Phylogeny of the Bacillariaceae with emphasis on the genus Pseudo-nitzschia (Bacillariophyceae) based on partial LSU rDNA

In order to elucidate the phylogeny and evolutionary history of the Bacillariaceae we conducted a phylogenetic analysis of 42 species (sequences were determined from more than two strains of many of the Pseudo-nitzschia species) based on the first 872 base pairs of nuclear-encoded large subunit (LSU) rDNA, which include some of the most variable domains. Four araphid genera were used as the outgroup in maximum likelihood, parsimony and distance analyses. The phylogenetic inferences revealed the Bacillariaceae as monophyletic (bootstrap support ≥90%). A clade comprising Pseudo-nitzschia, Fragilariopsis and Nitzschia americana (clade A) was supported by high bootstrap values (≥94%) and agreed with the morphological features revealed by electron microscopy. Data for 29 taxa indicate a subdivision of clade A, one clade comprising Pseudo-nitzschia species, a second clade consisting of Pseudo-nitzschia species and Nitzschia americana, and a third clade comprising Fragilariopsis species. Pseudo-nitzschia as presently defined is paraphyletic and emendation of the genus is probably needed. The analyses suggested that Nitzschia is not monophyletic, as expected from the great morphological diversity within the genus. A cluster characterized by possession of detailed ornamentation on the frustule is indicated. Eighteen taxa (16 within the Bacillariaceae) were tested for production of domoic acid, a neurotoxic amino acid. Only P. australis, P. multiseries and P. seriata produced domoic acid, and these clustered together in all analyses. Since Nitzschia navis-varingica also produces domoic acid, but is distantly related to the cluster comprising the Pseudo-nitzschia domoic acid producers, it is most parsimonious to suggest that the ability of species in the Bacillariaceae to produce domoic acid has evolved at least twice.     

The influence of light quality on the development of the brown algae Petalonia and Scytosiphon

Petalonia fascia (O. F. Müll.) Kuntze, P. zosterifolia (Reinke) Kuntze and Scytosiphon lomentaria (Lyngb.) J. Ag. have been cultured in white, blue and red light of equal quantum irradiance at 15°C. Hairs, knot-filaments and Ralfsia-like crusts were formed only in blue light, whereas the prostrate system of red-grown plants consisted entirely of sparingly-branched and mostly uniseriate filaments. The production of erect thalli from the prostrate system was controlled or stimulated by red light, but these erect thalli became fertile only in the presence of blue light. All three species exhibited all of these types of response, although specific differences in the degree of certain types of response were observed.     

New gammaroid family, genera and species from subterranean waters of Japan, and their phylogenetic relationships (Crustacea: Amphipoda)

Luciobliviidae, a new family in the superfamily Gammaroidea (Amphipoda: Crustacea), is described on the basis of species in the genus Lucioblivio gen. nov. from subterranean waters of Japan. Mesogammaridae Bousfield, 1977 is rediagnosed; Octopupilla gen. nov. from subterranean waters of Japan is described and Eoniphargus (Uéno, 1955) from subterranean waters of Japan and Korea is included. The members of Lucioblivio , Octopupilla and Eoniphargus share several characters, including reduced eyes, a setose body, reduced coxae, feeble appendages and pedunculate coxal gills. To elucidate the phylogeny of the three genera among others, a sequence analysis of the 28S rRNA gene was conducted for 14 species in six families, including the three genera, from the superfamilies, Gammaroidea, Crangonyctoidea and Hadzioidea. The tree from a neighbour-joining analysis and the strict consensus tree from a maximum-parsimony analysis indicate monophyly of Mesogammaridae. Luciobliviidae is embedded within a clade of taxa belonging to the superfamily Gammaroidea. These results and the occurrence of gammarid-type calceoli in species of the new family indicate that Luciobliviidae should be placed within the superfamily Gammaroidea. © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 149 , 643–670.     

