Nuclear Large Subunit Ribosomal DNA Research Articles

Blood flukes of Asiatic softshell turtles: revision of Coeuritrema Mehra, 1933 (Digenea: Schistosomatoidea) and a new species infecting Chinese softshell turtles, Pelodiscus sinensis (Trionychidae), from Vietnam.

Coeuritrema Mehra, 1933, previously regarded as a junior subjective synonym of Hapalorhynchus Stunkard, 1922, herein is revised to include Coeuritrema lyssimus Mehra, 1933 (type species), Coeuritrema rugatus (Brooks et Sullivan, 1981) comb. n., and Coeuritrema platti Roberts et Bullard sp. n. These genera are morphologically similar by having a ventral sucker, non-fused caeca, two testes, a pre-testicular cirrus sac, an intertesticular ovary, and a common genital pore that opens dorsally and in the sinistral half of the body. Phylogenetic analysis of the D1-D3 domains of the nuclear large subunit ribosomal DNA (28S) suggested that Coeuritrema and Hapalorhynchus share a recent common ancestor. Coeuritrema is morphologically most easily differentiated from Hapalorhynchus by having ventrolateral tegumental papillae and a definitive metraterm that is approximately 3-7× longer than the uterus. Coeuritrema comprises species that reportedly infect Asiatic softshell turtles (Testudines: Trionychidae) only, whereas Hapalorhynchus (as currently defined) comprises blood flukes that reportedly infect those hosts plus North American musk turtles (Sternotherus Bell in Gray) and mud turtles (Kinosternon Spix), both Kinosternidae, North American snapping turtles (Chelydridae), Asiatic hard-shelled turtles (Geoemydidae) and African pleurodirans (Pelomedusidae). Coeuritrema platti sp. n. infects the blood of Chinese softshell turtles, Pelodiscus sinensis (Wiegmann), cultured in the Da Rang River Basin (Phu Yen Province, Vietnam). It differs from C. lyssimus by having a narrow hindbody (< 1.6× forebody width), ventrolateral tegumental papillae restricted to the hindbody, a short cirrus sac (< 10% of corresponding body length), a transverse ovary buttressing the caeca, a short, wholly pre-ovarian metraterm (~ 10% of corresponding body length), and a submarginal genital pore. It differs from C. rugatus by having small ventrolateral tegumental papillae, testes without deep lobes, and a Laurer's canal pore that opens posterior to the vitelline reservoir and dorsal to the oviducal seminal receptacle. The new species is only the second turtle blood fluke reported from Vietnam.

New Primers for Discovering Fungal Diversity Using Nuclear Large Ribosomal DNA.

Metabarcoding has become an important tool in the discovery of biodiversity, including fungi, which are the second most speciose group of eukaryotes, with diverse and important ecological roles in terrestrial ecosystems. We have designed and tested new PCR primers that target the D1 variable region of nuclear large subunit (LSU) ribosomal DNA; one set that targets the phylum Ascomycota and another that recovers all other fungal phyla. The primers yield amplicons compatible with the Illumina MiSeq platform, which is cost-effective and has a lower error rate than other high throughput sequencing platforms. The new primer set LSU200A-F/LSU476A-R (Ascomycota) yielded 95–98% of reads of target taxa from environmental samples, and primers LSU200-F/LSU481-R (all other fungi) yielded 72–80% of target reads. Both primer sets have fairly low rates of data loss, and together they cover a wide variety of fungal taxa. We compared our results with these primers by amplifying and sequencing a subset of samples using the previously described ITS3_KYO2/ITS4_KYO3 primers, which amplify the internal transcribed spacer 2 (ITS2) of Ascomycota and Basidiomycota. With approximately equivalent read depth, our LSU primers recovered a greater number and phylogenetic diversity of sequences than the ITS2 primers. For instance, ITS3_KYO2/ITS4_KYO3 primers failed to pick up any members of Eurotiales, Mytilinidiales, Pezizales, Saccharomycetales, or Venturiales within Ascomycota, or members of Exobasidiomycetes, Microbotryomycetes, Pucciniomycetes, or Tremellomycetes within Basidiomycota, which were retrieved in good numbers from the same samples by our LSU primers. Among the OTUs recovered using the LSU primers were 127 genera and 28 species that were not obtained using the ITS2 primers, although the ITS2 primers recovered 10 unique genera and 16 species that were not obtained using either of the LSU primers These features identify the new primer sets developed in this study as useful complements to other universal primers for the study of fungal diversity and community composition.

