Molecular phylogenetic relationships of 30 grouper species in China Seas based on 16S rDNA fragment sequences
- 海洋环境－已发表论文 
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。The Subfamily Epinephelinae (Teleoste: Serranidae), commonly known as groupers, comprises about 159 species of marine fishes in 15 genera. They are bottom-associated fishes found in tropical and subtropical waters. Most species occur on coral reefs, but some live in estuaries or on rocky reefs. Groupers are of considerable economic value, however, the classification and evolutionary relationships of them have always been hindered by the overwhelming number of species, global distribution, and the lack of morphological specializations traditionally used in ichthyological classification. The confusion and debates have brought much trouble not only to the study of the phylogenetic relationships among groupers, but also to the identification of fry and parent in grouper aquaculture. In this study, to evaluate the phylogenetic relationship of the groupers from the China Seas, the 16S ribosomal DNA of thirty grouper species within six genera of subfamily Epinephelinae were amplified using PCR techniques, 572 bp DNA fragments were obtained and the sequences were analyzed. The genetic information indexes, including Kimura-2 parameter genetic distance and Ts/Tv ratios, were generated using a suite of biology software. Of the 572 aligned base pairs, among which insertion or deletion of base pairs was evident, 373 were constant, 151 were parsimony informative, comprising 26.4% of the total base pairs. The maximum pairwise nucleotide divergence value among all taxa was 0.186 between Epinephelus malabaricus and Plectropomus laevis and the minimum value was 0.007 between E.moara and E.bruneus. The average pairwise nucleotide divergence value among all taxa was 0.079. Transitions were found to be more common than transversions. The average transition/transversion ratio among all pairwise comparisons was 1.7, suggesting that the sequences had not reached saturation. The sequence analysis also showed an obvious adenine bias on the 16S ribosomal DNA fragment and no anti-guanine bias was detected. With Pronotogrammus multifasciatus (No.AF297330) and Johnius belengerii (No.AY336727) as the designated outgroups and additional homologous sequences information of other Cephalopolis and Epinephelus fishes invoked from GenBank, phylogenetic trees were constructed based on the neighbor-joining (NJ),maximum-parsimony (MP) and maximum-likelihood (ML) methods. Conclusions were drawn as follow: 1) all the phylogenic trees suggested that genus Plectropomus, which obviously showed monophyly, is the most primitive group among the subfamily Epinephelinae in this study; genus Cephalopolis is also recovered as a monophyletic group and is more primitive than genus Epinephelus; the evolutionary status of genus Variola is between genus Cephalopolis and genus Plectropomus; 2) Promicrops lanceolatus should be included in genus Epinephelus because it emerged as a cluster within the clade of Epinephelus and had a close relationship with E.coioides and E.malabaricus; Cromileptes altivelis also showed close relationship with genus Epinephelus; perhaps a specialization group within genus Epinephelus; 3) genus Epinephelus was located at the top of the phylogenetic tree indicating that it is the most recently diverged species, which is in accordance with the fact that it is also the most flourishing genus in Epinephelinae. There are two parallel evolutionary sister clades existing (with high bootstrap value support) in genus Epinephelus. However the species-level differences within these clads are not clear due to the lack of high bootstrap values support. The species within this two clades seem to be irrelevant to their biogeographic distributions, which suggested that there were two parallel evolutionary ancestors existing in the early evolution stage of genus Epinephelus and their on-going divergence should be earlier than the existence of geographic floras of genus Epinephelus.