Phenotypic divergence but not genetic distance predicts assortative mating among species of a cichlid fish radiation

The hypothesis of ecological divergence giving rise to premating isolation in the face of gene flow is controversial. However, this may be an important mechanism to explain the rapid multiplication of species during adaptive radiation following the colonization of a new environment when geographical barriers to gene flow are largely absent but underutilized niche space is abundant. Using cichlid fish, we tested the prediction of ecological speciation that the strength of premating isolation among species is predicted by phenotypic rather than genetic distance. We conducted mate choice experiments between three closely related, sympatric species of a recent radiation in Lake Mweru (Zambia/DRC) that differ in habitat use and phenotype, and a distantly related population from Lake Bangweulu that resembles one of the species in Lake Mweru. We found significant assortative mating among all closely related, sympatric species that differed phenotypically, but none between the distantly related allopatric populations of more similar phenotype. Phenotypic distance between species was a good predictor of the strength of premating isolation, suggesting that assortative mating can evolve rapidly in association with ecological divergence during adaptive radiation. Our data also reveals that distantly related allopatric populations that have not diverged phenotypically, may hybridize when coming into secondary contact, e.g. upon river capture because of diversion of drainage systems.

Driving the refactoring of Java Enterprise applications by evaluating the distance between application elements

Java Enterprise Applications (JEAs) are complex systems composed using various technologies that in turn rely on languages other than Java, such as XML or SQL. Given the complexity of these applications, the need to reverse engineer them in order to support further development becomes critical. In this paper we show how it is possible to split a system into layers and how is possible to interpret the distance between application elements in order to support the refactoring of JEAs. The purpose of this paper is to explore ways to provide suggestions about the refactoring operations to perform on the code by evaluating the distance between layers and elements belonging those layers. We split JEAs into layers by considering the kinds and the purposes of the elements composing the application. We measure distance between elements by using the notion of the shortest path in a graph. Also we present how to enrich the interpretation of the distance value with enterprise pattern detection in order to refine the suggestion about modifications to perform on the code.

Distance-based kriging relying on proxy simulations for inverse conditioning

Let us consider a large set of candidate parameter fields, such as hydraulic conductivity maps, on which we can run an accurate forward flow and transport simulation. We address the issue of rapidly identifying a subset of candidates whose response best match a reference response curve. In order to keep the number of calls to the accurate flow simulator computationally tractable, a recent distance-based approach relying on fast proxy simulations is revisited, and turned into a non-stationary kriging method where the covariance kernel is obtained by combining a classical kernel with the proxy. Once the accurate simulator has been run for an initial subset of parameter fields and a kriging metamodel has been inferred, the predictive distributions of misfits for the remaining parameter fields can be used as a guide to select candidate parameter fields in a sequential way. The proposed algorithm, Proxy-based Kriging for Sequential Inversion (ProKSI), relies on a variant of the Expected Improvement, a popular criterion for kriging-based global optimization. A statistical benchmark of ProKSI’s performances illustrates the efficiency and the robustness of the approach when using different kinds of proxies.

