Bulk de novo mitogenome assembly from pooled total DNA elucidates the phylogeny of weevils (Coleoptera: Curculionoidea)

Complete mitochondrial genomes have been shown to be reliable markers for phylogeny reconstruction among diverse animal groups. However, the relative difficulty and high cost associated with obtaining de novo full mitogenomes have frequently led to conspicuously low taxon sampling in ensuing studies. Here, we report the successful use of an economical and accessible method for assembling complete or near-complete mitogenomes through shot-gun next-generation sequencing of a single library made from pooled total DNA extracts of numerous target species. To avoid the use of separate indexed libraries for each specimen, and an associated increase in cost, we incorporate standard polymerase chain reaction-based “bait” sequences to identify the assembled mitogenomes. The method was applied to study the higher level phylogenetic relationships in the weevils (Coleoptera: Curculionoidea), producing 92 newly assembled mitogenomes obtained in a single Illumina MiSeq run. The analysis supported a separate origin of wood-boring behavior by the subfamilies Scolytinae, Platypodinae, and Cossoninae. This finding contradicts morphological hypotheses proposing a close relationship between the first two of these but is congruent with previous molecular studies, reinforcing the utility of mitogenomes in phylogeny reconstruction. Our methodology provides a technically simple procedure for generating densely sampled trees from whole mitogenomes and is widely applicable to groups of animals for which bait sequences are the only required prior genome knowledge

A Catalog of Candidate Intermediate-luminosity X-ray Objects

ROSAT, and now Chandra, X-ray images allow studies of extranuclear X-ray point sources in galaxies other than our own. X-ray observations of normal galaxies with ROSAT and Chandra have revealed that off-nuclear, compact, Intermediate-luminosity (Lx[2-10 keV] >= 1e39 erg/s) X-ray Objects (IXOs, a.k.a. ULXs [Ultraluminous X-ray sources]) are quite common. Here we present a catalog and finding charts for 87 IXOs in 54 galaxies, derived from all of the ROSAT HRI imaging data for galaxies with cz <= 5000 km/s from the Third Reference Catalog of Bright Galaxies (RC3). We have defined the cutoff Lx for IXOs so that it is well above the Eddington luminosity of a 1.4 Msun black hole (10^38.3 erg/s), so as not to confuse IXOs with ``normal'' black hole X-ray binaries. This catalog is intended to provide a baseline for follow-up work with Chandra and XMM, and with space- and ground-based survey work at wavelengths other than X-ray. We demonstrate that elliptical galaxies with IXOs have a larger number of IXOs per galaxy than non-elliptical galaxies with IXOs, and note that they are not likely to be merely high-mass X-ray binaries with beamed X-ray emission, as may be the case for IXOs in starburst galaxies. Approximately half of the IXOs with multiple observations show X-ray variability, and many (19) of the IXOs have faint optical counterparts in DSS optical B-band images. Follow-up observations of these objects should be helpful in identifying their nature.Comment: 29 pages, ApJS, accepted (catalog v2.0) (full resolution version of paper and future releases of catalog at http://www.xassist.org/ixocat_hri

Chandra Snapshot Observations of Low-Luminosity AGNs with a Compact Radio Source

The results of Chandra snapshot observations of 11 LINERs (Low-Ionization Nuclear Emission-line Regions), three low-luminosity Seyfert galaxies, and one HII-LINER transition object are presented. Our sample consists of all the objects with a flat or inverted spectrum compact radio core in the VLA survey of 48 low-luminosity AGNs (LLAGNs) by Nagar et al. (2000). An X-ray nucleus is detected in all galaxies except one and their X-ray luminosities are in the range 5x10^38 to 8x10^41 erg/s. The X-ray spectra are generally steeper than expected from thermal bremsstrahlung emission from an advection-dominated accretion flow (ADAF). The X-ray to Halpha luminosity ratios for 11 out of 14 objects are in good agreement with the value characteristic of LLAGNs and more luminous AGNs, and indicate that their optical emission lines are predominantly powered by a LLAGN. For three objects, this ratio is less than expected. Comparing with properties in other wavelengths, we find that these three galaxies are most likely to be heavily obscured AGN. We use the ratio RX = \nu L\nu (5 GHz)/LX, where LX is the luminosity in the 2-10 keV band, as a measure of radio loudness. In contrast to the usual definition of radio loudness (RO = L\nu(5 GHz)/L\nu(B)), RX can be used for heavily obscured (NH >~ 10^23 cm^-2, AV>50 mag) nuclei. Further, with the high spatial resolution of Chandra, the nuclear X-ray emission of LLAGNs is often easier to measure than the nuclear optical emission. We investigate the values of RX for LLAGNs, luminous Seyfert galaxies, quasars and radio galaxies and confirm the suggestion that a large fraction of LLAGNs are radio loud.Comment: 15 pages, accepted for publication in Ap

