基于细胞色素b基因片段序列研究中国近海石斑鱼类系统进化关系

石斑鱼的分类一直是鱼类系统分类学中的一个难题. 为探讨中国近海石斑鱼类系统进化关系, 通过PCR扩增获得了石斑鱼亚科(Epinephelinae)6属28个种类的线粒体细胞色素b基因片段序列. 采用多个生物软件对序列变异和碱基组成进行分析, 计算了Kimura 2-parameter遗传距离、转换/颠换比等遗传信息指数, 并结合GenBank上石斑鱼属的同源序列, 以东洋鲈(Niphon spinosus)、真鲷(Pagrus major)等为外群构建NJ, MP, ML和ME系统树. 从分子系统学的角度并结合形态学特征得出了如下结果: (i) 鳃棘鲈属(Plectropomus)最先分化, 是石斑鱼亚科中原始的类群; (ii) 侧牙鲈属(Variola)与九棘鲈属(Cephalopholis)具有较近的亲缘关系; (iii) 九棘鲈属是一个单系群, 并且较石斑鱼属(Epinephelus)原始; (iv) 宽额鲈(Promicrops lanceolatus)和驼背鲈(Cromileptes altivelis)可以归入石斑鱼属; (v) 石斑鱼属内部存在两个平行进化的姐妹分支.     

从细胞色素b部分序列探讨石斑鱼属的分子系统发育关系

石斑鱼的分类在学术界尚存在很多争议。本文采用PCR技术,测定了分布于中国的点带石斑鱼(Epinepheluscoioiaes)、青石斑鱼(E.awoara)、六带石斑鱼(E.sexfasciatus)、褐石斑鱼(E.brunneus),长棘石斑鱼(E.longispinis),吻斑石斑鱼(E.spilotoceps),巨石斑鱼(E.tauvina)以及石斑鱼亚科侧牙鲈属的侧牙鲈(Variola louti)的线粒体细胞色素b基因402bp的序列,结合GenBank提供的7种中国无记录的石斑鱼:青铜石斑鱼(E.aeneus)、海丰石斑鱼(E.haifensis)、犬牙石斑鱼(E.caninus)、东大西洋石斑鱼(E.marginatus)、白斑石斑鱼(E.multinotatus)、德氏石斑鱼(E.drummondhayi)、淡点石斑鱼(E.labriformis),把这14种石斑鱼作为内群,对他们的序列组成和结构特点进行了分析;并以同为科(Serranidae)、石斑鱼亚科(Epinephelinae)的侧牙鲈属(Variola)的侧牙鲈作外群,分别用MP法、NJ法对内、外群构建了分子系统树,结果表明:(1)14种石斑鱼402bp的mtDNA Cytb部分序列的碱基组成上,A T的含量为53.6%高于G C含量(46.4%),序列中转换颠换比为4.78,没有突变饱和;(2)青石斑鱼与六带石斑鱼、点带石斑鱼与巨石斑鱼、长棘石斑鱼与吻斑石斑鱼分别聚在一起,与形态分类结果一致;(3)系统树中,大西洋与太平洋种类各枝交替汇合,表明石斑鱼的Cytb序列有严格的保守性,也可能是协同进化的结果;(4)揭示在良种选配或遗传管理时,避免居于同枝的石斑鱼混交,将大西洋种类与太平洋种类杂交可能是遗传改良的一种途径。     

云南曲靖下泥盆统西山村组四营鱼属(Siyingia)一新种(英文)

主要采用形态学与比较解剖学的方法,对采自云南曲靖地区下泥盆统西山村组中的1件盔甲鱼类标本进行了详细的形态学研究,建立了多鳃鱼类四营鱼属1新种:宽棘四营鱼(Siyingia perlatuspinosa sp.nov.),并据此修订了四营鱼属的特征。在此基础上,应用分支系统学对多鳃鱼类属一级的系统发育关系进行了重新分析与探讨,确定了四营鱼在多鳃鱼类中的系统发育位置。系统发育分析结果显示,四营鱼(Siyingia)与多鳃鱼(Polybranchiaspis)亲缘关系最近,二者形成了一个单系类群,与宽甲鱼(Laxaspis)+坝鱼(Damaspis)组成的单系类群互为姊妹群。宽棘四营鱼的发现不仅拓宽了四营鱼在华南的时空分布范围,而且丰富了多鳃鱼类的多样性,并为多鳃鱼类的深入研究提供了可靠的化石新证据。     

