用核糖体DNA的ITS序列探讨滇桐属的系统学位置

采用PCR直接测序方法 ,对来自椴树科、梧桐科、木棉科 17属的 33个种和作为外类群的锦葵科 2属4个种的核糖体DNAITS区 (含 5 8S区 )序列进行了分析。结果表明 ,滇桐属 (Craigia)与椴树属为姐妹群关系 ,二者构成单系类群 ,因而将滇桐属置于椴树科中较为合理 ;刺果藤属和翅子树属有较近的亲缘关系 ,并与蚬木属和柄翅果属构成一个单系类群 ,二者可能与椴树科有更近的亲缘关系 ;榴莲属与椴树科的破布叶属构成单系类群 ;山芝麻属与椴树科、梧桐科和木棉科构成并系关系 ;因此 ,这些属的系统位置尚需进一步确定。综合分析的结果支持将椴树科、梧桐科和木棉科归并到锦葵科中的观点。     

基于膜盘菌属的两种系统发育研究方法的比较研究

以rDNA ITS1-5.8S-ITS2序列作为分子标记,采用直接优化和常规分析两种方法,探讨膜盘菌属内种间及其与相关属间的亲缘关系,并比较了两种建树方法在解决该属内种间关系的效果。以Lachnum spartinae为外群,选取31条序列构建了最小进化树、最大简约树和直接优化树。结果表明,Hymenoscyphus ericae复合种与其他膜盘菌属的成员关系较远,除了H.ericae外,其他膜盘菌形成一个单系群。模式种Hymenoscyphus fructigenus与H.caudatus,H.fucatus,H.scutulus等构成一个高支持率的分支,与另一分支(H.epiphyllus,H.lasiopodium)形成姐妹群。相对于常规的两步分析法,直接优化所产生的系统树与当前形态学特征基本相符合,因而更合理地反映膜盘菌属的分类地位和种间关系,表明该分析方法在真菌系统发育分析中具有较大的应用价值。     

唐松草及近缘植物ITS序列和5S rRNA基因间隔区序列的分析

通过对毛茛科的唐松草(Thalicrum L.)及其近缘植物黄连、毛莨和芍药科的牡丹等植物的ITS序列和5SrRNA基因间隔区的克隆、扩增及构建系统发育树的分析研究,结果显示,唐松草扩增后ITS序列长607 bp,5SrRNA基因基因间隔区序列长323 bp;系统树证明唐松草属与黄连属和毛茛属的亲缘关系较近,结合形态学与化学等其它学科证据,本研究结论支持唐松草和黄连在进化上更接近,为含木兰花碱生物碱及毛茛甙植物的鉴别以及毛茛科相关植物的亲缘关系初步提供了分子依据.     

鲑科鱼类线粒体全基因组序列结构特征及其系统发育信息分析

为了深入开展鲑科鱼类的线粒体全基因组序列的结构特征和系统发育信息的研究,利用生物信息学的方法分析了已获得的40种鲑科鱼类的线粒体全基因组序列.通过软件Clustal X进行对比,然后用软件MEGA5.05分析DNA的序列差异,并用邻接法生成系统进化树.结果发现:1)鲑科鱼类线粒体基因组的结构和基因排列顺序和其他硬骨鱼类的相同,其全长为16 526~16 997 bp.2)从系统进化树可以看出白鲑亚科(Coregonidaeinae)位于祖先的位置,是最早出现分化的一枝,鲑亚科(Salmoninae)和茴鱼亚科(Thymallinae)亲缘关系较近,互为姐妹群.3)在所有编码基因中,序列变异程度最大的是ND2基因(47.6%),最小的是16S rRNA基因(11.0);Kimura双参数遗传距离最大的是ND2基因(0.203),最小的是12S rRNA基因(0.037).     

华南湍蛙东、南沿海种群间系统发育关系研究

测定了华南湍蛙东南沿海8个种群共55个样品以及2个外群香港湍蛙的线粒体上ND2和CO1两个基因片段,比对后有2382 bp的序列,发现446个变异位点,391个为简约信息位点.分别用NJ法和Mrbayes法建立系统发育树,得到一致的结果:华南湍蛙东、南各种群主要分为四支,其中广西龙胜种群与湖南张家界种群聚在一起形成A支;广西防城种群(B支)与A形成姐妹群;广东深圳种群与香港大屿山种群形成姐妹群构成C支;而广东南昆山种群与南岭种群及福建三港种群形成姐妹群D.     

