基于线粒体ND2基因的直翅目部分种类分子系统学发育研究

本文的研究目的是通过对直翅目部分种类的线粒体ND2基因进行分析,重建直翅目内部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。基于80个物种ND2基因的研究结果显示直翅目ND2基因存在碱基偏向性A T含量平均为73%,第三位点A T含量79.9%最高,推测这与氨基酸变异有关。直翅目具有单系性,而蝗亚目内部的剑角蝗科、网翅蝗科、槌角蝗科和斑腿蝗科均不是单系群,锥头蝗科和瘤锥蝗科亲缘关系较近,这与Otte分类系统相一致,建议将锥头蝗科和瘤锥蝗科合并为一个科。癞蝗科的分类地位存在争议有待进一步深入的研究。     

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。     

利用线粒体16S rRNA基因全序列分析直翅目主要类群的系统发生关系

为了构建稳健的直翅目主要类群间的系统发生关系并探讨16S rRNA基因序列在构建直翅目昆虫不同分类阶元系统发生关系时的可行性、功效以及性能,文章测定了直翅目4总科9科18种昆虫的16S rRNA基因全序列,联合已知该基因全序列的其他40种昆虫,构建了直翅目主要类群之间的系统发生关系,并分析了16SrRNA基因全序列的系统发生性能和功效。结果表明,直翅目昆虫的16S rRNA基因全长平均为1 310 bp;除生活方式特化的蚤蝼总科和蝼蛄总科的地位无法确定外,直翅目其他主要类群系统发生关系比较稳定;蝗总科下除了斑翅蝗科和槌角蝗科外,剑角蝗科、斑腿蝗科、网翅蝗科都不是单系群,且用不同的方法构建的系统发生树中聚类情况完全一致,各科间遗传距离差异不大,建议将其合为一科;锥头蝗科、瘤锥蝗科和癞蝗科间的遗传距离差异也不大;在构建系统发生树时,16S rRNA基因环区的信息量要比茎区的大;16S rRNA基因可以构建可靠的直翅目属与种水平和目与亚目高级阶元的系统发生关系,但对科和总科阶元缺乏足够的分辨力。     

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。     

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。     

基于线粒体基因Cytb和COI的蝗科中五亚科分子系统发育关系分析（直翅目: 蝗总科）（英文）

本研究基于Cytb 基因和COI基因的部分序列来推断17种蝗虫之间的系统发育关系。这17种蝗虫均采自国内，代表了蝗科(Acrididae)5个亚科：黑蝗亚科(Melanoplinae)、斑腿蝗亚科(Catantopinae)、刺胸蝗亚科(Cyrtacanthacridinae)、斑翅蝗亚科(Oedipodinae)和大足蝗亚科(Gomphocerinae)。采用联合序列方法进行分析，结果显示：Cytb 和COI联合序列长度为1 998 bp，其中A和T总含量为72.13%，G和C总含量为27.87%。联合序列共包含了889个保守位点，1 109个变异位点，在这些变异位点中有838个简约信息位点。系统发生树采用邻接法（NJ）、最大简约法（MP）和最大似然法（ML）进行构建。使用蜢总科的变色乌蜢Erianthus versicolor 和 Erianthus sp. 两个种作为外群。结果表明：大足蝗亚科和斑腿蝗亚科的单系性没有得到支持。斑翅蝗亚科内部各种聚成一个大支，在本研究中该亚科的单系性得到支持，与前人的研究结论相同。大足蝗亚科、斑腿蝗亚科、刺胸蝗亚科和黑蝗亚科这4科关系非常近，可以考虑将其合并为一个亚科。同时，我们发现基于Cytb和COI基因联合序列推断蝗科内各亚科间的系统发生关系并不十分可靠。     

