Alignments of mitochondrial genome arrangements: Applications to metazoan phylogeny

Mitochondrial genomes provide a valuable dataset for phylogenetic studies, in particular of metazoan phylogeny because of the extensive taxon sample that is available. Beyond the traditional sequence-based analysis it is possible to extract phylogenetic information from the gene order. Here we present a novel approach utilizing these data based on cyclic list alignments of the gene orders. A progressive alignment approach is used to combine pairwise list alignments into a multiple alignment of gene orders. Parsimony methods are used to reconstruct phylogenetic trees, ancestral gene orders, and consensus patterns in a straightforward approach. We apply this method to study the phylogeny of protostomes based exclusively on mitochondrial genome arrangements. We, furthermore, demonstrate that our approach is also applicable to the much larger genomes of chloroplasts

Plant clonal morphologies and spatial patterns as self-organized responses to resource-limited environments

We propose here to interpret and model peculiar plant morphologies (cushions, tussocks) observed in the Andean altiplano as localized structures. Such structures resulting in a patchy, aperiodic aspect of the vegetation cover are hypothesized to self-organize thanks to the interplay between facilitation and competition processes occurring at the scale of basic plant components biologically referred to as 'ramets'. (Ramets are often of clonal origin.) To verify this interpretation, we applied a simple, fairly generic model (one integro-differential equation) emphasizing via Gaussian kernels non-local facilitative and competitive feedbacks of the vegetation biomass density on its own dynamics. We show that under realistic assumptions and parameter values relating to ramet scale, the model can reproduce some macroscopic features of the observed systems of patches and predict values for the inter-patch distance that match the distances encountered in the reference area (Sajama National Park in Bolivia). Prediction of the model can be confronted in the future to data on vegetation patterns along environmental gradients as to anticipate the possible effect of global change on those vegetation systems experiencing constraining environmental conditions.Comment: 14 pages, 6figure

A Multiscale Approach for Statistical Characterization of Functional Images

Increasingly, scientific studies yield functional image data, in which the observed data consist of sets of curves recorded on the pixels of the image. Examples include temporal brain response intensities measured by fMRI and NMR frequency spectra measured at each pixel. This article presents a new methodology for improving the characterization of pixels in functional imaging, formulated as a spatial curve clustering problem. Our method operates on curves as a unit. It is nonparametric and involves multiple stages: (i) wavelet thresholding, aggregation, and Neyman truncation to effectively reduce dimensionality; (ii) clustering based on an extended EM algorithm; and (iii) multiscale penalized dyadic partitioning to create a spatial segmentation. We motivate the different stages with theoretical considerations and arguments, and illustrate the overall procedure on simulated and real datasets. Our method appears to offer substantial improvements over monoscale pixel-wise methods. An Appendix which gives some theoretical justifications of the methodology, computer code, documentation and dataset are available in the online supplements

Studying Evolutionary Change: Transdisciplinary Advances in Understanding and Measuring Evolution

