鸢尾属分子系统发育学研究进展

鸢尾属植物具有重要的观赏价值和经济价值,研究该属属内系统演化关系对该属种质保存、利用和遗传育种具有重要意义.目前,有关鸢尾属各分类单元的系统学关系长期处于争议状态.因此,该文以经典分类系统主要观点为基础,从不同分类单元的系统关系总结了鸢尾属分子系统发育学研究进展.结果表明:现有分子系统发育学研究结果大多支持鸢尾属为并系...     

分子伴娘60类群的系统发育学分析

有充分的证据支持线粒体和叶绿体起源的内共生假说,即:紫色细菌、α—类群的成员是线粒体的祖先,而蓝细菌的成员是叶绿体的祖先。这一证据来自分子伴娘60蛋白为基础的系统发育学分析,并且与16S rRNA序列为基础的分析结果是完全一致的。这一结果还说明,嗜碱芽胞杆菌C-125菌株在系统发育地位上更接近枯草芽孢杆菌。     

基于线粒体基因组的白甲鱼属分子系统发育学研究

从基本形态上分类, 白甲鱼属(Onychostoma)隶属鲤形目(Cypriniformes)、鲤科(Cyprinidae)、鲃亚科(Barbinae), 其中包含19个种。然而, 白甲鱼属内的分子系统发育学关系并不是很清楚。基于整个线粒体基因组序列, 以斑马鱼(Danio rerio)和倒刺鲃(Spinibarbus denticulatus)为外类群, 分析了8种白甲鱼属的分子系统发育学关系。结果表明, 白甲鱼属内的8个物种不是1个单类群, 其中包括3个分支: 多鳞白甲鱼(Onychostoma macrolepis)、小口白甲鱼(Onychostoma lini)、粗须白甲鱼(Onychostoma barbatum)和台湾白甲鱼(Onychostoma barbatulum)为一个分支, 南方白甲鱼(Onychostoma gerlachi)和白甲鱼(Onychostoma simum)一个分支, 稀有白甲鱼(Onychostoma rara)和高身白甲鱼(Onychostoma alticorpus)为一个分支。研究结果和传统的形态学分类学结果大致一样, 均分为3个分支。研究使用线粒体全基因组进行白甲鱼属系统发育学研究, 为白甲鱼属的系统发育学填补相关方面空白。     

西藏温泉两种中国新记录纤毛虫第一双小核草履虫和明布雷斯四膜虫的形态学和系统发育学研究

研究利用活体观察、蛋白银和氨银染色技术对采自西藏温泉的寡膜纲咽膜类纤毛虫第一双小核草履虫(Paramecium primaurelia)和膜口类纤毛虫明布雷斯四膜虫(Tetrahymena mimbres)进行了形态学研究,首次描述了这两种纤毛虫细胞核器的形态和位置、纤毛图式和口膜的排布模式;并且测定了SSU rDNA和COXⅠ标记基因序列,基于这两种基因的系统发育树均支持P. primaurelia聚在草履虫P. aurelia复合种中, T. mimbres聚在四膜虫T. borealis类群中。两种纤毛虫均为中国新记录种,且首次在高原温泉中发现,不仅为西藏地区温泉原生动物生物资源的发掘提供新的方法和思路,也为原生动物环境适应性研究提供基础资料。     

核基因在鸟类分子系统发育学研究中的应用

核基因作为一种新的遗传标记,近年来被广泛应用于鸟类分子系统发育研究中.核基因与线粒体基因位于不同的遗传载体上,因此被引入到系统发育学研究中为物种树的重建提供独立的证据.常用的外显子标记为重组激活基因1(RAG-1),重组激活基因2(RAG-2),癌基因c-myc,原癌基因c-mos,它们由于缓慢的进化速率而被用于鸟类高级分类阶元的系统学研究中.常用的内含子标记是β纤维蛋白原基因内含子7(β-fibrinogen intron7,β-fibint7),肌红蛋白基因内含子Ⅱ(myoglobin intionⅡ).内含子标记通常与线粒体序列联合使用,形成具有互补系统发育信号的数据集,应用于各种分类阶元的系统学研究中.     

