scholarly journals Molecular Clock and Phylogeny ofAnophelesspecies of the subgenusNyssorhynchus(Diptera: Culicidae)

2018 ◽  
Author(s):  
Richard Hoyos-López
Keyword(s):  
Molecular Markers ◽  
Molecular Clock ◽  
Phylogenetic Hypothesis ◽  
Bayesian Approaches ◽  
Natural Group ◽  
Phylogenetic Studies ◽  
The Times

AbstractThe main Phylogenetic hypothesis supporting the Myzorhynchella section as a natural group, but the sections Albimanus and Argyritarsis, do not present clearly resolved relationships, nor is it possible to recover the monophyly of both sections, even within these sections ofNyssorhynchus; it has not been possible identify the relationships between the species that make up these taxonomic subdivisions (Sallum, 2000, Sallum, 2002, Bourke, 2011, Foster, 2013). This lack of resolution has been attributed to the effect of few species for phylogenetic studies, making difficult the determination of monophyly of many groups, subgroups and complexes within sections Albimanus and ArgyritarsisWe infer the phylogeny of the subgenusNyssorhynchusthrough the sequences characterized for the molecular markers ND6, COI-Barcode, White and CAD, in addition we calculate the times of divergence for the main lineages corresponding to the sections Albimanus, Argyritarsis and Myzorhynchella using Bayesian approaches.

scholarly journals Optimal markers for the identification ofColletotrichumspecies

2019 ◽  
Author(s):  
Willie Anderson dos Santos Vieira ◽  
Priscila Alves Bezerra ◽  
Anthony Carlos da Silva ◽  
Josiene Silva Veloso ◽  
Marcos Paz Saraiva Câmara ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Species Complex ◽  
Plant Pathogens ◽  
Phylogenetic Signal ◽  
Intergenic Spacer ◽  
Internal Transcribed Spacers ◽  
Type Locus ◽  
Phylogenetic Studies ◽  
Fungal Plant Pathogens ◽  
Species Complexes

ABSTRACTColletotrichumis among the most important genera of fungal plant pathogens. Molecular phylogenetic studies over the last decade have resulted in a much better understanding of the evolutionary relationships and species boundaries within the genus. There are now approximately 200 species accepted, most of which are distributed among 13 species complexes. Given their prominence on agricultural crops around the world, rapid identification of a large collection ofColletotrichumisolates is routinely needed by plant pathologists, regulatory officials, and fungal biologists. However, there is no agreement on the best molecular markers to discriminate species in each species complex. Here we calculate the barcode gap distance and intra/inter-specific distance overlap to evaluate each of the most commonly applied molecular markers for their utility as a barcode for species identification. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), histone-3 (HIS3), DNA lyase (APN2), intergenic spacer between DNA lyase and the mating-type locusMAT1-2-1 (APN2/MAT-IGS), and intergenic spacer between GAPDH and a hypothetical protein (GAP2-IGS) have the properties of good barcodes, whereas sequences of actin (ACT), chitin synthase (CHS-1) and nuclear rDNA internal transcribed spacers (nrITS) are not able to distinguish most species. Finally, we assessed the utility of these markers for phylogenetic studies using phylogenetic informativeness profiling, the genealogical sorting index (GSI), and Bayesian concordance analyses (BCA). Although GAPDH, HIS3 and β-tubulin (TUB2) were frequently among the best markers, there was not a single set of markers that were best for all species complexes. Eliminating markers with low phylogenetic signal tends to decrease uncertainty in the topology, regardless of species complex, and leads to a larger proportion of markers that support each lineage in the Bayesian concordance analyses. Finally, we reconstruct the phylogeny of each species complex using a minimal set of phylogenetic markers with the strongest phylogenetic signal and find the majority of species are strongly supported as monophyletic.

Positional information and pattern regulation in Hydra. Dynamics of regions at the boundary

Development ◽  
1975 ◽  
Vol 33 (2) ◽  
pp. 499-510
Author(s):  
J. Hicklin ◽  
A. Hornbruch ◽  
L. Wolpert
Keyword(s):  
Positional Information ◽  
Boundary Region ◽  
The Times ◽  
Pattern Regulation ◽  
Cut Surface

The dynamics of boundary regions have been investigated mainly by axial grafting and with the emphasis on the head end. The time to lesist inhibition of head-end formation and the ability to inhibit head-end formation have been assayed under a variety of conditions. The times increase with distance from the head end. The times required by a boundary region to acquire the inhibitory properties of a head end are longer than those required to acquire resistance to inhibition. Determination of a head end is faster at a cut surface and at higher temperatures. The results are discussed in terms of a model involving two gradients. Some anomalous results are reported.

