Error, Bias, and Long-Branch Attraction in Data for Two Chloroplast Photosystem Genes in Seed Plants

Sequences of two chloroplast photosystem genes, psaA and psbB, together comprising about 3,500 bp, were obtained for all five major groups of extant seed plants and several outgroups among other vascular plants. Strongly supported, but significantly conflicting, phylogenetic signals were obtained in parsimony analyses from partitions of the data into first and second codon positions versus third positions. In the former, both genes agreed on a monophyletic gymnosperms, with Gnetales closely related to certain conifers. In the latter, Gnetales are inferred to be the sister group of all other seed plants, with gymnosperms paraphyletic. None of the data supported the modern ‘‘anthophyte hypothesis,’’ which places Gnetales as the sister group of flowering plants. A series of simulation studies were undertaken to examine the error rate for parsimony inference. Three kinds of errors were examined: random error, systematic bias (both properties of finite data sets), and statistical inconsistency owing to long-branch attraction (an asymptotic property). Parsimony reconstructions were extremely biased for third-position data for psbB. Regardless of the true underlying tree, a tree in which Gnetales are sister to all other seed plants was likely to be reconstructed for these data. None of the combinations of genes or partitions permits the anthophyte tree to be reconstructed with high probability. Simulations of progressively larger data sets indicate the existence of long-branch attraction (statistical inconsistency) for third-position psbB data if either the anthophyte tree or the gymnosperm tree is correct. This is also true for the anthophyte tree using either psaA third positions or psbB first and second positions. A factor contributing to bias and inconsistency is extremely short branches at the base of the seed plant radiation, coupled with extremely high rates in Gnetales and nonseed plant outgroups. M. J. Sanderson,* M. F. Wojciechowski,*† J.-M. Hu,* T. Sher Khan,* and S. G. Brady

A Bias in ML Estimates of Branch Lengths in the Presence of Multiple Signals

Sequence data often have competing signals that are detected by network programs or Lento plots. Such data can be formed by generating sequences on more than one tree, and combining the results, a mixture model. We report that with such mixture models, the estimates of edge (branch) lengths from maximum likelihood (ML) methods that assume a single tree are biased. Based on the observed number of competing signals in real data, such a bias of ML is expected to occur frequently. Because network methods can recover competing signals more accurately, there is a need for ML methods allowing a network. A fundamental problem is that mixture models can have more parameters than can be recovered from the data, so that some mixtures are not, in principle, identifiable. We recommend that network programs be incorporated into best practice analysis, along with ML and Bayesian trees.

Branch-length estimation bias misleads molecular dating for a vertebrate mitochondrial phylogeny

Despite recent methodological advances in inferring the time-scale of biological evolution from molecular data, the fundamental question of whether our substitution models are sufficiently well specified to accurately estimate branch-lengths has received little attention. I examine this implicit assumption of all molecular dating methods, on a vertebrate mitochondrial protein-coding dataset. Comparison with analyses in which the data are RY-coded (AG → R; CT → Y) suggests that even rates-across-sites maximum likelihood greatly under-compensates for multiple substitutions among the standard (ACGT) NT-coded data, which has been subject to greater phylogenetic signal erosion. Accordingly, the fossil record indicates that branch-lengths inferred from the NT-coded data translate into divergence time overestimates when calibrated from deeper in the tree. Intriguingly, RY-coding led to the opposite result. The underlying NT and RY substitution model misspecifications likely relate respectively to “hidden” rate heterogeneity and changes in substitution processes across the tree, for which I provide simulated examples. Given the magnitude of the inferred molecular dating errors, branch-length estimation biases may partly explain current conflicts with some palaeontological dating estimates.

Observability analysis of electric networks considering branch impedance

This paper presents an analytical method to analyze the effect of X to R ratio as well as impedance value of branches on observability of a network based on un-decoupled formulation of state estimation (SE) and null space of matrices. The results showed that the X to R ratio of branches had no effect on the observability of networks. In addition, it was shown that observability of some networks was affected by impedance values while some others were not affected. In addition, for branch observability analysis of radial network, a simple and quick method is developed. Illustrative examples of the network under transmission and distribution voltages demonstrate the effectiveness of the proposed methods.

The special branch : governing mentalities through alternative-site placement

"…one should try to locate power at the extreme points of its exercise, where it is always less legal in character." (Foucault, 1980, p.97) Studies of schooling practices as techniques deriving from a particular art of governing that Foucault (2003b) called ‘governmentality’ have shown how psychopathologising discourses work to construct particular student-subjects and legitimise various practices of exclusion (Gram, 2007b). Here I extend this work to consider the use of alternative-site placement as an intensification in response to governmentality being put ‘at risk’. Governing ‘at a distance’ conjures an illusion of individual freedom which relies on the production of subjects who ‘choose’ to make choices that are consistent with the aspirations of government. In this chapter, it is argued that the designation of a child as ‘disorderly’ legitimises the intrusion of state into the private domain of the family via the Trojan horse of early intervention. This is enabled by the psy-sciences, whose technologies and aims amount to the moral retraining of ‘improper’ future-citizens who, in choosing to choose otherwise, threaten to make visible invisible relations of power. Alternative-site placement in special schools running intensive behaviour modification programs allows for a ‘redoubled insistence’ (Ewald, 1992) of these norms and limits that a ‘disorderly’ child threatens to transgress.

