Resolving higher-level relationships of the Cypriniformes (Teleostei) : A mitochondrial phylogenomic approach

解决鲤形目（Teleostei）的高级关系：线粒体系统发育学方法

基本信息

批准号：
17207007
负责人：
MIYA Masaki
金额：
$ 32.28万
依托单位：
Natural History Museum and Institute, Chiba
依托单位国家：
日本
项目类别：
Grant-in-Aid for Scientific Research (A)
财政年份：
2005
资助国家：
日本
起止时间：
2005 至 2008
项目状态：
已结题

项目摘要

Fishes of the order Cypriniformes are almost completely restricted to freshwaters and number over 3500 species placed in six families, each with poorly-defined subfamilies and/or tribes. The first purpose of this study was to resolve the higher-level relationships of the World's largest freshwater-fish clade based on whole mitochondrial (mt) genome sequences from a number of cypriniforms in a short period of time. This has been accomplished by the new sequencing method developed by Miya et al.(2006) and subsequent publication of Saitoh et al.(2006). In the latter paper we assembled the mt genome sequences from 56 cypriniforms and analyzed the datasets using the Bayesian method. The resulting phylogenies in Saitoh et al.(2006) have had a great impact on the cypriniform systematics, being cited by 45 papers up to now. We have determined over 400 mt genome sequences during this study and are currently constructing a large dataset comprising those mt genome sequences and numerous partial sequences downloaded from the DNA databases. This mixed dataset is called a "mitogenomic supermatrix" and is currently analyzed by a cluster of 4 desktop machines each with 4 CPUs. The second purpose was to gain the initiative in molecular phylogenetics of fishes by publishing a number of papers based on numerous whole mt genome sequences from various groups of fishes. It appears that our mt genomic papers have attracted considerable attention from the scientific community, with being cited over 2,000 scientific papers during these 10 years. Also our outreaches to the public are outstanding, with numerous newspapers and scientific journals having featured our papers, such as Johnson et al.(2009) on the whalefish families, Setiamarga et al.(2009) on the divergence times of medaka, and Inoue et al.(2010) on deep-ocean origin of the freshwater eels.

Cypriniformes的鱼类几乎完全局限于淡水，数量超过3500种在六个家庭中，每个家庭中的亚科和/或部落定义较差。这项研究的第一个目的是基于整个线粒体（MT）基因组序列，从短时间内从许多塞氏菌中的整个线粒体（MT）基因组序列解决世界上最大的淡水基枝的高层关系。这是通过Miya等人（2006年）和随后的Saitoh等人（2006）开发的新测序方法来完成的。在后一篇论文中，我们组装了来自56个氰基的MT基因组序列，并使用贝叶斯方法分析了数据集。 Saitoh等人（2006年）中产生的系统发育对氰型系统的影响很大，到目前为止，有45篇论文引用了。我们在这项研究中确定了超过400吨基因组序列，目前正在构建一个大型数据集，其中包括这些MT基因组序列和从DNA数据库下载的大量部分序列。该混合的数据集称为“有丝分裂基因组的超级元素”，目前由4个台式机的群集分析，每个台式机的四个CPU。第二目的是通过根据来自各种鱼类的许多整个MT基因组序列发表许多论文来获得鱼类分子系统发育的倡议。看来，我们的MT基因组论文引起了科学界的极大关注，在这10年中被引用了2,000多篇科学论文。同样，我们对公众的宣传也非常出色，许多报纸和科学期刊都有我们的论文，例如Johnson等人（2009年），《鲸鱼家族》，Setiamarga等人（2009年）关于Medaka的分歧时代，以及Inoue等人（Inoue等人（2010年），有关淡水埃尔斯的深度启动。