Intergeneric phylogenetic relationships in catfishes of the Loricariinae (Siluriformes: Loricariidae), with the description of Fonchiiloricaria nanodon: a new genus and species from Peru

Recent investigations in the upper Río Huallaga in Peru revealed the presence of an intriguing species of the Loricariinae. To characterize and place this species within the evolutionary tree of the subfamily, a molecular phylogeny of this group was inferred based on the 12S and 16S mitochondrial genes and the nuclear gene F-reticulon4. The phylogeny indicated that this distinctive species was a member of the subtribe Loricariina. Given its phylogenetic placement, and its unusual morphology, this species is described as a new genus and new species of Loricariinae: Fonchiiloricaria nanodon. This new taxon is diagnosed by usually possessing one to three premaxillary teeth that are greatly reduced; lips with globular papillae on the surface; the distal margin of lower lip bearing short, triangular filaments; the premaxilla greatly reduced; the abdomen completely covered by plates, with the plates between lateral abdominal plates small and rhombic; a caudal fin with 14 rays; the orbital notch absent; five lateral series of plates; dorsal-fin spinelet absent; preanal plate present, large and solid, and of irregular, polygonal shape, the caudal peduncle becoming more compressed posteriorly for the last seven to 10 plates.     

Comparative morphology and systematics of Chondrymenia lobata from the Mediterranean Sea and a phylogeny of the Chondrymeniaceae fam. nov. (Rhodophyta) based on rbcL sequence analyses

The Chondrymeniaceae Rodríguez-Prieto, G. Sartoni, S.-M. Lin & Hommersand, fam. nov., is proposed for Chondrymenia lobata. Analyses of rbcL sequences place the new family in a large gigartinalean assemblage that comprises the Cystocloniaceae–Solieriaceae complex. Plants are decumbent and growth takes place by division of multiple apical cells at the margin of the blade. Thalli consist of an outer cortex of subspherical to elongate cortical cells arranged in anticlinal rows, a subcortex of cells cross-linked by lateral arms, and a large central medulla composed of primary medullary filaments intermixed with numerous rhizoidal filaments. Male stages are reported in monoecious individuals. Inactive carpogonial branches consist of a two-celled filament that is directed inwards from the supporting cell. Functional carpogonial branches are oriented outwardly, with the carpogonia and trichogynes pointed towards the thallus surface. After presumed fertilization, the carpogonium fuses with the hypogynous cell and transfers the zygote nucleus. The hypogynous cell, in turn, fuses with the supporting cell which contains many haploid nuclei. The resulting fusion cell functions as an auxiliary cell that cuts off a single gonimoblast initial, which produces the gonimoblast filaments. Gametophytic cells close to the auxiliary cell unite with it to form a placental fusion network of variable size and outline, and a placental fusion cell. Proximal gonimoblast cells fuse with the placental fusion cell, while the distal cells differentiate into branched chains of subspherical carposporangia. The superficial similarity of the outwardly developed osteolate cystocarp is responsible for Kylin's (1956) placement of Chondrymenia in his family Sarcodiaceae; however, the manner in which the placenta is formed is more like that seen in the Cystocloniaceae–Solieriaceae complex.     

Phylogeny of the order Tintinnida (Ciliophora, Spirotrichea) inferred from small- and large-subunit rRNA genes

Concatenated sequences of small- and large-subunit rRNA genes were used to infer the phylogeny of 29 species in six genera of Tintinnida. We confirmed previous results on the positions of major clusters and the grouping of various genera, including Stenosemella, the paraphyletic Tintinnopsis, the newly investigated Helicostomella, and some species of the polyphyletic Favella. Tintinnidium and Eutintinnus were found to be monophyletic. This study contributes to tintinnid phylogenetic reconstruction by increasing both the number of species and the range of genetic markers analyzed.     

The blood alga: phylogeny of Haematococcus (Chlorophyceae) inferred from ribosomal RNA gene sequence data

The status of the green algal genera Haematococcus and Stephanosphaera has been a source of debate among algal systematists. A phylogenetic alliance between Haematococcus (sensu lato) and the colonial Stephanosphaera was affirmed by earlier molecular phylogenetic investigations. Although the data suggested that the genus Haematococcus may not be a monophyletic group, taxon sampling limited the scope of any potential taxonomic revision. Results from new molecular phylogenetic analyses of data from the 18S and 26S rRNA genes support the establishment of a separate genus, Balticola, as originally proposed by Droop in 1956. Haematococcus remains as a valid genus, with H. pluvialis as its only member. The monotypic status of H. pluvialis is supported both by molecular phylogenetic analyses of the ribosomal RNA genes and assessments of molecular evolution in the ITS2 sequences of H. pluvialis strains. The near-complete absence of compensatory base changes in a sequence-structure analysis of the highly variable ITS2 gene from more than 40 geographically diverse isolates of H. pluvialis corroborates the unity of the species inferred from molecular phylogenetic analyses of 18S and 26S rRNA gene sequence data.     

