Game Characterizations and the PSPACE-Completeness of Tree Resolution Space

2007 ◽  
pp. 527-541 ◽  
Author(s):  
Alexander Hertel ◽  
Alasdair Urquhart
Keyword(s):  
Tree Resolution

scholarly journals Monophyly of Heterandriini (Teleostei: Poeciliidae) revisited: a critical review of the data

2012 ◽  
Vol 10 (1) ◽  
pp. 19-44 ◽  
Author(s):  
Alfy Morales-Cazan ◽  
James S. Albert
Keyword(s):  
Biological Sciences ◽  
Morphological Characters ◽  
Model Systems ◽  
Morphological Data ◽  
Maximum Parsimony Analysis ◽  
Fin Ray ◽  
Outgroup Species ◽  
Tree Topologies ◽  
Tree Resolution ◽  
Shape Morphometrics

The systematics and taxonomy of poeciliid fishes (guppies and allies) remain poorly understood despite the relative importance of these species as model systems in the biological sciences. This study focuses on testing the monophyly of the nominal poeciliine tribe Heterandriini and the genus Heterandria, through examination of the morphological characters on which the current classification is based. These characters include aspects of body shape (morphometrics), scale and fin-ray counts (meristics), pigmentation, the cephalic laterosensory system, and osteological features of the neurocranium, oral jaws and suspensorium, branchial basket, pectoral girdle, and the gonopodium and its supports. A Maximum Parsimony analysis was conducted of 150 characters coded for 56 poeciliid and outgroup species, including 22 of 45 heterandriin species (from the accounted in Parenti & Rauchenberger, 1989), or seven of nine heterandriin species (from the accounted in Lucinda & Reis, 2005). Multistate characters were analyzed as both unordered and ordered, and iterative a posteriori weighting was used to improve tree resolution. Tree topologies obtained from these analyses support the monophyly of the Middle American species of "Heterandria," which based on available phylogenetic information, are herein reassigned to the genus Pseudoxiphophorus. None of the characters used in previous studies to characterize the nominal taxon Heterandriini are found to be unambiguously diagnostic. Some of these characters are shared with species in other poeciliid tribes, and others are reversed within the Heterandriini. These results support the hypothesis that Pseudoxiphophorus is monophyletic, and that this clade is not the closest relative of H. formosa (the type species) from southeastern North America. Available morphological data are not sufficient to assess the phylogenetic relationships of H. formosa with respect to other members of the Heterandriini. The results further suggest that most tribe-level taxa of the Poeciliinae are not monophyletic, and that further work remains to resolve the evolutionary relationships of this group.

Discriminating the effects of phylogenetic hypothesis, tree resolution and clade age estimates on phylogenetic signal measurements

Plant Biology ◽  
2012 ◽  
Vol 15 (5) ◽  
pp. 858-867 ◽  
Author(s):  
G. D. S. Seger ◽  
L. D. S. Duarte ◽  
V. J. Debastiani ◽  
A. Kindel ◽  
J. A. Jarenkow
Keyword(s):  
Phylogenetic Signal ◽  
Phylogenetic Hypothesis ◽  
Tree Resolution ◽  
Age Estimates

Large-Eddy Simulation Study of the Effects on Flow of a Heterogeneous Forest at Sub-Tree Resolution

2014 ◽  
Vol 154 (1) ◽  
pp. 27-56 ◽  
Author(s):  
Fabian Schlegel ◽  
Jörg Stiller ◽  
Anne Bienert ◽  
Hans-Gerd Maas ◽  
Ronald Queck ◽  
...  
Keyword(s):  
Large Eddy Simulation ◽  
Simulation Study ◽  
Eddy Simulation ◽  
Large Eddy ◽  
Tree Resolution

scholarly journals Comparative anatomy and phylogeny of the Forcipulatacea (Echinodermata: Asteroidea): insights from ossicle morphology

2019 ◽  
Vol 189 (3) ◽  
pp. 921-952 ◽  
Author(s):  
Marine Fau ◽  
Loïc Villier
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
Phylogenetic Analysis ◽  
Comparative Anatomy ◽  
Morphological Diversity ◽  
Consensus Tree ◽  
Sea Stars ◽  
Extant Species ◽  
Tree Resolution ◽  
Scanning Electron

Abstract A new phylogenetic analysis of the superorder Forcipulatacea is presented. Forcipulatacea is one of the three major groups of sea stars (Asteroidea: Echinodermata), composed of 400 extant species. The sampled taxa are thought to represent the morphological diversity of the group. Twenty-nine forcipulate taxa were sampled belonging to Asteriidae, Stichasteridae, Heliasteridae, Pedicellasteridae, Zoroasteridae and Brisingida. Specimens were dissected with bleach. Detailed description of the skeleton and the anatomy of the ossicles were investigated using scanning electron microscopy. Comparative anatomy allowed the scoring of 115 phylogenetically informative characters. The consensus tree resulting from the analysis recovers Asteriidae, Stichasteridae, Zoroasteridae and Brisingida as monophyletic. All types of morphological features contribute to tree resolution and may be appropriate for taxon diagnosis. The synapomorphies supporting different clades are described and discussed. Brisingida and Zoroasteridae are the best-supported clades. The potentially challenging position of Brisingida in the tree may be explained by homoplastic changes, but also by the presence of numerous non-applicable characters.

