Molecular phylogeny of Phoma and allied anamorph genera: Towards a reclassification of the Phoma complex

The present generic concept of Phoma is broadly defined, with nine sections being recognised based on morphological characters. Teleomorph states of Phoma have been described in the genera Didymella, Leptosphaeria, Pleospora and Mycosphaerella, indicating that Phoma anamorphs represent a polyphyletic group. In an attempt to delineate generic boundaries, representative strains of the various Phoma sections and allied coelomycetous genera were included for study. Sequence data of the 18S nrDNA (SSU) and the 28S nrDNA (LSU) regions of 18 Phoma strains included were compared with those of representative strains of 39 allied anamorph genera, including Ascochyta, Coniothyrium, Deuterophoma, Microsphaeropsis, Pleurophoma, Pyrenochaeta, and 11 teleomorph genera. The type species of the Phoma sections Phoma, Phyllostictoides, Sclerophomella, Macrospora and Peyronellaea grouped in a subclade in the Pleosporales with the type species of Ascochyta and Microsphaeropsis. The new family Didymellaceae is proposed to accommodate these Phoma sections and related anamorph genera. The present study demonstrated that Phoma radicina, the type species of Phoma sect. Paraphoma and Phoma heteromorphospora, the type species of Phoma sect. Heterospora can be assigned to the Phaeosphaeriaceae and Leptosphaeriaceae respectively.     

AFLPs detect low genetic diversity for Phytophthora nemorosa and P. pseudosyringae in the US and Europe

In California and Oregon, two recently described oomycete forest pathogens, Phytophthora nemorosa and P. pseudosyringae, overlap in their host and geographic ranges with the virulent P. ramorum, causal agent of “sudden oak death.” Epidemiological observations, namely broader geographic distribution and lack of landscape-level mortality, led to the hypothesis they are native to this region, whereas multiple lines of evidence indicate P. ramorum is exotic to North America. We used AFLP analysis to measure genetic variability in the homothallic P. nemorosa and P. pseudosyringae and to evaluate the hypothesis of endemism. We analysed 39 P. nemorosa and 48 P. pseudosyringae isolates (29 American and 19 European) from throughout their geographic and host ranges. In the US, both P. nemorosa and P. pseudosyringae have a dominant AFLP clone with several closely related variants. There is no evidence that genetic diversity is partitioned by host or location in P. nemorosa, but the US P. pseudosyringae clonal lineage is largely nested within a more genetically variable European group. Though the absence of highly variable sampled source populations does not allow us to determine whether each species is native or introduced in the western US with certainty, the results are most consistent with the hypothesis that both are introduced — P. pseudosyringae perhaps from Europe. Invasive Phytophthora species are increasingly being implicated in emergent forest diseases, highlighting the need to identify and characterize both native and previously unknown introduced forest Phytophthoras.     

Septal pore complex morphology in the Agaricomycotina (Basidiomycota) with emphasis on the Cantharellales and Hymenochaetales

The ultrastructure of septa and septum-associated septal pore caps are important taxonomic markers in the Agaricomycotina (Basidiomycota, Fungi). The septal pore caps covering the typical basidiomycetous dolipore septum are divided into three main phenotypically recognized morphotypes: vesicular-tubular (including the vesicular, sacculate, tubular, ampulliform, and globular morphotypes), imperforate, and perforate. Until recently, the septal pore cap-type reflected the higher-order relationships within the Agaricomycotina. However, the new classification of Fungi resulted in many changes including revision of existing and addition of new orders. Therefore, the septal pore cap ultrastructure of more than 325 species as reported in literature was related to this new classification. In addition, the septal pore cap ultrastructures of Rickenella fibula and Cantharellus formosus were examined by transmission electron microscopy. Both fungi have dolipore septa associated with perforate septal pore caps. These results combined with data from the literature show that the septal pore cap-type within orders of the Agaricomycotina is generally monomorphic, except for the Cantharellales and Hymenochaetales.It appears from the fungal phylogeny combined with the septal pore cap ultrastructure that the vesicular-tubular and the imperforate type both may have arisen from endoplasmic reticulum. Thereafter, the imperforate type eventually gave rise to the perforate septal pore cap-type.     