基于叶绿体基因组数据的芸香科属间系统发育初步分析

为探究花椒属种水平系统进化关系以及为新品种培育研究奠定理论基础，该研究以芸香科物种的叶片为材料，采用改良CTAB法提取叶绿体DNA,利用BGISEQ-500平台进行叶绿体基因组测序，并对叶绿体基因组进行组装、注释，联合NCBI数据库数据，共获得芸香科19属49个物种的全叶绿体基因组序列。构建了芸香科属间系统进化关系。结果表明，(1)基于叶绿体基因组序列矩阵(总长196 641 bp),ML和BI 2种方法得到的系统发育树的拓扑结够基本一致，系统发育树各分支具有较强的支持率，叶绿体基因组数据可以解决芸香科属间的系统发育关系。(2)芸香科为单系类群，并进一步形成两大分支，其中柑橘亚科为单系，与芸香亚科内的芸香属聚为分支I,分支Ⅱ由芸香亚科和飞龙掌血亚科组成，两亚科均不是单系，其中飞龙掌血亚科的香肉果属，茵芋属与芸香亚科的白鲜属，臭常山属是最早分化出来的类群，其次是蜜茱萸属和山油柑属；黄檗属和吴茱萸属与花椒属类群形成姊妹群，飞龙掌血属的物种飞龙掌血嵌套于花椒属分支中，支持飞龙掌血物种并入花椒属的处理。     

基于髭鲷属鱼类Cyt b基因全序列探讨髭鲷属在鲈总科的分类地位

为探讨髭鲷属鱼类的分类地位,克隆了两种髭鲷属鱼类(横带髭鲷和斜带髭鲷)的线粒体Cyt 6基因全长序列,并利用线粒体Cyt b基因序列分析了鲈总科6个科29种的分子系统进化关系.结果表明:髭鲷属与石鲈科的其他5个属的遗传距离超过了科问水平的遗传距离,存在较远的遗传分化.29种鲈总科鱼类分成了两大类群,石鲈科的矶鲈属、仿石鲈属、厚唇椒鲷属、异孔石鲈属和石鲈属的物种聚为一起形成石鲈科的一个独立分支,与亲缘关系较近的鲷科、梅鲷科和笛鲷科形成一个类群;而隶属于石鲈科的髭鲷属与石鲷科及雀鲷科形成另一个类群.髭鲷属与其他石鲈科鱼类的亲缘关系已经超过了科问的遗传分化水平,而在遗传距离及系统进化分析上髭鲷属仍然隶属于鲈总科.本研究支持将髭鲷属提升为髭鲷科的观点.     

基于ITS序列探讨杜鹃属的亚属和组间系统关系

首次报道了 15种杜鹃属 (Rhododendron)植物、1种杜香属 (Ledum)植物和Cassiopefastigiata的内转录间隔区(ITS) (包括 5 .8S)序列。加上从GenBank下载的 13种杜鹃属植物和Bajiariaracemosa的ITS序列 ,以C .fastigiata和B .racemosa为外类群 ,用最大简约法对杜鹃属的亚属和组间的系统关系进行了分析。结果表明 :1)杜鹃属是一个单系类群 ,叶状苞亚属为杜鹃属的基部类群 ;2 )杜香属确应归并到杜鹃属中 ,且与有鳞杜鹃亚属有较近的亲缘关系 ;3)有鳞杜鹃亚属和杜香构成一个单系分支 ,该分支是其余无鳞杜鹃花的姐妹群 ;4 )由无鳞杜鹃花组成的一个分支的内部支持率较低 ,其中常绿杜鹃亚属和映山红亚属均为内部支持率很高的单系类群 ,而羊踯躅亚属和马银花亚属均为多系类群 ;5 )在马银花亚属中 ,长蕊杜鹃组和马银花组均分别得到强烈支持 ,马银花组与异蕊杜鹃亚属可能构成姐妹群关系 ,异蕊杜鹃亚属和马银花组组成的一个分支可能与映山红亚属构成姐妹群关系。     

