Phylogenetic artifacts can be caused by leucine, serine, and arginine codon usage heterogeneity: dinoflagellate plastid origins as a case study.

@article{Inagaki2004PhylogeneticAC,
  title={Phylogenetic artifacts can be caused by leucine, serine, and arginine codon usage heterogeneity: dinoflagellate plastid origins as a case study.},
  author={Yuji Inagaki and Alastair G. B. Simpson and Joel B Dacks and Andrew J. Roger},
  journal={Systematic biology},
  year={2004},
  volume={53 4},
  pages={582-93}
}
Phylogenetic analyses of first and second codon positions (DNA1 + 2 analysis) and amino acid sequences (protein analysis) are often thought to provide similar estimates of deep-level phylogeny. However, here we report a novel artifact influencing DNA level phylogenetic inference of protein-coding genes introduced by codon usage heterogeneity that causes significant incongruities between DNA1 + 2 and protein analyses. DNA1 + 2 analyses of plastid-encoded psbA genes (encoding of photosystem II D1… CONTINUE READING
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