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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A reappraisal of the evolution of Asian snakehead fishes (Pisces, Channidae) using molecular data from multiple genes and fossil calibration.
TL;DR: A multi-locus molecular phylogeny was constructed and calibrated using two fossil dates to estimate divergence times within the Channidae, suggesting that after divergence from African taxa 40-50 Ma, evolution of Asian snakeheads has been heavily influenced by multiple broad scale dispersal events across India and Southeast Asia.
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Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements
Sarah J. Longo,Brant C. Faircloth,Axel Meyer,Mark W. Westneat,Michael E. Alfaro,Peter C. Wainwright +5 more
TL;DR: This study uses a dataset of ultraconserved elements (UCEs) to conduct the first phylogenomic study of Syngnathiformes, finding consistent support for the monophyly of traditional long-snouted syngnATHiform lineages, which better agrees with morphological hypotheses than previously published topologies from molecular data.
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Phylogeny and biogeography of a shallow water fish clade (Teleostei: Blenniiformes).
TL;DR: The first comprehensive phylogenetic hypothesis for a monophyletic Labrisomidae with five tribes is presented and global distributions of blenny genera included in the analysis support the evolution of a largely Neotropical clade whose closest relatives are temperate in distribution.
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To see in different seas: spatial variation in the rhodopsin gene of the sand goby (Pomatoschistus minutus)
Maarten Larmuseau,Joost A. M. Raeymaekers,Kevin G. Ruddick,Jeroen K. J. Van Houdt,Filip Volckaert +4 more
TL;DR: The usefulness of sensory genes, like rhodopsin, for studying the characteristics of local adaptation in marine nonmodel organisms is highlighted, including nonsynonymous mutations on amino acids known as spectral tuning sites.
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The mitogenomic contributions to molecular phylogenetics and evolution of fishes: a 15-year retrospect
TL;DR: It is argued that intensive taxonomic sampling from an interface between species and populations together with the massive character sampling from mitogenome sequences using next-generation sequencing (NGS) technologies would enable simultaneous attempts to delimit species boundaries and to reconstruct evolutionary relationships at much finer scale, eventually unraveling the fish part of the Tree of Life in a bottom-up manner with more accurate estimations of species diversity.
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.