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MBE Advance Access published online on October 27, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msi028
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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Accepted October 20, 2004

Research Article

Physicochemical Evolution and Molecular Adaptation of the Cetacean and Artiodactyl Cytochrome b Proteins

D. A. McClellan 1*, E. J. Palfreyman 2, M. J. Smith 1, J. L. Moss 2, R. G. Christensen 3, and J. K. Sailsbery 4

1 Dept. Integrative Biology, Brigham Young University, Provo, UT
2 Dept. Microbiology & Molecular Biology, Brigham Young University, Provo, UT
3 Dept. Integrative Biology, Brigham Young University, Provo, UT; Dept. Physiology & Developmental Biology, Brigham Young University, Provo, UT
4 Dept. Integrative Biology, Brigham Young University, Provo, UT; Dept. Microbiology & Molecular Biology, Brigham Young University, Provo, UT; Dept. Computer Science, Brigham Young University, Provo, UT

* To whom correspondence should be addressed.
D. A. McClellan, E-mail: david_mcclellan{at}byu.edu


  Abstract

Cetaceans have most likely experienced metabolic shifts since evolutionarily diverging from their terrestrial ancestors, shifts that may be reflected in the proteins like cytochrome b that are responsible for metabolic efficiency. However, accepted statistical methods for detecting molecular adaptation are largely biased against even moderately conservative proteins because the primary criterion involves a comparison of nonsynonymous and synonymous substitution rates (dN/dS); they do not allow for the possibility that adaptation may come in the form of very few amino acid changes. We apply the MM01 model (McClellan and McCracken 2001) to the possible molecular adaptation of cytochrome b among cetaceans because it does not rely on a dN/dS ratio, instead opting to evaluate positive selection in terms of the amino acid properties that comprise protein phenotypes that selection at the molecular level may act upon. We also apply the codon-degeneracy model (CDM; McClellan 2000), which focuses on evaluating overall patterns of nucleotide substitution in terms of base-exchange, codon position, and synonymy, to estimate the overall effect of selection. Using these relatively new models, we characterize the molecular adaptation that has occurred in the cetacean cytochrome b protein by comparing revealed amino acid replacement patterns to those found among artiodactyls, the modern terrestrial mammals found to be most closely related to cetaceans. Our findings suggest that several regions of the cetacean cytochrome b protein have experienced molecular adaptation. Also that these adaptations are spatially associated with domain structure, protein function, and the structure and function of the cytochrome bc1 complex and its constituents. We also have found a general correlation between the results of the analytical software programs TreeSAAP (which implements the MM01 model) and CDM (which implements the codon-degeneracy model).

Keywords: Molecular adaptation; Cytochrome b; Artiodactyla; Cetacea; Protein evolution; Physicochemical amino acid properties.
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