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Optimality Criterion (optimality + criterion)
Selected AbstractsReconstructing ancestral ecologies: challenges and possible solutionsDIVERSITY AND DISTRIBUTIONS, Issue 1 2006Christopher R. Hardy ABSTRACT There are several ways to extract information about the evolutionary ecology of clades from their phylogenies. Of these, character state optimization and ,ancestor reconstruction' are perhaps the most widely used despite their being fraught with assumptions and potential pitfalls. Requirements for robust inferences of ancestral traits in general (i.e. those applicable to all types of characters) include accurate and robust phylogenetic hypotheses, complete species-level sampling and the appropriate choice of optimality criterion. Ecological characters, however, also require careful consideration of methods for accounting for intraspecific variability. Such methods include ,Presence Coding' and ,Polymorphism Coding' for discrete ecological characters, and ,Range Coding' and ,MaxMin Coding' for continuously variable characters. Ultimately, however, historical inferences such as these are, as with phylogenetic inference itself, associated with a degree of uncertainty. Statistically based uncertainty estimates are available within the context of model-based inference (e.g. maximum likelihood and Bayesian); however, these measures are only as reliable as the chosen model is appropriate. Although generally thought to preclude the possibility of measuring relative uncertainty or support for alternative possible reconstructions, certain useful non-statistical support measures (i.e. ,Sharkey support' and ,Parsimony support') are applicable to parsimony reconstructions. [source] A comparison between new adaptive remeshing strategies based on point wise stress error estimation and energy norm error estimationINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING, Issue 7 2002G. Bugeda Abstract Traditionally, the most commonly used mesh adaptive strategies for linear elastic problems are based on the use of an energy norm for the measurement of the error, and a mesh refinement strategy based on the equal distribution of the error between all the elements. However, little attention has been paid to the study of alternative error norms and alternative refinement strategies. This paper studies the feasibility of using alternative mesh refinement strategies based on , the use of the classical error energy norm and an optimality criterion based on the equal distribution of the density of error, , the use of alternative error norms based on measurements of the point wise error contained in the main magnitudes that control the equilibrium problem and/or the material constitutive equations such as the stresses (e.g. the Von Mises stress). The feasibility of using all the described strategies is demonstrated through the solution of a benchmark example. This example is also used for comparison between the described refinement criteria. Copyright © 2002 John Wiley & Sons, Ltd. [source] Prospects and challenges for parametric models in historical biogeographical inferenceJOURNAL OF BIOGEOGRAPHY, Issue 7 2009Richard H. Ree Abstract In historical biogeography, phylogenetic trees have long been used as tools for addressing a wide range of inference problems, from explaining common distribution patterns of species to reconstructing ancestral geographic ranges on branches of the tree of life. However, the potential utility of phylogenies for this purpose has yet to be fully realized, due in part to a lack of explicit conceptual links between processes underlying the evolution of geographic ranges and processes of phylogenetic tree growth. We suggest that statistical approaches that use parametric models to forge such links will stimulate integration and propel hypothesis-driven biogeographical inquiry in new directions. We highlight here two such approaches and describe how they represent early steps towards a more general framework for model-based historical biogeography that is based on likelihood as an optimality criterion, rather than having the traditional reliance on parsimony. The development of this framework will not be without significant challenges, particularly in balancing model complexity with statistical power, and these will be most apparent in studies of regions with many component areas and complex geological histories, such as the Mediterranean Basin. [source] 1 Taxon sampling and inferences about diatom phylogenyJOURNAL OF PHYCOLOGY, Issue 2003A. J. Alverson Proper taxon sampling is one of the greatest challenges to understanding phylogenetic relationships, perhaps as important as choice of optimality criterion or data type. This has been demonstrated in diatoms where centric diatoms may either be strongly supported as monophyletic or paraphyletic when analyzing SSU rDNA sequences using the same optimality criterion. The