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.     

A new fungal genus, Teracosphaeria, with a phialophora-like anamorph (Sordariomycetes, Ascomycota)

The new genus and species Teracosphaeria petroica is described for a perithecial ascomycete and its anamorph occurring on decayed wood collected in New Zealand. The fungus produces immersed, non-stromatic ceratosphaeria-like perithecia in nature, with hyaline, septate ascospores produced in unitunicate, non-amyloid asci. The anamorph produced in vitro is phialophora-like with lightly pigmented phialides terminating in flaring, deep collarettes that are often noticeably brown with conspicuous periclinal thickening. Phylogenetic analysis of LSU rDNA sequence data indicates that this fungus is distinct from morphologically similar fungi classified in the Chaetosphaeriales, the Trichosphaeriales or the Magnaporthaceae. It forms a monophyletic group with recently described, chaetosphaeria-like ascomycetes, such as the pyrenomycete genus Mirannulata, and shows affinity with the anamorphic species Dictyochaeta cylindrospora. The usefulness of describing anamorph genera for morphologically reduced anamorphs, when anamorph characteristics are actually part of the holomorph diagnosis, is discussed. An apparently contradictory example of the so-called Cordana and Pseudobotrytis anamorphs of Porosphaerella spp. is also discussed.     

Phylogenetic investigations of Sordariaceae based on multiple gene sequences and morphology

The family Sordariaceae incorporates a number of fungi that are excellent model organisms for various biological, biochemical, ecological, genetic and evolutionary studies. To determine the evolutionary relationships within this group and their respective phylogenetic placements, multiple-gene sequences (partial nuclear 28S ribosomal DNA, nuclear ITS ribosomal DNA and partial nuclear β-tubulin) were analysed using maximum parsimony and Bayesian analyses. Analyses of different gene datasets were performed individually and then combined to generate phylogenies. We report that Sordariaceae, with the exclusion Apodus and Diplogelasinospora, is a monophyletic group. Apodus and Diplogelasinospora are related to Lasiosphaeriaceae. Multiple gene analyses suggest that the spore sheath is not a phylogenetically significant character to segregate Asordaria from Sordaria. Smooth-spored Sordaria species (including so-called Asordaria species) constitute a natural group. Asordaria is therefore congeneric with Sordaria. Anixiella species nested among Gelasinospora species, providing further evidence that non-ostiolate ascomata have evolved from ostiolate ascomata on several independent occasions. This study agrees with previous studies that show heterothallic Neurospora species to be monophyletic, but that homothallic ones may have a multiple origins. Although Gelasinospora and Neurospora are closely related and not resolved as monophyletic groups, there is insufficient evidence to place currently accepted Gelasinospora and Neurospora species into the same genus.     

Molecular phylogeny of Phebalium (Rutaceae: Boronieae) and related genera based on the nrDNA regions ITS 1+2

Parsimony analyses of the internal transcribed spacer regions of nuclear ribosomal DNA (ITS 1 & ITS 2) for 38 taxa sampled from the Phebalium group (Rutaceae: Boronieae) and two outgroups confirm that, with the exception of Phebalium sensu stricto and Rhadinothamnus, six of the currently recognised genera within the group are monophyletic. The data indicate that Phebaliums. str. is paraphyletic with respect to Microcybe, and Rhadinothamnus is paraphyletic with respect to Chorilaena. Rhadinothamnus and Chorilaena together are the sister group to Nematolepis. Drummondita, included as an outgroup taxon, clustered within the ingroup as sister to Muiriantha and related to Asterolasia.The phylogeny suggests that the evolution of major clades within a number of these genera (e.g. Phebalium) relates to vicariance events between eastern and south-western Australia. Leionema is an eastern genus, with the most basal taxon being the morphologically distinct Leionema ellipticum from northern Queensland. Leionema also includes one species from New Zealand, but this species (as with some others) proved difficult to sequence and its phylogenetic position remains unknown. Taxonomic changes at the generic level are recommended.The authors wish to thank Paul G.Wilson, PERTH, for advice and discussion, and Paul Forster, BRI, for collecting and providing material of Leionema ellipticum. The project was supported by a Melbourne University Postgraduate Award (to BM), the Australian Biological Resources Study (ABRS), Australian Systematic Botany Society and Wolf Den (Australia) Investments.     

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.     