Homo floresiensis: a cladistic analysis

The announcement of a new species, Homo floresiensis, a primitive hominin that survived until relatively recent times is an enormous challenge to paradigms of human evolution. Until this announcement, the dominant paradigm stipulated that: 1) only more derived hominins had emerged from Africa, and 2) H. sapiens was the only hominin since the demise of Homo erectus and Homo neanderthalensis. Resistance to H. floresiensis has been intense, and debate centers on two sets of competing hypotheses: 1) that it is a primitive hominin, and 2) that it is a modern human, either a pygmoid form or a pathological individual. Despite a range of analytical techniques having been applied to the question, no resolution has been reached. Here, we use cladistic analysis, a tool that has not, until now, been applied to the problem, to establish the phylogenetic position of the species. Our results produce two equally parsimonious phylogenetic trees. The first suggests that H. floresiensis is an early hominin that emerged after Homo rudolfensis (1.86 Ma) but before H. habilis (1.66 Ma, or after 1.9 Ma if the earlier chronology for H. habilis is retained). The second tree indicates H. floresiensis branched after Homo habilis.     

Three new species and two new combinations in the Aizoaceae from the Western and Northern Cape of South Africa

Three new species of Aizoaceae from the Western Cape are described. Octopoma tanquanum Klak and Vlokia montana Klak are dwarf shrubby or mat-forming succulents which belong to the Ruschieae in the Ruschioideae. Mesembryanthemum knolfonteinense Klak of the Mesembryanthemoideae is a geophyte. Octopoma tanquanum inhabits relatively low lying arid areas within the Tanqua Karoo and the Little Karoo and is thought to be closely allied to the two species of Octopoma found in the Little Karoo. Both V. montana and M. knolfonteinense grow at relatively high altitudes within the fynbos biome. In addition, Ruschia littlewoodii L.Bolus is transferred to Phiambolia, and two new combinations are made in Antimima for Ruschia hexamera L.Bolus and Ruschia radicans L.Bolus.     

The ITS region as a taxonomic discriminator between Fusarium verticillioides and Fusarium proliferatum

The maize pathogens Fusarium verticillioides (Fv) and Fusarium proliferatum (Fp) are morphologically very similar to one another, so Fp isolates have been often mistaken as Fusarium moniliforme (the former name of Fv). The only presently accepted morphological discriminator between these species is the presence/absence of polyphialides. Here, a collection of 100 Fusarium strains, isolated from infected maize kernels on plants grown in north-western Italy, were assigned as Fv or Fp on the basis of the presence/absence of polyphialides. This classification was tested on a subset of isolates by sexual crosses, ITS and calmodulin sequencing and AFLP profiling. An ITS-RFLP assay was extended to the full collection and to a number of Fv and Fp isolates of different geographical origin and hosts. The ITS region is proposed as taxonomically informative for distinguishing between Fp and Fv.     

The deubiquitinase emperor's thumb is a regulator of apoptosis in Drosophila

We have characterized the gene emperor's thumb (et) and showed that it is required for the regulation of apoptosis in Drosophila. Loss-of-function mutations in et result in apoptosis associated with a decrease in the concentration of DIAP1. Overexpression of one form of et inhibits apoptosis, consistent with et having an anti-apoptotic function; however, overexpression of a second form of et induces apoptosis, indicating that the two forms of et may have competing functions. et encodes a protein deubiquitinase, suggesting it regulates apoptosis by controlling the stability of apoptotic regulatory proteins.     

