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MBE Advance Access originally published online on January 12, 2005
Molecular Biology and Evolution 2005 22(4):894-904; doi:10.1093/molbev/msi081
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Molecular Biology and Evolution vol. 22 no. 4 © Society for Molecular Biology and Evolution 2005; all rights reserved.

Research Article

Protein Structural Influences in Rhodopsin Evolution

Lorraine Marsh* and Carole S. Griffiths*,{dagger}

* Department of Biology, Long Island University; and {dagger} Ornithology Department, American Museum of Natural History

E-mail: lorraine.marsh{at}liu.edu.

Incorporating specific structural information can be important for developing a realistic model of evolution for phylogenetic reconstruction of protein-coding genes. We analyzed 62 sequences of vertebrate rhodopsin. The bovine rhodopsin structure was used to label residue sites by surface accessibility, secondary structure, and transmembrane (TM) location. Residue sites with amino acid differences were identified; using maximum parsimony (MP), homoplasious residues were identified. Residues were analyzed for patterns that would indicate correlation of rate with secondary structure, surface accessibility, or position relative to the lipid bilayer. Surface residues, especially those residing in one of the seven TM helices, were significantly correlated with high rates of amino acid substitution. This category of residues, defined solely by protein structural characteristics, potentially defined a class enriched in homoplasious residues. MP analysis using all sites led to a tree with anomalies in the relationships of amphibian, mammalian, bird, and alligator species. Analysis excluding the structurally defined residue class recovered a more accurate phylogeny. A model is presented for including structural influences on rate in phylogenetic inference.

Key Words: protein structure • substitution rate • rhodopsin • homoplasy • extra steps


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[Abstract] [Full Text] [PDF]


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