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.     

A further phylogenetic study of the heterotrophic dinoflagellate genus, Protoperidinium (Dinophyceae) based on small and large subunit ribosomal RNA gene sequences

The heterotrophic marine dinoflagellate genus Protoperidinium is the largest genus in the Dinophyceae. Previously, we reported on the intrageneric and intergeneric phylogenetic relationships of 10 species of Protoperidinium, from four sections, based on small subunit (SSU) rDNA sequences. The present paper reports on the impact of data from an additional 5 species and, therefore, an additional two sections, using the SSU rDNA data, but now also incorporating sequence data from the large subunit (LSU) rDNA. These sequences, in isolation and in combination, were used to reconstruct the evolutionary history of the genus. The LSU rDNA trees support a monophyletic genus, but the phylogenetic position within the Dinophyceae remains ambiguous. The SSU, LSU and SSU + LSU rDNA phylogenies support monophyly in the sections Avellana, Divergentia, Oceanica and Protoperidinium, but the section Conica is paraphyletic. Therefore, the concept of discrete taxonomic sections based on the shape of 1′ plate and 2a plate is upheld by molecular phylogeny. Furthermore, the section Oceanica is indicated as having an early divergence from other groups within the genus. The sections Avellana and Excentrica and a clade combining the sections Divergentia/Protoperidinium derived from Conica‐type dinoflagellates independently. Analysis of the LSU rDNA data resulted in the same phylogeny as that obtained using SSU rDNA data and, with increased taxon sampling, including members of new sections, a clearer idea of the evolution of morphological features within the genus Protoperidinium was obtained. Intraspecific variation was found in Protoperidinium conicum (Gran) Balech, Protoperidinium excentricum (Paulsen) Balech and Protoperidinium pellucidum Bergh based on SSU rDNA data and also in Protoperidinium claudicans (Paulsen) Balech, P. conicum and Protoperidinium denticulatum (Gran et Braarud) Balech based on LSU rDNA sequences. The common occurrence of base pair substitutions in P. conicum is indicative of the presence of cryptic species.     

Molecular phylogeny of parabasalids based on small subunit rRNA sequences, with emphasis on the Trichomonadinae subfamily

We determined small subunit ribosomal DNA sequences from three parabasalid species, Trichomitus batrachorum strain R105, Tetratrichomonas gallinarum, and Pentatrichomonas hominis belonging to the Trichomonadinae subfamily. Unrooted molecular phylogenetic trees inferred by distance, parsimony, and likelihood methods reveal four discrete clades among the parabasalids. The Trichomonadinae form a robust monophyletic group. Within this subfamily T. gallinarum is closely related to Trichomonas species as supported by morphological data, with P. hominis and Pseudotrypanosoma giganteum occupying basal positions. Our analysis does not place T. batrachorum within the Trichomonadinae. Trichomitus batrachorum (strains R105 and BUB) and Hypotrichomonas acosta form a well-separated cluster, suggesting the genus Trichomitus is polyphyletic. The emergence of T. batrachorum precedes the Trichomonadinae-Tritrichomonadinae dichotomy, emphasizing its pivotal evolutionary position among the Trichomonadidae. A third cluster unites the Devescovinidae and the Calonymphidae. The fourth clade contains the three hypermastigid sequences from the genus Trichonympha, which exhibit the earliest emergence among the parabasalids. The addition of these three new parabasalid species did not however resolve ambiguities regarding the relative branching order of the parabasalid clades. The phylogenetic positions of Tritrichomonas faetus, Monocercomonas sp., Dientamoeba fragilis, and the unidentified Reticulitermes flavipes gut symbiont 1 remain unclear.     

