基因序列在小蜂总科分子系统发育研究中的应用

总结了线粒体基因和核基因在膜翅目小蜂总科分子系统发育研究中的应用.核基因中,28S rDNA序列应用最广泛,探讨的问题从种级到科级不等;其次是ITS序列,主要用于探讨种及种级以下阶元问题;18S rDNA适于探讨科级以上高级阶元的问题.线粒体基因中,16S rDNA和3个蛋白编码基因COⅠ、COⅡ和Cytb,主要用于属种级系统发育关系研究.核基因间、线粒体基因间、核基因和线粒体基因间以及分子数据和形态数据间进行的联合分析,在解决不同层次的问题中均有应用.建议对更多的小蜂类群测定线粒体基因和核基因的序列,不断寻找新的基因对小蜂分子系统发育研究进行充实和拓展.     

广西姬小蜂科分类学研究(膜翅目:小蜂总科)

根据1998－2000年作者在广西南部山区的采集,结合中国科学院动物研究所昆虫标本馆馆藏标本的研究,报道了该科4亚科27属81种在广西的分布,其中,4属60种是中国新纪录,本文对前人和作者最近对中国姬小蜂科的分类研究简单作了综述,并对广西的姬小蜂科物种进行了初步的组分分析,根据现有材料得出结论是：1）广西的姬小蜂科区系成分以东洋区和古北成分为主;2）多个区纱成分分布相互重叠,交错。     

伊朗寄生蓟马的侧姬小蜂属Ceranisus种类记述(膜翅目:姬小蜂科:凹面姬小蜂亚科)(英文)

侧姬小蜂属Ceranisus Walker,1841隶属膜翅目Hymenoptera、小蜂总科Chalcidoidea、姬小蜂科Eulophidae、凹面姬小蜂亚科Entedoninae,是蓟马幼虫重要的寄生蜂,迄今世界上已知16种。该属颜面凹陷,额V字形,槽沟伸达中单眼水平,侧单眼后部有1条完整的沟横穿颅顶,颚眼沟一般不分叉,上颚退化;雌性触角索节2分节,棒节2或3分节;盾纵沟不明显,一般中胸盾片中叶着生2对刚毛,小盾片1对刚毛;前翅缘毛短于翅宽,后翅末端尖锐;腹柄短,宽明显大于(或至少等于)长等特征明显,较易识别。本文首次报道该属伊朗的3种类:月侧姬小蜂Ceranisus menes(Walker,1839),平侧姬小蜂C.planitianus Erds,1966和爱侧姬小蜂C.amanosus Doganlar et al.,2009,这也是该属在伊朗的首次记录。并对近缘种爱侧姬小蜂C.amanosus Doganlar et al.,2009和乌侧姬小蜂C.udnamtak Tryapitsin,2005的鉴别进行了简要讨论。     

基于分子系统学的可疑瑟姬小蜂分类修订及姬小蜂亚科盾纵沟的演化分析

姬小蜂为寄生蜂的演化研究提供了很好的材料。在姬小蜂分类中,盾纵沟是一个重要性状, 曾被用来区分亚科、族、属及种。非同源性相似形态特征的存在使得物种准确鉴定存在困难。从盾纵沟形状上,可疑瑟姬小蜂Cirrospilus ambiguu 和双斑潜蝇姬小蜂Diglyphus bimaculatus应介于瑟姬小蜂属Cirrospilus 和潜蝇姬小蜂属Diglyphus之间。确定这两种姬小蜂的系统发育位置将有助于分析盾纵沟的演化模式。本文用贝叶斯方法分析了线粒体COⅠ 部分序列、核糖体ITS1 序列及核糖体28S D2 区部分序列等3个基因序列,结果显示可疑瑟姬小蜂应被移到潜蝇姬小蜂属中; 研究结果支持潜蝇姬小蜂属是单系,而不支持瑟姬小蜂属是单系。结合28S D2 区部分序列的贝叶斯分析结果,分析了在姬小蜂亚科中盾纵沟的演化模式。结果显示,完整且延伸到中胸背板后缘的盾纵沟代表其原始类型;完整且延伸到三角片的盾纵沟类型分别出现在5个独立的枝上,代表了该特征5次独立的演化;不完整的盾纵沟类型出现在4个独立的枝上,表明该类型独立演化了4次     