effect of ingroup and outgroup taxon sampling on relationships of diatoms is explored for diatoms as a whole and for the order Thalassiosirales. In the latter case, SSU rDNA and rbcL sequence data result in phylogenetic relationships that appear to be strongly incongruent with morphology and broadly incongruent with the fossil record. For example, Cyclotella stelligera Cleve & Grunow behaves like a rogue taxon, jumping from place to place throughout the tree. Morphological data place C. stelligera near the base of the freshwater group as sister to the extinct genus Mesodictyon Theriot and Bradbury, suggesting that it is an old, long branch that might be expected to "misbehave" in poorly sampled trees. Cyclotella stelligera and C. bodanica Grunow delimit the diameter of morphological diversity in Cyclotella, so increased sampling of intermediate taxa will be critical to resolving this part of the tree. Morphology is sampled for a much greater number of taxa and many transitional states of putative synapomorphies seem to suggest a robust morphological hypothesis. The Thalassiosirales are unstable with regards to taxon sampling in the genetic data, suggesting that perhaps the morphological hypothesis is (for now) preferable. [source] Optimization-seeking experimentations: Design of an RL -circuit via the vs-optimality criterionQUALITY AND RELIABILITY ENGINEERING INTERNATIONAL, Issue 2 2010Hilla Ginsburg Abstract In this paper we explore the Vs-optimality criterion that was proposed in Ginsburg and Ben-Gal (IIE Trans. 2006; 38:445,461) as a new design-of-experiment (DOE) alphabetic optimality criterion. The Vs-optimality criterion seeks to minimize the variance of the optimal solution of an empirically fitted model. We show that the Vs-optimality citerion is well related to known alphabetic DOE criteria. However, it focuses on an 'optimization-seeking' experimental approach rather than an 'information-seeking' approach, which is often adopted by traditional optimality criteria. We illustrate the differences between these two approaches by a detailed example of a robust design of an RL -circuit. Copyright © 2009 John Wiley & Sons, Ltd. [source] Optimal predictive densities and fractional momentsAPPLIED STOCHASTIC MODELS IN BUSINESS AND INDUSTRY, Issue 1 2009Emanuele Taufer Abstract The maximum entropy approach used together with fractional moments has proven to be a flexible and powerful tool for density approximation of a positive random variable. In this paper we consider an optimality criterion based on the Kullback,Leibler distance in order to select appropriate fractional moments. We discuss the properties of the proposed procedure when all the available information comes from a sample of observations. The method is applied to the size distribution of the U.S. family income. Copyright © 2008 John Wiley & Sons, Ltd. [source] The molecular phylogeny of the Miarus campanulae (Coleoptera: Curculionidae) species group inferred from CO1 and ITS2 sequencesCLADISTICS, Issue 3 2006Varpu Vahtera Miarus is a Holarctic weevil genus with morphologically very similar species, all breeding on Campanula plants or their close relatives. Two European members of this genus, Miarus campanulae (L.), the type species, and Miarus graminis (Bohemann) have recently been split into several new species on the basis of slight external variations. The separation of these new forms has proved impossible and new data was needed. Molecular data were gathered from specimens from a number of locations in Finland, Estonia, Denmark and Sweden. The regions sequenced were mitochondrial CO1 and nuclear ITS2. Both combined and separate datasets were analyzed using the optimization alignment program POY, with parsimony as the optimality criterion. The recently separated Miarus species was found to be indistinguishable from the traditionally recognized form on the basis of this sequence data. On the other hand, the traditionally recognized species were characterized by numerous synapomorphies. Our data suggest that recent studies have underestimated the morphological variation in this genus. We propose that this may also be true for many taxonomically problematic beetle complexes in well-studied European regions. The idea that molecular evidence will inevitably reveal unnoticed cryptic variation may only apply to poorly known regions. Miarus fennicusKangas, 1978 is placed as a junior synonym of Miarus campanulae (Linnaeus, 1767) syn. nov. © The Willi Hennig Society 2006. [source] Gnathostomulid phylogeny inferred from a combined approach of four molecular loci and morphologyCLADISTICS, Issue 1 2006Martin V. Sørensen The phylogeny of the obscure metazoan phylum Gnathostomulida has previously only been addressed with cladistic analyses of morphological data. In the present study DNA sequence data from four molecular loci, including 18S rRNA, 28S rRNA, histone H3 and cytochrome c oxidase subunit I, are