PHYLOGENY OF THE EUGLENALES INFERRED FROM PLASTID LSU rDNA SEQUENCES1

To gain insights into the phylogeny of the Euglenales, we analyzed the plastid LSU rDNA sequences from 101 strains of the photosynthetic euglenoids belonging to nine ingroup genera (Euglena, Trachelomonas, Strombomonas, Monomorphina, Cryptoglena, Colacium, Discoplastis, Phacus, and Lepocinclis) and two outgroup genera (Eutreptia and Eutreptiella). Bayesian and maximum‐likelihood (ML) analyses resulted in trees of similar topologies and four major clades: a Phacus and Lepocinclis clade; a Colacium clade; a Trachelomonas, Strombomonas, Monomorphina, and Cryptoglena clade; and a Euglena clade. The Phacus and Lepocinclis clade was the sister group of all other euglenalian genera, followed by Discoplastis spathirhyncha (Skuja) Triemer and the Colacium clade, respectively, which was inconsistent with their placement based on nuclear rDNA genes. The Trachelomonas, Strombomonas, Monomorphina, and Cryptoglena clade was sister to the Euglena clade. The loricate genera, Trachelomonas and Strombomonas, were closely related to each other, while Monomorphina and Cryptoglena also grouped together. The Euglena clade formed a monophyletic lineage comprising most species from taxa formerly allocated to the subgenera Calliglena and Euglena. However, within this genus, none of the subgenera was monophyletic.     

SSU rDNA phylogeny of cladoniiform lichens

To examine phylogenetic relationships among the "cladoniiform" lichenized fungi, i.e., the families Cladoniaceae, Baeomycetaceae, Icmadophilaceae, Stereocaulaceae, and Siphulaceae, and to provide evidence for the anticipated independent origins of podetia and pseudopodetia, we conducted phylogenetic analyses of SSU (small subunit) rDNA sequences from 39 lichen-forming fungi. These fungi represent all of the major growth forms of lichen associations, fruticose (including "cladoniiform"), foliose, and crustose. Our analysis suggests that lichen-forming fungi with a "cladoniiform" morphology arose multiple times within the ascomycetes. Additionally, each of the other thallus growth forms, crustose, foliose, and fruticose, have originated multiple times. It also seems to be clear that neither all podetiate nor all pseudopodetiate taxa form a monophyletic group. Therefore the term "podetium" should be restricted to homologous structures that are most probably limited to the genera Cladonia, Cladina, Pycnothelia, and allies. The "pseudopodetia" of Stereocaulon (Stereocaulaceae) and Cladia (Cladiaceae) may represent different states of the same homologous character. Our phylogenetic hypothesis supports the monophyletic origin of the order Lecanorales sensu stricto, including representatives of five suborders Cladoniineae, Lecanorineae, Teloschistineae, Agyriineae and Peltigerineae, but excluding representatives of the suborders Acarosporineae (Acarospora schleicheri and Megaspora verrucosa), Pertusariineae (Pertusaria trachythallina), and Umbilicarineae. The suborder Cladoniineae and the family Cladoniaceae both appear to be polyphyletic assemblages.     

Molecular data and phylogeny of Nosema infecting lepidopteran forest defoliators in the genera Choristoneura and Malacosoma

ABSTRACT. Nosema isolates from five lepidopteran forest defoliators, Nosema fumiferanae from spruce budworm, Choristoneura fumiferana ; a Nosema sp. from jack pine budworm, Choristoneura pinus pinus and western spruce budworm, Choristoneura occidentalis ( Nosema sp. CPP and Nosema sp. CO, respectively); Nosema thomsoni from large aspen tortrix, Choristoneura conflictana ; and Nosema disstriae , from the forest tent caterpillar, Malacosoma disstria were compared based on their small subunit (SSU) ribosomal RNA (rRNA) gene sequences. Four of the species sequenced, N. fumiferanae , Nosema sp. CPP, Nosema sp. CO, and N . disstriae have a high SSU rDNA sequence identity (0.6%–1.5%) and are members of the "true Nosema " clade. They all showed the reverse arrangement of the (large subunit [LSU]–internal transcribed spacer [ITS]–SSU) of the rRNA gene. The fifth species, N. thomsoni has the usual (SSU–ITS–LSU) arrangement and is not a member of this clade showing only an 82% sequence similarity. We speculate, therefore, that a genetic reversal may have occurred in the common ancestor to the "true Nosema " clade. Although, the mechanism for rearrangement of the rRNA gene subunits is not known we provide a possible explanation for the localization. N. fumiferanae , Nosema sp. CPP, and Nosema sp. CO clustered together on the inferred phylogenetic tree. The high sequence similarities, the reverse arrangement in the rRNA gene subunits, and the phylogenetic clustering suggest that these three species are closely related but separate species.     