基于28S rDNA序列的姬小蜂科(膜翅目,小蜂总科)分类

选择28S rDNA D2区基因,针对GenBank中姬小蜂科总计542条相关序列,借助Blast Align、MUSCLE及TNT等生物信息学软件进行计算分析,提出了一种基于亚科水平的姬小蜂科快速DNA分类鉴定方法。建树结果对目前分类系统中姬小蜂科4亚科分类体系(Bouek,1988)予以支持;综合分析结果基本支持对于姬小蜂亚科以及灿小蜂亚科的分族、分属方法。同时对地位不明的两属Anselmella和Ophelimus的分类学地位提出了假设。     

由12S rDNA序列探讨中国狼蛛科主要类群的分子系统发育关系

将自测的我国蜘蛛目狼蛛科4属6个种和从互联网GenBank中检索到相关物种的线粒体基因组12SrDNA的序列进行同源性比较,计算核苷酸使用频率。然后据此进行分子分析,利用2个外群(漏斗蛛科的机敏漏斗蛛Agelena difficilis和缘漏斗蛛Agelena limbat)和2种建树方法(邻近法Neighbour Joining,NJ和最大简约法Maximum Parsimony,MP)分析我国狼蛛科内的亲缘关系。获得平均为291.6 bp的序列中,A T平均含量为78.13%,而G C含量只要21.87%,颠换取代(tranversion)的速度多数大于或接近转换取代(transition)的速度,其中161个核苷酸位点存在变异。研究结果表明:在蜘蛛目狼蛛科有差异的161 bp中,属内种间仅为1.08%,狼蛛科属间为6.85%~14.80%。所构建的分子系统树表明:科内的属和属内的种均优先聚在一起;狼蛛科现行分类系统中各亚科的演化关系顺序为:马蛛亚科→狼蛛亚科→豹蛛亚科;狼蛛科各属的演化关系顺序为:水狼蛛属→马蛛属(或水狼蛛属和马蛛属)→獾蛛属→狼蛛属→豹蛛属;水狼蛛属为最早分出的一支或者水狼蛛属和马蛛属...     

基于18S rDNA的蝗总科分子系统发育关系研究及分类系统探讨

将自测的我国直翅目蝗总科7科7种和从GenBank中下载的17种直翅目昆虫的18S rDNA序列片段进行了同源性比较,用似然比检验的方法对序列比对结果进行了碱基替代模型的选择,以蚱总科的Paratettix cucullatus和蜢总科的Stiphra robusta作外群,用NJ、MP、ML和贝叶斯法构建了分子系统树。在获得的1 849 bp的序列中,有205个变异位点,74个简约信息位点; A、T、C和G的碱基平均含量分别为23.9%、24.3%、23.8%和28.0%,碱基组成基本上无偏异。分子系统树表明：所研究的内群聚为4支,锥头蝗科、瘤锥蝗科、斑腿蝗科、网翅蝗科、槌角蝗科和剑角蝗科都不是单系。建议将蝗总科分为4科,即锥头蝗科、大腹蝗科、癞蝗科和蝗科。     

基于18S rRNA基因序列的直翅目主要类群系统发育关系研究

基于78种直翅目昆虫的18S rRNA基因全序列构建了直翅目各主要类群间的系统发育关系。本研究的结果支持直翅目的单系性,但不支持蝗亚目和螽亚目各自的单系性;直翅目下除蜢总科和蝗总科外各总科的划分多数与Otte系统相一致;蜢总科的单系性得不到支持;蝗总科的剑角蝗科、斑腿蝗科、斑翅蝗科、网翅蝗科和槌角蝗科5科均不是单系群,各物种间的遗传距离差异不大,应合并为一科,即蝗科;本研究支持将Otte系统中蚱总科和螽蟖总科下各亚科级阶元提升为科级阶元;18S rRNA基因全序列可以作为划分科级阶元的工具,当位于同一分支上互成姐妹群的类群间的遗传距离超过1%时,这几个类群属于不同的科;但由于其在进化上的保守性,18S rRNA基因只能用于纲目等高级阶元间关系的研究,而由其获得的总科以下阶元间的关系并不可靠。     