叶蝉科昆虫分子系统发育的研究进展

从基因组DNA的提取、研究的基因片段、PCR引物选用、扩增条件以及叶蝉科不同阶元的分子系统发育分析等方面,综述叶蝉科(半翅目:叶蝉科)昆虫分子系统发育的研究进展。目前角顶叶蝉类的研究成果相对较多,大叶蝉亚科次之,其余类群的研究较少或无。线粒体基因与核基因序列联合分析以及线粒体全序列分析以及基因序列与形态数据相结合分析,分子鉴定叶蝉与共生菌之间的协同进化的研究,将是叶蝉分子系统学未来发展的主要研究手段。     

旋唇纲纤毛虫系统发育分子树构建的影响因素

以36种旋唇类高等类群纤毛虫的核糖体小亚基核苷酸(Small subunit ribosomal RNA,SS rRNA)基因序列为素材,比较研究了不同条件(包括外类群、内类群的选择,同一基因不同序列长度的组合,不同建树方法和不同分析软件的使用)对纤毛虫分子系统树构建结果的影响。结果表明,上述因素均可不同程度地影响拓扑结构。结果同时提示,在利用有限数据进行相关研究,特别是在对未明类群的系统关系分析中,必须充分考虑因建树条件的不同所带来的影响。作者同时也建议,在当前可用的分子信息欠充分的前提下,对于纤毛虫任何类群的分子系统学探讨而言,慎重形成结论并尽可能地结合和参照形态学、发生学等资讯,仍是需优先考虑的工作路线。     

西藏三种苔藓栖生纤毛虫的形态和系统发育分析

本研究利用活体观察和蛋白银染色方法对采自西藏日喀则和那曲的3种苔藓栖生纤毛虫,鬃异源棘尾虫(Tetmemena pustulata)、棘毛虫未定种(Sterkiella sp.)和殖口虫未定种(Gonostomum sp.)进行了形态学研究,描述了活体、核器以及纤毛图式等形态学特征.同时,测定了这3种纤毛虫的SSU r...     

八种纤毛虫减数分裂基因的分子进化研究

减数分裂是真核生物适应性进化的重要机制,以8种纤毛虫作为实验对象,通过生物信息学方法对其14个减数分裂基因进行了鉴定及分子进化研究。结果表明:(1)不同的纤毛虫种类存在一些特异性的减数分裂基因的丢失与复制现象;(2)减数分裂相关基因在纤毛虫中很保守;(3)纤毛虫减数分裂重要的同源重组过程是在真核生物中不常见的Ⅱ型。本研究表明,纤毛虫减数分裂可能代表了真核生物较原始的减数分裂方式,在进化的过程中很保守,为研究真核生物减数分裂起源与进化提供了重要线索。     

两种缘毛类纤毛虫胞质Hsp70基因序列的克隆及其系统发育分析

克隆得到2种缘毛类纤毛虫——钟形钟虫(Vorticella campanula)和螅状独缩虫(Carchesium polypinum)的胞质Hsp70基因部分序列,长度均为438bp,编码146个氨基酸。以细菌为外类群,利用最大似然法和邻接法构建包括其他5种纤毛虫在内的共26个物种的Hsp70基因氨基酸序列系统发育树,其拓扑结构显示：V．campanula和C．polypinum聚在一起,并与另2种寡膜纲的嗜热四膜虫(Tetrahymena thermophila)及草履虫(Paramecium tetraurelia)聚为姊妹枝,提示了缘毛类纤毛虫为单系,且隶属于寡膜纲的系统发育地位。     