基于ITS序列探讨杜鹃属的亚属和组间系统关系

首次报道了15种杜鹃属(Rhododendron)植物、1种杜香属(Ledum)植物和Cassiope fastigiata的内转录间隔区(ITS) (包括5.8S)序列.加上从GenBank下载的13种杜鹃属植物和Bajiaria racemosa的ITS序列,以C. fastigiata和B. racemosa为外类群,用最大简约法对杜鹃属的亚属和组间的系统关系进行了分析.结果表明: 1)杜鹃属是一个单系类群,叶状苞亚属为杜鹃属的基部类群; 2)杜香属确应归并到杜鹃属中,且与有鳞杜鹃亚属有较近的亲缘关系; 3)有鳞杜鹃亚属和杜香构成一个单系分支,该分支是其余无鳞杜鹃花的姐妹群; 4)由无鳞杜鹃花组成的一个分支的内部支持率较低,其中常绿杜鹃亚属和映山红亚属均为内部支持率很高的单系类群,而羊踯躅亚属和马银花亚属均为多系类群; 5)在马银花亚属中,长蕊杜鹃组和马银花组均分别得到强烈支持,马银花组与异蕊杜鹃亚属可能构成姐妹群关系,异蕊杜鹃亚属和马银花组组成的一个分支可能与映山红亚属构成姐妹群关系.     

10种棘豆属植物的trnL-F序列及其分子系统学研究

选择内蒙古27个样地采集的10种棘豆属植物54个单株,提取样品的基因组DNA,对其叶绿体trnL-F序列进行扩增、测序,所得序列利用ClustalX软件进行对位排列,并用MEGA5.0软件采用最大似然法构建系统发育树,以探讨棘豆属的种间关系与系统进化.结果显示:(1)10种棘豆属trnL-F的变异位点54个,信息位点46个,种间碱基差异百分率为1.9％,GC含量变化范围在30.69％～31.50％之间.(2)棘豆属与黄芪属各为一支,自展支持率达99％,支持棘豆属植物为单系起源.(3)系统树中小花棘豆的样本自成一支,为相对独立进化;多叶棘豆、砂珍棘豆和黄毛棘豆的样本相互混杂,表明亲缘关系很近,从而支持《内蒙古植物志》将三者归入真棘豆亚属轮叶棘豆组的观点.(4)刺叶柄棘豆的样本不同样地形成2个分支,对其亚属水平上的分类需进一步探讨.(5)缘毛棘豆与阴山棘豆的样本聚成一支,支持将二者归入矮生棘豆组.研究表明,trnL-F序列可为棘豆属下种间系统发育关系研究提供分子证据.     

凤蝶亚科(凤蝶科,鳞翅目)16S rRNA基因的分子系统发生分析

对15种凤蝶亚科蝶类线粒体16S rRNA基因部分序列进行了测定,并结合GenBank中其它相关类群的序列,采用邻接法(NJ)、最大简约法(MP)、最大似然法(ML)和贝叶斯法构建凤蝶亚科的分子系统树,探讨该亚科各类群间的系统发生关系.结果表明,燕凤蝶族构成凤蝶亚科蝶类系统树基部的一个独立分支;燕凤蝶族和裳凤蝶族为单系发生,且裳凤蝶族聚在凤蝶族内部;喙凤蝶族的单系性尚不能确定.综合分子系统学、形态学及寄主植物等相关证据,推测斑凤蝶类为凤蝶族中早期分化的一支;较之裳凤蝶类,斑凤蝶类可能更早从二者最近的共同祖先中分化出来.     

