Prediction and systematic study of protein-protein interaction networks of Leptospira interrogans

Leptospirosis, a serious and contagious zoonotic bacterial disease that havocs livers and kidneys in hu-mans and some animals, occurs in both urban and rural environments worldwide. It is caused by the genus lep- tospira, a corkscrew-shaped bacterium[1]. Though the genomes of Leptospira interrogans serovars Lai strain lai[2] and Leptospira interrogans serovars Copenhageni strain L1-130[3] were recently sequenced and many molecular and cellular studies on leptospires have been conducted, the …     

Complete mitochondrial DNA sequence of Chinese alligator,Alligator sinensis, and phylogeny of crocodiles

The 16746-neueleotide (nt) sequence of mitochondrial DNA(mtDNA) of Chinese alligator,Alligator sinensis,was determined using the Long-PCR and primer walking methods.As is typical in vertebrates,the mtDNA encodes 13 proteins,2 rDNA,22 tRNA genes,and a noncoding control region.The Composition of bases is respectively 29.43%A,24.59%T,14.86%G,31.12% C.The gene arrangement differs from the common vertebrate gene arrangement,but is similar to that of other crocodiles,DNA sequence data from 12S rRNA,168 rRNA,protein-coding genes and combined sequence data were used to reconstruct the phylogeny of reptiles with the MP and ML methods.With this large data set and an appropriate range of outgroup taxa,the authors demonstrate that Chinese alligator is most closely related to American alligator among three crocodilian species,which suppors the traditional viewpoint.According to the branch lengths of ML tree from the combined data set,the primary divergence between Alligator and Caiman genus was dated at about 74.9 Ma,the split between Chinese alligator and American alligator was dated at 50.9Ma.     

Mitochondrial 16S rRNA sequence variations and phylogeny of the Chinese sisorid catfishes

Partial sequences of mitochondrial 16S rRNA gene were obtained by PCR amplification for comparisons among nine species of glyptosternoid fishes and six species of non-glyptosternoids representing 10 sisorid genera. There are compositional biases in the A-rich unpaired regions and G-rich paired regions. A-G transitions are primarily responsible for the Ts/Tv bias in unpaired regions. The overall substitution rate in unpaired regions is almost two times higher than that in the paired regions. Saturation plots at comparable levels of sequence divergence demonstrate no saturation effects. Phylogenetic analyses using both maximum likelihood and Bayesian methods support the monophyly of Sisoridae. Chinese sisorid catfishes are composed of two majorlineages, one represented by (Gagata (Bagarius, Glyptothorax)) and the other by “glyptosternoids Pseudecheneis“. The glyptosternoids may not be a monophyletic group. A previous hypothesis referring to Pseudecheneis as the sister group of monophyletic glyptosternoids, based on morphological evidence, is not supported by the molecular data. Pseudecheneis is shown to be a sister taxon of Glaridoglanis. Pareuchiloglanis might be paraphyletic with Pseudexostoma and Euchiloglanis. Our results also support the hypothesis that Pareuchiloglanis anteanalis might be considered as the synonyms of Pareuchiloglanis sinensis, and genus Euchiloglanis might have only one valid species, Euchiloglanis davidi.     

Bayesian mixed models and divergence time estimation of Chinese cavefishes （Cyprinidae： Sinocyclocheilus）

The genus Sinocyclocheilus is distributed in Yun-Gui Plateau and its surrounding region only, within more than 10 cave species showing different degrees of degeneration of eyes and pigmentaUon with wonderful adaptations. To present, published morphological and molecular phylogenetic hypotheses of Slnocyclocheilus from prior works are very different and the relationships within the genus are still far from clear. We obtained the sequences of cytochrome b （cyt b） and NADH dehydrogenase subunlt 4 （ND4） of 34 species within Sinocyclocheilus, which represent the most dense taxon sampling to date. We performed Bayesian mixed models analyses with this data set. Under this phylogenetic framework, we estimated the divergence times of recovered clades using different methods under relaxed molecular clock. Our phyloegentic results supported the monophyly of Sinocyclocheilus and showed that this genus could be subdivided into 6 major clades. In addition, an earlier finding demonstrating the polyphyletlc of cave species and the most basal position of S. jii was corroborated. Relaxed divergence-time estimation suggested that Sinocyclocheilus originated at the late Miocene, about 11 million years ago （Ma）, which is older than what have been assumed.     

