PHYLOGENETIC POSITION OF ATTHEYA LONGICORNIS AND ATTHEYA SEPTENTRIONALIS (BACILLARIOPHYTA)1

The phylogenetic position of diatoms belonging to the genus Attheya is presently under debate. Species belonging to this genus have been placed in the subclasses Chaetocerotophycidae and Biddulphiophycidae, but published phylogenetic trees based on 18S rDNA, morphology, and sexual reproduction indicate that this group of diatoms may be a sister group of the pennates. To clarify the position of Attheya, we studied the morphology, 18S rDNA, 16S rDNA of the chloroplasts, the rbcL large subunit (LSU) sequences of the chloroplasts, and the sterol composition of three different strains of Attheya septentrionalis (Østrup) R. M. Crawford and one strain of Attheya longicornis R. M. Crawford et C. Gardner. These data were compared with data from more than 100 other diatom species, covering the whole phylogenetic tree, with special emphasis on species belonging to the genera that have been suggested to be related to the genus Attheya. All data suggest that the investigated Attheya species form a separate group of diatoms, and there is no indication that they belong to either the Chaetocerotophycidae or the Biddulphiophycidae. Despite applying these various approaches, we were unable to determine the exact phylogenetic position of the investigated Attheya species within the diatoms.     

Phylogenetic Analysis of the Genus Bifidobacterium and Related Genera Based on 16S rDNA Sequences

The 16S rRNA gene sequences were determined for type strains of 21 Bifidobacterium species. A phylogenetic tree was constructed using the determined sequences and sequences from DNA databases, which contain the sequences of 11 type strains of Bifidobacterium species and 11 strains of related genera. All species of the genus Bifidobacterium and Gardnerella vaginalis ATCC 14018 belonged to a cluster phylogenetically distinct from the other genera. The cluster was divided into two subclusters: subcluster 1 composed of most species of Bifidobacterium and G. vaginalis, and subcluster 2 consisting of two species, B. denticolens and B. inopinatum; both of which were isolated from human dental caries. In the genus Bifidobacterium, four groups of species are known to be moderately to highly related by DNA-DNA hybridization. The four groups of species exhibited more than 99% similarity among their 16S rDNA sequences within each group. These results indicated that species with around 99% or more similarity in their 16S rDNA sequences should be confirmed for species identities.     

Phylogenetic studies in <Emphasis Type="Italic">Ravenelia esculenta</Emphasis> and related rust fungi

Ravenelia esculenta Naras. and Thium. is a rust fungus, which infects mostly thorns, inflorescences, flowers and fruits of Acacia eburnea Willd. Aecial stages of the rust produce hypertrophy in infected parts. DNA of the rust fungus was isolated from aeciospores by ‘freeze thaw’ method. 18S rDNA was amplified and sequenced by automated DNA sequencer. BLAST of the sequence at NCBI retrieved 96 sequences producing significant alignments. Multiple sequence alignment of these sequences was done by ClustalW. Phylogenetic analysis was done by using MEGA 3.1. UPGMA Minimum Evolution tree with bootstrap value of 1000 replicates was constructed using these sequences. From phylogenetic tree it is observed that Ravenelia esculenta and the genus Gymnosporangium share a common ancestry, though Ravenelia esculenta is autoecious on angiosperm and the genus Gymnosporangium is heteroecious with pycnia, aecia on angiosperm and uredia, telia on gymnosperm. Two major clades are recognized which are based on the nature of aecial host (gymnosperm or angiosperm). These clades were also showing shift from pteridophytes to angiosperms as telial hosts. The tree can be interpreted in the other way also where there is separation of 14 families of Uredinales depending upon nature of teliospores, nature of aeciospores and structure of pycnia. These studies determine the phylogenetic position of Ravenelia esculenta among other rust fungi besides broad separation of Uredinales into two clades. These studies also show that there is phylogenetic correlation between molecular and morphological data. This is first report of DNA sequencing and phylogenetic positioning in genus Ravenelia from India.     

