Four new species of the genus Hymenoscyphus (fungi) based on morphology and molecular data

Four new species of Hymenoscyphus (H. brevicellulus, H. hyaloexcipulus, H. microcaudatus, and H. subsymmetricus) and a new Chinese record (H. subpallescens) are described. These five species share common characteristics: small apothecia (<3mm in diameter); hymenium whitish, pale yellow, to yellow in color; ectal excipulum of textura prismatica; asci arising from simple septa; ascospores scutuloid and guttulate; saprophytic nutrition; and leaf habitats, except for H. subsymmetricus, which grows on herbaceous stems. Phylogenetic analyses of internal transcribed spacer nuclear ribosomal DNA sequences, the universal DNA barcode for fungi, for 16 species in the genus indicated that these taxa were closely related to H. microserotinus, in accordance with their morphological features, but represented independent species. The distinguishing features of each new species from its relatives are discussed, and their phylogenetic relationships explored.     

<Emphasis Type="Italic">Cryptodiscus muriformis</Emphasis> and <Emphasis Type="Italic">Schizoxylon gilenstamii</Emphasis>, two new species of Stictidaceae (Ascomycota)

Cryptodicus muriformis and Schizoxylon gilenstamii (Stictidaceae, Ostropales, Lecanoromycetes, Ascomycota) are described as new to science from collections made in Europe (Sweden, Austria, Switzerland) and North America (Arizona), based on phylogenetic analyses of three loci. Both species show unique morphological characters that distinguish them from closely related species; Cryptodiscus muriformis, growing on decorticated or sometimes corticated branches of Picea abies and Pseudotsuga menziesii, that resembles C. foveolaris and C. tabularum in the yellowish-orange ascomatal disc, but is clearly distinguished by the muriform ascospores. Schizoxylon gilenstamii grows on dead stems of Globularia vulgaris and has a characteristic unique red-purple pigment in the epithecium and upper part of the excipulum that changes to bluish-green with KOH. We also report for the first time the anamorph of Stictis brunnescens.     

PHAEODISCUS,A NEW GENUS OF SCLEROTINIACEAE (INOPERCULATAE: DISCOMYCETES)

Phaeodiscus, a new genus of Sclerotiniaceae, is described with P. rhamnicola Batra as the single species. It is characterized by an ectal excipulum of subhyaline textura prismatica and textura porrecta; dichotomously branched, golden brown, aculeate paraphyses; and golden brown, narrowly ellipsoid, usually biguttulate ascospores. The two guttules fuse at maturity to form a single central guttule. The apothecia arise from pseudosclerotia consisting of numerous interconnected sclerotules. A number of other Sclerotiniaceae related to the new fungus are compared with it.     

Crossing test among floating Ulva thalli forming `green tide' in Japan

Crossing tests were made to determine the relationship between the identified Ulva pertusa, which commonly grows in Japan as an attached form on exposed rocks, and the floating Ulva forming "green tide" inside calm bays. The floating Ulva thalli were collected from five major green tide sites in Japan (Yokohama, Mikawa, Miyajima, Kochi and Hakata). Reproductive maturation was induced in U. pertusa and the floating thalli from each site. Mating between induced gametes was observed. It is therefore believed that the floating thalli from Yokohama, Mikawa and Miyajima were mainly U. pertusa, while those from Kochi and Hakata were of a different species (Ulva sp.1). Furthermore, the Ulva species found in Mikawa is also a species (Ulva sp.2) different from both U. pertusa and Ulva sp.1.     

Xylodon kunmingensis sp. nov. (Hymenochaetales,Basidiomycota) from southern China

A new wood-inhabiting fungal species, Xylodon kunmingensis, is proposed based on morphological and molecular evidences. The species is characterized by an annual growth habit, resupinate basidiocarps with cream to buff hymenial, odontioid surface, a monomitic hyphal system with generative hyphae bearing clamp connections and oblong-ellipsoid, hyaline, thin-walled, smooth, inamyloid and indextrinoid, acyanophilous basidiospores, 5–5.8 × 2.8–3.5 μm. The phylogenetic analyses based on molecular data of ITS sequences showed that X. kunmingensis belongs to the genus Xylodon and formed a single group with a high support (100% BS, 100% BP, 1.00 BPP) and grouped with the related species X. astrocystidiatus, X. crystalliger and X. paradoxus. Both morphological and molecular evidences confirmed the placement of the new species in Xylodon.     

