Phylogeny of cardinalfishes (Teleostei: Gobiiformes: Apogonidae) and the evolution of visceral bioluminescence

The cardinalfishes (Apogonidae) are a diverse clade of small, mostly reef-dwelling fishes, for which a variety of morphological data have not yielded a consistent phylogeny. We use DNA sequence to hypothesize phylogenetic relationships within Apogonidae and among apogonids and other acanthomorph families, to examine patterns of evolution including the distribution of a visceral bioluminescence system. In conformance with previous studies, Apogonidae is placed in a clade with Pempheridae, Kurtidae, Leiognathidae, and Gobioidei. The apogonid genus Pseudamia is recovered outside the remainder of the family, not as sister to the superficially similar genus Gymnapogon. Species sampled from the Caribbean and Western Atlantic (Phaeoptyx, Astrapogon, and some Apogon species) form a clade, as do the larger-bodied Glossamia and Cheilodipterus. Incidence of visceral bioluminescence is found scattered throughout the phylogeny, independently for each group in which it is present. Examination of the fine structure of the visceral bioluminescence system through histology shows that light organs exhibit a range of morphologies, with some composed of complex masses of tubules (Siphamia, Pempheris, Parapriacanthus) and others lacking tubules but containing chambers formed by folds of the visceral epithelium (Acropoma, Archamia, Jaydia, and Rhabdamia). Light organs in Siphamia, Acropoma, Pempheris and Parapriacanthus are distinct from but connected to the gut; those in Archamia, Jaydia, and Rhabdamia are simply portions of the intestinal tract, and are little differentiated from the surrounding tissues. The presence or absence of symbiotic luminescent bacteria does not correlate with light organ structure; the tubular light organs of Siphamia and chambered tubes of Acropoma house bacteria, those in Pempheridae and the other Apogonidae do not.     

Phylogeny and Megasystematics of Phagotrophic Heterokonts (Kingdom Chromista)

Heterokonts are evolutionarily important as the most nutritionally diverse eukaryote supergroup and the most species-rich branch of the eukaryotic kingdom Chromista. Ancestrally photosynthetic/phagotrophic algae (mixotrophs), they include several ecologically important purely heterotrophic lineages, all grossly understudied phylogenetically and of uncertain relationships. We sequenced 18S rRNA genes from 14 phagotrophic non-photosynthetic heterokonts and a probable Ochromonas, performed phylogenetic analysis of 210–430 Heterokonta, and revised higher classification of Heterokonta and its three phyla: the predominantly photosynthetic Ochrophyta; the non-photosynthetic Pseudofungi; and Bigyra (now comprising subphyla Opalozoa, Bicoecia, Sagenista). The deepest heterokont divergence is apparently between Bigyra, as revised here, and Ochrophyta/Pseudofungi. We found a third universal heterokont signature sequence, and deduce three independent losses of ciliary hairs, several of 1-2 cilia, 10 of photosynthesis, but perhaps only two plastid losses. In Ochrophyta, heterotrophic Oikomonas is sister to the photosynthetic Chrysamoeba, whilst the abundant freshwater predator Spumella is biphyletic; neither clade is specifically related to Paraphysomonas, indicating four losses of photosynthesis by chrysomonads. Sister to Chrysomonadea (Chrysophyceae) is Picophagea cl. nov. (Picophagus, Chlamydomyxa). The diatom-parasite Pirsonia belongs in Pseudofungi. Heliozoan-like actinophryids (e.g. Actinosphaerium) are Opalozoa, not related to pedinellids within Hypogyristea cl. nov. of Ochrophyta as once thought. The zooflagellate class Bicoecea (perhaps the ancestral phenotype of Bigyra) is unexpectedly diverse and a major focus of our study. We describe four new biciliate bicoecean genera and five new species: Nerada mexicana, Labromonas fenchelii (=Pseudobodo tremulans sensu Fenchel), Boroka karpovii (=P. tremulans sensu Karpov), Anoeca atlantica and Cafeteria mylnikovii; several cultures were previously misidentified as Pseudobodo tremulans. Nerada and the uniciliate Paramonas are related to Siluania and Adriamonas; this clade (Pseudodendromonadales emend.) is probably sister to Bicosoeca. Genetically diverse Caecitellus is probably related to Anoeca, Symbiomonas and Cafeteria (collectively Anoecales emend.). Boroka is sister to Pseudodendromonadales/Bicoecales/Anoecales. Placidiales are probably divergent bicoeceans (the GenBank Placidia sequence is a basidiomycete/heterokont chimaera). Two GenBank ‘opalinid’ sequences are fungal; Pseudopirsonia is cercozoan; two previous GenBank ‘Caecitellus’ sequences are Adriamonas. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editior: Patnck J. Keeling]     

Die GattungKarschia — Bindeglied zwischen bitunicaten Ascomyceten und lecanoralen Flechtenpilzen?

