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
Citations
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Phylogeny of Gobioidei and Placement within Acanthomorpha, with a New Classification and Investigation of Diversification and Character Evolution
TL;DR: This study integrates and expands previous molecular phylogenetic hypotheses to infer a comprehensive gobioid phylogeny, including a variety of outgroup taxa included to confirm sister taxon identity and position of the group among other acanthomorphs.
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Hidden Likelihood Support in Genomic Data: Can Forty-Five Wrongs Make a Right?
John Gatesy,Richard Baker +1 more
TL;DR: Reanalysis of a large comparative genomic data set for yeast demonstrates that hidden support can be an important factor in maximum likelihood analyses of multiple data sets as well, and shows that isolated analyses of individual data sets can mask congruence and distort interpretations of clade stability.
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Barcoding and border biosecurity: identifying cyprinid fishes in the aquarium trade.
Rupert A. Collins,Karen F. Armstrong,Rudolf Meier,Youguang Yi,Samuel D. J. Brown,Robert H. Cruickshank,Suzanne Keeling,Colin Johnston +7 more
TL;DR: It is demonstrated that DNA barcoding provides a highly effective biosecurity tool for rapidly identifying high-risk fishes in the aquarium trade, and is improved on previous studies by consolidating supplementary information from multiple data sources.
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To name or not to name: Criteria to promote economy of change in Linnaean classification schemes.
TL;DR: It is concluded that not all TNCs lead to equally informative and stable taxonomies and provides a workflow scheme to guide the procedure of taxonomic decisions concerning the creation or modification of supraspecific classifications.
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Systematics of the subfamily Danioninae (Teleostei: Cypriniformes: Cyprinidae).
Kevin L. Tang,Mary K. Agnew,M. Vincent Hirt,Tetsuya Sado,Leah M. Schneider,Jörg Freyhof,Zohrah Sulaiman,Ernst R. Swartz,Chavalit Vidthayanon,Masaki Miya,Kenji Saitoh,Andrew M. Simons,Robert M. Wood,Richard L. Mayden +13 more
TL;DR: The phylogenetic relationships of the Danioninae are examined and the resulting topology supports some conclusions drawn by recent studies on the group and certain portions of the traditional classification, but the results also contradict key aspects of theTraditional classification.
References
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The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Naruya Saitou,Masatoshi Nei +1 more
TL;DR: The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.
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Confidence limits on phylogenies: an approach using the bootstrap.
TL;DR: The recently‐developed statistical method known as the “bootstrap” can be used to place confidence intervals on phylogenies and shows significant evidence for a group if it is defined by three or more characters.
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The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
TL;DR: ClUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W, providing an integrated system for performing multiple sequence and profile alignments and analysing the results.
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MODELTEST: testing the model of DNA substitution.
David Posada,Keith A. Crandall +1 more
TL;DR: The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data.