Discovery of a novel type of body scale in the marine dinoflagellate,Amphidinium cupulatisquama sp. nov. (Dinophyceae)

A new species of Amphidinium, A. cupulatisquama Tamura et Horiguchi, from sand samples from Ikei Island, Okinawa Prefecture in subtropical Japan, is described based on light, scanning and transmission electron microscopy and the partial sequencing of the large subunit rDNA gene. The species has a typical morphology for the genus, but is distinguished from previously described species by having a combination of the following characteristics: (i) a relatively large cell (over 30 µm in length); (ii) possessing an eyespot on the dorsal side of the cingulum; (iii) the longitudinal flagellum emerging from a point close to the cingulum; (iv) cell division taking place in the motile phase; and (v) possessing body scales. This is the third species of this genus to possess body scales. The body scales of A. cupulatisquama are uniform and cup‐shaped in side view and elliptical in face view. Their dimensions are 136.4 nm by 91.0 nm by 81.8 nm high. In side view, the scale is seen to have a thick lower half and a thin upper half. This scale type is very different from those of previously reported Amphidinium species (HG114 and HG115). The molecular tree indicated that A. cupulatisquama and the two other strains of body scale‐bearing Amphidinium are distantly related within the Amphidinium clade.     

基于28S rDNA序列的鞘藻目系统发育研究

作者进行了较广泛的样品采集,通过实验分离纯化培养得到多个鞘藻目种类的株系,并采用PCR技术新获得鞘藻目2属8个种类的部分28S rDNA序列,连同GenBank中的另两条序列,分析的物种涵盖了鞘藻目中的每个属。通过比较分析绿藻纲中包括此10条序列的共36个种类的同一基因序列,并选取Trebouxiophyceae中的椭圆小球藻（Chlorella ellipsoidea）和Fusochloris perforata作外类群,运用多种方法构建分子系统树,包括邻接法（Neighbor-Joining）、最大简约法（Maximum Parsimony）和Bayesian方法。3种方法所得的结果非常相似,在形态上就在整个绿藻中界限分明的鞘藻目从分子水平上再次证明为单系起源的类群;构建的系统发育树还在一定程度上表明毛鞘藻属处于鞘藻目内三个属中较分离的位置,而枝鞘藻属与鞘藻属植物并无明显界限。     

Plagiodinium ballux sp. nov. (Dinophyceae), a deep (36 m) sand dwelling dinoflagellate from subtropical Japan

A new species of marine sand‐dwelling dinoflagellate, Plagiodinium ballux N. Yamada, Dawut, R. Terada & T. Horiguchi is described from a deep (36 m) seafloor off Takeshima Island, Kagoshima Prefecture, Japan in the subtropical region of the northwest Pacific. The species is thecate and superficially resembles species of Prorocentrum, but possesses an extremely small epitheca. The cell varies from ovoid to a rounded square, and is small (15.0–22.5 μm in length) and laterally compressed. The thecal plates are smooth and the thecal plate arrangement (Po, 1′, 0a, 5″, 5C, 2S, 5?, 0p, 1″″) is similar to that of Plagiodinium belizeanum, the type species of the genus. Molecular phylogenetic analyses based on SSU rDNA and partial LSU rDNA reveal that the dinoflagellate is closely related to P. belizeanum, but it can be clearly distinguished by its size and cell shape. This suite of morphological and molecular differences leads to the conclusion that this deep benthic dinoflagellate represents a new species of the genus Plagiodinium.     

Bayesian inference of cetacean phylogeny based on mitochondrial genomes

The phylogeny of Cetacea (whales, dolphins, porpoises) has long attracted the interests of biologists and has been investigated by many researchers based on different datasets. However, some phylogenetic relationships within Cetacea still remain controversial. In this study, Bayesian analyses were performed to infer the phylogeny of 25 representative species within Cetacea based on their mitochondrial genomes for the first time. The analyses recovered the clades resolved by the previous studies and strongly supported most of the current cetacean classifications, such as the monophyly of Odontoceti (toothed whales) and Mysticeti (baleen whales). The analyses provided a reliable and comprehensive phylogeny of Cetacea which can provide a foundation for further exploration of cetacean ecology, conservation and biology. The results also showed that: (i) the mitochondrial genomes were very informative for inferring phylogeny of Cetacea; and (ii) the Bayesian analyses outperformed other phylogenetic methods on inferring mitochondrial genome-based phylogeny of Cetacea.     