scholarly journals psbE-psbL and ndhA Intron, the Promising Plastid DNA Barcode of Fagopyrum

2019 ◽  
Vol 20 (14) ◽  
pp. 3455 ◽  
Author(s):  
Yue Huang ◽  
Zhiqiang Li ◽  
Chenglong Wang ◽  
Chenyan Zou ◽  
Wen Wen ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Phylogenetic Relationship ◽  
Dna Barcode ◽  
Plastid Dna ◽  
Food Material ◽  
Wild Buckwheat ◽  
Phylogenetic Studies ◽  
Related Wild Species ◽  
The Relationship ◽  
Species Hybridization

Buckwheat is an important functional food material with high nutritional value. However, it is still a difficult task for the taxonomy studies of wild buckwheat that are only based on morphology. In order to demonstrate the most efficient DNA barcode in the phylogenetic research of buckwheat, promote the investigation of wild buckwheat, and also reveal the phylogenetic relationship between Fagopyrum species, psbE-psbL and ndhA intron were validated here, which previously have been proved to be promising DNA barcode candidates for phylogenetic studies in genera Fagopyrum. Meanwhile, ndhA intron + psbE-psbL and matK + psbE-psbL could distinguish the relationship between species clearly. Combining the results of morphology and molecular markers, we suggested the buckwheat species should be divided into two subgroups, one subgroup consisted of F. tataricum, F. esculentum, F. cymosum and its related wild species, and the other subgroup included other wild buckwheat species. Our results could fulfill molecular markers of taxonomy research in genera Fagopyrum, promote wild buckwheat species identification, and assist in the use of wild buckwheat resources in the future. Additionally, the phylogenetic relationship revealed here could provide valuable information for molecular breeding of buckwheat and provide reference for inter-species hybridization.

IX. Contributions to terrestrial magnetism.—No. IV

1843 ◽  
Vol 133 ◽  
pp. 113-143 ◽  
Keyword(s):  
Pacific Ocean ◽  
West Coast ◽  
China Seas ◽  
North West ◽  
The North ◽  
The Pacific ◽  
The Pacific Ocean ◽  
The Times ◽  
The China Seas

In the present number of these Contributions, I resume the consideration of Captain Sir Edward Belcher’s magnetic observations, of which the first portion, viz. that of the stations on the north-west coast of America and adjacent islands, was discussed in No. II. The return to England of Her Majesty’s ship Sulphur by the route of the Pacific Ocean, and her detention for some months in the China Seas, have enabled Sir Edward Belcher to add magnetic determinations at thirty-two stations to those at the twenty-nine stations previously recorded. In the notice of the earlier observations, a provisional coefficient was employed in the formula for the temperature corrections of the results with the intensity needles, as no experiments had then been made for the determination of their individual co­efficients. As soon therefore as Sir Edward Belcher had completed the observation of the times of vibration of those needles at Woolwich, as the concluding station of the series made with them, Lieut. Riddell, R. A. undertook the determination of their several coefficients, which was performed in the manner and with the results described in the subjoined memorandum.

Phylogenetic studies of Saprolegniomycetidae and related groups based on nuclear large subunit ribosomal DNA sequences

2000 ◽  
Vol 77 (12) ◽  
pp. 1790-1800 ◽  
Author(s):  
Alexandra Riethmüller ◽  
Michael Weiß ◽  
Franz Oberwinkler
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Bootstrap Method ◽  
Large Subunit ◽  
Phytophthora Megasperma ◽  
Parsimony Method ◽  
Natural Group ◽  
Maximum Parsimony Method ◽  
Phylogenetic Studies ◽  
Main Emphasis

To reveal phylogenetic relationships within the Peronosporomycetes (Oomycetes), we sequenced a part of the nuclear rDNA coding for the ribosomal large subunit of 46 Peronosporomycetes species and one representative of the Xanthophyta. The main emphasis of our study was put on the phylogenetic relationships within the Saprolegniomycetidae. We supplemented our data with a sequence of Phytophthora megasperma Drechsler from GenBank. Two sets of sequences were analysed using the neighbor-joining method, statistically supported by the bootstrap method, as well as the maximum parsimony method. Our results are well compatible with the tripartite subclassification of the Peronosporomycetes into Saprolegniomycetidae, Rhipidiomycetidae and Peronosporomycetidae, as well as with the placement of the orders Saprolegniales and Leptomitales in the Saprolegniomycetidae. Pachymetra chaunorhiza Croft & Dick, which has been placed in the Sclerosporales, was grouped within the Saprolegniales. Within the Peronosporomycetidae, the orders Peronosporales and Pythiales could not be separated. There are indications that Phytophthora de Bary and the Peronosporales form a common natural group. The genus Achlya Nees proved to be a heterogeneous group.