Morphological and genetic species diversity in ostracods (Crustacea: Oligostraca) from Caribbean reefs

The taxonomy and ecology of ostracods in the Caribbean remain incomplete, even though they are among the most successful and ubiquitous microcrustaceans of marine ecosystems. In an effort to enhance our knowledge of the biodiversity, abundance, and distribution of benthic ostracods, several sediment samples were collected from mesophotic coral ecosystems (MCEs) of Puerto Rico and U.S. Virgin Islands at different depths (30–102 m) using technical diving. The highest densities of ostracods were found in the deepest samples (≥61 m), and these were the most abundant and diverse assemblages. All ostracods collected belong to the subclasses Myodocopa Sars and Podocopa Sars. Myodocopa was represented by the families Cypridinidae Baird, Polycopidae Sars, Sarsiellidae Brady & Norman, Rutidermatidae Brady & Norman, Cylindroleberididae Muller, and Philomedidae Muller. On the other hand, Podocopa was represented by the following families: Bairdiidae Sars, Pontocyprididae Muller, Candonidae Kaufmann (subfamily Paracypridinae Sars), Macrocyprididae Muller, Loxoconchidae Sars, Xestoleberididae Sars, Cytherellidae Sars and Cytheromatidae Elofson. The subclass Podocopa showed the highest number of individuals and species. There was a ~100 % correspondence between morphologically identified species and genetically defined species through a short region of the nuclear large subunit ribosomal DNA, which was shown to be appropriate for species recognition and discrimination in ostracods. Using a morphological (shell shape and ornamentation) and molecular barcoding approach (28S rDNA), we provide the first report of the biodiversity of ostracods in the mesophotic coral ecosystems of northeastern Caribbean.

Phylloporia minutipora and P. radiata spp. nov. (Hymenochaetales, Basidiomycota) from China and a key to worldwide species of Phylloporia

Phylloporia is a monophyletic genus within the Hymenochaetaceae as recovered by nuclear large subunit ribosomal DNA (nLSU) sequences. According to the summarization of 38 species accepted in this genus, Phylloporia is characterized by an absence of setae and the presence of abundant thick-walled, colored and tiny basidiospores, although its other morphological characters are highly diverse. Nine herbarium specimens from China, fitting the morphological concept of Phylloporia, were morphologically and phylogenetically studied in detail. The phylogeny inferred from nLSU sequences shows that the nine specimens formed three terminal lineages within the Phylloporia clade. Two lineages being composed of four specimens from Hainan and three from Guizhou were newly described as Phylloporia minutipora and P. radiata, respectively. In Phylloporia, P. minutipora is distinct by a combination of annual, sessile and imbricate basidiocarps, distinctly concentrically sulcate pileal surface with obtuse margin, angular pores of 12–15 per mm, duplex context separated by a black zone, a dimitic hyphal system, and broadly ellipsoid basidiospores of 2.5–3 × 2–2.5 μm, while P. radiata is distinct by a combination of annual, sessile and imbricate basidiocarps, faintly sulcate and radially striate pileal surface, sharp pileal margin, angular pores of 8–10 per mm, duplex context separated by a black zone, a monomitic hyphal system, and broadly ellipsoid basidiospores of 2.5–3.5 × 2–2.5 μm. The third lineage, comprising two specimens from Hainan, was morphologically determined as Phylloporia pulla. This species was recently combined to Phylloporia based on only morphological characters, and the current study for the first time generated its molecular sequences for phylogenetic reference. A key to all 40 species of Phylloporia is provided.

New Genus of Blood Fluke (Digenea: Schistosomatoidea) from Malaysian Freshwater Turtles (Geoemydidae) and its Phylogenetic Position Within Schistosomatoidea.

