scholarly journals Detecting destabilizing species in the phylogenetic backbone of Potentilla (Rosaceae) using low-copy nuclear markers

AoB Plants ◽  
2020 ◽  
Vol 12 (3) ◽  
Author(s):  
Nannie L Persson ◽  
Ingrid Toresen ◽  
Heidi Lie Andersen ◽  
Jenny E E Smedmark ◽  
Torsten Eriksson
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Data Sets ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Nuclear Markers ◽  
Data Set ◽  
Multispecies Coalescent ◽  
Single Marker ◽  
Named Groups

Abstract The genus Potentilla (Rosaceae) has been subjected to several phylogenetic studies, but resolving its evolutionary history has proven challenging. Previous analyses recovered six, informally named, groups: the Argentea, Ivesioid, Fragarioides, Reptans, Alba and Anserina clades, but the relationships among some of these clades differ between data sets. The Reptans clade, which includes the type species of Potentilla, has been noticed to shift position between plastid and nuclear ribosomal data sets. We studied this incongruence by analysing four low-copy nuclear markers, in addition to chloroplast and nuclear ribosomal data, with a set of Bayesian phylogenetic and Multispecies Coalescent (MSC) analyses. A selective taxon removal strategy demonstrated that the included representatives from the Fragarioides clade, P. dickinsii and P. fragarioides, were the main sources of the instability seen in the trees. The Fragarioides species showed different relationships in each gene tree, and were only supported as a monophyletic group in a single marker when the Reptans clade was excluded from the analysis. The incongruences could not be explained by allopolyploidy, but rather by homoploid hybridization, incomplete lineage sorting or taxon sampling effects. When P. dickinsii and P. fragarioides were removed from the data set, a fully resolved, supported backbone phylogeny of Potentilla was obtained in the MSC analysis. Additionally, indications of autopolyploid origins of the Reptans and Ivesioid clades were discovered in the low-copy gene trees.

scholarly journals IMPAct: A Holistic Framework for Mixed Reality Robotic User Interface Classification and Design

2019 ◽  
Vol 3 (2) ◽  
pp. 25
Author(s):  
Dennis Krupke ◽  
Jianwei Zhang ◽  
Frank Steinicke
Keyword(s):  
User Interfaces ◽  
Mixed Reality ◽  
Scientific Literature ◽  
Card Sorting ◽  
Precise Description ◽  
Scientific Publications ◽  
System Description ◽  
Technical Factors ◽  
Effective Use ◽  
Named Groups

The number of scientific publications combining robotic user interfaces and mixed reality highly increased during the 21st Century. Counting the number of yearly added publications containing the keywords “mixed reality” and “robot” listed on Google Scholar indicates exponential growth. The interdisciplinary nature of mixed reality robotic user interfaces (MRRUI) makes them very interesting and powerful, but also very challenging to design and analyze. Many single aspects have already been successfully provided with theoretical structure, but to the best of our knowledge, there is no contribution combining everything into an MRRUI taxonomy. In this article, we present the results of an extensive investigation of relevant aspects from prominent classifications and taxonomies in the scientific literature. During a card sorting experiment with professionals from the field of human–computer interaction, these aspects were clustered into named groups for providing a new structure. Further categorization of these groups into four different categories was obvious and revealed a memorable structure. Thus, this article provides a framework of objective, technical factors, which finds its application in a precise description of MRRUIs. An example shows the effective use of the proposed framework for precise system description, therefore contributing to a better understanding, design, and comparison of MRRUIs in this growing field of research.

scholarly journals The social class of the Baptist: Dissident retainer or peasant millennialist?

2004 ◽  
Vol 60 (1/2) ◽  
Author(s):  
Johan Strijdom
Keyword(s):  
Social Class ◽  
Social Ethics ◽  
Lower Class ◽  
Status Quo ◽  
The Other ◽  
Upper Class ◽  
The Social ◽  
Psalms Of Solomon ◽  
The One ◽  
Named Groups

In this article the Baptist is compared with the upper-class/literate millennialists behind the Psalms of Solomon, the Testament of Moses, the Similitudes of 1 Enoch, and the Qumran scrolls on the one hand, and with the lower-class/illiterate millennialist movements in Josephus on the other hand. The argument is developed in constant dialogue with the analyses of John Dominic Crossan. After an initial statement of historical facts about the Baptist, these are compared with the named groups in terms of each one’s (1) criticism of the social-political and religious status quo, (2) depiction of the imagined mediator through whom God was expected to intervene, (3) portrayal of the violent/non-violent intervention of God and the group respectively, and (4) social ethics. It is concluded that John shows closer resemblance to the literate than illiterate millennialists, and should therefore rather be considered as a dissident retainer.

