Inference of the Distribution of Selection Coefficients for New Nonsynonymous Mutations Using Large Samples.

The distribution of fitness effects (DFE) has considerable importance in population genetics. To date, estimates of the DFE come from studies using a small number of individuals. Thus, estimates of the proportion of moderately to strongly deleterious new mutations may be unreliable because such variants are unlikely to be segregating in the data. Additionally, the true functional form of the DFE is unknown, and estimates of the DFE differ significantly between studies. Here we present a flexible and computationally tractable method, called Fit∂a∂i, to estimate the DFE of new mutations using the site frequency spectrum from a large number of individuals. We apply our approach to the frequency spectrum of 1300 Europeans from the Exome Sequencing Project ESP6400 data set, 1298 Danes from the LuCamp data set, and 432 Europeans from the 1000 Genomes Project to estimate the DFE of deleterious nonsynonymous mutations. We infer significantly fewer (0.38-0.84 fold) strongly deleterious mutations with selection coefficient |s| > 0.01 and more (1.24-1.43 fold) weakly deleterious mutations with selection coefficient |s| < 0.001 compared to previous estimates. Furthermore, a DFE that is a mixture distribution of a point mass at neutrality plus a gamma distribution fits better than a gamma distribution in two of the three data sets. Our results suggest that nearly neutral forces play a larger role in human evolution than previously thought

SWEEPFINDER2: Increased sensitivity, robustness, and flexibility

SweepFinder is a popular program that implements a powerful likelihood-based method for detecting recent positive selection, or selective sweeps. Here, we present SweepFinder2, an extension of SweepFinder with increased sensitivity and robustness to the confounding effects of mutation rate variation and background selection, as well as increased flexibility that enables the user to examine genomic regions in greater detail and to specify a fixed distance between test sites. Moreover, SweepFinder2 enables the use of invariant sites for sweep detection, increasing both its power and precision relative to SweepFinder

SMARTSNP, an R package for fast multivariate analyses of big genomic data

Abstract Principal component analysis (PCA) is a powerful tool for the analysis of population structure, a genetic property that is essential to understand the evolutionary processes driving biological diversification and (pre)historical colonizations, migrations and extinctions. In the current era of high‐throughput sequencing technologies, population structure can be quantified from scores of genetic markers across hundreds to thousands of genomes. However, these big genomic datasets pose substantial computing and analytical challenges. We present the r package smartsnp for fast and user‐friendly computation of PCA on single‐nucleotide polymorphism (SNP) data. Inspired by the current field‐standard software EIGENSOFT, smartsnp includes appropriate SNP scaling for genetic drift and allows projection of ancient samples onto a modern genetic space while also providing permutation‐based multivariate tests for population differences in genetic diversity (both location and dispersion). Our extensive benchmarks show that smartsnp's PCA is 2–4 times faster than EIGENSOFT's SMARTPCA algorithm across a wide range of sample and SNP sizes. All four smartsnp functions (smart_pca, smart_permanova, smart_permdisp and smart_mva) process datasets with up to 100 samples and 1 million simulated SNPs in less than 30 s and accurately recreate previously published SMARTPCA of ancient‐human and wolf genotypes. The package smartsnp provides fast and robust multivariate ordination and hypothesis testing for big genomic data that is also suitable for ancient and low‐coverage modern DNA. The simple implementation should appeal to biological conservation, evolutionary, ecological and (palaeo)genomic researchers, and be useful for phenotype, ancestry and lineage studies

Dismantling a dogma: the inflated significance of neutral genetic diversity in conservation genetics

The current rate of species extinction is rapidly approaching unprecedented highs and life on Earth presently faces a sixth mass extinction event driven by anthropogenic activity, climate change and ecological collapse. The field of conservation genetics aims at preserving species by using their levels of genetic diversity, usually measured as neutral genome-wide diversity, as a barometer for evaluating population health and extinction risk. A fundamental assumption is that higher levels of genetic diversity lead to an increase in fitness and long-term survival of a species. Here, we argue against the perceived importance of neutral genetic diversity for the conservation of wild populations and species. We demonstrate that no simple general relationship exists between neutral genetic diversity and the risk of species extinction. Instead, a better understanding of the properties of functional genetic diversity, demographic history, and ecological relationships, is necessary for developing and implementing effective conservation genetic strategies.Comment: 31 pages, 4 figures, 1 Table, 1 Bo