Phylogenetic position of Ephedra rhytidosperma, a species endemic to China： Evidence from chloroplast and ribosomal DNA sequences

The chloroplast genes matK and rbcL, ribosomal gene 18S and ITS regions of nuclear ribosomal DNA from Ephedra rhytidosperma, a species endemic to China, were sequenced and its phylogenetic position was investigated. Independent and combined phylogenetic analyses for the DNA sequences from 16 taxa representing 15 species of the genus Ephedra were performed using the maximum parsimony （MP）, neighbor-joining （N J）, minimum evolution （ME） and maximum likelihood （ML） methods. The results indicate that E. rhytidosperma is closely related to E. equisetina. The divergence time between them is estimated to be 10.85±2.44 Ma based on the results of the relative-rate tests and the evolutionary rate of rbcL gene.     

系统发育分析在古DNA研究中的应用

介绍了系统发育分析的基本原理及各种构树方法的统计学基础,阐述了各种分析方法在古DNA数据分析中的具体应用,并对各种方法的优缺点进行了评价.分析了系统发育分析的局限性和发展趋势,以及古DNA研究的不断发展对其所提出的问题.     

Investisations into the perplexing interrelationship of the Genus Takifugu Abe, 1949 （Tetraodontiformes,Tetraodontidae）

The phylogenetic relationships within the genus Takifugu Abe, 1949 （Tetraodontiformes, Tetraodontidae） remain unresolved. Because of the use of Takifugu as model organisms, the resolution of these relationships is crucial for the interpretation of evolutionary trends in biology. Pufferfishes of this genus are comprised of a comparatively small number of species and are mainly distributed along the coastal region of the western part of the Sea of Japan and the coastline of China. Mitochondrial gene sequences were employed to test the phylogenetic hypotheses within the genus. Seventeen species of the genus were examined. Molecular phylogenetic trees were constructed using the maximum parsi- mony, neighbor-joining, maximum likelihood and Bayesian methods. Our hypothesis of internal relationships within the genus differs from previous hypotheses. Our results indicate that （1） the genus Takifugu is a monophyletic assemblage; （2） the genus is divided into 6 subgroups based on the moecular data; and （3） there is low genetic diversity among the species within this genus. In addition, speciation within Takifugu appears to be driven by hybridization and isolation by distribution. Our results also suggested that the taxonomy in the genus should be clarified based on both molecular and morphological data.     

从部分科的系统学区系学特点论被子植物的起源问题

从若干重要科在被子植物系统发育过程中的地位及其地理分布特点等方面进行综合分析,论述被子植物的起源问题,结论认为被子植物的起源时间始于三叠纪,起源的地点应在东亚与东南亚地区,核心区是东亚.     

长蝽类高级阶元系统发育初探(半翅目)

本文运用支序分析的原理和方法,采用Hennig86程序研究长蝽类（lygaeoidcomplex）亚科以上阶元间的系统发育关系．研究用分类单元代表共计21种,选用性状共48个,内群共包括19个OTUs,并采用“理想祖先”作为单一外群．计算得到的首选最简约树步长＝165,CI＝0．32,RI＝0．51．相应支序图所提示的系统发育再建景象主要包括：（1）原有意义上的长蝽科为一并系群或复系群．（2）Rhyparochrominae与红蝽类互成姐妹群．（3）Artheneinae似为一较原始而孤立的支系．（4）支持Cyminae与Berytidae接近的意见．（5）支持“malcidline”意见．     

枝孢属11个种18S rDNA序列测定及与近似属序列分析

本文对枝孢属11个种单孢分离菌株18S rDNA进行了序列测定,并与其近似属尾孢菌属、假尾孢属、钉孢属、色链隔孢属、柱隔孢属及其有性型属球腔菌属进行了序列分析,构建系统发育树.结果显示色链隔孢属与枝孢属之间系统关系较近,尾孢属、钉孢属和柱隔孢属相互之间系统关系很近,而与假尾孢属系统关系较远.球腔菌属与所有参比无性型属的关系较远.     

