Multivariate Analysis Confirms the Continuum View of Plant Form

Multivariate analysis, specifically principal components analysis,shows that in flowering plants structures occur that arc intermediatebetween the typical representatives of a root, a caulome (stemand stem homologues), a phyllome (leaf and leaf homologues),a shoot and a trichome. Since these intermediates span the wholerange between the typical forms, a morphological continuum isdocumented. Implications and consequences of these findingsare discussed (e.g. homology, homeosis). The telome theory andHagemann's theory of the evolution of plant form are interpretedas referring to changes in the patterning of the morphologicalcontinuum. Plant morphology, principal components analysis, morphological continoum, angiosperms, flower, shoot, stem, leaf, enation, trichome, root, telome, thallus, morphological categories, homology, partial homology, homeosis     

An Invasive Mammal (the Gray Squirrel,Sciurus carolinensis) Commonly Hosts Diverse and Atypical Genotypes of the Zoonotic Pathogen Borrelia burgdorferi Sensu Lato

Invasive vertebrate species can act as hosts for endemic pathogens and may alter pathogen community composition and dynamics. For the zoonotic pathogen Borrelia burgdorferi sensu lato, the agent of Lyme borreliosis, recent work shows invasive rodent species can be of high epidemiological importance and may support host-specific strains. This study examined the role of gray squirrels (Sciurus carolinensis) (n = 679), an invasive species in the United Kingdom, as B. burgdorferi sensu lato hosts. We found that gray squirrels were frequently infested with Ixodes ricinus, the main vector of B. burgdorferi sensu lato in the United Kingdom, and 11.9% were infected with B. burgdorferi sensu lato. All four genospecies that occur in the United Kingdom were detected in gray squirrels, and unexpectedly, the bird-associated genospecies Borrelia garinii was most common. The second most frequent infection was with Borrelia afzelii. Genotyping of B. garinii and B. afzelii produced no evidence for strains associated with gray squirrels. Generalized linear mixed models (GLMM) identified tick infestation and date of capture as significant factors associated with B. burgdorferi sensu lato infection in gray squirrels, with infection elevated in early summer in squirrels infested with ticks. Invasive gray squirrels appear to become infected with locally circulating strains of B. burgdorferi sensu lato, and further studies are required to determine their role in community disease dynamics. Our findings highlight the fact that the role of introduced host species in B. burgdorferi sensu lato epidemiology can be highly variable and thus difficult to predict.     

The shoot apex of Podostemaceae: De novo structure or reduction of the conventional type?

The paper reviews and discusses various interpretations of the shoot apex of Podostemaceae with special reference to subfamily Podostemoideae. Main questions concern (1) the proposed absence of a shoot apical meristem (SAM) in apical “meristemless” shoot tips of Podostemoideae and, as the consequence, the endogenous inception of leaf-borne leaves and branches and (2) the predicted stem bifurcation below a “terminal” dithecous (double-sheathed) leaf positioned instead of a shoot apex, as it is reported for subfamily Podostemoideae. Does the “meristemless” shoot apex represent a true evolutionary novelty? Does the view of stem bifurcation represent a new ramification pattern with the consequence that the “classical root–shoot model” of angiosperms is not valid for Podostemaceae? Both interpretations do not conform to previous studies that are complemented here by new data on the SAM of Zeylanidium olivaceum and Thelethylax minutiflora (Podostemoideae). Although a SAM is difficult to observe in the vegetative shoots of many Podostemoideae, it becomes well visible when the shoot passes into the flowering stage approaching the conspicuous shoot apex of floriferous shoots. The arguments of the absence of a SAM in vegetative shoots are not convincing and the endogenous origin of “leaf-borne leaves” appears questionable. Consequently, the “meristemless” shoot apex cannot be considered as a structure having evolved de novo. In the less advanced subfamilies Tristichoideae and Weddellinoideae, the leaf primordia develop only from a few apical cells of the outer shoot layer. This allows the conclusion that the surface layer of the apex in these subfamilies corresponds to the horizontally spread single-layered apical meristem of subfamily Podostemoideae. Similarly, the view of shoot bifurcation does not conform to the diachsial–sympodial branching pattern occurring in the cymose inflorescences of many Podostemoideae. This fact contradicts the presence of a terminal leaf.     

