r2cat: synteny plots and comparative assembly

Summary: Recent parallel pyrosequencing methods and the increasing number of finished genomes encourage the sequencing and investigation of closely related strains. Although the sequencing itself becomes easier and cheaper with each machine generation, the finishing of the genomes remains difficult. Instead of the desired whole genomic sequence, a set of contigs is the result of the assembly. In this applications note, we present the tool r2cat (related reference contig arrangement tool) that helps in the task of comparative assembly and also provides an interactive visualization for synteny inspection

Resolving galaxies in time and space: II: Uncertainties in the spectral synthesis of datacubes

In a companion paper we have presented many products derived from the application of the spectral synthesis code STARLIGHT to datacubes from the CALIFA survey, including 2D maps of stellar population properties and 1D averages in the temporal and spatial dimensions. Here we evaluate the uncertainties in these products. Uncertainties due to noise and spectral shape calibration errors and to the synthesis method are investigated by means of a suite of simulations based on 1638 CALIFA spectra for NGC 2916, with perturbations amplitudes gauged in terms of the expected errors. A separate study was conducted to assess uncertainties related to the choice of evolutionary synthesis models. We compare results obtained with the Bruzual & Charlot models, a preliminary update of them, and a combination of spectra derived from the Granada and MILES models. About 100k CALIFA spectra are used in this comparison. Noise and shape-related errors at the level expected for CALIFA propagate to 0.10-0.15 dex uncertainties in stellar masses, mean ages and metallicities. Uncertainties in A_V increase from 0.06 mag in the case of random noise to 0.16 mag for shape errors. Higher order products such as SFHs are more uncertain, but still relatively stable. Due to the large number statistics of datacubes, spatial averaging reduces uncertainties while preserving information on the history and structure of stellar populations. Radial profiles of global properties, as well as SFHs averaged over different regions are much more stable than for individual spaxels. Uncertainties related to the choice of base models are larger than those associated with data and method. Differences in mean age, mass and metallicity are ~ 0.15 to 0.25 dex, and 0.1 mag in A_V. Spectral residuals are ~ 1% on average, but with systematic features of up to 4%. The origin of these features is discussed. (Abridged)Comment: A&A, accepte

Old and new major mergers in the SOSIMPLE galaxy, NGC 7135

The simultaneous advancement of high resolution integral field unit spectroscopy and robust full-spectral fitting codes now make it possible to examine spatially resolved kinematic, chemical composition, and star-formation history from nearby galaxies. We take new MUSE data from the snapshot optical spectroscopic imaging of mergers and pairs for legacy Exploration (SOSIMPLE) survey to examine NGC 7135. With counter-rotation of gas, disrupted kinematics and asymmetric chemical distribution, NGC 7135 is consistent with an ongoing merger. Though well hidden by the current merger, we are able to distinguish stars originating from an older merger, occurring 6–10 Gyr ago. We further find a gradient in ex-situ material with galactocentric radius, with the accreted fraction rising from 0 per cent in the galaxy centre, to ∼7 per cent within 0.6 effective radii

The dependence of oxygen and nitrogen abundances on stellar mass from the CALIFA survey

We analysed the optical spectra of HII regions extracted from a sample of 350 galaxies of the CALIFA survey. We calculated total O/H abundances and, for the first time, N/O ratios using the semi-empirical routine HII-CHI-mistry, which, according to P\'erez-Montero (2014), is consistent with the direct method and reduces the uncertainty in the O/H derivation using [NII] lines owing to the dispersion in the O/H-N/O relation. Then we performed linear fittings to the abundances as a function of the de-projected galactocentric distances. The analysis of the radial distribution both for O/H and N/O in the non-interacting galaxies reveals that both average slopes are negative, but a non-negligible fraction of objects have a flat or even a positive gradient (at least 10\% for O/H and 4\% for N/O). The slopes normalised to the effective radius appear to have a slight dependence on the total stellar mass and the morphological type, as late low-mass objects tend to have flatter slopes. No clear relation is found, however, to explain the presence of inverted gradients in this sample, and there is no dependence between the average slopes and the presence of a bar. The relation between the resulting O/H and N/O linear fittings at the effective radius is much tighter (correlation coefficient $\rho_s$ = 0.80) than between O/H and N/O slopes ($\rho_s$ = 0.39) or for O/H and N/O in the individual \hii\ regions ($\rho_s$ = 0.37). These O/H and N/O values at the effective radius also correlate very tightly (less than 0.03 dex of dispersion) with total luminosity and stellar mass. The relation with other integrated properties, such as star formation rate, colour, or morphology, can be understood only in light of the found relation with mass.Comment: Accepted for publication in A&A. 20 pages, 19 figure

Stellar Population gradients in galaxy discs from the CALIFA survey

While studies of gas-phase metallicity gradients in disc galaxies are common, very little has been done in the acquisition of stellar abundance gradients in the same regions. We present here a comparative study of the stellar metallicity and age distributions in a sample of 62 nearly face-on, spiral galaxies with and without bars, using data from the CALIFA survey. We measure the slopes of the gradients and study their relation with other properties of the galaxies. We find that the mean stellar age and metallicity gradients in the disc are shallow and negative. Furthermore, when normalized to the effective radius of the disc, the slope of the stellar population gradients does not correlate with the mass or with the morphological type of the galaxies. Contrary to this, the values of both age and metallicity at $\sim$2.5 scale-lengths correlate with the central velocity dispersion in a similar manner to the central values of the bulges, although bulges show, on average, older ages and higher metallicities than the discs. One of the goals of the present paper is to test the theoretical prediction that non-linear coupling between the bar and the spiral arms is an efficient mechanism for producing radial migrations across significant distances within discs. The process of radial migration should flatten the stellar metallicity gradient with time and, therefore, we would expect flatter stellar metallicity gradients in barred galaxies. However, we do not find any difference in the metallicity or age gradients in galaxies with without bars. We discuss possible scenarios that can lead to this absence of difference.Comment: 24 pages, 17 figures, accepted for publication in A&

