基于16S rDNA部分序列探讨中国近海30种石斑鱼类的分子系统进化关系

石斑鱼因其种类繁多、分布广泛及缺乏显著的形体特征,使其系统分类的研究颇为困难。为探讨中国近海石斑鱼类的系统进化关系,通过PCR扩增获得了石斑鱼亚科(Epinephelinae)6属30个种类的线粒体16SrDNA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Kimura2parameter遗传距离、转换/颠换比等遗传信息指数,并结合GenBank石斑鱼属的同源序列,以多纹长尾(Pronotogrammusmultifasciatus)和皮氏叫姑鱼(Johniusbelengerii)为外群构建NJ、MP和ML系统树。根据所得分子依据并结合形态学特征,推论如下:1)在本研究的30种石斑鱼中,鳃棘鲈属(Plectropomus)最先分化,并呈明显单系性;九棘鲈属(Cephalopholis)是一个单系群,并且较石斑鱼属(Epinephelus)原始;侧牙鲈属(Variola)的进化地位介于鳃棘鲈属与九棘鲈属之间;2)宽额鲈(Promicropslanceolatus)可以归入石斑鱼属,而驼背鲈(Cromileptesaltivelis)也与石斑鱼属有很近的亲缘关系,甚至可能是石斑鱼属内的特化类群;3)石斑鱼属内部存在两个平行进化的姐妹分支,分支内部的种类组成与地理分布无关,暗示了石斑鱼属早期的分化模式。     

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.     

鲹科鱼类线粒体DNA控制区结构及系统发育关系

采用PCR技术获得了9种鲹科鱼类的线粒体DNA控制区全序列,并结合从GenBank中下载的3种鲹科鱼类的相应序列采用ClustalW排序后,对控制区结构进行分析,识别了其终止序列区、中央保守区和保守序列区3个区域,指出了终止相关序列的主体是TACAT与其反向互补序列ATGTA以及一系列保守序列(CSB-F、CSB-E、CSB-D和CSB-1、CSB-2、CSB-3),并给出了它们的一般形式,同时在康氏似鲹控制区的5′和3′两端发现重复序列。以尖吻鲈作为外类群,应用邻接法构建的分子系统树表明:鲹科鱼类分为鲹亚科、鰤亚科、鲳鲹亚科和鰆鲹亚科4个亚科,各自形成单系群;鲹亚科与鰤亚科形成姐妹群,鲳鲹亚科再与他们聚在一起,鰆鲹亚科处于鲹科鱼类的基部,与前面3个亚科聚在一起。     

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。     

鲹科鱼类线粒体DNA控制区结构及系统发育关系

采用PCR技术获得了9种鲹科鱼类的线粒体DNA控制区全序列,并结合从GenBank中下载的3种鲹科鱼类的相应序列采用Clustal W排序后,对控制区结构进行分析,识别了其终止序列区、中央保守区和保守序列区3个区域,指出了终止相关序列的主体是TACAT与其反向互补序列ATGTA以及一系列保守序列（CSB-F、CSB-E、CSB-D和CSB-1、CSB-2、CSB-3）,并给出了它们的一般形式,同时在康氏似鲹控制区的5′和3′两端发现重复序列。以尖吻鲈作为外类群,应用邻接法构建的分子系统树表明：鲹科鱼类分为鲹亚科、鰤亚科、鲳鲹亚科和鰆鲹亚科4个亚科,各自形成单系群;鲹亚科与鰤亚科形成姐妹群,鲳鲹亚科再与他们聚在一起,鰆鲹亚科处于鲹科鱼类的基部,与前面3个亚科聚在一起。     

