2008 Fiscal Year Final Research Report
Resolving higher-level relationships of the Cypriniformes (Teleostei) : A mitochondrial phylogenomic approach
| Project/Area Number |
17207007
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| Research Category |
Grant-in-Aid for Scientific Research (A)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
Biodiversity/Systematics
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| Research Institution | Natural History Museum and Institute, Chiba |
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Principal Investigator |
MIYA Masaki Natural History Museum and Institute, Chiba, 動物学研究科, 上席研究員 (30250137)
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| Co-Investigator(Kenkyū-buntansha) |
NISHIDA Mutsumi 東京大学, 海洋研究所, 教授 (90136896)
SAITOH Kenji 独立行政法人水産総合研究センター, 東北区水産研究所, 室長
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| Project Period (FY) |
2005 – 2008
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| Keywords | 遺伝子 / 動物 / ゲノム / 進化 / 分類学 |
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| Research Abstract |
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.
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Research Products
(26 results)
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[Journal Article] Deep-ocean origin of the freshwater eels2010
Author(s)
Inoue, J.G., M. Miva, M.J. Miller, T. Sado, R. Hanel, K. Hatooka, J. Aoyama, Y. Minegishi, M. Nishida, K. Tsukamoto
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Journal Title
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[Journal Article] Reconstructing the phylogenetic relationships of the Earth's most diverse Glade of freshwater fishes-Order Cypriniformes (Actinopterygii : Ostariophysi) : A case study using multiple nuclear loci and the mitochondrial genome2009
Author(s)
Mayden, R.L., W.-J. Chen, H.L. Bart, M.H. Doosey, A.M. Simons, K.L. Tang, R.M. Wood, M.K. Agnew, L. Yang, M.V. Hirt, M.D. Clements, K. Saitoh, M. Miva, M. Nishida
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Journal Title
Mol. Phylogenet. Evol 51(3)
Pages: 500-514
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[Journal Article] Inferring the Tree of Life of the order Cypriniformes, the earth's most diverse Glade of freshwater fishes : Implications of varied taxon and character sampling2008
Author(s)
Mayden, R.L., K.L. Tang, R. M. Wood, W.-J. Chen, M.K. Agnew, K.W. Conway, L. Yang, A.M. Simons, H.L. Bart, P.M. Harris, L.I. Junbing, X. Wang, K. Saitoh, S. He, H. Liu, Y. Chen, M. Nishida, M. Miva
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Journal Title
J. Syst. Evol 46(3)
Pages: 424-438
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[Journal Article] Phylogenetic relationships of Danio within the order Cypriniformes : A framework for comparative and evolutionary studies of a model species2007
Author(s)
Mayden, R.L., K.W. Conway, K. Tang, J. Freyhof, S. Chamberlain, M. Haskins, L. Schneider, M. Sudkamp, R.M. Wood, M. Agnew, A. Bufalino, Z. Sulaiman, M. Miya, K. Saitoh, S. He
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Journal Title
J Exp. Zool. Part B, Mol. Devel. Evol 308B(5)
Pages: 642-654
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