Genetic relationship among species in the genus Sonneratia in China as revealed by inter-simple sequence repeat (ISSR) markers

Inter-simple sequence repeat (ISSR) analysis was used to establish the genetic relationship among six Sonneratia species in China. A total of 100 primers were screened, of which 11 polymorphic and informative patterns were selected to determine the genetic relationship. Four hundred and eighty five DNA bands were amplified, among which 481 bands (99.18%) were polymorphic. The average number of DNA bands amplified by each primer was 44. Similarity coefficients were calculated and a dendrogram was constructed by using UPGMA algorithm. The six Sonneratia species were divided into two major groups. Group I consisted of Sonneratia caseolaris, Sonneratia × gulngai, Sonneratia alba, and Group II included Sonneratia × hainanensis, Sonneratia ovata and Sonneratia apetala. In Group I, S. × gulngai was close to S. alba, and in Group II, S. × hainanensis was close to S. ovata. The genetic relationships estimated by the polymorphism of ISSR markers are basically in agreement with those previously inferred by morphological data. Thus, ISSR approach is a reliable marker system that can be used to study genetic relationship in the genus Sonneratia.     

Phylogenetic and biosystematic relationships in four highly disjunct polyploid complexes in the subgenera Ceterach and Phyllitis in Asplenium (Aspleniaceae)

Phylogenetic studies using DNA sequences of two chloroplast regions, rbcL and trnL-F, demonstrate that the proposed genus Ceterach is a small clade within the large genus Asplenium, and sister to the Phyllitis clade. The Ceterach clade is characterised by irregular anastomosing veins and often densely scaled leaf blades. Its taxonomic status as a group nested within Asplenium is confirmed, and it is accepted here as a subgenus with seven species. The Ceterach clade comprises four lineages that correspond to disjunct polyploid complexes: the A. aureum clade forming a polyploid complex (4×, 6×, 8×) in Macaronesia, the A. ceterach clade forming a polyploid complex (2×, 4×, 6×) in the Mediterranean Basin, the A. paucivenosum clade (4×, 6×) in central Asia, and the A. dalhousiae clade (2×) with a disjunct distribution in the Himalaya, Yemen and Eritrea, and southwestern North America. Asplenium paucivenosum is sister to all other members of the Ceterach clade, whereas A. dalhousiae is sister to the A. aureum clade that includes tetraploid A. aureum, hexaploid A. lolegnamense, and octoploid A. parvifolium. Asplenium ceterach and its variations – including the hexaploid A. ceterach subsp. mediterraneum subsp. nov. first described below – form a monophyletic unit, sister to a clade consisting of A. aureum and A. dalhousiae. Asplenium cordatum from Africa and A. haugthonii from the isolated atlantic island of St. Helena are not members of the Ceterach clade, which suggests that leaf blades with dense indumenta have evolved at least twice within asplenioid ferns. The allotetraploid species A. hybridum has the chloroplast DNA from A. ceterach, and therefore the latter species is the maternal ancestor of the former. The other parent of this hybrid species is A. sagittatum that is nested within the sister clade of Ceterach, the Phyllitis clade comprising A. sagittatum and A. scolopendrium. The findings suggest that the current distribution of Ceterach is either the result of long-distance dispersal or represents fragmented relicts of a previously more widely distributed species.     

The Peniophorella praetermissa species complex (Basidiomycota)

The corticioid basidiomycete Peniophorella praetermissa has long been regarded as a morphologically variable species complex. An ITS-based phylogenetic study based on a worldwide sampling was carried out using parsimony and Bayesian inference. The resulting trees feature three major clades, further divided into well-supported subclades. These could be considered as distinct species, a contention that is further supported by crossing test data. Only two out of the eight phylogenetic lineages identified can be distinctly morphologically characterized: P. odontiaeformis and P. subpraetermissa. P. odontiaeformis is an odontioid species with a paleotropical distribution whereas the taxa in the remaining subclades have smooth basidiomata and are distributed in temperate areas. P. subpraetermissa is known only from the type collection and is distinguished microscopically by its reddish brown apically encrustated cystidia. Taxa in the remaining subclades are impossible to distinguish from each other morphologically, and therefore, are viewed as a species complex, P. praetermissa s. lat. One of the subclades, which is widely distributed but restricted to the Northern hemisphere, is proposed to represent P. praetermissa s. str. An epitype is selected from the same area as the holotype, among the specimens studied here. However, the geographically most widespread clade with many representatives from both hemispheres is here referred to as P. pertenuis, a taxon that was previously considered a synonym to P. praetermissa.     

