Stochastic search variable selection based on two mixture components and continuous‐scale weighting

Stochastic search variable selection (SSVS) is a Bayesian variable selection method that employs covariate‐specific discrete indicator variables to select which covariates (e.g., molecular markers) are included in or excluded from the model. We present a new variant of SSVS where, instead of discrete indicator variables, we use continuous‐scale weighting variables (which take also values between zero and one) to select covariates into the model. The improved model performance is shown and compared to standard SSVS using simulated and real quantitative trait locus mapping datasets. The decision making to decide phenotype‐genotype associations in our SSVS variant is based on median of posterior distribution or using Bayes factors. We also show here that by using continuous‐scale weighting variables it is possible to improve mixing properties of Markov chain Monte Carlo sampling substantially compared to standard SSVS. Also, the separation of association signals and nonsignals (control of noise level) seems to be more efficient compared to the standard SSVS. Thus, the novel method provides efficient new framework for SSVS analysis that additionally provides whole posterior distribution for pseudo‐indicators which means more information and may help in decision making.     

Phylogeography of lethal male fighting in a social spider mite

When males fight for access to females, such conflict rarely escalates into lethal fight because the risks and costs involved, that is, severe injury or death, are too high. The social spider mite, Stigmaeopsis miscanthi, does exhibit lethal male fights, and this male–male aggressiveness varies among populations. To understand the evolution of lethal fighting, we investigated aggressiveness in 42 populations and phylogenetic relationships in 47 populations along the Japanese archipelago. By analysis of the male weapon morph, a proxy for aggressiveness, we confirmed the existence of a mildly aggressive (ML) form, besides the low aggression (LW) and high aggression (HG) forms reported earlier. To evaluate demographic history of these three forms, we employed the approximate Bayesian computation approach using mtCOI sequences and taking into consideration the postlast glacial expansion history of the host plant, Miscanthus sinensis. As results, hierarchical split models are more likely to explain the observed genetic pattern than admixture models, and the ML form in the subtropical region was considered the ancestral group. The inferred demographic history was consistent with the one reconstructed for the host plant in a previous study. The LW form was split from the ML form during the last glacial period (20,000–40,000 years BP), and subsequently, the HG form was split from the ML form at the end of or after the last glacial period (5,494–10,988 years BP). The results also suggest that the mite invaded Japan more than once, resulting in the present parapatric distribution of LW and HG forms in eastern Japan.     

Flow‐injection chemiluminescence method for the determination of chloramphenicol based on luminol–sodium periodate order‐transform second‐chemiluminescence reaction

A new chemiluminescence (CL) reaction was observed when chloramphenicol solution was injected into the mixture after the end of the reaction of alkaline luminol and sodium periodate or sodium periodate was injected into the reaction mixture of chloramphenicol and alkaline luminol. This reaction is described as an order‐transform second‐chemiluminescence (OTSCL) reaction. The OTSCL method combined with a flow‐injection technique was applied to the determination of chloramphenicol. The optimum conditions for the order‐transform second‐chemiluminescence emission were investigated. A mechanism for OTSCL has been proposed on the basis of the chemiluminescence kinetic characteristics, the UV‐visible spectra and the chemiluminescent spectra. Under optimal experimental conditions, the CL response is proportional to the concentration of chloramphenicol over the range 5.0 × 10^?7–5.0 × 10^?5 mol/L with a correlation coefficient of 0.9969 and a detection limit of 6.0 × 10^?8 mol/L (3σ). The relative standard deviation (RSD) for 11 repeated determinations of 5.0 × 10^?6 mol/L chloramphenicol is 1.7%. The method has been applied to the determination of chloramphenicol in pharmaceutical samples with satisfactory results. Copyright © 2011 John Wiley & Sons, Ltd.     

Climate change alters plant biogeography in Mediterranean prairies along the West Coast,USA

Projected changes in climate are expected to have widespread effects on plant community composition and diversity in coming decades. However, multisite, multifactor climate manipulation studies that have examined whether observed responses are regionally consistent and whether multiple climate perturbations are interdependent are rare. Using such an experiment, we quantified how warming and increased precipitation intensity affect the relative dominance of plant functional groups and diversity across a broad climate gradient of Mediterranean prairies. We implemented a fully factorial climate manipulation of warming (+2.5–3.0 °C) and increased wet‐season precipitation (+20%) at three sites across a 520‐km latitudinal gradient in the Pacific Northwest, USA. After seeding with a nearly identical mix of native species at all sites, we measured plant community composition (i.e., cover, richness, and diversity), temperature, and soil moisture for 3 years. Warming and the resultant drying of soils altered plant community composition, decreased native diversity, and increased total cover, with warmed northern communities becoming more similar to communities further south. In particular, after two full years of warming, annual cover increased and forb cover decreased at all sites mirroring the natural biogeographic pattern. This suggests that the extant climate gradient of increasing heat and drought severity is responsible for a large part of the observed biogeographic pattern of increasing annual invasion in US West Coast prairies as one moves further south. Additional precipitation during the rainy season did little to relieve drought stress and had minimal effects on plant community composition. Our results suggest that the projected increase in drought severity (i.e., hotter, drier summers) in Pacific Northwest prairies may lead to increased invasion by annuals and a loss of forbs, similar to what has been observed in central and southern California, resulting in novel species assemblages and shifts in functional composition, which in turn may alter ecosystem functions.     

