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MBE Advance Access published online on October 16, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl136
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted September 25, 2006

Letter

MtArt: A New Model of Amino Acid Replacement for Arthropoda

Federico Abascal 1 *, David Posada 2, and Rafael Zardoya 3

1 Departamento de Bioquímica, Genética, e Inmunología, Universidad de Vigo, 36310 Vigo, Spain; Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, José Gutiérrez Abascal, 2, 28006 Madrid, Spain
2 Departamento de Bioquímica, Genética, e Inmunología, Universidad de Vigo, 36310 Vigo, Spain
3 Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, José Gutiérrez Abascal, 2, 28006 Madrid, Spain

* To whom correspondence should be addressed.
Federico Abascal, E-mail: fabascal{at}uvigo.es


  Abstract

A statistical approach was applied to select which models best fit each individual mitochondrial protein at different taxonomic levels of metazoans. The existing mitochondrial replacement matrices, MtREV and MtMam, were found to be the best-fit models for the mt-proteins of vertebrates, with the exception of Nd6, at different taxonomic levels. Remarkably, existing mitochondrial matrices generally failed to best-fit invertebrate mt-proteins. In an attempt to better modeling the evolution of invertebrate mt proteins a new replacement matrix, named MtArt, was constructed based on arthropod mt-proteomes. The new model was found to best fit almost all analyzed invertebrate mt-protein data sets. The observed pattern of model fit across the different data sets indicates that no single replacement matrix is able to describe the general evolutionary properties of mt-proteins, but rather that taxonomical biases and/or the existence of different mt genetic codes have great influence on which model is selected.

Keywords: mitochondrial genomes; protein evolution; model selection; arthropods.
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