双壳纲贝类18S rRNA基因序列变异及系统发生

双壳纲贝类栖息于环境多变的海域,是一个形态学和生态学都具有多样性的类群,清晰而可靠的进化关系对于养殖与相关种类的管理具重要意义。然而,目前对双壳类宏观分子系统学研究的报道较少。研究用18S rRNA基因(18S)分析了双壳类3个亚纲贝类的系统发育关系。从GenBank下载帘蛤目、海螂目、贻贝目、胡桃蛤目、蚶目、珍珠贝目6个目94个种类的18S全/部分序列107个,通过ClustalX软件进行序列比对, 用MEGA4.1软件和PHyML软件计算遗传距离, 构建系统发育树, 研究了双壳类18S变异规律及其在系统发生研究中的应用。结果显示18S有插入/缺失序列, 存在长度多态性。序列比对显示有5段约30 70bp的保守区, 4段约130 550bp的高变区。碱基组成平均为T:24.4%, C:23.6%, A:24.5%, G:27.5%。G+C含量为51.1%。在1796个比对位点中, 变异位点占31.7%, 简约信息位点占24.0%。目内科间遗传距离为0.003 0.043, 目间遗传距离为0.026 0.093。NJ树和ML树显示贻贝目、珍珠贝目、胡桃蛤目、蚶目和海螂目的缝栖蛤科先分别聚为支持率很高(BPN=94 100)的单系支, 后聚为一大支(BPN=100)。蛤蜊科与帘蛤目的其他科分离形成一置信度很高的单系支(BPN=93)。帘蛤科种类聚为置信度较低(BPN=60)的一支。海螂目、帘蛤目的种类没能完全聚到所属支系, 彼此嵌套,缝栖蛤科的种类从海螂目中分离出来。18S资料揭示帘蛤目的蛤蜊科、海螂目的缝栖蛤科已经进化为独立的支系。

18S rRNA gene variation and phylogenetic analysis among 6 orders of Bivalvia class

The class Bivalvia(phylum Mollusca) is a morphologically and ecologically diverse group that inhabits a variety of marine environments. Worldwide, there are approximately 20,000 species of marine bivalves that display a rich genetic diversity. Clear and reliable evolutionary relationship information is important for the culture and management of related species. Recently, it has been shown that comparative phylogenetic analyses based on small subunit rRNA gene(18S) sequences may be useful for resolving phylogenetic relationships within and among bivalve families. However, a comprehensive examination of bivalves is lacking so far. In this paper, 18S nucleotide variations were analyzed and used to investigate the evolutionary relationships among 3 subclasses of the Bivalvia. 18S sequences of ninety-four species, which belongs to six orders, were obtained from GenBank. Sequences were aligned by using the profile alignment function of ClustalX, and regions which could not be unambiguously aligned were excluded. The phylogenetic analyses were conducted using the Neighbor-Joining method(in MEGA 4.1) and the maximum likelihood method(in PHyML). The alignment results showed that many indels(insertions/deletions) were observed, so there is polymorphism in sequence length of these sequences. The 18S alignments for the 107 sequences contained 1796 sites in total, comprising 569 variable sites(31.7%) and 431 informative sites(24.0%). We observed 5 regions of highly conserved sequences and 4 regions of high variability. The mean composition of T, C, A, G, was 24.4%, 23.6%, 24.5%, 27.5%, respectively, and this dataset shows a higher proportion of G in all 18S sequences. Genetic distances among families and among orders were from 0.003 to 0.043 and from 0.026 to 0.093, respectively. The present analysis of the 18S data supports the proposal that each of the following 4 orders forms a distinct clade: Arcoida, Nucubida, Mytiloida and Pterioida. The monophyly of each order is supported by a relatively high bootstrap value(BPN=94 100). NJ and ML trees supports the placement of orders Arcoida, Nucubida, Mytiloida and Pterioida in one clade(BPN=100, and clustered with the family Hiatellidae(Order Myoida)(BPN=97). The Veneroida and Myoida were not recovered as monophyletic clade. In the case of the order Veneroida, the species of the family Mactridae grouped closest to one another(BPN=98) but separate from the other species of Veneroida. The Veneroidae clustered as a monophyletic clade with lower confidence level(BPN=60), and the species of the family Hiatellidae separate from the order Myoida. The Mactridae and Hiatellidae each formed a monophyletic clade.