Mafic explosive volcanism at Llaima Volcano: 3D x-ray microtomography reconstruction of pyroclasts to constrain shallow conduit processes

Mafic volcanic activity is dominated by effusive to mildly explosive eruptions. Plinian and ignimbrite-forming mafic eruptions, while rare, are also possible; however, the conditions that promote such explosivity are still being explored. Eruption style is determined by the ability of gas to escape as magma ascends, which tends to be easier in low-viscosity, mafic magmas. If magma permeability is sufficiently high to reduce bubble overpressure during ascent, volatiles may escape from the magma, inhibiting violent explosive activity. In contrast, if the permeability is sufficiently low to retain the gas phase within the magma during ascent, bubble overpressure may drive magma fragmentation. Rapid ascent may induce disequilibrium crystallization, increasing viscosity and affecting the bubble network with consequences for permeability, and hence, explosivity. To explore the conditions that promote strongly explosive mafic volcanism, we combine microlite textural analyses with synchrotron x-ray computed microtomography of 10 pyroclasts from the 12.6 ka mafic Curacautín Ignimbrite (Llaima Volcano, Chile). We quantify microlite crystal size distributions (CSD), microlite number densities, porosity, bubble interconnectivity, bubble number density, and geometrical properties of the porous media to investigate the role of magma degassing processes at mafic explosive eruptions. We use an analytical technique to estimate permeability and tortuosity by combing the Kozeny-Carman relationship, tortuosity factor, and pyroclast vesicle textures. The groundmass of our samples is composed of up to 44% plagioclase microlites, \u3e 85% of which are \u3c 10 µm in length. In addition, we identify two populations of vesicles in our samples: (1) a convoluted interconnected vesicle network produced by extensive coalescence of smaller vesicles (\u3e 99% of pore volume), and (2) a population of very small and completely isolated vesicles (\u3c 1% of porosity). Computed permeability ranges from 3.0 × 10−13 to 6.3 × 10−12 m2, which are lower than the similarly explosive mafic eruptions of Tarawera (1886; New Zealand) and Etna (112 BC; Italy). The combination of our CSDs, microlite number densities, and 3D vesicle textures evidence rapid ascent that induced high disequilibrium conditions, promoting rapid syn-eruptive crystallization of microlites within the shallow conduit. We interpret that microlite crystallization increased viscosity while simultaneously forcing bubbles to deform as they grew together, resulting in the permeable by highly tortuous network of vesicles. Using the bubble number densities for the isolated vesicles (0.1-3−3 × 104 bubbles per mm3), we obtain a minimum average decompression rate of 1.4 MPa/s. Despite the textural evidence that the Curacautín magma reached the percolation threshold, we propose that rapid ascent suppressed outgassing and increased bubble overpressures, leading to explosive fragmentation. Further, using the porosity and permeability of our samples, we estimated that a bubble overpressure \u3e 5 MPa could have been sufficient to fragment the Curacautín magma. Other mafic explosive eruptions report similar disequilibrium conditions induced by rapid ascent rate, implying that syn-eruptive disequilibrium conditions may control the explosivity of mafic eruptions more generally

Influence of static electric fields on an optical ion trap

We recently reported on a proof-of-principle experiment demonstrating optical trapping of an ion in a single-beam dipole trap superimposed by a static electric potential [Nat. Photonics 4, 772--775 (2010)]. Here, we first discuss the experimental procedures focussing on the influence and consequences of the static electric potential. These potentials can easily prevent successful optical trapping, if their configuration is not chosen carefully. Afterwards, we analyse the dipole trap experiments with different analytic models, in which different approximations are applied. According to these models the experimental results agree with recoil heating as the relevant heating effect. In addition, a Monte-Carlo simulation has been developed to refine the analysis. It reveals a large impact of the static electric potential on the dipole trap experiments in general. While it supports the results of the analytic models for the parameters used in the experiments, the analytic models cease their validity for significantly different parameters. Finally, we propose technical improvements for future realizations of experiments with optically trapped ions.Comment: 16 pages, 16 figure