Otolith shape lends support to the sensory drive hypothesis in rockfishes

The sensory drive hypothesis proposes that environmental factors affect both signalling dynamics and the evolution of signals and receivers. Sound detection and equilibrium in marine fishes are senses dependent on the sagittae otoliths, whose morphological variability appears intrinsically linked to the environment. The aim of this study was to understand if and which environmental factors could be conditioning the evolution of this sensory structure, therefore lending support to the sensory drive hypothesis. Thus, we analysed the otolith shape of 42 rockfish species (Sebastes spp.) to test the potential associations with the phylogeny, biological (age), ecological (feeding habit and depth distribution) and biogeographical factors. The results showed strong differences in the otolith shapes of some species, noticeably influenced by ecological and biogeographical factors. Moreover, otolith shape was clearly conditioned by phylogeny, but with a strong environmental effect, cautioning about the use of this structure for the systematics of rockfishes or other marine fishes. However, our most relevant finding is that the data supported the sensory drive hypothesis as a force promoting the radiation of the genus Sebastes. This hypothesis holds that adaptive divergence in communication has significant influence relative to other life history traits. It has already been established in Sebastes for visual characters and organs; our results showed that it applies to otolith transformations as well (despite the clear influence of feeding and depth), expanding the scope of the hypothesis to other sensory structures.     

Begomoviruses Infecting Tomato Crops in Panama

The key regions in Panama involved in open field‐ and greenhouse‐grown commercial tomato production, including the Chiriquí, Veraguas, Herrera, Los Santos, Coclé and Panama Oeste provinces, were surveyed for the incidence and distribution of begomoviruses in the growing seasons of 2011 and 2012. The surveys took place in 14 of the 51 districts of the above‐mentioned provinces and comprised all relevant tomato production areas of the provinces. A total of 28 tomato plots were surveyed. The exact location of each plot was geo‐referenced using a hand‐held Global Positioning System unit. In total, 319 individual tomato plants (181 in 2011 and 138 in 2012) were sampled. Plants displayed diverse combinations of virus‐like symptoms of different severity, including necrosis, yellowing, mosaic, mottling, rolling, curling, distortion and puckering of leaves, reduced leaf size, and stunted growth. DNA was extracted from each plant for a subsequent polymerase chain reaction (PCR) analysis, using two sets of degenerate primers able to detect members of the genus Begomovirus. The samples displaying a positive reaction were subsequently analysed with specific primer pairs to identify the affecting begomoviruses. A total of 42.3% of all collected samples showed a positive signal to PCRs. Three begomovirus species were detected with the species‐specific set of primers; in particular, in the samples obtained in 2011, Potato yellow mosaic Panama virus (PYMPV), Tomato leaf curl Sinaloa virus (ToLCSiV) and Tomato yellow mottle virus (TYMoV) were detected, while in the 2012 samples, only PYMPV and ToLCSiV were found. To our knowledge, this is the first reported incidence of ToLCSiV and TYMoV in Panamanian tomato crops.     

Square‐Centimeter‐Sized High‐Efficiency Polymer Solar Cells: How the Processing Atmosphere and Film Quality Influence Performance at Large Scale

Organic solar cells based on two benzodithiophene‐based polymers (PTB7 and PTB7‐Th) processed at square centimeter‐size under inert atmosphere and ambient air, respectively, are investigated. It is demonstrated that the performance of solar cells processed under inert atmosphere is not limited by the upscaling of photoactive layer and the interfacial layers. Thorough morphological and electrical characterizations of optimized layers and corresponding devices reveal that performance losses due to area enlargement are only caused by the sheet resistance of the transparent electrode reducing the efficiency from 9.3% of 7.8% for PTB7‐Th in the condition that both photoactive layer and the interfacial layers are of high layer quality. Air processing of photoactive layer and the interfacial layers into centimeter‐sized solar cells lead to additional, but only slight, losses (<10%) in all photovoltaic parameters, which can be addressed to changes in the electronic properties of both active layer and ZnO layers rather than changes in layer morphology. The demonstrated compatibility of polymer solar cells using solution‐processed photoactive layer and interfacial layers with large area indicates that the introduction of a standard active area of 1 cm² for measuring efficiency of organic record solar cells is feasible. However electric standards for indium tin oxides (ITO) or alternative transparent electrodes need to be developed so that performance of new photovoltaic materials can be compared at square centimeter‐size.     

MOLECULAR CHARACTERIZATION OF AUTOPHAGY‐RELATED GENE 5 FROM Spodoptera exigua AND EXPRESSION ANALYSIS UNDER VARIOUS STRESS CONDITIONS

Autophagy is not only involved in development, but also has been proved to attend immune response against invading pathogens. Autophagy protein 5 (ATG5) is an important autophagic protein, which plays a crucial role in autophagosome elongation. Although ATG5 has been well studied in mammal, yeast, and Drosophila, little is known about ATG5 in lepidopteran insects. We cloned putative SeAtg5 gene from Spodoptera exigua larvae by the rapid amplification of cDNA ends method, and its characteristics and the influences of multiple exogenous factors on its expression levels were then investigated. The results showed that the putative S. exigua SeATG5 protein is highly homologous to other insect ATG5 proteins, which has a conserved Pfm domain and multiple phosphorylation sites. Next, fluorescence microscope observation showed that mCherry‐SeATG5 was distributed in both nucleus and cytoplasm of Spodoptera litura Sl‐HP cells and partially co‐localized with BmATG6‐GFP, but it almost has no significant co‐localization with GFP‐HaATG8. Then, the Western blot analysis demonstrated that GFP‐SeATG5 conjugated with ATG12. Moreover, real‐time PCR revealed that its expression levels significantly increased at the initiation of pupation and the stage of adult. In addition, the expression levels of SeAtg5 can be enhanced by the starvation, UV radiation, and infection of baculovirus and bacterium. However, the expression levels of SeAtg5 decreased at 24 h post treatments in all these treatments except in starvation. These results suggested that SeATG5 might be involved in response of S. exigua under various stress conditions.