Why are there so many opsin genes in fish?

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Over the next five years there are two significant questions I aim to answer as part of my long-term study of gene duplication and divergence: 1) Why do fish have so many opsins genes? 2) Is opsin mRNA transcript abundance a good proxy for opsin protein abundance? By day, most humans are trichromatic. Different light-sensitive cone cells in our retinas express short, medium, or long wavelength-sensitive opsin genes. This repertoire, while larger than that of most mammals, pales in comparison to fish. For example, guppies have nine and zebrafish have eight different cone cell opsins. Not only do fish have lots of opsin genes, they have an enormous diversity. Why? The data we will collect from flatfish, guppies, stickleback and zebrafish will allow us to test four hypotheses: i) A large opsin gene 'toolkit' improves the ability of fish to match their vision to variation in their spectral environment. ii) 'Visual opsins' have non-ocular roles, specifically in the skin, that are better served by a large opsin repertoire. iii) There is selection for regional specialization in the retina (i.e., different opsins expressed in different parts of the retina). iv. Opsin duplication and divergence enhances wavelength discrimination and/or wavelength sensitivity. Three of these hypotheses will be tested by measuring opsin transcript (mRNA) abundance. However, recent experiments suggest that the differential expression of mRNA captures at most 40% of the variation of protein expression. I will use two model species (zebrafish and stickleback), opsin genes, and two new technologies, digital droplet PCR and multi reaction monitoring-based mass spectrophotometry or 'MRM MS' to answer my second question. This research will be of great importance to an enormous number of scientists who quantify gene transcript abundance (e.g., using qPCR) under the assumption that these data are correlated with gene function, that is, with protein abundance.