Journal ArticleDOI
Repeatability of clades as a criterion of reliability: a case study for molecular phylogeny of Acanthomorpha (Teleostei) with larger number of taxa.
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TLDR
This study represents the most extensive taxonomic sampling effort to date to collect new molecular characters for phylogenetic analysis of acanthomorph fishes, with new and reliable clades emerging from this study of the acanthomorphic radiation.About:
This article is published in Molecular Phylogenetics and Evolution.The article was published on 2003-02-01. It has received 350 citations till now. The article focuses on the topics: Acanthomorpha & Zoarcoidei.read more
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The tree of life and a new classification of bony fishes.
Ricardo Betancur-R.,Richard E. Broughton,Edward O. Wiley,Kent E. Carpenter,J. Andrés López,Chenhong Li,Nancy I. Holcroft,Dahiana Arcila,Millicent D. Sanciangco,James C. Cureton,Feifei Zhang,Thaddaeus John Buser,Matthew A. Campbell,Jesús A. Ballesteros,Adela Roa-Varon,Stuart C. Willis,W. Calvin Borden,Thaine W. Rowley,Paulette C. Reneau,Daniel J. Hough,Guoqing Lu,Terry Grande,Gloria Arratia,Guillermo Ortí +23 more
TL;DR: A comprehensive molecular phylogeny for bony fishes that includes representatives of all major lineages and the order Perciformes, considered by many a polyphyletic taxonomic waste basket, is defined for the first time as a monophyletic group in the global phylogeny.
Journal ArticleDOI
Phylogenetic classification of bony fishes.
Ricardo Betancur-R.,Ricardo Betancur-R.,Edward O. Wiley,Edward O. Wiley,Gloria Arratia,Arturo Acero,Nicolas Bailly,Masaki Miya,Guillaume Lecointre,Guillermo Ortí,Guillermo Ortí +10 more
TL;DR: This version of the phylogenetic classification of bony fishes is substantially improved, providing resolution for more taxa than previous versions, based on more densely sampled phylogenetic trees.
Journal ArticleDOI
Taxon sampling and the accuracy of phylogenetic analyses
TL;DR: Thorough taxon sampling is one of the most practical ways to improve the accuracy of phylogenetic estimates, as well as the accuracyof biological inferences that are based on these phylogenetic trees.
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The nature of the diversity of Antarctic fishes
TL;DR: The species diversity of the Antarctic fish fauna changed notably during the ≈40 million years from the Eocene to the present, and in some notothenioid clades phyletic diversification was accompanied by considerable morphological and ecological diversification.
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Mitogenomic evolution and interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): the first evidence toward resolution of higher-level relationships of the world's largest freshwater fish clade based on 59 whole mitogenome sequences.
Kenji Saitoh,Tetsuya Sado,Richard L. Mayden,Naoto Hanzawa,K. Nakamura,Mutsumi Nishida,Masaki Miya +6 more
TL;DR: The present study represents the first attempt toward resolution of the higher-level relationships of the world’s largest freshwater-fish clade based on whole mitochondrial genome sequences from 53 cypriniforms plus 6 outgroups, and it is advocated that RY-coding, which takes only transversions into account, effectively removes this likely “noise” from the data set and avoids the apparent lack of signal by retaining all available positions in the dataSet.
References
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Journal ArticleDOI
Homoplasy Increases Phylogenetic Structure
TL;DR: Analysis of the largest nucleotide matrix treated to date—2538 rbc L sequences covering all major lineages of green plants— shows that although rapidly evolving and highly homoplastic, third positions contain most of the phylogenetic structure in the data.
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Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny.
TL;DR: The relative efficiencies of different protein-coding genes of the mitochondrial genome and different tree-building methods in recovering a known vertebrate phylogeny was evaluated, and the utility of the currently used optimization principles in phylogenetic construction is questioned.
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How good are deep phylogenetic trees
TL;DR: This work has shown that species branching deep in molecular trees are often fast-evolving ones, misplaced because of the long-branch artefact, and that the detection of genuinely deep-branchesing organisms remains an elusive task.
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Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used.
Kei Takahashi,Masatoshi Nei +1 more
TL;DR: It is shown that when ME methods are used, the simple p distance generally gives better results in phylogenetic inference than more complicated distance measures such as the Hasegawa-Kishino-Yano (HKY) distance, even when nucleotide substitution follows the HKY model.