Pike and salmon as sister taxa: detailed intraclade resolution and divergence time estimation of Esociformes + Salmoniformes based on whole mitochondrial genome sequences.

@article{Campbell2013PikeAS,
  title={Pike and salmon as sister taxa: detailed intraclade resolution and divergence time estimation of Esociformes + Salmoniformes based on whole mitochondrial genome sequences.},
  author={Matthew A. Campbell and J. Andr{\'e}s L{\'o}pez and Tetsuya Sado and Masaki Miya},
  journal={Gene},
  year={2013},
  volume={530 1},
  pages={
          57-65
        }
}

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References

SHOWING 1-10 OF 60 REFERENCES

Phylogeny of salmonids (Salmoniformes: Salmonidae) and its molecular dating: Analysis of nuclear RAG1 gene

TLDR
The phylogenetic relationships among 26 species of salmonid fishes were studied using the RAG1 gene as phylogenetic marker, and it seems likely that divergence of the Prosopium and Coregonus ancestral lineages occurred during the same time interval.

Framing the Salmonidae Family Phylogenetic Portrait: A More Complete Picture from Increased Taxon Sampling

TLDR
It is found that some groups in Salmonidae are older than previously thought and that the mitochondrial rate of molecular divergence varies markedly among genes and clades, and some species require taxonomic revision, including two monotypic genera, Stenodus and Salvethymus.

Phylogenetic Relationships of Extant Esocid Species (Teleostei: Salmoniformes) Based on Morphological and Molecular Characters

TLDR
This study is the first study to integrate both morphological and molecular data into a phylogenetic analysis of Esox to provide a better understanding of esocid evolution and lay the foundation for the interpretation of fossil material assigned to E sox.

Phylogenetic Relationships of Esocoid Fishes (Teleostei) Based on Partial Cytochrome b and 16S Mitochondrial DNA Sequences

TLDR
The phylogenetic analyses revealed previously undiscovered affinities between species of umbrids and esocids that imply the paraphyly of the Umbridae as currently defined.

Remarkable morphological stasis in an extant vertebrate despite tens of millions of years of divergence

TLDR
Morphological stasis in these two allopatric lineages of Pantodon offers a living vertebrate model for investigating phenotypic stability over millions of generations in the face of profound fluctuations in environmental conditions.

Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes

TLDR
The results suggest that the causes of diversification in large clades are likely to be complex and not easily ascribed to a single event, even a dramatic one such as a whole genome duplication.

Resolution of ray-finned fish phylogeny and timing of diversification

  • T. NearR. Eytan W. Smith
  • Biology, Environmental Science
    Proceedings of the National Academy of Sciences
  • 2012
Ray-finned fishes make up half of all living vertebrate species. Nearly all ray-finned fishes are teleosts, which include most commercially important fish species, several model organisms for

Calibrating and constraining molecular clocks

TLDR
In explaining the role of fossils in establishing timescales, the historical sequ ence in which key observations were made is reviewed, and a list of 63 key dates is presented, with thorough evidence and error expressions, for a wide range of organisms.

Relaxed Phylogenetics and Dating with Confidence

TLDR
This work describes how it can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times and provides a means for measuring the clocklikeness of datasets and comparing this measure between different genes and phylogenies.
...