Euploid and aneuploid evolution in Potamogeton (Potamogetonaceae): a factual basis for interpretation

In a review of chromosome numbers in the genus Potamogeton, we highlight numerous errors that have crept into the literature. These have resulted chiefly from reliance on abstracts in chromosome number indices and compilations, rather than on the original publications, but partly also because of misleading summaries even in the primary literature. We present a list of counts that we believe are original and genuine, and a list of those that were never made but which nevertheless appear in the literature. Scrutiny of the list of accepted counts indicates that aneuploidy is widespread in the genus and that transition between the two common chromosome numbers (2n=26 and 2n=28) has occurred several times. Currently available data are insufficient to resolve the question of the ancestral base number. We also present details of the first chromosome counts from English populations of five taxa: P. polygonifolius Pourr. (2n=28), P. pectinatus L. (2n=ca. 78), P. perfoliatus L. (2n=ca. 52), P.×nitens Weber (P. gramineus×P. perfoliatus) (2n=ca. 52) and P.×salicifolius Wolfg. (P. lucens×P. perfoliatus) (2n=ca. 52).     

Effects of competition on an endangered limpet Patella ferruginea (Gastropoda: Patellidae): Implications for conservation

Spatial and trophic competitive interactions were analysed for the seldom-studied limpet Patella ferruginea (which is considered as an “extinction risk”). Spatial patterns of distribution of P. ferruginea were studied using quadrats of 1 × 1 m² at several transects along the coastline, whereas trophic interactions were studied through manipulations of densities of P. ferruginea and Patella caerulea in experimental plots located at the mid-shore. Physical parameters were measured inside each plot to determine the microenvironmental differences between fenced and unfenced plots. Fenced plots of 50 × 50 cm² were used with six different treatments. Mortality was recorded every 15 days and length was measured monthly during the 3.5 months of the experiment. At the beginning and end of the experiment, lengths and weights of limpets were recorded and chlorophyll concentration was measured by spectrophotometric analysis of rock surface. Both species showed increased mortality and reduced size and weight in treatments with greater densities. High intraspecific competition was detected in P. caerulea compared with P. ferruginea whereas asymmetrical interspecific competition was observed. The results suggest that P. caerulea is the superior competitor, possibly due to differences in radular morphology and mobility between the two species. Microalgal food assessment showed that it is probably a limiting resource, especially for P. caerulea, although this species has a lower biomass than P. ferruginea. The high intraspecific competition observed in P. caerulea could be responsible for the coexistence of both species. The present study may be useful in helping to conserve P. ferruginea, which is presently under serious threat of extinction, because the results show that experimental fences are a viable means of concentrating breeding individuals.     

Phylogenetic relationships and the maternal donor of Roegneria (Triticeae: Poaceae) based on three nuclear DNA sequences (ITS,Acc1, and Pgk1) and one chloroplast region (trnL-F)