Redescription of the western Balkan species Xerocampylaea waldemari and its phylogenetic relationships to other Urticicolini (Gastropoda: Hygromiidae)

The proper identification of species has significant implications for conservation and general knowledge of ecosystem variety. It is especially important for biodiversity hotspots and former Pleistocene refugia, such as the Balkans. In this paper, we evaluate the taxonomic status of the endemic Balkan species Fruticicola waldemari A. J. Wagner, 1912, using both recently collected material and museum specimens. Phylogenetic analyses based on two mitochondrial markers, 16S rRNA and cytochrome c oxidase subunit I, show that this species is closely related to the representatives of Xerocampylaea, including a conchologically similar and partly sympatric species, X. erjaveci. Analyses of shell and genital morphology as well as mitochondrial DNA sequences indicate that X. waldemari and X. erjaveci are separate but closely related species. These species differ in shell morphology (size, umbilicus diameter, microsculpture) as well as genital morphology. Nevertheless, a further study with more comprehensive sampling of both taxa is required to fully understand the complex pattern of genetic and morphological variation observed.     

Ailadinium reticulatum gen. et sp. nov. (Dinophyceae), a New Thecate,Marine, Sand‐Dwelling Dinoflagellate from the Northern Red Sea

A new photosynthetic, sand‐dwelling marine dinoflagellate, Ailadinium reticulatum gen. et sp. nov., is described from the Jordanian coast in the Gulf of Aqaba, northern Red Sea, based on detailed morphological and molecular data. A. reticulatum is a large (53–61 μm long and 38–48 μm wide), dorsoventrally compressed species, with the epitheca smaller than the hypotheca. The theca of this new species is thick and peculiarly ornamented with round to polygonal depressions forming a foveate‐reticulate thecal surface structure. The Kofoidian thecal tabulation is APC (Po, cp), 4′, 2a, 6′′, 6c, 4s, 6′′′, 1p, 1′′′′ or alternatively it can be interpreted as APC, 4′, 2a, 6′′, 6c, 4s, 6′′′, 2′′′′. The plate pattern of A. reticulatum is noticeably different from described dinoflagellate genera. Phylogenetic analyses based on the SSU and LSU rDNA genes did not show any supported affinities with currently known thecate dinoflagellates.     

On detection of pseudo-nitzschia (bacillariophyceae) species using whole cell hybridization: sample fixation and stability

Some species within the genus Pseudo‐nitzschia H. Peragallo are associated with production of domoic acid, the agent responsible for amnesic shellfish poisoning (ASP). Identification and enumeration of particular Pseudo‐nitzschia in natural populations is often difficult and time consuming because of the need for detailed morphological observations, which often require scanning or transmission electron microscopy. In earlier publications we described the development of large subunit ribosomal RNA (LSU rRNA)‐targeted fluorescent DNA probes for discriminating among a variety of Pseudo‐nitzschia species collected from Monterey Bay, California. Probes are applied using whole cell hybridization and a custom filtration manifold, enabling rapid identification and quantification of target species in cultured as well as field samples. In this work we compared a variety of preservation techniques and assessed the stability of stored samples with respect to their reactivity towards the probes. Of the preservatives tested, a saline ethanol‐based treatment gave the best results in terms of probes yielding a bright and uniform cell label. Culture samples treated with this fixative continued to react well with the probes for at least 6 weeks post‐fixation whether stored in the preservative or dried post‐preservation, with samples being kept at either room temperature or ?20° C. Likewise, field samples containing a variety of diatoms and dinoflagellate species stored in the saline ethanol solution at room temperature were also stable for at least 4–6 weeks, reacting brilliantly towards a positive control probe. After prolonged storage, however, cell reactivity towards the probes diminished dramatically. Post‐hybridization, samples stored at 4° C were found to retain their fluorescence for at least 1 week. These results indicate a wider window of opportunity for Pseudo‐nitzschia analysis using whole cell hybridization than previously reported. Sample collection, preservation, and probing protocols optimized for Pseudo‐nitzschia are also applicable to a wide range of phytoplankton species. The time required to execute the whole cell hybridization protocol was reduced by premixing probe with hybridization buffer. The premixed probe solutions as well as fixative and wash solutions are all stable at room temperature for at least 6 weeks. Application of two different species‐specific probes, each labeled with a different fluorochrome, allowed detection of two species on a single filter. The latter could be adopted in the future to increase the rate of sample processing and decrease the cost of sample analysis.     

