Microsatellites retain phylogenetic signals across genera in eucalypts (Myrtaceae)

The utility of microsatellites (SSRs) in reconstructing phylogenies is largely confined to studies below the genus level, due to the potential of homoplasy resulting from allele size range constraints and poor SSR transferability among divergent taxa. The eucalypt genus Corymbia has been shown to be monophyletic using morphological characters, however, analyses of intergenic spacer sequences have resulted in contradictory hypotheses- showing the genus as either equivocal or paraphyletic. To assess SSR utility in higher order phylogeny in the family Myrtaceae, phylogenetic relationships of the bloodwood eucalypts Corymbia and related genera were investigated using eight polymorphic SSRs. Repeat size variation using the average square and Nei’s distance were congruent and showed Corymbia to be a monophyletic group, supporting morphological characters and a recent combination of the internal and external transcribed spacers dataset. SSRs are selectively neutral and provide data at multiple genomic regions, thus may explain why SSRs retained informative phylogenetic signals despite deep divergences. We show that where the problems of size-range constraints, high mutation rates and size homoplasy are addressed, SSRs might resolve problematic phylogenies of taxa that have diverged for as long as three million generations or 30 million years. Key word

On the Suppression and Distortion of Non-Equilibrium Fluctuations by Transpiration

A fluid in a non-equilibrium state exhibits long-ranged correlations of its hydrodynamic fluctuations. In this article, we examine the effect of a transpiration interface on these correlations -- specifically, we consider a dilute gas in a domain bisected by the interface. The system is held in a non-equilibrium steady state by using isothermal walls to impose a temperature gradient. The gas is simulated using both direct simulation Monte Carlo (DSMC) and fluctuating hydrodynamics (FHD). For the FHD simulations two models are developed for the interface based on master equation and Langevin approaches. For appropriate simulation parameters, good agreement is observed between DSMC and FHD results with the latter showing a significant advantage in computational speed. For each approach we quantify the effects of transpiration on long-ranged correlations in the hydrodynamic variables

A Staggered Scheme for the Compressible Fluctuating Hydrodynamics of Multispecies Fluid Mixtures

We present a numerical formulation for the solution of non-isothermal, compressible, Navier-Stokes equations with thermal fluctuations to describe mesoscale transport phenomena in multispecies fluid mixtures. The novelty of our numerical method is the use of staggered grid momenta along with a finite volume discretization of the thermodynamic variables to solve the resulting stochastic partial differential equations. The key advantages of the numerical scheme are significantly simplified and compact discretization of the diffusive and stochastic momentum fluxes, and an unambiguous prescription of boundary conditions involving pressure. The staggered grid scheme more accurately reproduces the equilibrium static structure factor of hydrodynamic fluctuations in gas mixtures compared to a collocated scheme described previously in Balakrishnan et al., Phys. Rev. E 89:013017, 2014. The numerical method is tested for ideal noble gases mixtures under various nonequilibrium conditions, such as applied thermal and concentration gradients, to assess the role of cross-diffusion effects, such as Soret and Dufour, on the long-ranged correlations of hydrodynamic fluctuations, which are also more accurately reproduced compared to the collocated scheme. We numerically study giant nonequilibrium fluctuations driven by concentration gradients, and fluctuation-driven Rayleigh-Taylor instability in gas mixtures. Wherever applicable, excellent agreement is observed with theory and measurements from the direct simulation Monte Carlo (DSMC) method.Comment: 20 pages, 9 figures, 9 pages supplementary materia

Keeping Pace with Changes - Towards Supporting Continuous Improvements and Extensive Updates in Manufacturing Automation Software

Every long-term used software system ages. Even though intangible goods like software do not degenerate in the proper sense, each software system degenerates in relation to the everlasting changes of requirements, usage scenarios and environmental conditions. Accordingly, operational software is commonly situated in a continuous evolution process in which manually conducted modifications and adaptations try to preserve or reinforce its quality. Unfortunately, such an unmanaged evolution inevitably leads to a discrepancy between the obsolete originally documented requirements and the updated software itself. For this reason, our contribution presents a coherent vision of an anti-aging cycle that preserves (non-)functional requirements as explicit runtime artefacts. The fulfilment of these requirements is validated based on conditionally triggered online test cases. In order to achieve an enhanced semantic test coverage, these test cases are adapted by monitoring, analysing and learning typical system behaviours. To explain our vision in more detail and demonstrate the benefit of a managed software evolution, our anti-aging cycle is exemplarily applied on the domain of manufacturing automation

Assessing the long‐term carbon‐sequestration potential of the semi‐natural salt marshes in the European Wadden Sea

Salt marshes and other blue carbon ecosystems have been increasingly recognized for their carbon (C)‐sink function. Yet, an improved assessment of organic carbon (OC) stocks and C‐sequestration rates is still required to include blue C in C‐crediting programs. Particularly, factors inducing variability in the permanence of sequestration and allochthonous contributions to soil OC stocks require an improved understanding. This study evaluates the potential for long‐term C sequestration in the semi‐natural salt marshes of the European Wadden Sea (WS), conducting deep (1.3 m) down‐core OC‐density assessments in sites with known site histories and accretion records. Because these young marshes have developed from tidal‐flat ecosystems and have undergone rapid succession during the last 80–120 yr, the identification of different ecosystem stages down‐core was crucial to interpret possible changes in OC density. This was conducted based on the down‐core distribution of different foraminiferal taxa and grain sizes. Comparisons of historic and recent accretion rates were conducted to understand possible effects of accretion rate on down‐core changes in OC density. δ13C in OC was used to assess the origin of accumulated OC (autochthonous vs. allochthonous sources). We show that large amounts of short‐term accumulated OC are lost down‐core in the well‐aerated marsh soils of the WS region and thus emphasize the importance of deep sampling to avoid overestimation of C sequestration. Despite steep declines in OC‐density down‐core, minimum values of OC density in the salt‐marsh soils were considerably higher than those of the former tidal‐flat sediments that the marshes were converted from, illustrating the greater C‐sequestration potential of the vegetated ecosystem. However, our data also suggest that marine‐derived allochthonous OC makes up a large fraction of the effectively, long‐term preserved OC stock, whereas atmospheric CO2 removal by marsh vegetation contributes relatively little. The implication of this finding for C‐crediting approaches in blue C ecosystems has yet to be clarified