications where many trees have to be reconstructed, e.g., bootstrapping and genome wide applications. RESULTS: We give an advanced algorithm for Computing the number of mutational events between DNA sequences which is significantly faster than both Phylip and Paup. Moreover, we give a new method for estimating pairwise distances between sequences which contain ambiguity Symbols. This new method is shown to be more accurate as well as faster than earlier methods. CONCLUSION: Our novel algorithm for Computing distance estimators provides a valuable tool in phylogeny reconstruction. Since the running time of our distance estimation algorithm is comparable to that of most distance methods, the previous bottleneck is removed. All distance methods, such as NJ, require a distance matrix as input and, hence, our novel algorithm significantly improves the overall running time of all distance methods. In particular, we show for real world biological applications how the running time of phylogeny reconstruction using NJ is improved from a matter of hours to a matter of seconds

Mitochondrial and nuclear genes suggest that stony corals are monophyletic but most families of stony corals are not (Order Scleractinia, Class Anthozoa, Phylum Cnidaria)

Modern hard corals (Class Hexacorallia; Order Scleractinia) are widely studied because of their fundamental role in reef building and their superb fossil record extending back to the Triassic. Nevertheless, interpretations of their evolutionary relationships have been in flux for over a decade. Recent analyses undermine the legitimacy of traditional suborders, families and genera, and suggest that a non-skeletal sister clade (Order Corallimorpharia) might be imbedded within the stony corals. However, these studies either sampled a relatively limited array of taxa or assembled trees from heterogeneous data sets. Here we provide a more comprehensive analysis of Scleractinia (127 species, 75 genera, 17 families) and various outgroups, based on two mitochondrial genes (cytochrome oxidase I, cytochrome b), with analyses of nuclear genes (ßtubulin, ribosomal DNA) of a subset of taxa to test unexpected relationships. Eleven of 16 families were found to be polyphyletic. Strikingly, over one third of all families as conventionally defined contain representatives from the highly divergent "robust" and "complex" clades. However, the recent suggestion that corallimorpharians are true corals that have lost their skeletons was not upheld. Relationships were supported not only by mitochondrial and nuclear genes, but also often by morphological characters which had been ignored or never noted previously. The concordance of molecular characters and more carefully examined morphological characters suggests a future of greater taxonomic stability, as well as the potential to trace the evolutionary history of this ecologically important group using fossils