A phylogenetic overview of the family Pyronemataceae (Ascomycota, Pezizales)

Partial sequences of nuLSU rDNA were obtained to investigate the phylogenetic relationships of Pyronemataceae, the largest and least studied family of Pezizales. The dataset includes sequences for 162 species from 51 genera of Pyronemataceae, and 39 species from an additional 13 families of Pezizales. Parsimony, ML, and Bayesian analyses suggest that Pyronemataceae is not monophyletic as it is currently circumscribed. Ascodesmidaceae is nested within Pyronemataceae, and several pyronemataceous taxa are resolved outside the family. Glaziellaceae forms the sister group to Pyronemataceae in ML analyses, but this relationship, as well as those of Pyronemataceae to the other members of the lineage, are not resolved with support. Fourteen clades of pyronemataceous taxa are well supported and/or present in all recovered trees. Several pyronemataceous genera are suggested to be non-monophyletic, including Anthracobia, Cheilymenia, Geopyxis, Humaria, Lasiobolidium, Neottiella, Octospora, Pulvinula, Stephensia, Tricharina, and Trichophaea. Cleistothecial and truffle or truffle-like ascomata forms appear to have evolved independently multiple times within Pyronemataceae. Results of these analyses do not support previous classifications of Pyronemataceae, and suggest that morphological characters traditionally used to segregate the family into subfamilial groups are not phylogenetically informative above the genus level.     

Morphology and phylogenetic interpretation of a new Cambrian edrioasteroid (Echinodermata) from Spain

Abstract: The edrioasteroid, Aragocystites belli gen. nov. sp. nov. from the middle Cambrian Murero Formation of Spain, is described based on a small number of very well‐preserved specimens. Important anatomical characteristics include star‐shaped and pseudoclavate theca, rare or absent epispires, well‐developed interradially positioned oral plates and several unorganized cover plates associated with each widely exposed flooring plate. A phylogenetic analysis including several Cambro–Ordovician species shows it is more derived than Stromatocystites and Totiglobus but is a sister group to a clade comprising Cambraster and Edriodiscus. Ontogenetic observations based on juveniles of 5 mm in diameter suggest that this species changed thecal shape markedly during growth. A. belli gen. nov. sp. nov. probably lived in quiet environments where it attached directly to the sea floor on stabilized substrates.     

Morphological and phylogenetic studies of Cytospora (Valsaceae,Diaporthales) isolates from Chinese scholar tree,with description of a new species

Cytospora species are the most serious and widespread pathogens associated with canker disease on multiple plants. In this study, three species, i.e., Cytospora sophoricola, C. chrysosperma, and C. sophorae, which were isolated from Sophora in China, are described and illustrated based on their morphological characteristics and phylogenetic analyses. Cytospora sophoricola was distinguished clearly by its larger disc, multiple ostioles, cystic and multiple locules, and specific cultural characteristics, i.e., protruding fruiting bodies. Maximum parsimony and maximum likelihood analysis showed that it did not cluster with any known species of Cytospora, so it is described as a new species. Cytospora sophorae is a previously reported species from Sophora, which is redescribed based on new isolates and additional observations. Another species was identified as C. chrysosperma, which is reported for the first time on Sophora, so Papilionaceae is shown to be a new host family for C. chrysosperma. The morphological affinities of these species with related taxa are discussed, while the phylogenetic relationships of these species with other fungus in the genus Cytospora were elucidated based on their internal transcribed spacer (ITS) rRNA region sequences.     

Cystobasidiopsis nirenbergiae, a new agaricostilbomycete (Pucciniomycotina)

A new genus, Cystobasidiopsis, and a new species, Cystobasidiopsis nirenbergiae, are described for a fungus isolated from an arable loess soil in Ahlum near Braunschweig, Niedersachsen, Germany. An integrated analysis of morphological, ecological, ultrastructural and molecular data indicates that the new species belongs to the Chionosphaeraceae within the Agaricostilbales. Relevant characteristics of the new species are discussed and compared with those of related taxa.     