Comparative study of floral development in Onobrychis melanotricha, Hedysarum varium and Alhagi persarum (Leguminosae: Papilionoideae: Hedysareae)

Floral initiation and development of Hedysarum varium, Onobrychis melanotricha and Alhagi persarum was studied using epi-illumination light-microscopy techniques. The studied species belong to the tribe Hedysareae of the inverted repeat loss clade (IRLC clade), which is characterized by missing the large inverted repeat in the chloroplast genome. The main aim of our study was to determine developmental bases for similarities and differences among the three taxa and to verify the position of Alhagi relative to other genera of the IRLC clade. According to our observations, bracteoles are missing in Onobrychis melanotricha, but are present in the other two species. All three species share unidirectional sepal initiation starting with a median abaxial sepal and bidirectional petal initiation. Stamen initiation is unidirectional in all except in the outer stamen whorl of Hedysarum varium, where it is bidirectional. An important ontogenetic feature in O. melanotricha is the existence of five common primordia, which give rise to petal and stamen primordia. Although in H. varium and O. melanotricha common primordia are observed at some stages in floral organ initiations, in Alhagi all organs are initiated separately. Moreover, overlap in time of floral organs initiation occurs in H. varium and O. melanotricha, but not in A. persarum. The carpel initiates concurrently with the petal primordia in all. It might be presumed that Alhagi is primitive in relation to the other studied Hedysareae taxa, due to the presence of bracteoles, the absence of common primordia, and the lack of overlap in time of different organ initiations.     

Lavandula angustifolia essential oil as a novel and promising natural candidate for tick (Rhipicephalus (Boophilus) annulatus) control

Lavandula angustifolia is a well known herbal medicine with a variety of useful properties, including its acaricidal effect. This experiment was carried out to study the bioacaricidal activity of L. angustifolia essential oil (EO) against engorged Rhipicephalus (Boophilus) annulatus (Acari; Ixodidae) females. For this purpose six serial concentrations (0.5, 1.0, 2.0, 4.0, 6.0 and 8.0% w/v) of L. angustifolia EO were used. There was considerable mortality in concentrations more than 4.0% although there were no differences between 6.0 and 8.0% in all measured criteria. The mortality rate 24 h after inoculation was 73.26 and 100% in groups treated with 4.0 and 8.0% EO, respectively. Lavender EO also reduced tick egg weight in a concentration-dependent manner. The amount of eggs produced varied from 0.12 g (at 0.5% EO) to 0.00 g (at 8.0% EO) but did not differ statistically from the control. L. angustifolia EO caused 100% failure in egg laying at 6.0 and 8.0% whereas this value in the control group was zero. A positive correlation between L. angustifolia EO concentration and tick control, assessed by relative mortality rate and egg-laying weight, was observed by the EO LC/EC₅₀, which, when calculated using the Probit test, was 2.76-fold higher than the control. Lavender is a promising acaricidal against R. (B.) annulatusin vitro.     

The Rieske/cytochrome b complex of Heliobacteria

Heliobacteria have a Rieske/cytochrome b complex composed of a Rieske protein, a cytochrome b_6, a subunit IV and a di-heme cytochrome c. The overall structure of the complex seems close to the b₆f complex from cyanobacteria and chloroplasts to the exception of the di-heme cytochrome. We show here by biochemical and biophysical studies that a heme c_i is covalently attached to the Rieske/cytochrome b complex from Heliobacteria. We studied the EPR signature of this heme in two different species, Heliobacterium modesticaldum and Heliobacillus mobilis. In contrast to the case of b₆f complex, a strong axial ligand to the heme is present, most probably a protonatable amino acid residue.     

Phylogenetic relationships among Southeast Asian climbing bamboos (Poaceae: Bambusoideae) and the Bambusa complex

A phylogenetic analysis of Bambusa and allies based on the plastid DNA non-coding regions rps16-trnQ, trnC-rpoB, trnH-psbA and trnD-T, and a partial nuclear GBSSI gene, was carried out. This included representatives from all four Bambusa subgenera (including type species), a group of segregate Southeast Asian genera distinctive by their climbing–scrambling culms (Dinochloa, Holttumochloa, Kinabaluchloa, Maclurochloa, Soejatmia, Sphaerobambos), and two other Bambusinae genera (Dendrocalamus, Gigantochloa). The results do not support the present subgeneric classification of Bambusa. The climbing Southeast Asian genera, all of which include species previously placed in Bambusa, are distinct from the “core Bambusa group” (type species and alliance) and the Bambusa complex generally.     

