The efficiency of different search strategies in estimating parsimony jackknife, bootstrap, and Bremer support

BACKGROUND: For parsimony analyses, the most common way to estimate confidence is by resampling plans (nonparametric bootstrap, jackknife), and Bremer support (Decay indices). The recent literature reveals that parameter settings that are quite commonly employed are not those that are recommended by theoretical considerations and by previous empirical studies. The optimal search strategy to be applied during resampling was previously addressed solely via standard search strategies available in PAUP*. The question of a compromise between search extensiveness and improved support accuracy for Bremer support received even less attention. A set of experiments was conducted on different datasets to find an empirical cut-off point at which increased search extensiveness does not significantly change Bremer support and jackknife or bootstrap proportions any more. RESULTS: For the number of replicates needed for accurate estimates of support in resampling plans, a diagram is provided that helps to address the question whether apparently different support values really differ significantly. It is shown that the use of random addition cycles and parsimony ratchet iterations during bootstrapping does not translate into higher support, nor does any extension of the search extensiveness beyond the rather moderate effort of TBR (tree bisection and reconnection branch swapping) plus saving one tree per replicate. Instead, in case of very large matrices, saving more than one shortest tree per iteration and using a strict consensus tree of these yields decreased support compared to saving only one tree. This can be interpreted as a small risk of overestimating support but should be more than compensated by other factors that counteract an enhanced type I error. With regard to Bremer support, a rule of thumb can be derived stating that not much is gained relative to the surplus computational effort when searches are extended beyond 20 ratchet iterations per constrained node, at least not for datasets that fall within the size range found in the current literature. CONCLUSION: In view of these results, calculating bootstrap or jackknife proportions with narrow confidence intervals even for very large datasets can be achieved with less expense than often thought. In particular, iterated bootstrap methods that aim at reducing statistical bias inherent to these proportions are more feasible when the individual bootstrap searches require less time

Increased vegetative development and sturdiness of storekeeper-transgenic tobacco

The STOREKEEPER (STK) family of DNA-binding proteins work as transcription factors and the ectopic expression of two stk-like genes from Arabidopsis thaliana, stk01 (At1g61730) and stk03 (At4g00238), in tobacco increased the number of vegetative internodes and promoted plant and leaf size, stem diameter and sturdiness. The development of these plants started with rosette formation while pronounced shoot elongation and flowering was delayed. Moreover, when the STK01 and STK03 proteins were fused to the Herpes Simplex Virus VP16 transcriptional activation domain and expressed in tobacco the vigorous storekeeper-phenotype did not appear indicating that transgenic STK-like proteins in part worked as repressors of tobacco reproductive development. Furthermore, Yeast Two-Hybrid screenings proved that STK01 and STK03 can form homodimers and heterodimers with further members of the STKlike family. Therefore, we assume that interactions between transgenic Arabidopsis STKs and resident tobacco STKs could have contributed to the observed developmental changes in transgenic tobacco. Our findings open up promising applications for overexpression of stk-like genes in crops that benefit from increased sturdiness and vegetative organ development, such as tobacco in molecular farming approaches, biomass-based energy crops and medicinal plants that produce bioactive compounds in leaves

Noticing and weighing alternatives in the reflection of regular classroom teaching: Evidence of expertise using mobile eye-tracking

Instructional videos are widely used to study teachers’ professional vision. A new technological development in video research is mobile eye-tracking (MET). It has the potential to provide fine-grained insights into teachers’ professional vision in action, but has yet been scarcely employed. We addressed this research gap by using MET video feedback to examine how expert and novice teachers differed in their noticing and weighing of alternative teaching strategies. Expert and novice teachers’ lessons were recorded with MET devices. Then, they commented on what they observe while watching their own teaching videos. Using a mixed methods approach, we found that expert and novice teachers did not differ in the number of classroom events they noticed and alternative teaching strategies they mentioned. However, novice teachers were more critical of their own teaching than expert teachers, particularly when they considered alternative teaching strategies. Practical implications for the field of teacher education are discussed

Noticing and weighing alternatives in the reflection of regular classroom teaching: Evidence of expertise using mobile eye-tracking

Instructional videos are widely used to study teachers’ professional vision. A new technological development in video research is mobile eye-tracking (MET). It has the potential to provide fine-grained insights into teachers’ professional vision in action, but has yet been scarcely employed. We addressed this research gap by using MET video feedback to examine how expert and novice teachers differed in their noticing and weighing of alternative teaching strategies. Expert and novice teachers’ lessons were recorded with MET devices. Then, they commented on what they observe while watching their own teaching videos. Using a mixed methods approach, we found that expert and novice teachers did not differ in the number of classroom events they noticed and alternative teaching strategies they mentioned. However, novice teachers were more critical of their own teaching than expert teachers, particularly when they considered alternative teaching strategies. Practical implications for the field of teacher education are discussed. © 2021, The Author(s)