Multilocus sequence analysis of homologous recombination and diversity in Arthrobacter sensu lato named species and glacier-inhabiting strains

Members of the bacterial genus Arthrobacter sensu lato are Gram-positive actinomycetes distributed worldwide and found in numerous environments including soil, water, glacier ice, and sewage. Homologous recombination is an important driving force in bacterial evolution, but its impact on Arthrobacter sensu lato evolution is poorly understood. We evaluated homologous recombination among 41 Arthrobacter sensu lato named species, using multilocus sequence analysis (MLSA). A high level of recombination was found, associated with strong diversification and a reticulate evolutionary pattern of Arthrobacter sensu lato. We also collected a total of 31 cold-adapted Arthrobacter sensu lato strains from two cold glaciers located in northwest China and two temperate glaciers in southwest China, and evaluated their diversity and population structure by MLSA. The glacier strains displayed high diversity, but rates of recombination among the four glacier groups were quite low, indicating that barriers to homologous recombination formed in the past among the populations on different glaciers. Our findings indicate that historical glaciation events shaped the contemporary distributions, taxonomic relationships, and phylogeographic patterns of Arthrobacter sensu lato species on glaciers.     

A critical rebuttal of the proposed division of the genus Arcobacter into six genera using comparative genomic,phylogenetic, and phenotypic criteria

The proposal to restructure the genus Arcobacter into six distinct genera was critically examined using: comparative analyses of up to 80 Epsilonproteobacterial genome sequences (including 26 arcobacters); phylogenetic analyses of three housekeeping genes and also 342 core genes; and phenotypic criteria. Genome sequences were analysed with tools to calculate Percentage of Conserved Proteins, Average Amino-acid Identity, BLAST-based Average Nucleotide Identity, in silico DNA–DNA hybridisation values, genome-wide Average Nucleotide Identity, Alignment Fractions and G + C percentages. Genome analyses revealed the genus Arcobacter sensu lato to be relatively homogenous, and phylogenetic analyses clearly distinguished the group from other Epsilonproteobacteria. Genomic distinction of the genera proposed by Pérez-Cataluña et al. [2018] was not supported by any of the measures used and a subsequent risk of strain misidentification clearly identified. Similarly, phenotypic analyses supported the delineation of Arcobacter sensu lato but did not justify the position of the proposed novel genera. The present polyphasic taxonomic study strongly supports the continuance of the classification of “aerotolerant campylobacters” as Arcobacter and refutes the proposed genus-level subdivision of Pérez-Cataluña et al. [2018].     

Plasmidome Interchange between Clostridium botulinum,Clostridium novyi and Clostridium haemolyticum Converts Strains of Independent Lineages into Distinctly Different Pathogens

Clostridium botulinum (group III), Clostridium novyi and Clostridium haemolyticum are well-known pathogens causing animal botulism, gas gangrene/black disease, and bacillary hemoglobinuria, respectively. A close genetic relationship exists between the species, which has resulted in the collective term C. novyi sensu lato. The pathogenic traits in these species, e.g., the botulinum neurotoxin and the novyi alpha toxin, are mainly linked to a large plasmidome consisting of plasmids and circular prophages. The plasmidome of C. novyi sensu lato has so far been poorly characterized. In this study we explored the genomic relationship of a wide range of strains of C. novyi sensu lato with a special focus on the dynamics of the plasmidome. Twenty-four genomes were sequenced from strains selected to represent as much as possible the genetic diversity in C. novyi sensu lato. Sixty-one plasmids were identified in these genomes and 28 of them were completed. The genomic comparisons revealed four separate lineages, which did not strictly correlate with the species designations. The plasmids were categorized into 13 different plasmid groups on the basis of their similarity and conservation of plasmid replication or partitioning genes. The plasmid groups, lineages and species were to a large extent entwined because plasmids and toxin genes had moved across the lineage boundaries. This dynamic process appears to be primarily driven by phages. We here present a comprehensive characterization of the complex species group C. novyi sensu lato, explaining the intermixed genetic properties. This study also provides examples how the reorganization of the botulinum toxin and the novyi alpha toxin genes within the plasmidome has affected the pathogenesis of the strains.     

