How challenging RADseq data turned out to favor coalescent-based species tree inference. A case study in Aichryson (Crassulaceae)

Analysing multiple genomic regions while incorporating detection and qualification of discordance among regions has become standard for understanding phylogenetic relationships. In plants, which usually have comparatively large genomes, this is feasible by the combination of reduced-representation library (RRL) methods and high-throughput sequencing enabling the cost effective acquisition of genomic data for thousands of loci from hundreds of samples. One popular RRL method is RADseq. A major disadvantage of established RADseq approaches is the rather short fragment and sequencing range, leading to loci of little individual phylogenetic information. This issue hampers the application of coalescent-based species tree inference. The modified RADseq protocol presented here targets ca. 5,000 loci of 300-600nt length, sequenced with the latest short-read-sequencing (SRS) technology, has the potential to overcome this drawback. To illustrate the advantages of this approach we use the study group Aichryson Webb & Berthelott (Crassulaceae), a plant genus that diversified on the Canary Islands. The data analysis approach used here aims at a careful quality control of the long loci dataset. It involves an informed selection of thresholds for accurate clustering, a thorough exploration of locus properties, such as locus length, coverage and variability, to identify potential biased data and a comparative phylogenetic inference of filtered datasets, accompanied by an evaluation of resulting BS support, gene and site concordance factor values, to improve overall resolution of the resulting phylogenetic trees. The final dataset contains variable loci with an average length of 373nt and facilitates species tree estimation using a coalescent-based summary approach. Additional improvements brought by the approach are critically discussed

Transit timing analysis of CoRoT-1b

CoRoT, the pioneer space-based transit search, steadily provides thousands of high-precision light curves with continuous time sampling over periods of up to 5 months. The transits of a planet perturbed by an additional object are not strictly periodic. By studying the transit timing variations (TTVs), additional objects can be detected in the system. A transit timing analysis of CoRoT-1b is carried out to constrain the existence of additional planets in the system. We used data obtained by an improved version of the CoRoT data pipeline (version 2.0). Individual transits were fitted to determine the mid-transit times, and we analyzed the derived $O-C$ diagram. N-body integrations were used to place limits on secondary planets. No periodic timing variations with a period shorter than the observational window (55 days) are found. The presence of an Earth-mass Trojan is not likely. A planet of mass greater than $\sim 1$ Earth mass can be ruled out by the present data if the object is in a 2:1 (exterior) mean motion resonance with CoRoT-1b. Considering initially circular orbits: (i) super-Earths (less than 10 Earth-masses) are excluded for periods less than about 3.5 days, (ii) Saturn-like planets can be ruled out for periods less than about 5 days, (iii) Jupiter-like planets should have a minimum orbital period of about 6.5 days.Comment: 6 pages, accepted at A&

CoRoT-22 b: a validated 4.9 RE exoplanet in 10-day orbit

The CoRoT satellite has provided high-precision photometric light curves for more than 163,000 stars and found several hundreds of transiting systems compatible with a planetary scenario. If ground-based velocimetric observations are the best way to identify the actual planets among many possible configurations of eclipsing binary systems, recent transit surveys have shown that it is not always within reach of the radial-velocity detection limits. In this paper, we present a transiting exoplanet candidate discovered by CoRoT whose nature cannot be established from ground-based observations, and where extensive analyses are used to validate the planet scenario. They are based on observing constraints from radial-velocity spectroscopy, adaptive optics imaging and the CoRoT transit shape, as well as from priors on stellar populations, planet and multiple stellar systems frequency. We use the fully Bayesian approach developed in the PASTIS analysis software, and conclude that the planet scenario is at least 1400 times more probable than any other false positive scenario. The primary star is a metallic solar-like dwarf, with Ms = 1.099+-0.049 Msun and Rs = 1.136 (+0.038,-0.090) Rsun . The validated planet has a radius of Rp = 4.88 (+0.17,-0.39) RE and mass less than 49 ME. Its mean density is smaller than 2.56 g/cm^3 and orbital period is 9.7566+-0.0012 days. This object, called CoRoT-22 b, adds to a large number of validated Kepler planets. These planets do not have a proper measurement of the mass but allow statistical characterization of the exoplanet population

Assessing urban methane emissions using column-observing portable Fourier transform infrared (FTIR) spectrometers and a novel Bayesian inversion framework

Cities represent a large and concentrated portion of global greenhouse gas emissions, including methane. Quantifying methane emissions from urban areas is difficult, and inventories made using bottom-up accounting methods often differ greatly from top-down estimates generated from atmospheric observations. Emissions from leaks in natural gas infrastructure are difficult to predict and are therefore poorly constrained in bottom-up inventories. Natural gas infrastructure leaks and emissions from end uses can be spread throughout the city, and this diffuse source can represent a significant fraction of a city\u27s total emissions. We investigated diffuse methane emissions of the city of Indianapolis, USA, during a field campaign in May 2016. A network of five portable solar-tracking Fourier transform infrared (FTIR) spectrometers was deployed throughout the city. These instruments measure the mole fraction of methane in a total column of air, giving them sensitivity to larger areas of the city than in situ sensors at the surface. We present an innovative inversion method to link these total column concentrations to surface fluxes. This method combines a Lagrangian transport model with a Bayesian inversion framework to estimate surface emissions and their uncertainties, together with determining the concentrations of methane in the air flowing into the city. Variations exceeding 10 ppb were observed in the inflowing air on a typical day, which is somewhat larger than the enhancements due to urban emissions (<5 ppb downwind of the city). We found diffuse methane emissions of 73(±22) mol s−1, which is about 50 % of the urban total and 68 % higher than estimated from bottom-up methods, although it is somewhat smaller than estimates from studies using tower and aircraft observations. The measurement and model techniques developed here address many of the challenges present when quantifying urban greenhouse gas emissions and will help in the design of future measurement schemes in other cities

A review of assessment methods for river hydromorphology

The work leading to this paper has received funding for the EU’s FP7 under Grant Agreement No. 282656 (REFORM

PaperClip:rapid multi-part DNA assembly from existing libraries

Assembly of DNA ‘parts ’ to create larger constructs is an essential enabling technique for bioengineer-ing and synthetic biology. Here we describe a sim-ple method, PaperClip, which allows flexible assem-bly of multiple DNA parts from currently existing libraries cloned in any vector. No restriction en-zymes, mutagenesis of internal restriction sites, or reamplification to add end homology are required. Order of assembly is directed by double stranded oligonucleotides––‘Clips’. Clips are formed by lig-ation of pairs of oligonucleotides corresponding to the ends of each part. PaperClip assembly can be performed by polymerase chain reaction or by cell extract-mediated recombination. Once multi-use Clips have been prepared, assembly of at least six DNA parts in any order can be accomplished with high efficiency within several hours