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

鲤形目鱼类几乎完全局限于淡水，有6个科3500多种，每个亚科和/或部落界定不清。这项研究的第一个目的是解决世界上最大的淡水鱼支系在短时间内基于许多鲤科鱼类的全线粒体(Mt)基因组序列的更高级别的关系。这是通过Miya等人(2006年)开发的新测序方法和随后发表的Saitoh等人(2006年)完成的。在后一篇论文中，我们组装了56条鲤科鱼类的mt基因组序列，并使用贝叶斯方法对数据集进行了分析。Saitoh等人(2006年)的系统发育对鲤科系统学产生了很大的影响，到目前为止被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。这一混合数据集被称为“有丝分裂组超矩阵”，目前由4台台式机组成的集群进行分析，每台台式机有4个CPU。第二个目的是通过发表一些基于各种鱼类的大量线粒体全基因组序列的论文，获得鱼类分子系统发育的主动权。看来，我们的Mt基因组论文已经引起了科学界的相当大的关注，在这10年中被引用了2000多篇科学论文。此外，我们面向公众的外展活动也很出色，许多报纸和科学期刊都刊登了我们的论文，例如Johnson等人(2009年)关于鲸鱼科的论文，Setiamarga等人(2009)关于青竹的分歧时间的论文，以及井上等人(2010)关于淡水鳗鱼的深海起源的论文。

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.