Productivity differences between dandelion (Taraxacum officinale; Asteraceae) clones from pollution impacted versus non-impacted soils

Common dandelions (Taraxacum officinale Weber, sensu lato; Asteraceae) introduced to North America form an assemblage of asexual (agamospermous), clonal lineages derived from Eurasian mixed sexual and asexual populations. We investigated whether selection for more pollution tolerant clonal lineages occurs at polluted sites and selection for more pollution intolerant lineages occurs at unpolluted sites. We tested the above hypothesis by performing reciprocal greenhouse productivity experiments in which unique dandelion clones (12 clones, identified by DNA fingerprinting, from each site type) sampled from two unpolluted and two polluted (moderately enhanced Cu, Pb and Zn soil concentrations) sites were grown pairwise in both unpolluted (nutrient solution only) and polluted (nutrient solution + Cu, Pb and Zn) media (n?=?48 paired tests for each media type). Dandelion clones from polluted sites produced fewer and smaller leaves, shorter roots and smaller root diameters, reduced shoot and root dry weights, and reduced total biomass compared to clones from unpolluted sites when clones were grown in unpolluted-media (P?≤?0.05). In contrast, clones taken from unpolluted sites were shown to produce significantly fewer and shorter leaves, shorter roots and smaller root diameters, reduced shoot and root dry weights, reduced total biomass, a reduced shoot : root biomass ratio, and have much lower survival compared to clones from polluted sites when both were grown in polluted-media (P?≤?0.05). These results reveal that there was increased selection against unpolluted-site clonal lineages in polluted-media and against polluted-site clonal lineages in unpolluted-media. Across all treatments, clones from unpolluted sites growing in unpolluted-media had the highest proximate measures of fitness. Overall, these findings provide insight into the relationships among anthropogenic environmental contamination and the consequent effects of selective forces acting on dandelion clones and their population genetic architecture.     

NaCl effect on the distribution of wall ingrowth polymers and arabinogalactan proteins in type A transfer cells of Medicago sativa Gabès leaves

In most species of the Genlisea–Utricularia sister lineage, the organs arising directly after germination comprise a single leaf-like structure, followed by a bladder-trap/stolon, with the lack of an embryonic primary root considered a synapomorphic character. Previous anatomical work suggests that the most common recent ancestor of Utricularia possessed an embryo comprising storage tissue and a meristematic apical region minus lateral organs. Studies of embryogenesis across the Utricularia lineage suggest that multiple primary organs have only evolved in the viviparous Utricularia nelumbifolia, Utricularia reniformis, and Utricularia humboldtii within the derived Iperua/Orchidioides clade. All three of these species are specialized for growth as “aquatic epiphytes” in the tanks of bromeliads, with recent phylogenetic evidence suggesting the possibility that multiple primary organs may have evolved twice independently within this clade. The primary organs of viviparous Utricularia also possess epidermal surface glands, and our study suggests that these may function as root hairs for uptake of solutes from the external environment—a possible adaptation for the “aquatic–epiphytic” habitat.     

Lower Emsian biostratigraphy and event stratigraphy of Ha Giang Province,northern Vietnam

A new species of rugose coral, Sanidophyllum dubium n. sp., and the typical Emsian (Early Devonian) rugose coral Xystriphylloides nobilis are described from the Mia Le Formation in northern Vietnam. The lower Emsian index conodonts ranging from the Polygnathus excavatus zone to the P. nothoperbonus zone are illustrated. The biostratigraphic correlation between northern Vietnam and South China shows that the Mia Le Formation in northern Vietnam is early Emsian in age, and its upper part can be correlated with the lower part of the Shizhou Member of the Yukiang Formation in Liujing, Guangxi and its equivalents in South China. Based on the study of the lower Emsian biostratigraphic sequence, the disappearance of Xystriphylloides nobilis fauna in the overlying bed of the uppermost Mia Le Formation and the extinction of the “tonkinensis fauna” (sensu lato) in the interval between the basal Si Phai Formation and the uppermost Mia Le Formation demonstrate the influence of the Yujiang Event in northern Vietnam.     

Development of the epiphyllous inflorescence of Phyllonoma integerrima (Turcz.) Loes.: implications for comparative morphology*

The inflorescence primordium of Phyllonoma integerrima (Turcz.) Loes. is initiated on the adaxial side of the leaf primordium. At about the same time, a vegetative bud is formed at the base of the same leaf primordium. The vascular anatomy is the same in the fertile and sterile leaves, except that in the fertile leaf an inflorescence trace departs from the midvein of the leaf at the point where the inflorescence is inserted. Neither the inception nor the procambial supply of the inflorescence provide evidence of “congenital fusion”of inflorescence and leaf. It is also argued that the idea of an “adventitious”origin of the inflorescence is not useful in this case. Consequences for our conception of shoot construction are pointed out. It is argued that positional changes in the initiation of organs is an evolutionary process that may have remarkable effects on plant construction.     

