Mapping the Space of Genomic Signatures

We propose a computational method to measure and visualize interrelationships among any number of DNA sequences allowing, for example, the examination of hundreds or thousands of complete mitochondrial genomes. An "image distance" is computed for each pair of graphical representations of DNA sequences, and the distances are visualized as a Molecular Distance Map: Each point on the map represents a DNA sequence, and the spatial proximity between any two points reflects the degree of structural similarity between the corresponding sequences. The graphical representation of DNA sequences utilized, Chaos Game Representation (CGR), is genome- and species-specific and can thus act as a genomic signature. Consequently, Molecular Distance Maps could inform species identification, taxonomic classifications and, to a certain extent, evolutionary history. The image distance employed, Structural Dissimilarity Index (DSSIM), implicitly compares the occurrences of oligomers of length up to $k$ (herein $k=9$) in DNA sequences. We computed DSSIM distances for more than 5 million pairs of complete mitochondrial genomes, and used Multi-Dimensional Scaling (MDS) to obtain Molecular Distance Maps that visually display the sequence relatedness in various subsets, at different taxonomic levels. This general-purpose method does not require DNA sequence homology and can thus be used to compare similar or vastly different DNA sequences, genomic or computer-generated, of the same or different lengths. We illustrate potential uses of this approach by applying it to several taxonomic subsets: phylum Vertebrata, (super)kingdom Protista, classes Amphibia-Insecta-Mammalia, class Amphibia, and order Primates. This analysis of an extensive dataset confirms that the oligomer composition of full mtDNA sequences can be a source of taxonomic information.Comment: 14 pages, 7 figures. arXiv admin note: substantial text overlap with arXiv:1307.375

Phase Transition in Evolutionary Games

The evolution of cooperative behaviour is studied in the deterministic version of the Prisoners' Dilemma on a two-dimensional lattice. The payoff parameter is set at the critical region $1.8 < b < 2.0$ , where clusters of cooperators are formed in all spatial sizes. Using the factorial moments developed in particle and nuclear physics for the study of phase transition, the distribution of cooperators is studied as a function of the bin size covering varying numbers of lattice cells. From the scaling behaviour of the moments a scaling exponent is determined and is found to lie in the range where phase transitions are known to take place in physical systems. It is therefore inferred that when the payoff parameter is increased through the critical region the biological system of cooperators undergoes a phase transition to defectors. The universality of the critical behaviour is thus extended to include also this particular model of evolution dynamics.Comment: 12 pages + 3 figures, latex, submitted to Natur

Automated thematic mapping and change detection of ERTS-A images

The author has identified the following significant results. For the recognition of terrain types, spatial signatures are developed from the diffraction patterns of small areas of ERTS-1 images. This knowledge is exploited for the measurements of a small number of meaningful spatial features from the digital Fourier transforms of ERTS-1 image cells containing 32 x 32 picture elements. Using these spatial features and a heuristic algorithm, the terrain types in the vicinity of Phoenix, Arizona were recognized by the computer with a high accuracy. Then, the spatial features were combined with spectral features and using the maximum likelihood criterion the recognition accuracy of terrain types increased substantially. It was determined that the recognition accuracy with the maximum likelihood criterion depends on the statistics of the feature vectors. Nonlinear transformations of the feature vectors are required so that the terrain class statistics become approximately Gaussian. It was also determined that for a given geographic area the statistics of the classes remain invariable for a period of a month but vary substantially between seasons

Evolution of secondary cellular circulation flow above submarine bedforms imaged by remote sensing techniques

Normalized radar cross section (NRCS) modulation and acoustic Doppler current profiler (ADCP) measurements above submarine sand ribbons and sand waves are presented. The two study areas are located in the Southern Bight of the North Sea at the Birkenfels wreck and in the sand wave field of the Lister Tief in the German Bight of the North Sea. These measurements reveal the developments of secondary cellular circulations in tidally induced coastal sea areas. Secondary circulation cells can develop perpendicular as well as parallel to the direction of the dominant tidal current flow. Circulation cells developed perpendicular to the direction of the dominant tidal current flow are associated with marine sand ribbons manifested near an underwater wreck. Secondary circulation cells within the water column observed parallel to the direction of the dominant tidal current flow have been initiated during flood and ebb tidal current phases associated with submarine sand waves. These two types of cellular circulations must obey the Hamiltonian principle of classical mechanics. The current–short surface wave interaction is described by the action balance or radiation balance-equation based on weak hydrodynamic interaction theory. The calculated current gradient or strain rate of the applied imaging theory has the same order of magnitude for both bedforms such as marine sand ribbons and sand waves, respectively