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     

四个DNA 片段在山茶属分子系统学研究中的应用

选取山茶属14 个组中的10 组21 种植物对目前常用于属内种间的4 个DNA 片段( ITS、waxy 、trnLF
、rpL16) 进行序列测定。结果表明: ( 1) 来自叶绿体基因组的2 个片段( trnL- F、rpL 16) 其PCR 扩增和
测序都很容易, 但两者的进化速率都非常慢, 序列矩阵只有很少信息位点( trnL-F 含9 个, rpL16 为20
个) , 不能提供必要的系统发育信息。( 2) 来自核基因组的ITS 片段其PCR 产物比较容易获得, 但其序列
的测定存在较多问题。( 3) waxy 是来自核基因组的另一个片段, 其PCR 扩增因受模板DNA 的数量和质量
的影响很大而有一定难度, 但其进化速率较快, 序列矩阵具有较多信息位点( 92 个) , 并且在山茶属是单
拷贝, 这对于解决山茶属这类具有许多近缘物种的类群的系统关系有重要价值。基于tsnL- F、rpL16 和
waxy 三组数据所建分子系统树支持山茶属为一单系, 但属下系统由于取样等原因有待进一步研究。     

四个DNA片段在山茶属分子系统学研究中的应用

选取山茶属14个组中的10组21种植物对目前常用于属内种间的4个DNA片段（ITS、waxy、trnL-F、rpL16）进行序列测定。结果表明：（1）来自叶绿体基因组的2个片段（trnL-F、rpL16）其PCR扩增和测序都很容易,但两者的进化速率都非常慢,序列矩阵只有很少信息位点（trnL-F含9个,rpL16为20个）,不能提供必要的系统发育信息。（2）来自核基因组的ITS片段其PCR产物比较容易获得,但其序列的测定存在较多问题。（3）waxy是来自核基因组的另一个片段,其PCR扩增因受模板DNA的数量和质量的影响很大而有一定难度,但其进化速率较快,序列矩阵具有较多信息位点（92个）,并且在山茶属是单拷贝,这对于解决山茶属这类具有许多近缘物种的类群的系统关系有重要价值。基于tsnL-F、rpL16和waxy三组数据所建分子系统树支持山茶属为一单系,但属下系统由于取样等原因有待进一步研究。     

Phylogenetic relationships among genera of Massonieae (Hyacinthaceae) inferred from plastid DNA and seed morphology

The tribe Massonieae Baker (Hyacinthaceae-Hyacinthoideae) presently consists of about 19 genera and 230 species distributed from Africa (south of the Sahara) to Madagascar and India. Based on atpB and trnL-F DNA sequences the tribe is monophyletic only when the genus Pseudoprospero is excluded from Massonieae. In most trnL-F trees, this genus occupies a basal position within subfamily Hyacinthoideae and is sister to the rest of the subfamily. Molecular data suggest that the remaining genera of Massonieae do not share common ancestry with the Eurasian/North-African tribe Hyacintheae Dumort. (Scilla, Hyacinthus and allies), and thus a narrow concept of the essentially Eurasian genus Scilla is supported. Members of well-supported clades in Massonieae usually show similarities in seed characteristics as determined by scanning electron microscopy. Phylogenetic position and seed morphology indicate that Massonia angustifolia and M. zeyheri do not belong to the genus Massonia but fall into a clade together with Daubenya, Androsiphon and Amphisiphon. The genus Whiteheadia appears paraphyletic in the 50% majority rule trnL-F tree and occupies a basal position next to Massonia. However, in the strict consensus tree neither monophyly nor polyphyly can be excluded for this genus. Seed appendages are documented for members of the genera Ledebouria and Lachenalia. Within the genera of Massonieae there is a tendency towards bending of the seed axis. This phenomenon is most obvious within the genus Lachenalia. Delimitation of genera based on seed morphology largely agrees with the results of molecular studies. Correlation between number, size and color of seeds, geographical distribution and phylogenetic position of the genera are discussed. Electronic Publication     

Molecular phylogeny of litostome ciliates (Ciliophora, Litostomatea) with emphasis on free-living haptorian genera

