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Internal Nodes (internal + node)
Selected AbstractsCladistic coding of genomic mapsCLADISTICS, Issue 5 2002Cyril Gallut A new method of genomic maps analysis is described. The purpose of the method is to reconstruct phylogenetic relationships from the genomic organization of taxa. Our approach is based on gene order coding. This coding allows the description of genome topology without a prior hypothesis about evolutionary events and phylogenetic relationships. Different characters are used for each gene: (1) presence/absence, (2) orientation, and (3) relative position. The relative position of a particular gene inside the genome is the pair of genes surrounding it. The relative position character represents all the positions of a gene in the sampled genomes. It is coded as a multistate character. Our coding method has a priori variable cost implications on operators such as inversion, transposition, and gene loss/gain, which we discuss. The overall approach best fits the "duplication, random loss" evolutionary model. The coding method allows the reconstitution of a possible hypothetical common ancestor genome at each node of the tree. This reconstitution is based on the character states' optimization; it comes down to choosing, among all possible optimizations, the optimization compatible with a complete genome topology at each internal node. The multistate coding of gene relative position, which is an undeniable advantage of this method, permits this reconstitution. [source] PHYLOGENETICALLY NESTED COMPARISONS FOR TESTING CORRELATES OF SPECIES RICHNESS: A SIMULATION STUDY OF CONTINUOUS VARIABLESEVOLUTION, Issue 1 2003NICK J. B. ISAAC Abstract., Explaining the uneven distribution of species among lineages is one of the oldest questions in evolution. Proposed correlations between biological traits and species diversity are routinely tested by making comparisons between phylogenetic sister clades. Several recent studies have used nested sister-clade comparisons to test hypotheses linking continuously varying traits, such as body size, with diversity. Evaluating the findings of these studies is complicated because they differ in the index of species richness difference used, the way in which trait differences were treated, and the statistical tests employed. In this paper, we use simulations to compare the performance of four species richness indices, two choices about the branch lengths used to estimate trait values for internal nodes and two statistical tests under a range of models of clade growth and character evolution. All four indices returned appropriate Type I error rates when the assumptions of the method were met and when branch lengths were set proportional to time. Only two of the indices were robust to the different evolutionary models and to different choices of branch lengths and statistical tests. These robust indices had comparable power under one nonnull scenario. Regression through the origin was consistently more powerful than the t -test, and the choice of branch lengths exerts a strong effect on both the validity and power. In the light of our simulations, we re-evaluate the findings of those who have previously used nested comparisons in the context of species richness. We provide a set of simple guidelines to maximize the performance of phylogenetically nested comparisons in tests of putative correlates of species richness. [source] Robust support for tardigrade clades and their ages from three protein-coding nuclear genesINVERTEBRATE BIOLOGY, Issue 2 2004Jerome C. Regier Abstract. Coding sequences (5,334 nt total) from elongation factor-1,, elongation factor-2, and the largest subunit of RNA polymerase II were determined for 6 species of Tardigrada, 2 of Arthropoda, and 2 of Onychophora. Parsimony and likelihood analyses of nucleotides and amino acids yielded strong support for Tardigrada and all internal nodes (i.e., 100% bootstrap support for Tardigrada, Eutardigrada, Parachela, Hypsibiidae, and Macrobiotidae). Results are in agreement with morphology and an earlier molecular study based on analysis of 18S ribosomal sequences. Divergence times have been estimated from amino acid sequence data using an empirical Bayesian statistical approach, which does not assume a strict molecular clock. Divergence time estimates are pre-Vendian for Tardigrada/Arthropoda, Vendian or earlier for Eutardigrada/Heterotardigrada, Silurian to Ordovician for Parachela/Apochela, Permian to Carboniferous for Hypsibiidae and Macrobiotidae, and Mesozoic for Isohypsibius/Thulinia (both within Hypsibiidae) and Macrobiotus/Richtersius (both within Macrobiotidae). [source] A dynamic shortest path algorithm using multi-step ahead link travel time predictionJOURNAL OF ADVANCED TRANSPORTATION, Issue 1 2005Young-Ihn Lee Abstract In this paper, a multi-step ahead prediction algorithm of link travel speeds has been developed using a Kalman filtering technique in order to calculate a dynamic shortest path. The one-step and the multi-step ahead link travel time prediction models for the calculation of the dynamic shortest path have been applied to the directed test network that is composed of 16 nodes: 3 entrance nodes, 2 exit nodes and 11 internal nodes. Time-varying traffic conditions such as flows and travel time data for the test network have been generated using the CORSIM model. The