鼬科动物线粒体DNA控制区结构分析

利用PCR技术获得紫貂(Martes zibellina)和黄喉貂(Martes flavigula)线粒体DNA控制区全序列,并结合从GenBank中下载的9种鼬科动物相应序列,用ClustalX排序后对控制区结构进行分析,识别出延长终止序列区、中央区和保守序列区3个区域,指出了一个终止相关序列ETAS1及8个保守序列(CSB-F、E、D、C、B、1、2和3),并给出了序列通式,在CSB1和CSB2之间发现不同形式的短重复序列.此外,以狼为外类群,应用邻接法构建鼬科线粒体控制区全序列的系统进化树,结果表明:臭鼬亚科最先从鼬科中分化出来,随后剩余类群分为两大支系,即貂属种类与貂熊聚为一支,并与獾亚科的狗獾形成姐妹群;另一支为水獭亚科的物种与鼬属的林鼬形成姐妹群,再与虎鼬聚在一起,狗獾与貂属的紫貂亲缘关系最近,水獭亚科与鼬属亲缘关系最近.     

缘蝽亚科和巨缘蝽亚科部分种类细胞色素b基因序列及系统进化研究的探讨(半翅目:缘蝽科)

以线粒体细胞色素b(Cytb)基因作为分子标记,首次对缘蝽亚科和巨缘蝽亚科9种昆虫进行序列测定,获得Cytb基因412bp序列片段,该片段中碱基T、C、A、G的平均含量分别为34.0%、11.6%、34.5%和19.9%,A T平均含量为68.5%,明显高于G C含量(31.5%)。密码子第3位点的A T含量高达79.8%,属种间序列变异大,有188个核苷酸位点发生变异,碱基替换多发生于第3位点。以筛豆龟蝽为外群构建系统发育树,表明黑缘蝽属与缘蝽亚科其它属关系较远,同缘蝽属与巨缘蝽亚科关系较近,结合形态特征与序列变异情况,建议将黑缘蝽属和同缘蝽属从缘蝽亚科划出,同缘蝽归属于巨缘蝽亚科,并将黑缘蝽属提升为亚科。     

基于线粒体Cyt b,16S rDNA和核28S rDNA的中国斑腿蝗科(直翅目,蝗总科)九亚科间的系统发育关系研究

基于线粒体Cytb、16S rDNA和核28S rDNA的部分序列的联合数据集,重建了中国斑腿蝗科9亚科26种蝗虫和癞蝗科笨蝗(外群)间的系统发育关系。结果显示:1)除黑蝗亚科、秃蝗亚科和切翅蝗亚科外,其余6亚科的单系性都得到支持;2)黑蝗亚科似乎应当与秃蝗亚科合并为一个亚科,且与其他几个亚科亲缘关系相对较远;3)凸额蝗属应该由切翅蝗亚科中独立出来;4)卵翅蝗亚科和稻蝗亚科是姐妹群;5)星翅蝗亚科、黑背蝗亚科、斑腿蝗亚科、刺胸蝗亚科及切翅蝗亚科中的凸额蝗属间的关系较近。     

中国南方海域4种石斑鱼的遗传多样性及分子系统发生关系的分析

对中国南方海域的青石斑鱼(Epinephelus awoara)、赤点石斑鱼(E.akaara)、橙点石斑鱼(E.bleekeri)及蜂巢石斑鱼(E.merra)进行了遗传多样性和分子系统发生关系的分析。对9个微卫星DNA标记的基因型测定结果进行计算,发现这4个地理分布重叠且形态相似的石斑鱼均具有较丰富的遗传多样性,其平均等位基因数、平均多态信息含量(PIC)、平均观测杂合度(Ho)及平均期望杂合度(He)的取值范围分别为(8.22±5.02)～(18.67±9.38)、(0.56±0.21)～(0.83±0.13)、(0.62±0.03)～(0.85±0.02)和(0.60±0.07)～(0.86±0.04)。经哈迪-温伯格平衡(HWE)检验,除橙点石斑鱼外,其他3种鱼的微卫星DNA位点都基本符合平衡。利用微卫星DNA标记和线粒体细胞色素b基因对这4种鱼重建的分子系统树均显示,青石斑鱼与赤点石斑鱼的亲缘关系较近。以微卫星DNA标记对所研究石斑鱼的全部个体进行贝叶斯聚类分析的结果表明,4个鱼物种之间的分化关系明确。     

