LP-VIcode: a program to compute a suite of variational chaos indicators

An important point in analysing the dynamics of a given stellar or planetary system is the reliable identification of the chaotic or regular behaviour of its orbits. We introduce here the program LP-VIcode, a fully operational code which efficiently computes a suite of ten variational chaos indicators for dynamical systems in any number of dimensions. The user may choose to simultaneously compute any number of chaos indicators among the following: the Lyapunov Exponents, the Mean Exponential Growth factor of Nearby Orbits, the Slope Estimation of the largest Lyapunov Characteristic Exponent, the Smaller ALignment Index, the Generalized ALignment Index, the Fast Lyapunov Indicator, the Othogonal Fast Lyapunov Indicator, the dynamical Spectra of Stretching Numbers, the Spectral Distance, and the Relative Lyapunov Indicator. They are combined in an efficient way, allowing the sharing of differential equations whenever this is possible, and the individual stopping of their computation when any of them saturates.Comment: 26 pages, 9 black-and-white figures. Accepted for publication in Astronomy and Computing (Elsevier

Forming first-ranked early-type galaxies through hierarchical dissipationless merging

We have developed a computationally competitive N-body model of a previrialized aggregation of galaxies in a flat LambdaCDM universe to assess the role of the multiple mergers that take place during the formation stage of such systems in the configuration of the remnants assembled at their centres. An analysis of a suite of 48 simulations of low-mass forming groups (of about 1E13 solar masses) demonstrates that the gravitational dynamics involved in their hierarchical collapse is capable of creating realistic first-ranked galaxies without the aid of dissipative processes. Our simulations indicate that the brightest group galaxies (BGGs) constitute a distinct population from other group members, sketching a scenario in which the assembly path of these objects is dictated largely by the formation of their host system. We detect significant differences in the distribution of Sersic indices and total magnitudes, as well as a luminosity gap between BGGs and the next brightest galaxy that is positively correlated with the total luminosity of the parent group. Such gaps arise from both the grow of BGGs at the expense of lesser companions and the decrease in the relevance of second-ranked objects in equal measure. This results in a dearth of intermediate-mass galaxies which explains the characteristic central dip detected in their luminosity functions in dynamically young galaxy aggregations. The fact that the basic global properties of our BGGs define a thin mass fundamental plane strikingly similar to that followed giant early-type galaxies in the local universe reinforces confidence in the results obtained.Comment: 25 pages, 14 figures, 3 tables. Accepted to MNRA

The State of Software for Evolutionary Biology

With Next Generation Sequencing data being routinely used, evolutionary biology is transforming into a computational science. Thus, researchers have to rely on a growing number of increasingly complex software. All widely used core tools in the field have grown considerably, in terms of the number of features as well as lines of code and consequently, also with respect to software complexity. A topic that has received little attention is the software engineering quality of widely used core analysis tools. Software developers appear to rarely assess the quality of their code, and this can have potential negative consequences for end-users. To this end, we assessed the code quality of 16 highly cited and compute-intensive tools mainly written in C/Cþþ (e.g., MrBayes, MAFFT, SweepFinder, etc.) and JAVA (BEAST) from the broader area of evolutionary biology that are being routinely used in current data analysis pipelines. Because, the software engineering quality of the tools we analyzed is rather unsatisfying, we provide a list of best practices for improving the quality of existing tools and list techniques that can be deployed for developing reliable, high quality scientific software from scratch. Finally, we also discuss journal as well as science policy and, more importantly, funding issues that need to be addressed for improving software engineering quality as well as ensuring support for developing new and maintaining existing software. Our intention is to raise the awareness of the community regarding software engineering quality issues and to emphasize the substantial lack of funding for scientific software developmen

Forming first-ranked early-type galaxies through hierarchical dissipationless merging

We have developed a computationally competitive N-body model of a previrialized aggregation of galaxies in a flat Λ cold dark matter Universe to assess the role of the multiple mergers that take place during the formation stage of such systems in the configuration of the remnants assembled at their centres. An analysis of a suite of 48 simulations of low-mass forming groups (Mtot,gr ∼ 1013 h−1 M⊙) demonstrates that the gravitational dynamics involved in their hierarchical collapse is capable of creating realistic first-ranked galaxies without the aid of dissipative processes. Our simulations indicate that the brightest group galaxies (BGGs) constitute a distinct population from other group members, sketching a scenario in which the assembly path of these objects is dictated largely by the formation of their host system. We detect significant differences in the distribution of Sérsic indices and total magnitudes, as well as a luminosity gap between BGGs and the next brightest galaxy that is positively correlated with the total luminosity of the parent group. Such gaps arise from both the grow of BGGs at the expense of lesser companions and the decrease in the relevance of second-ranked objects in equal measure. This results in a dearth of intermediate-mass galaxies which explains the characteristic central dip detected in their luminosity functions in dynamically young galaxy aggregations. The fact that the basic global properties of our BGGs define a thin mass Fundamental Plane strikingly similar to that followed by giant early-type galaxies in the local Universe reinforces confidence in the results obtained