Structure and palaeoenvironmental implications of inter-branch coenosteum-rich skeleton in corymbose Acropora species

Coral reefs provide an increasingly important archive of palaeoclimate data that can be used to constrain climate model simulations. Reconstructing past environmental conditions may also provide insights into the potential of reef systems to survive changes in the Earth’s climate. Reef-based palaeoclimate reconstructions are predominately derived from colonies of massive Porites, with the most abundant genus in the Indo-Pacific—Acropora—receiving little attention owing to their branching growth trajectories, high extension rates and secondary skeletal thickening. However, inter-branch skeleton (consisting of both coenosteum and corallites) near the bases of corymbose Acropora colonies holds significant potential as a climate archive. This region of Acropora skeleton is atypical, having simple growth trajectories with parallel corallites, approximately horizontal density banding, low apparent extension rates and a simple microstructure with limited secondary thickening. Hence, inter-branch skeleton in Acropora bears more similarities to the coralla of massive corals, such as Porites, than to traditional Acropora branches. Cyclic patterns of Sr/Ca ratios in this structure suggest that the observed density banding is annual in nature, thus opening up the potential to use abundant corymbose Acropora for palaeoclimate reconstruction.

The long and short of it: branch lengths and the problem of placing the New Zealand short-tailed bat.

The taxonomic position of the endemic New Zealand bat genus Mystacina has vexed systematists ever since its erection in 1843. Over the years the genus has been linked with many microchiropteran families and superfamilies. Most recent classifications place it in the Vespertilionoidea, although some immunological evidence links it with the Noctilionoidea (=Phyllostomoidea). We have sequenced 402 bp of the mitochondrial cytochrome b gene for M. tuberculata (Gray in Dieffenbach, 1843), and using both our own and published DNA sequences for taxa in both superfamilies, we applied different tree reconstruction methods to find the appropriate phylogeny and different methods of estimating confidence in the parts of the tree. All methods strongly support the classification of Mystacina in the Noctilionoidea. Spectral analysis suggests that parsimony analysis may be misleading for Mystacina's precise placement within the Noctilionoidea because of its long terminal branch. Analyses not susceptible to long-branch attraction suggest that the Mystacinidae is a sister family to the Phyllostomidae. Dating the divergence times between the different taxa suggests that the extant chiropteran families radiated around and shortly after the Cretaceous–Tertiary boundary. We discuss the biogeographical implications of classifying Mystacina within the Noctilionoidea and contrast our result with those classifications placing Mystacina in the Vespertilionoidea, concluding that evidence for the latter is weak.

An observation about circular shortest paths: Dealing with additional constraints using branch and bound

Circular shortest paths represent a powerful methodology for image segmentation. The circularity condition ensures that the contour found by the algorithm is closed, a natural requirement for regular objects. Several implementations have been proposed in the past that either promise closure with high probability or ensure closure strictly, but with a mild computational efficiency handicap. Circularity can be viewed as a priori information that helps recover the correct object contour. Our "observation" is that circularity is only one among many possible constraints that can be imposed on shortest paths to guide them to a desirable solution. In this contribution, we illustrate this opportunity under a volume constraint but the concept is generally applicable. We also describe several adornments to the circular shortest path algorithm that proved useful in applications. © 2011 IEEE.

The Long and Short of It: Branch Lengths and the Problem of Placing the New Zealand Short-Tailed Bat, Mystacina

The taxonomic position of the endemic New Zealand bat genus Mystacina has vexed systematists ever since its erection in 1843. Over the years the genus has been linked with many microchiropteran families and superfamilies. Most recent classifications place it in the Vespertilionoidea, although some immunological evidence links it with the Noctilionoidea (=Phyllostomoidea). We have sequenced 402 bp of the mitochondrial cytochrome b gene for M. tuberculata (Gray in Dieffenbach, 1843), and using both our own and published DNA sequences for taxa in both superfamilies, we applied different tree reconstruction methods to find the appropriate phylogeny and different methods of estimating confidence in the parts of the tree. All methods strongly support the classification of Mystacina in the Noctilionoidea. Spectral analysis suggests that parsimony analysis may be misleading for Mystacina's precise placement within the Noctilionoidea because of its long terminal branch. Analyses not susceptible to long-branch attraction suggest that the Mystacinidae is a sister family to the Phyllostomidae. Dating the divergence times between the different taxa suggests that the extant chiropteran families radiated around and shortly after the Cretaceous-Tertiary boundary. We discuss the biogeographical implications of classifying Mystacina within the Noctilionoidea and contrast our result with those classifications placing Mystacina in the Vespertilionoidea, concluding that evidence for the latter is weak.

Evaluation of ANPR trials for traffic policing in Queensland. Report to the Queensland Police Service, State Traffic Support Branch

In response to the Travelsafe Committee Report No. 51 – report on the inquiry into Automatic Plate Recognition Technology – it was recommended that the Queensland Police Service continue to trial the deployment of ANPR technology for traffic enforcement work and to evaluate the road safety impacts and operational effectiveness of the technology. As such, the purpose of this report is to provide an independent evaluation of a trial of ANPR that was conducted by a project team within the State Traffic Support Branch of the Queensland Police Service (QPS) and provide recommendations as to the applicability and usability of the technology for use throughout Queensland...

A low-cost attack on branch-based software watermarking schemes

In 2005, Ginger Myles and Hongxia Jin proposed a software watermarking scheme based on converting jump instructions or unconditional branch statements (UBSs) by calls to a fingerprint branch function (FBF) that computes the correct target address of the UBS as a function of the generated fingerprint and integrity check. If the program is tampered with, the fingerprint and integrity checks change and the target address will not be computed correctly. In this paper, we present an attack based on tracking stack pointer modifications to break the scheme and provide implementation details. The key element of the attack is to remove the fingerprint and integrity check generating code from the program after disassociating the target address from the fingerprint and integrity value. Using the debugging tools that give vast control to the attacker to track stack pointer operations, we perform both subtractive and watermark replacement attacks. The major steps in the attack are automated resulting in a fast and low-cost attack.