On the Selection and Analysis of Clades in Comparative Evolutionary Studies

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.]

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

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.

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

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.

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

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.

The Image of Region in Ordinary Language Consciousness of its Residents (on an Example of an Image of Kuzbass)

The article solves a topical problem, i.e. it develops the idea about the relevance of the psycholinguistic techniques’ usage in the image-building and branding of the regions. In particular it develops the thesis that an initial point of the region successful image’s formation is the studying of its image existing in the ordinary language consciousness of its residents and then and in the consciousness of other regions’ residents. Such psycholinguistic researches will give an opportunity to define strong and weak points of the regions in the consciousness of a mass audience. In other words they will let reveal and neutralize risk factors which can negatively affect the region’s image and define characteristics which will become a basis for successful region’s self-presentation. In order to demonstrate the efficiency of psycholinguistic techniques’ application in the studying of the territory’s representation the image of Kuzbass is described. Kuzbass is one of the strategically significant regions of Russia. In the course of the research an experimental psycholinguistic technique was used, including three complementary procedures: 1) а method of subjective definitions; 2) the directed associative experiment; 3) a method of non-complete sentences. The analysis has shown that the kernel of Kuzbass’s image is formed by three semantic groups: «Homeland», «Territory» and «Coal». The named groups are reflected both in the knowledge about the region and in the differently ranked concepts and evaluations which proves their fundamental character. It is also necessary to note that positive evaluations prevail which shows that the doubtless positive attitude of the residents to native region dominates. The developed coal industry and the positive personal attitude to the region can become meaningful points for an effective Kuzbass brand development. Nevertheless, negative issues are also reflected in the reactions, such as problems in social and recreational areas which should be paid attention to while working on the positive image of Kuzbass.

A review of the Neotropical genus Diochus Erichson, 1840 (Coleoptera: Staphylinidae: Staphylininae)