Evolutionary relationship and species separation of four morphologically similar stichotrichous ciliates （Protozoa, Ciliophora）

Phylogenetic and taxonomic studies on ciliate protists using molecular approaches have been demonstrated to be very reliable to form strong conclusions and results. In the present work, species separation of some morphologically similar stichotrichous ciliates, two species of Pseudokeronopsis and two species of Apokeronopsis, was reexamined using amplified ribosomal DNA restriction analysis (PCRRFLP). Five of 10 restriction enzymes revealed species-specific polymorphic patterns, of which four similar stichotrichs could be significantly separated and identified. Among them, EcoR I offered almost no significantly different restriction fragment patterns, but the four species could be separated from one another and identified with Hae III. Distinctly different restriction digestion haplotypes and similarity indices separated the species, and were used to construct a phylogeny. Phylogenies based on ITS2 nucleotide sequences and ITS2 secondary structures supported the separation of Pseudokeronopsis and Apokeronopsis using RFLP analysis, although three Pseudokeronopsis carnea populations did not cluster together. In addition, phylogenetic analyses using multiple algorithms confirmed that these two genera formed two distinct groups within the urostylids.     

中国斑翅蝗科(直翅目:蝗总科)11属的系统发育关系支序分析

在比较形态学研究的基础上，本文选择了25个性状，利用Hennig86程序包，以支序分析探讨了中国斑翅蝗科11属昆虫间的系统发育关系，结果表明：斑翅蝗科11属昆虫可分为3支：由小车蝗属(11)与车蝗属(4)和飞蝗属(5)这一对姐妹群组成第1支，相互间关系不明确的尖翅蝗属(9)和绿纹蝗属(10)组成第2支，剩余的赤翅蝗属(12)、束颈蝗属(14)、疣蝗属(13)、异痴蝗属(6)、痴蝗属(7)及皱膝蝗属(8)6属构成第3支，其中痴蝗属与皱膝蝗属为1对姐妹群，它俩的最近共同祖先与异痴蝗属构成姐妹群关系，然后依次与疣蝗属、束颈蝗属、赤翅蝗属分别构成关系上渐远的单系群，它们的亲缘关系可表示为：((11(4，5))(9，10(12(14(13(6(7，8)))))))。     

基于16S rRNA和POMC基因序列的中国北方林蛙属动物系统发生关系

基于16S rRNA和POMC基因部分序列研究了中国北方林蛙属动物的系统发生关系.利用ClustalX软件对序列进行对位排列后,长度为1148bp,内群变异位点259,简约位点110.利用MP法、ML法和BI法构建系统进化树,结果显示林蛙属物种构成单系群,其中东北种群聚为一支,中国林蛙聚为一支,支持东北林蛙为有效物种.桓仁林蛙和核型为2n=26的林蛙属物种聚为一支,因此不支持核型为2n=24的林蛙形成单系群.桓仁林蛙、昆嵛林蛙、黑龙江林蛙单独聚为一支,表明三者之间的亲缘关系较近.     

