THE SPECIES EUGLENA DESES (EUGLENACEAE) REVISITED: NEW MORPHOLOGICAL AND MOLECULAR DATA1

For this study, we have examined the literature and the morphological diversity, as well as analyzed the nuclear SSU rDNA sequences of two very common and cosmopolitan species formerly known as Euglena deses Ehrenb. and Euglena intermedia (G. A. Klebs) F. Schmitz. Our studies have shown that there is evidence for distinguishing only one species (E. deses). Here, we define new diagnostic features for E. deses, namely, periplast ornamentation (the presence of small papillae—discovered for the first time in this species) and the lateral location of the anterior canal opening, from which the flagellum emerges. We also designate the epitype and emend the diagnosis for E. deses.     

TAXONOMY OF THE PHACUS OSCILLANS (EUGLENACEAE) AND ITS CLOSE RELATIVES—BALANCING MORPHOLOGICAL AND MOLECULAR FEATURES1

The establishment of epitypes (together with emended diagnoses) for seven species of Phacus Dujard. [Phacus oscillans G. A. Klebs, Phacus parvulus G. A. Klebs, Phacus pusillus Lemmerm., Phacus skujae Skvortzov, Phacus inflexus (Kisselew) Pochm., Phacus polytrophos Pochm., and Phacus smulkowskianus (Zakry?) Kusber] was achieved by literature studies, verification of morphological diagnostic features (cell size, cell shape), as well as molecular characters (SSU rDNA). The investigated Phacus species are mostly well distinguished morphologically, with an SSU rDNA interspecific sequence similarity of 95.1%–99.0% and an intraspecific sequence similarity of 99.0%–99.9%. Some of the phylogenetic relationships among the seven species have not been resolved, but the topology obtained indicates their assignment into two sister clades. The first clade is composed of two sister groups (P. parvulus and P. pusillus), while the second constitutes an assemblage of the remaining five species. The relationships between the clades remain unresolved.     

基于线粒体16S rRNA基因部分序列探讨贵州9种菊头蝠(翼手目:菊头蝠科)的分子系统进化关系

依据部分线粒体16S rRNA基因序列,我们对贵州九种菊头蝠进行了分子系统进化关系研究.结果表明:马铁菊头蝠与其他菊头蝠亲缘关系较远,它可能是最原始的种类.中华菊头蝠和贵州菊头蝠聚在同一分支,表明它们之间亲缘关系非常接近,高鞍菊头蝠和贵州菊头蝠的DNA差异百分比最小(1.13%),因此认为这两个种亲缘关系也非常接近.     

蝗总科部分种类16S rDNA的分子系统发育关系

将自测的我国直翅目蝗总科8科8个种和从互联网GenBank中检索到相关物种的线粒体基因组：16S rDNA序列片段进行同源性比较,计算核苷酸使用频率,并构建分子系统树。在获得的480bp的序列中。A T约占70．7％,G C为29．3％,颠换取代(transversion)的速率大于或接近转换取代(transition)的速率,其中188个核苷酸位点存在变异。研究结果表明：在直翅目蝗总科有差异的188bp中,属内种间的碱基序列差异仅为1．5％,科内属间为3．5％～3．6％,科间差异为4．8％～15．8％,亚目间差异达到15．2％～25．6％。分子系统树表明：科内的属和属内的种均优先聚在一起;蝗总科8科的起源关系为：锥头蝗科→瘤锥蝗科→癞蝗科→斑翅蝗科→剑角蝗科→网翅蝗科和槌角蝗科→斑腿蝗科;锥头蝗科与瘤锥蝗科关系较近,是蝗总科内最原始的类群;槌角蝗科和网翅蝗科互为姐妹群,与最进化的斑腿蝗科关系较近;蚤蝼科为独立的一支,最先分出,似为一个亚目,与现用的分类系统有明显差别;哈螽科(螽嘶总科)和蟋蟀科聚在一起为剑瓣亚目(Ensifera),蚱科和蝗总科的8科组成短瓣亚目(Caehfera),同现用的分类系统。     