Evolutionary processes can be found in almost any historical, i.e. evolving, system that erroneously copies from the past. Well studied examples do not only originate in evolutionary biology but also in historical linguistics. Yet an approach that would bind together studies of such evolving systems is still elusive. This thesis is an attempt to narrowing down this gap to some extend. An evolving system can be described using characters that identify their changing features. While the problem of a proper choice of characters is beyond the scope of this thesis and remains in the hands of experts we concern ourselves with some theoretical as well data driven approaches. Having a well chosen set of characters describing a system of different entities such as homologous genes, i.e. genes of same origin in different species, we can build a phylogenetic tree. Consider the special case of gene clusters containing paralogous genes, i.e. genes of same origin within a species usually located closely, such as the well known HOX cluster. These are formed by step- wise duplication of its members, often involving unequal crossing over forming hybrid genes. Gene conversion and possibly other mechanisms of concerted evolution further obfuscate phylogenetic relationships. Hence, it is very difficult or even impossible to disentangle the detailed history of gene duplications in gene clusters. Expanding gene clusters that use unequal crossing over as proposed by Walter Gehring leads to distinctive patterns of genetic distances. We show that this special class of distances helps in extracting phylogenetic information from the data still. Disregarding genome rearrangements, we find that the shortest Hamiltonian path then coincides with the ordering of paralogous genes in a cluster. This observation can be used to detect ancient genomic rearrangements of gene clus- ters and to distinguish gene clusters whose evolution was dominated by unequal crossing over within genes from those that expanded through other mechanisms. While the evolution of DNA or protein sequences is well studied and can be formally described, we find that this does not hold for other systems such as language evolution. This is due to a lack of detectable mechanisms that drive the evolutionary processes in other fields. Hence, it is hard to quantify distances between entities, e.g. languages, and therefore the characters describing them. Starting out with distortions of distances, we first see that poor choices of the distance measure can lead to incorrect phylogenies. Given that phylogenetic inference requires additive metrics we can infer the correct phylogeny from a distance matrix D if there is a monotonic, subadditive function ζ such that ζ^−1(D) is additive. We compute the metric-preserving transformation ζ as the solution of an optimization problem. This result shows that the problem of phylogeny reconstruction is well defined even if a detailed mechanistic model of the evolutionary process is missing. Yet, this does not hinder studies of language evolution using automated tools. As the amount of available and large digital corpora increased so did the possibilities to study them automatically. The obvious parallels between historical linguistics and phylogenetics lead to many studies adapting bioinformatics tools to fit linguistics means. Here, we use jAlign to calculate bigram alignments, i.e. an alignment algorithm that operates with regard to adjacency of letters. Its performance is tested in different cognate recognition tasks. Using pairwise alignments one major obstacle is the systematic errors they make such as underestimation of gaps and their misplacement. Applying multiple sequence alignments instead of a pairwise algorithm implicitly includes more evolutionary information and thus can overcome the problem of correct gap placement. They can be seen as a generalization of the string-to-string edit problem to more than two strings. With the steady increase in computational power, exact, dynamic programming solutions have become feasible in practice also for 3- and 4-way alignments. For the pairwise (2-way) case, there is a clear distinction between local and global alignments. As more sequences are consid- ered, this distinction, which can in fact be made independently for both ends of each sequence, gives rise to a rich set of partially local alignment problems. So far these have remained largely unexplored. Thus, a general formal frame- work that gives raise to a classification of partially local alignment problems is introduced. It leads to a generic scheme that guides the principled design of exact dynamic programming solutions for particular partially local alignment problems

A study of the usefulness of Skylab EREP data for earth resources studies in Australia

The author has identified the following significant results. In subhumid, vegetated areas, S190B photography: (1) has a potentially operational role in detecting lineaments in 1:100,000 scale geological mapping and in major civil engineering surveys; (2) is of limited value for regional lithological mapping at 1:500,000 scale; and (3) provided much useful synoptic information and some detailed information of direct value to the mapping of nonmineral natural resources such as vegetation, land soil, and water. In arid, well exposed areas, S190B photography could be used: (1) with a limited amount of field traverses, to produce reliable 1:500,000 scale geological maps of sedimentary sequences; (2) to update superficial geology on 1:250,000 scale maps; and (3) together with the necessary field studies, to prepare landform, soil, and vegetation maps at 1:1,000,000 scale. Skylab photography was found to be more useful than LANDSAT images for small scale mapping of geology and land types, and for the revision of topographic maps at 1:100,000 scale, because of superior spatial resolution and stereoscopic coverage

Optimal control of the heave motion of marine cable subsea-unit systems

One of the key problems associated with subsea operations involving tethered subsea units is the motions of support vessels on the ocean surface which can be transmitted to the subsea unit through the cable and increase the tension. In this paper, a theoretical approach for heave compensation is developed. After proper modelling of each element of the system, which includes the cable/subsea-unit, the onboard winch, control theory is applied to design an optimal control law. Numerical simulations are carried out, and it is found that the proposed active control scheme appears to be a promising solution to the problem of heave compensation