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- W2145164089 abstract "Knowledge of the correct phylogenetic relationships among animals is crucial for the valid interpretation of evolutionary trends in biology. Zebrafish, medaka, pufferfish and cichilds are fish models for development, genomics and comparative genetics studies, although their phylogenetic relationships have not been tested rigorously. The results of phylogenomic analysis based on 20 nuclear protein-coding genes confirmed the basal placement of zebrafish in the fish phylogeny but revealed an unexpected relationship among the other three species, contrary to traditionally held systematic views based on morphology. Our analyses show that medaka (Beloniformes) and cichlids (Perciformes) appear to be more closely related to each other than either of them is to pufferfish (Tetraodontiformes), suggesting that a re-interpretation of some findings in comparative biology might be required. In addition, phylogenomic analyses show that fish typically have more copies of nuclear genes than land vertebrates, supporting the fish-specific genome duplication hypothesis. Knowledge of the correct phylogenetic relationships among animals is crucial for the valid interpretation of evolutionary trends in biology. Zebrafish, medaka, pufferfish and cichilds are fish models for development, genomics and comparative genetics studies, although their phylogenetic relationships have not been tested rigorously. The results of phylogenomic analysis based on 20 nuclear protein-coding genes confirmed the basal placement of zebrafish in the fish phylogeny but revealed an unexpected relationship among the other three species, contrary to traditionally held systematic views based on morphology. Our analyses show that medaka (Beloniformes) and cichlids (Perciformes) appear to be more closely related to each other than either of them is to pufferfish (Tetraodontiformes), suggesting that a re-interpretation of some findings in comparative biology might be required. In addition, phylogenomic analyses show that fish typically have more copies of nuclear genes than land vertebrates, supporting the fish-specific genome duplication hypothesis. a clade of ‘bony fish’ in the animal phylum Chordata, comprising the ray-finned fish, which evolved during the end of the Silurian period, ∼408 million years ago. They dominate the modern fauna and can be found in most aquatic habitats from the abyssal depths of the ocean, >10 000 m, to high altitude freshwater streams and ponds. Both ‘fish’ and ‘bony fish’ (fish, other than lampreys, sharks and their relatives, with bony skeletons including ray-finned fish, lungfish and so on) are general terms in popular use but they are not derived from formal taxonomic classifications, in the sense of being derived from a single ancestral lineage (monophyletic group). In contrast, ray-finned fish are considered a monophyletic group. Traditionally three grades of Actinopterygii have been recognized: the Chondrostei (sturgeons, bichirs), Holostei (gars, bowfins) and Teleostei (the vast majority of extant ray-finned species). An example of how a ray-finned species are placed into a systematic hierarchical (cladistic) classification based on grouping taxa by their shared possession of derived characters is shown in a cluster of taxa derived from a single common ancestor. a similarity in character state (e.g. nucleotide in molecular phylogeny) resulting from chance or a selection constraint but not due to common history. a potential pitfall of phylogenetic reconstruction when the rate of sequence evolution among lineages is significantly different. That is, if a dataset contains some taxa that are placed at the tips of long branches (because of rapid evolution) and some other branches (both external and internal) that are short, then the long branches will attract each other and appear as sister taxa on the tree, even if they do not share recent common ancestry. two homologous genes that evolved directly from their most recent common ancestor via speciation that did not undergo a gene duplication; otherwise they are termed paralogous, if they result from gene duplication. an analytical approach in phylogenetics using large-scale or multiple gene loci sequence data (usually with less number of taxonomic representatives) obtained from intensive sequencing efforts and/or available genomic databases in order to reconstruct a well-supported phylogenetic tree of organisms or to understand the evolution of the individual gene trees (i.e. does a gene genealogy tree result from speciation, duplication or both of these two evolutionary processes?). Phylogenomics can be considered as an extension of molecular phylogenetics because it consists of the use of molecular data (not morphological characters) for evolutionary analysis. However, molecular phylogenetics is concerned with attempts to determine the rates and patterns of nucleotide and/or amino acid change occurring within a gene, whereas the focus of phylogenomics is on the evolutionary change among genes or the evolutionary trends of a group of genes such as a gene family. A sophisticated application of phylogenomics is to improve functional predictions for uncharacterized genes" @default.
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- W2145164089 date "2004-09-01" @default.
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- W2145164089 title "Novel evolutionary relationship among four fish model systems" @default.
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- W2145164089 doi "https://doi.org/10.1016/j.tig.2004.07.005" @default.
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