Phylogenetic estimation under codon models can be biased by codon usage heterogeneity

Molecular Phylogenetics and Evolution
Yuji Inagaki, Andrew J Roger

Abstract

In theory, codon models that account for the dependence of nucleotide substitutions between codon positions as well as differences between synonymous and non-synonymous changes best describe the sequence evolution in protein coding genes. However, in practice we know little about the degree to which violations of the assumptions of codon model-based estimates occur, and how significant these artifacts may be. In nucleotide-based phylogenies from first and second codon positions in a concatenated plastid gene data set, two distantly related taxa--dinoflagellate and haptophyte plastids--were robustly grouped together. This artifactual grouping is attributed to the parallel heterogeneity in leucine (Leu) and serine (Ser) codon usages in the data set. Here, by using this data set, we demonstrated that codon-based phylogenetic estimations are seriously biased, robustly uniting the dinoflagellate and haptophyte plastids into a monophyletic clade, when the model assumption of homogeneity of codon composition was violated. Our results suggest that similar phylogenetic artifacts may occur via codon usage heterogeneity in any amino acids in codon model-based estimations. We advise that homogeneity in codon usage across taxa in a data set...Continue Reading

References

Mar 15, 1979·Journal of Molecular Evolution·T MiyataT Yasunaga
Nov 21, 1997·Computer Applications in the Biosciences : CABIOS·Z Yang
Mar 27, 1999·Journal of Molecular Evolution·P G Foster, D A Hickey
Apr 6, 2002·Bioinformatics·Heiko A SchmidtArndt von Haeseler
Nov 16, 2002·Current Opinion in Genetics & Development·Laurent Duret
Jul 25, 2003·Molecular Phylogenetics and Evolution·Matthew J Phillips, David Penny
Aug 13, 2003·Bioinformatics·Fredrik Ronquist, John P Huelsenbeck
Jan 24, 2004·Molecular Biology and Evolution·G L Abby HarrisonDavid Penny
Apr 16, 2004·Molecular Biology and Evolution·Matthew J PhillipsDavid Penny
Jan 18, 2005·International Journal of Systematic and Evolutionary Microbiology·James T HarperPatrick J Keeling
Mar 5, 2005·Molecular Biology and Evolution·Hwan Su YoonDebashish Bhattacharya
May 27, 2005·Molecular Biology and Evolution·Tsvetan R BachvaroffCharles F Delwiche
Sep 24, 2005·Molecular Biology and Evolution·Beth ShapiroAlexei J Drummond
Nov 26, 2005·Molecular Biology and Evolution·Alastair G B SimpsonAndrew J Roger

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Citations

Nov 28, 2007·Genetics·Andreas Heger, Chris P Ponting
May 20, 2009·Journal of Molecular Evolution·Caroline MichelleChristian R Andres
Oct 12, 2010·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Mary J O'ConnellCharles Spillane
Feb 28, 2013·Journal of Molecular Evolution·Rachael A Bay, Joseph P Bielawski
Apr 24, 2007·Molecular Phylogenetics and Evolution·M Virginia Sanchez-PuertaCharles F Delwiche
Oct 1, 2008·Journal of Phycology·M Virginia Sanchez-Puerta, Charles F Delwiche
Dec 30, 2006·PLoS Genetics·Laura Wegener ParfreyLaura A Katz
Jul 24, 2008·PloS One·E Alejandro HerradaCarlos M Duarte
Oct 29, 2015·PloS One·Alicia Abadía-CardosoFrancisco Javier García de León
Sep 11, 2012·Systematic Biology·Omar Rota-StabelliDavide Pisani
Jan 3, 2018·Molecular Biology and Evolution·Seunggwan ShinDuane D McKenna

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