Bipolar-Hyper-Shell Galactic Center Statrburst Model: Further Evidence from ROSAT Data and New Radio and X-ray Simulations

Using the all-sky ROSAT soft X-ray and 408-MHz radio continuum data, we show that the North Polar Spur and its western and southern counter-spurs draw a giant dumbbell-shape necked at the galactic plane. We interpret these features as due to a shock front originating from a starburst 15 million years ago with a total energy of the order of $\sim 10^{56}$ ergs or $10^5$ type II supernovae. We simulate all-sky distributions of radio continuum and soft X-ray intensities based on the bipolar-hyper-shell galactic center starburst model. The simulations can well reproduce the radio NPS and related spurs, as well as radio spurs in the tangential directions of spiral arms. Simulated X-ray maps in 0.25, 0.75 and 1.5 keV bands reproduce the ROSAT X-ray NPS, its western and southern counter-spurs, and the absorption layer along the galactic plane. We propose to use the ROSAT all-sky maps to probe the physics of gas in the halo-intergalactic interface, and to directly date and measure the energy of a recent Galactic Center starburst.Comment: To appear in ApJ, Latex MS in ApJ macro, 8 figures in jpg (original quality ps figs available on request

The evolutionary genetics of highly divergent alleles of the mimicry locus in Papilio dardanus

Background: The phylogenetic history of genes underlying phenotypic diversity can offer insight into the evolutionary origin of adaptive traits. This is especially true where single genes have large phenotypic effects, for example in determining polymorphic mimicry in butterflies. Here, we characterise the evolutionary history of two candidate genes for the mimicry switch in the polymorphic Batesian mimic Papilio dardanus coding for the transcription factors engrailed and invected. Results: We show that phased haplotypes associated with the dominant morphs f. poultoni and f. planemoides are phylogenetically highly divergent, in particular at non-synonymous sites. Some non-synonymous changes are shared between the divergent alleles suggesting either convergence or a shared ancestry. Gene trees for invected do not show this pattern. Despite their great divergence, all engrailed alleles of P. dardanus were monophyletic with respect to alleles of closely related species. Phylogenetic analyses therefore reveal no evidence for introgression from other species. A McDonald-Kreitman test conducted on a population sample from South Africa confirms a significant excess of intraspecific non-synonymous diversity in P. dardanus engrailed, suggesting long-term balanced polymorphism at this locus. Conclusions: The divergence between engrailed haplotypes suggests an evolutionary history distorted by selection with multiple changes reflecting recurrent selective sweeps. The high level of intraspecific polymorphism observed is characteristic of balancing selection on this locus, as expected if the gene engrailed is under phenotypic selection for the maintenance of multiple mimetic morphs. Non-synonymous changes in key functional portions of a major transcription factor are likely to be deleterious but if maintained in a dominant allele at low frequency, heterozygosity would reduce the associated genetic load

Quantification of mechanical forces and physiological processes involved in pollen tube growth using microfluidics and microrobotics

Pollen tubes face many obstacles on their way to the ovule. They have to decide whether to navigate around cells or penetrate the cell wall and grow through it or even within it. Besides chemical sensing, which directs the pollen tubes on their path to the ovule, this involves mechanosensing to determine the optimal strategy in specific situations. Mechanical cues then need to be translated into physiological signals, which eventually lead to changes in the growth behavior of the pollen tube. To study these events, we have developed a system to directly quantify the forces involved in pollen tube navigation. We combined a lab-on-a-chip device with a microelectromechanical systems-based force sensor to mimic the pollen tube's journey from stigma to ovary in vitro. A force-sensing plate creates a mechanical obstacle for the pollen tube to either circumvent or attempt to penetrate while measuring the involved forces in real time. The change of growth behavior and intracellular signaling activities can be observed with a fluorescence microscope

Chandra View of the Dynamically Young Cluster of Galaxies A1367 I. Small-Scale Structures

The 40 ks \emph{Chandra} ACIS-S observation of A1367 provides new insights into small-scale structures and point sources in this dynamically young cluster. Here we concentrate on small-scale extended structures. A ridge-like structure around the center (``the ridge'') is significant in the \chandra\ image. The ridge, with a projected length of $\sim$ 8 arcmin (or 300 h$_{0.5}^{-1}$ kpc), is elongated from northwest (NW) to southeast (SE), as is the X-ray surface brightness distribution on much larger scales ($\sim$ 2 h$_{0.5}^{-1}$ Mpc). The ridge is cooler than its western and southern surroundings while the differences from its eastern and northern surroundings are small. We also searched for small-scale structures with sizes $\sim$ arcmin. Nine extended features, with sizes from $\sim$ 0.5$'$ to 1.5$'$, were detected at significance levels above 4 $\sigma$. Five of the nine features are located in the ridge and form local crests. The nine extended features can be divided into two types. Those associated with galaxies (NGC 3860B, NGC 3860 and UGC 6697) are significantly cooler than their surroundings (0.3 - 0.9 keV vs. 3 - 4.5 keV). The masses of their host galaxies are sufficient to bind the extended gas. These extended features are probably related to thermal halos or galactic superwinds of their host galaxies. The existence of these relatively cold halos imply that galaxy coronae can survive in cluster environment (e.g., Vikhlinin et al. 2001). Features of the second type are not apparently associated with galaxies. Their temperatures may not be significantly different from those of their surroundings. This class of extended features may be related to the ridge. We consider several possibilities for the ridge and the second type of extended features. The merging scenario is preferred.Comment: To appear in ApJ, Vol 576, 2002, Sep., a high-resolution version is in http://cfa160.harvard.edu/~sunm/a1367_a.ps.g