The Neotropical species of the genus Diochus are reviewed. Two species are synonymised: D. flavicans Sharp, 1876 = D. vicinus Sharp, 1876 and D. vilis Sharp, 1885 = D. schaumii Kraatz, 1860. Six species groups are differentiated containing the following species: D. longicornis-group with the species D. adisi spec. nov., D. ashei spec. nov., D. guianensis spec. nov., D. longicornis Sharp, 1876, D. tarsalis Sharp, 1876, and D. unicolor spec. nov.; D. inornatusgroup with the species D. antennalis Cameron, 1922, D. amazonensis spec. nov., D. hanagarthi spec. nov., D. hermani spec. nov., D. hibbsi spec. nov., D. inornatus Sharp, 1885, D. newtoni spec. nov., D. novus spec. nov., D. plaumanni spec. nov., D. schuelkei spec. nov., D. tricolor spec. nov., and D. vicinus Sharp, 1876; D. maculicollis-group with the species: D. brooksi spec. nov., D. ecuadoriensis spec. nov., D. maculicollis Fauvel, 1891, D. mexicanus spec. nov., D. panamaensis spec. nov., D. peruvianus spec. nov., and D. pumilio Bernhauer, 1929; D. schaumii-group with the species D. angustiformis spec. nov., D. argentinus spec. nov., D. brunneus spec. nov., D. curtipennis spec. nov., and D. schaumii Kraatz, 1860; D. verhaaghi-group with the two species D. verhaaghi spec. nov. and D. santacatarinae spec. nov.; D. nanus-group with the species D. apicipennis Cameron, 1922, D. nanus Erichson, 1839, D. parvulus Kraatz, 1860, and D. perplexus Cameron, 1922. D. formicetorum Bernhauer, 1927 is with unclear position among the named groups. A key to the species groups and to species is provided. The relation among groups, the ecology, and the geographic distribution is discussed. Nomenclatural Acts Diochus adisi spec. nov. – urn:lsid:zoobank.org:act:33DAA72A-B7E0-4806-BD59-8FC17FE1EF58 Diochus amazonensis spec. nov. – urn:lsid:zoobank.org:act:D2230764-A93A-46CF-B5F0-F4E6963E26DF Diochus angustiformis spec. nov. – urn:lsid:zoobank.org:act:BB731197-AF1B-458F-AE6B-BC32865D30C9 Diochus argentinae spec. nov. – urn:lsid:zoobank.org:act:2353FF33-7AEB-4B05-A9C8-EF6CCCC95684 Diochus ashei spec. nov. – urn:lsid:zoobank.org:act:949EFF27-4323-46C9-8F5D-F4731958CA14 Diochus brooksi spec. nov. – urn:lsid:zoobank.org:act:E45E737C-D6F4-45D2-AD3A-712C3578AE37 Diochus brunneus spec. nov. – urn:lsid:zoobank.org:act:7B393143-5E9A-4DE2-92D7-4458FAEF5B2B Diochus curtipennis spec. nov. – urn:lsid:zoobank.org:act:9F36420A-6AD4-4940-AAB0-A0535101A319 Diochus ecuadoriensis spec. nov. – urn:lsid:zoobank.org:act:0B0B68AB-0348-412D-A77B-EA722A5130C9 Diochus guianensis spec. nov. – urn:lsid:zoobank.org:act:BDD3E1B7-96A0-4ACE-BC32-4D24ADA1D2DB Diochus hanagarthi spec. nov. – urn:lsid:zoobank.org:act:00554886-6F3A-4FBA-9639-39AF0EE7E01B Diochus hermani spec. nov. – urn:lsid:zoobank.org:act:5C2FD0E5-BAFB-4AC4-8E80-9199884948B0 Diochus hibbsi spec. nov. – urn:lsid:zoobank.org:act:FA01A055-A996-4C60-9FE8-6756FDFA9A36 Diochus mexicanus spec. nov. – urn:lsid:zoobank.org:act:10213825-70EC-4B7F-BE1A-4FFD11B5D988 Diochus newtoni spec. nov. – urn:lsid:zoobank.org:act:FD5C80C7-1C1E-4C8C-9D48-8FEC23D9365F Diochus novus spec. nov. – urn:lsid:zoobank.org:act:3B902DCA-F381-4754-B88C-5825BC6E0B94 Diochus panamaensis spec. nov. – urn:lsid:zoobank.org:act:989703D5-6335-4E97-8772-B999831203C3 Diochus peruvianus spec. nov. – urn:lsid:zoobank.org:act:A3ED9480-CAC6-459D-9046-D1FE793F01EC Diochus plaumanni spec. nov. – urn:lsid:zoobank.org:act:4169DC68-8683-4290-A14A-62492505A4CA Diochus santacatarinae spec. nov. – urn:lsid:zoobank.org:act:99209529-EE6A-43A3-BE1F-413C5DF5CA1C Diochus schuelkei spec. nov. – urn:lsid:zoobank.org:act:4551D562-B65C-42EB-A4C5-5AA6F195F8D5 Diochus tricolor spec. nov. – urn:lsid:zoobank.org:act:5A551701-6B51-4659-B6A6-D2CBF83EA095 Diochus unicolor spec. nov. – urn:lsid:zoobank.org:act:5D7AB086-BCE1-4FEF-A732-1E210D4B3A87 Diochus verhaaghi spec. nov. – urn:lsid:zoobank.org:act:BBD1EC47-8638-4417-AE87-AC006B318FE1

Neisseria Adhesin A Variation and Revised Nomenclature Scheme

ABSTRACTNeisseriaadhesin A (NadA), involved in the adhesion and invasion ofNeisseria meningitidisinto host tissues, is one of the major components of Bexsero, a novel multicomponent vaccine licensed for protection against meningococcal serogroup B in Europe, Australia, and Canada. NadA has been identified in approximately 30% of clinical isolates and in a much lower proportion of carrier isolates. Three protein variants were originally identified in invasive meningococci and named NadA-1, NadA-2, and NadA-3, whereas most carrier isolates either lacked the gene or harbored a different variant, NadA-4. Further analysis of isolates belonging to the sequence type 213 (ST-213) clonal complex identified NadA-5, which was structurally similar to NadA-4, but more distantly related to NadA-1, -2, and -3. At the time of this writing, more than 89 distinctnadAallele sequences and 43 distinct peptides have been described. Here, we present a revised nomenclature system, taking into account the complete data set, which is compatible with previous classification schemes and is expandable. The main features of this new scheme include (i) the grouping of the previously named NadA-2 and NadA-3 variants into a single NadA-2/3 variant, (ii) the grouping of the previously assigned NadA-4 and NadA-5 variants into a single NadA-4/5 variant, (iii) the introduction of an additional variant (NadA-6), and (iv) the classification of the variants into two main groups, named groups I and II. To facilitate querying of the sequences and submission of new allele sequences, the nucleotide and amino acid sequences are available athttp://pubmlst.org/neisseria/NadA/.

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

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.