基于12S rRNA和16S rRNA基因序列探讨中国蚤蝇科部分属间的系统发育关系

基于线粒体12S rRNA和16S rRNA基因序列联合分析,采用最大简约法、最大似然法和贝叶斯法分别构建了中国蚤蝇科14属的系统发育树.结果表明:联合分析序列总长度为819 bp,其中可变位点277个,简约信息位点200个;A+T平均含量为77.7%,具A、T偏倚性.系统发育分析显:中国蚤蝇科为单系发生,分为蚤蝇亚科和裂蚤蝇亚科两个单系群.蚤蝇亚科内脉蚤蝇属、锥蚤蝇属和刺蚤蝇属亲缘关系较近,栅蚤蝇属与栓蚤蝇属亲缘关系较近;裂蚤蝇亚科中虼蚤蝇属与裂蚤蝇属互为姐妹群,寡蚤蝇属与伐蚤蝇属互为姐妹群.     

六种灵猫科动物的分子系统关系研究

对六种灵猫科物种线粒体12 S rRNA基因及其中四种的Cytb基因部分序列进行了测定,并从Gen-Bank获得斑林狸(Prionodon pardicolor)、熊狸(Arctictis binturong)的Cytb基因同源序列。两基因整合序列比对后长755 bp,12 S rRNA基因序列中有70个变异位点,31个简约信息位点,在Cytb基因序列中,共有120个位点呈现变异,60个简约信息位点,Cytb基因的碱基变异百分比高于12 S rRNA基因的碱基变异百分比。使用邻接法(NJ)、最大似然法(ML)重建的分子系统树显示:斑林狸从灵猫亚科中分离出来,支持灵猫亚科的多系起源,而且斑林狸可能是中国起源最早且最特化的灵猫科动物。另外,同属于灵猫亚科的大灵猫(Viverra zibe-tha)、小灵猫(Viverricula indica)聚为一支,同属于棕榈狸亚科的果子狸(Viverricula indica)、熊狸聚为姐妹群,这些与传统形态学分类观点一致。     

基于线粒体ND1和16S rRNA基因序列探讨中国蝴蝶12科的系统发育关系(鳞翅目: 双孔次亚目: 蝶类)

对中国12科共32种代表蝶类的ND1基因和16S rRNA 基因进行了序列测定（包括新测30种ND1基因和9种16S rRNA基因）和比较分析, 同时采用邻接法、最大似然法和贝叶斯法构建了12科蝶类的系统发育树, 探讨了其高级分类群的系统发育关系。序列分析的结果显示: 经比对处理后的两个基因总长度为869 bp, 其中保守位点373个, 可变位点496个, 简约信息位点375个; A+T的平均含量为80.2％, 明显高于C+G的平均含量19.8％。分子系统树表明: 蛱蝶科不是单系群; 珍蝶类、斑蝶类和喙蝶类位于蛱蝶科内; 粉蝶科和凤蝶科具有共同祖先。据此建议: 绢蝶科应归入凤蝶科; 蚬蝶科归入灰蝶科; 珍蝶类、斑蝶类和喙蝶类作为蛱蝶科中的亚科, 眼蝶类从蛱蝶科中分离出来独立成科。另外, 环蝶类的系统分类地位还有待于进一步研究。     

基于线粒体DNA序列探讨斑头鱼分类地位

测定了斑头鱼Agrammus agrammus和大泷六线鱼Hexagrammos otakii的线粒体COⅠ、Cyt b和16S rRNA基因的部分序列,结合从GenBank中获得的六线鱼属3种的同源序列,以单鳍多线鱼Pleurogrammus monopterygius为外群,运用邻接法(NJ)、最大简约法(MP)和贝叶斯法(BI)构建了分子系统树。同时联合了3个基因片段序列,运用贝叶斯联合模型综合探讨了六线鱼类的系统发育关系。结果显示:除16S rRNA基因外,其余2个基因片段以及联合模型所构建的系统树拓扑结构完全一致,即斑头鱼与大泷六线鱼亲缘关系最近,应归为六线鱼属,拉丁学名应为Hexagrammos agrammus。Cyt b基因片段序列分析结果显示,斑头鱼和大泷六线鱼分歧时间约为175万年。结合形态学研究资料,支持将斑头鱼归为六线鱼属的观点,斑头鱼和大泷六线鱼亲缘关系最近,属于六线鱼科中分化较晚的种类。     

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。     

基于线粒体16S rDNA序列探讨蛱蝶科(鳞翅目, 蝶亚目)主要分类群的系统发生关系

本文测定了蛱蝶科7亚科27种蛱蝶和斑蝶科2种蝴蝶的线粒体16S rRNA基因部分序列,并从GenBank中下载了6种蛱蝶的同源序列。以斑蝶科的幻紫斑蝶和绢斑蝶作外群,通过遗传分析软件对这些序列进行了比较分析,用邻接法和贝叶斯法重建了蛱蝶科的系统发育树,探讨了蛱蝶科主要类群间的系统发育关系。序列分析的结果显示:经比对处理后获得494bp长度序列,其中有可变位点206个,简约信息位点145个;A T平均含量78.4%,C G平均含量为21.6%,具A、T偏倚性。分子系统树显示:蛱蝶亚科并非单系群;蛱蝶族中眼蛱蝶属应移入斑蛱蝶族;闪蛱蝶和蛱蝶亚科与蛱蝶亚科具有较近的系统关系;结果支持豹蛱蝶和釉蛱蝶合为一亚科即釉蛱蝶亚科;支持将秀蛱蝶和蛱蝶亚科从线蛱蝶亚科中分离出来。     

