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
Molecular Evolution: A Phylogenetic Approach.—Roderic D. M. Page and Edward C. Holmes.
General time reversible distances with unequal rates across sites
Peter J. Waddell,Mike Steel +1 more
TL;DR: This work illustrates graphically ways to interpret the reliability of distance-based transformations, using the corrected transition to transversion ratio returned for pairs of sequences which are successively more diverged.
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Congruence Between Molecular and Morphological Phylogenies
TL;DR: Phylogenies based on molecular sequence data and on morphology are surveyed and compared within animals and within plants and it is found that incongruence between molecular trees (generated from different data sets or by different analytical methods) is as striking or pervasive as is incongrience between trees generated by morphologists in the long history of their discipline.
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General Time-Reversible Distances with Unequal Rates across Sites: Mixing Γ and Inverse Gaussian Distributions with Invariant Sites
Peter J. Waddell,Mike Steel +1 more
TL;DR: In this paper, a series of new results useful to the study of DNA sequences using Markov models of substitution are presented with proofs, including the divergence time of humans and chimps from mtDNA sequence data.
Journal ArticleDOI
Amphioxus mitochondrial DNA, chordate phylogeny, and the limits of inference based on comparisons of sequences.
TL;DR: In this paper, the authors show that the phylogeny of the lancelet Branchiostoma floridae ("amphioxus") is almost certainly incorrect, despite their being supported by equally weighted parsimony, distance, and maximum likelihood analyses.