Seed plant phylogeny: Demise of the anthophyte hypothesis?

Recent molecular phylogenetic studies indicate, surprisingly, that Gnetales are related to conifers, or even derived from them, and that no other extant seed plants are closely related to angiosperms. Are these results believable? Is this a clash between molecules and morphology?     

Bacteriophage biocontrol of plant pathogens: fact or fiction?

Bacterial resistance due to the misuse of antibiotics has become a global issue and alternative methods are being developed that might decrease the use of antimicrobials in agricultural settings. Bacteriophage therapy represents a novel way to control the growth of plant-based bacterial pathogens. Although this method shows promise, a recent paper by Gill and Abedon has shown that the complex bacteriophage-host interactions in the plant environment must be investigated further.     

Do plant and human pathogens have a common pathogenicity strategy?

Recently, a novel 'two-step' model of pathogenicity has been described that suggests host-cell-derived vasculoproliferative factors play a crucial role in the pathogenesis of bacillary angiomatosis, a disease caused by the human pathogenic bacterium Bartonella henselae. The resulting proliferation of endothelial cells could be interpreted as bacterial pathogens triggering the promotion of their own habitat: the host cell. Similar disease mechanisms are well known in the plant pathogen Agrobacterium tumefaciens, which causes crown gall disease. There are notable similarities between the pathogenicity of A. tumefaciens leading to tumourous disease in plants and to the B. henselae-triggered proliferation of endothelial cells in humans. Here, we hypothesize that this pathogenicity strategy might be common to several bacterial species in different hosts owing to shared pathogenicity factors.     

Global pattern of plant utilization across different organisms: Does plant apparency or plant phylogeny matter?

The present study is the first to consider human and nonhuman consumers together to reveal several general patterns of plant utilization. We provide evidence that at a global scale, plant apparency and phylogenetic isolation can be important predictors of plant utilization and consumer diversity. Using the number of species or genera or the distribution area of each plant family as the island “area” and the minimum phylogenetic distance to common plant families as the island “distance”, we fitted presence–area relationships and presence–distance relationships with a binomial GLM (generalized linear model) with a logit link. The presence–absence of consumers among each plant family strongly depended on plant apparency (family size and distribution area); the diversity of consumers increased with plant apparency but decreased with phylogenetic isolation. When consumers extended their host breadth, unapparent plants became more likely to be used. Common uses occurred more often on common plants and their relatives, showing higher host phylogenetic clustering than uncommon uses. On the contrary, highly specialized uses might be related to the rarity of plant chemicals and were therefore very species‐specific. In summary, our results provide a global illustration of plant–consumer combinations and reveal several general patterns of plant utilization across humans, insects and microbes. First, plant apparency and plant phylogenetic isolation generally govern plant utilization value, with uncommon and isolated plants suffering fewer parasites. Second, extension of the breadth of utilized hosts helps explain the presence of consumers on unapparent plants. Finally, the phylogenetic clustering structure of host plants is different between common uses and uncommon uses. The strength of such consistent plant utilization patterns across a diverse set of usage types suggests that the persistence and accumulation of consumer diversity and use value for plant species are determined by similar ecological and evolutionary processes.     

Is analysing the nitrogen use at the plant canopy level a matter of choosing the right optimization criterion?

Herbivores can have strong deleterious effects on plant growth, reproduction, and even survival. Because these effects might be strongly interrelated, the direct consumptive effects of herbivores and a variety of indirect effects are difficult to untangle. Reductions in growth, for example, may strongly impact the flowering behaviour of plant species in the current season, but at the same time incur costs to survival, growth and reproduction in the next growing season(s). To get better insights in the effects of herbivory on the flowering behaviour of the long-lived polycarpic grassland herb Primula veris L., flowering patterns were monitored over ten consecutive years under two treatments (grazing and control mowing regimes). We tested the hypothesis that the size at flowering was affected by the presence of herbivores, and whether this translated into costs to future reproduction and survival. Overall, grazed plants were significantly smaller than control plants, and the size at which plants flowered was also significantly smaller when herbivores were present. The transition probability of flowering and of surviving into the next year was significantly smaller for all plants in the current year if they had been grazed than if they had been mown, indicating that herbivory incurred costs to both flowering and survival. Grazed plants also needed longer to start flowering, had fewer flowers and flowered less frequently, causing a significantly lower proportion of flowering adults in the population. These results suggest that the observed regression in plant size due to herbivory does not allow plants to capture enough resources to guarantee regular flowering in the longer run.     

Is the originality of a species measurable?