从叶绿体DNA rbcL序列分析探讨五味子科的系统发育

以广玉兰Magnolia grandiflora，蝙蝠葛Menispermum dauricum，牡丹Paeonia suffruticosa和Illicium parviflorum为外类群，对五味子科的叶绿体rbcL基因进行序列分析，探讨其系统发育关系．结果表明，五味子科为一单系类群，与八角科关系最近，与木兰科关系较远．在严格一致性树中(Length=256，CI=0．8725，RI=0．8192)，五味子科被分为二支，一支由五味子属中的中华五味子亚属Subgen．Sinoschisandra，多蕊五味子亚属Subgen．Pleiostema和少蕊五味子亚属Subgen．Maximowixzia构成，支持率82％；另一支包括南五味子属和五味子属中的团蕊五味子亚属Subgen．Sphaerostema，重瓣五味子亚属Subgen．Plenischisandra．由此推断，五味子属和南五味子属关系密切，它们之间存在交叉和重叠，两属可能起源于共同的祖先．通过基因树分析，结合形态学、解剖学和化学证据认为，五味子S．chinensis和红花五味子S．rubriflora是五味子属中的原始类群．     

亚洲Chiloscyphus-Heteroscyphus-Lophocolea类群的系统分类研究进展

裂萼苔属Chiloscyphus,异萼苔属Heteroscyphus及齿萼苔属Lophocolea是地萼苔科（Geocaly-caceae）中亲缘关系非常接近的三个属,由于植物体特征变化极大,且缺乏足够的分类修订研究,长期以来它们的系统分类地位和属间关系存有很大争议,属及某些种的概念和界线极其模糊.亚洲为该类群的分布中心之一,目前对该类群的分类学研究也不够深入全面.故拟通过文献考证法、经典分类学方法并结合形态特征和数量分类,必要时利用分子系统学的方法对这一类群进行一次较为详尽的分类修订.     

ITS序列在天门冬属物种DNA条形码构建中的应用研究

在对天门冬属4个种ITS(internal transcribed spacer)序列克隆测序的基础上,并对4个种进行序列比较分析.结果表明:(1)4个物种的亲缘关系很近,它们间的ITS序列的变异小,GC含量高,在60％左右.(2)4个物种在系统树上聚为一类,文竹与其他3种天门冬的亲缘关系相对较远,处于系统树的一支,其...     

基于线粒体基因组全序列的鳅科(Cobitidae)鱼类进化关系分析

为了解鳅科(Cobitidae)鱼类线粒体全基因组序列的结构特征和系统发育信息,利用生物信息学方法对已知的40种鳅科鱼类线粒体全基因组进行比对分析,用邻接法(NJ)构建系统发育树。结果显示：(1)鳅科鱼类线粒体基因组全序列长度在16 553～16 937 bp之间,基因组的结构特征及基因排列顺序与其他硬骨鱼类一致。(2)鳅科鱼类线粒体全基因组一致序列长度为17 483 bp,变异位点数为8039(45.9%),Kimura双参数平均遗传距离为0.19。在13个蛋白质编码基因中,ND2的变异程度(58.9%)和平均遗传距离(0.28)最大,变异程度最小的是12S rRNA(30.5%),tRNA拼接序列的平均遗传距离最小(0.07)。(3)Cox1、ND5、Cytb基因是进行鳅科鱼类系统发育分析较为理想的分子标记,NJ系统发育树显示,条鳅亚科(Noemacheilinae)是最早分化出来的一枝群系,位于祖先位置,沙鳅亚科(Botiinae)和花鳅亚科(Cobitinae)亲缘关系更近,互为姐妹群系。本研究为鳅科鱼类进化学研究和分子标记的选取提供参考依据。     

9种拟步甲16S rDNA部分序列及其亲缘关系

测定了9种拟步甲的16S rDNA部分基因序列,并与GenBank中的1种步甲的基因序列作同源性比较,计算其核苷酸使用频率并构建了分子系统树.在获得的435 bp的序列中,A+T约占74.4%,颠换(transversion)取代的速率大于转换(transition)取代的速率,其中277个核苷酸位点存在变异.结果表明:属内种间的碱基序列差异范围为3.4%～6.2%;族内属间为9.4%～11.0%;科内族间为10.8%～17.7%;科与科间的差异达到46.7%～50.3%.分子系统树表明:拟步甲科为一单系群,其中琵甲族较为进化,漠甲族与漠王族相对原始;琵甲族与土甲族的亲缘关系较近;漠甲族、漠王族与鳖甲族的亲缘关系较近.本结果与传统的分类观点相吻合.     

