Correlated patterns of genetic diversity and differentiation across an avian family

Comparative studies of closely related taxa can provide insights into the evolutionary forces that shape genome evolution and the prevalence of convergent molecular evolution. We investigated patterns of genetic diversity and differentiation in stonechats (genus Saxicola), a widely distributed avian species complex with phenotypic variation in plumage, morphology, and migratory behavior, to ask whether similar genomic regions have become differentiated in independent, but closely related, taxa. We used whole-genome pooled sequencing of 262 individuals from 5 taxa and found that levels of genetic diversity and divergence are strongly correlated among different stonechat taxa. We then asked if these patterns remain correlated at deeper evolutionary scales and found that homologous genomic regions have become differentiated in stonechats and the closely related Ficedula flycatchers. Such correlation across a range of evolutionary divergence and among phylogenetically independent comparisons suggests that similar processes may be driving the differentiation of these independently evolving lineages, which in turn may be the result of intrinsic properties of particular genomic regions (e.g., areas of low recombination). Consequently, studies employing genome scans to search for areas important for reproductive isolation or adaptation should account for corresponding regions of differentiation, as these regions may not necessarily represent speciation islands or evidence of local adaptation

The evolutionary history and genomics of European blackcap migration

Seasonal migration is a taxonomically widespread behaviour that integrates across many traits. The European blackcap exhibits enormous variation in migration and is renowned for research on its evolution and genetic basis. We assembled a reference genome for blackcaps and obtained whole genome resequencing data from individuals across its breeding range. Analyses of population structure and demography suggested divergence began ~30,000 ya, with evidence for one admixture event between migrant and resident continent birds ~5000 ya. The propensity to migrate, orientation and distance of migration all map to a small number of genomic regions that do not overlap with results from other species, suggesting that there are multiple ways to generate variation in migration. Strongly associated single nucleotide polymorphisms (SNPs) were located in regulatory regions of candidate genes that may serve as major regulators of the migratory syndrome. Evidence for selection on shared variation was documented, providing a mechanism by which rapid changes may evolve

Analysis of the iron coatings formed during marcasite and arsenopyrite oxidation at neutral-alkaline conditions

In order to study the nature of the precipitates formed on arsenopyrite and marcasite after reacting with neutral to alkaline solutions, a combination of techniques including Scanning Electron Microscope-Energy Dispersive Spectroscopy (SEM-EDS), X-ray Photoelectron Spectroscopy (XPS) and synchrotron-based techniques such as micro-X-Ray diffraction (µXRD) and Micro-X-ray Absorption Near Edge Structure (µXANES) have been used. The results showed that the oxidation of marcasite and arsenopyrite under neutral to alkaline conditions leads to the formation of an Fe rich coating which seems to prevent the oxidation of these sulphides. SEM observations confirmed the presence newly-formed phases after the sulphides reaction under the studied conditions. XPS analysis showed that iron, sulphur and arsenic in the case of the arsenopyrite are in oxidized states in the sulphide surfaces. The microscale analysis of the S and Fe speciation performed by µXANES suggested that due to the sulphide oxidation an increase in the oxidation state of those elements took place together with an increase of the sulphate content in the surface layer (grain boundary). Micro-X-ray diffraction results indicated that goethite (a-FeOOH) is the only crystalline newly-formed phase when the reaction occurs at pH 12 whereas at lower pH the products formed on the sulphide surfaces seem to be poorly crystalline and they do not contribute to the diffraction effects in the XRD diagrams

A Transfer Hamiltonian Model for Devices Based on Quantum Dot Arrays

We present a model of electron transport through a random distribution of interacting quantum dots embedded in a dielectric matrix to simulate realistic devices. The method underlying the model depends only on fundamental parameters of the system and it is based on the Transfer Hamiltonian approach. A set of noncoherent rate equations can be written and the interaction between the quantum dots and between the quantum dots and the electrodes is introduced by transition rates and capacitive couplings. A realistic modelization of the capacitive couplings, the transmission coefficients, the electron/hole tunneling currents, and the density of states of each quantum dot have been taken into account. The effects of the local potential are computed within the self-consistent field regime. While the description of the theoretical framework is kept as general as possible, two specific prototypical devices, an arbitrary array of quantum dots embedded in a matrix insulator and a transistor device based on quantum dots, are used to illustrate the kind of unique insight that numerical simulations based on the theory are able to provide

A Transfer Hamiltonian Model for Devices Based on Quantum Dot Arrays

We present a model of electron transport through a random distribution of interacting quantum dots embedded in a dielectric matrix to simulate realistic devices. The method underlying the model depends only on fundamental parameters of the system and it is based on the Transfer Hamiltonian approach. A set of noncoherent rate equations can be written and the interaction between the quantum dots and between the quantum dots and the electrodes is introduced by transition rates and capacitive couplings. A realistic modelization of the capacitive couplings, the transmission coefficients, the electron/hole tunneling currents, and the density of states of each quantum dot have been taken into account. The effects of the local potential are computed within the selfconsistent field regime. While the description of the theoretical framework is kept as general as possible, two specific prototypical devices, an arbitrary array of quantum dots embedded in a matrix insulator and a transistor device based on quantum dots, are used to illustrate the kind of unique insight that numerical simulations based on the theory are able to provide

Effect of cold plasma on polyphenol oxidase inactivation in cloudy apple juice and on the quality parameters of the juice during storage

Direct cold plasma treatment has been investigated as an alternative non-thermal technology as a means of maintaining and improving quality of fresh cloudy apple juice. Process variables studied included type of plasma discharge, input voltage and treatment time on polyphenol oxidase (PPO) inactivation. Spark discharge plasma at 10.5 kV for 5 min was the best treatment, with near total inactivation of PPO achieved, although good PPO inactivation was also recorded using shorter treatment times. Residual activity (RA) of PPO was 16 and 27.6% after 5 and 4 min of treatment respectively. This PPO inactivation was maintained throughout the storage trials, but decreased with samples treated for a shorter time. Plasma treatment improved key quality parameters of Golden delicious cloudy apple juice, with retention of critical quality parameters during extended storage trials. Color was the most noticeable change, which was enhanced with retention of a greener color. An increase of 69 and 64% was obtained in the total phenolic content after 4 and 5 min of treatment, respectively. Therefore, cold plasma was demonstrated to be a good alternative to traditional heat treatments for enhanced quality retention of fresh cloudy apple juice and over its storage.Spanish Government (MINECO) and the European Regional Development Fund (ERDF) [Project CTQ2015-64396-R] and in part by a research grant from Science Foundation Ireland (SFI) under the Grant Number SFI/16/BBSRC/3391 and the BBSRC under the Grant Reference BB/P008496/