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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.

鲤形目的鱼类几乎完全局限于淡水和数量超过3500种放置在六个家庭，每个家庭有定义不明确的亚科和/或部落。本研究的第一个目的是解决世界上最大的淡水鱼类分支的高层次的关系的基础上，整个线粒体（mt）的基因组序列在很短的时间内从一些鲤形目。这已经通过Miya等人开发的新测序方法完成。（2006）和Saitoh et al.（2006年）。在后一篇论文中，我们组装了56个鲤形目的mt基因组序列，并使用贝叶斯方法分析了数据集。在Saitoh et al.（2006）对鲤科鱼类的系统学研究产生了重大影响，至今被45篇论文引用。我们在这项研究中已经确定了400多个mt基因组序列，目前正在构建一个大型数据集，包括这些mt基因组序列和从DNA数据库下载的许多部分序列。这种混合数据集被称为“有丝分裂基因组超矩阵”，目前由4台台式机组成的集群进行分析，每台台式机都有4个CPU。第二个目的是通过发表大量基于不同鱼类类群的全基因组序列的论文，在鱼类分子遗传学方面取得主动。看来我们的mt基因组论文已经引起了科学界的极大关注，在这10年中被引用的科学论文超过2,000篇。此外，我们对公众的影响也很突出，许多报纸和科学期刊都刊登了我们的论文，如约翰逊等人。（2009）关于鲸鱼科，Setiamarga et al.（2009）关于青鳉的分歧时间，和Inoue et al.（2010）淡水鳗鱼的深海起源。