Phylogeny of anaerobic fungi (phylum <Emphasis Type="Italic">Neocallimastigomycota</Emphasis>), with contributions from yak in China

The phylum Neocallimastigomycota contains eight genera (about 20 species) of strictly anaerobic fungi. The evolutionary relationships of these genera are uncertain due to insufficient sequence data to infer their phylogenies. Based on morphology and molecular phylogeny, thirteen isolates obtained from yak faeces and rumen digesta in China were assigned to Neocallimastix frontalis (nine isolates), Orpinomyces joyonii (two isolates) and Caecomyces sp. (two isolates), respectively. The phylogenetic relationships of the eight genera were evaluated using complete ITS and partial LSU sequences, compared to the ITS1 region which has been widely used in this phylum in the past. Five monophyletic lineages corresponding to six of the eight genera were statistically supported. Isolates of Caecomyces and Cyllamyces were present in a single lineage and could not be separated properly. Members of Neocallimastigomycota with uniflagellate zoospores represented by Piromyces were polyphyletic. The Piromyces-like genus Oontomyces was consistently closely related to the traditional Anaeromyces, and separated the latter genus into two clades. The phylogenetic position of the Piromyces-like genus Buwchfawromyces remained unresolved. Orpinomyces and Neocallimastix, sharing polyflagellate zoospores, were supported as sister genera in the LSU phylogeny. Apparently ITS, specifically ITS1 alone, is not a good marker to resolve the generic affinities of the studied fungi. The LSU sequences are easier to align and appear to work well to resolve generic relationships. This study provides a comparative phylogenetic revision of Neocallimastigomycota isolates known from culture and sequence data.     

Molecular systematics of the critically-endangered North American spinymussels (Unionidae: <Emphasis Type="Italic">Elliptio</Emphasis> and <Emphasis Type="Italic">Pleurobema</Emphasis>) and description of <Emphasis Type="Italic">Parvaspina</Emphasis> gen. nov.

Despite being common in numerous marine bivalve lineages, lateral spines are extremely rare among freshwater bivalves (Bivalvia: Unionidae), with only three known species characterized by the presence of spines: Elliptio spinosa, Elliptio steinstansana, and Pleurobema collina. All three taxa are endemic to the Atlantic Slope of southeastern North America, critically endangered, and protected by the US Endangered Species Act. Currently, these species are recognized in two genera and remain a source of considerable taxonomic confusion. Because spines are rare in freshwater mussels and restricted to a small region of North America, we hypothesized that spinymussels represent a monophyletic group. We sequenced two mtDNA gene fragments (COI and ND1) and a fragment of the nuclear ITS-1 locus from >70 specimens. Bayesian and maximum-likelihood phylogenetic reconstructions suggest that the spinymussels do not comprise a monophyletic group. Elliptio steinstansana is sister to P. collina, forming a monophyletic clade that was estimated to have diverged from its most recent ancestor in the late Miocene and is distinct from both Elliptio and Pleurobema; we describe a new genus (Parvaspina gen. nov.) to reflect this relationship. Additionally, E. spinosa forms a monophyletic clade that diverged from members of the core Elliptio lineage in the mid-Pliocene. Furthermore, E. spinosa is genetically divergent from the other spinymussel species, suggesting that spines, while extremely rare in freshwater mussels worldwide, may have evolved independently in two bivalve lineages. Recognizing the genetic distinctiveness and inter-generic relationships of the spinymussels is an important first step towards effectively managing these imperiled species and lays the groundwork for future conservation genetics studies.     