Transport of 234U in the Opalinus Clay on centimetre to decimetre scales

The Opalinus Clay formation in North Switzerland is a potential host rock for a deep underground radioactive waste repository. The distribution of U-238, U-234 and Th-230 was studied in rock samples of the Opalinus Clay from an exploratory borehole at Benken (Canton of Zurich) using MC-ICP-MS. The aim of U-234 was to assess the in situ, long-term migration behaviour in this rock. Very low hydraulic conductivities of the Opalinus Clay, reducing potential of the pore water and its chemical equilibrium with the host rock are expected to render both U-238 and Th-230 immobile. If U is heterogeneously distributed in the Opalinus Clay, gradients in the supply of U-234 from the rock matrix to the pore water by the decay of U-238 will be established. Diffusive redistribution separates U-234 from its immobile parent U-238 resulting in bulk rock U-234/U-238 activity disequilibria. These may provide a means of estimating the mobility of U-234 in the rock if the diffusion rate of U-234 is significant compared to its decay rate. Sampling was carried out on two scales. Drilling of cm-spaced samples from the drill-core was done to study mobility over short distances and elucidate possible small-scale lithological control. Homogenized 25-cm-long portions of a 2-m-long drill-core section were prepared to provide information on transport over a longer distance. Variations in U and/or Th content on the cm-scale between clays and carbonate-sandy layers are revealed by beta-scanning, which shows that the (dominant) clay is richer in both elements. Samples were digested using aqua regia followed by total HF dissolution, yielding two fractions. in all studied samples U was found to be concentrated in the HF digestion fraction. It has a high U/Th ratio and a study by SEM-EDS points to sub-mu m up to several mu m in size zircon grains as the main U-rich phase. This fraction consistently has U-234/U-238 activity ratios below unity. The minute zircon grains constitute the major reservoir of U in the rock and act as constant rate suppliers of U-234 into the rock matrix and the pore water. The aqua regia leach fraction was found to be enriched in Th, and complementary to the HF fraction, having U-234/U-238 activity ratios above unity. It is believed that these U activity ratios reflect the surplus of having U-234 delivered from the zircon grains. Some cm-spaced samples show bulk rock U-234/U-238 activity ratios that are markedly out of equilibrium. In most of them a striking negative correlation between the total U content and the bulk rock U-234/U-238 activity ratios is observed. This is interpreted to indicate net U-234 transfer from regions of higher supply of U-234 towards those of lower supply which is, in most cases, equivalent to transfer from clayey towards carbonate/sandy portions of the rock. In contrast, the 25 cm averaged samples all have uniform bulk rock U-234/U-238 activity ratios in equilibrium, indicating U immobility in the last 1-1.5 Ma on this spatial scale. It is concluded that the small-scale lithological variations which govern U spatial distribution in the Opalinus Clay are the major factor determining U-234 in situ supply rates, regulating its diffusive fluxes and controlling the observed bulk rock U-234/U-238 activity ratios. A simple box-model is presented to simulate the measured bulk rock U-234/U-238 activity ratios and to give an additional insight into the studied system. (C) 2008 Elsevier Ltd. All rights reserved.

Probing interactions of NMD factors in a distance‐dependent manner by BioID

The understanding of molecular mechanisms requires the elucidation of protein-­‐protein interaction in vivo. For large multi-­‐factor complexes like those assembling on mRNA, co-­‐immunoprecipitation assays often identify many peripheral interactors that complicate the interpretation of such results and that might conceal other insightful mechanistic connections. Here we address the protein-­‐protein interaction network for key factors in the nonsense-­‐mediated mRNA decay (NMD) pathway in a distant-­‐dependent manner using BioID1,2. In this novel approach, the mutant E. coli biotin-­‐protein ligase BirAR118G is fused to the bait protein and biotinylates proximal proteins promiscuously. Hence, interactors positioned close to the bait in vivo are enriched by streptavidin purification and identified by mass spectrometry or western blotting. We present a validation of the BioID assay and preliminary results for close interactors of UPF1 and other key players in NMD.

Long-distance photogrammetric trait estimation in free-ranging animals: A new approach

The acquisition of accurate information on the size of traits in animals is fundamental for the study of animal ecology and evolution and their management. We demonstrate how morphological traits of free-ranging animals can reliably be estimated on very large observation distances of several hundred meters by the use of ordinary digital photographic equipment and simple photogrammetric software. In our study, we estimated the length of horn annuli in free-ranging male Alpine ibex (Capra ibex) by taking already measured horn annuli of conspecifics on the same photographs as scaling units. Comparisons with hand-measured horn annuli lengths and repeatability analyses revealed a high accuracy of the photogrammetric estimates. If length estimations of specific horn annuli are based on multiple photographs measurement errors of <5.5 mm can be expected. In the current study the application of the described photogrammetric procedure increased the sample size of animals with known horn annuli length by an additional 104%. The presented photogrammetric procedure is of broad applicability and represents an easy, robust and cost-efficient method for the measuring of individuals in populations where animals are hard to capture or to approach.