: Baracktrema obamai n. gen., n. sp. infects the lung of geoemydid turtles (black marsh turtle, Siebenrockiella crassicollis [type host] and southeast Asian box turtle, Cuora amboinensis ) in the Malaysian states of Perak, Perlis, and Selangor. Baracktrema and Unicaecum Stunkard, 1925 are the only accepted turtle blood fluke genera having the combination of a single cecum, single testis, oviducal seminal receptacle, and uterine pouch. Baracktrema differs from Unicaecum by having a thread-like body approximately 30-50× longer than wide and post-cecal terminal genitalia. Unicaecum has a body approximately 8-12× longer than wide and terminal genitalia that are anterior to the distal end of the cecum. The new genus further differs from all other accepted turtle blood fluke genera by having a cecum that is highly convoluted for its entire length, a spindle-shaped ovary between the cirrus sac and testis, a uterine pouch that loops around the primary vitelline collecting duct, a Laurer's canal, and a dorsal common genital pore. Phylogenetic analysis of the D1-D3 domains of the nuclear large subunit ribosomal DNA (28S) revealed, with high nodal support and as predicted by morphology, that Baracktrema and Unicaecum share a recent common ancestor and form a clade sister to the freshwater turtle blood flukes of Spirorchis, paraphyletic Spirhapalum, and Vasotrema and that, collectively, these flukes were sister to all other tetrapod blood flukes (Hapalorhynchus + Griphobilharzia plus the marine turtle blood flukes and schistosomes). Pending a forthcoming emended morphological diagnosis of the family, the clade including Spirorchis spp., paraphyletic Spirhapalum, Vasotrema, Baracktrema, and Unicaecum is a likely placeholder for "Spirorchiidae Stunkard, 1921 " (type genus Spirorchis MacCallum, 1918 ; type species Spirorchis innominatus Ward, 1921 ). The present study comprises the 17th blood fluke known to infect geoemydid turtles and the first proposal of a new genus of turtle blood fluke in 21 yr.

Fulvifomes imbricatus and F. thailandicus (Hymenochaetales, Basidiomycota): two new species from Thailand based on morphological and molecular evidence

Fulvifomes, which belongs to Hymenochaetaceae, is characterized by a combination of annual to perennial and non-resupinate basidiocarps with an homogeneous or duplex context, a monomitic to dimitic hyphal system, lack of hyphoid and hymenial setae, and subglobose to ellipsoid, yellowish to brown and thick-walled basidiospores. Specimens collected in Chiang Mai, Thailand, and subjected to morphological examination and phylogenetic analysis were determined as F. fastuosus and the newly described species F. imbricatus and F. thailandicus. Fulvifomes imbricatus is characterized by perennial and imbricate basidiocarps, a concentrically sulcate and uncracked pileal surface, a duplex context with a black cuticle, thin tube layers (less than 3 mm thick), a dimitic hyphal system and an absence of cystidioles, whereas F. thailandicus is distinguished by perennial basidiocarps, applanate pilei, a concentrically sulcate and cracked pileal surface, an homogeneous context, a dimitic hyphal system and the presence of cystidioles. The phylogenies inferred from nuclear large subunit ribosomal DNA and internal transcribed spacer sequences showed that the two new species formed distinct lineages from other sampled species in the Fulvifomes clade. In addition, Inonotus luteoumbrinus and I. porrectus were nested within the Fulvifomes clade.

Molecular systematics of Barbatosphaeria (Sordariomycetes): multigene phylogeny and secondary ITS structure.

Thirteen morphologically similar strains of barbatosphaeria- and tectonidula-like fungi were studied based on the comparison of cultural and morphological features of sexual and asexual morphs and phylogenetic analyses of five nuclear loci, i.e. internal transcribed spacer rDNA operon (ITS), large and small subunit nuclear ribosomal DNA, β-tubulin, and second largest subunit of RNA polymerase II. Phylogenetic results were supported by in-depth comparative analyses of common core secondary structure of ITS1 and ITS2 in all strains and the identification of non-conserved, co-evolving nucleotides that maintain base pairing in the RNA transcript. Barbatosphaeria is defined as a well-supported monophyletic clade comprising several lineages and is placed in the Sordariomycetes incertae sedis. The genus is expanded to encompass nine species with both septate and non-septate ascospores in clavate, stipitate asci with a non-amyloid apical annulus and non-stromatic ascomata with a long decumbent neck and carbonised wall often covered by pubescence. The asexual morphs are dematiaceous hyphomycetes with holoblastic conidiogenesis belonging to Ramichloridium and Sporothrix types. The morphologically similar Tectonidula, represented by the type species T. hippocrepida, grouped with members of Barbatosphaeria and is transferred to that genus. Four new species are introduced and three new combinations in Barbatosphaeria are proposed. A dichotomous key to species accepted in the genus is provided.

