Molecular phylogenetics and new (infra)generic classification to alleviate polyphyly in tribe Hydrangeeae (Cornales : Hydrangeaceae)

Tribe Hydrangeeae of Hydrangeaceae currently contains nine morphologically diverse genera, many of which are well-known garden ornamentals. Previous studies have shown eight of these genera to be phylogenetically nested within Hydrangea, rendering the latter polyphyletic. To clarify the phylogeny of tribe Hydrangeeae, the present study sequenced four chloroplast regions and ITS for an extensive set of taxa, including the type for all nine genera involved. The resulting phylogenetic hypotheses corroborate the polyphyly of Hydrangea. Since polyphyletic taxa are deemed unacceptable by both sides in the ongoing debate concerning the adherence to strict monophyly in biological classifications, a new (infra)generic classification for tribe Hydrangeeae is proposed. In order to create a stable, evolutionary informative classification a broader circumscription of the genus Hydrangea is proposed, to include all eight satellite genera of the tribe. Such treatment is considered highly preferable to an alternative where Hydrangea is to be split into several morphologically potentially unidentifiable genera. To facilitate the acceptance of the new classification proposed here, and in order to create a classification with high information content, the familiar generic names were maintained as section names where possible

A genome-scale mining strategy for recovering novel rapidly-evolving nuclear single-copy genes for addressing shallow-scale phylogenetics in Hydrangea

Background: Identifying orthologous molecular markers that potentially resolve relationships at and below species level has been a major challenge in molecular phylogenetics over the past decade. Non-coding regions of nuclear low-or single-copy markers are a vast and promising source of data providing information for shallow-scale phylogenetics. Taking advantage of public transcriptome data from the One Thousand Plant Project (1KP), we developed a genome-scale mining strategy for recovering potentially orthologous single-copy markers to address low-scale phylogenetics. Our marker design targeted the amplification of intron-rich nuclear single-copy regions from genomic DNA. As a case study we used Hydrangea section Cornidia, one of the most recently diverged lineages within Hydrangeaceae (Cornales), for comparing the performance of three of these nuclear markers to other "fast" evolving plastid markers. Results: Our data mining and filtering process retrieved 73 putative nuclear single-copy genes which are potentially useful for resolving phylogenetic relationships at a range of divergence depths within Cornales. The three assessed nuclear markers showed considerably more phylogenetic signal for shallow evolutionary depths than conventional plastid markers. Phylogenetic signal in plastid markers increased less markedly towards deeper evolutionary divergences. Potential phylogenetic noise introduced by nuclear markers was lower than their respective phylogenetic signal across all evolutionary depths. In contrast, plastid markers showed higher probabilities for introducing phylogenetic noise than signal at the deepest evolutionary divergences within the tribe Hydrangeeae (Hydrangeaceae). Conclusions: While nuclear single-copy markers are highly informative for shallow evolutionary depths without introducing phylogenetic noise, plastid markers might be more appropriate for resolving deeper-level divergences such as the backbone relationships of the Hydrangeaceae family and deeper, at which non-coding parts of nuclear markers could potentially introduce noise due to elevated rates of evolution. The herein developed and demonstrated transcriptome based mining strategy has a great potential for the design of novel and highly informative nuclear markers for a range of plant groups and evolutionary scales

Comparative genomics of Flavobacterium columnare unveils novel insights in virulence and antimicrobial resistance mechanisms

This study reports the comparative analyses of four Flavobacterium columnare isolates that have different virulence and antimicrobial resistance patterns. The main research goal was to reveal new insights into possible virulence genes by comparing the genomes of bacterial isolates that could induce tissue damage and mortality versus the genome of a non-virulent isolate. The results indicated that only the genomes of the virulent isolates possessed unique genes encoding amongst others a methyl-accepting chemotaxis protein possibly involved in the initial colonization of tissue, and several VgrG proteins engaged in interbacterial competition. Furthermore, comparisons of genes unique for the genomes of the highly virulent (HV) carp and trout isolates versus the, respectively, low and non-virulent carp and trout isolates were performed. An important part of the identified unique virulence genes of the HV-trout isolate was located in one particular gene region identified as a genomic island. This region contained araC and nodT genes, both linked to pathogenic and multidrug-resistance, and a luxR-gene, functional in bacterial cell-to-cell communication. Furthermore, the genome of the HV-trout isolate possessed unique sugar-transferases possibly important in bacterial adhesion. The second research goal was to obtain insights into the genetic basis of acquired antimicrobial resistance. Several point-mutations were discovered in gyrase-genes of an isolate showing phenotypic resistance towards first and second-generation quinolones, which were absent in isolates susceptible to quinolones. Tetracycline-resistance gene tetA was found in an isolate displaying acquired phenotypic resistance towards oxytetracycline. Although not localized on a prophage, several flanking genes were indicative of the gene's mobile character

Distinct transcriptome signatures of Helicobacter suis and Helicobacter heilmannii strains upon adherence to human gastric epithelial cells