Phylogenetic Relationships and Morphological Character Evolution of Photosynthetic Euglenids (Excavata) Inferred from Taxon‐rich Analyses of Five Genes

Photosynthetic euglenids acquired chloroplasts by secondary endosymbiosis, which resulted in changes to their mode of nutrition and affected the evolution of their morphological characters. Mapping morphological characters onto a reliable molecular tree could elucidate major trends of those changes. We analyzed nucleotide sequence data from regions of three nuclear‐encoded genes (nSSU, nLSU, hsp90), one chloroplast‐encoded gene (cpSSU) and one nuclear‐encoded chloroplast gene (psbO) to estimate phylogenetic relationships among 59 photosynthetic euglenid species. Our results were consistent with previous works; most genera were monophyletic, except for the polyphyletic genus Euglena, and the paraphyletic genus Phacus. We also analyzed character evolution in photosynthetic euglenids using our phylogenetic tree and eight morphological traits commonly used for generic and species diagnoses, including: characters corresponding to well‐defined clades, apomorphies like presence of lorica and mucilaginous stalks, and homoplastic characters like rigid cells and presence of large paramylon grains. This research indicated that pyrenoids were lost twice during the evolution of phototrophic euglenids, and that mucocysts, which only occur in the genus Euglena, evolved independently at least twice. In contrast, the evolution of cell shape and chloroplast morphology was difficult to elucidate, and could not be unambiguously reconstructed in our analyses.     

Molecular phylogeny of the Pooideae (Poaceae) based on nuclear rDNA (ITS) sequences

Phylogenetic relationships of the Poaceae subfamily, Pooideae, were estimated from the sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA. The entire ITS region of 25 species belonging to 19 genera representing seven tribes was directly sequenced from polymerase chain reaction (PCR)-amplified DNA fragments. The published sequence of rice, Oryza saliva, was used as the outgroup. Sequences of these taxa were analyzed with maximum parsimony (PAUP) and the neighbor-joining distance method (NJ). Among the tribes, the Stipeae, Meliceae and Brachypodieae, all with small chromosomes and a basic number more than x=7, diverged in succession. The Poeae, Aveneae, Bromeae and Triticeae, with large chromosomes and a basic number of x=7, form a monophyletic clade. The Poeae and Aveneae are the sister group of the Bromeae and Triticeae. On the ITS tree, the Brachypodieae is distantly related to the Triticeae and Bromeae, which differs from the phylogenies based on restriction-site variation of cpDNA and morphological characters. The phylogenetic relationships of the seven pooid tribes inferred from the ITS sequences are highly concordant with the cytogenetic evidence that the reduction in chromosome number and the increase in chromosome size evolved only once in the pooids and pre-dated the divergence of the Poeae, Aveneae, Bromeae and Triticeae.This paper reports factually on available data; however, the USDA neither guarantees nor warrants the standard of the product, and the use of the name by USDA implies no approval of the product to the exclusion of others that may also be suitableThis paper is a cooperative investigation of USDA-ARS and the Utah Agricultural Experiment Station. Logan, Utah 84322. Journal Paper No. 4581     

Morphological and Molecular Characterisation of Notosolenus urceolatus Larsen and Patterson 1990, a Member of an Understudied Deep‐branching Euglenid Group (Petalomonads)