Hoffmannoscypha, a novel genus of brightly coloured, cupulate Pyronemataceae closely related to Tricharina and Geopora

The rare apothecial, cupulate fungus Geopora pellita (Pyronemataceae) is characterized by a uniquely bright yellow-orange excipulum. We here re-examine its affiliations by use of morphological, molecular phylogenetic and ultrastructural analyses. G. pellita appears as phylogenetically rather isolated, being the sister group of a clade comprising Phaeangium, Picoa, the majority of the Tricharina species, and the remaining Geopora species. Based on its phylogenetic position and its unique combination of morphological characters, we assign G. pellita to Hoffmannoscypha, gen. nov., as H. pellita, comb. nov. As in a previous study, analyses of both large subunit (LSU) and internal transcribed spacer (ITS) ribosomal DNA suggest that the remaining genus Geopora is paraphyletic, with the hypogeous, ptychothecial type species more closely related to Picoa and Phaeangium than to the greyish-brownish cupulate and apothecial Geopora spp., indicating that the latter should be reassigned to the genus Sepultaria. The current study also shows that ITS confirm LSU data regarding the polyphyly of Tricharina.     

A new Liopropoma sea bass (Serranidae,Epinephelinae, Liopropomini) from deep reefs off Cura?ao,southern Caribbean,with comments on depth distributions of western Atlantic liopropomins

Collecting reef-fish specimens using a manned submersible diving to 300 m off Curaçao, southern Caribbean, is resulting in the discovery of numerous new fish species. The new Liopropoma sea bass described here differs from other western Atlantic members of the genus in having VIII, 13 dorsal-fin rays; a moderately indented dorsal-fin margin; a yellow-orange stripe along the entire upper lip; a series of approximately 13 white, chevron-shaped markings on the ventral portion of the trunk; and a reddish-black blotch on the tip of the lower caudal-fin lobe. The new species, with predominantly yellow body and fins, closely resembles the other two “golden basses” found together with it at Curaçao: L. aberrans and L. olneyi. It also shares morphological features with the other western Atlantic liopropomin genus, Bathyanthias. Preliminary phylogenetic data suggest that western Atlantic liopropomins, including Bathyanthias, are monophyletic with respect to Indo-Pacific Liopropoma, and that Bathyanthias is nested within Liopropoma, indicating a need for further study of the generic limits of Liopropoma. The phylogenetic data also suggest that western Atlantic liopropomins comprise three monophyletic clades that have overlapping depth distributions but different depth maxima (3–135 m, 30–150 m, 133–411 m). The new species has the deepest depth range (182–241 m) of any known western Atlantic Liopropoma species. Both allopatric and depth-mediated ecological speciation may have contributed to the evolution of western Atlantic Liopropomini.     

Sedum plumbizincicola X.H. Guo et S.B. Zhou ex L.H. Wu (Crassulaceae): a new species from Zhejiang Province, China

Sedum plumbizincicola X.H. Guo et S.B. Zhou ex L.H. Wu (Crassulaceae), a new species restricted to lead–zinc mining areas in Zhejiang Province, China, is described and illustrated. This taxon belongs to sect. Sedum (H. Ohba) S.H. Fu based on the adaxially gibbous carpels and follicles. It superficially resembles S. alfredii Hance and three other Sedum species found in the same area, but differs from these other taxa in bearing 4-merous flowers. Differences in geographical distribution, growth habit, phenology, macromorphology, leaf and stem anatomy, as well as seed micromorphology among S. plumbizincicola, S. alfredii and other related taxa in the genus Sedum are also reported. nrDNA internal transcribed spacers (ITS) sequences from seven populations of S. plumbizincicola support the recognition of this as a taxonomic entity distinct from S. alfredii.     

A revision of Dryopteris sect. Diclisodon (Dryopteridaceae) based on morphological and molecular evidence with description of a new species

Dryopteris sect. Diclisodon is a small section of ferns with about 12 species mainly distributed in East Asia. Here, we carried out morphological and phylogenetic analyses of this section. A new species from southwest China, D. gaoligongensis, is described and illustrated. Dryopteris gaoligongensis resembles D. indonesiana and D. sparsa, but differs by having a creeping rhizome and large 4-pinnate fronds. We also show that D. glabrior Ching & Z.Y. Liu is a distinct species; however, because it is a later homonym of D. glabrior Copel., it should be renamed D. renchangiana. We conclude that a species previously known as D. nitidula, also an illegitimate homonym, should be recognized with a new name, D. sinonepalensis. We resolve the phylogenetic position of D. yoroii as sister to other sampled species of D. sect. Diclisodon. Our phylogenetic analyses confirm the distinctiveness of D. gaoligongensis, D. renchangiana, and D. sinonepalensis. A key to species of D. sect. Diclisodon in China is provided.     