Roegneria is a polyploid perennial genus in the tribe Triticeae. Some species of Roegneria are morphologically similar to genus Elymus and have been classified in Elymus. To investigate the delimitation and phylogenetic relationships of Roegneria, nuclear (ITS, Acc1, and Pgk1) and chloroplast (trnL–trnF) DNA regions were sequenced for 38 allopolyploid species and 32 diploid species of Triticeae. Phylogenetic analyses of nuclear DNA revealed that all Roegneria species were included in the St and Y genome clades, and that the Y genome was closely related to the V and Xp genomes. The chloroplast DNA dataset showed that Roegneria species were grouped with Pseudoroegneria species. The Pseudoroegneria species from the Middle East (P. libanotica and P. tauri) and Central Asia (P. strigosa) were more closely related to Roegneria species. The results suggested that: (i) the species containing the St and Y genomes should be segregated from Elymus and treated as a distinct genus, Roegneria, based on the genomic constitution; (ii) P. libanotica, P. tauri, and/or P. strigosa potentially served as the maternal donor of the St genome in Roegneria; (iii) The Y genome of Roegneria originated from a diploid Y genome species, and the V and Xp genomes may have contributed to Y genome formation; (iv) among Roegneria species of previously uncertain genomic constitution, R. seriotina was tetraploid and possessed the StY genomes, E. calcicolus was hexaploid with the StYH genomic constitution and should be classified in Campeiostachys, R. glaucifolia possessed the StStY genomes, and R. tschimganica had the genomic constitution St₁St₂Y.     

Alexandrium catenella and Alexandrium minutum blooms in the Mediterranean Sea: Toward the identification of ecological niches

Annual recurrent blooms of the toxic dinoflagellates Alexandrium catenella and Alexandrium minutum were detected from 2000 to 2003 in harbours along the Catalan coast. The interrelation study between the occurrence of the blooms and specific external conditions at the study sites demonstrated that different factors are required for the bloom of each Alexandrium species. Concentrations higher than 10⁵ cells l⁻¹ of A. catenella were only detected in Tarragona harbour. These blooms were associated with water surface temperature between 21 and 25 °C and salinities of around 34 psu or higher than 37 psu. A. minutum appeared widely spread along the Catalan coast, though the most intensive and recurrent blooms of this species were observed in Arenys de Mar harbour. Concentrations of millions of cells per litre of A. minutum were associated with water temperatures below 14 °C and salinities of around 34–36 psu. A. minutum cell densities showed a positive significant correlation with NO₃ but a negative correlation with NH₄. On the other hand, A. catenella blooms dominated when both NO₃ and NH₄ levels were high. The prevailing inorganic nitrogen form (NO₃ vs. NH₄) could explain why these two species rarely coincide in the same harbours. Accumulation of cysts in the sediment was found to be an important potential factor for the recurrence of these species. The 4.3 × 10³ A. catenella cysts cm⁻³ of wet sediment in Tarragona harbour and the 3.02 × 10³ A. minutum cysts cm⁻³ of wet sediment in Vilanova harbour were the highest concentrations observed from the cyst study. Confined waters such as harbours play an important role as reservoirs for the accumulation of cysts and vegetative cells, which contributes to the expansion of these dinoflagellates in the region. However, the particular environmental conditions are also decisive factors of bloom intensity.     

Paralygodium meckertii sp. nov. (Schizaeaceae) from the Upper Cretaceous (Coniacian) of Vancouver Island, British Columbia, Canada

More than 50 specimens of permineralized fertile pinnules with abaxially borne sporangia have been discovered in calcareous marine nodules from the Upper Cretaceous (Coniacian) Comox Formation from the Eden Main localities on Vancouver Island, British Columbia, Canada. Isolated pinnules 1.6–3.0 mm wide × 1.6–2.8 mm long are lobed and abaxially enrolled to form irregular globose structures. Pyriform sporangia 216–300 μm wide × 360–468 μm long occur in two rows on the abaxial surface of pinnule lobes. Sporangia have an apical annulus of 15–18 cells. Spores are tetrahedral and trilete, 33–42 μm in diameter, with straight to concave interradial sides, laesurae extending nearly to the equator, and a psilate exine. Spores are assignable to the sporae dispersae genus Deltoidospora. Fertile pinnules are compared to fossils of Anemia poolensis and two previously described species of Paralygodium, and show closest similarities to P. vancouverensis from the Eocene of British Columbia. The Cretaceous Eden Main specimens differ in number of pinnule lobes and their morphology and are described as a new taxon: P. meckertii sp. nov. This discovery extends the Cretaceous geographic range of Paralygodium from Japan to North America and adds to our knowledge of the diversity of extinct schizaeaceous ferns.     