Heterostyly in species ofNarcissus (Amaryllidaceae) andHugonia (Linaceae) and other disputed cases

The hypothesis ofHenriques andFernandes that several Iberian species ofNarcissus (Amaryllidaceae) are tristylous is reconsidered. Contrary to the opinion ofBateman and most subsequent authors, we believe that the available evidence indicates that some populations ofN. triandrus andN. fernandesii, at least, are tristylous; other populations ofN. triandrus are distylous.Hugonia cf.penicillanthemum (Linaceae) from new Caledonia is distylous, but it remains possible that other species ofHugonia are tristylous. The disputed occurrence of heterostyly in S. African species ofBauhinia (Leguminosae),Cleome (Capparaceae) andAneilema (Commelinaceae), and inAgelaea (Connaraceae) is discussed.     

Phylogenetic relationships in theCampanulales based onrbcL sequences

Phylogenetic relationships within the angiosperm orderCampanulales were investigated by comparative sequencing of the chloroplast generbcL. CompleterbcL sequences were obtained for ten species in six families within the order. These data were analyzed along with previously publishedrbcL sequences from other taxa (for a total of 117 species) within the subclassAsteridae and outgroups, producing 32 equally parsimonious trees. A subset consisting of 44 of these taxa was then chosen and more rigorous analyses performed, resulting in four equally parsimonious trees. Results indicate that two major clades roughly corresponding to traditionally circumscribedAsterales andCampanulales exist as sister taxa. In particular, therbcL trees indicate thatSphenoclea is not a member ofCampanulales orAsterales, thatPentaphragma is more closely allied toAsterales thanCampanulales, that theCyphiaceae are not monophyletic, thatCampanulaceae andLobeliaceae are not sister taxa, and thatStylidiaceae are correctly placed withinCampanulales.     

Evolutionary relationships among aquatic anamorphs and teleomorphs: Lemonniera, Margaritispora, and Goniopila

The hypothesis that similar conidial morphologies in aquatic hyphomycetes are a result of convergent evolution was tested using molecular sequence data. Cladistic analyses were performed on partial sequences of 28S rDNA of seven species of Lemonniera, one species of Margaritispora and one species of Goniopila. Lemonniera has tetraradiate conidia with long arms, whereas Margaritispora and Goniopila have typically globose (isodiametric) conidia, with short conical protuberances in a stellate or quadrangular arrangement. Lemonniera and Margaritispora have phialidic conidiogenesis and both produce dark, minute sclerotia in culture whereas Goniopila has holoblastic conidiogenesis and does not produce sclerotia in culture. Goniopila produces a microconidial phialidic synanamorph in culture. All three genera have schizolytic conidial secession. Molecular analyses demonstrate that Lemonniera species are placed in two distinct clades: one within Leotiomycetes; the other within Pleosporales, Dothideomycetes. Margaritispora is placed with Lemonniera species within Leotiomycetes. Goniopila and Lemonniera pseudofloscula are placed within Dothideomycetes. No morphological character was entirely congruent with the molecular derived phylogeny. This suggests that for the group of species studied, conidial shape is not a reliable indicator of phylogeny but more likely the result of convergent evolution in response to the aquatic environment.     

Synopsis of the tribe Bocageeae (Annonaceae), with revisions of Cardiopetalum,Froesiodendron, Trigynaea,Bocagea, and Hornschuchia

The tribal name Bocageeae Endlicher is reestablished and the tribe is circumscribed on the basis of solitary internodal ebracteate pedicels that are articulated at the base, and pollen shed in polyads of eight or more grains. Septate anther locules, large pollen size, and seed appendages are prevalent in the tribe. Intectate pollen with free-standing columellae, rare in Annonaceae, occurs not only in the genusTrigynaea but also in some species ofBocagea andHornschuchia. As defined here, the Bocageeae include seven neotropical genera:Cymbopetalum, Porcelia, Bocagea, Cardiopetalum, Froesiodendron, Hornschuchia, andTrigynaea. The latter five genera are revised and the treatments include ten new species:Cardiopetalum plicatum, Froesiodendron urceocalyx, Hornschuchia lianarum, H. santosii, H. leptandra, Trigynaea cinnamomea, T. lanceipetala, T. triplinervis, T. lagaropoda, andT. axilliflora, all from tropical South America. A new combination,Froesiodendron longicuspe, changes the rank of that taxon from subspecies to species.Cardiopetalum surinamense is removed fromFroesiodendron and reassigned toCardiopetalum on the basis of its connate petals, dehiscent monocarps, and seeds with bilobed arils. A cladogram provides an explicit hypothesis of intergeneric relationships in the tribe. The new combinationOnychopetalum periquino, based onTrigynaea periquino, is made.     