Molecular systematics and taxonomic overview of the bird's nest fungi (Nidulariaceae)

Fungi in the Nidulariaceae, otherwise known as ‘bird's nest fungi’, are among the least studied groups of Agaricomycetes (Basidiomycota). Bird's nest fungi are globally distributed and typically grow on woody debris or animal dung as saprotrophs. This group of fungi is morphologically diverse with ca. 200 described species. Phylogenetic relationships of bird's nest fungi were investigated with four commonly used loci (ITS, LSU, tef, and rpb2). The family was resolved as a monophyletic group with Squamanitaceae as a potential sister taxon. Cyathus and Crucibulum each formed its own independent and well-supported clade. Nidula and Nidularia formed a clade together, but each genus is polyphyletic. Two Mycocalia species included in our analyses were on their own separate branches, indicating that this genus is also polyphyletic. Misidentifications were detected in most genera, suggesting that species concepts need to be revisited and refined throughout Nidulariaceae. Several bird's nest fungi species have global geographical distributions whereas others may have more limited ranges. Basic morphological characters of bird's nest fungi have likely been lost or gained multiple times. The phylogenetic placement of Crucibulum is unclear and the sister lineage of bird's nest fungi is not conclusive. Further studies with data from rare species and additional informative genes are needed to fully resolve the topology of Nidulariaceae and identify its sister group with more certainty.     

Phylogenetic relationships among Boleosoma darter species (Percidae: Etheostoma)

Darters represent a species rich group of North American freshwater fishes studied in the context of their diverse morphology, behavior, and geographic distribution. We report the first molecular phylogenetic analyses of the Boleosoma darter clade that includes complete species sampling. We estimated the relationship among the species of Boleosoma using DNA sequence data from a mitochondrial (cytochrome b) and a nuclear gene (S7 ribosomal protein intron 1). Our analyses discovered that the two Boleosoma species with large geographic distributions (E. nigrum and E. olmstedi) do not form reciprocally monophyletic groups in either gene trees. Etheostoma susanae and E. perlongum were phylogenetically nested in E. nigrum and E. olmstedi, respectively. While analysis of the nuclear gene resulted in a phylogeny where E. longimanum and E. podostemone were sister species, the mitochondrial gene tree did not support this relationship. Etheostoma vitreum was phylogenetically nested within Boleosoma in the mitochondrial DNA and nuclear gene trees. Our analyses suggest that current concepts of species diversity underestimate phylogenetic diversity in Boleosoma and that Boleosoma species likely provide another example of the growing number of discovered instances of mitochondrial genome transfer between darter species.     

Molecular phylogenetic analyses of snakeheads (Perciformes: Channidae) using mitochondrial DNA sequences

Mitochondrial DNA sequences of approximately 1.5 kbp including the NADH dehydrogenase subunit 2 (ND2) gene and its flanking gene regions were determined for 20 species from the freshwater fish family Channidae and 3 species from Nandidae, Badidae, and Osphronemidae. Channa orientalis and C. gachua had an approximately 170-bp insertion between the tRNA^Met and ND2 genes, where a 5′-half of the insertion was similar to the 5′-end portion of the ND2 gene and a 3′-half was homologous to the tRNA^Met gene. This insertion may thus have originated from a tandem gene duplication that occurred in a common ancestor of these two sister species. Molecular phylogenetic analyses from different tree-building methods consistently suggested the mutual monophyly of the African and Asian taxa and the existence of several clades within the Asian taxa, some of which correspond to distinct morphological features. Our molecular phylogeny clearly supported multiple independent losses of pelvic fins on Asian lineages in parallel. Divergence time estimation based on some reasonable assumptions without assuming the molecular clock suggested the early Cretaceous divergence of the African and Asian channids. The results thus support an ancient vicariant divergence of the African and Asian channids, rather than the more recent dispersal between African and Eurasian continents.     

Molecular phylogeny of the Herpestidae (Mammalia, Carnivora) with a special emphasis on the Asian Herpestes

Until now, phylogenetic studies of the mongooses (Carnivora, Herpestidae) have not included an exhaustive sampling of the Asian members of this family. In this study, we used mitochondrial (Cytochrome b and ND2), nuclear (β-fibrinogen intron 7 and Transthyretin intron 1) sequences from almost all of the recognized mongoose species to produce a well-resolved phylogeny of the Herpestidae. We also performed molecular dating analyses to infer divergence dates of the different lineages within the Herpestidae. Our results confirmed the paraphyly of the Herpestes genus and other phylogenetic relationships, which previously had only been moderately supported. The Asian herpestid species were found to form a monophyletic group within the Herpestidae. Within the Asian species, a cyto-nuclear conflict was discovered between the small Indian mongoose (Herpestes auropunctatus), the Indian gray mongoose (Herpestes edwardsii) and the Javan mongoose (Herpestes javanicus), which may have occurred through interspecific hybridization. This study inferred an Early Miocene origin for the Herpestidae and a Middle Miocene origin for the Asian mongooses.     