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COⅡ基因序列的斑腿蝗科部分亚科的分子系统学研究

采用PCR产物直接测序法测定了斑腿蝗科10个亚科16属22种的COⅡ基因585 bp的片段, 对序列的碱基组成进行了分析,并评估了数据集的系统发育信号;最后,以癞蝗科的肃南 短鼻蝗作为外群,采用NJ法、MP法、ML法以及贝叶斯推论法构建了系统树,以解决这些物种所代表的亚科之间的系统发育关系。结果表明：22种斑腿蝗科昆虫的COⅡ基因序列碱基组成表现强烈的A+T含量偏向性。对COⅡ基因585 bp序列片段构成的全数据组和根据密码子不同位点划分的密码子第一、第二和第三位点数据组的系统发育信号分析显示,所有数据组都具有一定的系统发育信息。在4种方法得到的合一树中发现： （1）星翅蝗亚科、刺胸蝗亚科、黑背蝗亚科、斑腿蝗亚科的亲缘关系较近;（2）卵翅蝗亚科与稻蝗亚科亲缘关系较近,建议卵翅蝗亚科似乎应归入稻蝗亚科中,板胸蝗亚科与这两个亚科的关系较近;（3）黑蝗亚科和秃蝗亚科似乎应合并为一个亚科;（4）切翅蝗亚科的4个属未聚在一起,表明这些属的区别较大,不是一个单系群;（5）黑蝗亚科和秃蝗亚科关系较近,且与本研究中其他几个亚科的亲缘关系相对较远。研究结果表明COⅡ基因在解决斑腿蝗科的亚科以下属种间的系统发育关系时是一个有效的分子标记。     

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。     

Comparative mitogenome analysis of three species and monophyletic inference of Catantopinae (Orthoptera: Acridoidea)

To enrich the genomic database of Catantopinae (Orthoptera: Acrididae), mitogenomes of three species from different genera, Traulia nigritibialis (15,701 bp), Choroedocus capensis (16,293 bp) and Stenocatantops splendens (15,574 bp), were characterized and compared with those of other grasshoppers in the subfamily. All 13 protein-coding genes (PCGs) were initiated by ATN codons except COI with ACC (C. capensis and S.splendens) and ND6 with TTG (S. splendens). All transfer RNA (tRNA) genes had a typical clover-leaf structure, except tRNA^Ser(AGN) in which the base pairs of the dihydrouridine (DHU) arm were reduced. The phylogenetic relationships were constructed among 22 species from four subfamiles of Acrididae by classical classifications based on two datasets of their mitogenomes using both Bayesian Inference (BI) and Maximum Likelihood (ML). The phylogenetic analysis confirmed the monophyly of the three other subfamilies, but did not provided support of the monophyly of Catantopinae.     

The complete mitochondrial genome of the small yellow croaker and partitioned Bayesian analysis of Sciaenidae fish phylogeny

To understand the phylogenetic position of Larimichthys polyactis within the family Sciaenidae and the phylogeny of this family, the organization of the mitochondrial genome of small yellow croaker was determined herein. The complete, 16,470 bp long, mitochondrial genome contains 37 mitochondrial genes (13 protein-coding, 2 ribosomal RNA and 22 transfer RNA genes), as well as a control region (CR), as in other bony fishes. Comparative analysis of initiation/termination codon usage in mitochondrial protein-coding genes of Percoidei species, indicated that COI in Sciaenidae entails an ATG/AGA codon usage different from other Percoidei fishes, where absence of a typical conserved domain or motif in the control regions is common. Partitioned Bayesian analysis of 618 bp of COI sequences data were used to infer the phylogenetic relationships within the family Sciaenidae. An improvement in harmonic mean -lnL was observed when specific models and parameter estimates were assumed for partitions of the total data. The phylogenetic analyses did not support the monophyly of Otolithes, Argyrosomus, and Argyrosominae. L. polyactis was found to be most closely related to Collichthys niveatus, whereby, according to molecular systematics studies, the relationships within the subfamily Pseudosciaenidae should be reconsidered.     

基于16S rDNA序列探讨中国剑角蝗科的单系性及其六属的系统发育关系

在中国学者夏凯龄的分类系统中,剑角蝗科Acrididae一直被看作是单系群,包含6个亚科。但是,近年来的研究对其单系性争议较大。为探讨其单系性和剑角蝗属等6属的系统发育关系,我们测定了剑角蝗科14种蝗虫的16S rRNA基因部分序列,并从GenBank中下载了1种蝗虫的同源序列。以蚱科的2个种作外群,用NJ、MP及ML法重建系统发生树。由三棵分子系统树中得出的系统发生关系与中国的分类系统差别较大,都不支持剑角蝗科是单系群,但与国外Kevan的系统相一致,提示我们国内的分类系统亟待修改和完善。长腹蝗亚科与斑腿蝗科的亲缘关系要近于与剑角蝗科的其他种类的关系。另外,尽管所测的红足剑角蝗和上海剑角蝗的16S rDNA的片段序列完全相同,我们仍不能断定二者是同一个物种[动物学报52 (2) : 302 -308 , 2006]。     

A new perspective on phylogeny and evolution of tetraodontiform fishes (Pisces: Acanthopterygii) based on whole mitochondrial genome sequences: Basal ecological diversification?