The porcine Helicobacter suis and canine-feline H. heilmannii are gastric Helicobacter species with zoonotic potential. However, little is known about the pathogenesis of human infections with these Helicobacter species. To gain more insight into the interactions of both zoonotic Helicobacter species with human gastric epithelial cells, we investigated bacterial genes that are differentially expressed in a H. suis and H. heilmannii strain after adhesion to the human gastric epithelial cell line MKN7. In vitro Helicobacter-MKN7 binding assays were performed to obtain bacterial RNA for sequencing analysis. H. suis and H. heilmannii bacteria attached to the gastric epithelial cells (i.e. cases) as well as unbound bacteria (i.e. controls) were isolated, after which prokaryotic RNA was purified and sequenced. Differentially expressed genes were identified using the DESeq2 package and SARTools pipeline in R. A list of 134 (83 up-regulated and 51 down-regulated) and 143 (60 up-regulated and 83 down-regulated) differentially expressed genes (p(adj)= 2) were identified for the adherent H. suis and H. heilmannii strains, respectively. According to BLASTp analyses, only 2 genes were commonly up-regulated and 4 genes commonly down-regulated in both pathogens. Differentially expressed genes of the H. suis and H. heilmannii strains belonged to multiple functional classes, indicating that adhesion of both strains to human gastric epithelial cells evokes pleiotropic adaptive responses. Our results suggest that distinct pathways are involved in human gastric colonization of H. suis and H. heilmannii. Further research is needed to elucidate the clinical significance of these findings

The explanatory role of rumours in the reciprocal relationship between organizational change communication and job insecurity: A within-person approach

© 2016 Informa UK Limited, trading as Taylor & Francis Group. The current study highlights rumours as an explanation of the reciprocal relationship between perceived organizational change communication and job insecurity. First, we predict that perceiving insufficient organizational change communication may result in rumours, which in turn may shape job insecurity perceptions. Second, we propose that rumours may also mediate the relationship between job insecurity and perceiving insufficient organizational change communication. To test the hypotheses, a multilevel approach was used, in which three measurements were nested within 1994 employees. This enabled us to probe within-person processes, while controlling for possible between-person variation. The results demonstrated a negative reciprocal relationship between perceived organizational change communication and job insecurity. Additionally, rumours mediated both the negative relationship between perceived organizational change communication and subsequent job insecurity, and the negative relationship between job insecurity and subsequent perceived organizational change communication. This study contributes to the literature on job insecurity by offering initial evidence on the relationship between job insecurity and rumours, and by highlighting rumours as a process through which perceived organizational change communication and job insecurity may mutually affect each other.peerreview_statement: The publishing and review policy for this title is described in its Aims & Scope. aims_and_scope_url: http://www.tandfonline.com/action/journalInformation?show=aimsScope&journalCode=pewo20status: publishe

Know your limits: the importance of species and generic boundaries for conservation

Species are a fundamental unit of biology, being the only objective entity within the framework of more artificial taxonomical hierarchy. Using species as a unit for conservation assessment and management requires well defined, stable boundaries for these entities. Recognizing species as separately evolving metapopulation lineages (GLCS, General Lineage Concept of Species), their description and delimitation becomes objective, requiring multiple sources of evidence. Therefore, this method has high potential for creating stable lists of taxa for conservation. The Hydrangea aspera complex is a group of closely related taxa, which have been subjected to considerable taxonomic changes. Each of these changes results from a bias towards a particular combination of characters in defining species boundaries. Applying the GLCS to this complex, the number of recognizable taxa is examined, under different lines of evidence. As one recognized taxon, H. sargentiana is limited to a single population in the province of Hubei. China, correct delimitation of species in this group is crucial for conservation of unique evolutionary lineages

Additional evidence for recent divergence of Chinese Epimedium (Berberidaceae) derived from AFLP, chloroplast and nuclear data supplemented with characterisation of leaflet pubescence

Background - The genus Epimedium is well known for its ornamental representatives. However, species boundaries and evolutionary relationships within the genus remain uncertain due to several difficulties. First, potentially diagnostic characters are generally not described with enough detail, hampering linkage of specimens to recognized taxa. Second, previous molecular studies failed to gain resolution, especially within the Chinese distribution area of the genus. Nevertheless, growing scientific interest in the medicinal properties of Epimedium has prompted the need for reliable identification of species. Aims and methods - This study aims at: (1) assessing genetic diversity within Epimedium, using nuclear and chloroplast DNA sequences in combination with AFLP fingerprinting, (2) delivering a detailed description for one potentially diagnostic character, pubescence of leaflets. Key results - The DNA sequences and AFLP fingerprints resulted in an unresolved polytomy for the Chinese representatives of Epimedium. Furthermore, this study provided detailed scanning electron microscope images of four clearly distinguishable types of leaflet pubescence. Conclusions - As AFLP is considered capable of detecting rare genetic differences in groups with low sequence variation, we suggest the lack of resolution in the Chinese clade to represent a hard polytomy. This is interpreted as additional evidence for the hypothesis of a recent origin for these taxa. As this implies that several recognized species are still in the process of differentiation, these difficulties in resolving evolutionary relationships are linked to difficulties in species delimitation. Furthermore, the lack of details in some species descriptions has led to the description of new taxa based on small variations. To tackle these problems, we propose a change in view on Epimedium taxonomy. In this view, broader taxonomic entities are recognized, characterized by clearly defined characters. The four types of pubescence described in this study can serve as a first step towards this new interpretation of Epimedium taxonomy

Rediscovering Hydrangea sargentiana, a taxon in need of conservation action

The genus Hydrangea, famous for its ornamental representatives, faces several taxonomic and systematic difficulties at different levels. Unclear species boundaries are one of these difficulties, which require an in-depth study of molecular and morphological variability of Hydrangea taxa. This paper concentrates on gathering more specimens for studying the variability in H. sargentiana, which is recognized as a subspecies of H. aspera by some authors