从核rDNA序列探讨隙蛛亚科Coelotinae的分类地位

隙蛛亚科Coelotinae主要分布于东亚地区,其中我国的已有种类占到全世界种数的一半以上,因此对于我国隙蛛类蜘蛛的研究已经成为世界暗蛛科研究的重点之一。隙蛛亚科属于无筛器类群,于1893年,由Cambridge以隙蛛属为模式属而建立,归属于无筛器的漏斗蛛科。之后,虽然经历了数次修订     

蝗科高级阶元的分子系统发育(英文）

迄今,蝗科内各分类阶元之间的系统发生关系大部分是未知的。本文用来自中国24种蝗科昆虫的12SrDNA和16SrDNA2个基因的联合序列(共795bp)数据,以锥头蝗科的锥头蝗(Pyrgomorpha conica)为外群,重建了分子系统树。研究结果表明,在12SrDNA与16SrDNA组成的联合数据中,转换的替代速率明显比颠换的替代速率高得多,核酸的替代已经发生了饱和。分子系统树表明:斑翅蝗亚科是一单系群,该亚科是一个合法的亚科,但斑腿蝗亚科和蝗亚科都不是单系群;斑翅蝗亚科在蝗科内是一个相对原始的类群,而稻蝗亚科比斑翅蝗亚科相对进化,比蝗科的其他亚科的种类相对原始。     

5S rDNA variation and its phylogenetic inference in the genus <Emphasis Type="Italic">Leporinus</Emphasis> (Characiformes: Anostomidae)

5S rDNA sequences have proven to be valuable as genetic markers to distinguish closely related species and also in the understanding of the dynamic of repetitive sequences in the genomes. In the aim to contribute to the knowledge of the evolutionary history of Leporinus (Anostomidae) and also to contribute to the understanding of the 5S rDNA sequences organization in the fish genome, analyses of 5S rDNA sequences were conducted in seven species of this genus. The 5S rRNA gene sequence was highly conserved among Leporinus species, whereas NTS exhibit high levels of variations related to insertions, deletions, microrepeats, and base substitutions. The phylogenetic analysis of the 5S rDNA sequences clustered the species into two clades that are in agreement with cytogenetic and morphological data.     

Molecular systematics of the genus Troglophilus (Rhaphidophoridae,Orthoptera) in Turkey: mitochondrial 16S rDNA evidences

This study focuses on the evolutionary relationships among Turkish species of the cave cricket genus Troglophilus.Fifteen populations were studied for sequence variation in a fragment (543 base pairs) of the mitochondrial DNA (mtDNA) 16S rDNA gene (16S) to reconstruct their phylogenetic relationships and biogeographic history. Genetic data retrieved three main clades and at least three divergent lineages that could not be attributed to any of the taxa known for the area. Molecular time estimates suggest that the diversification of the group took place between the Messinian and the Plio-Pleistocene.     

基于线粒体Cyt b,16S rDNA和核28S rDNA的中国斑腿蝗科(直翅目,蝗总科)九亚科间的系统发育关系研究

基于线粒体Cytb、16S rDNA和核28S rDNA的部分序列的联合数据集,重建了中国斑腿蝗科9亚科26种蝗虫和癞蝗科笨蝗(外群)间的系统发育关系。结果显示:1)除黑蝗亚科、秃蝗亚科和切翅蝗亚科外,其余6亚科的单系性都得到支持;2)黑蝗亚科似乎应当与秃蝗亚科合并为一个亚科,且与其他几个亚科亲缘关系相对较远;3)凸额蝗属应该由切翅蝗亚科中独立出来;4)卵翅蝗亚科和稻蝗亚科是姐妹群;5)星翅蝗亚科、黑背蝗亚科、斑腿蝗亚科、刺胸蝗亚科及切翅蝗亚科中的凸额蝗属间的关系较近。     