The genusKarschia, in the earlier sense, including saprophytes and parasites on lichens, has been thought to be a non-lichenized parallel genus of the lichen genusBuellia. Modern workers included it on the one hand inBuellia, on the other hand combined it with bitunicate ascomycetes. It is now proved thatKarschia is heterogeneous and contains but superficially similar members both of the genusBuellia of theLecanorales and of typical or masked bitunicateAscomycetes. Therefore, it can not be regarded as a link betweenLecanorales andDothideales. The type species ofKarschia belongs to theDothideales.

     

A molecular phylogeny of Hebeloma species from Europe

In order to widen the scope of existing phylogenies of the ectomycorrhizal agaric genus Hebeloma a total of 53 new rDNA ITS sequences from that genus was generated, augmented by sequences retrieved from GenBank, and analysed using Bayesian, strict consensus and neighbour joining methods. The lignicolous Hebelomina neerlandica, Gymnopilus penetrans, and two species of Galerina served as outgroup taxa. Anamika indica, as well as representatives of the genera Hymenogaster and Naucoria, were included to test the monophyly of Hebeloma, which is confirmed by the results. Hebeloma, Naucoria, Hymenogaster and Anamika indica cluster in a strongly supported monophyletic hebelomatoid clade. All trees largely reflect the current infrageneric classification within Hebeloma, and divide the genus into mostly well-supported monophyletic groups surrounding H. crustuliniforme, H. velutipes, H. sacchariolens, H. sinapizans, and H. radicosum, with H. sarcophyllum being shown at an independent position; however this is not well supported. The section Indusiata divides with strong support into three groups, the position of the pleurocystidiate Hebeloma cistophilum suggests the possible existence of a third subsection within sect. Indusiata. Subsection Sacchariolentia is raised to the rank of section.     

Five additional genera of conidial lichen-forming fungi from Europe

Three remarkable new genera of conidial lichen-forming fungi, with pycnidial or acervular conidiomata are described and illustrated.Hastifera tenuispora gen. et spec. nov. from the South-Tyrol, Italy, is characterized by very long and narrow hyaline conidia produced in pycnidial conidiomata immersed in thalline warts.Lichingoldia gyalectiformis gen. et spec. nov. from rocks subject to inundation by freshwater in Norway has long sigmoidly curved conidia which appear to be adapted to dispersal in water.Woessia fusarioides gen. et spec. nov. from aQuercus stump in the Burgenland, Austria, has a finely granular thallus and disc-like conidiomata producing falcate conidia; this species is also of interest in that it hasChlorella as the photobiont. The recently described hyphomyceteCheiromycina flabelliformis B. Sutton is reported from Austria for the first time, and is also lichenized. Recent collections ofNigropuncta rugulosa D. Hawksw. from Austria and Italy also show that this species is lichenized rather than parasymbiotic. In all five cases the fungal hyphae of the conidiogenous structures are continuous with those in intimate contact with cells of the algal partners and the biological relationship appears to be mutualistic giving rise to stable crustose lichen thalli.     

Phylogenetic relationships of Auriculoscypha based on ultrastructural and molecular studies

The phylogeny of Auriculoscypha anacardiicola, an associate of scale insects in India, is investigated using subcellular characters and MP and Bayesian analyses of combined nuLSU-rDNA, nuSSU-rDNA and 5.8S rDNA sequence data. It has simple septa with a pulley-wheel-shaped pore plug, which is diagnostic of phytoparasitic members of the Pucciniomycetes, and hyphal wall break on branching, a phenomenon unique to some simple septate heterobasidiomycetes. The septal ultrastructure of A. anacardiicola is similar to that of the genus Septobasidium. The close relationship to Septobasidium is also confirmed by rDNA sequence analyses. The polyphyletic nature of the order Platygloeales, noted in earlier studies, is evident from the present molecular analysis as well. The placement of Auriculoscypha in the Platygloeales can no longer be justified and both ultrastructural and molecular evidence strongly support the placement of Auriculoscypha in the Septobasidiales.     

