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。     

基于线粒体COI基因全序列的直翅目部分类群系统发育关系分析

该研究基于直翅目56种昆虫的COI基因全序列构建了该目部分类群间的系统发育关系,同时也分析了COI基因编码的氨基酸序列构建直翅目系统发育关系的可靠性。将COI序列按照密码子一、二、三位点划分,分别计算PBS(partioned Bremer support)值,评估蛋白质编码基因密码子不同位点的系统发生信号强度。分析结果支持螽亚目和蝗亚目的单系性;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,科间的遗传距离在0.107~0.153之间变化,与其他科相比遗传距离较小,符合将这5科合并为一科(即蝗科)的分类系统,瘤锥蝗科和锥头蝗科归为锥头蝗总科,癞蝗科单独成为一科,这也与Otte(1997)系统的划分一致。根据PBS值的大小推断密码子第三、第一位点对系统树分支的贡献比第二位点大,并且较长的序列含有较多的信息位点。研究也证实将各物种COI基因之间的遗传距离作为直翅目划分科级阶元的工具是可行的。     

直翅目昆虫线粒体基因组特征及系统发育研究

目前GenBank数据库共收录167种直翅目昆虫全线粒体基因组序列,涉及蝗亚目9个总科22个科99个物种,螽亚目7个总科12个科68个物种。在此基础上,该文分析了直翅目昆虫线粒体基因组的基本特征,概述了线粒体全基因组在直翅目昆虫系统发育研究上的应用;同时基于线粒体全基因组序列重建了直翅目昆虫的系统发育关系。主要结果如下:(1)直翅目昆虫存在8种线粒体基因组排列类型,其中trnK-trnD重排现象仅发生在蝗总科中,trnN-trnS-trnE重排现象仅发生在蟋蟀总科中,trnM-trnI-(-trnQ)重排现象仅发生在拟叶蟲亚科中;(2)直翅目昆虫全线粒体基因组的碱基组成具有明显的AT偏向性;(3)不同的蛋白质编码基因在直翅目昆虫中的进化速率不同;(4)支持直翅目以及螽亚目和蝗亚目的单系性;(5)不支持沙螽总科单系性;(6)支持蝗亚目各总科阶元的单系性,且各总科间的系统发育关系为:(蚤蝼总科+(蚱总科+(?蜢总科+(蜢总科+(长角蝗总科+(牛蝗总科+叶翅蝗总科)+(锥头蝗总科+蝗总科))))))。     

基于线粒体ND2基因的直翅目部分种类分子系统发育分析

测定了39种直翅目昆虫线粒体ND2基因全长序列,联合GenBank中41种直翅目昆虫的ND2基因序列,探讨ND2基因在解决直翅目系统发育分析上的功效,为建立直翅目的主要类群之间稳定的系统发育关系提供更多的数据。研究结果表明,直翅目昆虫的ND2基因序列全长为996～1 029 bp,平均长度为1 020 bp,A+T含量平均为73%。用贝叶斯法(Bayesian,BI)、最简约法(maximum parsimony,MP)和最大似然法(maximum likelihood,ML)构建系统树,SH检验显示,RAxML法构建的ML树似然值最大,与PAUP*的ML法构建的ML树差异显著,而与贝叶斯树和简约树没有明显差异。所有系统树都显示直翅目为单系群;而蝗亚目的剑角蝗科、网翅蝗科、槌角蝗科和斑腿蝗科均不是单系群,锥头蝗科与瘤锥蝗科亲缘关系较近,这与Otte分类系统一致。螽亚目基本由两大分支构成,一支是蝼蛄总科和蟋蟀总科聚集而成,且具有很高的置信度;另一大分支由螽斯总科独自构成。     

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。     

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。     

基于线粒体ND2基因的中国斑翅蝗科部分种类分子系统学研究（直翅目：蝗总科）

本文的目的是通过对斑翅蝗科部分种类的线粒体ND2基因进行分析,重建斑翅蝗科昆虫的系统发育关系,并探讨分子系统发育关系和传统分类结果的异同。扩增并测定了我国斑翅蝗科10属16种蝗虫的线粒体ND2全基因1 023 bp的序列,对序列的碱基组成、转换颠换、系统发育信号等进行了分析。并基于ND2全基因序列数据,分别采用邻接法（NJ）、最简约法（MP）、最大似然法（ML）和贝叶斯法重建了10属16种蝗虫的系统发育关系。结果表明：斑翅蝗科蝗虫ND2全基因A+T含量平均为74.6%;痂蝗亚科和异痂蝗亚科没能得到区分,建议合并为一个亚科;而斑翅蝗亚科和飞蝗亚科的分类地位还存在争议。     