基于核基因和线粒体基因序列的中国Singhardina亚属系统发育（半翅目：叶蝉科：小叶蝉亚科：小叶蝉族）

测定了中国Singhardina亚属15个代表种的核糖体28S基因D2区和线粒体16S基因、COI基因部分序列,分别采用最大简约法、最大似然法和贝叶斯法构建分子系统树。系统发育树显示了相似的拓扑结构,明晰了各分支间的关系。首次探讨了中国Singhardina亚属4个种团间的系统发育关系。结果显示,Singhardina亚属构成了1个独立支系,代表1个单系群。本研究首次提出种团Eurhadina(Singhardina)rubra,并推测该种团可能是Singhardina亚属中最原始的种团。种团Eurhadina(Singhardina)robusta和E.(Singhardina)mamata为姐妹群。种团E.(Singhardina)vittata不能从种团E.(Singhardina)punjabensis中分出得到了分子数据的支持。     

Isolation and Phylogenetic Analysis of Halophilic Archaeon AJ6

Halophilic archaeon AJ6 was isolated and purified from the Altun Mountain National Nature Reserve of the Xinjiang Uygur Autonomous Region. Strain AJ6 is a Gram-negative rod whose size is 0.2–0.6 by 1.6–4.2 μm, wherein a few cells are globular. The optimum salt concentration for its growth is 20% NaCl and 0.6% Mg²⁺, and the optimum pH is 6.0–7.0. Morphological, physiological, and biochemical characteristics of strain AJ6 were observed. The 16S rRNA encoding gene (16S rDNA) sequence of strain AJ6 was amplified by PCR, and its nucleotide sequence was determined subsequently. “Clustalw” and “PHYLIP” software bags were used to analyze the 16S rDNA sequence; the homology was compared, and then the phylogenetic tree was established. The results indicate that strain AJ6 is a novel species of the genus Natrinema. The GenBank accession number of the 16S rDNA sequences of strain AJ6 is AY277584. Translated from Journal of Zhejiang University (Science Edition), 2005, 32(1) (in Chinese)     

Molecular phylogeny of the family Tephritidae (Insecta: Diptera): New insight from combined analysis of the mitochondrial 12S, 16S,and COII genes

The phylogeny of the family Tephritidae (Diptera: Tephritidae) was reconstructed from mitochondrial 12S, 16S, and COII gene fragments using 87 species, including 79 tephritid and 8 outgroup species. Minimum evolution and Bayesian trees suggested the following phylogenetic relationships: (1) A sister group relationship between Ortalotrypeta and Tachinisca, and their basal phylogenetic position within Tephritidae; (2) a sister group relationship between the tribe Acanthonevrini and Phytalmiini; (3) monophyly of Plioreocepta, Taomyia and an undescribed new genus, and their sister group relationship with the subfamily Tephritinae; (4) a possible sister group relationship of Cephalophysa and Adramini; and (5) reconfirmation of monophyly for Trypetini, Carpomyini, Tephritinae, and Dacinae. The combination of 12S, 16S, and COII data enabled resolution of phylogenetic relationships among the higher taxa of Tephritidae.     