Phylogenetic implication of the chloroplast rpoC1 intron loss in the Aizoaceae (Caryophyllales)

A representative sample of 69 species from all recognized infrafamilial taxa of the family Aizoaceae (angiosperms, eudicotyledons, Caryophyllales) was surveyed for the presence/absence of the rpoC1 intron. PCR fragments of the samples fall into two size classes: a long fragment of approximately 1200 bp, and a short fragment of approximately 500 bp which was found in all samples from the tribes Drosanthemeae and Ruschieae of subfamily Ruschioideae. The length difference of about 700 bp corresponds to the length of the intron (738 bp in tobacco). Sequencing of the short fragment from Monilaria moniliformis revealed the precise excision of the intron as found in a previous study of the cactus family. It is concluded that the intron lacks in all samples from the clade including the tribes Drosanthemeae and Ruschieae of subfamily Ruschioideae, thus providing valuable PCR-based, sequence- and morphology-independent evidence for the monophyly of this lineage.     

RPB2 sequences reveal a close phylogenetic relationship between tetraploid Hordelymus and diploid Hordeum species in Triticeae (Poaceae)

The origin of Hordelymus genome has been debated for years, and no consensus conclusion was reached. In this study, we sequenced and analyzed the RPB2 (RNA polymerase subunit II) gene from Hordelymus europaeus (L.) Harz, and its potential diploid ancestor species those were suggested in previous studies. The focus of this study was to examine the phylogenetic relationship of Hordelymus genomes with its potential donor Hordeum, Psathyrostachys, and Taeniatherum species. Two distinguishable copies of sequences were obtained from H. europaeus. The obvious difference between the two copies of sequences is a 24 bp indel (insertion/deletion). Phylogenetic analysis showed a strong affinity between Hordeum genome and Hordelymus with 85% bootstrap support. These results suggested that one genome in tetraploid H. europaeus closely related to the genome in Hordeum species. Another genome in H. europaeus is sister to the genomes in Triticeae species examined here, which corresponds well with the recently published EF-G data. No obvious relationship was found between Hordelymus and either Ta genome donor, Taeniatherum caput-medusae or Ns genome donor, Psathyrostachys juncea. Our data does not support the presence of Ta and Ns genome in H. europaeus, and further confirms that H. europaeus is allopolyploid.     

Tetraploid European Salicornia species are best interpreted as ecotypes of multiple origin

Salicornia procumbens and S. stricta are two tetraploid European salt marsh species of locally adjacent but ecologically differentiated distribution. Whereas S. procumbens grows in the lowest part of the salt marsh, it is replaced by S. stricta in the middle part (and diploid Salicornias in the upper part). Using AFLPs and a reciprocal transplantation experiment, we investigated whether the two species represent distinct evolutionary lineages. The analysis of AFLP variation clearly showed that both species are not monophyletic. Also, accessions do not cluster according to geographical origin. The transplantation experiment revealed that S. procumbens shows significantly reduced fitness when transplanted into the habitat of S. stricta. Reduction of fitness of S. stricta in the habitat of S. procumbens is less obvious. In both habitats S. procumbens performs better than S. stricta in terms of seed production and dry weight. On the background of these results, it is hypothesized that S. procumbens and S. stricta represent intraspecific ecotypes which originated repeatedly in adaptation to their specific environments and which dispersed widely. We hypothesize that the ecologically vicariant distribution of S. procumbens and S. stricta along the inundation gradient in the saltmarsh in spite of their good performance in the respective non-native habitats results from strong selection during seed germination and seedling establishment. Reproductive isolation between locally adjacent or even intermingled ecotypes is suggested to be achieved by high levels of selfing.     

Phylogeny of Phaeomollisia piceae gen. sp. nov.: a dark, septate, conifer-needle endophyte and its relationships to Phialocephala and Acephala