Morphology and molecular phylogeny of Thalassiosira sinica sp. nov. (Bacillariophyta) with delicate areolae and fultoportulae pattern

Thalassiosira Cleve is one of the most species-rich marine diatom genera. Previous studies have mainly focused on polar and temperate areas, but recent studies on material from Asian waters suggested that a high and undescribed species diversity of Thalassiosira occurs in Asia. On the basis of plankton samples collected from the South China Sea, a new species, T. sinica sp. nov. Y. Li & Y. Q. Guo is described. The morphology of the cells was examined by light and scanning electron microscopy. The hypervariable region of the nuclear large-subunit ribosomal DNA and the relatively conserved region of the nuclear small-subunit ribosomal DNA were sequenced for information on phylogenetic relationships. The living cells are usually solitary and drum-shaped. The areolae on the valve are delicate, small and arranged in fascicles. In addition to a regular ring of marginal fultoportulae on the valve edge, T. sinica possesses one central fultoportula and a number of fultoportulae arranged into 2–3 irregular rings on the valve face. A rimoportula located inside the ring of marginal fultoportulae possesses a long and strong external tube. The valvocopula and the copulae have rows of pores, but the pores on the valvocopula are larger than those on the copulae. Thalassiosira sinica appears to be included in subgroup C sensu Gedde because of a rimoportula with a distinct external tube located on the valve face. The molecular phylogeny, inferred from both SSU and LSU sequences, does, however, not support the validity of subgroup C, as the closest allies of T. sinica here turned out to be T. diporocyclus and T. lundiana, species in which the rimoportulae are located on the valve margin.     

Divergent Histories of rDNA Group I Introns in the Lichen Family Physciaceae

The wide but sporadic distribution of group I introns in protists, plants, and fungi, as well as in eubacteria, likely resulted from extensive lateral transfer followed by differential loss. The extent of horizontal transfer of group I introns can potentially be determined by examining closely related species or genera. We used a phylogenetic approach with a large data set (including 62 novel large subunit [LSU] rRNA group I introns) to study intron movement within the monophyletic lichen family Physciaceae. Our results show five cases of horizontal transfer into homologous sites between species but do not support transposition into ectopic sites. This is in contrast to previous work with Physciaceae small subunit (SSU) rDNA group I introns where strong support was found for multiple ectopic transpositions. This difference in the apparent number of ectopic intron movements between SSU and LSU rDNA genes may in part be explained by a larger number of positions in the SSU rRNA, which can support the insertion and/or retention of group I introns. In contrast, we suggest that the LSU rRNA may have fewer acceptable positions and therefore intron spread is limited in this gene. Reviewing Editor: Dr. W. Ford Doolittle     

The evolution of the diatoms (Bacillariophyta). I. Origin of the group and assessment of the monophyly of its major divisions

The diatoms are one of the best characterised algal groups. Despite this, little is known of the evolution of the group from the earliest cell to the myriad of taxa known today. Relationships among taxa at the family or generic level have been recognised in some diatoms. However, relationships at higher taxonomic levels are poorly understood and have often been strongly influenced by the first appearances of key taxa in the fossil record. An independent assessment of relationships among the diatoms at these higher taxonomic levels has been made using rRNA sequence data to infer phylogenetic relationships. In this paper we present an analysis of 18S rRNA data from several chosen centric, araphid and raphid pennate taxa. The phylogenetic inferences from these 18S rRNA sequences are supported by evidence from the fossil record and evidence from ontogenetic data. Ribosomal RNA data indicate that both the centric and araphid pennate lineages may not be monophyletic.     

Molecular phylogeny of parasitic Platyhelminthes based on sequences of partial 28S rDNA D1 and mitochondrial cytochrome c oxidase subunit I

The phylogenic relationships existing among 14 parasitic Platyhelminthes in the Republic of Korea were investigated via the use of the partial 28S ribosomal DNA (rDNA) D1 region and the partial mitochondrial cytochrome c oxidase subunit 1 (mCOI) DNA sequences. The nucleotide sequences were analyzed by length, G + C %, nucleotide differences and gaps in order to determine the analyzed phylogenic relationships. The phylogenic patterns of the 28S rDNA D1 and mCOI regions were closely related within the same class and order as analyzed by the PAUP 4.0 program, with the exception of a few species. These findings indicate that the 28S rDNA gene sequence is more highly conserved than are the mCOI gene sequences. The 28S rDNA gene may prove useful in studies of the systematics and population genetic structures of parasitic Platyhelminthes.     