基于28S rDNA D2基因片段与形态特征的矛茧蜂亚科系统发育研究（膜翅目：茧蜂科）

本研究选取矛茧蜂亚科Doryctinae（昆虫纲Insecta：膜翅目Hymenoptera：茧蜂科Braconidae）的6族15属18种做内群,茧蜂科其它7亚科11属11种做外群,首次结合同源核糖体28S rDNA D2基因序列片段和100个形态学和解剖学特征对该亚科进行了系统发育学研究。利用“非圆口类"的小腹茧蜂亚科Microgastrinae为根,以PAUP*4.0和MrBayes 3.0B4软件分别应用最大简约法（MP）和贝叶斯法对矛茧蜂亚科的分子数据和分子数据与非分子数据的结合体进行了运算分析;并以PAUP*4.0对矛茧蜂亚科的28S rDNA D2基因序列片段的碱基组成与碱基替代情况进行了分析。结果表明：矛茧蜂亚科的28S rDNA D2基因序列片段的GC含量在39.33%～48.28%之间变动,而对于碱基替代情况来讲,矛茧蜂亚科各成员间序列变异位点上颠换（transversion）大于转换（transition）。不同的分析算法所产生的系统发育树都表明矛茧蜂亚科是一个界限分明的单系群;在矛茧蜂亚科内,除了吉丁茧蜂族Siragrini为单系群外,其他族（矛茧蜂族Doryctini和方头茧蜂族Hecabolini）都是并系群。对于矛茧蜂亚科内各属之间的相互亲缘关系,不同算法所得的系统发育树的拓扑结构不完全一致,表明矛茧蜂亚科内（属及族）的系统发育关系还有待于进一步研究。     

Evolutionary Relationships Among Old World Fruitbats (Megachiroptera: Pteropodidae) Based on 12S rRNA, tRNA Valine, and 16S rRNA Gene Sequences

Old World fruitbats were divided into the cynopterine, epomophorine, rousettine, eonycterine, and notopterine sections by Knud Andersen (1912). Among these, the eonycterine and notopterine sections together comprise the subfamily Macroglossinae, which includes forms with specializations for nectarivory. Single-copy DNA hybridization data argue against the monophyly of four of Andersen's sections and further suggest paraphyly or polyphyly of the Macroglossinae. DNA hybridization data provide support for an endemic African clade that includes Megaloglossus (an eonycterine), Epomophorus (an epomophorine), and Lissonycteris (a rousettine). Analyses of mitochondrial 12S rRNA-tRNA valine gene sequences corroborate the African clade but provide less resolution than hybridization data for most branches on the pteropodid tree. Here, we report 11 new 16S rRNA sequences and analyze a mitochondrial data set that includes 12S rRNA, tRNA valine, and 16S rRNA for 18 pteropodid genera. Parsimony, minimum evolution, and maximum likelihood were all employed in phylogenetic analyses. The addition of 16S rRNA sequences to the mitochondrial data set resulted in increased support for several clades, including Macroglossus + Syconycteris, Cynopterus + Thoopterus, Rousettus + the endemic African clade, and Eonycteris + Rousettus + the endemic African clade. Statistical tests suggest that another endemic African genus, Eidolon, is dissociated from the African clade and represents an independent invasion into Africa. We constructed a molecular phylogenetic framework that incorporated clades that were strongly supported by both single-copy DNA hybridization and 12S rRNA-tRNA valine-16S rRNA sequences. Using this framework as a backbone phylogenetic constraint, we then analyzed a morphological data matrix for 34 pteropodid genera with parsimony. Results of this analysis suggest that other epomophorines and Myonycteris (a cynopterine) are also part of the endemic African clade.     

Rhodotorula lamellibrachii sp. nov., a new yeast species from a tubeworm collected at the deep-sea floor in Sagami Bay and its phylogenetic analysis

A new species of the genus Rhodotorula was isolated from a tubeworm (Lamellibrachia sp.) collected at a depth of 1156 m in Sagami Bay, Japan. Strain SY-89 had physiological properties quite similar to R. aurantiaca. Two phylogenetic trees, one based on internal transcribed spacer (ITS) regions and 5.8S rDNA sequences and the other based on the D1/D2 region of the large subunit (26S) rDNA sequences, united strain SY-89 to the type strain of Sakaguchia dacryoides through a considerable evolutionary distance. Strain SY-89 was differentiated from S. dacryoides by the G+C content of the nuclear DNA and differences in the ability to utilize specific carbon and nitrogen compounds. The low complementarity of strain SY-89 DNA to that of the type strain of S. dacryoides confirmed that this strain was genetically unrelated to previously known species. The tubeworm isolates are described as R. lamellibrachii sp. nov. The type strain of R. lamellibrachii is strain SY-89 (= JCM 10907). R. lamellibrachii formed a cluster with Erythrobasidium hasegawianum, R. lactosa, S. dacryoides and Sporobolomyces elongatus on the ITS and 5.8S rDNA phylogenetic tree. These five species shared a signature sequence in 26S rDNA, although this relationship was not supported by phylogeny based on the D1/D2 region of 26S rDNA.     

