Evolutionary history limits species' ability to match colour sensitivity to available habitat light

Dietary carotenoids enhance SWS1 expression in female western mosquitofish (Gambusia affinis) but do not impair their likelihood of pregnancy in the presence of male guppy

The various cone opsin genes are responsible for distinct ecological tasks, with the altered expression profiles in teleost fishes representing an excellent paradigm for studying how fishes can quickly adapt to diverse habitats within their lifecycles. The molecular mechanisms underlying transcriptional switching among cone opsin genes are still being investigated, but factors such as light conditions, developmental stages, sex hormones, and diet are known to play a role in changing cone opsin expression profiles. Based on previous research on guppies, we hypothesized that a diet rich in carotenoids could enhance expression of the opsin gene LWS in western mosquitofish (Gambusia affinis) and potentially influence female mate choice. We raised female western mosquitofish under low-level or high-level carotenoid diets and then conducted female mating preference experiments, with or without the presence of male guppy (Poecilia reticulata). qPCR revealed that high carotenoid intake upregulates SWS1 rather than LWS transcription. This positive feedback loop may promote foraging efficiency and also protect the visual system from UV damage. The carotenoid diets had no effect on pregnancy likelihood, possibly because UV light is not a critical cue in western mosquitofish female mate choice and/or the light source we used did not encompass the UV spectrum. Presence of male guppies had no effect on pregnancy likelihood, though a previous study reported that it significantly reduced brood size. Therefore, interactions between male guppies and western mosquitofish likely reduces the number of copulations and/or disrupts parenting to reduce the number of offspring.

Red vision in animals is broadly associated with lighting environment but not types of visual task

Red sensitivity is the exception rather than the norm in most animal groups. Among species with red sensitivity, there is substantial variation in the peak wavelength sensitivity (λmax) of the long wavelength sensitive (LWS) photoreceptor. It is unclear whether this variation can be explained by visual tuning to the light environment or to visual tasks such as signalling or foraging. Here, we examine long wavelength sensitivity across a broad range of taxa showing diversity in LWS photoreceptor λmax: insects, crustaceans, arachnids, amphibians, reptiles, fish, sharks and rays. We collated a list of 161 species with physiological evidence for a photoreceptor sensitive to red wavelengths (i.e. λmax ≥ 550 nm) and for each species documented abiotic and biotic factors that may be associated with peak sensitivity of the LWS photoreceptor. We found evidence supporting visual tuning to the light environment: terrestrial species had longer λmax than aquatic species, and of these, species from turbid shallow waters had longer λmax than those from clear or deep waters. Of the terrestrial species, diurnal species had longer λmax than nocturnal species, but we did not detect any differences across terrestrial habitats (closed, intermediate or open). We found no association with proxies for visual tasks such as having red morphological features or utilising flowers or coral reefs. These results support the emerging consensus that, in general, visual systems are broadly adapted to the lighting environment and diverse visual tasks. Links between visual systems and specific visual tasks are commonly reported, but these likely vary among species and do not lead to general patterns across species.

Discovering genotype-phenotype relationships with machine learning and the Visual Physiology Opsin Database (VPOD)

BACKGROUND

Predicting phenotypes from genetic variation is foundational for fields as diverse as bioengineering and global change biology, highlighting the importance of efficient methods to predict gene functions. Linking genetic changes to phenotypic changes has been a goal of decades of experimental work, especially for some model gene families, including light-sensitive opsin proteins. Opsins can be expressed in vitro to measure light absorption parameters, including λmax-the wavelength of maximum absorbance-which strongly affects organismal phenotypes like color vision. Despite extensive research on opsins, the data remain dispersed, uncompiled, and often challenging to access, thereby precluding systematic and comprehensive analyses of the intricate relationships between genotype and phenotype.

RESULTS

Here, we report a newly compiled database of all heterologously expressed opsin genes with λmax phenotypes that we call the Visual Physiology Opsin Database (VPOD). VPOD_1.0 contains 864 unique opsin genotypes and corresponding λmax phenotypes collected across all animals from 73 separate publications. We use VPOD data and deepBreaks to show regression-based machine learning (ML) models often reliably predict λmax, account for nonadditive effects of mutations on function, and identify functionally critical amino acid sites.

CONCLUSION

The ability to reliably predict functions from gene sequences alone using ML will allow robust exploration of molecular-evolutionary patterns governing phenotype, will inform functional and evolutionary connections to an organism's ecological niche, and may be used more broadly for de novo protein design. Together, our database, phenotype predictions, and model comparisons lay the groundwork for future research applicable to families of genes with quantifiable and comparable phenotypes.