Calculation of coercivity of magnetic nanostructures at finite temperatures

We report a finite temperature micromagnetic method (FTM) that allows for the calculation of the coercive field of arbitrary shaped magnetic nanostructures at time scales of nanoseconds to years. Instead of directly solving the Landau-Lifshitz-Gilbert equation, the coercive field is obtained without any free parameter by solving a non linear equation, which arises from the transition state theory. The method is applicable to magnetic structures where coercivity is determined by one thermally activated reversal or nucleation process. The method shows excellent agreement with experimentally obtained coercive fields of magnetic nanostructures and provides a deeper understanding of the mechanism of coercivity.Comment: submitted to Phys. Rev.

Intraspecific genetic variation in complex assemblages from mitochondrial metagenomics: comparison with DNA barcodes

Metagenomic shotgun sequencing, using Illumina technology, and de novo genome assembly of mixed field-collected amples of invertebrates readily produce mitochondrial genome sequences, allowing rapid identification and quantification of species diversity. However, intraspecific genetic variability present in the specimen pools is lost during mitogenome assembly, which limits the utility of ‘mitochondrial metagenomics’ for studies of population diversity. 2. Using 10 natural communities (>2600 individuals) of leaf beetles (Chrysomelidae), DNA variation in the mitochondrial cox1-5’ ‘barcode’ was compared for Sanger sequenced individuals and Illumina shotgun sequenced specimen pools. 3. Generally, only a single mitochondrial contig was assembled per species, even in the presence of intraspecific variation. Ignoring ambiguity from the use of two different assemblers, the cox1 barcode regions from these assemblies were exact nucleotide matches of a Sanger sequenced barcode in 90.7% of cases, which dropped to 76.0% in assemblies from samples with large intra and interspecific variability. Nucleotide differences between barcodes from both data types were almost exclusively in synonymous 3rd codon position, although the number of affected sites was very low, and the greatest discrepancies were correlated with poor quality of Sanger sequences. 4. Unassembled shotgun reads were also used to score single nucleotide polymorphisms and to calculate intraspecific nucleotide diversity (pi) for all available populations at each site. These values correlated with Sanger sequenced cox1 variation but were significantly higher. 5. Overall, the assemblage-focused shotgun sequencing of pooled samples produced nucleotide variation data comparable to the well-established specimen-focused Sanger approach. The findings thus extend the application of mitochondrial metagenomics of complex biodiversity samples to the estimation of diversity below the species level

Radio Continuum Jet in NGC 7479

The barred galaxy NGC 7479 hosts a remarkable jet-like radio continuum feature: bright, 12-kpc long in projection, and hosting an aligned magnetic field. The degree of polarization is 6%-8% along the jet, and remarkably constant, which is consistent with helical field models. The radio brightness of the jet suggests strong interaction with the ISM and hence a location near the disk plane. We observed NGC 7479 at four wavelengths with the VLA and Effelsberg radio telescopes. The equipartition strength is 35-40 micro-G for the total and >10 micro-G for the ordered magnetic field in the jet. The jet acts as a bright, polarized background. Faraday rotation between 3.5 and 6 cm and depolarization between 6 and 22 cm can be explained by magneto-ionic gas in front of the jet, with thermal electron densities of ~0.06 cm**(-3) in the bar and ~0.03 cm**(-3) outside the bar. The regular magnetic field along the bar points toward the nucleus on both sides. The regular field in the disk reveals multiple reversals, probably consisting of field loops stretched by a shearing gas flow in the bar. The projection of the jet bending in the sky plane is in the sense opposite to that of the underlying stellar and gaseous spiral structure. The bending in 3-D is most easily explained as a precessing jet, with an age less than 10**6 years. Our observations are consistent with very recent triggering, possibly by a minor merger. NGC 7479 provides a unique opportunity to study interaction-triggered 15-kpc scale radio jets within a spiral galaxy.Comment: 18 pages, 21 figures, accepted for publication in the Astrophysical Journa