A functional interpretation ofLactuceae (Compositae) pollen

Pollen morphology and ultrastructure inLactuceae pollen is considered in relation to the accomodation of volume changes, pollination biology and exine-held substances. Echinate pollen grains, such as those ofCatananche, are shown to accomodate volume changes by folding along the colpi and possibly by volume changes in the cavea. The different patterns of echinolophate pollen respond in different ways. Folding along the colpi is important inScorzonera andTragopogon and to a limited extent inCichorium andEpilasia whilst inScolymus the colpi are almost immobilized. Movements of the lacunar floors take over the harmomegathic function to compensate for lack of colpus mobility. Bulging of the intine at the apertures and changes in the size of the cavea may account for part of the volume change accomodated in any pollen type. Echinolophate pollen is interpreted as being a superior means of regulating volume changes with the most economical and mechanically efficient use of wall material which has evolved independently in several tribes ofCompositae.     

黑粉菌属一新种及中国黑粉菌补遗VI

本文描述采自河北小五台山的黑粉菌一新种,即寄生在野青茅(Deyeuxia arundinacea(L.) Beauv)上的野青茅黑粉菌(Ustilago deyeuxiae L. Guo)。此种与网优黑粉菌(Ustilago scrobiculata Liro)近似,但野青茅黑粉菌网纹明显,网眼高。并报道三种黑粉菌中国新记录。1)酢浆草黑粉菌(Ustilago oxalidis Ellis&Tracy)寄生于醉浆草(Oxalis corniculata L.),此种是我国首次在酢浆草科(Oxalidaceae)植物上发现的黑粉菌。2)网状黑粉菌(Ustilago polygoni-alati Thirum. & Pavgi)寄生于尼泊尔萝(Polygonum nepalense Meisn.),作者对此种进行了订正研究。3)臭草条黑粉菌(Urocystis melicae (Lagerheim & Liro) Zundel)寄生于细叶臭草(Melica radula Fr.)。     

A reconsideration of the genusRabdosiella (Lamiaceae,Nepetoideae, Ocimeae)

The two generaPlectranthus andIsodon are compared and found to be very dissimilar.Isodon ist considered to be misplaced inOcimeae subtribePlectranthinae and apparently is more closely related to subtribeHyptidinae. The disjunct genusRabdosiella is compared to these two genera and regarded to be polyphyletic. The AfricanR. calycina (Benth.)Codd is returned toPlectranthus and calledP. calycinus Benth., while the AsianR. ternifolia (D. Don)Codd is placed inIsodon sect.Pyramidium and calledI. ternifolius (D. Don)Kudo.     

下延叉蕨和芽胞叉蕨配子体发育的研究

利用光学显微镜详细观察了叉蕨属(Tectaria)下延叉蕨(Tectaria decurrens)和芽胞叉蕨(T.fauriei)的配子体发育过程,记录了配子体各发育阶段的特征。结果表明:(1)下延叉蕨和芽胞叉蕨的孢子均为单裂缝,具周壁,由周壁形成纹饰,孢子极面观椭圆形,赤道面观豆形或肾形。(2)孢子萌发方式为向心型。(3)原叶体发育方式为三叉蕨型。(4)成熟原叶体心脏形,两翼向斜上方扩展。(5)均具单细胞和多细胞毛状体,在丝状体或片状体阶段出现。研究认为,从配子体发育角度看,叉蕨属是较进化的陆生真蕨类;毛状体的类型、位置和出现时间等特征在叉蕨属种间存在差异,可作为该属种间分类的特征。     

