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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Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics
Lily C. Hughes,Lily C. Hughes,Guillermo Ortí,Guillermo Ortí,Hadeel Saad,Chenhong Li,William T. White,Carole C. Baldwin,Keith A. Crandall,Dahiana Arcila,Dahiana Arcila,Dahiana Arcila,Ricardo Betancur-R. +12 more
TL;DR: It is shown that legacy loci with known paralogues are at risk of assembling duplicated sequences with target‐capture, but it is also assembled many useful orthologous sequences that can be integrated with many PCR‐generated matrices.
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Tracking the history of an invasion: the freshwater croakers (Teleostei: Sciaenidae) in South America
TL;DR: The results were compatible with the hypothesis of a single colonisation event of South American freshwater habitats by a marine lineage, and the parsimony and BI phylogenetic hypotheses for the concatenated sequences supported the monophyly of the freshwater Sciaenidae.
Journal ArticleDOI
Eekaulostomus cuevasae gen. and sp. nov., an ancient armored trumpetfish (Aulostomoidea) from Danian (Paleocene) marine deposits of Belisario Domínguez, Chiapas, southeastern Mexico
TL;DR: Alvarado et al. as discussed by the authors identified Eekaulostomus cuevasae as a new member of the superfamily Aulostomoidea, which differs from other aulostomoids in the presence of two spines preceding the soft rays of both dorsal and anal fins.
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Short-wavelength sensitive opsin (SWS1) as a new marker for vertebrate phylogenetics
TL;DR: The results suggest that SWS1 may be a good marker for vertebrate phylogenetics due to the variable yet consistent patterns of sequence evolution exhibited across fairly wide taxonomic groups.
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.