We developed grenepipe, an all-in-one Snakemake workflow to streamline the data processing from raw high-throughput sequencing data of individuals or populations to genotype variant calls. Our pipeline offers a range of popular software tools within a single configuration file, automatically installs software dependencies, is highly optimized for scalability in cluster environments and runs with a single command.

Species-abundance distributions (SADs) describe the spectrum of commonness and rarity in a community. Beyond the universal observation that most species are rare and only a few common, more-precise description of SAD shape is controversial. Furthermore, the mechanisms behind SADs and how they vary along environmental gradients remain unresolved. We lack a general, non-neutral theory of SADs. Here, we develop a trait-based framework, focusing on a local community coupled to the region by dispersal. The balance of immigration and exclusion determines abundances, which vary over orders-of-magnitude. The local trait-abundance distribution (TAD) reflects a transformation of the regional TAD. The left-tail of the SAD depends on scaling exponents of the exclusion function and the regional species pool. More-complex local dynamics can lead to multimodal TADs and SADs. Connecting SADs with trait-based ecological theory provides a way to generate more-testable hypotheses on the controls over commonness and rarity in communities.

We employed an idealized macro-energy system model to examine how the value of unidirectionally- and bidirectionally-charging electric vehicles (EVs) varies with EV penetration and mix of electricity generators. We find that EVs can help wind and solar-based electricity generation systems to be less costly by making better use of power that would otherwise be curtailed and, potentially, by giving electricity back to the grid at times of peak net load. At low levels of EV penetration, bidirectional EVs are valuable because they can provide electricity at times of main load peak. At today's low levels of EV penetration, bidirectional EVs stimulate investments in solar and wind generation and substantially reduce the need for grid-battery storage compared to unidirectional EVs. At high levels of EV penetration, generation capacity must be increased, and most peaks in main net load demand can be met by reductions in charging by unidirectional EVs.

The hypersaline sediment and groundwater of playa lake, Lake Lucero, at the White Sands National Monument in New Mexico were examined for microbial community composition, geochemical gradients, and mineralogy during the dry season along a meter and a half depth profile of the sediment vs. the groundwater interface. Lake Lucero is a highly dynamic environment, strongly characterized by the capillary action of the groundwater, the extreme seasonality of the climate, and the hypersalinity. Sediments are predominantly composed of gypsum with minor quartz, thenardite, halite, quartz, epsomite, celestine, and clays. Geochemical analysis has revealed the predominance of nitrates over ammonium in all of the analyzed samples, indicating oxygenated conditions throughout the sediment column and in groundwater. Conversely, the microbial communities are primarily aerobic, gram-negative, and are largely characterized by their survival adaptations. Halophiles and oligotrophs are ubiquitous for all the samples. The very diverse communities contain methanogens, phototrophs, heterotrophs, saprophytes, ammonia-oxidizers, sulfur-oxidizers, sulfate-reducers, iron-reducers, and nitrifiers. The microbial diversity varied significantly between groundwater and sediment samples as their temperature adaptation inferences that revealed potential psychrophiles inhabiting the groundwater and thermophiles and mesophiles being present in the sediment. The dynamism of this environment manifests in the relatively even character of the sediment hosted microbial communities, where significant taxonomic distinctions were observed. Therefore, sediment and groundwater substrates are considered as separate ecological entities. We hope that the variety of the discussed playa environments and the microorganisms may be considered a useful terrestrial analog providing valuable information to aid future astrobiological explorations.

The Sloan Digital Sky Survey V (SDSS-V) is an all-sky spectroscopic survey of more than 6 million objects, designed to decode the history of the Milky Way, reveal the inner workings of stars, investigate the origin of solar systems, and track the growth of supermassive black holes across the Universe. SDSS-V presents significant innovations in both hardware and software, chiefly due to the introduction of a robotic Focal Plane System (FPS) that replaces plug-plate operations. This new mode of operations introduces new challenges with respect to target scheduling, fibre robot positioner reconfiguration optimisation, telescope guiding, observer interfaces, and observatory operations. During normal operations SDSS-V will observe a new field every 15 minutes. For each field requiring a new telescope pointing the FPS will reconfigure 500 robotic fibre positioners with feedback from an external Field Viewing Camera (FVC) in less than two minutes. Six CCD cameras mounted on the FPS will be used to automatically acquire the field and maintain the necessary guiding accuracy. These strict requirements highlight the need for streamlined operations software and procedures to minimise the time spent during FPS reconfigurations. We describe the overall design and implementation of the SDSS-V survey operations, with special emphasis on software development, conventions, and observing procedures. While specific to SDSS-V, the solutions we describe can be readily applied to other astronomical surveys and are of special interest given the rapid increase in projects employing robotic fibre positioners.