Molecular phylogenetic perspective on the evolution of the deep-sea fish genusCyclothone (Stomiiformes: Gonostomatidae)

A portion of mitochondrially encoded 12S and 16S ribosomal RNA genes were sequenced from 13 currently recognized species of the midwater deep-sea fish genusCyclothone (Stomiiformes: Gonostomatidae) and three gonostomatid outgroup taxa. Phylogenetic analyses using maximum parsimony and maximum likelihood methods were performed on unambiguously aligned, combined sequences (803 bp) of the two genes. The resultant tree topologies from the two methods were congruent, being robust and supported by various tree statistics, enabling the evolutionary history ofCyclothone to be described in detail. The molecular phylogeny demonstrated striking inconsistencies with previously proposed “natural groups”, although the latter could be confidently refuted by the molecular data. The most significant characteristic of the evolutionary history ofCyclothone was the independent acquisition of an apomorphic depth habitat from the relatively ancestral, lower mesopelagic habitat, by each of three major distinct lineages that had diverged earlier in their evolution. Moreover, such macroevolutionary habitat shifts had been necessarily accompanied by morphological and ecological novelties, presumably originating from paedomorphosis. Repeated evolution of such changes strongly suggests ontogenetic plasticity inCyclothone which could enable these fishes to acquire larval-like, simple organization of body structure. Such a body plan could help them subsist in food-poor surroundings and regulate reproductive variables that take advantage of increasing larval survival toward shallower depths. Recent speciation events, on the contrary, have produced contemporary sister species of allopatric (or microallopatric) distributions, but few morphological and ecological differences. Even if remarkable miniaturization has occurred, such as in the Mediterranean endemicC. pygmaea, it had to have been a simple truncation of ancestral species' ontogeny without attendance of any discernible paedomorphic features. On the basis of the fossil record, geological history of the Mediterranean region, and ectotherm molecular divergence rate, it was estimated thatCyclothone radiation had already started in the early-middle Miocene (17–20 million years ago).     

中国甘肃省狭义丝盖伞属二新种

依据形态学和分子系统学研究结果,描述了产自中国甘肃省的狭义丝盖伞属2个新种,即拟黄囊丝盖伞Inocybe muricellatoides和甘肃丝盖伞I. gansuensis。对新种的ITS、LSU和rpb2片段进行了测序和分析,并提供了详细描述、线条图、生态照片及与相似种的区别。拟黄囊丝盖伞以菌盖翘起的鳞片、菌柄纤维状、孢子光滑和厚壁的侧生囊状体为主要识别特征。甘肃丝盖伞具有粗壮的子实体、较大的孢子和厚壁侧生囊状体。基于LSU和rpb2联合数据的分子系统发育分析显示这两个新种隶属于狭义丝盖伞属且分别占据独特的分支。     

Molecular identification and phylogenetic analysis of nuclear rDNA sequences among three opisthorchid liver fluke species (Opisthorchiidae: Trematoda)

In this study, we describe the development of a fast and accurate molecular identification system for human-associated liver fluke species (Opisthorchis viverrini, Opisthorchis felineus, and Clonorchis sinensis) using the PCR-RFLP analysis of the 18S-ITS1-5.8S nuclear ribosomal DNA region. Based on sequence variation in the target rDNA region, we selected three species-specific restriction enzymes within the ITS1 regions, generating different restriction profiles among the species: MunI for O. viverrini, NheI for O. felineus, and XhoI for C. sinensis, respectively. Each restriction enzyme generated different-sized fragments specific to the species examined, but no intraspecific polymorphism or cross-reaction between the species was detected in their restriction pattern. These results indicate that PCR-linked restriction analysis of the ITS1 region allows for the rapid and reliable molecular identification among these opisthorchid taxa. In addition, phylogenetic analysis of rDNA sequences using different methods (MP, ML, NJ, and Bayesian inference) displayed O. viverrini and O. felineus as a sister group, but this relationship was not strongly supported. The failure of recovering a robust phylogeny may be due to the relatively small number of synapomorphic characters shared among the species, yielding weak phylogenetic signal. Alternatively, rapid speciation within a very short period time could be another explanation for the relatively poorly resolved relationships among these species. Our data are insufficient for discriminating between sudden cladogenesis and other potential causes of poor resolution. Further information from independent loci might help resolve this phylogeny.     