Armed and accurate: engineering cytotoxic T cells for eradication of leukemia

After publication we discovered an error in the identification of the origin of the cell line reported in our article in BMC Biotechnology (2010, 10:50), entitled "Ao38, a new cell line from eggs of the black witch moth, Ascalapha odorata (Lepidoptera: Noctuidae), is permissive for AcMNPV infection and produces high levels of recombinant proteins". Upon analysis of primary A. odorata cultures, we found that they were contaminated with cells of Trichoplusia ni origin. The origin of the Ao38 cell line was determined as T. ni using three marker genes and the Ao38 cell line was renamed BTI-Tnao38. References to the origin of the cell line as Ascalapha odorata should be replaced with "a cell line of Trichoplusia ni origin". The absence of TNCL virus detection in the BTI-Tnao38 (Ao38) cell line was confirmed using a highly sensitive RT-PCR protocol capable of detecting TNCL virus RNA at approximately 0.018 copies/cell. Because of these observations, we have revised the title of the original article to "Correction: BTI-Tnao38, a new cell line derived from Trichoplusia ni, is permissive for AcMNPV infection and produces high levels of recombinant proteins" and two additional authors were added to reflect their contributions to the analysis of this cell line.     

BACIDIA NEOSQUAMULOSA,A NEW AND RAPIDLY SPREADING CORTICOLOUS LICHEN SPECIES FROM WESTERN EUROPE

Bacidia neosquamulosaAptroot & van Herk, a new corticolous lichen species, is described from the Netherlands, where it seems to be rapidly spreading and where it is considered to be a neophytic species. It is also reported from Belgium and Great Britain. It resembles corticolous morphs of the rather variableB. arnoldiana, but differs from this and other species by the longer, conspicuously septate, filiform, curved, macroconidia, the longer ascospores and the squamulose-isidiate thallus.     

Distribution of Xiphinema americanum and Related Species in North America

All species of the Xiphinema americanum-group and their synonyms are listed. The North American species reported are listed by state or province. Among these species, X. rivesi has the most widely reported distribution. Six species (X. diffusum, X. floridae, X. laevistriatum, X. luci, X. shell, and X. tarjanense) have been reported from only Florida. The reports of X. pachtaicum, X. sheri, and X. luci did not include morphometrics and need to be confirmed; X. brevicolle from California was identified before Lamberti and Bleve-Zacheo described 15 new species in 1979 and similarly needs to be confirmed. Because of the proliferation of species in this group, reports of X. americanum (sensu stricto) before 1979 are questionable. Extraction techniques for longidorids are discussed.     

Impact of weed control on arbuscular mycorrhizal fungi in a tropical agroecosystem: a long-term experiment

Cover crop species represent an affordable and effective weed control method in agroecosystems; nonetheless, the effect of its use on arbuscular mycorrhizal fungi (AMF) has been scantily studied. The goal of this study was to determine root colonization levels and AMF species richness in the rhizosphere of maize plants and weed species growing under different cover crop and weed control regimes in a long-term experiment. The treatment levels used were (1) cover of Mucuna deeringian (Muc), (2) "mulch" of Leucaena leucocephala (Leu), (3) "mulch" of Lysiloma latisiliquum (Lys), (4) herbicide (Her), (5) manual weeding (CD), (6) no weeding (SD), and (7) no maize and no weeding (B). A total of 18 species of AMF belonging to eight genera (Acaulospora, Ambispora, Claroideoglomus, Funneliformis, Glomus, Rhizophagus, Sclerocystis, and Scutellospora) were identified from trap cultures. Muc and Lys treatments had a positive impact on AMF species richness (11 and seven species, respectively), while Leu and B treatments on the other hand gave the lowest richness values (six species each). AMF colonization levels in roots of maize and weeds differed significantly between treatment levels. Overall, the use of cover crop species had a positive impact on AMF species richness as well as on the percentage of root colonized by AMF. These findings have important implications for the management of traditional agroecosystems and show that the use of cover crop species for weed control can result in a more diverse AMF community which should potentially increase crop production in the long run.     

