Journal of Phylogenetics & Evolutionary Biology

M.L. Bean Museum, Brigham Young University, Provo, UT 84602, USA

Publications

• Review   
  How Codon Usage Biases Affect Our Ability to Recover the Tree of Life
  Author(s): Justin B. Miller, Michael F. Whiting, John S.K. Kauwe and Perry G. Ridge*
  
  Many common phylogenomic algorithms that were well-adapted to classify limited numbers of species have become increasingly intractable as large whole-genome sequencing datasets have emerged. Various novel approaches use characteristics of DNA sequences, including variations in codon usage biases, to establish the phylogenetic relatedness of species. Codon choice affects transcription and translational efficiencies, which can lead to differential protein expression and phenotypic variation that may be a target of selection. Several functional biases exist within genes, including the number of codons that are used, the position of the codons, and the overall nucleotide composition of the genome. Although recent algorithms capitalize on specific codon usage biases to improve phylogenetic tree inference, the phylogenies produced by these algorithms vary significantly and indicate differen.. Read More»
  DOI: 10.37421/2329-9002.2021.9.211

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