A metagenetic approach for revealing community structure of marine planktonic copepods.

Marine planktonic copepods are an ecologically important group with high species richness and abundance. Here, we propose a new metagenetic approach for revealing the community structure of marine planktonic copepods using 454 pyrosequencing of nuclear large subunit ribosomal DNA. We determined an appropriate similarity threshold for clustering pyrosequencing data into molecular operational taxonomic units (MOTUs) using an artificial community containing 33 morphologically identified species. The 99% similarity threshold had high species-level resolution for MOTU clustering but overestimated species richness. The artificial community was appropriately clustered into MOTUs at 97% similarity, with little inflation in MOTU numbers and with relatively high species-level resolution. The number of sequence reads of each MOTU was correlated with dry weight of that taxon, suggesting that sequence reads could be used as a proxy for biomass. Next, we applied the method to field-collected samples, and the results corresponded reasonably well with morphological analysis of these communities. Numbers of MOTUs were well correlated with species richness at 97% similarity, and large numbers of sequence reads were generally observed in MOTUs derived from species with large biomass. Further, MOTUs were successfully classified into taxonomic groups at the family level at 97% similarity; similar patterns of species richness and biomass were revealed within families with metagenetic and morphological analyses. At the 99% similarity threshold, MOTUs with high proportions of sequence reads were identified as biomass-dominant species in each field-collected sample. The metagenetic approach reported here can be an effective tool for rapid and comprehensive assessment of copepod community structure.

Wood Decay Fungi in South Korea: Polypores from Seoul

In Seoul, a majority of plant communities have undergone significant changes over the last few decades; however, how wood decay fungi have responded and adapted to the changes in vegetation remains unknown. Through an ongoing investigation of Korean indigenous fungi, ca. 300 specimens with poroid basidiocarp were collected in Seoul during 2008~2012. Morphological examination and molecular analysis using the internal transcribed spacer and nuclear large subunit ribosomal DNA region sequences helped identify 38 species belonging to 28 genera, 10 families, and 5 orders in this area. Among them, three polypores, Abundisporus pubertatis, Coriolopsis strumosa, and Perenniporia maackiae were found to be new to South Korea.

A floristic survey of marine tube-forming diatoms reveals unexpected diversity and extensive co-habitation among genetic lines of the Berkeleya rutilans complex (Bacillariophyceae)

Limited molecular data for marine tube-forming diatoms are available currently and this study provides the first molecular survey of these taxa. To conduct this survey, we used a molecular-assisted alpha taxonomy (MAAT) approach that utilizes DNA barcode data. We used three DNA barcode markers: the 3´ end of the large subunit of RUBISCO (rbcL-3P); the variable D2/D3 region of the nuclear large subunit ribosomal DNA (LSU D2/D3); and the internal transcribed spacer 2 (ITS2) to assign marine tube-forming diatoms from Canada to genetic species groups. The rbcL-3P analysis uncovered 29 genetic groups including representatives of Haslea crucigera, Navicula bottnica, N. brunelii, N. ramosissima, Nitzschia fontifuga, N. tubicola, Parlibellus berkeleya and P. delognei f. elliptica, as well as a complex of 14 closely related groups morphologically consistent with Berkeleya rutilans. We sequenced ITS2 for representatives of the B. rutilans complex; these data were consistent with the rbcL-3P genetic clusters for 86% of the colonies tested. The remaining 14% were in conflict, possibly indicating that more than a single Berkeleya genetic species was present in each colony. To investigate this hypothesis further, we developed ‘species-specific’ ITS2 primers and confirmed heterogeneity of Berkeleya genetic species in 64% of the colonies tested (N = 91). Therefore, a taxonomic assessment of tube-forming species that were originally described on the basis of colony morphology (e.g. Berkeleya rutilans) can only proceed using clonal cultures or single-cell analysis.