Goodbye or welcome Gondwana? – insights into the phylogenetic biogeography of the leafy liverwort Plagiochila with a description of Proskauera, gen. nov. (Plagiochilaceae, Jungermanniales)

Molecular phylogenies based on chloroplast gene rps4 sequences and nuclear ribosomal ITS sequences have been generated to investigate relationships among species and putative segregates in Plagiochila (Plagiochilaceae), the largest genus of leafy liverworts. About a fourth of the ca. 450 accepted binomials of Plagiochilaceae are included in these phylogenetic analyses, several represented by multiple accessions. A clade with Chiastocaulon, Pedinophyllum, and Plagiochilion is placed sister to a clade with numerous accessions of Plagiochila. Plagiochila pleurata and P. fruticella are resolved sister to the remainder of Plagiochilaceae and transferred to the new Australasian genus Proskauera which differs from all other Plagiochilaceae by the occurrence of spherical leaf papillae. The historical biogeography of Plagiochilaceae is explored based on the reconstructions of the phylogeny, biogeographic patterns and diversification time estimates. The results indicate that the current distribution of Plagiochilaceae cannot be explained exclusively by Gondwanan vicariance. A more feasible explanation of the range is a combination of short distance dispersal, rare long distance dispersal events, extinction, recolonization and diversification.     

A preliminary molecular phylogeny shows Japanese and Austrian populations of the red mite <Emphasis Type="Italic">Balaustium murorum</Emphasis> (Acari: Trombidiformes: Erythraeidae) to be closely related

The red mite Balaustium murorum (Hermann) inhabits the Western Palaearctic realm and is well adapted to man-made structures. In Japan, B. murorum had been reported more frequently after the 1980s. A molecular phylogeny based on the nuclear 18S rRNA and mitochondrial COI genes, and including B. murorum individuals from Japan and Austria and representatives of related species from Japan showed four Balaustium species-level lineages in Japan (B. murorum, Balaustium sp. 1, Balaustium sp. 2, Balaustium sp. 3). The B. murorum lineage shared identical 18S sequence and COI haplotype with the Austrian population. Balaustium sp. 1 was detected from the Tokyo and Misaki area (Honshu Island) and was the sister group to B. murorum; the other two lineages inhabited coastal environments of Erimo, Hokkaido Island (Balaustium sp. 2) and Ainan, Shikoku Island (Balaustium sp. 3). The high genetic distances among these four lineages indicate that each lineage is a distinct species, with three of the lineages representing undescribed species. Our results are compatible with the conclusion that B. murorum was introduced to Japan from Europe, although our study did not resolve the polarity or timing of migration events.     

Systematic relationships of <Emphasis Type="Italic">Mosgovoyia</Emphasis> Spasskii, 1951 (Cestoda: Anoplocephalidae) and related genera inferred from mitochondrial and nuclear sequence data

The present study evaluates the phylogenetic position and systematic relationships of two species of Mosgovoyia Spasskii, 1951 and related genera (Cestoda: Anoplocephalidae) based on sequences of 28S ribosomal RNA and mitochondrial NADH dehydrogenase subunit 1 (Nad1) genes. Both molecular data-sets show that M. pectinata (Goeze, 1782) and Schizorchis caballeroi Rausch, 1960 are sister species and that they are phylogenetically independent from M. ctenoides (Railliet, 1890). This shows unambiguously that Mosgovoyia [sensu Beveridge (1978)] is a non-monophyletic assemblage, supporting the validity of Neoctenotaenia Tenora, 1976, erected for M. ctenoides. The results also show that the morphologically related Ctenotaenia marmotae (Fröhlich, 1802) is the sister species of Andrya rhopalocephala (Riehm, 1881) and therefore represents a more derived lineage. Modified diagnoses are provided for Mosgovoyia and Neoctenotaenia.     

Revisiting phylogenetic diversity and cryptic species of <Emphasis Type="Italic">Cenococcum geophilum</Emphasis> sensu lato