直翅目昆虫线粒体基因组研究进展

本文总结了本实验室对40余种直翅目昆虫的线粒体基因组序列的研究方法和主要结果.直翅目线粒体基因组研究中最重要的发现包括：（1）在直翅目昆虫线粒体基因组中发现了3种基因排列次序.蝗亚目除蜢总科外都具有DK排列.蜢总科的变色乌蜢为KD 排列,与蝗亚目其他总科不同,而与螽亚目昆虫的排序方式相同.已测出的螽亚目大多数昆虫的KD 排列顺序与典型节肢动物的完全相同,但在黄脸油葫芦Teleogryllus emma发生了tRNA^Glu,tRNA^Ser和tRNA^Asn的倒置;（2）在疑钩额螽Ruspolia dubia中发现了一种到目前为止具有最短控制区（70 bp）的线粒体基因组;（3）采用多种方法分析了昆虫A+T富集区存在的调控序列和二级结构特征,获得了昆虫A+T富集区保守序列的一致结构.采用Z曲线分析蝗虫的A+T富集区,表明也存在与原核生物复制起点类似的信号;（4）构建了30种蝗虫12S rRNA和16S rRNA的二级结构.在昆虫线粒体基因组非编码链中发现了一些类tRNA结构和tRNA异构体;（5）构建了基于线粒体基因组数据的直翅目昆虫主要亚科以上分类单元之间的系统发育关系.     

应用16S rDNA序列探讨斑腿蝗科的单系性及其亚科的分类地位

本文测定了斑腿蝗科10亚科20种蝗虫和其他蝗科3种蝗虫的线粒体16S rDNA部分序列,并从GenBank中下载了15种蝗亚目昆虫的16S rRNA基因相应序列片段。比对后的序列长度是397 bp,其中有196个变异位点,157个简约信息位点,A+T平均含量为71.7%,C+G平均含量为28.3%。以序列差异比值为横坐标,以碱基转换数和颠换数为纵坐标作散点图,结果表明颠换多于转换,且随着差异程度的增加,转换明显出现了饱和。以蚱总科的日本蚱Tetrix japonica和卡尖顶蚱Teredorus carmichaeli作外群,用ME、等权MP、加权MP及贝叶斯法重建系统发生树。分子系统树表明,斑腿蝗科并非是一单系群,该科的切翅蝗亚科与稻蝗亚科也均不是一单系群;卵翅蝗、伪稻蝗和稻蝗三者有很近的亲缘关系;支持将黑蝗亚科和秃蝗亚科合为一个亚科——秃蝗亚科;现行的稻蝗亚科并非一单系群,而是一多系群。分子系统学研究结果和传统的基于形态特征的斑腿蝗科的分类体系有很大的不同。     

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。     

Evaluation of ribosomal RNA gene restriction patterns for the classification of Bacillus species and related genera

AIMS: To identify Bacillus species and related genera by fingerprinting based on ribosomal RNA gene restriction patterns; to compare ribosomal RNA gene restriction patterns-based phylogenetic trees with trees based on 16S rRNA gene sequences; to evaluate the usefulness of ribosomal RNA gene restriction patterns as a taxonomic tool for the classification of Bacillus species and related genera. METHODS AND RESULTS: Seventy-eight bacterial species which include 42 Bacillus species, 31 species from five newly created Bacillus-related genera, and five species from five phenotypically related genera were tested. A total of 77 distinct 16S rRNA gene hybridization banding patterns were obtained. The dendrogram resulting from UPGMA analysis showed three distinct main genetic clusters at the 75% banding pattern similarity. A total of 77 distinct 23S and 5S rRNA genes hybridization banding patterns were obtained, and the dendrogram showed four distinct genetic clusters at the 75% banding pattern similarity. A third dendrogram was constructed using a combination of the data from the 16S rRNA gene fingerprinting and the 23S and 5S rRNA genes fingerprinting. It revealed three distinct main phylogenetic clusters at the 75% banding pattern similarity. CONCLUSIONS: The Bacillus species along with the species from related genera were identified successfully and differentiated by ribosomal RNA gene restriction patterns, and most were distributed with no apparent order in various clusters on each of the three dendrograms. SIGNIFICANCE AND IMPACT OF THE STUDY: Our data indicate that ribosomal RNA gene restriction patterns can be used to reconstruct the phylogeny of the Bacillus species and derived-genera that approximates, but does not duplicate, phylogenies based on 16S rRNA gene sequences.     