In this paper, we introduce the concept of 'originality of a species within a set' in order to indicate the average rarity of all the features belonging to this species. Using a phylogenetic tree of 70 species of New World terrestrial Carnivora, we suggest measuring the originality by a probability distribution. This maximizes the expected number of features shared by two species randomly drawn from the set. By using this new index, we take account of branch lengths whereas current indices of originality focus on tree topology. As a supplement to Nee and May's optimizing algorithm, we find that originality must be one of the criteria used in conservation planning.     

Is palatability of a root-hemiparasitic plant influenced by its host species?

Palatability of parasitic plants may be influenced by their host species, because the parasites take up nutrients and secondary compounds from the hosts. If parasitic plants acquired the full spectrum of secondary compounds from their host, one would expect a correlation between host and parasite palatability. We examined the palatability of leaves of the root-hemiparasite Melampyrum arvense grown with different host plants and the palatability of these host plants for two generalist herbivores, the caterpillar of Spodoptera littoralis and the slug Arion lusitanicus. We used 19 species of host plants from 11 families that are known to contain a wide spectrum of anti-herbivore compounds. Growth of M. arvense was strongly influenced by the host species. The palatability of the individual host species for the two herbivores differed strongly. Both A. lusitanicus and S. littoralis discriminated also between hemiparasites grown with different host plants. There was no correlation between the palatability of a host species and that of the parasites grown on that host, i.e., hemiparasites grown on palatable host species were not more palatable than those grown on unpalatable hosts. We suggest an interacting pattern of specific effects of chemical anti-herbivore defences and indirect effects of the hosts on herbivores through effects on growth and tissue quality of the parasites.     

Is multiple-sequence alignment required for accurate inference of phylogeny?

The process of inferring phylogenetic trees from molecular sequences almost always starts with a multiple alignment of these sequences but can also be based on methods that do not involve multiple sequence alignment. Very little is known about the accuracy with which such alignment-free methods recover the correct phylogeny or about the potential for increasing their accuracy. We conducted a large-scale comparison of ten alignment-free methods, among them one new approach that does not calculate distances and a faster variant of our pattern-based approach; all distance-based alignment-free methods are freely available from http://www.bioinformatics.org.au (as Python package decaf+py). We show that most methods exhibit a higher overall reconstruction accuracy in the presence of high among-site rate variation. Under all conditions that we considered, variants of the pattern-based approach were significantly better than the other alignment-free methods. The new pattern-based variant achieved a speed-up of an order of magnitude in the distance calculation step, accompanied by a small loss of tree reconstruction accuracy. A method of Bayesian inference from k-mers did not improve on classical alignment-free (and distance-based) methods but may still offer other advantages due to its Bayesian nature. We found the optimal word length k of word-based methods to be stable across various data sets, and we provide parameter ranges for two different alphabets. The influence of these alphabets was analyzed to reveal a trade-off in reconstruction accuracy between long and short branches. We have mapped the phylogenetic accuracy for many alignment-free methods, among them several recently introduced ones, and increased our understanding of their behavior in response to biologically important parameters. In all experiments, the pattern-based approach emerged as superior, at the expense of higher resource consumption. Nonetheless, no alignment-free method that we examined recovers the correct phylogeny as accurately as does an approach based on maximum-likelihood distance estimates of multiply aligned sequences.     

Is the meniscus of the knee joint a fibrocartilage?

A histological analysis of the structure of intact knee joint menisci was carried out in adult dogs. By means of specific histochemical methods for the connective tissue and cartilage, it was found that the meniscus as a whole does not have a unique structure. The anterior and posterior horns are populated by round chondroid cells encircled by abundant interstitial substance and branched wavy connective fibers; blood vessels are present. The outer third of the meniscus is constituted of cross bundles of connective fibers, fibrocytes and spindle-like areas of loose connective tissue with blood vessels. The inner avascular two thirds of the meniscus are filled with parallel circumferentially oriented fascicles of connective fibers, ovally elongated chondroid cells, and a small quantity of chondroid interstitial substance. In some menisci, in the inner two thirds of the body, there are isles of typical cartilage, which show metachromasia of the beta type and rarely of the gamma type. The occurrence and way of the manifestation of cartilage are of an individual character. The structural duality of the knee meniscus is accounted for by its functional duality manifested in offering resistance to the forces of traction and pressure, the latter ones favoring the process of evolution of tissue from connective, through chondroid, to cartilaginous.     

What limits the evolutionary emergence of pathogens?