The fungus Cenococcum geophilum Fr. (Dothideomycetes, Ascomycota) is one of the most common ectomycorrhizal fungi in boreal to temperate regions. A series of molecular studies has demonstrated that C. geophilum is monophyletic but a heterogeneous species or a species complex. Here, we revisit the phylogenetic diversity of C. geophilum sensu lato from a regional to intercontinental scale by using new data from Florida (USA) along with existing data in GenBank from Japan, Europe, and North America. The combination of internal transcribed spacer (ITS) ribosomal DNA and the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene resolved six well-supported lineages (87–100 % bootstrap values) that are closely related to each other and a seventh lineage that is phylogenetically distinct. A multi-locus analysis (small subunit (SSU), large subunit (LSU), translational elongation factor (TEF), and the largest and second-largest subunits of RNA polymerase II (RPB1 and RPB2)) revealed that the divergent lineage is the sister group to all other known Cenococcum isolates. Isolates of the divergent lineage grow fast on nutrient media and do not form ectomycorrhizas on seedlings of several pine and oak species. Our results indicate that C. geophilum sensu lato includes more phylogenetically distinct cryptic species than have previously been reported. Furthermore, the divergent lineage appears to be a non-mycorrhizal sister group. We discuss the phylogenetic diversity of C. geophilum sensu lato and argue in favor of species recognition based on phylogenetic and ecological information in addition to morphological characteristics. A new genus and species (Pseudocenococcum floridanum gen. et sp. nov.) is proposed to accommodate a divergent and putatively non-mycorrhizal lineage.     

Myrothecium-like (Ascomycota,Hypocreales) species from tropical areas: <Emphasis Type="Italic">Digitiseta</Emphasis> gen. nov. and additions to <Emphasis Type="Italic">Inaequalispora</Emphasis> and <Emphasis Type="Italic">Parvothecium</Emphasis>

Inaequalispora and Parvothecium are two myrothecium-like, closely related genera of Hypocreales. They are also morphologically similar, sharing sporodochial conidiomata, penicillate conidiophores, fusiform to ellipsoidal conidia accumulating in a green slimy drop, and hypha-like setoid extensions emerging through the conidial mass. During a revision of myrothecium-like isolates originating from rainforest areas of South America (Ecuador, Brazil) and Southeast Asia (Singapore), multilocus phylogenetic inferences (based on DNA sequence data of ITS, partial nuc 28S, and partial tef1a, rpb2 and tub2) and morphological studies concordantly revealed the occurrence of two undescribed species of Inaequalispora (I. longiseta sp. nov. and I. cylindrospora sp. nov.) and one undescribed species of Parvothecium (P. amazonensesp. nov.). Myrothecium setiramosum, M. dimorphum, and two undescribed taxa form the base of a new lineage, sister to the current Parvothecium lineage. This lineage is recognized as Digitiseta gen. nov., typified by D. setiramosa comb. nov. Digitiseta dimorpha comb. nov. is also proposed, and the new species D. parvodigitata sp. nov. and D. multidigitata sp. nov. are described.     

New phylogenetic insights into <Emphasis Type="Italic">Saprolegniales</Emphasis> (Oomycota,Straminipila) based upon studies of specimens isolated from Brazil and Argentina

Saprolegniales is a complex and monophyletic order of oomycetes. Their members inhabit terrestrial, freshwater, and marine ecosystems and have a worldwide distribution. In these ecosystems, they are found as saprobes, parasites, or even pathogens of animals and plants of economic importance. In this study, a concatenate phylogeny of the partial LSU and complete ITS rDNA regions is presented, including isolates from Brazil and Argentina, which were sequenced after a detailed morphological analysis. Among the sequenced species, Achlya orion, Leptolegnia eccentrica, Phragmosporangium uniseriatum, and Pythiopsis irregularis are included for the first time in a phylogeny. Our results are in agreement with the recent informal proposals outlined in taxonomic overviews of the Oomycota of G.W. Beakes and collaborators, who placed the family Verrucalvaceae into the Saprolegniales and introduced the family Achlyaceae to group Achlya s.s., Brevilegnia, Dictyuchus, and Thraustotheca. These results also support the transference of Achlya androgyna to Newbya. Leptolegnia appears as paraphyletic, with the separation of L. eccentrica from the other species of this genus. In addition, Phragmosporangium, which is herein sequenced for the first time, clustered as sister to some species of Aphanomyces, including the type species, A. stellatus.     