Morphology and molecular phylogeny of coccoid green algae Coelastrella sensu lato (Scenedesmaceae,Sphaeropeales), including the description of three new species and two new varieties

The genus Coelastrella was established by Chodat (Bull. Soc. Bot. Geneve, 13 [1922] 66), and was characterized as being unicellular or in few‐celled aggregations with many longitudinal ribs on the cell wall. Many species of this genus showed strong ability to accumulate carotenoids and oils, so they have recently attracted much attention from researchers due to its potential applicability in the energy and food industries. In this study, a total of 23 strains of Coelastrella were sampled from China, and three new species and two new varieties were described: C. thermophila sp. nov., C. yingshanensis sp. nov., C. tenuitheca sp. nov., C. thermophila var. globulina var. nov., C. rubescens var. oocystiformis var. nov. Besides 18S rDNA and ITS2 sequences, we have newly sequenced the tufA gene marker for this taxon. Phylogenetic analysis combined with morphological studies revealed four morphotypes within the Coelastrella sensu lato clade, which contained the morphotype of original Coelastrella, original Scotiellopsis, Asterarcys, and morphotype of C. vacuolata and C. tenuitheca sp. nov. The relationships between morphological differences and phylogenic diversity based on different markers were discussed. Our results support that 18S rDNA was too conserved to be used a species‐specific or even a genus‐specific marker in this clade. The topology of tufA gene‐based phylogenetic tree had a better match with the morphological findings.     

基于16S rDNA和28S rDNA D2基因序列与形态特征联合分析的中国角顶叶蝉亚科系统发育研究（半翅目： 叶蝉科）

首次在国内利用28S rDNA D2区段和16S rDNA基因序列,结合50个形态特征对角顶叶蝉亚科(Deltocephalinae)［半翅目（Hemiptera）: 叶蝉科（Cicadellidae）］19个属进行系统发育分析研究。从无水乙醇浸泡保存的标本中提取基因组DNA并扩增了19个内群和1种外群Typhlocybinae［半翅目(Hemiptera): 叶蝉科(Cicadellidae)］种类的28S rDNA D2基因片段并测序,同时扩增了16S rDNA基因片段并测序11条,采用了GenBank中1个种类的16S rDNA同源序列。采用PAUP*4.0和MrBayes3.0两个分析软件和3种建树方法,利用同源28S D2 rDNA和16S rDNA两个基因序列与形态特征结合进行系统发育分析研究。分析结果表明,二叉叶蝉族Macrostelini是一个单系,并在角顶叶蝉亚科的系统发育中处于基部的位置,是内群中最原始的族;角顶叶蝉族Deltocephalini中除了纹翅叶蝉属Nakaharanus,其余各属构成单系;殃叶蝉族Euscelini内属的归属比较混乱,可能是一个并系群,属间差异有待进一步研究。隆额叶蝉族Paralimnini与顶带叶蝉族Athysanini是姐妹群。带叶蝉属Scaphoideus与纹翅叶蝉属Nakaharanus是姐妹群,二者与木叶蝉属Phlogotettix的关系最近,三者构成一个单系,建议将三者归为带叶蝉族Scaphoideini。研究结果还表明,小眼叶蝉族Xestocephalini和Balcluthini的系统发育位置不明,有待进一步研究。     

Evaluation of the efficacy of mitochondrial ATP 6 and 8, Cyt b and 16S rDNA genes for differentiation of Iranian honeybees (Apis mellifera meda) from commercial subspecies of Apis mellifera L. and comparison with geometric morphometric method