added to a revised morphological data matrix. The data set represents 23 gnathostomulid species that are analyzed under direct optimization using parsimony as the optimality criterion. The results obtained from analyzing the four molecular loci and combined morphological and molecular data under different parameter sets are generally very congruent, and differ only on minor points. The results clearly support gnathostomulid monophyly, as well as the basal division of Gnathostomulida into Filospermoidea and Bursovaginoidea. Filospermoidea were represented by species of Haplognathia and Cosmognathia, and generic monophyly is supported for both groups. Within Bursovaginoidea, Conophoralia (= Austrognathiidae) and Scleroperalia appear as sister groups. Monophyly of Mesognathariidae was confirmed as well, whereas the relationships between species of Gnathostomulidae and Onychognathiidae were contradicted by the molecular data when compared to morphological observations. ©The Willi Hennig Society 2006. [source] A combined approach to the phylogeny of Cephalopoda (Mollusca)CLADISTICS, Issue 5 2004A. R. Lindgren Cephalopoda represents a highly diverse group of molluscs, ranging in habitat from coastal regions to deep benthic waters. While cephalopods remain at the forefront of modern biology, in providing insight into fields such as neurobiology and population genetics, little is known about the relationships within the group. This study provides a comprehensive phylogenetic analysis of Cephalopoda (Mollusca) using a combination of molecular and morphological data. Four loci (three nuclear 18S rRNA, fragments of 28S rRNA and histone H3 and one mitochondrial cytochrome c oxidase subunit I) were combined with 101 morphological characters to test the relationships of 60 species of cephalopods, with emphasis within Decabrachia (squids and cuttlefishes). Individual and combined data sets were analyzed using the direct optimization method, with parsimony as the optimality criterion. Analyses were repeated for 12 different parameter sets accounting for a range of indel/change and transversion/transition cost ratios. Most analyses support the monophyly of Cephalopoda, Nautiloidea, Coleoidea and Decabrachia, however, the monophyly of Octobrachia was refuted due to the lack of support for a Cirroctopoda + Octopoda group. When analyzing all molecular evidence in combination and for total evidence analyses, Vampyromorpha formed the sister group to Decabrachia under the majority of parameters, while morphological data and some individual data sets supported a sister relationship between Vampyromorpha and Octobrachia. Within Decabrachia, a relationship between the sepioids Idiosepiida, Sepiida, Sepiolida and the teuthid Loliginidae was supported. Spirulida fell within the teuthid group in most analyses, further rendering Teuthida paraphyletic. Relationships within Decabrachia and specifically Oegopsida were found to be highly parameter-dependent. © The Willi Hennig Society 2004. [source] Phylogeny and Systematic Position of Opiliones: A Combined Analysis of Chelicerate Relationships Using Morphological and Molecular Data,CLADISTICS, Issue 1 2002Gonzalo Giribet The ordinal level phylogeny of the Arachnida and the suprafamilial level phylogeny of the Opiliones were studied on the basis of a combined analysis of 253 morphological characters, the complete sequence of the 18S rRNA gene, and the D3 region of the 28S rRNA gene. Molecular data were collected for 63 terminal taxa. Morphological data were collected for 35 exemplar taxa of Opiliones, but groundplans were applied to some of the remaining chelicerate groups. Six extinct terminals, including Paleozoic scorpions, are scored for morphological characters. The data were analyzed using strict parsimony for the morphological data matrix and via direct optimization for the molecular and combined data matrices. A sensitivity analysis of 15 parameter sets was undertaken, and character congruence was used as the optimality criterion to choose among competing hypotheses. The results obtained are unstable for the high-level chelicerate relationships (except for Tetrapulmonata, Pedipalpi, and Camarostomata), and the sister group of the Opiliones is not clearly established, although the monophyly of Dromopoda is supported under many parameter sets. However, the internal phylogeny of the Opiliones is robust to parameter choice and allows the discarding of previous hypotheses of opilionid phylogeny such as the "Cyphopalpatores" or "Palpatores." The topology obtained is congruent with the previous hypothesis of "Palpatores" paraphyly as follows: (Cyphophthalmi (Eupnoi (Dyspnoi + Laniatores))). Resolution within the Eupnoi, Dyspnoi, and Laniatores (the latter two united as Dyspnolaniatores nov.) is also stable to the superfamily level, permitting a new classification system for the Opiliones. 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