Petalomonads are particularly important for understanding the early evolution of euglenids, but are arguably the least studied major group within this taxon. We have established a culture of the biflagellate petalomonad Notosolenus urceolatus, and conducted electron microscopy observations and molecular phylogenetic analysis. Notosolenus urceolatus has eight pellicular strips bordered by grooves and underlain by close‐set microtubules. There are ventral and dorsal Golgi bodies. Mitochondria apparently contain fibrous inclusions, as in Petalomonas cantuscygni. A previously undocumented type of large, globular extrusome is present instead of the tubular extrusomes characteristic of Euglenozoa. The feeding apparatus lacks rods and vanes, and is partly supported by an “MTR”. The flagella have complex transition zones that are extremely elongated but unswollen. Only the emergent portion of the anterior flagellum has an organised paraxonemal rod, and also has very fine mastigonemes. The basal bodies are offset and lack connecting fibres. 18S rRNA gene phylogenies show that N. urceolatus is closely related to Petalomonas sphagnophila and P. cantuscygni, not Notosolenus ostium, confirming that current generic assignments based on the number of emergent flagella are phylogenetically unreliable, and making it difficult to infer whether features shared by N. urceolatus and P. cantuscygni (for example) are general for petalomonads.     

18S rDNA phylogeny of the Tubificidae (Clitellata) and its constituent taxa: dismissal of the Naididae

The phylogeny of the Tubificidae, and of most of its subfamilies and some of its genera, is revisited, on the basis of sequences of 18S ribosomal DNA in a selection of species. Forty-six new 18S sequences of Naididae (6), Tubificidae (37), Phreodrilidae (1), Lumbriculidae (1), and Enchytraeidae (1) are reported and aligned together with corresponding sequences of 21 previously studied taxa. The 18S gene of Insulodrilus bifidus provides the first molecular evidence that phreodrilids are closely related to tubificids, corroborating previous conclusions based on morphology. The data further support the monophyletic status of Tubificidae, provided that the "Naididae" is regarded a part of this family; "naidids" may not even constitute a monophyletic group. It is thus suggested that the family name Naididae is formally suppressed as a junior synonym of the Tubificidae. The 18S gene also resolves a number of relationships within the tubificids. Among the subfamilies, Tubificinae is supported, Rhyacodrilinae and Phallodrilinae are revealed as nonmonophyletic, and Limnodriloidinae remains unresolved. Most tubificid genera tested for monophyly are corroborated by the data, only one (Tubifex) is refuted, and two (Tubificoides and Limnodriloides) are unresolved from other taxa. It is concluded that it will be valuable to expand the taxonomic sampling for 18S rDNA in clitellates, and in annelids in general, as this is likely to improve the resolution at many levels. However, it will be equally important to combine the annelid 18S data with other gene sequences and nonmolecular characters, to estimate the phylogeny of these common and diverse worms with greater precision.     

中国西南特有翅茎草属的种间界定——基于形态学和分子系统学分析

翅茎草属(Pterygiella)是中国西南地区特有的半寄生植物.翅茎草属4种植物形态差异不显著,种的界定依据较模糊;此外,杜氏翅茎草2变种的划分依据也存在疑问.本研究选取了翅茎草属4种13个居群,通过数量性状的主成分分析和质量性状的非加权组平均法聚类分析;结合叶绿体4个片段(即atpB-rbcL、trnD-trnT、trnS-trnG和sbA-trnH)和核基因组的ITS片段研究,对该属下的种类划分作了重新界定.研究表明:翅茎草属应包括3种,即翅茎草、杜氏翅茎草和圆茎翅茎草;川滇翅茎木应作为圆茎翅茎草的变种.对杜氏翅茎草指定了后选模式,该种仅包括茎无毛的个体,而茎疏被毛的个体应归入翅茎草中.基于以上研究结果,本文提出了一个新的翅茎草属分种检索表,并做了分类修订.     