Dark, septate endophytes (DSE) were isolated from roots and needles of dwarf Picea abies and from roots of Vaccinium spp. growing on a permafrost site in the Jura Mountains in Switzerland. Two of the isolates sporulated after incubation for more than one year at 4 °C. One of them was a hitherto undescribed helotialean ascomycete Phaeomollisia piceae gen. sp. nov., the other was a new species of Phialocephala, P. glacialis sp. nov. Both species are closely related to DSE of the Phialocephala fortinii s. lat.-Acephala applanata species complex (PAC) as revealed by phylogenetic analyses of the ITS and 18S rDNA regions. Morphologically dissimilar fungi, such as Vibrissea and Loramyces species, are phylogenetically also closely linked to the new species and the PAC. Cadophora lagerbergii and C. (Phialophora) botulispora are moved to Phialocephala because Phialocephala dimorphospora and P. repens are the closest relatives. Several Mollisia species were closely related to the new species and the PAC according to ITS sequence comparisons. One DSE from needles of Abies alba and one from shoots of Castanea sativa formed Cystodendron anamorphs in culture. Their identical 18S sequences and almost identical ITS sequences indicated Mollisia species as closest relatives, suggesting that Mollisia species are highly euryoecious.     

The effect of different primary producers on Hydrobia ulvae population dynamics: a case study in a temperate intertidal estuary

The effect of macroalgal blooms and the consequent disappearance of Zostera noltii meadows on Hydrobia ulvae population dynamics and production was studied in the Mondego estuary based on data obtained from January 1993 to September 1995. Sampling was carried out at a non-eutrophicated area, covered with Z. noltii, and also at an eutrophicated area, where seasonal Enteromorpha spp. blooms occur.Stable populations represented by individuals of all age classes were found only at the Z. noltii meadows throughout the study period. On the contrary, at the eutrophicated area, during most of the time, solely juveniles were present, with adults appearing only during the macroalgal bloom (>1.5 mm width).During the algal bloom (e.g. 1993), H. ulvae population density was clearly higher in the eutrophicated area due to the combined effect of stronger benthic recruitments (99% of veliger larvae newly recruited) and dispersion of juveniles proceeding from the Z. noltii meadows to this area. On the other hand, in the absence of macroalgae (spring of 1994), 98.9% of veliger larvae was recruited in the Z. noltii meadows. Therefore, H. ulvae seems to respond rapidly to macroalgal dynamics and its presence at the eutrophicated area depends on the existence of green macroalgae.H. ulvae presented the same benthic recruitment pattern at the two sampling areas, with new cohorts being produced in March, June, July and September. Depending on the time of the year in which the recruitment took place, cohorts showed different growth rhythms. However, after 12 months they reached a similar size.A three-generation life cycle involving a short-lived (16 months), fast growing spring generation, a medium growing (17-19 months) summer generation and a longer-lived (20 months) slower growing generation that overwinters is identified.As a general trend, productivity and mean population standing biomass were higher at the Z. noltii meadows, during the entire study, except for a short period, during the macroalgal bloom, when production was higher at the eutrophicated area. On the contrary, P/B? ratios were higher at the eutrophicated area. According to our results, H. ulvae population structure and yearly productivity are clearly affected by eutrophication, namely by the dynamics of macroalgal blooms.In the long run, we may infer that, following the disappearance of the Z. noltii meadows, due to eutrophication, H. ulvae would also tend to disappear, since reproductive adults were almost exclusively found in this area.     

Hybridizations and genetic relationships among Lindernia species (Scrophulariaceae): L. procumbens and two subspecies of L. dubia

Lindernia procumbens and L. dubia are common annual weeds in flooded rice fields of Japan. Two subspecies of L. dubia, subsp. major and subsp. dubia, are usually recognized in Japan but they are both regarded as synonyms of L. dubia elsewhere. In a cluster analysis based on AFLP, most L. dubia subsp. major formed a separate cluster from L. dubia subsp. dubia although 11% of haplotypes classified using AFLP were not coincident with classification using the shape of leaf bases, which is the commonly used identification trait. Artificial F₁ plants between L. procumbens and L. dubia subsp. major, and between L. procumbens and L. dubia subsp. dubia did not produce seed. Forty percent of capsules produced by F₁ plants from these two subspecies were slimmer and 80% pollen were sterile in slimmer capsules. However, seed number of most F₁ capsules was not different from that of self-fertilized plants, suggesting that there was no complete reproductive isolation between the subspecies. Natural hybridization of these subspecies may have occurred but we are not aware of it because F₁ plants are rare and F₂ plants are indistinguishable from these subspecies.