Chaetoceros rotosporus sp. nov. (Bacillariophyceae), a species with unusual resting spore formation

Li Y., Lundholm N. and Moestrup Ø. 2013. Chaetoceros rotosporus sp. nov. (Bacillariophyceae), a species with unusual resting spore formation. Phycologia 52: 600–608. DOI: 10.2216/13-168.1With more than 400 species, the diatom genus Chaetoceros Ehrenberg is one of the most species-rich genera of marine planktonic diatoms. Although many Chaetoceros taxa are considered to be cosmopolitan, research has mainly focused on polar and temperate areas. Studies on material from tropical waters suggested that a high and undescribed species diversity of Chaetoceros occur here. On the basis of plankton samples collected in Daya Bay, South China Sea, a new species, C. rotosporus sp. nov., is described. Vegetative cells and resting spores were examined by light microscopy as well as transmission and scanning electron microscopy. The most variable part of the nuclear large-subunit ribosomal DNA was sequenced for information on phylogenetic relationships. Characteristic traits of C. rotosporus were a 90° rotation of the resting spore during spore maturation and a nearly rectangular silica wing that extended around the girdle of the immature resting spore. Neither character has been observed in previously described Chaetoceros species. Other distinguishing characters were the very large apertures and the single chloroplast, which formed a shallow bowl with four arms within each cell and appeared H-shaped in broad girdle view. Chaetoceros rotosporus sp. nov. belongs to the subgenus Hyalochaete Gran, but it could not be placed in any of the traditional sections of Chaetoceros, indicating a need for revision of Chaetoceros using a combination of morphological and molecular data.

Novel Evolutionary Lineages Revealed in the Chaetothyriales (Fungi) Based on Multigene Phylogenetic Analyses and Comparison of ITS Secondary Structure

Cyphellophora and Phialophora (Chaetothyriales, Pezizomycota) comprise species known from skin infections of humans and animals and from a variety of environmental sources. These fungi were studied based on the comparison of cultural and morphological features and phylogenetic analyses of five nuclear loci, i.e., internal transcribed spacer rDNA operon (ITS), large and small subunit nuclear ribosomal DNA (nuc28S rDNA, nuc18S rDNA), β-tubulin, DNA replication licensing factor (mcm7) and second largest subunit of RNA polymerase II (rpb2). Phylogenetic results were supported by comparative analysis of ITS1 and ITS2 secondary structure of representatives of the Chaetothyriales and the identification of substitutions among the taxa analyzed. Base pairs with non-conserved, co-evolving nucleotides that maintain base pairing in the RNA transcript and unique evolutionary motifs in the ITS2 that characterize whole clades or individual taxa were mapped on predicted secondary structure models. Morphological characteristics, structural data and phylogenetic analyses of three datasets, i.e., ITS, ITS-β-tubulin and 28S-18S-rpb2-mcm7, define a robust clade containing eight species of Cyphellophora (including the type) and six species of Phialophora. These taxa are now accommodated in the Cyphellophoraceae, a novel evolutionary lineage within the Chaetothyriales. Cyphellophora is emended and expanded to encompass species with both septate and nonseptate conidia formed on discrete, intercalary, terminal or lateral phialides. Six new combinations in Cyphellophora are proposed and a dichotomous key to species accepted in the genus is provided. Cyphellophora eugeniae and C. hylomeconis, which grouped in the Chaetothyriaceae, represent another novel lineage and are introduced as the type species of separate genera.

New Species of the Genus Metschnikowia Isolated from Flowers in Indonesia, Metschnikowia cibodasensis sp. nov.

