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.

鲤形目鱼类几乎完全局限于淡水中，共有 3500 多种鱼类，分为六个科，每个科都有不明确的亚科和/或部落。这项研究的第一个目的是在短时间内根据多种鲤鱼的完整线粒体（mt）基因组序列来解决世界上最大的淡水鱼进化枝的高级关系。这是通过 Miya 等人 (2006) 开发的新测序方法以及 Saitoh 等人 (2006) 随后发表的文章实现的。在后一篇论文中，我们组装了 56 种鲤科动物的 mt 基因组序列，并使用贝叶斯方法分析了数据集。 Saitoh et al.(2006) 所得出的系统发育对鲤科系统学产生了巨大影响，迄今为止已被 45 篇论文引用。在这项研究中，我们已经确定了 400 多个 mt 基因组序列，目前正在构建一个包含这些 mt 基因组序列和从 DNA 数据库下载的大量部分序列的大型数据集。这个混合数据集被称为“线粒体基因组超级矩阵”，目前由 4 台台式机组成的集群（每台配有 4 个 CPU）进行分析。第二个目的是通过发表多篇基于不同鱼类的整个 mt 基因组序列的论文来获得鱼类分子系统发育的主动权。看来我们的 mt 基因组论文引起了科学界的广泛关注，在这 10 年里被引用了 2000 多篇科学论文。此外，我们对公众的宣传也非常出色，许多报纸和科学期刊都刊登了我们的论文，例如 Johnson 等人 (2009) 关于鲸鱼科的文章、Setiamarga 等人 (2009) 关于青鳉的分歧时间的文章以及 Inoue 等人的文章。等人（2010）关于淡水鳗鱼的深海起源。