从18S rRNA基因序列探讨盾腹吸虫的系统发育关系

盾腹亚纲吸虫被认为是寄生扁形动物中古老的类群,包括盾腹科、多萼科、裂杯科和皱腹科,科间系统发育关系尚存争议。本研究收集GenBank数据库中所有的盾腹吸虫18S rRNA基因序列,测定了三种盾腹吸虫的相应序列,分别采用最大简约法和最大似然法构建分子系统发育树。结果显示,多萼科的分类地位不成立,多萼属应还原到盾腹科;盾腹科的盾腹亚科和杯盾亚科均非单系,吸槽列数可能是平行进化特征,不能反映盾腹科各亚科间的系统发育关系。建议将具有边缘器的吸槽型腹吸盘,以及不具边缘器的吸杯型和皱褶型腹吸盘分别鉴定为盾腹科、裂杯科和皱腹科种类的共裔性状。     

蝗总科部分种类16S rDNA的分子系统发育关系

将自测的我国直翅目蝗总科8科8个种和从互联网GenBank中检索到相关物种的线粒体基因组：16S rDNA序列片段进行同源性比较,计算核苷酸使用频率,并构建分子系统树。在获得的480bp的序列中。A T约占70．7％,G C为29．3％,颠换取代(transversion)的速率大于或接近转换取代(transition)的速率,其中188个核苷酸位点存在变异。研究结果表明：在直翅目蝗总科有差异的188bp中,属内种间的碱基序列差异仅为1．5％,科内属间为3．5％～3．6％,科间差异为4．8％～15．8％,亚目间差异达到15．2％～25．6％。分子系统树表明：科内的属和属内的种均优先聚在一起;蝗总科8科的起源关系为：锥头蝗科→瘤锥蝗科→癞蝗科→斑翅蝗科→剑角蝗科→网翅蝗科和槌角蝗科→斑腿蝗科;锥头蝗科与瘤锥蝗科关系较近,是蝗总科内最原始的类群;槌角蝗科和网翅蝗科互为姐妹群,与最进化的斑腿蝗科关系较近;蚤蝼科为独立的一支,最先分出,似为一个亚目,与现用的分类系统有明显差别;哈螽科(螽嘶总科)和蟋蟀科聚在一起为剑瓣亚目(Ensifera),蚱科和蝗总科的8科组成短瓣亚目(Caehfera),同现用的分类系统。     

Flatworm phylogeny from partial 18S rDNA sequences

Partial 18S rDNA sequences from 29 flatworms and 2 outgroup taxa were used in a cladistic analysis of the Platyhelminthes. Support for the clades in the resulting single most parsimonious tree was estimated through bootstrap analysis, jack-knife analysis and decay indices. The Acoelomorpha (Acoela and Nemertodermatida) were absent from the most parsimonious tree. The Acoela and the Fecampiidae form a strongly supported clade, the sister group of which may be the Tricladida. There is some support for monophyly of the rhabdocoel taxon Dalyellioida, previously regarded as paraphyletic. The sister group of the Neodermata remains unresolved. This revised version was published online in July 2006 with corrections to the Cover Date.     

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     

Phylogenetic relationships of conifers inferred from partial 28S rRNA gene sequences

The conifers, which traditionally comprise seven families, are the largest and most diverse group of living gymnosperms. Efforts to systematize this diversity without a cladistic phylogenetic framework have often resulted in the segregation of certain genera and/or families from the conifers. In order to understand better the relationships between the families, we performed cladistic analyses using a new data set obtained from 28S rRNA gene sequences. These analyses strongly support the monophyly of conifers including Taxaceae. Within the conifers, the Pinaceae are the first to diverge, being the sister group of the rest of conifers. A recently discovered Australian genus Wollemia is confirmed to be a natural member of the Araucariaceae. The Taxaceae are nested within the conifer clade, being the most closely related to the Cephalotaxaceae. The Taxodiaceae and Cupressaceae together form a monophyletic group. Sciadopitys should be considered as constituting a separate family. These relationships are consistent with previous cladistic analyses of morphological and molecular (18S rRNA, rbcL) data. Furthermore, the well-supported clade linking the Araucariaceae and Podocarpaceae, which has not been previously reported, suggests that the common ancestor of these families, both having the greatest diversity in the Southern Hemisphere, inhabited Gondwanaland.     

