A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study

  title={A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study},
  author={Chenhong Li and Guillermo Ort{\'i} and Gong Zhang and Guoqing Lu},
  journal={BMC Evolutionary Biology},
  pages={44 - 44}
BackgroundMolecular systematics occupies one of the central stages in biology in the genomic era, ushered in by unprecedented progress in DNA technology. The inference of organismal phylogeny is now based on many independent genetic loci, a widely accepted approach to assemble the tree of life. Surprisingly, this approach is hindered by lack of appropriate nuclear gene markers for many taxonomic groups especially at high taxonomic level, partially due to the lack of tools for efficiently… 

Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data

It is suggested that most lineages of living fishes were already established in the Mesozoic Period, more than 65 million years ago, and genome-scale data support the structure of the fish phylogeny.

FishPIE: A universal phylogenetically informative exon markers set for ray-finned fishes

Gene markers for exon capture and phylogenomics in ray-finned fishes

A suite of “single-copy” protein coding sequence (CDS) markers was identified through comparing eight fish genomes, and tested them empirically in 83 species (33 families and 11 orders) of ray-finned fishes, resulting in a selection of 4,434 markers which were proven to be useful in reconstructing phylogenies of the ray- Finned fishes at different taxonomic level.

Multiple genome alignments facilitate development of NPCL markers: a case study of tetrapod phylogeny focusing on the position of turtles.

This work takes advantage of the multiple genome alignment resources from the University of California-San Cruz Genome Browser and presents a simple and straightforward bioinformatic approach to automatically screen for candidate nuclear protein-coding locus (NPCL) markers.

PhyloMarker–-A Tool for Mining Phylogenetic Markers through Genome Comparison: Application of the Mouse Lemur (Genus Microcebus) Phylogeny

PhyloMarker, a phylogenomic tool designed to find nuclear gene markers for the inference of phylogeny through multiple genome comparison, was presented and nine markers confirmed the distinct lineage inferred from previous mtDNA data.

Genomic outposts serve the phylogenomic pioneers: designing novel nuclear markers for genomic DNA extractions of lepidoptera.

A genomic approach to finding new protein-coding genes for systematics in nonmodel taxa, which can be PCR amplified from standard, slightly degraded genomic DNA extracts is described.

Genomic Outposts Serve the Phylogenomic Pioneers: Designing Novel Nuclear Markers

A genomic approach to finding new protein-coding genes for systematics in nonmodel taxa, which can be PCR amplified from standard, slightly degraded genomic DNA extracts, is described.

Novel intron markers to study the phylogeny of closely related mammalian species

A new set of 224 nuclear introns with optimal features for the phylogeny of closely related mammalian species is designed, indicating that this marker set can be very helpful in multilocus phylogenetics of mammals.



The phylogenetic position of toadfishes (order Batrachoidiformes) in the higher ray-finned fish as inferred from partitioned Bayesian analysis of 102 whole mitochondrial genome sequences

The resultant phylogenies strongly suggest that the toadfishes are not members of relatively primitive higher actinopterygians (ParacanthopteryGii), but belong to a crown group of actinoperative groups (Percomorpha), as was demonstrated for ophidiiform eels and anglerfishes in the previous study.

Novel evolutionary relationship among four fish model systems.

C-mos, a nuclear marker useful for squamate phylogenetic analysis.

Partial sequences of c-mos were obtained from 13 squamate reptile families and outgroup representatives from the orders Rhynchocephalia, Chelonia, and Crocodylia and reveal a high degree of phylogenetic information contained within the sequence for both the synonymous and nonsynonymous substitutions.

Generating single-copy nuclear gene data for a recent adaptive radiation.

Genome-scale data, angiosperm relationships, and "ending incongruence": a cautionary tale in phylogenetics.

Novel Relationships Among Ten Fish Model Species Revealed Based on a Phylogenomic Analysis Using ESTs

A molecular phylogeny of higher-level relationships of derived teleosts is revealed, which indicates that the use of multiple genes produces robust phylogenies, a finding that is expected to apply to other phylogenetic issues among distantly related taxa.

Phylogenetic Relationships of New World Needlefishes (Teleostei: Belonidae) and the Biogeography of Transitions between Marine and Freshwater Habitats

Optimization of habitat on the total evidence tree, combined with paleogeographic data, suggests that four independent entries into freshwater have taken place—one in Central America, and three in South America.

From 2R to 3R: evidence for a fish-specific genome duplication (FSGD).

  • A. MeyerY. van de Peer
  • Biology
    BioEssays : news and reviews in molecular, cellular and developmental biology
  • 2005
An important mechanism for the evolution of phenotypic complexity, diversity and innovation, and the origin of novel gene functions is the duplication of genes and entire genomes. Recent phylogenomic

Nuclear gene sequences for higher level phylogenetic analysis: 14 promising candidates

Concordance among multiple indepen? dent data sets is the strongest form of cor? roboration for a phylogeny estimate (Mi? yamoto and Cracraft, 1991). Nuclear gene sequences are a potentially vast

Phylogenomics of eukaryotes: impact of missing data on large alignments.

This large data set provides a reliable phylogenetic framework for studying eukaryotic and animal evolution and will be easily extendable when large amounts of sequence information become available from a broader taxonomic range.