Phylogenetic Classification at Generic Level in the Absence of Distinct Phylogenetic Patterns of Phenotypical Variation: A Case Study in Graphidaceae (Ascomycota)

Molecular phylogenies often reveal that taxa circumscribed by phenotypical characters are not monophyletic. While re-examination of phenotypical characters often identifies the presence of characters characterizing clades, there is a growing number of studies that fail to identify diagnostic characters, especially in organismal groups lacking complex morphologies. Taxonomists then can either merge the groups or split taxa into smaller entities. Due to the nature of binomial nomenclature, this decision is of special importance at the generic level. Here we propose a new approach to choose among classification alternatives using a combination of morphology-based phylogenetic binning and a multiresponse permutation procedure to test for morphological differences among clades. We illustrate the use of this method in the tribe Thelotremateae focusing on the genus Chapsa, a group of lichenized fungi in which our phylogenetic estimate is in conflict with traditional classification and the morphological and chemical characters do not show a clear phylogenetic pattern. We generated 75 new DNA sequences of mitochondrial SSU rDNA, nuclear LSU rDNA and the protein-coding RPB2. This data set was used to infer phylogenetic estimates using maximum likelihood and Bayesian approaches. The genus Chapsa was found to be polyphyletic, forming four well-supported clades, three of which clustering into one unsupported clade, and the other, supported clade forming two supported subclades. While these clades cannot be readily separated morphologically, the combined binning/multiresponse permutation procedure showed that accepting the four clades as different genera each reflects the phenotypical pattern significantly better than accepting two genera (or five genera if splitting the first clade). Another species within the Thelotremateae, Thelotrema petractoides, a unique taxon with carbonized excipulum resembling Schizotrema, was shown to fall outside Thelotrema. Consequently, the new genera Astrochapsa, Crutarndina, Pseudochapsa, and Pseudotopeliopsis are described here and 39 new combinations are proposed.     

A new dugong species (Sirenia,Dugongidae) from the Eocene of Catalonia (NE Iberian Peninsula)

A new stem dugongid species, Prototherium ausetanum sp. nov. (Dugongidae, Halitheriinae), is described based on a cranium from the middle Eocene of Mas Vilageliu (Tona, NE Iberian Peninsula). The new species displays a combination of features that enables its distinction from other halitheriines, including Prototherium veronense (type species of the genus), Prototherium? intermedium (which likely belongs to a different genus), and Prototherium? montserratense (here considered a nomen dubium), as well as Eotheroides spp. In overall morphology (e.g., dolichocephaly) the new species more closely resembles species previously included in Prototherium. However, a cladistic analysis based on craniodental features recovers the new species as the sister taxon of Eotheroides aegyptiacum (type species of this genus), further constituting a polytomy with P. veronense, Eotheroides lambondrano and the remaining Halitheriinae. Our analysis further indicates that P.? intermedium is more derived than other species of Prototherium, but it does not conclusively resolve the phylogenetic relationships between the included species of Prototherium and Eotheroides. A deeper taxonomic revision of these two genera would be required in order to better resolve the phylogeny of early dugongids.     

When did Cuon reach Java? – Reinvestigation of canid fossils from Homo erectus faunas

The presence of the genus Cuon during the Pleistocene of Java is attested by the endemic species C. sangiranensis and C. crassidens, sometimes classified as C. alpinus, a species that is also part of the Holocene fauna and has persisted until today. The current study revises the fossil canid material from the Sangiran Dome, previously assigned variously to C. sangiranensis, C. crassidens, C. alpinus, C. javanicus, and C. trinilensis. It aims to reinvestigate the arrival of Cuon in Java, in particular in relation to the late early Pleistocene endemic canid of Java: the Cuon-sized Xenocyon trinilensis, which had evolved in situ on Java from the large X. merriami, and which could be a potential competitor to early Cuon in case of contemporaneity. We found that a mandible fragment from Pandejan (holotype of C. crassidens) shows a morphology typical for C. alpinus. However, a maxilla and a mandible from the Bapang Formation at Sangiran, including the holotype of C. sangiranensis, is here assigned to the early dhole species C. priscus. Our results indicate that Cuon was already present in Java during the early middle Pleistocene and probably arrived as part of the immigration events during the Kedung Brubus faunal stage. Since X. trinilensis and Cuon are both hypercarnivorous medium-sized dogs, similar ecological niches are expected for both species. Thus, X. trinilensis probably was outcompeted and replaced by C. priscus. In turn, the latter species was replaced by the extant species, C. alpinus, during the Nangdong faunal stage, likely as part of the next immigration phase, which then disappeared during the tropical rainforest fauna of the Punung faunal stage and re-entered at the onset of the Holocene.     