天漠嗜盐和耐盐细菌产淀粉酶活性及菌株多样性

采用平板水解圈法对分离自张家口天漠沙土的嗜盐和耐盐细菌（含放线菌）进行淀粉酶活性筛选,运用基于16S rRNA基因序列的分析方法对活菌株进行系统发育多样性分析.结果表明,76个受试菌株中,有34株淀粉水解酶活性呈阳性（44.7%）,其中有6株具有较强的淀粉水解酶活性;系统发育分析显示34个阳性菌株类群多样性和物种多样性较高,可以归为18个物种,分属于细菌域（Bacteria）的2门（Actinobacteria,Firmicutes）2科（Streptomycetaceae,Bacillaceae）8属（Streptomyces,Bacillus,Gracilibacillus,Halobacillus,Oceanobacillus,Piscibacillus,Thalassobacillus,Virgibacillus）;产淀粉酶活性较强的6株菌均属于厚壁菌门（Firmicutes）芽孢杆菌科（Bacillaceae）,分属于该科的3个属.其中菌株JSM 1684012,JSM 1684041和JSM 1685098属于芽孢杆菌属（Bacillus）;JSM 1684067和JSM 1685082属于纤长芽孢杆菌属（Gracilibacillus）;JSM 1685081属于喜盐芽孢杆菌属（Halobacillus）.以上结果说明分离自张家口天漠沙土的嗜盐和耐盐菌中存在较高比例的产淀粉酶菌株,且这些菌株具有较高的类群多样性和物种多样性.     

基于16S rRNA序列的鳃金龟亚科5族种类的系统发育关系

测定了鳃金龟亚科部分种类的线粒体16SrRNA部分序列,运用MEGA 4.0、PAUP*4.0b10和MrBayes等软件,对5个族29个代表种的序列变异和系统关系进行了研究.序列变异分析结果显示:绢金龟族Sericini、哦鳃金龟族Hopliini、鳃金龟族Melolonthini的族内遗传距离分别为7.7%,11.3%,10.6%,族间遗传距离在12.6%～19.2%.最大似然树(ML)和贝叶斯树(BI)结果表明,所有种类分别聚集在所属的族下,哦鳃金龟族、绢金龟族分别为单系.齿爪鳃金龟属Holotrichia、云鳃金龟属Polyphylla、胸突鳃金龟属Hoplosternus、Hilyotrogus、双绺鳃金龟属Amphimallon、Hoplochelus、婆鳃金龟属Brahmina和皱鳃金龟属Trematodes聚在鳃金龟族分支下,没有形成明显的根鳃金龟族Rhizotrogini分支.齿爪鳃金龟属的非单系性与前人研究结果一致.皱鳃金龟属Trematodes和婆鳃金龟属Brahmina的代表种为姐妹种.绢金龟族的绢金龟属Serica和玛绢金龟属Maladera多数种类聚在本属分支下.证明16SrRNA序列可探讨鳃金龟亚科高级阶元的系统发育关系.     

Phylogenetic relationships and divergence times of the family Araucariaceae based on the DNA sequences of eight genes

Araucariaceae is one of the most primitive families of the living conifers, and its phylogenetic relationships and divergence times are critically important issues. The DNA sequences of 8 genes, i.e., nuclear ribosomal 18S and 26S rRNA, chloroplast 16S rRNA, rbcL, matK and rps4, and mitochondrial coxl and atpl, obtained from this study and GenBank were used for constructing the molecular phylogenetic trees of Araucariaceae, indicating that the phyiogenetic relationships among the three genera of this family should be （（Wollemia, Agathis）, Araucaria）. On the basis of the fossil calibrations of Wollemia and the two tribes Araucaria and Eutacta of the genus Araucaria, the divergence time of Araucariaceae was estimated to be （308± 53） million years ago, that is, the origin of the family was in the Late Carboniferous rather than Triassic as a traditional view. With the same gene combination, the diver- gence times of the genera Araucaria and Agathis were （246 ± 47） and （61 ±15） Ma, respectively. Statis- tical analyses on the phylogenetic trees generated by using different genes and comparisons of the divergence times estimated by using those genes suggested that the chloroplast matK and rps4 genes are most suitable for investigating the phylogenetic relationships and divergence times of the family Araucariaceae.     