Phylogenetic relationships of graminicolous downy mildews based on cox2 sequence data

Graminicolous downy mildews (GDM) are an understudied, yet economically important, group of plant pathogens, which are one of the major constraints to poaceous crops in the tropics and subtropics. Here we present a first molecular phylogeny based on cox2 sequences comprising all genera of the GDM currently accepted, with both lasting (Graminivora, Poakatesthia, and Viennotia) and evanescent (Peronosclerospora, Sclerophthora, and Sclerospora) sporangiophores. In addition, all other downy mildew genera currently accepted, as well as a representative sample of other oomycete taxa, have been included. It was shown that all genera of the GDM have had a long, independent evolutionary history, and that the delineation between Peronosclerospora and Sclerospora is correct. Sclerophthora was found to be a particularly divergent taxon nested within a paraphyletic Phytophthora, but without support. The results confirm that the placement of Peronosclerospora and Sclerospora in the Saprolegniomycetidae is incorrect. Sclerophthora is not closely related to Pachymetra of the family Verrucalvaceae, and also does not belong to the Saprolegniomycetidae, but shows close affinities to the Peronosporaceae. In addition, all GDM are interspersed throughout the Peronosporaceae s lat., suggesting that a separate family for the Sclerosporaceae might not be justified.     

Oriole pollination ofErythrina breviflora (Leguminosae): Evidence for a polytypic view of ornithophily

Erythrina breviflora is visited by large numbers of passerine birds of which orioles (Icterus: Icteridae) are the primary pollinators. The flowers produce large quantities of nectar but they are rarely visited by hummingbirds. Inflorescence and floral morphology, and low levels of sucrose in the nectar probably explain the rarity of foraging hummingbirds. A comparison of Old WorldErythrina and their pollinators with New World species pollinated by orioles and hummingbirds suggests that parallel evolution has occurred. When the comparison is expanded to include other species pollinated by orioles, it is clear that various New WorldIcteridae, Thraupidae, etc. are ecological equivalents of Old WorldOriolidae, Pycnonotidae, Sturnidae, etc. and that flowers pollinated by these birds have similar characteristics.     

Comparative ultrastructure of the zoospores of nine species ofNeochloris (Chlorophyta)

Nine species ofNeochloris can be divided into three groups on the basis of comparative ultrastructure of the flagellar apparatus, the cell wall and the pyrenoid of zoospores. In Group I,N. wimmeri andN. minuta, zoospores are thin-walled, pyrenoids are penetrated by stromal channels, and the basal bodies are in the clockwise absolute orientation and connected by the distal and two proximal fibers. In Group II,N. aquatica, N. vigenis, N. terrestris, N. pyenoidosa, andN. pseudostigmatica, zoospores are naked or covered by fuzzy material, pyrenoids are covered by a continuous starch sheath or invaginated by cytoplasmic channels, basal bodies are directly opposed, the distal fiber is differentiated into a ribbed structure at the central region, a striated microtubule-associated component (SMAC) is continuous between opposite two-membered rootlets and connected to the ribbed structure, proximal ends of basal bodies are covered by partial caps, each two-membered rootlet and a basal body are connected by a striated fiber to the X-membered rootlet associated with the opposite basal body, and the basal bodies, when oriented at wide angles, are joined at their proximal ends by core extensions. In Group III,N. pseudoalveolaris andN. cohaerens, zoospores are naked, pyrenoids are traversed by parallel thylakoids, basal bodies are in the counterclockwise absolute orientation and overlapped, and each X-membered rootlet is connected to the end of the opposite basal body by a terminal cap. It is suggested that the genusChlorococcopsis gen. nov. be erected for the Group I species. Group II, which includes the type species,N. aquatica, should be preserved asNeochloris. The group appears to be closely related to the coenobial generaPediastrum, Hydrodictyon, andSorastrum, and to have affinities with the coenocytic generaSphaeroplea andAtractomorpha as well. It is also suggested that the genusParietochloris gen. nov. be erected in thePleurastrophyceae for the species of Group III.     

The <Emphasis Type="Italic">Caenorhabditis</Emphasis><Emphasis Type="Italic">briggsae</Emphasis> genome contains active <Emphasis Type="Italic">CbmaT1</Emphasis> and <Emphasis Type="Italic">Tcb1</Emphasis> transposons

The maT clade of transposons is a group of transposable elements intermediate in sequence and predicted protein structure to mariner and Tc transposons, with a distribution thus far limited to a few invertebrate species. We present evidence, based on searches of publicly available databases, that the nematode Caenorhabditis briggsae has several maT-like transposons, which we have designated as CbmaT elements, dispersed throughout its genome. We also describe two additional transposon sequences that probably share their evolutionary history with the CbmaT transposons. One resembles a fold back variant of a CbmaT element, with long (380-bp) inverted terminal repeats (ITRs) that show a high degree (71%) of identity to CbmaT1. The other, which shares only the 26-bp ITR sequences with one of the CbmaT variants, is present in eight nearly identical copies, but does not have a transposase gene and may therefore be cross mobilised by a CbmaT transposase. Using PCR-based mobility assays, we show that CbmaT1 transposons are capable of excising from the C. briggsae genome. CbmaT1 excised approximately 500 times less frequently than Tcb1 in the reference strain AF16, but both CbmaT1 and Tcb1 excised at extremely high frequencies in the HK105 strain. The HK105 strain also exhibited a high frequency of spontaneous induction of unc-22 mutants, suggesting that it may be a mutator strain of C. briggsae.     