results show that the multi-step ahead algorithm is compared more favorably for searching the dynamic shortest time path than the other algorithm. [source] Neural network-based state prediction for strategy planning of an air hockey robotJOURNAL OF FIELD ROBOTICS (FORMERLY JOURNAL OF ROBOTIC SYSTEMS), Issue 4 2001Jung Il Park We analyze a neural network implementation for puck state prediction in robotic air hockey. Unlike previous prediction schemes which used simple dynamic models and continuously updated an intercept state estimate, the neural network predictor uses a complex function, computed with data acquired from various puck trajectories, and makes a single, timely estimate of the final intercept state. Theoretically, the network can account for the complete dynamics of the table if all important state parameters are included as inputs, an accurate data training set of trajectories is used, and the network has an adequate number of internal nodes. To develop our neural networks, we acquired data from 1500 no-bounce and 1500 one-bounce puck trajectories, noting only translational state information. Analysis showed that performance of neural networks designed to predict the results of no-bounce trajectories was better than the performance of neural networks designed for one-bounce trajectories. Since our neural network input parameters did not include rotational puck estimates and recent work shows the importance of spin in impact analysis, we infer that adding a spin input to the neural network will increase the effectiveness of state estimates for the one-bounce case. © 2001 John Wiley & Sons, Inc. [source] PHYLOGENY OF THE EUGLENALES BASED UPON COMBINED SSU AND LSU RDNA SEQUENCE COMPARISONS AND DESCRIPTION OF DISCOPLASTIS GEN.JOURNAL OF PHYCOLOGY, Issue 3 2006NOV. (EUGLENOPHYTA) A Bayesian analysis, utilizing a combined data set developed from the small subunit (SSU) and large subunit (LSU) rDNA gene sequences, was used to resolve relationships and clarify generic boundaries among 84 strains of plastid-containing euglenophytes representing 11 genera. The analysis produced a tree with three major clades: a Phacus and Lepocinlis clade, a Discoplastis clade, and a Euglena, Colacium, Trachelomonas, Strombomonas, Monomorphina, and Cryptoglena clade. The majority of the species in the genus Euglena formed a well-supported clade, but two species formed a separate clade near the base of the tree. A new genus, Discoplastis, was erected to accommodate these taxa, thus making the genus Euglena monophyletic. The analysis also supported the monophyly of Colacium, Trachelomonas, Strombomonas, Monomorphina, and Cryptoglena, which formed two subclades sister to the Euglena clade. Colacium, Trachelomonas, and Strombomonas, all of which produce copious amounts of mucilage to form loricas or mucilaginous stalks, formed a well-supported lineage. Our analysis supported retaining Strombomonas and Trachelomonas as separate genera. Monomorphina and Cryptoglena formed two well-supported clades that were sister to the Colacium, Trachelomonas, and Strombomonas clade. Phacus and Lepocinclis, both of which have numerous small discoid chloroplasts without pyrenoids and lack peristaltic euglenoid movement (metaboly), formed a well-supported monophyletic lineage that was sister to the larger Euglena through Cryptoglena containing clade. This study demonstrated that increased taxon sampling, multiple genes, and combined data sets provided increased support for internal nodes on the euglenoid phylogenetic tree and resolved relationships among the major genera in the photosynthetic euglenoid lineage. [source] On the shape of the fringe of various types of random treesMATHEMATICAL METHODS IN THE APPLIED SCIENCES, Issue 10 2009Michael Drmota Abstract We analyze a fringe tree parameter w in a variety of settings, utilizing a variety of methods from the analysis of algorithms and data structures. Given a tree t and one of its leaves a, the w(t,,a) parameter denotes the number of internal nodes in the subtree rooted at a's father. The closely related w,(t,,a) parameter denotes the number of leaves, excluding a, in the subtree rooted at a's father. We define the cumulative w parameter as W(t) = ,aw(t,,a), i.e. as the sum of w(t,,a) over all leaves a of t. The w parameter not only plays an important rôle in the analysis of the Lempel,Ziv '77 data compression algorithm, but it is captivating from a combinatorial viewpoint too. In this report, we determine the asymptotic behavior of the w and W parameters on a variety of types of trees. In particular, we analyze simply generated trees, recursive trees, binary search trees, digital search trees, tries and Patricia tries. The final section of this report briefly summarizes and improves the previously known results about the w, parameter's behavior on tries and suffix trees, originally published in one author's thesis (see Analysis of the multiplicity matching parameter in suffix trees. Ph.D. Thesis, Purdue University, West Lafayette, IN, U.S.A., May 2005; Discrete Math. Theoret. Comput. Sci. 2005; AD:307,322; IEEE Trans. Inform. Theory 2007; 53:1799,1813). This survey of new results about the w parameter is very instructive since a variety of different combinatorial methods are used in tandem to carry out the analysis. Copyright © 2008 John Wiley & Sons, Ltd. [source] Phylogeography of the dusky shrew, Sorex