We present an overview of best practices for publishing data in astronomy and astrophysics journals. These recommendations are intended as a reference for authors to help prepare and publish data in a way that will better represent and support science results, enable better data sharing, improve reproducibility, and enhance the reusability of data. Observance of these guidelines will also help to streamline the extraction, preservation, integration and cross-linking of valuable data from astrophysics literature into major astronomical databases, and consequently facilitate new modes of science discovery that will better exploit the vast quantities of panchromatic and multidimensional data associated with the literature. We encourage authors, journal editors, referees, and publishers to implement the best practices reviewed here, as well as related recommendations from international astronomical organizations such as the International Astronomical Union for publication of nomenclature, data, and metadata. A convenient Checklist of Recommendations for Publishing Data in the Literature (Appendix A) is included for authors to consult before the submission of the final version of their journal articles and associated data files. We recommend that publishers of journals in astronomy and astrophysics incorporate a link to this document in their Instructions to Authors.

We define a large sample of galaxies for use in a study of the fundamental plane in the intermediate redshift cluster Cl 1358 + 62 at z = 0.33. We have analyzed high-resolution spectra for 55 members of the cluster. The data were acquired with the Low-Resolution Imaging Spectrograph on the Keck 1 10 m telescope. A new algorithm for measuring velocity dispersions is presented and used to measure the internal kinematics of the galaxies. This algorithm has been tested against the Fourier fitting method so that the data presented here can be compared with those measured previously in nearby galaxies. We have measured central velocity dispersions suitable for use in a fundamental plane analysis. The data have a high signal-to-noise ratio (S/N) and the resulting random errors on the dispersions are very low, typically less that 5%. Uncertainties due to mismatch of the stellar templates have been minimized through several tests, and the total systematic error is of order similar to 5%. Good seeing enabled us to measure velocity dispersion profiles and rotation curves for most of the sample, and although a large fraction of the galaxies display a high level of rotation, the gradients of the total second moment of the kinematics are all very regular and similar to those in nearby galaxies. We conclude that the data therefore can be reliably corrected for aperture size in a manner consistent with nearby galaxy samples.

Using wide-field, two-color Hubble Space Telescope (HST) imaging of the cluster Cl 1358 + 62 (z = 0.33), we derive structural parameters for a large, magnitude-limited sample of cluster members. These structural parameters are combined with accurate velocity dispersions in another paper to investigate the fundamental plane in the cluster. We fit integrated r(1/4) laws to the integrated surface brightness profiles and fit two-dimensional r(1/4)-law model galaxies to the images directly. A comparison of the results from the two methods shows that the derived half-light radii, r(e), agree very well, with an rms scatter of only 13%. The half-light radii range from approximately 1 to 20 kpc with a median of about 3 kpc (H(0) = 65 km s(-1) Mpc(-1), q(0) = 0.1).

We present a compilation of Cepheid distance moduli and data for four secondary distance indicators that employ stars in the old stellar populations: the planetary nebula luminosity function (PNLF), the globular cluster luminosity function (GCLF), the tip of the red giant branch (TRGB), and the surface brightness fluctuation (SBF) method. The database includes all data published as of 1999 July 15. The main strength of this compilation resides in the fact that all data are on a consistent and homogeneous system: all Cepheid distances are derived using the same calibration of the period-luminosity relation, the treatment of errors is consistent for all indicators, and measurements that are not considered reliable are excluded. As such, the database is ideal for comparing any of the distance indicators considered, or for deriving a Cepheid calibration to any secondary distance indicator, such as the Tully-Fisher relation, the Type Ia supernovae, or the fundamental plane for elliptical galaxies. This task has already been undertaken by Ferrarese et at, Sakai et al., Kelson et al., and Gibson et al. Specifically the database includes (1) Cepheid distances, extinctions, and metallicities; (2) reddened apparent lambda 5007 Angstrom magnitudes of the PNLF cutoff; (3) reddened apparent magnitudes and colors of the turnover of the GCLF (in both the V and B bands); (4) reddened apparent magnitudes of the TRGB (in the I band) and V-I colors at 0.5 mag fainter than the TRGB; and (5) reddened apparent surface brightness fluctuation magnitudes measured in Kron-Cousin I, K', and K-short, and using the F814W filter with the Hubble Space Telescope (HST) WFPC2. In addition, for every galaxy in the database we give reddening estimates from IRAS/DIRBE as well as H I maps, J2000 coordinates, Hubble and T-type morphological classification, apparent total magnitude in B, and systemic velocity.

The evolution of galaxies is likely to be complex, involving mergers, starbursts, and other dramatic changes in morphology and luminosity. The measurement of the evolution of the mass function of galaxies is therefore essential. This can be accomplished by measuring the evolution of the mass-to-light ratios of galaxies as a function of redshift. The Fundamental Plane relation is uniquely suited to measure the evolution of the mass-to-light ratio of early-type galaxies. We show that the evolution depends sensitively on cosmology and star-formation history. We present results on the evolution of the mass-to-light ratio from the Fundamental Plane out to z = 0.83. The early-type galaxies in clusters follow a well-defined relation out the highest redshift. The mass-to-light evolution is very slow, and implies a high mean stellar age in an open universe.