The complexity of analytic tableaux

2006 ◽  
Vol 71 (3) ◽  
pp. 777-790 ◽  
Author(s):  
Noriko H. Arai ◽  
Toniann Pitassi ◽  
Alasdair Urquhart
Keyword(s):  
Lower Bound ◽  
Theorem Proving ◽  
Automated Theorem Proving ◽  
Relative Complexity ◽  
Analytic Tableaux ◽  
Open Questions ◽  
Tree Resolution

AbstractThe method of analytic tableaux is employed in many introductory texts and has also been used quite extensively as a basis for automated theorem proving. In this paper, we discuss the complexity of the system as a method for refuting contradictory sets of clauses, and resolve several open questions. We discuss the three forms of analytic tableaux: clausal tableaux, generalized clausal tableaux, and binary tableaux. We resolve the relative complexity of these three forms of tableaux proofs and also resolve the relative complexity of analytic tableaux versus resolution. We show that there is a quasi-polynomial simulation of tree resolution by analytic tableaux; this simulation is close to optimal, since we give a matching lower bound that is tight to within a polynomial.

scholarly journals Full Likelihood Inference from the Site Frequency Spectrum based on the Optimal Tree Resolution

2017 ◽  
Author(s):  
Raazesh Sainudiin ◽  
Amandine Véber
Keyword(s):  
Frequency Spectrum ◽  
Likelihood Function ◽  
Simulation Studies ◽  
Genealogical Tree ◽  
Full Likelihood ◽  
Branch Lengths ◽  
Optimal Tree ◽  
Site Frequency Spectrum ◽  
Tree Resolution ◽  
Balance Parameter

AbstractWe develop a novel importance sampler to compute the full likelihood function of a demographic or structural scenario given the site frequency spectrum (SFS) at a locus free of intra-locus recombination. This sampler, instead of representing the hidden genealogy of a sample of individuals by a labelled binary tree, uses the minimal level of information about such a tree that is needed for the likelihood of the SFS and thus takes advantage of the huge reduction in the size of the state space that needs to be integrated. We assume that the population may have demographically changed and may be non-panmictically structured, as reflected by the branch lengths and the topology of the genealogical tree of the sample, respectively. We also assume that mutations conform to the infinitely-many-sites model. We achieve this by a controlled Markov process that generates ‘particles’ in the hidden space of SFS histories which are always compatible with the observed SFS.To produce the particles, we use Aldous’ Beta-splitting model for a one parameter family of prior distributions over genealogical topologies or shapes (including that of the Kingman coalescent) and allow the branch lengths or epoch times to have a parametric family of priors specified by a model of demography (including exponential growth and bottleneck models). Assuming independence across unlinked loci, we can estimate the likelihood of a population scenario based on a large collection of independent SFS by an importance sampling scheme, using the (unconditional) distribution of the genealogies under this scenario when the latter is available. When it is not available, we instead compute the joint likelihood of the tree balance parameter β assuming that the tree topology follows Aldous’ Beta-splitting model, and of the demographic scenario determining the distribution of the inter-coalescence times or epoch times in the genealogy of a sample, in order to at least distinguish different equivalence classes of population scenarios leading to different tree balances and epoch times. Simulation studies are conducted to demonstrate the capabilities of the approach with publicly available code.

scholarly journals A Complexity Gap for Tree-Resolution

1999 ◽  
Vol 6 (29) ◽  
Author(s):  
Søren Riis
Keyword(s):  
Predicate Logic ◽  
Proof Complexity ◽  
Polynomial Size ◽  
Combinatorial Principles ◽  
Resolution Proofs ◽  
Symmetrical Group ◽  
Tree Resolution ◽  
Single Proposition ◽  
Exponential Size ◽  
Recent Idea

<p>It is shown that any sequence  psi_n of tautologies which expresses the<br />validity of a fixed combinatorial principle either is "easy" i.e. has polynomial<br />size tree-resolution proofs or is "difficult" i.e requires exponential<br />size tree-resolution proofs. It is shown that the class of tautologies which<br />are hard (for tree-resolution) is identical to the class of tautologies which<br />are based on combinatorial principles which are violated for infinite sets.<br />Actually it is shown that the gap-phenomena is valid for tautologies based<br />on infinite mathematical theories (i.e. not just based on a single proposition).<br />We clarify the link between translating combinatorial principles (or<br />more general statements from predicate logic) and the recent idea of using<br /> the symmetrical group to generate problems of propositional logic.<br />Finally, we show that it is undecidable whether a sequence  psi_n (of the<br />kind we consider) has polynomial size tree-resolution proofs or requires<br />exponential size tree-resolution proofs. Also we show that the degree of<br />the polynomial in the polynomial size (in case it exists) is non-recursive,<br />but semi-decidable.</p><p>Keywords: Logical aspects of Complexity, Propositional proof complexity,<br />Resolution proofs.</p><p> </p>

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