Screening the physical properties of novel Pseudomonas exopolysaccharides by HPSEC with multi-angle light scattering and viscosity detection

The physical properties of three novel acidic exopolysaccharides obtained from P. marginalis types A, B and C, one from P. ‘gingen’, one from P. andropogenis and one from P. fluorescens have been partially characterized. These EPSs were chromatographed on three serially placed SE Shodex OH pak columns covering a molar mass range for pullulans from about 4 × 10⁷ to 1 × 10³. The mobile phase was 0.05 M NaNO₃. Physical measurements were performed on about 30 mg of sample for each EPS. The weight average molar mass of these EPSs ranged from about 0.71 to 2.85 × 10⁶, the weight average intrinsic viscosity from 7.15 to 35.3 dl/ g and the radius of gyration from 62 to 123nm. The polydispersities of these EPSs ranged from 1.01 to 1.37. The large molar mass, size and viscosities of these EPSs may indicate that they have potential for use as thickeners, stabilizers, emulsifiers, and gelling agents in the food and non-food industries.     

Leaf alkanes in Persea and related taxa

The normal-alkane range in leaf cuticular waxes from 22 Persea species and cultivars and from the closely related genus Beilschmiedia was C₂₃ H₄₈ to C₃₅, H₇₂; alkanes with an odd number of carbon atoms predominated, C₃₃ H₆₈ usually constituting about half of the total wax. The alkane profiles gave good agreement with established taxonomy. Beilschmiedia showed an alkane distribution quite different from that of the Persea taxa. Amongst Persea species, the geographical and phylogenetic distinctiveness of P. indica and P. donnell-smithii were reflected in the distinctiveness of their alkanes. Within the subgenus Persea. the morphologically most distinct entity. P. schiedeana, also had a distinct alkane profile. Cultivars of hybrid origin indicated in their alkane proportions pronounced gene interaction.     

Fruiting body-guided molecular identification of root-tip mantle mycelia provides strong indications of ectomycorrhizal associations in two species of Sistotrema (Basidiomycota)

Fruiting body guided sequence analysis of mycorrhizal root-tip mycelia is a powerful yet relatively sparsely explored method for species-level identification of mycorrhizal fungi. It is used in this study to indicate mycorrhizal associations in the corticioid (resupinate) genus Sistotrema of the cantharelloid clade through phylogenetic analysis of the ITS and nuLSU rDNA regions of two spatiotemporally co-occurring Sistotrema fruiting bodies and ectomycorrhizal root tips. The genus Sistotrema is confirmed to be polyphyletic, and the mycorrhizal species form a strongly supported monophyletic clade together with the stipitate genus Hydnum. The remaining lineages of Sistotrema may well be saprotrophic, the nutritional mode traditionally attributed to the genus, but the phylogenetic analyses show that they should be excluded from Sistotrema. The cantharelloid clade contains several mycorrhizal genera, but no symbiotic associations have previously been demonstrated for Sistotrema.     

PHYLOGENETIC ANALYSIS OF THE GENUS EUGLENA (EUGLENOPHYCEAE) WITH PARTICULAR REFERENCE TO THE TYPE SPECIES EUGLENA VIRIDIS1