西太平洋沿海石斑鱼属鱼类DNA条形码及分子系统进化研究

研究测定了分布于西太平洋沿海的35种石斑鱼属鱼类共142个个体线粒体基因COⅠ及核基因TMO-4C4标记序列, 基于最大似然法与贝叶斯法构建分析了石斑鱼类分子系统进化关系。同时, 探讨了COⅠ基因作为DNA条形码在石斑鱼属鱼类物种鉴定中的有效性问题。结果显示: 35种石斑鱼属鱼类COⅠ同源序列为636 bp, 编码212个氨基酸, TMO-4C4同源序列为486 bp, 编码162个氨基酸, 在COⅠ基因中, 种间遗传距离在0.030—0.202, 平均遗传距离为0.143, 物种间遗传距离均大于Hebert 推荐的物种鉴定最小种间遗传距离0.020(2%)。种内遗传距离0.000—0.008, 平均遗传距离为0.003, 种间平均遗传距离是种内平均遗传距离的48倍, 显著大于种内平均遗传距离, 表明COⅠ基因可作为石斑鱼属物种鉴定的有效条形码基因。基于COⅠ及TMO-4C4构建的系统进化树上, 35种石斑鱼主要形成2个主要类群, 类群Ⅰ由细点石斑鱼(Epinephelus cyanopodus)和蓝棕石斑鱼(Epinephelus multinotatus)等22种石斑鱼聚成, 类群Ⅱ由吊桥石斑鱼(Epinephelus morrhua)和小点石斑鱼(Epinephelus epistictus)等13种石斑鱼组成。部分存在同种异名争议的种类如云纹石斑鱼(Epinephelus moara)/褐石斑鱼(Epinephelus bruneus)和斜带石斑鱼(Epinephelus coioides)/马拉巴石斑鱼(Epinephelus malabaricus)经COⅠ及TMO-4C4序列差异及进化分析, 均存在较大的遗传分化。结果支持近期的分类研究, 云纹石斑鱼/褐石斑鱼和斜带石斑鱼/马拉巴石斑鱼均为独立的物种, 并非同种异名的分类。     

Molecular phylogenetic relationships of China Seas groupers based on cytochrome b gene fragment sequences

The classification and evolutionary relationships are important issues in the study of the groupers. Cytochrome b gene fragment of twenty-eight grouper species within six genera of subfamily Epinephelinae was amplified using PCR techniques and the sequences were analyzed to derive the phylogenetic relationships of the groupers from the China Seas. Genetic information indexes, including Kimura-2 parameter genetic distance and Ts/Tv ratios, were generated by using a variety of biology softwares. With Niphon spinosus, Pagrus major and Pagrus auriga as the designated outgroups, phylogenetic trees, which invoke additional homologous sequences of other Epinephelus fishes from GenBank, were constructed based on the neighbor-joining (NJ), maximum-parsimony (MP), maximum-likelihood (ML) and minimum-evolution (ME) methods. Several conclusions were drawn from the DNA sequences analysis: (1) genus Plectropomus, which was early diverged, is the most primitive group in the subfamily Epinephelinae; (2) genus Variola is more closely related to genus Cephalopolis than the other four genera; (3) genus Cephalopolis is a monophyletic group and more primitive than genus Epinephelus; (4) Promicrops lanceolatus and Cromileptes altivelis should be included in genus Epinephelus; (5) there exist two sister groups in genus Epinephelus.     