The larval development of an Australian limnadiid clam shrimp (Crustacea, Branchiopoda, Spinicaudata), and a comparison with other Limnadiidae

The adult morphology of the Australian Limnadopsis shows some remarkable differences to that of other Limnadiidae. These differences are not reflected in its larval development. In Limnadopsis parvispinus, larval development comprises six stages. In stages I and II only the three naupliar appendages are present: the antennule as a small bud, the biramous antenna as the main swimming organ, and the mandible. The antennal protopod bears two endites, the proximal naupliar process and a more distal endite. In stage III a bifid naupliar process (in earlier stages not bifid) and the first signs of the carapace and trunk limb anlagen (undifferentiated rudiments) appear. In stage IV the carapace anlagen become more pronounced. The number of trunk limb anlagens increases to five, and differentiation has commenced. In stage V the first five pairs of trunk limbs are differentiated to varying degrees. The anterior-most four pairs of trunk limbs are subdivided into five endites, a small endopod, an exopod and an epipod. The bivalved carapace covers the anterior-most limbs. In larval stage VI the carapace is larger and the trunk limbs are further differentiated. A general pattern in the sequence of larval stages is the increasing number of sensilla on the antennules. From the last larval to the first postlarval stage, a significant change in morphology takes place. The trunk limbs are now used for swimming. Typical larval organs are much smaller than in the last larval stage. A comparison with other representatives of the Limnadiidae shows a high degree of correspondence, with most differences explained by the heterochronous appearance of characters during development. Five to seven stages are described for all studied Limnadiidae, including one particular stage in which four fully developed setae, a bifid naupliar process and the first signs of carapace anlagen are present. These characters are found in stage III in L. parvispinus, Limnadia stanleyana, Eulimnadia texana, and Imnadia yeyetta but in stage IV in E. braueriana and L. lenticularis. Based on a comparison of the larval stages of six limnadiid and one cyzicid species, we conclude that at least six naupliar stages belong to the limnadiid ground pattern.     

Chromosome numbers and karyotypes within the Ranunculus alpestris-group (Ranunculaceae)

The Ranunculus alpestris-group comprises six white-flowered species growing in mostly alpine zones of central and southern European mountains. They all are diploid with 2n=16 chromosomes. The common karyotype of the group was established based on 75 metaphases (6–26 metaphases per species). The haploid karyotype consists of four metacentric (chromosomes 1, 3, 6, 7) and four more or less subtelocentric chromosomes (2, 4, 5, 8). This karyotype is similar to that of other white-flowered European Ranunculus species as well as the yellow-flowered R. thora-group. Analysis of karyotypes partly confirms relationships inferred from molecular phylogenies. Species with this karyotype are placed on rather basal branches in existing phylogenies, which may indicate that this karyotype is primitive within the genus Ranunculus.     

The C. elegans sex determination gene laf-1 encodes a putative DEAD-box RNA helicase

The Caenorhabditis elegans gene laf-1 is critical for both embryonic development and sex determination. Laf-1 is thought to promote male cell fates by negatively regulating expression of tra-2 in both hermaphrodites and males. We cloned laf-1 and established that it encodes a putative DEAD-box RNA helicase related to Saccharomyces cerevisiae Ded1p and Drosophila Vasa. Three sequenced laf-1 mutations are missense alleles affecting a small region of the protein in or near helicase motif III. We demonstrate that the phenotypes resulting from laf-1 mutations are due to loss or reduction of laf-1 function, and that both laf-1 and a related helicase vbh-1 function in germline sex determination. Laf-1 mRNA is expressed in both males and hermaphrodites and in both the germline and soma of hermaphrodites. It is expressed at all developmental stages and is most abundant in embryos. LAF-1 is predominantly, if not exclusively, cytoplasmic and colocalizes with PGL-1 in P granules of germline precursor cells. Previous results suggest that laf-1 functions to negatively regulate expression of the sex determination protein TRA-2, and we find that the abundance of TRA-2 is modestly elevated in laf-1/+ females. We discuss potential functions of LAF-1 as a helicase and its roles in sex determination.