Sample data processing in an additive and reproducible taxonomic workflow by using character data persistently linked to preserved individual specimens

We present the model and implementation of a workflow that blazes a trail in systematic biology for the re-usability of character data (data on any kind of characters of pheno- and genotypes of organisms) and their additivity from specimen to taxon level. We take into account that any taxon characterization is based on a limited set of sampled individuals and characters, and that consequently any new individual and any new character may affect the recognition of biological entities and/or the subsequent delimitation and characterization of a taxon. Taxon concepts thus frequently change during the knowledge generation process in systematic biology. Structured character data are therefore not only needed for the knowledge generation process but also for easily adapting characterizations of taxa. We aim to facilitate the construction and reproducibility of taxon characterizations from structured character data of changing sample sets by establishing a stable and unambiguous association between each sampled individual and the data processed from it. Our workflow implementation uses the European Distributed Institute of Taxonomy Platform, a comprehensive taxonomic data management and publication environment to: (i) establish a reproducible connection between sampled individuals and all samples derived from them; (ii) stably link sample-based character data with the metadata of the respective samples; (iii) record and store structured specimen-based character data in formats allowing data exchange; (iv) reversibly assign sample metadata and character datasets to taxa in an editable classification and display them and (v) organize data exchange via standard exchange formats and enable the link between the character datasets and samples in research collections, ensuring high visibility and instant re-usability of the data. The workflow implemented will contribute to organizing the interface between phylogenetic analysis and revisionary taxonomic or monographic work

Suppression of Heavy Ion gamma gamma Production of the Higgs by Coulomb Dissociation

Predicted two-photon Higgs production with heavy ions at LHC is shown to be reduced due to the large Coulomb dissociation cross section. Incorporating the effect of dissociation reduces the production of a 100 GeV Higgs by about a factor of three compared to rates in the literature calculated without this effect.Comment: 5 pages, latex, revtex source, two postscript figure

Towards resolving Lamiales relationships: insights from rapidly evolving chloroplast sequences

<p>Abstract</p> <p>Background</p> <p>In the large angiosperm order Lamiales, a diverse array of highly specialized life strategies such as carnivory, parasitism, epiphytism, and desiccation tolerance occur, and some lineages possess drastically accelerated DNA substitutional rates or miniaturized genomes. However, understanding the evolution of these phenomena in the order, and clarifying borders of and relationships among lamialean families, has been hindered by largely unresolved trees in the past.</p> <p>Results</p> <p>Our analysis of the rapidly evolving <it>trnK/matK</it>, <it>trnL-F </it>and <it>rps16 </it>chloroplast regions enabled us to infer more precise phylogenetic hypotheses for the Lamiales. Relationships among the nine first-branching families in the Lamiales tree are now resolved with very strong support. Subsequent to Plocospermataceae, a clade consisting of Carlemanniaceae plus Oleaceae branches, followed by Tetrachondraceae and a newly inferred clade composed of Gesneriaceae plus Calceolariaceae, which is also supported by morphological characters. Plantaginaceae (incl. Gratioleae) and Scrophulariaceae are well separated in the backbone grade; Lamiaceae and Verbenaceae appear in distant clades, while the recently described Linderniaceae are confirmed to be monophyletic and in an isolated position.</p> <p>Conclusions</p> <p>Confidence about deep nodes of the Lamiales tree is an important step towards understanding the evolutionary diversification of a major clade of flowering plants. The degree of resolution obtained here now provides a first opportunity to discuss the evolution of morphological and biochemical traits in Lamiales. The multiple independent evolution of the carnivorous syndrome, once in Lentibulariaceae and a second time in Byblidaceae, is strongly supported by all analyses and topological tests. The evolution of selected morphological characters such as flower symmetry is discussed. The addition of further sequence data from introns and spacers holds promise to eventually obtain a fully resolved plastid tree of Lamiales.</p

Chasing the hare - Evaluating the phylogenetic utility of a nuclear single copy gene region at and below species level within the species rich group Peperomia (Piperaceae)