Variability of the wood monoterpenoids from Pinus aristata

Striking differences in turpentine composition between California-Nevada-Utah populations and Colorado-New Mexico-Arizona populations of the Bristlecone pine (Pinus aristata) were demonstrated by GLC analyses of the wood extracts. These differences are in line with Bailey's taxonomic division of Pinus aristata sensu lato into western Pinus longaeva and eastern Pinus aristata sensu stricto.     

The systematics and population genetics of Opisthorchis viverrini sensu lato: implications in parasite epidemiology and bile duct cancer

Together with host and environmental factors, the systematics and population genetic variation of Opisthorchis viverrini may contribute to recorded local and regional differences in epidemiology and host morbidity in opisthorchiasis and cholangiocarcinoma (CCA). In this review, we address recent findings that O. viverrini comprises a species complex with varying degrees of population genetic variation which are associated with specific river wetland systems within Thailand as well as the Lao PDR. Having an accurate understanding of systematics is a prerequisite for a meaningful assessment of the population structure of each species within the O. viverrini complex in nature, as well as a better understanding of the magnitude of genetic variation that occurs within different species of hosts in its life cycle. Whether specific genotypes are related to habitat type(s) and/or specific intermediate host species are discussed based on current available data. Most importantly, we focus on whether there is a correlation between incidence of CCA and genotype(s) of O. viverrini. This will provide a solid basis for further comprehensive investigations of the role of genetic variation within each species of O. viverrini sensu lato in human epidemiology and genotype related morbidity as well as co-evolution of parasites with primary and secondary intermediate species of host.     

The “tropical lineage” of the brown dog tick Rhipicephalus sanguineus sensu lato identified as Rhipicephalus linnaei ()

The brown dog tick (Rhipicephalus sanguineus) parasitises dogs. Over the past decade, two distinct lineages have been recognised – R. sanguineus sensu lato “temperate lineage” and R. sanguineus sensu lato “tropical lineage”. The nominal taxon R. sanguineus (Latreille, 1806) was recently associated with the “temperate lineage”. We here identify the “tropical lineage” as Rhipicephalus linnaei (Audouin, 1826) using material from Australia, where no other Rhipicephalus species parasitises dogs. Whole genome sequencing of R. linnaei from Australia, Fiji and Laos, and assembly of their complete mitochondrial DNA (~15 kb) confirms the genetic identity and distinctness from all other known species within the brown dog tick species complex. Designation of the species R. linnaei is unequivocally supported by material available through the Australian National Insect Collection, Australia. Accordingly, we are formally justified in using R. linnaei for the “tropical lineage”.     

A case of human cystic echinococcosis acquired in Ireland

Cystic echinococcosis (CE) is caused by the cestodes of the Echinococcus granulosus sensu lato complex and, in the majority of cases, is associated with hepatic or pulmonary involvement. Human CE is not thought to be endemic in Ireland. We describe the first reported case of human CE possibly acquired in Ireland.     

The Principles of Data Formalization for Building Biological Model of Shoot Development in Flowering Plants

Shoot system of a plant can be divided into elementary molecules composed of phyllome, internode, and meristem of the lateral bud. The capacity of plants for open growth is manifested as multiple reproductions of the modules. These main principles of plant structural organization can be used to formalize and integrate the data from various disciplines studying shoot development—genetics of development, morphology, etc. At the example of a model species Arabidopsis thaliana we show that the data on genetic control of shoot development can be considered in terms of rearrangement of individual modules. Several variants of the module structural reorganization are allowed: reduction or transformation of phyllome, change in the internode length, and triggering active/inactive status of the lateral shoot meristem. Each variant of module structure corresponds to specific pattern of genes activity. Such integration of the data on genetic and structural aspects of morphogenesis can form a basis for mathematical modeling of plant development.     

Floral development of Phyllanthus chekiangensis (Phyllanthaceae), with special reference to androecium and gynoecium

The floral development of Phyllanthus chekiangensis has been studied by scanning electron microscopy. The perianth organs are initiated in two whorls, dimerous in male flowers and trimerous in female flowers, with a longer plastochron between whorls than between the organs within a whorl. Male flowers have two stamens. The prominent connective protrusions begin development simultaneously with the floral disk. The disk is two-lobed in male flowers but continuous in female flowers. In female flowers, the developing gynoecium remains open relatively long, so the developing ovules are visible from the outside for some time. The direction of the hemitropous ovules in the carpels is antitropous (epitropous). Two small obturators are formed per carpel, one above each ovule. The prominent nucellar beak extends far beyond the “micropyle”. A micropyle in the classical sense formed by integuments closing over the nucellus apex is not present at any stage of development. Thus, it is not correct to say that the nucellar beak “grows through the micropyle”. The exposed nucellar beak continues the curvature of the antitropous (epitropous) ovule and becomes contiguous with the obturator. The unusual length of the nucellar beak may be a potential synapomorphy of the enlarged Phyllanthus clade as inferred from molecular phylogenetics.     