Background  

The order Tetraodontiformes consists of approximately 429 species of fishes in nine families. Members of the order exhibit striking morphological diversity and radiated into various habitats such as freshwater, brackish and coastal waters, open seas, and deep waters along continental shelves and slopes. Despite extensive studies based on both morphology and molecules, there has been no clear resolution except for monophyly of each family and sister-group relationships of Diodontidae + Tetraodontidae and Balistidae + Monacanthidae. To address phylogenetic questions of tetraodontiform fishes, we used whole mitochondrial genome (mitogenome) sequences from 27 selected species (data for 11 species were newly determined during this study) that fully represent all families and subfamilies of Tetraodontiformes (except for Hollardinae of the Triacanthodidae). Partitioned maximum likelihood (ML) and Bayesian analyses were performed on two data sets comprising concatenated nucleotide sequences from 13 protein-coding genes (all positions included; third codon positions converted into purine [R] and pyrimidine [Y]), 22 transfer RNA and two ribosomal RNA genes (total positions = 15,084).     

Resolving deep phylogenetic relationships in salamanders: analyses of mitochondrial and nuclear genomic data

Phylogenetic relationships among salamander families illustrate analytical challenges inherent to inferring phylogenies in which terminal branches are temporally very long relative to internal branches. We present new mitochondrial DNA sequences, approximately 2,100 base pairs from the genes encoding ND1, ND2, COI, and the intervening tRNA genes for 34 species representing all 10 salamander families, to examine these relationships. Parsimony analysis of these mtDNA sequences supports monophyly of all families except Proteidae, but yields a tree largely unresolved with respect to interfamilial relationships and the phylogenetic positions of the proteid genera Necturus and Proteus. In contrast, Bayesian and maximum-likelihood analyses of the mtDNA data produce a topology concordant with phylogenetic results from nuclear-encoded rRNA sequences, and they statistically reject monophyly of the internally fertilizing salamanders, suborder Salamandroidea. Phylogenetic simulations based on our mitochondrial DNA sequences reveal that Bayesian analyses outperform parsimony in reconstructing short branches located deep in the phylogenetic history of a taxon. However, phylogenetic conflicts between our results and a recent analysis of nuclear RAG-1 gene sequences suggest that statistical rejection of a monophyletic Salamandroidea by Bayesian analyses of our mitochondrial genomic data is probably erroneous. Bayesian and likelihood-based analyses may overestimate phylogenetic precision when estimating short branches located deep in a phylogeny from data showing substitutional saturation; an analysis of nucleotide substitutions indicates that these methods may be overly sensitive to a relatively small number of sites that show substitutions judged uncommon by the favored evolutionary model.     

Sequences from 14 mitochondrial genes provide a well-supported phylogeny of the Charadriiform birds congruent with the nuclear RAG-1 tree

Because of the difficulties of constructing a robust phylogeny for Charadriiform birds using morphological characters, recent studies have turned to DNA sequences to resolve the systematic uncertainties of family-level relationships in this group. However, trees constructed using nuclear genes or the mitochondrial Cytochrome b gene suggest deep-level relationships of shorebirds that differ from previous studies based on morphology or DNA-DNA hybridization distances. To test phylogenetic hypotheses based on nuclear genes (RAG-1, myoglobin intron-2) and single mitochondrial genes (Cytochrome b), approximately 13,000 bp of mitochondrial sequence was collected for one exemplar species of 17 families of Charadriiformes plus potential outgroups. Maximum likelihood and Bayesian analyses show that trees constructed from long mitochondrial sequences are congruent with the nuclear gene topologies [Chardrii (Lari, Scolopaci)]. Unlike short mitochondrial sequences (such as Cytochrome b alone), longer sequences yield a well-supported phylogeny for shorebirds across various taxonomic levels. Examination of substitution patterns among mitochondrial genes reveals specific genes (especially ND5, ND4, ND2, and COI) that are better suited for phylogenetic analyses among shorebird families because of their relatively homogeneous nucleotide composition among lineages, slower accumulation of substitutions at third codon positions, and phylogenetic utility in both closely and distantly related lineages. For systematic studies of birds in which family and generic levels are examined simultaneously, we recommend the use of both nuclear and mitochondrial sequences as the best strategy to recover relationships that most likely reflect the phylogenetic history of these lineages.