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Adaptive molecular evolution in the opsin genes of rapidly speciating cichlid species.
Mol Biol Evol. 2005 Jun; 22(6):1412-22.MB

Abstract

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.

Authors+Show Affiliations

Hubbard Center for Genome Studies and Department of Zoology, University of New Hampshire, NH, USA. tspady@cisunix.unh.eduNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

15772376

Citation

Spady, Tyrone C., et al. "Adaptive Molecular Evolution in the Opsin Genes of Rapidly Speciating Cichlid Species." Molecular Biology and Evolution, vol. 22, no. 6, 2005, pp. 1412-22.
Spady TC, Seehausen O, Loew ER, et al. Adaptive molecular evolution in the opsin genes of rapidly speciating cichlid species. Mol Biol Evol. 2005;22(6):1412-22.
Spady, T. C., Seehausen, O., Loew, E. R., Jordan, R. C., Kocher, T. D., & Carleton, K. L. (2005). Adaptive molecular evolution in the opsin genes of rapidly speciating cichlid species. Molecular Biology and Evolution, 22(6), 1412-22.
Spady TC, et al. Adaptive Molecular Evolution in the Opsin Genes of Rapidly Speciating Cichlid Species. Mol Biol Evol. 2005;22(6):1412-22. PubMed PMID: 15772376.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Adaptive molecular evolution in the opsin genes of rapidly speciating cichlid species. AU - Spady,Tyrone C, AU - Seehausen,Ole, AU - Loew,Ellis R, AU - Jordan,Rebecca C, AU - Kocher,Thomas D, AU - Carleton,Karen L, Y1 - 2005/03/16/ PY - 2005/3/18/pubmed PY - 2005/9/17/medline PY - 2005/3/18/entrez SP - 1412 EP - 22 JF - Molecular biology and evolution JO - Mol Biol Evol VL - 22 IS - 6 N2 - 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. SN - 0737-4038 UR - https://www.unboundmedicine.com/medline/citation/15772376/Adaptive_molecular_evolution_in_the_opsin_genes_of_rapidly_speciating_cichlid_species_ DB - PRIME DP - Unbound Medicine ER -