Circumstances in which parsimony but not compatibility will be provably misleading

Phylogenetic methods typically rely on an appropriate model of how data evolved in order to infer an accurate phylogenetic tree. For molecular data, standard statistical methods have provided an effective strategy for extracting phylogenetic information from aligned sequence data when each site (character) is subject to a common process. However, for other types of data (e.g. morphological data), characters can be too ambiguous, homoplastic or saturated to develop models that are effective at capturing the underlying process of change. To address this, we examine the properties of a classic but neglected method for inferring splits in an underlying tree, namely, maximum compatibility. By adopting a simple and extreme model in which each character either fits perfectly on some tree, or is entirely random (but it is not known which class any character belongs to) we are able to derive exact and explicit formulae regarding the performance of maximum compatibility. We show that this method is able to identify a set of non-trivial homoplasy-free characters, when the number $n$ of taxa is large, even when the number of random characters is large. By contrast, we show that a method that makes more uniform use of all the data --- maximum parsimony --- can provably estimate trees in which {\em none} of the original homoplasy-free characters support splits.Comment: 37 pages, 2 figure

A matroid associated with a phylogenetic tree

A (pseudo-)metric D on a finite set X is said to be a `tree metric' if there is a finite tree with leaf set X and non-negative edge weights so that, for all x,y ∈X, D(x,y) is the path distance in the tree between x and y. It is well known that not every metric is a tree metric. However, when some such tree exists, one can always find one whose interior edges have strictly positive edge weights and that has no vertices of degree 2, any such tree is 13; up to canonical isomorphism 13; uniquely determined by D, and one does not even need all of the distances in order to fully (re-)construct the tree's edge weights in this case. Thus, it seems of some interest to investigate which subsets of X, 2 suffice to determine (`lasso') these edge weights. In this paper, we use the results of a previous paper to discuss the structure of a matroid that can be associated with an (unweighted) X-tree T defined by the requirement that its bases are exactly the `tight edge-weight lassos' for T, i.e, the minimal subsets of X, 2 that lasso the edge weights of T

A Southern Hemisphere radar meteor orbit survey

A meteor radar system has been operated on a routine basis near Christchurch, New Zealand, to determine the orbits of Earth-impacting interplanetary dust and meteoroids. The system sensitivity is +13 visual magnitude, corresponding to approximately 100 micron sized meteoroids. With an orbital precision of 2 degrees in angular elements and 10 percent in orbital energy (1/a), the operation yields an average of 1500 orbits daily with a total to date in excess of 10(exp 5). The use of pc's and automated data reduction permit the large orbital data sets we collect to be routinely reduced. Some illustrative examples are presented of the signal formats/processing and the results of data reduction, giving the individual orbital elements and hence the overall distributions. Current studies include the distribution of dust in the inner solar system; the influx of meteoroids associated with near-Earth asteroids; and the orbital structure existing in comet-produced streams

A tradeoff in simultaneous quantum-limited phase and loss estimation in interferometry

Interferometry with quantum light is known to provide enhanced precision for estimating a single phase. However, depending on the parameters involved, the quantum limit for the simultaneous estimation of multiple parameters may not attainable, leading to trade-offs in the attainable precisions. Here we study the simultaneous estimation of two parameters related to optical interferometry: phase and loss, using a fixed number of photons. We derive a trade-off in the estimation of these two parameters which shows that, in contrast to single-parameter estimation, it is impossible to design a strategy saturating the quantum Cramer-Rao bound for loss and phase estimation in a single setup simultaneously. We design optimal quantum states with a fixed number of photons achieving the best possible simultaneous precisions. Our results reveal general features about concurrently estimating Hamiltonian and dissipative parameters, and has implications for sophisticated sensing scenarios such as quantum imaging.Comment: 9 pages, 6 figure

Attacking Group Protocols by Refuting Incorrect Inductive Conjectures

Automated tools for finding attacks on flawed security protocols often fail to deal adequately with group protocols. This is because the abstractions made to improve performance on fixed 2 or 3 party protocols either preclude the modelling of group protocols all together, or permit modelling only in a fixed scenario, which can prevent attacks from being discovered. This paper describes Coral, a tool for finding counterexamples to incorrect inductive conjectures, which we have used to model protocols for both group key agreement and group key management, without any restrictions on the scenario. We will show how we used Coral to discover 6 previously unknown attacks on 3 group protocols

