Abstract
BackgroundPhenotypic evolution may occur through mutations that affect either the structure or expression of protein-coding genes. Although the evolution of color vision has historically been attributed to structural mutations within the opsin genes, recent research has shown that opsin regulatory mutations can also tune photoreceptor sensitivity and color vision. Visual sensitivity in African cichlid fishes varies as a result of the differential expression of seven opsin genes. We crossed cichlid species that express different opsin gene sets and scanned their genome for expression Quantitative Trait Loci (eQTL) responsible for these differences. Our results shed light on the role that different structural, cis-, and trans-regulatory mutations play in the evolution of color vision.ResultsWe identified 11 eQTL that contribute to the divergent expression of five opsin genes. On three linkage groups, several eQTL formed regulatory “hotspots” associated with the expression of multiple opsins. Importantly, however, the majority of the eQTL we identified (8/11 or 73%) occur on linkage groups located trans to the opsin genes, suggesting that cichlid color vision has evolved primarily via trans-regulatory divergence. By modeling the impact of just two of these trans-regulatory eQTL, we show that opsin regulatory mutations can alter cichlid photoreceptor sensitivity and color vision at least as much as opsin structural mutations can.ConclusionsCombined with previous work, we demonstrate that the evolution of cichlid color vision results from the interplay of structural, cis-, and especially trans-regulatory loci. Although there are numerous examples of structural and cis-regulatory mutations that contribute to phenotypic evolution, our results suggest that trans-regulatory mutations could contribute to phenotypic divergence more commonly than previously expected, especially in systems like color vision, where compensatory changes in the expression of multiple genes are required in order to produce functional phenotypes.
Highlights
Phenotypic evolution may occur through mutations that affect either the structure or expression of protein-coding genes
The evolution of vertebrate color vision has primarily been attributed to structural mutations within the opsin genes [1], a group of G-protein-coupled receptors expressed within the light-sensitive photoreceptor cells of the retina [2]
Some degree of autocorrelation between opsins is expected since we measure the expression of each gene relative to the total expression of all six opsins, compensatory trade-offs between these opsin pairs are expected since they must be alternatively expressed within identical photoreceptor classes in order to form the distinct visual palettes found among different cichlid species
Summary
Phenotypic evolution may occur through mutations that affect either the structure or expression of protein-coding genes. The evolution of vertebrate color vision has primarily been attributed to structural mutations within the opsin genes [1], a group of G-protein-coupled receptors expressed within the light-sensitive photoreceptor cells of the retina [2]. Since a complex network of both cis- and trans-regulatory factors controls vertebrate opsin expression [8,9,10], quantitative genetic studies of opsin gene regulation have the potential to clarify the role that different structural, cis-, and trans-regulatory mutations play in the evolution of color vision. The primary genetic mechanism responsible for this diversity is the differential regulation of seven opsin genes, structural mutations
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