基于线粒体16S rDNA序列探讨蛱蝶科(鳞翅目, 蝶亚目)主要分类群的系统发生关系

本文测定了蛱蝶科7亚科27种蛱蝶和斑蝶科2种蝴蝶的线粒体16S rRNA基因部分序列,并从GenBank中下载了6种蛱蝶的同源序列。以斑蝶科的幻紫斑蝶和绢斑蝶作外群,通过遗传分析软件对这些序列进行了比较分析,用邻接法和贝叶斯法重建了蛱蝶科的系统发育树,探讨了蛱蝶科主要类群间的系统发育关系。序列分析的结果显示:经比对处理后获得494bp长度序列,其中有可变位点206个,简约信息位点145个;A T平均含量78.4%,C G平均含量为21.6%,具A、T偏倚性。分子系统树显示:蛱蝶亚科并非单系群;蛱蝶族中眼蛱蝶属应移入斑蛱蝶族;闪蛱蝶和蛱蝶亚科与蛱蝶亚科具有较近的系统关系;结果支持豹蛱蝶和釉蛱蝶合为一亚科即釉蛱蝶亚科;支持将秀蛱蝶和蛱蝶亚科从线蛱蝶亚科中分离出来。     

Flamingomyces and Parvulago, new genera of marine smut fungi (Ustilaginomycotina)

Teliospore walls, teliospore germinations, hyphal septations, cellular interactions, and nucleotide sequences from the D1/D2 region of the nuLSU rRNA gene of the marine smut fungi Melanotaenium ruppiae and Ustilago marina were examined and compared with findings in other Ustilaginomycotina. The data show that Melanotaenium ruppiae belongs to the Urocystaceae and Ustilago marina to the Ustilaginaceae. Within the Urocystaceae, Melanotaenium ruppiae is morphologically similar to Melanustilospora and Vankya. However, according to the molecular results Melanotaenium ruppiae can neither be ascribed to Melanustilospora nor to Vankya. Therefore, the new genus Flamingomyces is proposed for Melanotaenium ruppiae. Ustilago marina differs from the other Ustilaginaceae in the mode of sporulation, which exclusively occurs at the base of the host plant culms. Accordingly, the new genus Parvulago is proposed for Ustilago marina.     

Cantharellus pleurotoides, a new and unusual basidiomycete from Guyana

Cantharellus pleurotoides sp. nov. (Cantharellaceae, Cantharellales, Basidiomycota) is described from the Pakaraima Mountains of Guyana, occurring in rainforests dominated by ectomycorrhizal Dicymbe spp. (Caesalpiniaceae). This fungus is singular among Cantharellus species described worldwide in possessing a pleurotoid basidioma. Macromorphological, micromorphological, and habitat data are provided for the new species.     

Sciuridae (Rodentia,Mammalia) from the Late Miocene of Venta del Moro (Cabriel Basin,Spain): biostratigraphical,phylogenetic and palaeoecological inferences

Abstract

Fossil squirrels are relatively abundant in Aragonian and Ramblian assemblages, but very scarce in the Late Turolian and Ruscinian of the Iberian Peninsula. Until now, the locality of Venta del Moro has yielded over 4500 micromammal dental remains, but just nine of them are sciurids. In this assemblage, we have identified the taxa Pliopetaurista pliocaenica, Heteroxerus cf. mariatheresae and Atlantoxerus cf. margaritae. This is the first co-occurrence of the genera Pliopetaurista, Heteroxerus and Atlantoxerus in the same locality, being also one of the oldest records of P. pliocaenica, the oldest record of a form that could be related to A. margaritae, and the youngest record of the genus Heteroxerus. In addition, we hypothesize about the phylogeny of Pliopetaurista in the light of recent discoveries. Finally, the presence of the genera Heteroxerus and Atlantoxerus suggests an open environment and relatively dry environmental conditions, while Pliopetaurista is purportedly a flying squirrel, dweller of forested habitats and wet climates. Based on this, we infer an open environment of grassland type, bordered by forested habitats, agreeing with the conditions supposed for Venta del Moro according to its macromammal and floral assemblages.     

