So many genes, so little time: A practical approach to divergence-time estimation in the genomic era

Phylogenomic datasets have been successfully used to address questions involving evolutionary relationships, patterns of genome structure, signatures of selection, and gene and genome duplications. However, despite the recent explosion in genomic and transcriptomic data, the utility of these data sources for efficient divergence-time inference remains unexamined. Phylogenomic datasets pose two distinct problems for divergence-time estimation: (i) the volume of data makes inference of the entire dataset intractable, and (ii) the extent of underlying topological and rate heterogeneity across genes makes model mis-specification a real concern. “Gene shopping”, wherein a phylogenomic dataset is winnowed to a set of genes with desirable properties, represents an alternative approach that holds promise in alleviating these issues. We implemented an approach for phylogenomic datasets (available in SortaDate) that filters genes by three criteria: (i) clock-likeness, (ii) reasonable tree length (i.e., discernible information content), and (iii) least topological conflict with a focal species tree (presumed to have already been inferred). Such a winnowing procedure ensures that errors associated with model (both clock and topology) mis-specification are minimized, therefore reducing error in divergence-time estimation. We demonstrated the efficacy of this approach through simulation and applied it to published animal (Aves, Diplopoda, and Hymenoptera) and plant (carnivorous Caryophyllales, broad Caryophyllales, and Vitales) phylogenomic datasets. By quantifying rate heterogeneity across both genes and lineages we found that every empirical dataset examined included genes with clock-like, or nearly clock-like, behavior. Moreover, many datasets had genes that were clock-like, exhibited reasonable evolutionary rates, and were mostly compatible with the species tree. We identified overlap in age estimates when analyzing these filtered genes under strict clock and uncorrelated lognormal (UCLN) models. However, this overlap was often due to imprecise estimates from the UCLN model. We find that “gene shopping” can be an efficient approach to divergence-time inference for phylogenomic datasets that may otherwise be characterized by extensive gene tree heterogeneity

Radar studies of the vertical distribution of insects migrating over southern Britain: the influence of temperature inversions on nocturnal layer concentrations

Insects migrating over two sites in southern UK (Malvern in Worcestershire, and Harpenden in Hertfordshire) have been monitored continuously with nutating vertical-looking radars (VLRs) equipped with powerful control and analysis software. These observations make possible, for the first time, a systematic investigation of the vertical distribution of insect aerial density in the atmosphere, over temporal scales ranging from the short (instantaneous vertical profiles updated every 15 min) to the very long (profiles aggregated over whole seasons or even years). In the present paper, an outline is given of some general features of insect stratification as revealed by the radars, followed by a description of occasions during warm nights in the summer months when intense insect layers developed. Some of these nocturnal layers were due to the insects flying preferentially at the top of strong surface temperature inversions, and in other cases, layering was associated with higher-altitude temperature maxima, such as those due to subsidence inversions. The layers were formed from insects of a great variety of sizes, but peaks in the mass distributions pointed to a preponderance of medium-sized noctuid moths on certain occasions

Current-voltage characteristic of parallel-plane ionization chamber with inhomogeneous ionization

The balances of particles and charges in the volume of parallel-plane ionization chamber are considered. Differential equations describing the distribution of current densities in the chamber volume are obtained. As a result of the differential equations solution an analytical form of the current-voltage characteristic of parallel-plane ionization chamber with inhomogeneous ionization in the volume is got.Comment: 8 pages, 4 figure

Quantum dot emission from site-controlled ngan/gan micropyramid arrays

InxGa1−xN quantum dots have been fabricated by the selective growth of GaN micropyramid arrays topped with InGaN/GaN quantum wells. The spatially, spectrally, and time-resolved emission properties of these structures were measured using cathodoluminescence hyperspectral imaging and low-temperature microphotoluminescence spectroscopy. The presence of InGaN quantum dots was confirmed directly by the observation of sharp peaks in the emission spectrum at the pyramid apices. These luminescence peaks exhibit decay lifetimes of approximately 0.5 ns, with linewidths down to 650 me

Effect of physical heterogeneity on the electromigration of nitrate in layered granular porous media