Phylogenetic systematics and biogeography of the poison frogs: evidence from mitochondrial DNA sequences

Regions of the mitochondrial genome were sequenced and analysed in representative species of poison frogs, in order to investigate phylogenetic relationships within the family Dendrobatidae. Mitochondrial DNA (mfDNA) fragments from three gene regions; cytochrome b, 16S ribosomal RNA (rRNA), and 12S rRNA, provided 1198 base pairs of DNA sequence and 589 informative sites. Phylogenetic analysis using parsimony was used to infer the evolutionary relationships among the species in the survey. Our analysis supported previous partitions of species into the genera Epipedobates, Phyllobates and Dendrobates , with two exceptions; Epipedobates (Allobates) femoralis was placed outside the clade containing the other toxic dendrobatids, and Minyobates minutus was placed within the genus Dendrobates. Genetic distances estimated between all pairs of taxa using the Kimura 2-parameter model indicated substantial genetic divergence between species, particularly those found in Amazonia. Time of divergence estimates were highly variable depending on gene region, but even the lowest estimates were inconsistent with the Pleistocene Refugia hypothesis.     

线粒体COⅠ和16S rRNA片段确定近江蛏和缢蛏属的分类地位

对5种双壳类软体动物(近江蛏Sinonovacula rivularis、缢蛏Sinonovacula constricta、小刀蛏Cultellus attenuatus、尖刀蛏Cultellus scalprum和大竹蛏Solen grandis)的线粒体基因COⅠ和16S rRNA部分序列进行测序和分析, 并结合GenBank中其他竹蛏超科和樱蛤超科物种COⅠ和16S rRNA片段, 计算种间遗传距离, 构建系统发育树, 探讨近江蛏及缢蛏属的分类地位。结果表明, 5个物种COⅠ和16S rRNA片段A+T含量均远高于G+C含量, 近江蛏与缢蛏之间的碱基序列差异和遗传距离均已达到种间差异水平, 确定近江蛏为缢蛏属的一个种。分别构建COⅠ(砂海螂为外群)和16S rRNA片段(密鳞牡蛎为外群)的Neighbor-Joining系统树, 两者的拓扑结构都明确显示, 缢蛏属为灯塔蛤科一个属, 灯塔蛤科录属于竹蛏超科, 而不录属于樱蛤超科。       

Phylogeny and molecular identification of vibrios on the basis of multilocus sequence analysis

We analyzed the usefulness of rpoA, recA, and pyrH gene sequences for the identification of vibrios. We sequenced fragments of these loci from a collection of 208 representative strains, including 192 well-documented Vibrionaceae strains and 16 presumptive Vibrio isolates associated with coral bleaching. In order to determine the intraspecies variation among the three loci, we included several representative strains per species. The phylogenetic trees constructed with the different genetic loci were roughly in agreement with former polyphasic taxonomic studies, including the 16S rRNA-based phylogeny of vibrios. The families Vibrionaceae, Photobacteriaceae, Enterovibrionaceae, and Salinivibrionaceae were all differentiated on the basis of each genetic locus. Each species clearly formed separated clusters with at least 98, 94, and 94% rpoA, recA, and pyrH gene sequence similarity, respectively. The genus Vibrio was heterogeneous and polyphyletic, with Vibrio fischeri, V. logei, and V. wodanis grouping closer to the Photobacterium genus. V. halioticoli-, V. harveyi-, V. splendidus-, and V. tubiashii-related species formed groups within the genus Vibrio. Overall, the three genetic loci were more discriminatory among species than were 16S rRNA sequences. In some cases, e.g., within the V. splendidus and V. tubiashii group, rpoA gene sequences were slightly less discriminatory than recA and pyrH sequences. In these cases, the combination of several loci will yield the most robust identification. We can conclude that strains of the same species will have at least 98, 94, and 94% rpoA, recA, and pyrH gene sequence similarity, respectively.     

The evolution of the diatoms (Bacillariophyta). I. Origin of the group and assessment of the monophyly of its major divisions

The diatoms are one of the best characterised algal groups. Despite this, little is known of the evolution of the group from the earliest cell to the myriad of taxa known today. Relationships among taxa at the family or generic level have been recognised in some diatoms. However, relationships at higher taxonomic levels are poorly understood and have often been strongly influenced by the first appearances of key taxa in the fossil record. An independent assessment of relationships among the diatoms at these higher taxonomic levels has been made using rRNA sequence data to infer phylogenetic relationships. In this paper we present an analysis of 18S rRNA data from several chosen centric, araphid and raphid pennate taxa. The phylogenetic inferences from these 18S rRNA sequences are supported by evidence from the fossil record and evidence from ontogenetic data. Ribosomal RNA data indicate that both the centric and araphid pennate lineages may not be monophyletic.     