蓟马科部分种类mtDNA-COⅠ序列变异及系统发育分析

【目的】蓟马科是一类重要的经济昆虫,目前一些种类的传统形态系统分类还存在争议,本研究采用分子标记对蓟马科的系统发育进行探讨。【方法】对蓟马科9属27种蓟马的mtDNA-COⅠ基因的变异进行分析,采用邻接法、最大似然法和贝叶斯法构建系统发育树。【结果】研究表明在比对的432 bp的序列中,有207个保守位点,222个变异位点,3个缺失位点,序列A+T含量为68.3%,具有A、T偏倚性;蓟马种间的序列分歧度变化在15.6~40.0之间。【结论】系统进化树支持针蓟马亚科为蓟马科最为原始的类群;棍蓟马亚科与绢蓟马亚科、蓟马亚科形成姐妹群;绢蓟马亚科与蓟马亚科有较近的亲缘关系,支持Mound四亚科的分类系统。     

基于细胞色素b序列的鲹科分子系统发育

测定了中国鲹科8属9种鱼的细胞色素b基因的全序列(1141bp),结合来自GenBank中分布于美国、安哥拉、希腊以及巴拿马的鲹科4属14种鱼的相应同源序列生成供系统发育分析的序列矩阵,用最大简约法和邻接法构建分子系统树。结果显示:(1)支持科下设四个亚科(鲹亚科,亚科,鲳鲹亚科,鰆鲹科)阶元的分类系统;(2)亚科属下不宜设亚属分类阶元;(3)及达副叶鲹与丽叶鲹亲缘关系较近,应同属于副叶鲹属;(4)我国传统的鱼类检索系统将狮鼻鲳鲹误鉴定为卵形鲳鲹,建议予以修正。     

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。     

中国黄粉蝶亚科六属间基于COⅡ和EF-1α基因部分序列的系统发育关系（鳞翅目：粉蝶科）

为了探讨中国黄粉蝶亚科属间的系统发育关系,我们对其中6属9种的细胞色素氧化酶Ⅱ（COⅡ）的部分序列和延伸因子基因（EF-1α）部分序列进行了分析。分别采用最大简约法（maximum parsimony, MP）、最大似然法（maximum likelihood, ML）和贝叶斯推论法（bayesian inference, BI）构建黄粉蝶亚科分子系统树。结果表明：在测得的COⅡ基因的648 bp序列和EF-1α基因的504 bp序列中,有261个变异位点,151个简约信息位点,黄粉蝶亚科内各属COⅡ基因A+T含量（77.3%）均明显偏高。系统发育分析显示黄粉蝶属为亚科中较为原始的类群,分化较早,豆粉蝶属和迁粉蝶属亲缘关系较近,但钩粉蝶属与豆粉蝶属、迁粉蝶属之间的亲缘关系还不能确定。本研究结果和传统的基于形态学的黄粉蝶亚科的分类体系有所不同,最显著的分歧是本研究支持内群中分化最早的属应为黄粉蝶属,而不是豆粉蝶属和迁粉蝶属。     

Complete nucleotide sequences and gene organization of mitochondrial genome of Bufo gargarizans

The complete mitochondrial genome of Bufo gargarizans was sequenced using overlapping polymerase chain reaction (PCR) amplicons (GenBank Accession No. DQ275350). The genome is 17,277 base pairs in length, containing 13 protein-coding genes (ATP6, ATP8, COI-III, ND1-6, ND4L, Cyt b), 2 ribosomal RNAs (12S rRNA and 16S rRNA), 22 transfer RNAs and a putative control region. We analyzed the sequence using bioinformatics methods comparing the obtained mtDNA sequence with other toads and frogs. Based on the concatenated nucleotide sequences of protein-coding genes, we constructed a phylogenetic tree with maximum likelihood (ML) and maximum parsimony (MP) methods and discussed the phylogenetic relationships among 11 species of Anura.     

Molecular phylogeny of Eastern Pacific porcelain crabs, genera Petrolisthes and Pachycheles, based on the mtDNA 16S rDNA sequence: phylogeographic and systematic implications

Porcelain crabs, genera Petrolisthes and Pachycheles, are diverse and abundant members of the eastern Pacific near-shore decapod crustacean community. Morphology-based taxonomic analyses of these crabs have determined groupings of affiliated species, but phylogenetic relationships remain unknown. We used sequence data from the mitochondrial 16S rRNA gene of 46 species of eastern Pacific porcelain crabs to perform phylogenetic analyses by distance and parsimony methods. Our results are used to compare the taxonomic significance of morphological and molecular characters, to examine sequence divergence rates of crab 16S rRNA genes, and to analyze the phylogeographic history of these crabs. Our phylogenetic trees indicate that the genus Petrolisthes is divided into two main clades, reflecting morphological features. One clade contains primarily tropical species, and the other contains species from throughout the eastern Pacific, as well as species in the genera Allopetrolisthes and Liopetrolisthes. Phylogenetic trees of Pachycheles suggest an antitropical distribution; north and south temperate species form one clade and tropical species form a second clade. Sequence divergence rates of the 16S rRNA gene from three pairs of geminate species can be used to date divergence times, and we discuss porcelain crab phylogeographic patterns in relation to paleogeographic events.     