monticolus (Insectivora, Soricidae): insight into deep and shallow history in northwestern North AmericaMOLECULAR ECOLOGY, Issue 5 2001John R. Demboski Abstract Phylogenetic relationships among the dusky shrew (Sorexmonticolus) and eight related species (S. bairdi, S. bendirii, S. neomexicanus, S.ornatus, S. pacificus, S. palustris, S. sonomae and S.vagrans) were assessed using sequences from the mitochondrial cytochrome b gene (801 bp). Analyses using parsimony and maximum likelihood revealed significant molecular variation not reflected in previous morphological studies of these species. Conversely, three morphologically defined species (S.bairdi, S.neomexicanusandS.pacificus) were poorly differentiated. SorexornatusandS.vagrans represented basal taxa for a more inclusive group that included: (i) a widespread Continental clade containing S.monticolus (Arizona to Alaska, including S. neomexicanus); (ii) a Coastal clade containing S.monticolus (Oregon to south-east Alaska, including S. bairdiandS. pacificus); (iii) the semiaquatic species (S. bendiriiandS. palustris); and (iv) S.sonomae. Additional subdivision was observed within the Continental clade corresponding to populations from the northern and southern Rocky Mountains. Average uncorrected sequence divergence between the Coastal and Continental clades was 5.3% (range 4.5,6.2%), which exceeds many interspecific comparisons within this species complex and within the genus Sorex. Lack of resolution of internal nodes within topologies suggests a deep history of rapid diversification within this group. Late Pleistocene/Holocene glacial perturbations are reflected in the shallow phylogeographic structure within these clades in western North America. Our results suggest also that S. monticolus is not monophyletic under current taxonomic nomenclature. This perspective on phylogeographic history was developed within a growing comparative framework for other organisms in western North America. [source] 2D internal flux compatibility equation of the flux Green element method for transient nonlinear potential problemsNUMERICAL METHODS FOR PARTIAL DIFFERENTIAL EQUATIONS, Issue 6 2010Akpofure E. Taigbenu Abstract This article presents the derivation and implementation of the normal directional flux compatibility equation (relationship) at internal nodes when the Green element formulation that consistently provides accurate estimates of the primary variable, and its normal directional derivative (normal flux) is applied in 2D heterogeneous media to steady and transient potential problems. Such a relationship is required to resolve the closure problem due to having fewer integral equations than the number of unknowns at internal nodes. The derivation of the relationship is based on Stokes' theorem, which transforms the contour integral of the normal directional fluxes into a surface integral that is identically zero. The numerical discretization of the compatibility equation is demonstrated with four numerical examples using the six-node quadratic triangular and the four and eight-node rectangular elements. The incorporation of triangular elements into the current formulation demonstrates that the internal compatibility equation can be successfully implemented on irregular grids. The direct calculation of the fluxes significantly enhances the accuracy of the formulation, so that high accuracy, exceeding that of the finite element method, is achieved with very coarse spatial discretization. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 2010 [source] A phylogeny of megachiropteran bats (Mammalia: Chiroptera: Pteropodidae) based on direct optimization analysis of one nuclear and four mitochondrial genesCLADISTICS, Issue 6 2003Norberto P Giannini The phylogeny of megachiropteran bats (Mammalia: Chiroptera: Pteropodidae) has been investigated using several different molecular datasets. These studies differed widely in taxonomic and locus sampling, and their results tended to lack resolution of internal nodes and were themselves largely incongruent. To address this, we assembled a data set of 5 loci (up to 3.5 kbp from 12S rDNA, 16S rDNA, tDNA-valine, cytochrome b, and the nuclear gene c -mos) for 43 species of megachiropterans and 6 microchiropteran outgroups. We analyzed these data with direct optimization under equal costs for substitutions and indels. We used POY in a parallel setting, and searches consisted of replicated swapping + refinements (ratcheting, tree fusing, and iterative pass optimization). Our results indicate that Megachiroptera and all recognized genera (including Pteropus) are monophyletic, and that Melonycteris is the sister group of the clade containing all the other genera. Clades previously proposed using molecular data, as well as many new and traditional groups, were well-supported, and various sources suggest that the degree of conflict with morphological data may be considerably less marked than previously supposed. Analysis of individual loci suffer 70% loss in the number of compatible groups recovered across all analyses with respect to combined analyses. Our results indicate that, within Megachiroptera, nectarivory and cave-dwelling originated several times, but echolocation (used for obstacle detection) evolved only once. Megachiropterans likely originated in SE Asia-Melanesia, and colonized Africa at least four times. [source] | ||||||||||||||||