scholarly journals Drying of green bean and okra under solar energy

2011 ◽  
Vol 17 (2) ◽  
pp. 199-205 ◽  
Author(s):  
İbrahim Doymaz
Keyword(s):  
Green Bean ◽  
Chi Square ◽  
Sun Drying ◽  
Constant Rate ◽  
Thin Layer Drying ◽  
Rate Period ◽  
Drying Models ◽  
Drying Curves ◽  
The Times

In this study, sun drying behaviours of green bean and okra were investigated. Drying experiments were conducted in Iskenderun-Hatay, Turkey. The drying study showed that the times taken for drying of green bean and okra from the initial moisture contents of 89.5% and 88.7% (w.b.) to final moisture content of around 15?0.5% (w.b.) were 60 and 100 h in open sun drying, respectively. The constant rate period is absent in drying curves. The drying process took place in the falling rate period. The drying data were fitted to thirteen thin-layer drying models. The performance of these models was investigated by comparing the determination of coefficient (R2), reduced chi-square (c2) and root mean square error (RMSE) between the observed and predicted moisture ratios. Estimations by Approximation of diffusion (for green bean) and Midilli et al. models (for okra) were in good agreement with the experimental data obtained.

scholarly journals CPT-Based Probabilistic Characterization of Undrained Shear Strength of Clay

2020 ◽  
Vol 2020 ◽  
pp. 1-15
Author(s):  
Mi Tian ◽  
Xiaotao Sheng
Keyword(s):  
Shear Strength ◽  
Correlation Function ◽  
Random Field ◽  
Site Investigation ◽  
Undrained Shear Strength ◽  
Bayesian Approaches ◽  
Probabilistic Characterization ◽  
Undrained Shear

Applying random field theory involves two important issues: the statistical homogeneity (or stationarity) and determination of random field parameters and correlation function. However, the profiles of soil properties are typically assumed to be statistically homogeneous or stationary without rigorous statistical verification. It is also a challenging task to simultaneously determine random field parameters and the correlation function due to a limited amount of direct test data and various uncertainties (e.g., transformation uncertainties) arising during site investigation. This paper presents Bayesian approaches for probabilistic characterization of undrained shear strength using cone penetration test (CPT) data and prior information. Homogeneous soil units are first identified using CPT data and subsequently assessed for weak stationarity by the modified Bartlett test to reject the null hypothesis of stationarity. Then, Bayesian approaches are developed to determine the random field parameters and simultaneously select the most probable correlation function among a pool of candidate correlation functions within the identified statistically homogeneous layers. The proposed approaches are illustrated using CPT data at a clay site in Shanghai, China. It is shown that Bayesian approaches provide a rational tool for proper determination of random field model for probabilistic characterization of undrained shear strength with consideration of transformation uncertainty.

scholarly journals Phylogenomic Reconstruction Sheds Light on New Relationships and Timescale of Rails (Aves: Rallidae) Evolution

Diversity ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 70 ◽  
Author(s):  
Juan C. Garcia-R ◽  
Emily Moriarty Lemmon ◽  
Alan R. Lemmon ◽  
Nigel French
Keyword(s):  
Evolutionary History ◽  
State Of The Art ◽  
Molecular Techniques ◽  
Evolutionary Significance ◽  
Phylogenetic Structure ◽  
Bayesian Approaches ◽  
Phylogenetic Studies ◽  
Anchored Phylogenomics ◽  
History Of ◽  
Phylogenomic Analyses

The integration of state-of-the-art molecular techniques and analyses, together with a broad taxonomic sampling, can provide new insights into bird interrelationships and divergence. Despite their evolutionary significance, the relationships among several rail lineages remain unresolved as does the general timescale of rail evolution. Here, we disentangle the deep phylogenetic structure of rails using anchored phylogenomics. We analysed a set of 393 loci from 63 species, representing approximately 40% of the extant familial diversity. Our phylogenomic analyses reconstruct the phylogeny of rails and robustly infer several previously contentious relationships. Concatenated maximum likelihood and coalescent species-tree approaches recover identical topologies with strong node support. The results are concordant with previous phylogenetic studies using small DNA datasets, but they also supply an additional resolution. Our dating analysis provides contrasting divergence times using fossils and Bayesian and non-Bayesian approaches. Our study refines the evolutionary history of rails, offering a foundation for future evolutionary studies of birds.

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