Large-scale phylogenetic analysis provides insights into the diversification and evolution of sessilid peritrich ciliates (Protista: Ciliophora)

The Peritrichia is a speciose and morphologically distinctive assemblage of ciliated protists that was first observed by Antonie van Leeuwenhoek over 340 years ago. In the last two decades, the phylogenetic relationships of this group have been increasingly debated as morphological and molecular analyses have generated contrasting conclusions, mainly owing to limited sampling. In the present study, we performed expanded phylogenetic analyses of 152 sessilid peritrichs collected from 14 different provinces of China and 141 SSU rDNA peritrich sequences from GenBank. The results of the analyses revealed new divergent relationships between and within major clades that challenge the morphological classification of this group including, (1) the recovery of four major phylogenetically divergent clades in the monophyletic order Sessilida, (2) aboral structures such as the stalk and spasmoneme were evolutionary labile, (3) the stalk or/and spasmoneme was lost in each divergent clade indicating that parallel evolution occurred in sessilid peritrichs and (4) the life cycle and habit drive the diversity of aboral structures as well as diversification and evolution in peritrichs.     

The phylogenetic relationships of introduced Aphelinus (Hymenoptera: Aphelinidae), biological control agents of the Russian wheat aphid (Homoptera: Aphididae)

Abstract  Several species of Aphelinus have been introduced to the US from the Old World for biological control of the Russian wheat aphid, Diuraphis noxia (Modvilko). Reproductive incompatibility has been observed among populations collected from different geographic areas. We examined whether or not the reproductive incompatibility between strains of A. asychis was caused by distant phylogenetic relationships. Ribosomal DNA sequences of internal transcribed spacers 2 (ITS2) were analyzed in several species of Aphelinus collected from multiple sites of Europe and Asia. The phylogenetic analysis showed that strains within the species A. albipodus and A. asychis are not monophyletic, and two clearly divergent clades were revealed among sequenced samples. Our results suggest that the reproductive incompatibility between three exotic strains of A. asychis was more likely caused by divergence of phylogeny than by symbiotic bacteria.     

Diatom Nitzschia navis-varingica (Bacillariophyceae) and its domoic acid production from the mangrove environments of Malaysia

The distribution of the toxic pennate diatom Nitzschia was investigated at four mangrove areas along the coastal brackish waters of Peninsular Malaysia. Eighty-two strains of N. navis-varingica were isolated and established, and their identity confirmed morphologically and molecularly. Frustule morphological characteristics of the strains examined are identical to previously identified N. navis-varingica, but with a sightly higher density of the number of areolae per 1 μm (4–7 areolae). Both LSU and ITS rDNAs phylogenetic trees clustered all strains in the N. navis-varingica clade, with high sequence homogeneity in the LSU rDNA (0–0.3%), while the intraspecific divergences in the ITS2 data set reached up to 7.4%. Domoic acid (DA) and its geometrical isomers, isodomoic A (IA) and isodomoic B (IB), were detected in cultures of N. navis-varingica by FMOC-LC-FLD, and subsequently confirmed by LC–MS/MS, with selected ion monitoring (SIM) and multiple reaction monitoring (MRM) runs. DA contents ranged between 0.37 and 11.06 pg cell⁻¹. This study demonstrated that the toxigenic euryhaline diatom N. navis-varingica is widely distributed in Malaysian mangrove swamps, suggesting the risk of amnesic shellfish poisoning and the possibility of DA contamination in the mangrove-related fisheries products.     

A new species of Dyrosaurus (Crocodylomorpha, Dyrosauridae) from the early Eocene of Morocco: phylogenetic implications

A new dyrosaurid is described from the Ypresian of the phosphatic deposits of the Oulad Abdoun Basin of Morocco. It is based on numerous cranial and postcranial remains, allowing an almost complete reconstruction. This new Dyrosaurus species, Dyrosaurus maghribensis sp. nov. , is currently only known from Morocco. It differs from D. phosphaticus , present in contemporaneous levels of Algeria and Tunisia, by several autapomorpies, including a smooth dorsal margin of the parietal and widely opened choanae. A phylogenetic analysis, using 47 taxa and 234 morphological characters, shows the dyrosaurids as the sister taxon of pholidosaurids, which include Elosuchus , Sarcosuchus , Terminonaris and Pholidosaurus , and the thalattosuchians. Goniopholididae is a non-monophyletic group; however, if dyrosaurids are not included in the analysis, the result differs and the goniopholidids form a distinct clade. If Thalattosuchia is excluded, both Goniopholididae and Pholidosauridae become paraphyletic assemblages. Thus, phylogenetic problems remain with respect to longirostrine clade, and more attention should be paid to resolving their evolutionary relationships amongst the crocodyliforms.  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 148 , 603–656.     