Molecular phylogeny and biogeography of caecilians from Southeast Asia (Amphibia, Gymnophiona, Ichthyophiidae), with special reference to high cryptic species diversity in Sundaland

We investigated the phylogenetic relationships and estimated the history of species diversification and character evolution in two ichthyophiid genera: Caudacaecilia and Ichthyophis. We estimated the phylogenetic relationships of 67 samples from 33 localities in Southeast Asia from 3840-bp sequences of the mitochondrial 12S rRNA, 16S rRNA, and cyt b genes using Bayesian inference, maximum likelihood, and maximum parsimony methods. The Southeast Asian samples formed a well-supported clade differentiated from a South Asian sample. The Southeast Asian clade was divided into two subclades, one containing samples from South China, Indochina, Malay Peninsula, and Java. The other consisted of samples from Borneo and the Philippines. Neither Caudacaecilia nor Ichthyophis was monophyletic, nor did samples with or without light stripes lateral to the body form clades. We found several distinct sympatric lineages and undescribed species, especially from Sundaland.     

Phylogenetic relationships among four species of Mullidae (Perciformes) inferred from DNA sequences of mitochondrial cytochrome b and 16S rRNA genes

DNA sequence comparisons of two mitochondrial DNA genes were used to infer phylogenetic relationships among four species of mullids. Approximately 238 bp of the mitochondrial 16S ribosomal RNA (rRNA) and 261 bp of the cytochrome b (cytb) genes were sequenced from representatives of three mullid genera (Mullus, Upeneus, Pseudopeneus), present in the Mediterranean Sea. Trees were constructed using three methods: maximum likelihood (ML), neighbor joining (NJ) and parsimony (MP). The results of the analyses of these data together with published data of the same mtDNA segments of two other perciform species (Sparus aurata, Perca fluviatilis), support the previous taxonomic classification of the three genera examined, as well as the classification of the two red mullet species in the same genus.     

鲤鱼野生群体线粒体部分基因片段序列比较

通过对线粒体16S rRNA基因、D-loop区和Cyt b基因部分片段测定,探讨我国鲤鱼C.carpio野生群体和云南大头鲤C.pellegrini的遗传变异和亲缘关系.数据和并后用于分析的序列共1 492 bp,变异位点221个,含简约信息位点217个,其中新疆群体用于分析的序列长度为1 478 bp.以云南大头鲤为外群,推测鲤鱼群体问的系统发育关系和分化时间,MP法和NJ法得到相似的系统树,新疆群体与其他群体的差异较大,遗传距离较远,单独聚为一支,其他群体间相似性较高聚在一起,新疆群体与其他群体间的分化时间约为2.42×106～2.45×106年前.     

Phylogenetic and systematic study of Korean <Emphasis Type="Italic">Orius</Emphasis> species (Heteroptera: Anthocoridae) on the basis of molecular and morphological data

A phylogenetic and systematic study of Orius species (Heteroptera: Anthocoridae) from Korea has been conducted using both morphological and molecular characters. Thirty morphological character states were coded for 10 strains of 9 species. Five molecular markers, partial cytochrome c oxidase I (COI), cytochrome b (CytB), 16S rRNA (16S), 18S rRNA (18S), and 28S rRNA (28S), from mitochondrial and nuclear genes, were tested. Phylogenetic analyses based on molecular data were conducted by minimum evolution, maximum parsimony, maximum likelihood, and Bayesian phylogenetic (BP) analyses. Analysis of morphological data was performed using the parsimony programs NONA, and the combined dataset of morphological and molecular data was analyzed using BP analyses. The results of this study indicate that use of COI and CytB enabled relatively effective identification of species, whereas the sequences of 16S, 18S and 28S did not enable identification of closely related species such as Orius minutus and O. strigicollis. We discuss the usefulness of the five molecular markers for determining phylogenetic relationships and identifying the species.     

尼罗鳄线粒体基因组全序列分析及鳄类系统发生关系的探讨

大多数脊椎动物的线粒体基因组（约16—18kb）的组成是相对较稳定的,但在不同类群中,线粒体基因组在基因结构和基因排列方式等方面均显示了极大的多样性,这种多样性可能反映了真核细胞不同的进化路线（Saccone et al．,1999）。就目前的研究而言,线粒体基因组是惟一一个能够从基因组水平上来分析动物系统发生的分子标记,可以从线粒体基因组序列信息、基因组成及基因排列方式等进行多方位的分子进化研究,因而线粒体基因组全序列将成为动物分子系统发生最有力的证据（Saccone et al．,1999）。     

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.     

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。