The effect of physical heterogeneity on the electrokinetic (EK) transport of nitrate, an electron acceptor frequently used for anaerobic biodegradation, was investigated experimentally within saturated granular porous media comprising two layers of high and low hydraulic conductivity (K) material. Two hypotheses were tested: firstly, that the presence of layered physical heterogeneity will generate non-uniformities in the electric field; and secondly that this would create non-uniform electromigration of ions resulting in an additional nitrate flux into the lower-K layer. Experiments were conducted in bench-top test cells that contained electrode and sediment chambers. An aqueous nitrate solution (0, 0.1, 1 and 5 g-NO3 L−1) was added at the cathode and the experiments run with an idealised mixture of glass beads and kaolinite, and natural sediment and kaolinite. A constant current (1.6 A m−2) was applied in all experiments. Results showed elevated voltage differences between layers in heterogeneous experiments compared to equivalent homogenous experiments. Furthermore, nitrate concentrations are elevated in the low-K material in heterogeneous compared with homogeneous systems. Using predicted values this is shown to be a function of a transverse flux associated with the voltage difference between layers. The importance of this phenomena at field scale for delivery of an amendment (i.e., electron acceptor, donor or nutrient) by EK for bioremediation is presented in an electron balance model. Overall, this research establishes and quantifies a previously unreported important phenomenon in the electrokinetic transport literature that enhance the application of this technology for bioremediation of contaminated aquifers

Physiological suitability of six West African gramineous borers (Lepidoptera: Noctuidae, Pyralidae) for development of Cotesia species complex (Hymenoptera: Braconidae)

Three gregarious, endoparasitic braconids, a Kenyan strain of Cotesia sesamiae, and the exotic Cotesia flavipes and Cotesia chilonis were imported into Benin as candidates for biological control of stem- and cob borers of maize and stemborers of millet. Host acceptability and host suitability of six gramineous borers occurring in western Africa, the noctuids Sesamia calamistis, Sesamia poephaga, Busseola fusca, the crambid Coniesta ignefusalis, and the pyralids Eldana saccharina and Mussidia nigrivenella, to these parasitoids were evaluated to test the hypothesis that new associations were superior over old association parasitoid-host relationships. All hosts were accepted by all Cotesia spp., except M. nigrivenella, which was not attacked by C. chilonis. Parasitoid progeny developed successfully in S. calamistis, S. poephaga and C. ignefusalis. S. calamistis was the most suitable host in terms of duration of developmental time, brood size and mortality of parasitoid progeny. It was concluded that because of its host specificity, the old association parasitoid C. sesamiae would have the highest chance of establishment in cereal systems in West Afric

Premature mortality in refractory partial epilepsy: does surgical treatment make a difference?

Background: Epilepsy carries an increased risk of premature death. For some people with intractable focal epilepsy, surgery offers hope for a seizure-free life. The authors aimed to see whether epilepsy surgery influenced mortality in people with intractable epilepsy. Methods: The authors audited survival status in two cohorts (those who had surgery and those who had presurgical assessment but did not have surgery). Results: There were 40 known deaths in the non-surgical group (3365 person years of follow-up) and 19 in the surgical group (3905 person-years of follow-up). Non-operated patients were 2.4 times (95% CI 1.4 to 4.2) as likely to die as those who had surgery. They were 4.5 times (95% CI 1.9 to 10.9) as likely to die a probable epilepsy-related death. In the surgical group, those with ongoing seizures 1 year after surgery were 4.0 (95% CI 1.2 to 13.7) times as likely to die as those who were seizure-free or who had only simple partial seizures. Time-dependent Cox analysis showed that the yearly outcome group did not significantly affect mortality (HR 1.3, 95% CI 0.9 to 1.8). Conclusion: Successful epilepsy surgery was associated with a reduced risk of premature mortality, compared with those with refractory focal epilepsy who did not have surgical treatment. To some extent, the reduced mortality is likely to be conferred by inducing freedom from seizures. It is not certain whether better survival is attributable only to surgery, as treatment decisions were not randomised, and there may be inherent differences between the groups.<br/

Elastic and Mechanical Properties of Human Dentin

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/67340/2/10.1177_00220345580370041801.pd