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.     

六种鱼巴亚科鱼类线粒体细胞色素b基因序列分析

测定了鱼巴亚科云南光唇鱼(Acrossocheilus yunnanensis)、宽头四须鱼巴(Barbodes laticeps)、抚仙金线鱼巴(Sinocyclocheilus tingi)和滇池金线鱼巴(Sinocyclocheilus grahami)4种鱼类线粒体细胞色素b基因DNA序列402bp,结合已知的云南倒刺鱼巴(Spinibarb denticulatus yunnanensis)和细尾长臀鱼巴(Mystacoleucus lepturus)的同源序列,组成1个6种代表鱼巴亚科5属鱼类的数据集.选用已知的云南鲴(Xenocypris yunnanensis)作为外群,采用邻接法、最大简约法和最大似然法构建了分子系统树.结果显示:倒刺鱼巴属(Spinibarbus)和光唇鱼属(Acrossocheilus)有较近的亲缘关系,四须鱼巴属(Barbodes)和长臀鱼巴属(Mystacoleucus)有较近的亲缘关系,而金线鱼巴属(Sinocyclocheilus)和它们的关系不能确定.上述结果与它们的地理分布基本吻合.       

Mitochondrial d-loop sequence variation and phylogeny of gobiobotine fishes

The mitochondrial DNA control region is amplified and sequenced from 8 genera and 10 species of gobiobotine fishes. The phylogenetic tree of Gobiobotinae and some representative species of other Cyprinid subfamilies obtained by the method of neighborhood joining, maximum likelihood and maximum parsimony with Danio rerio as an outgroup indicates that Gobiobotinae fishes are a monophyletic group which is close to Gobioninae subfamily. Gobiobotinae should be included into subfamily Gobioninae in terms of phylogenetic analysis. The research result supports that Gobiobotinae can be divided into genus Xenophysogobio and Gobiobotia. Xenophysogobio is the most primitive genera in the subfamily.     

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.     

六种鱼巴亚科鱼类线粒体细胞色素b基因序列分析

 测定了鱼巴亚科云南光唇鱼(Acrossocheilus yunnanensis)、宽头四须鱼巴(Barbodes laticeps)、抚仙金线鱼巴(Sinocyclocheilus tingi)和滇池金线鱼巴(Sinocyclocheilus grahami)4种鱼类线粒体细胞色素b基因DNA序列402bp,结合已知的云南倒刺鱼巴(Spinibarb denticulatus yunnanensis)和细尾长臀鱼巴(Mystacoleucus lepturus)的同源序列,组成1个6种代表鱼巴亚科5属鱼类的数据集.选用已知的云南鲴(Xenocypris yunnanensis)作为外群,采用邻接法、最大简约法和最大似然法构建了分子系统树.结果显示:倒刺鱼巴属(Spinibarbus)和光唇鱼属(Acrossocheilus)有较近的亲缘关系,四须鱼巴属(Barbodes)和长臀鱼巴属(Mystacoleucus)有较近的亲缘关系,而金线鱼巴属(Sinocyclocheilus)和它们的关系不能确定.上述结果与它们的地理分布基本吻合.     

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.     

Sequence variations of theS7 ribosomal protein gene in primitive cyprinid fishes: Implication on phylogenetic analysis

Cyprinidae is the largest fish family in the world and contains about 210 genera and 2010 species. Appropriate DNA markers must be selected for the phylogenetic analyses of Cyprinidae. In present study, the 1st intron of the S7 ribosomal protein (r-protein) gene is first used to examine the relationships among cyprinid fishes. The length of the 1st intron obtained by PCR amplification ranges from 655 to 859 bp in the 16 cyprinid species investigated, and is 602 bp in Myxocyprinus asiaticus. Out of the alignment of 925 nucleotide sites obtained, the parsimony informative sites are 499 and occupy 54% of the total sites. The results indicate that the 1st intron sequences of the S7 r-protein gene in cyprinids are rich in informative sites and vary remarkably in sequence divergence from 2.3% between close species to 66.6% between distant species. The bootstrap values of the interior nodes in the NJ (neighbor-joining) and MP (most- parsimony) trees based on the present S7 r-protein gene data are higher than those based on cytochrome b and the d-loop region respectively. Therefore, the 1st intron sequences of the S7 r-protein gene in cyprinids are sensitive enough for phylogenetic analyses, and the 1st intron is an appropriate genetic marker for the phylogenetic reconstruction of the taxa in different cyprinid subfamilies. However, attempts to discuss whether the present S7 r-protein gene data can be applied to the phylogeny of the taxa at the level of the family or the higher categories in Cypriniformes need further studies.     