Floral development and systematics ofCistaceae

The floral development of representatives of six genera ofCistaceae has been studied. Calyx development involves the formation of a ring primordium in several taxa. Androecium development in species with intermediate or higher stamen numbers starts with the formation of a ring meristem on which the stamens are initiated in a centrifugal direction. In many taxa five alternipetalous leading stamen primordia can be observed. In the apetalous (cleistogamous) flowers ofTuberaria inconspicua androecium development appears to be unordered; this is probably due to the lack of petals. InLechea intermedia (also cleistogamous) the corolla is trimerous and three complex stamen primordia are produced, which give rise either to one or three stamens. Relationships withinCistaceae are discussed. Floral development inCistaceae is compared with that in otherMalvanae. Among the eight families ofMalvanae from which information on floral development is availableCochlospermaceae andBixaceae exhibit the greatest similarities toCistaceae. InCistaceae the leading stamen primordia are alternipetalous. InBixa the same condition seems to be present. InMalvales s. str. mostTiliaceae also show earliest stamen initiation in alternipetalous sectors, whereas the stamens of the innermost alternipetalous position are retarded early or even suppressed inSterculiaceae, Bombacaceae, andMalvaceae. WithinMalvales s. str. the diversity of androecial developmental patterns seems to decrease inBombacaceae andMalvaceae due to increasing synorganization in the mature androecium. The derivation of polyandry inMalvanae from diplo- or obdiplostemony is discussed by comparison with the sister clades ofMalvanae as shown in recentrbcL studies (i.e.Sapindales, Rutales, the glucosinolate producing clade, andMyrtales).     

Progress on the genetics of the N2-fixing actinorhizal symbiont Frankia

The actinomycete Frankia is of fundamental and ecological interests for several reasons including its wide distribution, its ability to fix nitrogen, differentiate into sporangium and vesicle (specialized cell for nitrogen-fixation), and to nodulate plants from about 24 genera. Here, we present a review on the genetics performed so far on Frankia. At the end of July 2001, 293 kbp of Frankia DNA sequences were found in the databases. Thirty five percent of these sequences corresponded to full gene or gene cluster sequences. These genes could be divided according to their role into 6 key activities: gene translation (rrnA and tRNA ^pro gene), proteolysis (pcr genes), assimilation of ammonium (glnA and glnII), protection against superoxide ions (sodF), nitrogen fixation (nif cluster), and plasmid replication. We present a review of these genetic islands; their function, expression, localization and particular properties are discussed. A comparative analysis of Frankia nif genes from various strains and species is presented. An improved nomenclature for some of these genes is suggested to avoid conflicts. Frankia plasmids DNA sequences are also presented. The novel trends in Frankia genetics are described.     

Molecular phylogeny of the genus Stereocaulon (Stereocaulaceae, lichenized ascomycetes)

In the present study phylogenetic relationships of the genus Stereocaulon (lichenized ascomycetes) were examined using DNA sequences from the ITS1–5.8 S–ITS2 rDNA gene cluster and from the protein-coding β-tubulin gene. In addition to the fruticose species traditionally classified in Stereocaulon, representatives of the crustose species that have recently been transferred to the genus were included. Muhria, a monotypic genus that is morphologically similar to Stereocaulon, differing only in apothecia ontogeny, was also incorporated. The analyses included 101 specimens from the ingroup representing 49 taxa. Sequences from both DNA regions were analysed simultaneously using direct optimization under the parsimony optimality criterion. The results support the inclusion of the crustose species and Muhria in Stereocaulon, while the current infrageneric classification is not supported. As Muhria is securely nested within Stereocaulon the new combination Stereocaulon urceolatum comb. nov. (syn. Muhria urceolata) is made. Further, species concepts need to be re-examined, as some species do not appear as monophyletic entities in the phylogeny.     

Subdivision of the genus Pleuroxus (Anomopoda,Chydoridae) into subgenera worldwide

Examination of many species of Pleuroxus from the entire World has revealed a major dichotomy in morphology, one line related to aduncus: the other to laevis both from Europe. Pleuroxus trigonellus (the type species of the genus) and Peracantha truncata are in two other distinct lines. The new subgenus Tylopleuroxus is proposed for the species related to aduncus, and the subgenus Picripleuroxus for those related to laevis. Tylopleuroxus is primarily Southern Hemisphere in distribution, Picripleuroxus primarily Northern Hemisphere. Evidence thus far suggests that probably most, perhaps all, of the taxa are confined to single continents or land masses. Deceased     

Characterization of SLFL1, a pollen-expressed F-box gene located in the Prunus S locus

