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A mitogenomic supermatrix approach to resolve phylogeny and evolution of species-rich clades: Development of method and its applications to fishes

用于解决物种丰富的进化枝的系统发育和进化的线粒体基因组超级矩阵方法：方法的开发及其在鱼类中的应用

基本信息

批准号：
22370035
负责人：
MASAKI Miya
金额：
$ 11.98万
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 (B)
财政年份：
2010
资助国家：
日本
起止时间：
2010 至 2012
项目状态：
已结题

项目摘要

Resolution of phylogenetic relationships among members of a species-rich clade is inherently difficult because it requires longer sequences from a large number of taxa. Freshwater fishes of the order Cypriniformes represent one of such species-rich clades, with over 4,000 species currently recognized that have been placed in 6+ families, each with poorly defined subfamilies and/or tribes. This study attempted comprehensive resolution of the cypriniform phylogenies by combining a mitogenomic tree as a backbone constraint for the robust higher-level relationships and numerous partial sequences downloaded from GenBank for the reconstruction of lower-level relationships within the constrained clades. Also this supermatrix approaches were applied to fishes of Gobioidei and Otophysi, both including numerous species (ca. 2,000 spp. and 8,000 spp, respectively) and exhibiting different habitat preferences (principally marine vs. freshwater). The mitogenomic tree of the Cypriniformes was based … More on 602 sequences (including 6 outgroups) and the resulting best-scoring ML tree is congruent with the previous molecular phylogenies based on both mitogenomes and nuclear genes. A total of 17,057 partial sequences from cypriniforms were available from GenBank and they were sorted into 9 mitochondrial genes from 1,073 species, of which 1,039 species were those from the cyt b gene alone. 機関番号：８２５０３研究種目：基盤研究 (B) 研究期間：2011～2013 年課題番号：22370035 研究課題名（和文）ミトゲノム超行列による巨大クレードの包括的な進化史解明：方法論の確立と実際研究課題名（英文）A mitogenomic supermatrix approach to resolve phylogeny and evolution of species-rich clades: Development of method and its applications to fishes 研究代表者宮正樹（Masaki Miya）千葉県立中央博物館・自然誌・歴史研究部・動物学研究科・科長研究者番号：30250137 The supermatrix was constructed by combining 602 mitogenomic and 1,073 partial sequences and it was subjected to partitioned ML analysis using the mitogenomic tree as a backbone constraint. The best-scoring ML tree derived from 24 runs using a fast bootstrap (BS) option in RAxML places all species from the partial sequences (1,073 spp.) in reasonable positions, with 62.2% of the internal branches being supported by .80% BS probabilities. In addition whole mitogenome sequences from 152 gobioid and 120 otophysan were assembled to provide robust phylogenies for these groups of fishes and the trees will be used in the subsequent supermatrix analyses. Less

Resolution of phylogenetic relationships among members of a species-rich clade is inherently difficult because it requires longer sequences from a large number of taxa. Freshwater fishes of the order Cypriniformes represent one of such species-rich clades, with over 4,000 species currently recognized that have been placed in 6+ families, each with poorly defined subfamilies and/or tribes. This study attempted comprehensive resolution of the cypriniform phylogenies by combining a mitogenomic tree as a backbone constraint for the robust higher-level relationships and numerous partial sequences downloaded from GenBank for the reconstruction of lower-level relationships within the constrained clades. Also this supermatrix approaches were applied to fishes of Gobioidei and Otophysi, both including numerous species (ca. 2,000 spp. and 8,000 spp, respectively) and exhibiting different habitat preferences (principally marine vs. freshwater). The mitogenomic tree of the Cypriniformes was based … More on 602 sequences (including 6 outgroups) and the resulting best-scoring ML tree is congruent with the previous molecular phylogenies based on both mitogenomes and nuclear genes. A total of 17,057 partial sequences from cypriniforms were available from GenBank and they were sorted into 9 mitochondrial genes from 1,073 species, of which 1,039 species were those from the cyt b gene alone. Organ No.: 82503 Research project: Base plate research (B) Research period: 2011~2013 Project number: 22370035 Research project title (and text) A mitogenic supermatrix approach to resolve phylogenesis and evolution of species-rich clades: Development of method and its applications to fishes Research Representative Masaki Miyagi (Masaki Miya) Chiba Prefectural Central Museum·Natural History·History Research Department·Zoology Research Section·Head of Section Researcher No.: 30250137 The supermatrix was constructed by combining 602 mitogenomic and 1,073 partial sequences and it was subjected to partitioned ML analysis using the mitogenomic tree as a backbone constraint. The best-scoring ML tree derived from 24 runs using a fast bootstrap (BS) option in RAxML places all species from the partial sequences (1,073 spp.) in reasonable positions, with 62.2% of the internal branches being supported by .80% BS probabilities. In addition whole mitogenome sequences from 152 gobioid and 120 otophysan were assembled to provide robust phylogenies for these groups of fishes and the trees will be used in the subsequent supermatrix analyses. Less

项目成果

期刊论文数量（0）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Undetected evolutionary radiation in the pelagic realm: A novel clade in the percomorph fishes as revealed by bioinformatic and mitogenomic analyses

远洋领域未检测到的进化辐射：生物信息学和线粒体基因组分析揭示了鲈形目鱼类的一个新分支

DOI：
发表时间：
2013
期刊：
影响因子：
0
作者：
Miya;M.;Satoh;T.P.;Sado;T. & Nishida;M
通讯作者：
M

ウナギ目の新科を発見:パラオの海底洞窟に生息する「生きた化石」

发现新的鳗鱼目家族：生活在帕劳水下洞穴中的“活化石”

DOI：
发表时间：
2010
期刊：
影响因子：
0
作者：
Takeshita K.;Yamashita E.;Hyodo K;Matsuda M.Yamashita E.;宮正樹・井田齊・G. David Johnson・坂上治郎・佐土哲也・朝日田卓
通讯作者：
宮正樹・井田齊・G. David Johnson・坂上治郎・佐土哲也・朝日田卓

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