Electric-Field Gradient at Cd Impurities in In2o3. A FLAPW Study

We report an ab initio study of the electric-field gradient tensor (EFG) at Cd impurities located at both inequivalent cationic sites in the semiconductor In2O3. Calculations were performed with the FLAPW method, that allows us to treat the electronic structure of the doped system and the atomic relaxations introduced by the impurities in the host lattice in a fully self-consistent way. From our results for the EFG (in excellent agreement with the experiments), it is clear that the problem of the EFG at impurities in In2O3 cannot be described by the point-charge model and antishielding factors.Comment: 4 pages, 2 figures, and 2 table

Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes

This study was funded by the Sars Centre core budget to M. Adamska. Sequencing was performed at the Norwegian High Throughput Sequencing Centre funded by the Norwegian Research Council. O.M.R. and D.E.K.F. acknowledge support from the BBSRC and the School of Biology, University of St Andrews.Sponges are simple animals with few cell types, but their genomes paradoxically contain a wide variety of developmental transcription factors1,2,3,4, including homeobox genes belonging to the Antennapedia (ANTP) class5,6, which in bilaterians encompass Hox, ParaHox and NK genes. In the genome of the demosponge Amphimedon queenslandica, no Hox or ParaHox genes are present, but NK genes are linked in a tight cluster similar to the NK clusters of bilaterians5. It has been proposed that Hox and ParaHox genes originated from NK cluster genes after divergence of sponges from the lineage leading to cnidarians and bilaterians5,7. On the other hand, synteny analysis lends support to the notion that the absence of Hox and ParaHox genes in Amphimedon is a result of secondary loss (the ghost locus hypothesis)8. Here we analysed complete suites of ANTP-class homeoboxes in two calcareous sponges, Sycon ciliatum and Leucosolenia complicata. Our phylogenetic analyses demonstrate that these calcisponges possess orthologues of bilaterian NK genes (Hex, Hmx and Msx), a varying number of additional NK genes and one ParaHox gene, Cdx. Despite the generation of scaffolds spanning multiple genes, we find no evidence of clustering of Sycon NK genes. All Sycon ANTP-class genes are developmentally expressed, with patterns suggesting their involvement in cell type specification in embryos and adults, metamorphosis and body plan patterning. These results demonstrate that ParaHox genes predate the origin of sponges, thus confirming the ghost locus hypothesis8, and highlight the need to analyse the genomes of multiple sponge lineages to obtain a complete picture of the ancestral composition of the first animal genome.PostprintPeer reviewe

DNA barcoding reveals the coral “laboratory-rat”, Stylophora pistillata encompasses multiple identities

Stylophora pistillata is a widely used coral “lab-rat” species with highly variable morphology and a broad biogeographic range (Red Sea to western central Pacific). Here we show, by analysing Cytochorme Oxidase I sequences, from 241 samples across this range, that this taxon in fact comprises four deeply divergent clades corresponding to the Pacific-Western Australia, Chagos-Madagascar-South Africa, Gulf of Aden-Zanzibar-Madagascar, and Red Sea-Persian/Arabian Gulf-Kenya. On the basis of the fossil record of Stylophora, these four clades diverged from one another 51.5-29.6 Mya, i.e., long before the closure of the Tethyan connection between the tropical Indo-West Pacific and Atlantic in the early Miocene (16–24 Mya) and should be recognised as four distinct species. These findings have implications for comparative ecological and/or physiological studies carried out using Stylophora pistillata as a model species, and highlight the fact that phenotypic plasticity, thought to be common in scleractinian corals, can mask significant genetic variation

Extreme Food-Plant Specialisation in Megabombus Bumblebees as a Product of Long Tongues Combined with Short Nesting Seasons

© 2015 Huang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. http://creativecommons.org/licenses/by/4.0/ The attached file is the published version of the article

EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences

Next generation sequencing (NGS) technologies have led to a ubiquity of molecular sequence data. This data avalanche is particularly challenging in metagenetics, which focuses on taxonomic identification of sequences obtained from diverse microbial environments. Phylogenetic placement methods determine how these sequences fit into an evolutionary context. Previous implementations of phylogenetic placement algorithms, such as the evolutionary placement algorithm (EPA) included in RAxML, or PPLACER, are being increasingly used for this purpose. However, due to the steady progress in NGS technologies, the current implementations face substantial scalability limitations. Herein, we present EPA-NG, a complete reimplementation of the EPA that is substantially faster, offers a distributed memory parallelization, and integrates concepts from both, RAxML-EPA and PPLACER. EPA-NG can be executed on standard shared memory, as well as on distributed memory systems (e.g., computing clusters). To demonstrate the scalability of EPA-NG, we placed 1 billion metagenetic reads from the Tara Oceans Project onto a reference tree with 3748 taxa in just under 7 h, using 2048 cores. Our performance assessment shows that EPA-NG outperforms RAxML-EPA and PPLACER by up to a factor of 30 in sequential execution mode, while attaining comparable parallel efficiency on shared memory systems. We further show that the distributed memory parallelization of EPA-NG scales well up to 2048 cores. EPA-NG is available under the AGPLv3 license