The ability of a pathogen to cause an epidemic when introduced in a new host population often relies on its ability to adapt to this new environment. Here, we give a brief overview of recent theoretical and empirical studies of such evolutionary emergence of pathogens. We discuss the effects of several ecological and genetic factors that may affect the likelihood of emergence: migration, life history of the infectious agent, host heterogeneity, and the rate and effects of mutations. We contrast different modelling approaches and indicate how details in the way we model each step of a life cycle can have important consequences on the predicted probability of evolutionary emergence. These different theoretical perspectives yield important insights into optimal surveillance and intervention strategies, which should aim for a reduction in the emergence (and re-emergence) of infectious diseases.     

Is Sedum acre L. a CAM plant?

Summary Sedum acre L. collected from its natural stands south of Darmstadt (Germany) showed ¹³C values typical for C₃ plants. This suggests that in situ at the natural stand CO₂ was fixed mainly via the C₃ mode of photosynthesis rather than via the CAM mode. However, experimental water stress shifts the CO₂ exchange pattern from the C₃ type to CAM type. Simultaneously, a diurnal rhythm of malic acid oscillation, typical for CAM, and increase of PEP-carboxylase and malic enzyme activities developed. Hence, Sedum acre is obviously to be classified as a facultative CAM plant. Because of the temperature characteristics of CO₂ exchange in Sedum acre, in situ CO₂ should be harvested from the atmosphere mainly during the seasons where water stress situations capable of inducing CAM are unlikely to occur.     

Is Cyclocardia (Conrad) a wastebasket taxon? Exploring the phylogeny of the most diverse genus of the Carditidae (Archiheterodonta,Bivalvia)

The carditid genus Cyclocardia is currently the most diverse genus of the family, including nearly 180 nominal species encompassing wide stratigraphical (Cretaceous–Recent) and geographical (Antarctica, South and North America, Europe, Africa, Alaska, Russia, Japan and New Zealand) ranges. Due to the lack of autapomorphies in the diagnosis of the genus and its large account of species, we re-evaluate the systematic and phylogenetic status of Cyclocardia. We applied three approaches: bibliographic revision, phylogenetic analysis and an exploration of morphological disparity. We used a shell–character matrix comprising 65 taxa (2 outgroups, 29 non-Cyclocardia carditids and 28 species of Cyclocardia) for phylogenetic and disparity analyses. Maximum Observable Rescaled Distances was used to construct a distance matrix to compare Cyclocardia species and other carditid groups. According to our results, Cyclocardia represents a non-monophyletic taxon and is thus a ‘wastebasket taxon’, chiefly because its diagnosis was based mainly on plesiomorphic characters. The European species C. kickxi and C. chameformis are placed within Scalaricardita, and the previously proposed genus Crassicardia is monophyletic (including C. crassidens, C. crebricostata, C. isaotakii and C. rjabininae). Three new genera are proposed for new groups identified by the phylogenetic analysis: South American Oesterheldia gen. nov. (including O. cannada and O. dalek), western North American Coanicardita gen. nov. (including C. ventricosa and C. occidentalis), and North Pacific Hippocampocardia gen. nov. (including H. barbarensis, H. hamiltonensis and H. yakatagensis). The newly defined monophyletic Cyclocardia is restricted to the Atlantic Ocean species C. borealis, C. novangliae and C. compressa.     

Kodiak®—a successful biological-control product for suppression of soil-borne plant pathogens of cotton

Cotton (Gossypium spp) has been the first large-scale, agronomic crop in the United States treated with a biological-control agent (BCA) for suppression of seedling diseases and long-term chronic diseases of the rhizosphere. The vast majority of cotton seed planted in the United States is now treated with Bacillus subtilis strain GB03, registered as Kodiak^? (Gustafson, Inc, Plano, TX, USA). Responses are typically a mixture of growth promotion (increased root mass) and disease suppression (Rhizoctonia and Fusarium spp). Strain GB03 shows exceptional rhizosphere competence, colonizing the rhizosphere of monocots and dicots. Though the initial success of strain GB03 has been observed in the production of cotton, other crops have shown positive yield responses following bacterization. Since B. subtilis is a spore-forming organism, it is extremely tolerant of environmental stresses, including seed-treatment pesticides, soil and seed pH, cultivar effects, edaphic factors and long-term storage. More importantly, it is readily produced with current fermentation technology. Other BCAs, such as Pseudomonas spp, do not readily adapt to large-scale production methods, and stability is a limiting factor. In order to be successful, scale-up production must provide a product with efficacy equivalent to the laboratory model. A better understanding of how fermentation and other production processes affect the efficacy and rhizosphere competence of biocontrol organisms is now required by the industry. Processes have to be carefully optimized for both maximum production and maximum efficacy. A strong collaboration and understanding between the agricultural industry and industrial microbiologists are required to continue the advance of new biologicals such as Kodiak^?. Received 06 February 1997/ Accepted in revised form 16 April 1997