On depth zero L-packets for classical groups

By computing reducibility points of parabolically induced representations, we construct, to within at most two unramified quadratic characters, the Langlands parameter of an arbitrary depth zero irreducible cuspidal representation (Formula presented.) of a classical group (which may be not-quasi-split) over a non-archimedean local field of odd residual characteristic. From this, we can explicitly describe all the irreducible cuspidal representations in the union of one, two, or four (Formula presented.) -packets, containing (Formula presented.). These results generalize the work of DeBacker–Reeder (in the case of classical groups) from regular to arbitrary tame Langlands parameters

Phylogenetics and sequence analysis--some problems for the unwary.

DNA sequence comparisons can provide deep insight into phylogenetic relationships, but can also present problems for the unwary. Alignment comparisons are not always as straightforward as they might seem, and comparative models applied to deduce relationships need to be carefully chosen with full regard to the assumptions on which they are based. Most importantly perhaps, genes are not organisms, so some sequence analyses can be poorly informative about relationships - especially if evolution of those organisms has involved significant epigenetic factors, for example, in controlling gene expression. This review highlights some of the most prevalent problems in sequence-based phylogenetic studies of parasite systems

Trypanosomes are monophyletic: evidence from genes for glyceraldehyde phosphate dehydrogenase and small subunit ribosomal RNA.

The genomes of Trypanosoma brucei, Trypanosoma cruzi and Leishmania major have been sequenced, but the phylogenetic relationships of these three protozoa remain uncertain. We have constructed trypanosomatid phylogenies based on genes for glycosomal glyceraldehyde phosphate dehydrogenase (gGAPDH) and small subunit ribosomal RNA (SSU rRNA). Trees based on gGAPDH nucleotide and amino acid sequences (51 taxa) robustly support monophyly of genus Trypanosoma, which is revealed to be a relatively late-evolving lineage of the family Trypanosomatidae. Other trypanosomatids, including genus Leishmania, branch paraphyletically at the base of the trypanosome clade. On the other hand, analysis of the SSU rRNA gene data produced equivocal results, as trees either robustly support or reject monophyly depending on the range of taxa included in the alignment. We conclude that the SSU rRNA gene is not a reliable marker for inferring deep level trypanosome phylogeny. The gGAPDH results support the hypothesis that trypanosomes evolved from an ancestral insect parasite, which adapted to a vertebrate/insect transmission cycle. This implies that the switch from terrestrial insect to aquatic leech vectors for fish and some amphibian trypanosomes was secondary. We conclude that the three sequenced pathogens, T. brucei, T. cruzi and L. major, are only distantly related and have distinct evolutionary histories

Extreme radio-wave scattering associated with hot stars

We use data on extreme radio scintillation to demonstrate that this phenomenon is associated with hot stars in the solar neighbourhood. The ionized gas responsible for the scattering is found at distances up to 1.75pc from the host star, and on average must comprise 1.E5 distinct structures per star. We detect azimuthal velocities of the plasma, relative to the host star, up to 9.7 km/s, consistent with warm gas expanding at the sound speed. The circumstellar plasma structures that we infer are similar in several respects to the cometary knots seen in the Helix, and in other planetary nebulae. There the ionized gas appears as a skin around tiny molecular clumps. Our analysis suggests that molecular clumps are ubiquitous circumstellar features, unrelated to the evolutionary state of the star. The total mass in such clumps is comparable to the stellar mass.Comment: 9 pages, 1 figure, to appear in Ap

REFGEN and TREENAMER: Automated Sequence Data Handling for Phylogenetic Analysis in the Genomic Era

The phylogenetic analysis of nucleotide sequences and increasingly that of amino acid sequences is used to address a number of biological questions. Access to extensive datasets, including numerous genome projects, means that standard phylogenetic analyses can include many hundreds of sequences. Unfortunately, most phylogenetic analysis programs do not tolerate the sequence naming conventions of genome databases. Managing large numbers of sequences and standardizing sequence labels for use in phylogenetic analysis programs can be a time consuming and laborious task. Here we report the availability of an online resource for the management of gene sequences recovered from public access genome databases such as GenBank. These web utilities include the facility for renaming every sequence in a FASTA alignment file, with each sequence label derived from a user-defined combination of the species name and/or database accession number. This facility enables the user to keep track of the branching order of the sequences/taxa during multiple tree calculations and re-optimisations. Post phylogenetic analysis, these webpages can then be used to rename every label in the subsequent tree files (with a user-defined combination of species name and/or database accession number). Together these programs drastically reduce the time required for managing sequence alignments and labelling phylogenetic figures. Additional features of our platform include the automatic removal of identical accession numbers (recorded in the report file) and generation of species and accession number lists for use in supplementary materials or figure legends

Star-Formation in the Ultraluminous Infrared Galaxy F00183-7111

We report the detection of molecular CO(1-0) gas in F00183-7111, one of the most extreme Ultra-Luminous Infrared Galaxies known, with the Australia Telescope Compact Array. We measure a redshift of 0.3292 for F00183-7111 from the CO(1-0) line and estimate the mass of the molecular gas in 00183 to be 1 $\times$ 10$^{10}$ M$_{\odot}$. We find that F00183-7111 is predominately powered by the AGN and only $\sim$14 per cent of the total luminosity is contributed by star-formation (SFR $\sim$220 M$_{\odot}$ yr$^{-1}$). We also present an optical image of F00183-7111, which shows an extension to the East. We searched for star-formation in this extension using radio continuum observations but do not detect any. This suggests that the star-formation is likely to be predominately nuclear. These observations provide additional support for a model in which the radio emission from ULIRGs is powered by an intense burst of star-formation and by a radio-loud AGN embedded in its nucleus, both triggered by a merger of gas-rich galaxies.Comment: 5 pages, 2 figures, Accepted for publication in MNRAS Letters Accepted 2014 January 19. Received 2013 December 30; in original form 2013 November 2