A polyphasic approach to the study of the genus Nitzschia (Bacillariophyta): three new planktonic species from the Adriatic Sea

The paraphyletic diatom genus Nitzschia comprises over 1000 morphologically distinct pennate taxa, known from the benthos and plankton of freshwater, brackish, and marine environments. The principal diagnostic characters for delimitation of Nitzschia species include valve shape, the position and structure of the raphe, presence/absence and shape of the proximal raphe endings and terminal raphe fissures, areola structure, and specific morphometric features such as cell size, and stria and fibula density. In this study, we isolated 12 diatom strains into culture from samples collected at the surface or greater depths of the southeastern Adriatic Sea. Morphological analyses included LM, SEM, and TEM observations, which, along with specific morphometric features, allowed us to distinguish three new Nitzschia species. These findings were congruent with the results of phylogenetic analyses performed on nuclear‐encoded SSU (18S) rDNA and chloroplast‐encoded rbcL and psbC genes. One of the new species (Nitzschia dalmatica sp. nov.) formed a lineage within a clade of Bacillariaceae containing members of the Nitzschia sect. Dubiae, which was sister to Psammodictyon. A second lineage was part of a novel clade that is significantly distinct from other Nitzschia species sequenced so far and includes Nitzschia adhaerens sp. nov. and N. cf. adhaerens. A further new species was found, Nitzschia inordinata sp. nov., which appeared as the sister group to the N. adhaerens clade and the conopeoid Nitzschia species in our phylogenetic trees. Our findings contribute to the overall diversity of genus Nitzschia, especially in identifying some deep branches within the Bacillariaceae, and highlight under‐scoring of this genus in marine plankton.     

Sandwich hybridization probes for the detection of Pseudo-nitzschia (Bacillariophyceae) species: An update to existing probes and a description of new probes

New sandwich hybridization assay (SHA) probes for detecting Pseudo-nitzschia species (P. arenysensis, P. fraudulenta, P. hasleana, P. pungens) are presented, along with updated cross-reactivity information on historical probes (SHA and FISH; fluorescence in situ hybridization) targeting P. australis and P. multiseries. Pseudo-nitzschia species are a cosmopolitan group of diatoms that produce varying levels of domoic acid (DA), a neurotoxin that can accumulate in finfish and shellfish and transfer throughout the food web. Consumption of infected food sources can lead to illness in humans (amnesic shellfish poisoning; ASP) and marine wildlife (domoic acid poisoning; DAP). The threat of human illness, along with economic loss from fishery closures has resulted in the implementation of monitoring protocols and intensive ecological studies. SHA probes have been instrumental in some of these efforts, as the technique performs well in complex heterogeneous sample matrices and has been adapted to benchtop and deployable (Environmental Sample Processor) platforms. The expanded probe set will enhance future efforts towards understanding spatial, temporal and successional patterns in species during bloom and non-bloom periods.     

Ultrastructure of Gyrodinium spirale, the type species of Gyrodinium (Dinophyceae), including a phylogeny of G. dominans, G. rubrum and G. spirale deduced from partial LSU rDNA sequences

A detailed ultrastructural analysis of the type species of Gyrodinium, G. spirale, was made based on cells collected from Skagerrak and southern Kattegat (Denmark). This material is considered very similar to the type material studied by Bergh from southern Kattegat. The analysis revealed many characters typical for dinoflagellates as well as a number of previously undescribed features. Here, emphasis was given to a three-dimensional configuration of the flagellar apparatus, the surface ridges, and the nuclear capsule. The latter had a rather complex ultrastructure consisting of two wall-like layers surrounded by membranes, with nuclear pores restricted to globular invaginations of these layers. To overcome difficulties with culturing of many auto- and heterotrophic dinoflagellates, we designed a specific reverse primer to amplify ca. 1800 base pairs of nuclear-encoded LSU rDNA. Using this approach, LSU rDNA sequences were determined from three heterotrophic species of Gyrodinium, including the type species. Using other alveolates (i.e. ciliates and Apicomplexa) as outgroup species, phylogenetic analyses based on Maximum Likelihood, Maximum Parsimony, and Neighbor-Joining supported Gyrodinium as a separate lineage. Unfortunately, the nearest sister group to Gyrodinium could not be established due to low bootstraps support for the deep branching pattern.