Molecular phylogenetic relationship of Eplnephelus based on sequences of mtDNA Cty b

The mtDNA Cyt b gene was sequenced partially for Variola louti of Serranidae,Epinephelinae and seven endemic species of groupers-Epinephelus awoara,E.brunneus,E.coioides,E.longispinis,E.sexfasciatus,E.spilotoceps and E.tauvina in China.The seven endemic species and other seven foreign species of groupers--E,aeneus,E.caninus,E.drummondhayi,E,haifensis,E.labriformis,E.marginatus and E.multinotatus from the GenBank were combined and analysed as ingroup,while Variola louti was used as outgroup.We compared the 420 bp sequences of Cyt b among the 15 species and constructed two types of molecular phylogenetic trees with maximum parsimony method (MP)and neighbor-joining method (NJ) respectively.The results were as follows:(1) As to the base composition of mtDNA Cyt b sequence (402 bp) of 14 species of Epinepkelus,the content of (A + T) was 53.6%,higher than that of (G + C) (46.4%).The transition/transversion ratio was 4.78 with no mutation saturation.(2) The duster relationships between E.awoara and E.sexfasciatus,E.coioides and E.tauvina,E.longispinis and E.spilotoceps were consistent with phenotypes in taxonomy.(3) In the phylogenetic tree,the species in the Atlantic Ocean were associated closely with those in the Pacific Ocean,which suggested that the Cyt b sequences of Epinephelus were highly conserved.This may be attributed to the coordinate evolution.(4) In well-bred mating or heredity management,mating Epinephelus of the same branch should be avoided.It is likely to be an effective way to mate the species of the Atlantic Ocean with those of the Pacific Ocean to improve the inheritance species.     

Molecular phylogenetic relationship of Epinephelus based on sequences of mtDNA Cty b

The mtDNA Cyt b gene was sequenced partially for Variola louti of Serranidae, Epinephelinae and seven endemic species of groupers—Epinephelus awoara, E. brunneus, E. coioides, E. longispinis, E. sexfasciatus, E. spilotoceps and E. tauvina in China. The seven endemic species and other seven foreign species of groupers—E. aeneus, E. caninus, E. drummondhayi, E. haifensis, E. labriformis, E. marginatus and E. multinotatus from the GenBank were combined and analysed as ingroup, while Variola louti was used as outgroup. We compared the 420 bp sequences of Cyt b among the 15 species and constructed two types of molecular phylogenetic trees with maximum parsimony method (MP) and neighbor-joining method (NJ) respectively. The results were as follows: (1) As to the base composition of mtDNA Cyt b sequence (402 bp) of 14 species of Epinephelus, the content of (A + T) was 53.6%, higher than that of (G + C) (46.4%). The transition/transversion ratio was 4.78 with no mutation saturation. (2) The cluster relationships between E. awoara and E. sexfasciatus, E. coioides and E. tauvina, E. longispinis and E. spilotoceps were consistent with phenotypes in taxonomy. (3) In the phylogenetic tree, the species in the Atlantic Ocean were associated closely with those in the Pacific Ocean, which suggested that the Cyt b sequences of Epinephelus were highly conserved. This may be attributed to the coordinate evolution. (4) In wel1-bred mating or heredity management, mating Epinephelus of the same branch should be avoided. It is likely to be an effective way to mate the species of the Atlantic Ocean with those of the Pacific Ocean to improve the inheritance species.     

