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

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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