Euglena viridis (subgenus Euglena) serves as the type species for the genus Euglena. In this study, molecular phylogenetic analyses using a small subunit (SSU) and a combined SSU–partial large subunit rDNA data set for members of the genus Euglena showed that strains identified as E. viridis on the basis of morphology are distributed between two separate nonsister clades. Although all the E. viridis strains examined were morphologically indistinguishable and possessed spherical mucocysts and stellate chloroplasts with one paramylon center, there was a high degree of sequence divergence between the E. viridis strains in different clades, making this a cryptic species. Like E. viridis, all taxa from the subgenus Euglena are characterized by having one or more stellate chloroplasts with paramylon grains clustered around the center of the chloroplast. These additional taxa were divided into four clades in all the molecular analyses. Strains of Euglena stellata formed two nonsister clades whose members had a single aggregate chloroplast with paramylon center and spindle‐shaped mucocysts. A geniculata clade included species with one or two stellate chloroplasts with paramylon centers and spherical mucocysts, and the cantabrica clade had members with one stellate chloroplast with paramylon center and spherical mucocysts often arranged in spiral rows. Interspersed among these were three additional clades bearing taxa from the subgenus Calliglena that contains members with discoid plastids and pyrenoids that may or may not be capped with paramylon. These taxa formed a laciniata clade, mutabilis clade, and gracilis clade. This study demonstrates that E. viridis and E. stellata are cryptic species that can only be distinguished at the molecular level. Because E. viridis is the designated type species for the genus Euglena, we designated an epitype for E. viridis.     

Laboratory investigations on the potential of entomopathogenic fungi for biocontrol of Helicoverpa armigera (Lepidoptera: Noctuidae) larvae and pupae

The susceptibility of third instar Helicoverpa armigera to seven strains of three entomopathogenic fungal species, i.e. Metarhizium anisopliae, Beauveria bassiana and Paecilomyces fumosoroseus, was tested under laboratory conditions using the larval immersion method. High efficacies ranging from 68 to 100% corrected mortality were recorded with more profound effects in treatments with B. bassiana and P. fumosoroseus strains. The median lethal concentration (LC₅₀) for L3 was 6.0×10⁵ in M. anisopliae 79, 1.5×10⁵ in B. bassiana 124 and 4.2×10⁴ in P. fumosoroseus 14. These three strains were further used to characterize the age-dependent mortality of different larval stages (L2-L5) and the effect against pupae of H. armigera. Larval stages did not differ in their mortality but differed i in median lethal time, with shorter values recorded in the second instar. Tested fungi also caused a high reduction between 74.4 and 100% in the emergence of pupae using the soil inoculation method and the pupal immersion technique. All three fungal species, especially P. fumosoroseus, have a high potential for biocontrol of H. armigera larvae and also as a soil treatment targeting the pupae.     

Phylogenomic relationships and species identification of the olive genus Olea (Oleaceae)

The olive genus Olea includes c. 30–40 taxa in three subgenera (Olea, Tetrapilus, and Paniculatae) within the family Oleaceae. Historically, the Olea genus was classified into four groups that were overall well supported by reconstructed phylogenies, despite incomplete sampling of subgenus Tetrapilus and poor resolution within clades. These analyses also showed that the genus was not monophyletic. Reliable identification of Olea species is important for both their conservation and utilization of this economically important genus. In this study, we used phylogenomic data from genome skimming to resolve relationships within Olea and to identify molecular markers for species identification. We assembled the complete plastomes, and nrDNA of 26 individuals representing 13 species using next-generation sequencing and added 18 publicly available accessions of Olea. We also developed nuclear SNPs using the genome skimming data to infer the phylogenetic relationships of Olea. Large-scale phylogenomic analyses of 138 samples of tribe Oleeae supported the polyphyly of Olea, with Olea caudatilimba and Olea subgenus Tetrapilus not sharing their most recent common ancestor with the main Olea clade (subgenus Paniculatae and subgenus Olea). The interspecific phylogenetic resolution was poor owing to a possible rapid radiation. By comparing with the plastome data, we identified the markers ycf1b and psbE-petL as the best Olea-specific chloroplast DNA barcodes. Compared with universal barcodes, specific DNA barcodes and super-barcode exhibited higher discriminatory power. Our results demonstrated the power of phylogenomics to improve phylogenetic relationships of intricate groups and provided new insights into barcodes that allow for accurate identification of Olea species.     

Isolation of a new vahlkampfiid amoeba from soil: Paravahlkampfia lenta n. sp.