Molecular phylogeography of western Mediterranean dusky grouper Epinephelus marginatus

Intraspecific sequence variation in a portion of the gene coding for cytochrome b in the dusky grouper (Epinephelus marginatus Lowe 1834), an endangered fish species in various regions of the Mediterranean sea, was examined in 29 individuals from the western Mediterranean sea. Sixty-four phylogenetically informative nucleotide positions were present in a 353-base pair cytochrome b sequence, amplified using the polymerase chain reaction. Statistical analysis of the sequence data using a variety of tree-building algorithms separated the taxa into one group of dusky groupers corresponding to some of the Algerian individuals and another regrouped set of fishes originating in France, Tunisia and the remaining Algerian specimens. Although, on the basis of their morphology, E. marginatus are now considered as a single species, our results suggest that a subgroup of the Algerian dusky grouper constitutes a cryptic (undescribed) species. These results suggest that morphological and genetic evolution may be uncoupled in dusky grouper, resulting in morphological similarity between species despite extensive genetic divergence. In addition, we cannot rule out the possibility of gene introgression with other species of grouper. A more in depth phylogenetic analysis (i.e. between and within the different Epinephelus species) would likely affect many conservation management decisions about this assemblage of groupers.     

Molecular phylogenetic relationships of China Seas groupers based on cytochrome <Emphasis Type="Italic">b</Emphasis> gene fragment sequences

The classification and evolutionary relationships are important issues in the study of the groupers. Cytochrome b gene fragment of twenty-eight grouper species within six genera of subfamily Epinephelinae was amplified using PCR techniques and the sequences were analyzed to derive the phylogenetic relationships of the groupers from the China Seas. Genetic information indexes, including Kimura-2 parameter genetic distance and T _S/T _V ratios, were generated by using a variety of biology softwares. With Niphon spinosus, Pagrus major and Pagrus auriga as the designated outgroups, phylogenetic trees, which invoke additional homologous sequences of other Epinephelus fishes from GenBank, were constructed based on the neighbor-joining (NJ), maximum-parsimony (MP), maximum-likelihood (ML) and minimum-evolution (ME) methods. Several conclusions were drawn from the DNA sequences analysis: (1) genus Plectropomus, which was early diverged, is the most primitive group in the subfamily Epinephelinae; (2) genus Variola is more closely related to genus Cephalopolis than the other four genera; (3) genus Cephalopolis is a monophyletic group and more primitive than genus Epinephelus; (4) Promicrops lanceolatus and Cromileptes altivelis should be included in genus Epinephelus; (5) there exist two sister groups in genus Epinephelus.     

Molecular phylogenetic relationships of China Seas groupers based on cytochrome b gene fragment sequences

The classification and evolutionary relationships are important issues in the study of the groupers. Cytochrome b gene fragment of twenty-eight grouper species within six genera of subfamily Epinephelinae was amplified using PCR techniques and the sequences were analyzed to derive the phylogenetic relationships of the groupers from the China Seas. Genetic information indexes, including Kimura-2 parameter genetic distance and T _S/T _V ratios, were generated by using a variety of biology softwares. With Niphon spinosus, Pagrus major and Pagrus auriga as the designated outgroups, phylogenetic trees, which invoke additional homologous sequences of other Epinephelus fishes from GenBank, were constructed based on the neighbor-joining (NJ), maximum-parsimony (MP), maximum-likelihood (ML) and minimum-evolution (ME) methods. Several conclusions were drawn from the DNA sequences analysis: (1) genus Plectropomus, which was early diverged, is the most primitive group in the subfamily Epinephelinae; (2) genus Variola is more closely related to genus Cephalopolis than the other four genera; (3) genus Cephalopolis is a monophyletic group and more primitive than genus Epinephelus; (4) Promicrops lanceolatus and Cromileptes altivelis should be included in genus Epinephelus; (5) there exist two sister groups in genus Epinephelus. These authors contributed equally to this work.     