Molecular phylogeny of the Korean Rivellia species (Diptera: Tephritoidea: Platystomatidae) based on 16S rDNA sequences: Testing morphological hypotheses using molecular data

The phylogeny of the genus Rivellia Robineau‐Desvoidy was inferred from mitochondrial 16S ribosomal (r)DNA gene sequences of 13 Korean Rivellia species and six species representing other platystomatid genera and the family Tephritidae. We compared the inferred molecular phylogeny with the previously published morphological cladogram. As a result, the following phylogenetic relationships were recognized: (i) monophyly of the genus Rivellia; (ii) monophyly of the R. syngenesiae species group; (iii) R. depicta and R. apicalis (which were not previously placed in any species group) were recognized as a sister group of the R. syngenesiae species group; and (iv) monophyly of the R. basilaris species group was recognized to a limited extent. These results, even though geographically limited, provide a new insight into the phylogeny of the genus Rivellia. They clearly show the utility of 16S rDNA for phylogenetic analysis of the genus Rivellia. Additional study involving samples from different geographical areas will be needed to gain a better understanding of the adaptive radiation of this species‐rich genus.     

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。     

Reconstructing the phylogeny of the Sipuncula

Sipunculans are marine spiralian worms with possible close affinities to the Mollusca or Annelida. Currently 147 species, 17 genera, 6 families, 4 orders and 2 classes are recognized. In this paper we review sipunculan morphology, anatomy, paleontological data and historical affiliations. We have conducted cladistic analyses for two data sets to elucidate the phylogenetic relationships among sipunculan species. We first analyzed the relationships among the 45 species of Phascolosomatidea with representatives of the Sipunculidea as outgroups, using 35 morphological characters. The resulting consensus tree has low resolution and branch support is low for most branches. The second analysis was based on DNA sequence data from two nuclear ribosomal genes (18S rRNA and 28S rRNA) and one nuclear protein-coding gene, histone H3. Outgroups were chosen among representative spiralians. In a third analysis, the molecular data were combined with the morphological data. Data were analyzed using parsimony as the optimality criterion and branch support evaluated with jackknifing and Bremer support values. Branch support for outgroup relationships is low but the monophyly of the Sipuncula is well supported. Within Sipuncula, the monophyly of the two major groups, Phascolosomatidea and Sipunculidea is not confirmed. Of the currently recognized families, only Themistidae appears monophyletic. The Aspidosiphonidae, Phascolosomatidae and Golfingiidae would be monophyletic with some adjustments in their definition. The Sipunculidae is clearly polyphyletic, with Sipunculus nudus as the sister group to the remaining Sipuncula, Siphonosoma cumanense the sister group to a clade containing Siphonosoma vastumand the Phascolosomatidea, and Phascolopsis gouldi grouping within the Golfingiiformes, as suggested previously by some authors. Of the genera with multiple representatives, only Phascolosoma and Themiste are monophyletic as currently defined. We are aiming to expand our current dataset with more species in our molecular database and more detailed morphological studies.     

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     

FISH probes for the detection of the parasitic dinoflagellate Amoebophrya sp. infecting the dinoflagellate Akashiwo sanguinea in Chesapeake Bay

A comparison of the small subunit rRNA sequences of a Chesapeake Bay strain of the dinoflagellate Akashiwo sanguinea and the dinoflagellate Amoebophrya sp. parasitizing it revealed several potential target sites that could be used to detect the parasite through in situ hybridization. The fluorescence of probed cells under various conditions of hybridization was measured by using a spot meter on a Nikon UFX-II camera attachment so that the effect of various hybridization parameters on probe binding could be determined. Probes directed against both the junction between helices 8 and 11 and helix 46 could detect the parasite, although the helix 8/11 probe produced a stronger signal under the conditions tested. The fluorescence of the probed cells increased with increasing hybridization time up to approximately twelve hours. The background fluorescence was lower at the wavelengths used to detect Texas Red than at those used to detect fluorescein, so probed cells were more distinct when Texas Red was used as the label. Cells stored in cold paraformaldehyde for a year still bound the probes. Young stages of the parasite could be seen more readily after in situ hybridization than after protargol impregnation.