The S locus and its flanking regions in the genus Prunus (Rosaceae) contain four pollen-expressed F-box genes. These genes contain the S locus F-box genes with low allelic sequence polymorphism genes 1, 2, and 3 (SLFL1, SLFL2, and SLFL3) as well as the putative pollen S gene, named the S haplotype-specific F-box protein gene (SFB). As much less information is available on the function of SLFLs than that of SFB, we analyzed the SLFLs of six S haplotypes of sweet cherry (Prunus avium) in this study. Genomic DNA blot analysis and the isolation of SLFL1 showed that the SLFL1 gene in a functional self-incompatible S ³ haplotype is deleted and only a partial sequence resembling SLFL1 is left in the S ³ locus region, suggesting that SLFL1 by itself is not directly involved in either the GSI reaction or pollen-tube growth. Genomic DNA blot analysis showed that there was no substantial modification or mutation in SLFL2 and SLFL3. A phylogenic analysis of F-box genes in the rosaceous S locus and its border regions showed that Prunus SLFLs were more closely related to maloid S locus F-box brothers than to Prunus SFBs. The functions of SLFLs and the evolution of self-incompatibility in Prunus are discussed based on these results. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. The nucleotide sequence data reported appear in the DDBJ, EMBL, and GenBank Nucleotide Sequence Databases under the accession numbers, AB360339, AB360340, AB360341, and AB360342, for SLFL1-S ¹ , SLFL1-S ² , SLFL1-S ⁵ , and SLFL1-S ⁶ , respectively.     

Molecular and Structural Characterization of Barley Vernalization Genes

Vernalization, the requirement of a period of low temperature to induce transition from the vegetative to reproductive state, is an evolutionarily and economically important trait in the Triticeae. The genetic basis of vernalization in cultivated barley (Hordeum vulgare subsp. vulgare) can be defined using the two-locus VRN-H1/VRN-H2 model. We analyzed the allelic characteristics of HvBM5A, the candidate gene for VRN-H1, from ten cultivated barley accessions and one wild progenitor accession (subsp. spontaneum), representing the three barley growth habits – winter, facultative, and spring. We present multiple lines of evidence, including sequence, linkage map location, and expression, that support HvBM5A being VRN-H1. While the predicted polypeptides from different growth habits are identical, spring accessions contain a deletion in the first intron of HvBM5A that may be important for regulation. While spring HvBM5A alleles are typified by the intron-localized deletion, in some cases, the promoter may also determine the allele type. The presence/absence of the tightly linked ZCCT-H gene family members on chromosome 4H perfectly correlates with growth habit and we conclude that one of the three ZCCT-H genes is VRN-H2. The VRN-H2 locus is present in winter genotypes and deleted from the facultative and spring genotypes analyzed in this study, suggesting the facultative growth habit (cold tolerant, vernalization unresponsive) is a result of deletion of the VRN-H2 locus and presence of a winter HvBM5A allele. All reported barley vernalization QTLs can be explained by the two-locus VRN-H1/VRN-H2 model based on the presence/absence of VRN-H2 and a winter vs. spring HvBM5A allele. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users.     

The rust fungi (Uredinales) on ferns in South Africa

The rust fungi (Uredinales, basidiomycota) occuring on ferns (Pteridophyta) in South Africa are described, illustrated and keyed out. All species belong to the pucciniastraceous genera Milesina (M. blechni), Uredinopsis (U. pteridis) or to the related uredinial anamorph genus Milesia (M. nervisequa, M. cf. magellanica, M. silvae-knysnae). Milesia silvae-knysnae on Polystichum pungens is new to science; it probably belongs to the teleomorph genus Milesina. Milesina blechni is reported from South Africa for the first time on the new hosts Blechnum punctulatum and Rumohra adiantoides; it has hitherto been known only from the Northern Hemisphere on Blechnum spicant. Rust specimens collected on Asplenium aethiopicum and A. rutifolium were tentatively assigned to Milesia magellanica which has been known so far only from southern Chile. Hyalopsora neocheilanthis, Milesina neoexigua and M. neovogesiaca are proposed as new names for Hyalopsora cheilanthis, Milesia exigua and M. vogesiaca. It is discussed that the pucciniastraceous fern rusts could have reached South Africa either by migration (M. blechni) or by long-distance air dispersal. In the absence of their gametophyte hosts, species of Abies (Pinaceae), the rusts have to propagate in South Africa by urediniospores infecting fern to fern. Taxonomical novelties Milesia silvae-knysnae R. Berndt Milesina neoexigua R. Berndt Milesina neovogesiaca R. Berndt Hyalopsora neocheilanthis R. Berndt