Early-branching euteleost relationships: areas of congruence between concatenation and coalescent model inferences

@article{Campbell2017EarlybranchingER,
  title={Early-branching euteleost relationships: areas of congruence between concatenation and coalescent model inferences},
  author={Matthew A. Campbell and M. Alfaro and Max Belasco and J. Andr{\'e}s L{\'o}pez},
  journal={PeerJ},
  year={2017},
  volume={5}
}
Phylogenetic inference based on evidence from DNA sequences has led to significant strides in the development of a stable and robustly supported framework for the vertebrate tree of life. To date, the bulk of those advances have relied on sequence data from a small number of genome regions that have proven unable to produce satisfactory answers to consistently recalcitrant phylogenetic questions. Here, we re-examine phylogenetic relationships among early-branching euteleostean fish lineages… 
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References

SHOWING 1-10 OF 124 REFERENCES
Esociform Phylogeny
TLDR
An expanded dataset of DNA sequences from the mitochondrial and nuclear genomes is assembled to test existing hypotheses of esociform inter- and intraordinal relationships and offers support for the monophyly of the Osmeridae, for a sister-group relationship between the Retropinnidae and the Osmersoidei, and for a close relationship of Stomiiformes and Osmeriformes.
Origin and phylogenetic interrelationships of teleosts : honoring Gloria Arratia : proceedings of the international symposium at the ASIH Annual Meeting in St. Louis, Missouri, 2007
TLDR
A set of all 13 mitochondrial protein coding genes from 230 mitochondrial genomes is used in a large-scale phylogenetic analysis of teleost relationships and the resulting best phylogenetic hypothesis is discussed in the context of other recent molecular phylogenetic studies of Teleost and with respect to conventionally understood teleost interrelationships.
Estimating phylogenetic trees from genome‐scale data
TLDR
It is shown that approaches, such as binning, designed to augment the signal in species tree analyses can distort the distribution of gene trees and are inconsistent, and that Computationally efficient species tree methods incorporating biological realism are a key to phylogenetic analysis of whole‐genome data.
Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the "ancient fish".
Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye
TLDR
A phylogeny based on UCE loci that unequivocally supports flatfish monophyly and a single origin of asymmetry points to phenotypic divergence early within carangimorph history that broadly matches with the predictions of adaptive models of lineage diversification.
Contentious relationships in phylogenomic studies can be driven by a handful of genes
TLDR
A maximum likelihood framework is used to quantify the distribution of phylogenetic signal among genes and sites for 17 contentious branches and 6 well-established control branches in plant, animal and fungal phylogenomic data matrices, finding that resolution in some of these 17 branches rests on a single gene or a few sites.
The gene tree delusion.
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