Species Delimitation of Pterygiella (Orobanchaceae), a Genus Endemic to Southwestern China on the Basis of Morphometric and Molecular Analyses

Pterygiella, a genus endemic to southwestern China, belongs to hemiparasitic rhinanthoid Orobanchaceae. Since P.bartschioides was segregated as an independent genus of its own, i.e. Xizangia, the genus was treated to include four species, P.duclouxii, P.nigrescens, P.cylindrica, and P.suffruticosa. However, the discriminative characters are obscure among these species, and the delimitation of the two varieties in P.duclouxii remains problematic. To revise the taxonomy of the genus, thirteen populations from the four species were collected for both morphometric and molecular systematic analyses. Principal component analysis (PCA) and cluster analysis via unweighted pair group method with an arithmetic average (UPGMA) were used. In addition, four chloroplast sequences (i.e., atpB rbcL, psbA trnH, trnD trnT and trnS trnG) and nuclear ITS region were studied. The results showed that Pterygiella includes only three species, namely P.nigrescens, P.duclouxii, and P.cylindrica, while P.suffruticosa should be merged into P.cylindrica as a variety. The previous delimitation of the two varieties within P.duclouxii was probably caused by imperfect analysis of morphological characters. Thus, a lectotype was designated for P.duclouxii and the plants formerly treated as P.duclouxii that bear eglandular stem hairs should be put into P.nigrescens, while the individuals with glabrous stem should remain in P.duclouxii. A new key to the three species in the genus reflecting the results of this study was presented, and a taxonomic revision was given.     

Morphological and Molecular Diversity of the Neglected Genus Rhizomastix Alexeieff, 1911 (Amoebozoa: Archamoebae) with Description of Five New Species

The genus Rhizomastix is a poorly known group of amoeboid heterotrophic flagellates living as intestinal commensals of insects, amphibians or reptiles, and as inhabitants of organic freshwater sediments. Eleven Rhizomastix species have been described so far, but DNA sequences from only a single species have been published. Recently, phylogenetic analyses confirmed a previous hypothesis that the genus belongs to the Archamoebae; however, its exact position therein remains unclear. In this study we cultured nine strains of Rhizomastix, both endobiotic and free‐living. According to their light‐microscopic morphology and SSU rRNA and actin gene analyses, the strains represent five species, of which four are newly described here: R. bicoronata sp. nov., R. elongata sp. nov., R. vacuolata sp. nov. and R. varia sp. nov. In addition, R. tipulae sp. nov., living in the intestine of crane flies, is separated from the type species, R. gracilis. We also examined the ultrastructure of R. elongata sp. nov., which revealed that it is more complicated than the previously described R. libera. Our data show that either the endobiotic lifestyle of some Rhizomastix species has arisen independently from other endobiotic archamoebae, or the free‐living members of this genus represent a secondary switch from the endobiotic lifestyle.     

Molecular phylogenetic study of the basidiomycetous anamorphic yeast genusTrichosporon and related taxa based on small subunit ribosomal DNA sequences

Small subunit ribosomal DNA sequences of all species of the basidiomycetous anamorphic yeast genusTrichosporon were determined, and phylogenetic trees were constructed by the neighbor-joining and maximum likelihood methods. The sequence data showed that, with the exception ofT. pullulans, the genus is monophyletic, although its members have two different major ubiquinones, Q9 and Q10. The genus can be divided phylogenetically into three major clusters. Species with Q10 as the major ubiquinone constitute a single cluster, while those with Q9 form two clusters.Trichosporon pullulans was phylogenetically distinct from other taxa of the genus. It is located in a cluster containingCystofilobasidium capitatum, Mrakía frigida, Xanthophyllomyces dendrorhous and three species ofUdeniomyces. This result sugests thatT. pullulans does not belong to the genusTrichosporon.     

Molecular systematics of the suborder Trogiomorpha (Insecta: Psocodea: 'Psocoptera')