Phylogenetic position of three Condylostoma species （Protozoa,Ciliophora, Heterotrichea） inferred from the small subunit rRNA gene sequence

The systematically poorly known ciliate genus Condylostoma was erected by Vincent in 1826. About 10 morphotypes have been reported, but any molecular investigations concerning this group so far are lacking. In this work, the small subunit ribosomal RNA （SS rRNA） gene of three marine Condylostoma species was sequenced, by which the phylogenetic trees were constructed by distancematrix, maximum parsimony and Bayesian inference methods. The results show that （1） all the trees have similar topologies with high supports; （2） Condylostoma is mostly related to the genus Condylostentor; and （3） three Condylostoma species as well as Condylostentor auriculatus cluster together and form a sister group with other heterotrichs. This is moderately consistent with the assessment of phylogenetic relationships of Condylostoma-related heterotrichs from the morphological information. The phylogenetic relationship of some other related heterotrichs, Peritromus, Folliculina, Stentor and Blepharisma, has been also discussed.     

The c-myc coding DNA sequences of cyprinids （Teleostei： Cypriniformes）： Implications for phylogeny

The family Cyprinidae is one of the largest fish families in the world, which is widely distributed in East Asian, with obvious difference in characteristic size among species. The phylogeneUc analysis of cyprinid taxa based on the functionally important genes can help to understand the speciation and functional divergence of the Cyprinidae. The c-myc gene is an important gene regulating individual growth. In the present study, the sequence variations of the cyprinid c-myc gene and their phylogenetic significance were analyzed. The 41 complete sequences of the c-myc gene were obtained from cyprinids and outgroups through PCR amplification and clone. The coding DNA sequences of the c-myc gene were used to infer molecular phylogenetic relationships within the Cyprinidae. Myxocyprinus asiaticus （Catostomidae）, Misgurnus anguillicaudatus （CobiUdae） and Hemimyzon sinensis （Homalopteridae） were assigned to the outgroup taxa. Phylogenetic analyses using maximum parsimony （MP）, maximum likelihood （ML）, and Bayesian retrieved similar topology. Within the Cyprinidae, Leuciscini and Barbini formed the monophyletic lineage respectively with high nodal supports. Leuciscini comprises Xenocyprinae, CuItrinae, East Asian species of Leuciscinae and Danioninae, Gobioninae and Acheilognathinae, and Barbini contains Schizothoracinae, Barbinae, Cyprininae and Labeoninae. Danio rerio, D. myersi and Rasbora trilineata were supposed to separate from Leuciscinae and Barbini and to form another lineage. The positions of some Danioninae species were still unresolved. Analyses of both amino acid variation with parsimony information and two high variation regions indicated that there is no correlation between variations of single amino acid or high variation regions and characteristic size of cyprinids. In addition, the species with smaller size were usually found to be basal within clades in the tree, which might be the results of the adaptation to the primitive ecology and survival pressure.     

Phylogenetic position of three Condylostoma species(Protozoa,Ciliophora,Heterotricheal inferred from the small subunit rRNA gene sequence

The systematically poorly known ciliate genus Conadylostoma was erected by Vincent in 1826.About 10 morphotypes have been reported,but any molecular investigations concerning this group SO far are lacking.In this work,the small subunit ribosomal RNA (SS rRNA)gene of three marine Conaylostoma species was sequenced,by which the phylogenetic trees were constructed by distance-matrix,maximum parsimony and Bayesian inference methods.The results show that(1)all the trees have similar topologies with high supports;(2)Condylostoma is mostly related to the genus Condylostentor;and(3)three Condylostoma species as well as Conadylostentor auriculatus cluster together and form a sister group with other heterotrichs.This is moderately consistent with the assessment of phylo-genetic relationships of Conaylostoma-related heterotrichs from the morphological information.The phylogenetic relationship of some other related heterotrichs,Peritromus,Fotlictllina,Stentor and Blepharisma,has been also discussed.