Molecular phylogenetic relationship of Epinephelus based on sequences of mtDNA Cty b

The mtDNA Cyt b gene was sequenced partially for Variola louti of Serranidae, Epinephelinae and seven endemic species of groupers—Epinephelus awoara, E. brunneus, E. coioides, E. longispinis, E. sexfasciatus, E. spilotoceps and E. tauvina in China. The seven endemic species and other seven foreign species of groupers—E. aeneus, E. caninus, E. drummondhayi, E. haifensis, E. labriformis, E. marginatus and E. multinotatus from the GenBank were combined and analysed as ingroup, while Variola louti was used as outgroup. We compared the 420 bp sequences of Cyt b among the 15 species and constructed two types of molecular phylogenetic trees with maximum parsimony method (MP) and neighbor-joining method (NJ) respectively. The results were as follows: (1) As to the base composition of mtDNA Cyt b sequence (402 bp) of 14 species of Epinephelus, the content of (A + T) was 53.6%, higher than that of (G + C) (46.4%). The transition/transversion ratio was 4.78 with no mutation saturation. (2) The cluster relationships between E. awoara and E. sexfasciatus, E. coioides and E. tauvina, E. longispinis and E. spilotoceps were consistent with phenotypes in taxonomy. (3) In the phylogenetic tree, the species in the Atlantic Ocean were associated closely with those in the Pacific Ocean, which suggested that the Cyt b sequences of Epinephelus were highly conserved. This may be attributed to the coordinate evolution. (4) In wel1-bred mating or heredity management, mating Epinephelus of the same branch should be avoided. It is likely to be an effective way to mate the species of the Atlantic Ocean with those of the Pacific Ocean to improve the inheritance species. __________ Translated from Acta Hydrobiologica Sinica, 2006, 30(4): 432–438 [译自: 水生生物学报]     

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...     

Detection of species-specific long VNTRs in mitochondrial control region and their application to identifying sympatric Hong Kong grouper (Epinephelus akaara) and yellow grouper (Epinephelus awoara)

Length variation and heteroplasmy were observed in PCR products of the first half of mtDNA control region of both Hong Kong grouper (Epinephelus akaara) and yellow grouper (Epinephelus awoara). DNA sequencing unveiled the phenomena were caused by the presence of species-specific long variable number tandem repeats (VNTRs). This is the first report on the mtDNA VNTRs and their heteroplasmy in groupers. Moreover, these VNTRs are also the longest such structure found in teleost fish. Thereafter, we designed two species-specific PCR reverse primers according to the 3' end sequences of the VNTRs and successfully established assays for the identification of these two sympatric grouper species.     

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。     

Description of Pseudorhabdosynochus shenzhenensis n. sp. (Monogenea: Diplectanidae) and redescription of P. serrani Yamaguti, 1953 from Epinephelus coioides off Dapeng Bay, Shenzhen, China

One new species of diplectanid, Pseudorhabdosynochus shenzhenensis n. sp., is reported and described from the marine fish Epinephelus coioides off Nan'ao, Shenzhen, China. It can be differentiated from previously described species of the same genus by features of the haptoral and vaginal hard-parts. A second species, P. serrani Yamaguti, 1953, originally described from Serranus sp. from the western Pacific Ocean off the Celebes (now called Sulawesi), is redescribed based on new material from E. coioides.     

Origin, diversification, and historical biogeography of the genus Trachurus (Perciformes: Carangidae)

We addressed phylogenetic relationships in the genus Trachurus using cytochrome b gene and D-loop sequences. The trees showed five groups: (1) the Southwest Pacific species (T. japonicus, T. novaezelandiae, and T. declivis); (2) The Mediterranean Sea and Eastern Atlantic species (T. mediterraneus); (3) The Atlantic Ocean species (T. lathami and T. trecae); (4) Eastern Atlantic species (T. trachurus and T. capensis); and (5) a group of highly mobile pelagic species, two from the Eastern Pacific (T. symmetricus and T. murphyi) and one from the Eastern Atlantic (T. picturatus). The phylogeny based on Cyt b, supports the molecular clock hypothesis and our results agree with the reported fossil indicating that the origin of this genus occur when the Thetys Sea closed (around 18.4 MYA). In addition, a very slow neutral substitution rate is reported identified only two periods of maximum diversification: the first occurring between 18.4 and 15.0 MYA and the second between 8.4 MYA and present day.     

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.