Marine-freshwater colonizations of haptophytes inferred from phylogeny of environmental 18S rDNA sequences

The Haptophyta is a common algal group in many marine environments, but only a few species have been observed in freshwaters, with DNA sequences available from just a single species, Crysochromulina parva Lackey, 1939. Here we investigate the haptophyte diversity in a high mountain lake, Lake Finsevatn, Norway, targeting the variable V4 region of the 18S rDNA gene with PCR and 454 pyrosequencing. In addition, the freshwater diversity of Pavlovophyceae was investigated by lineage-specific PCR-primers and clone library sequencing from another Norwegian lake, Lake Svaersvann. We present new freshwater phylotypes belonging to the classes Prymnesiophyceae and Pavlovophyceae, as well as a distinct group here named HAP-1. This is the first molecular evidence of a freshwater species belonging to the class Pavlovophyceae. The HAP-1 and another recently detected marine group (i.e. HAP-2) are separated from both Pavlovophyceae and Prymnesiophyceae and may constitute new higher order taxonomic lineages. As all obtained freshwater sequences of haptophytes are distantly related to the freshwater species C. parva, the phylogeny demonstrates that haptophytes colonized freshwater on multiple independent occasions. One of these colonizations, which gave rise to HAP-1, took place very early in the history of haptophytes, before the radiation of the Prymnesiophyceae.     

Monophyly of the family Desmoscolecidae (Nematoda,Demoscolecida) and Its Phylogenetic position inferred from 18S rDNA sequences

To infer the monophyletic origin and phylogenetic relationships of the order Desmoscolecida, a unique and puzzling group of mainly free-living marine nematodes, we newly determined nearly complete 18S rDNA sequences for six marine desmoscolecid nematodes belonging to four genera (Desmoscolex, Greeffiella, Tricoma and Paratricoma). Based on the present data and those of 72 nematode species previously reported, the first molecular phylogenetic analysis focusing on Desmoscolecida was done by using neighbor joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) methods. All four resultant trees consistently and strongly supported that the family Desmoscolecidae forms a monophyletic group with very high node confidence values. The monophyletic clade of desmocolecid nematodes was placed as a sister group of the clade including some members of Monhysterida and Araeolaimida, Cyartonema elegans (Cyartonematidae) and Terschellingia longicaudata (Linhomoeidae) in all the analyses. However, the present phylogenetic trees do not show any direct attraction between the families Desmoscolecidae and Cyartonematidae. Within the monophyletic clade of the family Desmoscolecidae in all of the present phylogenetic trees, there were consistently observed two distinct sub-groups which correspond to the subfamilies Desmoscolecinae [Greeffiella sp. + Desmoscolex sp.] and Tricominae [Paratricoma sp. + Tricoma sp].     

Phylogenetic analysis of anostracans (Branchiopoda: Anostraca) inferred from nuclear 18S ribosomal DNA (18S rDNA) sequences

The nuclear small subunit ribosomal DNA (18S rDNA) of 27 anostracans (Branchiopoda: Anostraca) belonging to 14 genera and eight out of nine traditionally recognized families has been sequenced and used for phylogenetic analysis. The 18S rDNA phylogeny shows that the anostracans are monophyletic. The taxa under examination form two clades of subordinal level and eight clades of family level. Two families the Polyartemiidae and Linderiellidae are suppressed and merged with the Chirocephalidae, of which together they form a subfamily. In contrast, the Parartemiinae are removed from the Branchipodidae, raised to family level (Parartemiidae) and cluster as a sister group to the Artemiidae in a clade defined here as the Artemiina (new suborder). A number of morphological traits support this new suborder. The Branchipodidae are separated into two families, the Branchipodidae and Tanymastigidae (new family). The relationship between Dendrocephalus and Thamnocephalus requires further study and needs the addition of Branchinella sequences to decide whether the Thamnocephalidae are monophyletic. Surprisingly, Polyartemiella hazeni and Polyartemia forcipata ("Family" Polyartemiidae), with 17 and 19 thoracic segments and pairs of trunk limb as opposed to all other anostracans with only 11 pairs, do not cluster but are separated by Linderiella santarosae ("Family" Linderiellidae), which has 11 pairs of trunk limbs. All appear to be part of the Chirocephalidae and share one morphological character: double pre-epipodites on at least part of their legs. That Linderiella is part of the Polyartemiinae suggests that multiplication of the number of limbs occurred once, but was lost again in Linderiella. Within Chirocephalidae, we found two further clades, the Eubranchipus-Pristicephalus clade and the Chirocephalus clade. Pristicephalus is reinstated as a genus.     