The monophyly of the litostomes was tested using nine newly sequenced and four previously unpublished small subunit ribosomal RNA (SSrRNA) gene sequences from free-living Haptoria as well as from endosymbiotic Trichostomatia: the vestibuliferids Balantidium coli and Isotricha prostoma, the cyclotrichiid Mesodinium pulex, and the haptorids Loxophyllum rostratum, Dileptus sp., Enchelyodon sp., Enchelys polynucleata, Epispathidium papilliferum (isolates A and B), Spathidium stammeri, Arcuospathidium muscorum, Arcuospathidium cultriforme, and the unusual Teuthophrys trisulca. Phylogenetic analyses depicted the litostomes as a monophyletic group consisting of the trichostomes (subclass Trichostomatia) and the free-living haptorians (subclass Haptoria). The cyclotrichiids Mesodinium and Myrionecta (order Cyclotrichiida) branched either basally within or outside the Litostomatea. In most analyses, the haptorians did not receive support as a monophyletic group. Instead, Dileptus branched basally to all litostome taxa, and Epispathidium papilliferum grouped with the Subclass Trichostomatia. Some subgroupings, however, of haptorian genera corresponded to suggested superfamilial taxa (e.g., orders Spathidiida and Pleurostomatida). Within the monophyletic trichostomes, we can distinguish three clades: (1) an Australian clade; (2) the order Entodiniomorphida; and (3) the order Vestibuliferida. However, Balantidium, currently classified in the Vestibuliferida, did not group with the other vestibuliferids, suggesting that this order may be paraphyletic.     

Multiple origins of anural development in ascidians inferred from rDNA sequences

Ascidians exhibit two different modes of development. A tadpole larva is formed during urodele development, whereas the larval phase is modified or absent during anural development. Anural development is restricted to a small number of species in one or possibly two ascidian families and is probably derived from ancestors with urodele development. Anural and urodele ascidians constitute a model system in which to study the evolution of development, but the phylogeny of anural development has not been resolved. Classification based on larval characters suggests that anural species are monophyletic, whereas classification according to adult morphology suggests they are polyphyletic. In the present study, we have inferred the origin of anural development using rDNA sequences. The central region of 18S rDNA and the hypervariable D2 loop of 28S rDNA were amplified from the genomic DNA of anural and urodele ascidian species by the polymerase chain reaction and sequenced. Phylogenetic trees inferred from 18S rDNA sequences of 21 species placed anural developers into two discrete groups corresponding to the Styelidae and Molgulidae, suggesting that anural development evolved independently in these families. Furthermore, the 18S rDNA trees inferred at least four independent origins of anural development in the family Molgulidae. Phylogenetic trees inferred from the D2 loop sequences of 13 molgulid species confirmed the 18S rDNA phylogeny. Anural development appears to have evolved rapidly because some anural species are placed as closely related sister groups to urodele species. The phylogeny inferred from rDNA sequences is consistent with molgulid systematics according to adult morphology and supports the polyphyletic origin of anural development in ascidians. Correspondence to: W.R. Jeffery     

Patterns of nucleotide change in mitochondrial ribosomal RNA genes and the phylogeny of piranhas

The patterns and rates of nucleotide substitution in mitochondrial ribosomal RNA genes are described and applied in a phylogenetic analysis of fishes of the subfamily Serrasalminae (Teleostei, Characiformes, Characidae). Fragments of 345 bp of the 12S and 535 bp of the 16S genes were sequenced for 37 taxa representing all but three genera in the subfamily. Secondary-structure models based on comparative sequence analysis were derived to characterize the pattern of change among paired and unpaired nucleotides, forming stem and loop regions, respectively. Base compositional biases were in the direction of A-rich loops and G-rich stems. Ninety-five percent of substitutions in stem regions were compensatory mutations, suggesting that selection for maintenance of base pairing is strong and that independence among characters cannot be assumed in phylogenetic analyses of stem characters. The relative rate of nucleotide substitution was similar in both fragments sequenced but higher in loop than in stem regions. In both genes, C-T transitions were the most common type of change, and overall transitions outnumbered transversions by a factor of two in 16S and four in 12S. Phylogenetic analysis of the mitochondrial DNA sequences suggests that a clade formed by the generaPiaractus, Colossoma, andMylossoma is the sister group to all other serrasalmins and that the generaMyleus, Serrasalmus, andPristobrycon are paraphyletic. A previous hypothesis concerning relationships for the serrasalmins, based on morphological evidence, is not supported by the molecular data. However, phylogenetic analysis of host-specific helminth parasites and cytogenetic data support the phylogeny of the Serrasalminae obtained in this study and provide evidence for coevolution between helminth parasites and their fish hosts.