A novel species, Metschnikowia cibodasensis, is proposed to accommodate eight strains (ID03- 0093(T), ID03-0094, ID03-0095, ID03-0096, ID03-0097, ID03-0098, ID03-0099, and ID03-0109) isolated from flowers of Saurauia pendula, Berberis nepalensis, and Brunfelsia americana in Cibodas Botanical Garden, West Java, Indonesia. The type strain of M. cibodasensis is ID03- 0093(T) (= NBRC 101693(T) =UICC Y-335(T) = BTCC-Y25(T)). The common features of M. cibodasensis are a spherical to ellipsoidopedunculate shaped ascus, which contains one or two needleshaped ascospores, and lyse at maturity. Asci generally develop directly from vegetative cells but sometimes from chlamydospores. The neighbor-joining tree based on the D1/D2 domain of nuclear large subunit (nLSU) ribosomal DNA sequences strongly supports that M. cibodasensis (eight strains) and its closest teleomorphic species, M. reukaufii, are different species by a 100% bootstrap value. The type strain of M. cibodasensis, ID03-0093(T), differed from M. reukaufii NBRC 1679(T) by six nt (five substitutions and one deletion) in their D1/D2 region of nLSU rDNA, and by 18 nt (five deletions, four insertions, and nine substitutions) in their internal transcribed spacer regions of rDNA, respectively. Four strains representative of M. cibodasensis (ID03-0093(T), ID03-0095, ID03-0096, and ID03-0099) showed a mol% G+C content of 44.05 ± 0.25%, whereas that of M. reukaufii NBRC 1679(T) was 41.3%. The low value of DNADNA homology (5-16%) in four strains of M. cibodasensis and M. reukaufii NBRC 1679(T) strongly supported that these strains represent a distinct species.

Two taxonomic novelties in the Sordariomycetidae: Ceratolenta caudata gen. et sp. nov. and Platytrachelon abietis gen. et comb. nov. for Ceratosphaeria abietis

Wood-inhabiting taxa of the Sordariomycetidae comprise several distantly related monotypic or small genera, which lack familial or ordinal affiliation and share a simple and inconspicuous morphology of dark ascomata with carbonaceous walls and long necks, stipitate asci and hyaline ellipsoidal, fusiform to cylindrical ascospores. Recent collections of an undescribed fungus and of Ceratosphaeria abietis reveal two additional evolutionary lineages characterized by this simple and indistinct teleomorph morphology. Phylogenetic analysis of three genes, small and large subunit nuclear ribosomal DNA (nc28S and nc18S rDNA) combined with the second largest subunit of RNA polymerase II (rpb2), supports the recognition of two new genera, Ceratolenta and Platytrachelon for C. abietis. Platytrachelon abietis is redescribed and illustrated based on additional collections. In culture it produced a dematiaceous hyphomycetous anamorph with blastic conidiogenesis and ellipsoidal, septate, pale brown conidia. It was associated with a synanamorph producing cylindrical, strongly curved hyaline conidia. Molecular data suggest a relationship of Platytrachelon with the Papulosaceae, while Ceratolenta forms a monophylum on a separate branch. Both taxonomic novelties possess striking morphological similarities with Ceratosphaeria, Lentomitella and Rhodoveronaea, which recently were reinstated based on DNA sequence data. A key to morphologically similar wood-inhabiting fungi classified in the Sordariomycetidae is provided.

A new species of the genus Trematosphaeria from China

A new species of the genus Trematosphaeria was isolated and identified from the soil in Jiuzhaigou Nature Reserve, southwestern China. The new taxon was studied based on morphological characters and phylogenetic analyses of three nuclear loci, i.e., the internal transcribed spacer rDNA operon (ITS), and large and small subunit nuclear ribosomal DNA (nuc28S rDNA, nuc18S rDNA). The analyzed Trematosphaeria species were clustered in several clades within the Pleosporales and the genus was shown to be polyphyletic. The new species is introduced as Trematosphaeria terricola, and it is characterized by short-papillate ascomata with suborbicular ostiolum, 3-septate, cinnamon-brown, fusiform ascospores with narrowly rounded ends, verruculose at maturity. Trematosphaeria terricola is compared with morphologically similar species T. confusa, T. mangrovis, and T. pertusa, which differ from the former species in the number of septa, and the shape and size of the ascospores with or without a sheath. This is the first report of a Trematosphaeria isolate from alpine soil in China.

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The new genus Mangoldia Lücking, Parnmen &amp; Lumbsch is described based on the new species M. australiana and also including M. atronitens. Mangoldia combines thallus and ascoma features of Phaeographis s.str. (e.g., P. dendritica and P. lecanographa), i.e. a white, ecorticate thallus and ascoma with exposed, brown disc and thin, partially split, thalline margins, with hymenial and ascospore characters of Graphis, i.e. distoseptate, hyaline ascospores which react I+ violet-blue. DNA sequence data of the nuclear large subunit ribosomal DNA (nuLSU) of M. australiana place the taxon as separate lineage within subfamily Graphidoideae tribe Graphideae, but without a resolved and supported sister-group relationship with any of the accepted genera in this tribe.

