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MBE Advance Access originally published online on March 16, 2005
Molecular Biology and Evolution 2005 22(6):1412-1422; doi:10.1093/molbev/msi137
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© The Author 2005. 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@oupjournals.org

Adaptive Molecular Evolution in the Opsin Genes of Rapidly Speciating Cichlid Species

Tyrone C. Spady*, Ole Seehausen{dagger}, Ellis R. Loew{ddagger}, Rebecca C. Jordan§, Thomas D. Kocher* and Karen L. Carleton*

* Hubbard Center for Genome Studies and Department of Zoology, University of New Hampshire; {dagger} Institute of Zoology, Aquatic Ecology, University of Bern, Bern, Switzerland; {ddagger} Department of Biomedical Sciences, Cornell University; and § Ecology, Evolution, and Natural Resources, Cook College, Rutgers University

E-mail: tspady{at}cisunix.unh.edu.

Cichlid fish inhabit a diverse range of environments that vary in the spectral content of light available for vision. These differences should result in adaptive selective pressure on the genes involved in visual sensitivity, the opsin genes. This study examines the evidence for differential adaptive molecular evolution in East African cichlid opsin genes due to gross differences in environmental light conditions. First, we characterize the selective regime experienced by cichlid opsin genes using a likelihood ratio test format, comparing likelihood models with different constraints on the relative rates of amino acid substitution, across sites. Second, we compare turbid and clear lineages to determine if there is evidence of differences in relative rates of substitution. Third, we present evidence of functional diversification and its relationship to the photic environment among cichlid opsin genes. We report statistical evidence of positive selection in all cichlid opsin genes, except short wavelength–sensitive 1 and short wavelength–sensitive 2b. In all genes predicted to be under positive selection, except short wavelength–sensitive 2a, we find differences in selective pressure between turbid and clear lineages. Potential spectral tuning sites are variable among all cichlid opsin genes; however, patterns of substitution consistent with photic environment–driven evolution of opsin genes are observed only for short wavelength–sensitive 1 opsin genes. This study identifies a number of promising candidate-tuning sites for future study by site-directed mutagenesis. This work also begins to demonstrate the molecular evolutionary dynamics of cichlid visual sensitivity and its relationship to the photic environment.

Key Words: positive Darwinian selection • cichlid • opsin • photic environment


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