Comparison of articulate brachiopod nuclear and mitochondrial gene trees leads to a clade-based redefinition of protostomes (Protostomozoa) and deuterostomes (Deuterostomozoa)

Nuclear and mtDNA sequences from selected short-looped terebratuloid (terebratulacean) articulate brachiopods yield congruent and genetically independent phylogenetic reconstructions by parsimony, neighbor-joining and maximum likelihood methods, suggesting that both sources of data are reliable guides to brachiopod species phylogeny. The present-day genealogical relationships and geographical distributions of the tested terebratuloid brachiopods are consistent with a tethyan dispersal and subsequent radiation. Concordance of nuclear and mitochondrial gene phylogenies reinforces previous indications that articulate brachiopods, inarticulate brachiopods, phoronids and ectoprocts cluster with other organisms generally regarded as protostomes. Since ontogeny and morphology in brachiopods, ectoprocts and phoronids depart in important respects from those features supposedly diagnostic of protostomes, this demonstrates that the operational definition of protostomy by the usual ontological characters must be misleading or unreliable. New, molecular, operational definitions are proposed to replace the traditional criteria for the recognition of protostomes and deuterostomes, and the clade-based terms 'Protostomozoa' and 'Deuterostomozoa' are proposed to replace the existing terms 'Protostomia' and 'Deuterostomia'

Brachiopod molecular phylogeny

Analysis by parsimony, maximum likelihood and distance methods of newly determined nuclear-encoded SSU rRNA gene sequences from 23 species of articulate brachiopods, six inarticulate brachiopods, two phoronids and an ectoproct, together with other sequences from published and unpublished sources show that lophorates cluster with protostome, not deuterostome metazoa and the phoronids cluster with inarticulate brachiopods. Phoronids, inarticulate, and articulate brachiopods form a monophyletic assemblage. A chiton is the closest known out-group of brachiopods plus phoronids. With articulates, separate rhynchonellid and long and short-looped terebratulid clades are identified and a thecideidine falls within the short-looped articulate clade. Forms with incomplete loops belong either to the short or long-looped clades, thus, a three-fold division of articulate brachiopods suffices to encompass the range of extant diversity so far examined. A perfect correlation was found between clade rank and lineage age rank for five well-dated brachiopod lineages. The important underpinning role of classical brachiopod taxonomy for molecular phylogeny is stressed

A Smirnov-Bickel-Rosenblatt theorem for compactly-supported wavelets

In nonparametric statistical problems, we wish to find an estimator of an unknown function f. We can split its error into bias and variance terms; Smirnov, Bickel and Rosenblatt have shown that, for a histogram or kernel estimate, the supremum norm of the variance term is asymptotically distributed as a Gumbel random variable. In the following, we prove a version of this result for estimators using compactly-supported wavelets, a popular tool in nonparametric statistics. Our result relies on an assumption on the nature of the wavelet, which must be verified by provably-good numerical approximations. We verify our assumption for Daubechies wavelets and symlets, with N = 6, ..., 20 vanishing moments; larger values of N, and other wavelet bases, are easily checked, and we conjecture that our assumption holds also in those cases

System dynamics as a tool for exploring greenhouse gas emission mitigation potential in freight transport

In this study, system dynamics modelling is used to evaluate the impacts of decisions made by different decision makers in the freight subsector on the performance of the sector, as measured in terms of greenhouse gas (GHG) emissions, direct job creation, water usage and various externality costs. The focus is on gaining a deeper understanding of opportunities for reducing GHGs, and particularly on the shift of freight from road to rail. Transport of processed food along the Cape Town-Gauteng corridor is used as a case study. Decision makers considered include the freight owners and those responsible for decisions around the vehicle fleet. In the model, decision makers respond to a number of aspects of system performance, including cost, system reliability and taxes. These aspects inform their decision to shift freight on or off rail, or to invest in efficiency interventions. Decisions made in one year impact on overall system performance, which may change a decision maker?s actions in the following year. This paper describes in detail the structure of the model and how it functions. It also discusses the necessary input data, and how this was gathered. Finally, simulation results are presented and discussed.Paper presented at the 34th Annual Southern African Transport Conference 6-9 July 2015 "Working Together to Deliver - Sakha Sonke", CSIR International Convention Centre, Pretoria, South Africa.The Minister of Transport, South AfricaTransportation Research Board of the US

Understanding the barriers to a shift of processed food from road to rail through system dynamics

One of the most important greenhouse gas (GHG) mitigation opportunities identified for the freight transport sector is a mode shift from road to rail. A system dynamics model was constructed to evaluate the drivers and barriers to such a mode shift and the impact on the wider economy. This paper focuses on the decision-making process that determines the movement of corridor freight, using processed food on the Cape Town-Gauteng corridor as a case study. In order that the model was an accurate representation which would facilitate discussion amongst decision makers, stakeholders were consulted as to the most important considerations in transporting processed food, their current perception of rail and the barriers to shifting to rail. Stakeholders included not only the decision makers, which included manufacturers of processed food and major retailers, but also Transnet, logistics companies, bodies lobbying government for a switch from road to rail and other experts. The paper presents the insights gained from stakeholder engagement and describes how it informed the construction of the decision-making routines in the system dynamics model. The relative importance of different decision making criteria and the tipping points in the system have begun to be identified, together with the implications of this for achieving a road to rail shift.Paper presented at the 34th Annual Southern African Transport Conference 6-9 July 2015 "Working Together to Deliver - Sakha Sonke", CSIR International Convention Centre, Pretoria, South Africa.The Minister of Transport, South AfricaTransportation Research Board of the US

Quantum phase-space description of light polarization

We present a method to characterize the polarization state of a light field in the continuous-variable regime. Instead of using the abstract formalism of SU(2) quasidistributions, we model polarization in the classical spirit by superposing two harmonic oscillators of the same angular frequency along two orthogonal axes. By describing each oscillator by a $s$-parametrized quasidistribution, we derive in a consistent way the final function for the polarization. We compare with previous approaches and discuss how this formalism works in some relevant examples.Comment: 17 pages, 4 eps color figure

High Precision Mass Measurements in Ψ\Psi and Υ\Upsilon Families Revisited

High precision mass measurements in $\Psi$ and $\Upsilon$ families performed in 1980-1984 at the VEPP-4 collider with OLYA and MD-1 detectors are revisited. The corrections for the new value of the electron mass are presented. The effect of the updated radiative corrections has been calculated for the $J/\Psi(1S)$ and $\Psi(2S)$ mass measurements.Comment: 5 pages, 1 table, submitted to Phys. Lett.

Numerical approximation of the Euler-Poisson-Boltzmann model in the quasineutral limit

This paper analyzes various schemes for the Euler-Poisson-Boltzmann (EPB) model of plasma physics. This model consists of the pressureless gas dynamics equations coupled with the Poisson equation and where the Boltzmann relation relates the potential to the electron density. If the quasi-neutral assumption is made, the Poisson equation is replaced by the constraint of zero local charge and the model reduces to the Isothermal Compressible Euler (ICE) model. We compare a numerical strategy based on the EPB model to a strategy using a reformulation (called REPB formulation). The REPB scheme captures the quasi-neutral limit more accurately