Molecular characterization and phylogenetic inferences of Dermanyssus gallinae isolates in Italy within an European framework

In order to investigate the genetic relationships between Dermanyssus gallinae (Metastigmata: Dermanyssidae) (de Geer) isolates from poultry farms in Italy and other European countries, phylogenetic analysis was performed using a portion of the cytochrome c oxidase subunit 1 (cox1) gene of the mitochondrial DNA and the internal transcribed spacers (ITS1+5.8S+ITS2) of the ribosomal DNA. A total of 360 cox1 sequences and 360 ITS+ sequences were obtained from mites collected on 24 different poultry farms in 10 different regions of Northern and Southern Italy. Phylogenetic analysis of the cox1 sequences resulted in the clustering of two groups (A and B), whereas phylogenetic analysis of the ITS+ resulted in largely unresolved clusters. Knowledge of the genetic make‐up of mite populations within countries, together with comparative analyses of D. gallinae isolates from different countries, will provide better understanding of the population dynamics of D. gallinae. This will also allow the identification of genetic markers of emerging acaricide resistance and the development of alternative strategies for the prevention and treatment of infestations.     

Corylomyces: a new genus of Sordariales from plant debris in France

The new genus Corylomyces, isolated from the surface of a hazelnut (Corylus avellana) in the French Pyrenees, is described, illustrated and compared with morphologically similar taxa. It is characterised by tomentose, ostiolate ascomata possessing long necks composed of erect to sinuose hairs, and one- or two-celled, opaque, lunate to reniform ascospores. Analyses of the SSU and LSU fragments rDNA gene sequences support its placement in the Lasiosphaeriaceae (Sordariales).     

担子菌门总革菌科中国新记录种紫黑点壳菌

[背景] 在陕西省的毛泡桐腐木桩上观察和采集到一株绒毛状真菌子实体,编号为HMNWAFU-CF-HS002。[目的] 为了确定该菌的分类地位,对其进行形态观察及分子鉴定。[方法] 获取宏观彩色图像并对显微结构进行测量、统计和绘图。此外,用PDA培养基分离纯化该菌的培养物,并结合最大似然法、最大简约法和贝叶斯法进行rDNA ITS分子系统学研究。[结果] HMNWAFU-CF-HS002的形态特征与Punctularia atropurpurascens高度相似。系统发育分析将HMNWAFU-CF-HS002聚在P.atropurpurascens的单系分支中。[结论] 结合形态学特征与系统发育结果,HMNWAFU-CF-HS002被鉴定紫黑点壳菌（Punctularia atropurpurascens）,为中国的新记录种。此外,毛泡桐为其新记录寄主。至此,Punctularia属下的3个种,均在中国有分布记录。     

Revision of some Thecaphora species (Ustilaginomycotina) on Caryophyllaceae

Specimens of Thecaphora saponariae s. lat. from several caryophyllacean host plants belonging to the genera Cerastium, Dianthus, Petrorhagia, Saponaria, Silene, and Stellaria were studied by means of both LM, SEM, and molecular phylogenetic analyses using ITS and LSU rDNA sequences. The data show that T. saponariae s. lat. is not uniform but represents several taxa. Molecular phylogenetic analyses, correlated with morphology of the sori, spore balls, and spores, permitted the recognition of five species. Two new species, Thecaphora italica and T. cerastii are described, and two new combinations, T. alsinearum and T. melandrii are proposed. The anamorph of Thecaphora saponariae is reported for the first time. A lectotype is designated for Sorosporium silenes-inflatae. Evolutionary aspects are discussed.     

Clitopilus canariensis (Basidiomycota, Entolomataceae), a new species in the C. nitellinus-complex (Clitopilus subg. Rhodophana) from the Canary Islands (Spain)

Clitopilus canariensis is described as a new species belonging to Clitopilus subgenus Rhodophana on the basis of a collection from La Palma, Canary Islands. The new species grows on humus of Cistus monspeliensis and is known from a single site. A photograph of fresh basidiomes of the type-collection and line drawings are provided.