Background: The rapidly increasing number of available plant genomes opens up almost unlimited prospects for biology in general and molecular phylogenetics in particular. A recent study took advantage of this data and identified a set of nuclear genes that occur in single copy in multiple sequenced angiosperms. The present study is the first to apply genomic sequence of one of these low copy genes, agt1, as a phylogenetic marker for species-level phylogenetics. Its utility is compared to the performance of several coding and non-coding chloroplast loci that have been suggested as most applicable for this taxonomic level. As a model group, we chose Tildenia, a subgenus of Peperomia (Piperaceae), one of the largest plant genera. Relationships are particularly difficult to resolve within these species rich groups due to low levels of polymorphisms and fast or recent radiation. Therefore, Tildenia is a perfect test case for applying new phylogenetic tools. Results: We show that the nuclear marker agt1, and in particular the agt1 introns, provide a significantly increased phylogenetic signal compared to chloroplast markers commonly used for low level phylogenetics. 25% of aligned characters from agt1 intron sequence are parsimony informative. In comparison, the introns and spacer of several common chloroplast markers (trnK intron, trnK-psbA spacer, ndhF-rpl32 spacer, rpl32-trnL spacer, psbA-trnH spacer) provide less than 10% parsimony informative characters. The agt1 dataset provides a deeper resolution than the chloroplast markers in Tildenia. Conclusions: Single (or very low) copy nuclear genes are of immense value in plant phylogenetics. Compared to other nuclear genes that are members of gene families of all sizes, lab effort, such as cloning, can be kept to a minimum. They also provide regions with different phylogenetic content deriving from coding and non-coding parts of different length. Thus, they can be applied to a wide range of taxonomic levels from family down to population level. As more plant genomes are sequenced, we will obtain increasingly precise information about which genes return to single copy most rapidly following gene duplication and may be most useful across a wide range of plant groups

Accelerated physical emulation of Bayesian inference in spiking neural networks

The massively parallel nature of biological information processing plays an important role for its superiority to human-engineered computing devices. In particular, it may hold the key to overcoming the von Neumann bottleneck that limits contemporary computer architectures. Physical-model neuromorphic devices seek to replicate not only this inherent parallelism, but also aspects of its microscopic dynamics in analog circuits emulating neurons and synapses. However, these machines require network models that are not only adept at solving particular tasks, but that can also cope with the inherent imperfections of analog substrates. We present a spiking network model that performs Bayesian inference through sampling on the BrainScaleS neuromorphic platform, where we use it for generative and discriminative computations on visual data. By illustrating its functionality on this platform, we implicitly demonstrate its robustness to various substrate-specific distortive effects, as well as its accelerated capability for computation. These results showcase the advantages of brain-inspired physical computation and provide important building blocks for large-scale neuromorphic applications.Comment: This preprint has been published 2019 November 14. Please cite as: Kungl A. F. et al. (2019) Accelerated Physical Emulation of Bayesian Inference in Spiking Neural Networks. Front. Neurosci. 13:1201. doi: 10.3389/fnins.2019.0120

Article Fast Track Disproportional Plastome-Wide Increase of Substitution Rates and Relaxed Purifying Selection in Genes of Carnivorous Lentibulariaceae

Abstract Carnivorous Lentibulariaceae exhibit the most sophisticated implementation of the carnivorous syndrome in plants. Their unusual lifestyle coincides with distinct genomic peculiarities such as the smallest angiosperm nuclear genomes and extremely high nucleotide substitution rates across all genomic compartments. Here, we report the complete plastid genomes from each of the three genera Pinguicula, Utricularia, and Genlisea, and investigate plastome-wide changes in their molecular evolution as the carnivorous syndrome unfolds. We observe a size reduction by up to 9% mostly due to the independent loss of genes for the plastid NAD(P)H dehydrogenase and altered proportions of plastid repeat DNA, as well as a significant plastome-wide increase of substitution rates and microstructural changes. Protein-coding genes across all gene classes show a disproportional elevation of nonsynonymous substitutions, particularly in Utricularia and Genlisea. Significant relaxation of purifying selection relative to noncarnivores occurs in the plastid-encoded fraction of the photosynthesis ATP synthase complex, the photosystem I, and in several other photosynthesis and metabolic genes. Shifts in selective regimes also affect housekeeping genes including the plastid-encoded polymerase, for which evidence for relaxed purifying selection was found once during the transition to carnivory, and a second time during the diversification of the family. Lentibulariaceae significantly exhibit enhanced rates of nucleotide substitution in most of the 130 noncoding regions. Various factors may underlie the observed patterns of relaxation of purifying selection and substitution rate increases, such as reduced net photosynthesis rates, alternative paths of nutrient uptake (including organic carbon), and impaired DNA repair mechanisms