scholarly journals V.—Some Observations on the Zoantharia Rugosa

1866 ◽  
Vol 3 (26) ◽  
pp. 356-362 ◽  
Author(s):  
Gustave Lindström
Keyword(s):  
North America ◽  
The Other ◽  
Vesicular Structure ◽  
The Common ◽  
Named Groups

Professor Steenstrup, some years ago, questioned the fact as to whether the Zoantharia tabulata and rugosa, included by him under the common name of “Cyathophylla,” might be considered as true polyps. MM. Edwards and Haime in framing those great subdivisions of their “Coralliaria,” remarked their striking dissimilarity from the other Actinozoa. Professor Agassiz, in his grand monograph on the Acalephæ of North America, considers these differences so important that henceforth all connection between the above-named groups and the Zoantharia aporosa and perforata will be impossible. But besides these peculiar characteristics of the Rugosa, such, for instance, as the compact imperforate structure of the calyx and septa (the septa originating from four primary ones), the absence of costæ, the strange septal fossæ in the bottom of the calyx, the processes resembling rootlets, the transverse floors or tabulæ in the interior, which often have a cellular or vesicular structure; there is another peculiarity as yet not much known.

Reshaping fecal gut microbiota composition by growing with Polygonum cuspidatum, Houttuynia cordata, and Ipomoea aquatica

2019 ◽  
Vol 65 (7) ◽  
pp. 522-529 ◽  
Author(s):  
Yao Zheng ◽  
Gengdong Hu ◽  
Wei Wu ◽  
Liping Qiu ◽  
Dandan Li ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Pathogenic Bacteria ◽  
Medicinal Herbs ◽  
Chinese Medicinal Herbs ◽  
Polygonum Cuspidatum ◽  
Houttuynia Cordata ◽  
Ipomoea Aquatica ◽  
Houttuynia Cordata Thunb ◽  
Named Groups ◽  
Group D

We carried out sequencing of samples cultivated in floating beds with different Chinese medicinal herbs (Control, Houttuynia cordata Thunb., Polygonum cuspidatum, and a combination of H. cordata with Ipomoea aquatica Forssk.; named groups A, B, C, D, respectively) to analyze changes in the composition of gut microbiota of tilapia feces. Fusobacteria (ranging from 49.0% to 73.3%), Firmicutes (12.3%–37.8%), and Proteobacteria (5.1%–23.0%) were found to be the most dominant phyla present in all samples. The operational taxonomic units and the Ace and Chao1 indices of groups A and D were significantly higher than those of group C. Polygonum cuspidatum decreased the species richness and diversity of microbial communities in tilapia intestinal feces. The phylum WCHB1-60, order Enterobacteriales, and genus Plesiomonas significantly decreased (in group A); the species Plesiomonas shigelloides significantly decreased (in groups B and C); and the genus Leucobacter significantly increased (in group D) when compared with the control. The relative abundance of the class Verrucomicrobiae (groups B vs C) significantly decreased. In the presence of I. aquatica, the phylum Bacteroidetes significantly decreased, while the genera Leucobacter and Pelotomaculum significantly increased. The ratio of Bacteroidetes to Firmicutes was significantly higher in groups B and C relative to the controls, while it decreased significantly in group D. The algae (i.e., Anabaena and Microcystis) and beneficial pathogenic bacteria decreased in groups C and D, respectively. In addition, Enterovibrio decreased in all treatment groups. The present data demonstrate that floating bed cultivation with Chinese medicinal herbs significantly alters the gut microbiota of tilapia, which may enhance its immune activity.

scholarly journals On the Selection and Analysis of Clades in Comparative Evolutionary Studies

2020 ◽  
Vol 70 (1) ◽  
pp. 190-196 ◽  
Author(s):  
Steven Poe ◽  
Christopher Anderson ◽  
Joseph Barnett
Keyword(s):  
General Practice ◽  
Comparative Studies ◽  
Comparative Biology ◽  
Units Of Analysis ◽  
Evolutionary Studies ◽  
Biological Insight ◽  
Taxonomic Groups ◽  
Named Groups ◽  
Clade Selection

Abstract Researchers commonly present results of comparative studies of taxonomic groups. In this review, we criticize the focus on named clades, usually, comparably ranked groups such as families or orders, for comparative evolutionary analyses and question the general practice of using clades as units of analysis. The practice of analyzing sets of named groups persists despite widespread appreciation that the groups we have chosen to name are based on subjective human concerns rather than objective properties of nature. We demonstrate an effect of clade selection on results in one study and present some potential alternatives to selecting named clades for analysis that are relatively objective in clade choice. However, we note that these alternatives are only partial solutions for clade-based studies. The practice of analyzing named clades obviously is biased and problematic, but its issues portend broader problems with the general approach of employing clades as units of analysis. Most clade-based studies do not account for the nonindependence of clades, and the biological insight gained from demonstrating some pattern among a particular arbitrary sample of groups is arguable. [Clades; comparative biology; taxonomic groups.]

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