Observational hints of radial migration in disc galaxies from CALIFA

Context. According to numerical simulations, stars are not always kept at their birth galactocentric distances but they have a tendency to migrate. The importance of this radial migration in shaping galactic light distributions is still unclear. However, if radial migration is indeed important, galaxies with different surface brightness (SB) profiles must display differences in their stellar population properties. Aims: We investigate the role of radial migration in the light distribution and radial stellar content by comparing the inner colour, age, and metallicity gradients for galaxies with different SB profiles. We define these inner parts, avoiding the bulge and bar regions and up to around three disc scale lengths (type I, pure exponential) or the break radius (type II, downbending; type III, upbending). Methods: We analysed 214 spiral galaxies from the CALIFA survey covering different SB profiles. We made use of GASP2D and SDSS data to characterise the light distribution and obtain colour profiles of these spiral galaxies. The stellar age and metallicity profiles were computed using a methodology based on full-spectrum fitting techniques (pPXF, GANDALF, and STECKMAP) to the Integral Field Spectroscopic CALIFA data. Results: The distributions of the colour, stellar age, and stellar metallicity gradients in the inner parts for galaxies displaying different SB profiles are unalike as suggested by Kolmogorov-Smirnov and Anderson-Darling tests. We find a trend in which type II galaxies show the steepest profiles of all, type III show the shallowest, and type I display an intermediate behaviour. Conclusions: These results are consistent with a scenario in which radial migration is more efficient for type III galaxies than for type I systems, where type II galaxies present the lowest radial migration efficiency. In such a scenario, radial migration mixes the stellar content, thereby flattening the radial stellar properties and shaping different SB profiles. However, in light of these results we cannot further quantify the importance of radial migration in shaping spiral galaxies, and other processes, such as recent star formation or satellite accretion, might play a role

Beam test results of silicon sensor module prototypes for the Phase-2 Upgrade of the CMS Outer Tracker

The start of the High-Luminosity LHC (HL-LHC) in 2027 requires upgrades to the Compact Muon Solenoid (CMS) Experiment. In the scope of the upgrade program the complete silicon tracking detector will be replaced. The new CMS Tracker will be equipped with silicon pixel detectors in the inner layers closest to the interaction point and silicon strip detectors in the outer layers. The new CMS Outer Tracker will consist of two different kinds of detector modules called PS and 2S modules. Each module will be made of two parallel silicon sensors (a macro-pixel sensor and a strip sensor for the PS modules and two strip sensors for the 2S modules). Combining the hit information of both sensor layers it is possible to estimate the transverse momentum of particles in the magnetic field of 3.8 T at the full bunch-crossing rate of 40 MHz directly on the module. This information will be used as an input for the first trigger stage of CMS. It is necessary to validate the Outer Tracker module functionality before installing the modules in the CMS experiment. Besides laboratory-based tests several 2S module prototypes have been studied at test beam facilities at CERN, DESY and FNAL. This article concentrates on the beam tests at DESY during which the functionality of the module concept was investigated using the full final readout chain for the first time. Additionally the performance of a 2S module assembled with irradiated sensors was studied. By choosing an irradiation fluence expected for 2S modules at the end of HL-LHC operation, it was possible to investigate the particle detection efficiency and study the trigger capabilities of the module at the beginning and end of runtime of the CMS experiment.The start of the High-Luminosity LHC (HL-LHC) in 2027 requires upgrades to the Compact Muon Solenoid (CMS) experiment. In the scope of the upgrade program the complete silicon tracking detector will be replaced. The new CMS Tracker will be equipped with silicon pixel detectors in the inner layers closest to the interaction point and silicon strip detectors in the outer layers. The new CMS Outer Tracker will consist of two different kinds of detector modules called PS and 2S modules. Each module will be made of two parallel silicon sensors (a macro-pixel sensor and a strip sensor for the PS modules and two strip sensors for the 2S modules). Combining the hit information of both sensor layers, it is possible to estimate the transverse momentum of particles in the magnetic field of 3.8 T at the full bunch-crossing rate of 40 MHz directly on the module. This information will be used as an input for the first trigger stage of CMS. It is necessary to validate the Outer Tracker module functionality before installing the modules in the CMS experiment. Besides laboratory-based tests several 2S module prototypes have been studied at test beam facilities at CERN, DESY and FNAL. This article concentrates on the beam tests at DESY during which the functionality of the module concept was investigated using the full final readout chain for the first time. Additionally the performance of a 2S module assembled with irradiated sensors was studied. By choosing an irradiation fluence expected for 2S modules at the end of HL-LHC operation, it was possible to investigate the particle detection efficiency and study the trigger capabilities of the module at the beginning and end of the runtime of the CMS experiment