Species boundaries and host range of tortoise mites (Uropodoidea) phoretic on bark beetles (Scolytinae), using morphometric and molecular markers.

Understanding the ecology and evolutionary history of symbionts and their hosts requires accurate taxonomic knowledge, including clear species boundaries and phylogenies. Tortoise mites (Mesostigmata: Uropodoidea) are among the most diverse arthropod associates of bark beetles (Curculionidae: Scolytinae), but their taxonomy and host associations are largely unstudied. We tested the hypotheses that (1) morphologically defined species are supported by molecular data, and that (2) bark beetle uropodoids with a broad host range comprise cryptic species. To do so, we assessed the species boundaries of uropodoid mites collected from 51 host species, across 11 countries and 103 sites, using morphometric data as well as partial cytochrome oxidase I (COI) and nuclear large subunit ribosomal DNA (28S). Overall, morphologically defined species were confirmed by molecular datasets, with a few exceptions. Twenty-nine of the 36 uropodoid species (Trichouropoda, Nenteria and Uroobovella) collected in this study had narrow host ranges, while seven species had putative broad host ranges. In all but one species, U. orri, our data supported the existence of these host generalists, which contrasts with the typical finding that widespread generalists are actually complexes of cryptic specialists.

Four Unrecorded Wood Decay Fungi from Seoul in Korea

During the investigation of Korean indigenous fungi from Seoul, three genera-Fuscoporia, Porostereum, and Trametopsis, and four species-Fuscoporia senex, Phlebia acerina, Porostereum spadiceum, and Trametopsis cervina were found. Their morphological characteristics were examined and their identification was confirmed by molecular analysis based on internal transcribed spacer (ITS) and nuclear large subunit ribosomal DNA region sequences. These fungi are new to Korea and registered here with descriptions.

A new species of Lenzitopsis (Thelephorales, Basidiomycota) and its phylogenetic placement

Lenzitopsis (Thelephorales, Basidiomycota), typified by Lenzitopsis oxycedri, was monotypic before we described the second species of this genus, Lenzitopsis daii in this study. L. daii resembles L. oxycedri in producing lenzitoid hymenophore as well as brown hyphae and echinulate spores, but it differs from the type species by its annual basidiocarps, amyloid spores and growth exclusively on Juniperus chinensis (Cupressaceae). In the phylogenetic perspective inferred with nuclear large subunit ribosomal DNA sequences, the two species were separated from each other and formed a strongly supported clade in the Thelephorales. The two Lenzitopsis species showed a more than 5% difference in internal transcribed spacer sequences. Lenzitopsis species are wood-decaying fungi, and this is the second genus of the order where mycorrhizal life style is unknown, besides of Amaurodon.

Factors that affect large subunit ribosomal DNA amplicon sequencing studies of fungal communities: classification method, primer choice, and error.

Nuclear large subunit ribosomal DNA is widely used in fungal phylogenetics and to an increasing extent also amplicon-based environmental sequencing. The relatively short reads produced by next-generation sequencing, however, makes primer choice and sequence error important variables for obtaining accurate taxonomic classifications. In this simulation study we tested the performance of three classification methods: 1) a similarity-based method (BLAST + Metagenomic Analyzer, MEGAN); 2) a composition-based method (Ribosomal Database Project naïve Bayesian classifier, NBC); and, 3) a phylogeny-based method (Statistical Assignment Package, SAP). We also tested the effects of sequence length, primer choice, and sequence error on classification accuracy and perceived community composition. Using a leave-one-out cross validation approach, results for classifications to the genus rank were as follows: BLAST + MEGAN had the lowest error rate and was particularly robust to sequence error; SAP accuracy was highest when long LSU query sequences were classified; and, NBC runs significantly faster than the other tested methods. All methods performed poorly with the shortest 50–100 bp sequences. Increasing simulated sequence error reduced classification accuracy. Community shifts were detected due to sequence error and primer selection even though there was no change in the underlying community composition. Short read datasets from individual primers, as well as pooled datasets, appear to only approximate the true community composition. We hope this work informs investigators of some of the factors that affect the quality and interpretation of their environmental gene surveys.