On the status of the Serranid fish genus Epinephelus: evidence for paraphyly based upon 16S rDNA sequence

Historically, attempts to elucidate evolutionary relationships among members of the genus Epinephelus (Teleostei: Serranidae), commonly known as groupers, have been hindered by the overwhelming number of species (98, sensu stricto), a pan global distribution, and the lack of morphological specializations traditionally used in ichthyological classification. To date, no comprehensive phylogenetic study, morphological or molecular, to evaluate the monophyly of this genus has been presented. In this study, previous hypotheses regarding the relationships among the American grouper species and the allied genera were evaluated by examination of mitochondrial DNA sequences of the 16S ribosomal DNA region. A 590-bp region of the 16S rDNA gene was amplified using a universal primer pair for 42 serranid species, including members of the genera Epinephelus, Mycteroperca, and Paranthias from the New World and selected Indo-Pacific congeners. Maximum-parsimony criteria and neighbor-joining analysis dispute the monophyly of the American Epinephelus species as previously hypothesized. The data support the monophyly of Cephalopholis only with the inclusion of the morphologically distinct Paranthias and the monophyly of Mycteroperca with the inclusion of the Indo-Pacific Anyperodon leucogrammicus.     

Assessment of genetic diversity and phylogenetic relationship among grouper species Epinephelus spp. from the Saudi waters of the Arabian Gulf

Understanding of fish genetic characterization plays a vital role in the conservation and utilization of fish genetic resources of grouper species. The present study was carried out to assess the genetic diversity and phylogenetic relationships in five grouper species, Epinephelus spp. from eastern Saudi Arabian coast using two molecular marker systems, inter simple sequence repeat (ISSR) and microsatellite (SSR) markers. In total, 219 individuals grouper specimens (Epinephelus tauvina, E. coioides, E. bleekeri, E. malabaricus, and E. areolatus) were genotyped with 10 ISSR and 11 SSR selected primers. The ISSR produced 94 DNA fragments, of which 44 were polymorphic with an average of 2.13 fragment per primer. While SSR primers generated 107 alleles, all of them were polymorphic with an average 9.72 per primer. ISSR and SSR techniques demonstrated a high level of gene diversity and genetic distances illustrated by UPGMA dendrograms among the grouper species. The results proved that the SSR markers were highly informative and efficient in detecting genetic variability and relationships of the Epinephelus spp.     

Isolation and characterization of polymorphic microsatellites from red coral grouper (Plectropomus maculatus)

The red coral grouper, Plectropomus maculatus, is a high value marine food fish species. We isolated the first set of 10 polymorphic microsatellites and examined their polymorphism in two related species: the Malabar grouper Epinephelus malabaricus and the brown‐marbled grouper Epinephelus fuscoguttatus. The average allele number of these 10 microsatellite DNA loci is 9.1/locus with a range of four to 17, whereas the expected heterozygosity ranged from 0.18 to 0.94, averaging 0.76. Five of the 10 markers amplified polymorphic and specific products in E. malabaricus, whereas only four were amplified in E. fuscoguttatus. These microsatellites could be applicable to captive breeding and to the studies on genetic diversity and population structure of grouper wild stocks.     

9种石斑鱼遗传多样性和系统发生关系的微卫星分析

利用实验室克隆的13个青石斑鱼微卫星分子标记, 对中国南海海域9种石斑鱼(青石斑鱼、蜂巢石斑鱼、鲑点石斑鱼、黑边石斑鱼、鞍带石斑鱼、赤点石斑鱼、七带石斑鱼、斜带石斑鱼和棕点石斑鱼)进行了遗传多样性和系统发生关系的分析。研究结果显示, 13个微卫星标记共检测到了84个等位基因, 9种石斑鱼中的平均等位基因数、平均多态信息含量(PIC)、平均观测杂合度(Ho)、平均期望杂合度(He)和平均Hardy-Weinberg遗传偏离指数(D)分别在2.69~5.38、0.1976~0.4267、0.4615~0.6239、0.3510~0.4754和0.1097~0.2836之间变动, 说明9种石斑鱼的遗传多样性都处于中等水平。用NJ法进行聚类分析的结果将9种石斑鱼分为3个支系：斜带石斑鱼、棕点石斑鱼和鞍带石斑鱼为第1支; 青石斑鱼、赤点石斑鱼和七带石斑鱼为第2支系; 蜂巢石斑鱼、黑边石斑鱼和鲑点石斑鱼为第3支系, 该支系与第2支系的关系较近。本研究支持将宽额鲈(鞍带石斑鱼)归入石斑鱼属。