Interrelationships of Staphyliniform groups inferred from 18S and 28S rDNA sequences, with special emphasis on Hydrophiloidea (Coleoptera, Staphyliniformia)

The series Staphyliniformia is one of the mega‐diverse groups of Coleoptera, but the relationships among the main families are still poorly understood. In this paper we address the interrelationships of staphyliniform groups, with special emphasis on Hydrophiloidea and Hydraenidae, based on partial sequences of the ribosomal genes 18S rDNA and 28S rDNA. Sequence data were analysed with parsimony and Bayesian posterior probabilities, in an attempt to overcome the likely effect of some branches longer than the 95% cumulative probability of the estimated normal distribution of the path lengths of the species. The inter‐family relationships in the trees obtained with both methods were in general poorly supported, although most of the results based on the sequence data are in good agreement with morphological studies. In none of our analyses a close relationship between Hydraenidae and Hydrophiloidea was supported, contrary to the traditional view but in agreement with recent morphological investigations. Hydraenidae form a clade with Ptiliidae and Scydmaenidae in the tree obtained with Bayesian probabilities, but are placed as basal group of Staphyliniformia (with Silphidae as subordinate group) in the parsimony tree. Based on the analysed data with a limited set of outgroups Scarabaeoidea are nested within Staphyliniformia. However, this needs further support. Hydrophiloidea s.str., Sphaeridiinae, Histeroidea (Histeridae + Sphaeritidae), and all staphylinoid families included are confirmed as monophyletic, with the exception of Hydraenidae in the parsimony tree. Spercheidae are not a basal group within Hydrophiloidea, as has been previously suggested, but included in a polytomy with other Hydrophilidae in the Bayesian analyses, or its sistergroup (with the inclusion of Epimetopidae) in the parsimony tree. Helophorus is placed at the base of Hydrophiloidea in the parsimony tree. The monophyly of Hydrophiloidea s.l. (including the histeroid families) and Staphylinoidea could not be confirmed by the analysed data. Some results, such as a placement of Silphidae as subordinate group of Hydraenidae (parsimony tree), or a sistergroup relationship between Ptiliidae and Scydmaenidae, appear unlikely from a morphological point of view.     

Phylogenetic relationships ofPolemoniaceae inferred from 18S ribosomal DNA sequences

Cladistic analyses of chloroplast DNA disagree with current classifications by placingPolemoniaceae near sympetalous families with two staminal whorls, includingFouquieriaceae andDiapensiaceae, rather than near sympetalous families with a single staminal whorl, such asHydrophyllaceae andConvolvulaceae. To explore further the affinities ofPolemoniaceae, we sequenced 18S ribosomal DNA for eight genera ofPolemoniaceae and 31 families representing a broadly definedAsteridae. The distribution of variation in these sequences suggest some sites are hypervariable and multiple hits at these sites have obscured much of the hierarchical structure present in the data. Nevertheless, parsimony, least-squares minimum evolution, and maximum likelihood methods all support a monophyleticPolemoniaceae that is placed nearFouquieriaceae, Diapensiaceae and related ericalean families.     

基于部分18S rDNA, 28S rDNA和COI基因序列的索科线虫亲缘关系

通过PCR扩增获得我国常见昆虫病原索科线虫6属10种18S rDNA、28S rDNA(D3区)和COI基因序列,结合来自GenBank中6属10种索科线虫的18S rDNA同源序列,用邻接法和最大简约法构建系统进化树。结果显示:12属索科线虫分为三大类群,第一大类群是三种罗索属线虫(Romanomermis)先聚在一起,再与两索属(Amphimermis)和蛛索属(Aranimermis)线虫聚为一支;在第二大类群中,六索属(Hexamermis)、卵索属线虫(Ovomermis)和多索属(Agamermis)亲缘关系最近,先聚在一起,再与八腱索属(Octomyomermis)和Thaumamermis线虫聚为一支。第三大类群由索属(Mermis)和异索属(Allomermis)线虫以显著水平的置信度先聚在一起,再与蠓索属(Heleidomermis)和施特克尔霍夫索属(Strelkovimermis)线虫聚为一支。从遗传距离看,基于3个基因的数据集均显示索科线虫属内种间差异明显小于属间差异,武昌罗索线虫(R.wuchangensis)和食蚊罗索线虫(R.culicivorax)同属蚊幼寄生罗索属线虫,其种间的遗传距离最小。