Difficulties in Testing for Covarion-Like Properties of Sequences under the Confounding Influence of Changing Proportions of Variable Sites

The covarion (COV)-like properties of sequences are poorly described and their impact on phylogenetic analyses poorly understood. We demonstrate using simulations that, under an evolutionary model where the proportion of variable sites changes in nonadjacent lineages, log likelihood values for rates across site (RAS) and COV models become similar, making models difficult to distinguish. Further, although COV and RAS models provide a great improvement in likelihood scores over a homogeneous model with these simulated data, reconstruction accuracy of tree building is low, suggesting caution when it is suspected that proportions of variable sites differ in different evolutionary lineages. We study the performance of a recently developed contingency test that detects the presence of COV-type evolution modified for protein data. We report that if proportions of variable sites (pvar) change in a lineage-specific manner such that their distributions in different lineages become sufficiently nonoverlapping, then the contingency test can incorrectly suggest a homogeneous model. Also of concern is the possibility of different proportions of variable sites between the groups being studied. In a study of chloroplast proteins, interpretation of the test is found to be susceptible to different partitioning of taxon groups, making the test very subjective in its implementation. Extreme intergroup differences in the extent of divergence and difference in proportions of variable sites could be contributing to this effect

Polarization dependence of four-wave mixing in a degenerate two-level system

Nearly degenerate four-wave mixing (NDFWM) within a closed degenerate two-level atomic transition is theoretically and experimentally examined. Using the model presented by A. Lezama et al [Phys. Rev. A 61, 013801 (2000)] the NDFWM spectra corresponding to different pump and probe polarization cases are calculated and discussed. The calculated spectra are compared to the observation of NDFWM within the $6S_{1/2}(F=4)\to 6P_{3/2}(F=5)$ transition of cesium in a phase conjugation experiment using magneto optically cooled atomsComment: 10 pages, 13 figures; submitted to Phys. Rev.

Discretely-observable continuous time quantum walks on M\"obius strips and other exotic structures in 3D integrated photonics

We theoretically analyze the dynamical evolution of photonic quantum walks on M\"obius strips and other exotic structures in 3D integrated photonics. Our flexible design allows discrete observations of continuous time quantum walks of photons in a variety of waveguide arrays. Furthermore, our design allows one to inject photons during the evolution, allowing the possibility of interacting with the photons as they are 'walking'. We find that non-trivial array topologies introduce novel time-dependent symmetries of the two-photon correlations. These properties allow a large degree of control for quantum state engineering of multimode entangled states in these devices.Comment: 9 pages, 4 figure

Introducing national osteopathy practice-based research networks in Australia and New Zealand: an overview to inform future osteopathic research.

Both the Osteopathic Research Innovation Network (ORION) and the Osteopathy Research Connect-New Zealand (ORC-NZ) are practice-based research networks (PBRNs) recently established in Australia and New Zealand. This paper highlights the profile of the osteopaths participating in each PBRN in order to encourage and facilitate further related research in osteopathy. All registered osteopaths in Australia and New Zealand were invited to participate in the ORION and ORC-NZ PBRNs, respectively. This paper presents practice and sociodemographic characteristics of the osteopaths that elected to join the PBRN in their country. A total of 253 registered osteopaths in New Zealand (48.7%) agreed to join ORC-NZ while 992 registered osteopaths in Australia (44.5%) joined ORION. Membership of both PBRNs reflect national geographical spread, and diverse personal and practice characteristics. Combined membership of both PBRNs represents 45.3% of all registered osteopaths in Australasia and 7.7% of the global osteopathic profession. The PBRNs, independently and in combination, hold much potential to advance the evidence-base and capacity of osteopathy research. Both ORION and ORC-NZ PBRNs are powerful, innovative resources available to other interested parties to help conduct further osteopathy research in Australia and New Zealand