When the genus Paravahlkampfia was distinguished from the genus Vahlkampfia on the basis of significant differences in small subunit ribosomal DNA sequences, Paravahlkampfia ustiana was the only described species of this new genus. More recently, a vahlkampfiid strain has been isolated (from soil from an upland farm in Scotland) which has trophozoite and cyst morphology more similar to P. ustiana than to other non-flagellating vahlkampfiid species. Also, it clusters with P. ustiana in phylogenetic trees derived from 5.8S ribosomal DNA sequences. However, it is significantly different from P. ustiana in both phenotype and internal transcribed spacer sequence. Consequently, a new species, Paravahlkampfia lenta, is proposed.     

Synthesis of graft copolymer (k-carrageenan-g-N,N-dimethylacrylamide) and studies of metal ion uptake, swelling capacity and flocculation properties

Graft copolymer of k-carrageenan and N,N-dimethylacrylamide has been synthesized by free radical polymerization using peroxymonosulphate/glycolic acid redox pair in an inert atmosphere. The grafting parameters i.e. grafting ratio, add on and efficiency decrease with increase in concentration of k-carrageenan from 0.6 to 1.4 g dm⁻³ and hydrogen ion from 3 × 10⁻³ to 7 × 10⁻³ mol dm⁻³, but these grafting parameters increase with increase in concentration of N,N-dimethylacrylamide from 16 × 10⁻² to 32 × 10⁻² mol dm⁻³, and peroxymonosulphate from 0.8 × 10⁻² to 2.4 × 10⁻² mol dm⁻³. The metal ion sorption, swelling behaviour and flocculation properties have been studied. The intrinsic viscosity of pure and grafted samples has been measured by using Ubbelohde capillary viscometer. Flocculation capability of k-carrageenan and k-carrageenan-g-N,N-dimethylacrylamide for both coking and non-coking coals has been studied for the treatment of coal mine waste water. The graft copolymer has been characterized by Infrared (IR) spectroscopy and thermogravimetric analysis.     

Lack of effect of the nematophagous fungus Duddingtonia flagrans on the development of the dung beetle, Aphodius constans

The nematode-trapping fungus Duddingtonia flagrans may be used as a biological control agent of gastro-intestinal nematode larvae of ruminants by feeding the hosts with fungal spores. This trial was intended to search an eventual detrimental impact of the presence of spores of D. flagrans in high numbers in goat feces on the common dung beetle, Aphodius constans (Coleoptera: Aphodiidae). A. constans eggs were settled in feces derived from grazing goats fed spores at daily dose rates of 0, 0.25 × 10⁶, 0.5 × 10⁶ or 10⁶ spores/kg BW. At the end of the incubation period, the number of adults that have emerged from eggs were counted and compared between dose rates. No difference in emergence rate between treatments can be seen. The presence of D. flagrans spores in goat feces, even in large numbers, did not alter the development of A. constans.     

Phylogenetic reassessment of the Teloschistaceae (lichen-forming Ascomycota, Lecanoromycetes)

The Teloschistaceae is a widespread family with considerable morphological and ecological heterogeneity across genera and species groups. In order to provide a comprehensive molecular phylogeny for this family, phylogenetic analyses were carried out on sequences from the nuclear ribosomal ITS region obtained from 114 individuals that represent virtually all main lineages of Teloschistaceae. Our study confirmed the polyphyly of Caloplaca, Fulgensia and Xanthoria, and revealed that Teloschistes is probably non-monophyletic. We also confirm here that species traditionally included in Caloplaca subgenus Gasparrinia do not form a monophyletic entity. Caloplaca aurantia, C. carphinea and C. saxicola s. str. groups were recovered as monophyletic. The subgenera Caloplaca and Pyrenodesmia were also polyphyletic. In the subgenus Caloplaca, the traditionally recognized C. cerina group was recovered as monophyletic. Because this study is based solely on ITS, to maximize taxon sampling, the inclusion of phylogenetic signal from ambiguously aligned regions in MP (recoded INAASE and arc characters) resulted in the most highly supported phylogenetic reconstruction, compared with Bayesian inference restricted to alignable sites.