Phylogenetic relationships among extant families in the suborder Trogiomorpha (Insecta: Psocodea: 'Psocoptera') were inferred from partial sequences of the nuclear 18S rDNA and Histone 3 and mitochondrial 16S rDNA genes. Analyses of these data produced trees that largely supported the traditional classification; however, monophyly of the infraorder Psocathropetae (= Psyllipsocidae + Prionoglarididae) was not recovered. Instead, the family Psyllipsocidae was recovered as the sister taxon to the infraorder Atropetae (= Lepidopsocidae + Trogiidae + Psoquillidae), and the Prionoglarididae was recovered as sister to all other families in the suborder. Character states previously used to diagnose Psocathropetae are shown to be plesiomorphic. The sister group relationship between Psyllipsocidae and Atropetae was supported by two morphological apomorphies: the presence of a paraproctal anal spine and an anteriorly opened phallosome. Based on these sequence data and morphological observations, we propose a new classification scheme for the Trogiomorpha as follows: infraorder Prionoglaridetae (Prionoglarididae), infraorder Psyllipsocetae (Psyllipsocidae), infraorder Atropetae (Lepidopsocidae, Trogiidae, Psoquillidae).  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 146 , 287–299.     

Molecular phylogeny of onygenalean fungi based on small subunit ribosomal DNA (SSU rDNA) sequences

Phylogenetic analysis of nucleotide data from small subunit ribosomal DNA (SSU rDNA) sequences (ca. 1685 bp.) was performed on 19 taxa of the Onygenales and three related mitosporic fungi. Phylogenetic trees were constructed by the neighbor-joining method with the sequence data of related taxa obtained from DNA databases. The species in the Onygenales form two clusters and seven subclusters, and the tree topology reflects the traditional classification by Currah (1985) with some exceptions. The Myxotrichaceae is placed in the different lineage, separate from other plectomycetous taxa and among the Leotiales and the Erysiphales. Furthermore, two separate lineages in the Myxotrichaceae were found. Tree topology suggested the Onygenaceae is polyphyletic and composed of three subgroups; 1) most members of Onygenaceae, 2)Spiromastix warcupii, and 3) pathogenic dimorphic fungi classified inAjellomyces.     

Phylogenetic analysis of the non-pathogenic genusSpiromastix (Onygenaceae) and related onygenalean taxa based on large subunit ribosomal DNA sequences

The phylogenetic positioning of the non-pathogenic genusSpiromastix in the Onygenales was studied based on large subunit rDNA (LSU rDNA) partial sequences (ca. 570 bp.). FourSpiromastix species and 28 representative taxa of the Onygenales were newly sequenced. Phylogenetic trees were constructed by the neighbor-joining (NJ) method and evaluated by the maximum parsimony (MP) method with the data of 13 taxa retrieved from DNA databases.Spiromastix and dimorphic systemic pathogens,Ajellomyces andParacoccidioides, appear to be a monophyletic group with 74% bootstrap probability (BP) in the NJ tree constructed with the representative taxa of the Onygenales. The tree topology was concordant with the NJ tree based on SSU rDNA sequences of our previous work and corresponded to the classification system of the Onygenales by Currah (1985) and its minor modification by Udagawa (1997) with the exception of the classification of the Onygenaceae. The Onygeneceae sensu Udagawa may still be polyphyletic, since three independent lineages were recognized. The taxa forming helicoid peridial appendages were localized to two clades on the tree. The topology of the NJ tree constructed withSpiromastix and its close relatives suggested that the helicoid peridial appendages were apomorphic and acquired independently in the two clades of the Onygenales.     

Molecular characterization and revised systematics of Microdiaphanosoma arcuatum (Ciliophora, Colpodea)

Microdiaphanosoma arcuatum Wenzel, 1953 is a world-wide distributed ciliate, recorded mainly in soil samples, which we have also identified in ground water samples from South Africa. This ciliate has been frequently overlooked or not determined due to its small size, ～12 μm. The genus Microdiaphanosoma is nowadays included in the class Colpodea, order Bryometopida, family Kreyellidae. The first complete small subunit (SSU) rDNA gene sequence of this ciliate was obtained from a South African isolate. Phylogenetic analysis including available SSU rDNA sequences from another Colpodea species in the GenBank strongly supported the position of M. arcuatum within the order Cyrtolophosidida instead of the order Bryometopida. The analysis also suggested a sister relationship between this species and species from the family Cyrtolophosididae.