Mitochondrial DNA sequence variations and the geometric morphometric method can be used to differentiate honeybee subspecies and evolutionary lineages. Molecular markers are powerful tools for discriminating honeybee subspecies. In this study, 19 beekeeping sites were selected to collect Iranian honeybee samples. The honeybee forewing images stored at Oberursel (the Bee Data Bank) were used to compare with those of Iranian honeybees using the geometric morphometric method. Furthermore, the abilities of DNA markers to differentiate Iranian honeybees (A. m. meda) from the most common commercial subspecies (A. m. carnica and A. m. ligustica) were assessed. In the present research, 16S rDNA (Mitochondrial 16S rDNA Region) showed greater ability in differentiating Iranian honeybees from other subspecies compared with ATP 6 and 8 and Cyt b. The phylogenetic tree derived from 16S rDNA differentiated A. m. carnica and A. m. ligustica from Iranian honeybees. Principle component analysis (PCA) discriminated C lineage and Z subgroup from A and M lineages using 16S rDNA. In addition, the phylogenetic tree of the 16S rDNA affirmed the findings of the cluster analysis derived from the geometric morphometric method in differentiating A. m. carnica and A. m. ligustica from Iranian honeybees. The cluster analysis grouped reference subspecies of A. m. meda with Iranian honeybees. Moreover, the Discriminant Function Analyses (DFA) differentiated Iranian honeybees from A. m. ligustica and A. m. carnica.     

First Report of Aster Yellows Phytoplasma in Goldenrain Tree (Koelreuteria paniculata) in Korea

Aster yellows phytoplasma was detected for the first time in goldenrain tree (Koelreuteria paniculata) growing in Sinpyeong‐myeon, Jeollabuk‐do, South Korea. DNA was extracted from the infected leaf samples and part of the 16S rDNA, rp operon and tuf gene were amplified using R16F2n/R2 and gene‐specific primers. The sequence analysis showed that the phytoplasma was closely related (99%) to members of the Aster Yellows (AY) group, and belonging to 16Sr I, subgroup B. Moreover, the 16S rDNA sequences of the isolate showed 88–96% identity with members of other 16Sr and undesignated groups. Based on the sequence identity and phylogenetic studies, it was confirmed that phytoplasma infecting goldenrain tree in South Korea belongs to the AY group.     

Characterization of freshwater benthic biofilm‐forming Hydrocoryne (Cyanobacteria) isolates from Antarctica

The aims of this work were to study cyanobacterial isolates resembling the genus Hydrocoryne using a combination of morphology and phylogeny of 16S rRNA and nifH sequences and to investigate genes involved in cyanotoxin and protease inhibitor production. Four new cyanobacterial strains, isolated from biofilm samples collected from King George Island, Antarctica, were studied. In terms of morphology, these new strains share traits similar to true Anabaena morphotypes (benthic ones), whereas phylogenetic analysis of their 16S rRNA gene sequences grouped them with the sequence of the type species Hydrocoryne spongiosa (H. Schwabe ex Bornet and Flahault 1886–1888), but not with sequences of the type species from the genus Anabaena. This cluster is the sister group of Anabaena morphotypes isolated only from the Gulf of Finland. In addition, this cluster is related to two other clusters formed by sequences of Anabaena isolated from different sites. Partial nifH genes were sequenced from two strains and the phylogenetic tree revealed that the Antarctic nifH sequences clustered with sequences from Anabaena. Furthermore, two strains were tested, using PCR with specific primers, for the presence of genes involved in cyanotoxins (microcystin and saxitoxin) and protease inhibitor (aeruginosin, and cyanopeptolin). Only cyanopeptolin was amplified using PCR. These four Hydrocoryne strains are the first to be isolated and sequenced from Antarctica, which improves our knowledge on this poorly defined cyanobacterial genus.