Systematic Placement of Dasypogonaceae Among Commelinid Monocots: Evidence from Flowers and Fruits

Despite progress in clarifying the relationships of Dasypogonaceae (four genera, Baxteria, Calectasia, Dasypogon, and Kingia), their infrafamilial relationships and precise affinities within the commelinid clade remain unsatisfactorily resolved. This paper reviews existing data on the systematic affinities of Dasypogonaceae. It also presents new data on floral structure in all four genera, and data on floral ontogeny in Dasypogon. In Dasypogon, Kingia, and Baxteria the ovary is trilocular and septal nectaries are present around the ovary base. In Calectasia, the ovary is unilocular and septal nectaries are entirely absent. Two subfamilial groupings within Dasypogonaceae (Calectasia–Dasypogon and Baxteria–Kingia) are proposed on the basis of leaf anatomy and ovule and ovary morphology. Many floral characters are plesiomorphic in Dasypogonaceae, but some morphological characters support a close relationship with the order Poales sensu lato, especially the epidermal location of the silica bodies. The unusual long-stalked “drumstick” inflorescences of Dasypogon and Kingia resemble those of some Poales, in which flowers are frequently borne on condensed inflorescences. A possible close relationship between Dasypogonaceae and some Poales such as Rapateaceae and Thurniaceae merits further exploration.     

The principles of data formalization for building the genetic-morphological model of shoot development in flowering plants

Shoot system of a plant can be divided into elementary molecules composed of phyllome, internode, and meristem of the lateral bud. The capacity of plants for open growth is manifested as multiple reproductions of the modules. These main principles of plant structural organization can be used to formalize and integrate the data from various disciplines studying the shoot development--genetics of development, morphology, etc. At the example of model species Arabidopsis thaliana we show that the data on genetic control of shoot development can be considered in terms of individual modules reorganization. Several variants of the modules structural reorganization are allowed: reduction or transformation of phyllome, change in the internode length, and triggering active/inactive status of the lateral shoot meristem. Each variant of the module structure corresponds to specific pattern of genes activity. Such integration of the data on genetic and structural aspects of morphogenesis can form a basis for mathematical modeling of plant development.     

Systématique du groupe « Palaeochelys sensu lato – Mauremys » (Chelonii,Testudinoidea) du Tertiaire d’Europe occidentale : principaux résultats

Among fossil chelonians from the Tertiary of Western Europe, freshwater Testudinoidea (sensu Hirayama, 1985, Gaffney et Meylan, 1988) are abundant, and more particularly the “Palaeochelys sensu lato—Mauremys” group. This group has never been studied as a whole. Taxa of this group were before referred to extinct genera such as Ocadia, Clemmys, Emys or to the fossil genera Palaeochelys, Borkenia and Palaeoemys. These taxa are redefined, new taxa are described and a hypothesis of phylogenetic relationships is given.     

Evo-devo and the search for homology (“sameness”) in biological systems

Developmental biology and evolutionary studies have merged into evolutionary developmental biology (“evo-devo”). This synthesis already influenced and still continues to change the conceptual framework of structural biology. One of the cornerstones of structural biology is the concept of homology. But the search for homology (“sameness”) of biological structures depends on our favourite perspectives (axioms, paradigms). Five levels of homology (“sameness”) can be identified in the literature, although they overlap to some degree: (i) serial homology (homonomy) within modular organisms, (ii) historical homology (synapomorphy), which is taken as the only acceptable homology by many biologists, (iii) underlying homology (i.e., parallelism) in closely related taxa, (iv) deep evolutionary homology due to the “same” master genes in distantly related phyla, and (v) molecular homology exclusively at gene level. The following essay gives emphasis on the heuristic advantages of seemingly opposing perspectives in structural biology, with examples mainly from comparative plant morphology. The organization of the plant body in the majority of angiosperms led to the recognition of the classical root–shoot model. In some lineages bauplan rules were transcended during evolution and development. This resulted in morphological misfits such as the Podostemaceae, peculiar eudicots adapted to submerged river rocks. Their transformed “roots” and “shoots” fit only to a limited degree into the classical model which is based on either–or thinking. It has to be widened into a continuum model by taking over elements of fuzzy logic and fractal geometry to accommodate for lineages such as the Podostemaceae.