Increased gene sampling strengthens support for higher-level groups within leaf-mining moths and relatives (Lepidoptera: Gracillariidae)

Background: Researchers conducting molecular phylogenetic studies are frequently faced with the decision of what to do when weak branch support is obtained for key nodes of importance. As one solution, the researcher may choose to sequence additional orthologous genes of appropriate evolutionary rate for the taxa in the study. However, generating large, complete data matrices can become increasingly difficult as the number of characters increases. A few empirical studies have shown that augmenting genes even for a subset of taxa can improve branch support. However, because each study differs in the number of characters and taxa, there is still a need for additional studies that examine whether incomplete sampling designs are likely to aid at increasing deep node resolution. We target Gracillariidae, a Cretaceous-age (similar to 100 Ma) group of leaf-mining moths to test whether the strategy of adding genes for a subset of taxa can improve branch support for deep nodes. We initially sequenced ten genes (8,418 bp) for 57 taxa that represent the major lineages of Gracillariidae plus outgroups. After finding that many deep divergences remained weakly supported, we sequenced eleven additional genes (6,375 bp) for a 27-taxon subset. We then compared results from different data sets to assess whether one sampling design can be favored over another. The concatenated data set comprising all genes and all taxa and three other data sets of different taxon and gene sub-sampling design were analyzed with maximum likelihood. Each data set was subject to five different models and partitioning schemes of non-synonymous and synonymous changes. Statistical significance of non-monophyly was examined with the Approximately Unbiased (AU) test. Results: Partial augmentation of genes led to high support for deep divergences, especially when non-synonymous changes were analyzed alone. Increasing the number of taxa without an increase in number of characters led to lower bootstrap support; increasing the number of characters without increasing the number of taxa generally increased bootstrap support. More than three-quarters of nodes were supported with bootstrap values greater than 80% when all taxa and genes were combined. Gracillariidae, Lithocolletinae + Leucanthiza, and Acrocercops and Parectopa groups were strongly supported in nearly every analysis. Gracillaria group was well supported in some analyses, but less so in others. We find strong evidence for the exclusion of Douglasiidae from Gracillarioidea sensu Davis and Robinson (1998). Our results strongly support the monophyly of a G.B.R.Y. clade, a group comprised of Gracillariidae + Bucculatricidae + Roeslerstammiidae + Yponomeutidae, when analyzed with non-synonymous changes only, but this group was frequently split when synonymous and non-synonymous substitutions were analyzed together. Conclusions: 1) Partially or fully augmenting a data set with more characters increased bootstrap support for particular deep nodes, and this increase was dramatic when non-synonymous changes were analyzed alone. Thus, the addition of sites that have low levels of saturation and compositional heterogeneity can greatly improve results. 2) Gracillarioidea, as defined by Davis and Robinson (1998), clearly do not include Douglasiidae, and changes to current classification will be required. 3) Gracillariidae were monophyletic in all analyses conducted, and nearly all species can be placed into one of six strongly supported clades though relationships among these remain unclear. 4) The difficulty in determining the phylogenetic placement of Bucculatricidae is probably attributable to compositional heterogeneity at the third codon position. From our tests for compositional heterogeneity and strong bootstrap values obtained when synonymous changes are excluded, we tentatively conclude that Bucculatricidae is closely related to Gracillariidae + Roeslerstammiidae + Yponomeutidae

The effect of variable turbulent intensities on the distribution of zooplankton in the shallow, large Lake Balaton (Hungary)

The influence of current velocity on zooplankton organisms is manifold. Moderate current velocity is beneficial for zooplankton, but through various mechanisms too high a current velocity can have detrimental effects. We examined how current velocity acts on zooplankton in Lake Balaton at different levels and found a highly significant, negative relation between current velocity and the density of zooplankton assemblages. Of the studied assemblages, Daphnia galeata  ×  cucullata and Eudiaptomus gracilis exhibited the greatest sensitivity to the degree of current velocity. During calm weather, when the water surface was calm too, nocturnal migration was observed for both Daphnia galeata  ×  cucullata and Eudiaptomus gracilis. We demonstrated that the vertical migration of these two species started before the storm as the usual nocturnal migration, but during the storm the regular pattern was confused

Integrated effects of nitrogen form, row spacing, and herbicide treatment on maize

To control weeds and cultivate maize (Zea mays L.) with higher yields, production systems have to include more efficient forms of N and appropriate herbicide treatments. The timing of N release could give maize an advantage over weeds in competition for resources, whereas cultivation at lower row spacing often decreases weed biomass. Knowledge about the different factors affecting herbicide efficiency increases the accuracy and reliability of chemical control. This study tested the weed infestation level and the development and productivity of a recently developed maize hybrid grown with the application of several integrated practices. The maize hybrid was sown with application of standard and slow-releasing urea, with row spacing of 50 and 70 cm and treatment with either a pre-emergence or a post-emergence mix of herbicides. The numbers of plants of each weed species and their biomass were lower after the application of herbicides, although N form and row spacing produced no significant differences in the average weed infestation level for 3 yr. The post-emergence herbicide treatment was more effective than the pre-emergence treatment for weed biomass reduction and enhancing maize yield parameters. The N form did not influence any measured yield parameter, whereas the 70-cm row spacing resulted in significantly higher harvest index and grain yield (0.45 and 9.19 Mg ha(-1), respectively) than the 50-cm spacing (0.43 and 7.36 Mg ha(-1), respectively). The wider row spacing resulted in higher grain yield through its interaction with N form and herbicide treatment

Double matrix effect in Low Energy Ion Scattering from La surfaces

Low Energy Ion Scattering (LEIS) has been performed on several lanthanum-based surfaces. Strong subsurface matrix effects – dependence of surface scattered He+ ion yield on the composition of subsurface layer – have been observed. The ion yield of He+ scattered by La differed by a factor of up to 2.5 for different surfaces, while only the La peak was visible in the spectra. To study these effects and enable surface quantification, He+ ion yields have been measured in a range of incident He+ energies from 1000 to 7500 eV for LaB6, La2O3, oxidized La and pure La surfaces. The investigation showed that as many as two simultaneous matrix effects are present, each one driven by a separate charge exchange mechanism. The first one is a resonant neutralization from the conduction band of La to an excited state of the He+ ion. It depends on the work function of the surface, which is lowered significantly when La interacts with O or B. The second mechanism is quasiresonant charge transfer between bound La levels and He 1s, which creates characteristic oscillations in the energy dependence of ion yields. The exact structure of the oscillations depends on small changes in binding energies of interacting La levels. This is the first time quasiresonant charge transfer is proven to be present in La. It is likely that La 5p orbitals participate in this resonance, which can be the first clear observation of a resonance between p and s orbitals in LEIS. This type of resonance was previously believed to be absent because of strong damping. We also demonstrated that despite the complex matrix effect precise measurements over a wide energy range allow quantification of the atomic composition of La-based surfaces