On the phylogeny of Early Cardioceratidae (Ammonoidea) and Cadoceratinae from Central Russia at the Bathonian–Callovian boundary

The phylogeny of the Middle Jurassic Cardioceratidae is reconstructed on the basis of a study of their shell morphology and analysis of their stratigraphic distribution. The phylogenetic lineage Cranocephalites → Arctocephalites → Arcticoceras → Paracadoceras is assigned to the subfamily Arctocephalitinae (Upper Bajocian–lowermost Callovian). The subfamily Cadoceratinae (Upper Bajocian–Callovian) also originating from Cranocephalites includes the phylogenetic lineage Greencephalites → Cadoceras → Longaeviceras; and lateral branches Chamoussetia and Platychamoussetia. The origin of the Early Callovian Eckhardites, also assigned to Cardioceratidae, is not established. The generic names Rondiceras and Cadochamoussetia are considered as junior synonyms of Cadoceras and Chamoussetia, respectively. The Early Callovian species Cadoceras bellabimba sp. nov. is described.     

Cleaning up the grasses dustbin: systematics of the Arundinoideae subfamily (Poaceae)

Among the 12 subfamilies currently considered in the systematics of Poaceae, the Arundinoideae have long been considered as a dustbin group, with a diversity of forms putatively hiding incertae sedis. Because this subfamily has been poorly investigated using molecular markers for the last two decades, the present study provides the first complete phylogeny of the Arundinoideae based on five plastid DNA loci sequenced for 12 genera, and analysed with and without plastome data from previous studies. The refined Arundinoideae appear to be a robust evolutionary lineage of Poaceae, divided into three tribes with some biogeographical patterns: (1) tribe Arundineae, the most heterogeneous tribe, including Eurasian Arundo, Australian Amphipogon and Monachather, and South African Dregeochloa; (2) tribe Crinipedeae (described here), including Crinipes, Elytrophorus, Styppeiochloa and Pratochloa (described here), with a South and East African distribution; and (3) tribe Molinieae, including Hakonechloa, Molinia and Phragmites, with a Eurasian distribution. Despite reduction in size, this small subfamily conserves a high diversity of morphological forms, with several small but highly differentiated genera. Finally, the molecular dating approach provides an evolutionary framework to understand the diversification of Arundinoideae, refuting Gondwanan vicariance between genera and suggesting capability for long distance dispersal.     

Anatomical features of species of Cyperaceae from northeastern Brazil

Seventy-three species from 17 genera of Cyperaceae were studied with the aim of identifying and confirming those species with Kranz anatomy. Among the species studied, 36 exhibited Kranz anatomy; 37 did not. Of the four types of Kranz anatomy recognized in Cyperaceae, three were encountered: the chlorocyperoid type in the genera Cyperus, Kyllinga, Lipocarpha, Pycreus, and Remirea; the fimbristyloid type in Abildgaardia, Bulbostylis, and Fimbristylis; and the rhynchosporoid type in Rhynchospora. Non-Kranz anatomy was confirmed in species of the following genera: Becquerelia, Calyptrocarya, Cyperus, Diplacrum, Eleocharis, Fuirena, Hypolytrum, Pleurostachys, Rhynchospora, and Scleria. The anatomical data obtained corroborate earlier studies of species of Cyperaceae as to the presence of Kranz anatomy and the anatomical types in several species and the “Kranzkette” pattern in Cyperus ligularis and Cyperus pohlli.     