Phylogenetic positions of two marine ciliates, Metanophrys similis and Pseudocohnilembus hargisi (Protozoa, Ciliophora,Scuticociliatia), inferred from complete small subunit rRNA gene sequences

The small subunit rRNA (SSrRNA) gene was sequenced for two marine scuticociliates Metanophrys similis and Pseudocohnilembus hargisi. The results show that this gene comprises 1763 and 1753 nucleotides in the two marine ciliates respectively. Metanophrys similis is phylogenetically closely related to the clade containing Mesanophrys carcini and Anophyroides haemophila, which branches basally to other species within the order Philasterida. Pseudocohnilembus hargisi groups with its congener, P. marinus, with strong bootstrap support. Paranophrys magna groups with the clade including Cohnilembus and Uronema, representing a sister clade to that containing the two Pseudocohnilembus species.     

Phylogenetic positions of two marine ciliates, Metanophrys similis and Pseudocohnilembus hargisi (Protozoa, Ciliophora, Scuticociliatia), inferred from complete small subunit rRNA gene sequences

The small subunit rRNA (SSrRNA) gene was sequenced for two marine scuticociliates Metanophrys similis and Pseudocohnilembus hargisi. The results show that this gene comprises 1763 and 1753 nucleotides in the two marine ciliates respectively. Metanophrys similis is phylogenetically closely related to the clade containing Mesanophrys carcini and Anophyroides haemophila, which branches basally to other species within the order Philasterida. Pseudocohnilembus hargisi groups with its congener, P. marinus, with strong bootstrap support. Paranophrys magna groups with the clade including Cohnilembus and Uronema, representing a sister clade to that containing the two Pseudocohnilembus species.     

Phylogenetic positions of two marine ciliates, Metanophrys similis and Pseudocohnilembus hargisi (Protozoa, Ciliophora, Scuticociliatia), inferred from complete small subunit rRNA gene sequences

The small subunit rRNA (SSrRNA) gene was sequenced for two marine scuticociliates Metanophrys similis and Pseudocohnilembus hargisi. The results show that this gene comprises 1763 and 1753 nucleotides in the two marine ciliates respectively. Metanophrys similis is phylogenetically closely related to the clade containing Mesanophrys carcini and Anophyroides haemophila, which branches basally to other species within the order Philasterida. Pseudocohnilembus hargisi groups with its congener, P. marinus, with strong bootstrap support. Paranophrys magna groups with the clade including Cohnilembus and Uronema, representing a sister clade to that containing the two Pseudocohnilembus species.     

Phylogenetic position of Schnabelia, a genus endemic to China： Evidence from sequences of cpDNA matK gene and nrDNA ITS regions

The chloroplast gene matK and the internal transcribed spacers (ITS) of the nuclear ribosomal DNA from Schnabelia, a genus endemic to China, and 6 genera of Verbenaceae and 13 genera of Lamiaceae were sequenced. The phylogenetic signal and validity outgroups were measured and evaluated by means of the relatively apparent synapomorphy analysis (RASA). Independent and combined phylogenetic analyses for the matK and ITS sequences were performed using the maximum parsimony (MP), neighbor-joining (NJ) and maximum likelihood (ML) methods, indicating that Schnabelia oligophylla and Caryopteris terniflora form a sister-group relationship. The Caryopteris complex is not shown to be a monophyly because Trichostema, C. paniculata and C. forrestii are paraphyletic to the clade containing the remaining members of the complex. A monophyly of Ajugoideae proposed by Cantino et al., including 8 genera in this study, is strongly supported and the closest relatives of Schnabelia are in the Ajugoideae (Lamiaceae), especially near Caryopteris terniflora. The polygenetic analyses also showed that the genera of Lamiaceae and Verbenaceae sampled in this tudy are phylogenetically mixed and the genus Avicennia is distant to other genera of Verbenaceae. RASA and combined analysis can be used as effective approaches to determining the relationships among phylogenetically complex groups.