Phonon-Assisted Two-Photon Interference from Remote Quantum Emitters

Photonic quantum technologies are on the verge of finding applications in everyday life with quantum cryptography and quantum simulators on the horizon. Extensive research has been carried out to identify suitable quantum emitters and single epitaxial quantum dots have emerged as near-optimal sources of bright, on-demand, highly indistinguishable single photons and entangled photon-pairs. In order to build up quantum networks, it is essential to interface remote quantum emitters. However, this is still an outstanding challenge, as the quantum states of dissimilar “artificial atoms” have to be prepared on-demand with high fidelity and the generated photons have to be made indistinguishable in all possible degrees of freedom. Here, we overcome this major obstacle and show an unprecedented two-photon interference (visibility of 51 ± 5%) from remote strain-tunable GaAs quantum dots emitting on-demand photon-pairs. We achieve this result by exploiting for the first time the full potential of a novel phonon-assisted two-photon excitation scheme, which allows for the generation of highly indistinguishable (visibility of 71 ± 9%) entangled photon-pairs (fidelity of 90 ± 2%), enables push-button biexciton state preparation (fidelity of 80 ± 2%) and outperforms conventional resonant two-photon excitation schemes in terms of robustness against environmental decoherence. Our results mark an important milestone for the practical realization of quantum repeaters and complex multiphoton entanglement experiments involving dissimilar artificial atoms

Similarities and differences in altitudinal versus latitudinal variation for morphological traits in Drosophila melanogaster

Understanding how natural environments shape phenotypic variation is a major aim in evolutionary biology. Here, we have examined clinal, likely genetically based variation in morphology among 19 populations of the fruit fly (Drosophila melanogaster) from Africa and Europe, spanning a range from sea level to 3000 m altitude and including locations approximating the southern and northern range limit. We were interested in testing whether latitude and altitude have similar phenotypic effects, as has often been postulated. Both latitude and altitude were positively correlated with wing area, ovariole number, and cell number. In contrast, latitude and altitude had opposite effects on the ratio between ovariole number and body size, which was negatively correlated with egg production rate per ovariole. We also used transgenic manipulation to examine how increased cell number affects morphology and found that larger transgenic flies, due to a higher number of cells, had more ovarioles, larger wings, and, unlike flies from natural populations, increased wing loading. Clinal patterns in morphology are thus not a simple function of changes in body size; instead, each trait might be subject to different selection pressures. Together, our results provide compelling evidence for profound similarities as well as differences between phenotypic effects of latitude and altitude

Resonant tunneling through a C60 molecular junction in liquid environment

We present electronic transport measurements through thiolated C$_{60}$ molecules in liquid environment. The molecules were placed within a mechanically controllable break junction using a single anchoring group per molecule. When varying the electrode separation of the C$_{60}$-modified junctions, we observed a peak in the conductance traces. The shape of the curves is strongly influenced by the environment of the junction as shown by measurements in two distinct solvents. In the framework of a simple resonant tunneling model, we can extract the electronic tunneling rates governing the transport properties of the junctions.Comment: 13 pages, 4 figures. To appear in Nanotechnolog

Influence of CT Image Matrix Size and Kernel Type on the Assessment of HRCT in Patients with SSC-ILD

BACKGROUND Interstitial lung disease (ILD) is a frequent complication of systemic sclerosis (SSc), and its early detection and treatment may prevent deterioration of lung function. Different vendors have recently made larger image matrices available as a post-processing option for computed tomography (CT), which could facilitate the diagnosis of SSc-ILD. Therefore, the objective of this study was to assess the effect of matrix size on lung image quality in patients with SSc by comparing a 1024-pixel matrix to a standard 512-pixel matrix and applying different reconstruction kernels. METHODS Lung scans of 50 patients (mean age 54 years, range 23-85 years) with SSc were reconstructed with these two different matrix sizes, after determining the most appropriate kernel in a first step. Four observers scored the images on a five-point Likert scale regarding image quality and detectability of clinically relevant findings. RESULTS Among the eight tested kernels, the Br59-kernel (sharp) reached the highest score (19.48 ± 3.99), although differences did not reach statistical significance. The 1024-pixel matrix scored higher than the 512-pixel matrix HRCT overall (p = 0.01) and in the subcategories sharpness (p < 0.01), depiction of bronchiole (p < 0.01) and overall image impression (p < 0.01), and lower for the detection of ground-glass opacities (GGO) (p = 0.04). No significant differences were found for detection of extent of reticulations/bronchiectasis/fibrosis (p = 0.50) and image noise (p = 0.09). CONCLUSIONS Our results show that with the use of a sharp kernel, the 1024-pixel matrix HRCT, provides a slightly better subjective image quality in terms of assessing interstitial lung changes, whereby GGO are more visible on the 512-pixel matrix. However, it remains to be answered to what extent this is related to the improved representation of the smallest structures