Phylogeny and taxonomy of casebearer moths (Lepidoptera,Coleophoridae) based on morphological and molecular genetic data. 1. Reconstruction of phylogeny of coleophoridae using analysis of <Emphasis Type="Italic">COI</Emphasis> gene variability

A phylogenetic study of representatives of the family Coleophoridae was conducted using a comprehensive approach, including methods of morphological and molecular genetic analyses. The existent data on the family system were compared with the results of phylogenetic analysis of the COI mitochondrial gene sequences. Four of the five studied subfamilies (Coleophorinae, Ischnophaninae, Augasminae, and Tolleophorinae) corresponded to their location on the phylogram; representatives of Metriotinae were part of Coleophorinae. According to the aggregate data from molecular phylogeny and morphology, the most numerous subfamily of casebearers, Coleophorinae, is polyphyletic within its current boundaries. The results of our analysis of COI molecular divergence does not refute the monophyly of the tribes Casignetellini, Carpochenini, Klinzigedini, Goniodomini, Casasini, and Atractulini from the subfamily Coleophorinae. The allocation of the tribes Aporipturini and Sistrophoecini within the subfamily does not correspond to the molecular data. Monophyly of the genera Ecebalia, Perygra, and Casignetella was confirmed. These genera are well isolated, which reflects the evolutionary significance of the morphological characters chosen for their taxonomic division. The boundaries of the cluster containing these genera correspond to those of the tribe Casignetellini, justifying the allocation of this tribe within the subfamily. The existence of monophyletic tribes Goniodomini (genus Goniodoma) and Carpochenini (genera Ionescumia, Carpochena, and Falkmisa) was also supported. The exceptions were the genera Kasyfia, Tollsia, and Agapalsa, whose monophyly was not confirmed by our results. The distribution of the sequences of species of these genera indicated a paraphyletic origin of Kasyfia and Tollsia and a polyphyletic origin of Agapalsa.     

<Emphasis Type="Italic">Cortinarius</Emphasis> sect. <Emphasis Type="Italic">Riederi</Emphasis>: taxonomy and phylogeny of the new section with European and North American distribution

Cortinarius is one of the most species-rich genera of mushroom-forming fungi. Based on phylogenetic and morphological evidence, Cortinarius, sect. Riederi, is introduced at sectional level (= subsect. Riederi sensu Brandrud & Melot). The taxonomy, phylogeny, ecology and distribution of not only mainly European but also including some North American taxa of this section are treated, which includes nine species and two varieties. Of these, three taxa are described as new (C. burlinghamiae, C. pallidoriederi and C. argenteolilacinus var. dovrensis). The sect. Riederi species possess morphological features similar to Phlegmacium group(s) and forms a phylogenetically isolated lineage, with no supported affinity to other phlegmacioid groups. Three taxa are known from both Europe and North America, two species are known only from North America and five only from Europe. Altogether, eight of the ten taxa are associated with conifers or northern (boreal-subalpine) deciduous trees (Betula spp.). Only two species occur in more temperate forests (Fagus forests), and no species have so far been found in thermophilous Quercus forests     

Phylogeny of Polycladida (Platyhelminthes) based on mtDNA data

A phylogenetic analysis of Polycladida based on two partial mitochondrial genes (cox1 and 16S) is provided. The analysis includes 30 polyclad terminals that represent species from the two taxa which traditionally divide the groups Cotylea and Acotylea. Our phylogenetic analyses produced a well-supported hypothesis that confirms the monophyly of Polycladida, as well as Acotylea and Cotylea. Within Acotylea, there are two lineages not highly supported: on one hand, Leptoplanoidea (excluding Hoploplana elisabelloi) and one Stylochoidea member (Pseudostylochus intermedius) (classification sensu Faubel, 1983, 1984), and on the other hand, Stylochoidea members together with Discocelis tigrina and H. elisabelloi. The genera Stylochus and Imogine are not monophyletic. Within Cotylea, Pseudocerotidae and Euryleptidae are monophyletic, though not highly supported, while Prosthiostomidae is not. Euryleptoidea is paraphyletic. The genera Pseudobiceros and Pseudoceros are monophyletic and highly supported. Our results suggest that, within Acotylea, the prostatoid organs of Discocelis may have been derived from a prostatic vesicle. The genus Hoploplana could be included in Stylochoidea. Within Cotylea, the common ancestor of Euryleptidae and Pseudocerotidae might have been an aposematic animal with tentacles.     