贵州荔波发现弱须洞鳅

洞鳅属（Troglonectes Zhang, Zhao & Tang 2016）鱼类为中国特有的小型洞穴淡水鱼类,主要分布在贵州和广西喀斯特地区的地下河流中。2018至2019年在贵州省荔波县境内进行洞穴生物多样性调查时采集到4号洞鳅属标本,经过形态比较,与弱须洞鳅（Troglonectes barbatus）相似;基于线粒体16S rRNA和Cyt b重建的系统发育树及遗传距离分析显示,4号洞鳅属标本与来自模式产地的弱须洞鳅高度支持聚为一支;利用Kimura双参数模型计算基于16S rRNA和Cyt b的遗传距离,这些标本与弱须洞鳅之间的遗传距离分别为0.4%和0.2%,小于洞鳅属物种之间的遗传距离（16S rRNA遗传距离为2.4%,Cyt b遗传距离为6.1%）。本次研究使用16S rRNA和Cyt b分子标记研究洞鳅属部分物种的系统发育关系和遗传距离。综合形态和分子系统发育分析结果,确定采集自贵州省荔波县小七孔景区的4号标本为隶属于鲤形目条鳅科洞鳅属的弱须洞鳅,系贵州省洞穴鱼类新记录种。     

A molecular phylogenetic investigation of Opisthonecta and related genera (Ciliophora, Peritrichia, Sessilida)

The gene encoding 18S small subunit ribosomal RNA (ssu rRNA) was sequenced in the sessiline peritrichs Opisthonecta minima and Opisthonecta matiensis, whose free-swimming, paedomorphic trophonts resemble telotrochs. Using these new sequences, phylogenetic trees were constructed with four different methods to test a previously published association between Opisthonecta henneguyi and members of the families Vorticellidae and Astylozoidae. All trees had similar topologies, with O. minima, O. henneguyi, Vorticella microstoma, and Astylozoon enriquesi forming a well-supported, certainly monophyletic clade. On the basis of genetic evidence, genera of the families Opisthonectidae and Astylozoidae are assigned to the family Vorticellidae, which already includes some species with free-swimming morphotypes. The ssu rRNA sequence of O. matiensis places it in the family Epistylididae; its taxonomic revision will be left to another group of authors. A close association of Ophrydium versatile with members of the family Vorticellidae was confirmed, casting doubt on the validity of the family Ophrydiidae. Epistylis galea, Campanella umbellaria, and Opercularia microdiscum are confirmed as comprising an extremely distinct, monophyletic, but morphologically heterogeneous clade that is basal to other clades of sessiline peritrichs.     

Towards a genome-based taxonomy for prokaryotes

The ranks higher than the species in the prokaryotic taxonomy are primarily designated based on phylogenetic analysis of the 16S rRNA gene sequences, but no definite standards exist for the absolute relatedness (measured by 16S rRNA or other means) between the ranks. Accordingly, it remains unknown how comparable the ranks are between different organisms. To gain insights into this question, we studied the relationship between shared gene content and genetic relatedness for 175 fully sequenced strains, using as a robust measure of relatedness the average amino acid identity (AAI) of the shared genes. Our results reveal that adjacent ranks (e.g., phylum versus class) frequently show extensive overlap in terms of genetic and gene content relatedness of the grouped organisms, and hence, the current system is of limited predictive power in this respect. The overlap between nonadjacent ranks (e.g., phylum versus family) is generally limited and attributable to clear inconsistencies of the taxonomy. In addition to providing means for standardizing taxonomy, our AAI-based approach provides a means to evaluate the robustness of alternative genetic markers for phylogenetic purposes. For instance, the 23S rRNA gene was found to be as good a marker as the 16S rRNA gene, while several of the widely distributed protein-coding genes, such as the RNA polymerase and gyrase subunits, show a strong phylogenetic signal, albeit less strong than the rRNA genes (0.78 > R2 > 0.69 for the protein-coding genes versus R2 = 0.84 for the rRNA genes). The AAI approach outlined here could contribute significantly to a genome-based taxonomy for all microbial organisms.