Transcriptional profiling of Actinobacillus pleuropneumoniae under iron-restricted conditions

Background

Toll-like receptors (TLRs) play a central role in innate immunity. TLRs are membrane glycoproteins and contain leucine rich repeat (LRR) motif in the ectodomain. TLRs recognize and respond to molecules such as lipopolysaccharide, peptidoglycan, flagellin, and RNA from bacteria or viruses. The LRR domains in TLRs have been inferred to be responsible for molecular recognition. All LRRs include the highly conserved segment, LxxLxLxxNxL, in which "L" is Leu, Ile, Val, or Phe and "N" is Asn, Thr, Ser, or Cys and "x" is any amino acid. There are seven classes of LRRs including "typical" ("T") and "bacterial" ("S"). All known domain structures adopt an arc or horseshoe shape. Vertebrate TLRs form six major families. The repeat numbers of LRRs and their "phasing" in TLRs differ with isoforms and species; they are aligned differently in various databases. We identified and aligned LRRs in TLRs by a new method described here.

Results

The new method utilizes known LRR structures to recognize and align new LRR motifs in TLRs and incorporates multiple sequence alignments and secondary structure predictions. TLRs from thirty-four vertebrate were analyzed. The repeat numbers of the LRRs ranges from 16 to 28. The LRRs found in TLRs frequently consists of LxxLxLxxNxLxxLxxxxF/LxxLxx ("T") and sometimes short motifs including LxxLxLxxNxLxxLPx(x)LPxx ("S"). The TLR7 family (TLR7, TLR8, and TLR9) contain 27 LRRs. The LRRs at the N-terminal part have a super-motif of STT with about 80 residues. The super-repeat is represented by STTSTTSTT or _TTSTTSTT. The LRRs in TLRs form one or two horseshoe domains and are mostly flanked by two cysteine clusters including two or four cysteine residue.

Conclusion

Each of the six major TLR families is characterized by their constituent LRR motifs, their repeat numbers, and their patterns of cysteine clusters. The central parts of the TLR1 and TLR7 families and of TLR4 have more irregular or longer LRR motifs. These central parts are inferred to play a key role in the structure and/or function of their TLRs. Furthermore, the super-repeat in the TLR7 family suggests strongly that "bacterial" and "typical" LRRs evolved from a common precursor.     

Evidence from morphological and genetic data confirms that Colossendeis tenera Hilton, 1943 (Arthropoda: Pycnogonida), does not belong to the Colossendeis megalonyx Hoek, 1881 complex

Within the Pycnogonida, genetic studies have revealed that Colossendeis megalonyx Hoek (Challenger Report, Zoology, 3(X), 1–167, 1881), consists of a complex of several cryptic or overlooked species. Colossendeis megalonyx is a typical Southern Hemisphere species complex distributed primarily on the continental shelves in the Antarctic and Subantarctic. However, a different Colossendeis species with a completely different geographic distribution range, Colossendeis tenera Hilton (Journal of Entomology and Zoology, Pomona College, Claremont, 35(1), 2–4, 1943), was considered a subspecies of Colossendeis megalonyx by Turpaeva (Trudy Instituta Okeanology "P. P. Shirshova", Akademy Nauk SSSR, 103, 230–246, 1975). Colossendeis tenera occurs predominantly along the Pacific Coast of North America from the Bering Sea to central California. Prominent differences between these two currently distinct species are found in body proportions and other characters that were interpreted by Turpaeva as a possible case of pedomorphosis induced by deep-sea conditions. In this study, we tested the hypothesis that Colossendeis tenera belongs to the Colossendeis megalonyx complex by analyzing available and novel sequence data (CO1 and H3) of both Colossendeis megalonyx and Colossendeis tenera as well as a similar, apparently closely related species, Colossendeis angusta Sars (Archiv for Mathematik og Naturvidenskab, 2, 237–271, 1877). We compared morphometric data and SEM of the ovigera of these species. Our results clearly indicate that Colossendeis tenera and Colossendeis angusta are not a part of the Colossendeis megalonyx complex. A sister-group relationship of Colossendeis tenera and Colossendeis angusta is strongly supported, but Colossendeis tenera is not clearly resolved as monophyletic with respect to Colossendeis angusta. This work highlights the need for further examination of the variation found in the tenera-angusta clade. It also gives a first hint of the phylogenetic affinities of species within Colossendeis.     

Trillium sulcatum (Liliaceae), a new species of the southern Appalachians

Trillium sulcatum, a new species with two petal color forms, was first circumscribed by Barksdale as a variety in 1938, but without a Latin diagnosis. It superficially resembles the mainly northernT. erectum and appears to be closely related to the primarily midwesternT. flexipes. Its distinguishing features are ringent flowers, short sepals, and long pedicels; additional characters are presented in a chart contrasting it with species with which it has been confused. Distribution suggesting relictual significance is documented. Except that intermediates withT. flexipes are occasional,T. sulcatum maintains its distinctiveness throughout its southern Appalachian range.