Diversity and evolution of leaf anatomical characters in Taxaceae <Emphasis Type="Italic">s.l.—</Emphasis>fluorescence microscopy reveals new delimitating characters

Taxaceae s.l. comprise six genera (including Cephalotaxus) and about 35 species; The present study aims to give new insights into the evolution of this family, especially into the phylogenetic position of Cephalotaxus. Moreover, only little is known about comparative leaf anatomy of this family and this study aims to expose and interpret the diversity and evolution of leaf anatomical characters and to assess their applicability to identify taxa at the generic and species level. A detailed phylogeny was reconstructed, using both maximum likelihood and Bayesian inference, with a combined dataset of four molecular markers from the plastid and nuclear genomes. Leaf sections from 132 specimens, representing 32 species and four varieties (fresh and herbarium material) were inspected, using fluorescence microscopy. Ancestral characters were reconstructed using Mesquite. The phylogenetic analyses provided full support for Cephalotaxus as sister group to Taxaceae s.str. Within the latter, two monophyletic tribes Taxeae (comprising Austrotaxus, Pseudotaxus, and Taxus) and Torreyeae (comprising Amentotaxus and Torreya) were fully supported. Fluorescence microscopy was shown to be very useful for identifying leaf tissues and their constitution. We were able to show that particularly sclerified tissues have highest potential for the discrimination of both freshly collected samples and rehydrated herbarium specimens at the generic and species level. A correlation between the presence of different sclereid types could be shown and sclereids were hypothesized to pose a primitive trait in the evolution of Taxaceae s.l. New identification keys were generated on the basis of leaf anatomical characters. The microscopic method presented here is applicable for further studies within gymnosperms and probably in angiosperms, as well.     

First phylogenetic analysis of the tribe Oligaphorurini (Collembola: Onychiuridae) inferred from morphological data,with implications for generic classification

Oligaphorurini represent tribe of the subfamily Onychiurinae, which currently comprises 5 genera and 53 species. The present study evaluated the monophyly of Oligaphorurini genera. We investigated phylogenetic relationships among 39 species, representing all extant genera of Oligaphorurini. Both equal- and implied-weighting parsimony analyses were used in phylogenetic reconstruction. The cladistic analyses were based on comprehensive survey of adults’ morphological characters because specimens suitable for molecular studies were not available for the majority taxa. The phylogenetic analysis resulted in the recognition of a monophyletic Chribellphorura, and strongly supported non-monophyly of the previously recognized genera Archaphorura, Dimorphaphorura, Micraphorura, and Oligaphorura. The following new synonymy is recognized: Oligaphorura = Dimorphaphorura syn. nov., = Micraphorura syn. nov., = Archaphorura syn. nov. The general classification of Oligaphorurini is followed by the diagnoses of genera and key to the all known species.     

<Emphasis Type="Italic">Thyridariella</Emphasis>, a novel marine fungal genus from India: morphological characterization and phylogeny inferred from multigene DNA sequence analyses

A novel saprobic fungal genus, Thyridariella (Thyridariaceae), is herein described to include Thyridariella mangrovei, the type species and T. mahakoshae spp. nov. Both species were collected as saprobes on decaying wood of Avicennia marina, a common mangrove species found near Kaveri River Delta, Tamil Nadu, on the east coast of India. Thyridariella is diagnosed by having an exclusive combination of characters, such as ascomata with ostiolar necks thickened laterally, hyaline, and centrally constricted muriform ascospores with a single longitudinal septum in each segment and surrounded by a mucilaginous sheath. These characters demarcate these taxa from morphologically similar genera such as Halojulella and Julella. In addition, the new genus also differs from Parathyridaria and Thyridaria in having hyaline, muriform ascospores with distinct mucilaginous sheaths. The monophyly of Thyridariella is well supported in the phylogenetic analysis based on a concatenated dataset from two proteins and three nuclear gene regions. The phylogeny also depicts a sister group relationship of our new genus to Parathyridaria and Thyridaria and hence confirms its position within Thyridariaceae.