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

Systematic Biology
Yuji InagakiAndrew J Roger

Abstract

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 proteins) strongly suggest a relationship between haptophyte plastids and typical (peridinin-containing) dinoflagellate plastids. The psbA genes from haptophytes and a subset of the peridinin-type plastids display similar codon usage patterns for Leu, Ser, and Arg, which are each encoded by two separated codon sets that differ at first or first plus second codon positions. Our detailed analyses clearly indicate that these unusual preferences shared by haptophyte and some peridinin-type plastid genes are largely responsible for their strong affinity in DNA analyses. In particular, almost all of the support from DNA level analyses for the monophyly of haptophyte and peridinin-type plastids is lost when the codons corresponding to constant ...Continue Reading

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Citations

Dec 30, 2006·PLoS Genetics·Laura Wegener ParfreyLaura A Katz
May 23, 2015·Proceedings of the National Academy of Sciences of the United States of America·Richard G Dorrell, Christopher J Howe
Oct 1, 2008·Journal of Phycology·M Virginia Sanchez-Puerta, Charles F Delwiche
Jan 3, 2018·Molecular Biology and Evolution·Seunggwan ShinDuane D McKenna
Jul 1, 2006·American Journal of Botany·Jonathan R Bennett, Sarah Mathews
Oct 1, 2004·American Journal of Botany·Patrick J Keeling
Oct 1, 2004·American Journal of Botany·Jeremiah D HackettDebashish Bhattacharya
Jul 27, 2005·Journal of Molecular Evolution·Kerstin Hoef-EmdenShoshana Malis Arad
Jul 28, 2019·Biomolecules·Christen M Klinger, Elisabeth Richardson
Mar 5, 2005·Molecular Biology and Evolution·Hwan Su YoonDebashish Bhattacharya
Sep 11, 2012·Systematic Biology·Omar Rota-StabelliDavide Pisani
May 27, 2005·Molecular Biology and Evolution·Tsvetan R BachvaroffCharles F Delwiche
Nov 4, 2020·Scientific Reports·Alexandre Freitas da SilvaGabriel Luz Wallau
May 2, 2006·Molecular Phylogenetics and Evolution·Yuji Inagaki, Andrew J Roger

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