The visual systems of teleost fishes usually match their habitats and lifestyles. Since coral reefs are bright and colourful environments, the visual systems of their diurnal inhabitants have been more extensively studied than those of nocturnal species. In order to fill this knowledge gap, we conducted a detailed investigation of the visual system of the nocturnal reef fish family Holocentridae. Results showed that the visual system of holocentrids is well adapted to their nocturnal lifestyle with a rod-dominated retina. Surprisingly, rods in all species were arranged into 6-17 well-defined banks, a feature most commonly found in deep-sea fishes, that may increase the light sensitivity of the eye and/or allow colour discrimination in dim-light. Holocentrids also have the potential for dichromatic colour vision during the day with the presence of at least two spectrally different cone types: single cones expressing the blue-sensitive SWS2A gene, and double cones expressing one or two green-sensitive RH2 genes. Some differences were observed between the two subfamilies, with Holocentrinae (squirrelfish) having a slightly more developed photopic visual system than Myripristinae (soldierfish). Moreover, retinal topography of both ganglion cells and cone photoreceptors showed specific patterns for each cell type, likely highlighting different visual demands at different times of the day, such as feeding. Overall, their well-developed scotopic visual systems and the ease of catching and maintaining holocentrids in aquaria, make them ideal models to investigate teleost dim-light vision and more particularly shed light on the function of the multibank retina and its potential for dim-light colour vision.

Vision mediates important behavioural tasks such as mate choice, escape from predators and foraging. In fish, photoreceptors are generally tuned to specific visual tasks and/or to their light environment, according to depth or water colour to ensure optimal performance. Evolutionary mechanisms acting on genes encoding opsin, the protein component of the photopigment, can influence the spectral sensitivity of photoreceptors. Opsin genes are known to respond to environmental conditions on a number of time scales, including short time frames due to seasonal variation, or through longer-term evolutionary tuning. There is also evidence for 'on-the-fly' adaptations in adult fish in response to rapidly changing environmental conditions; however, results are contradictory. Here, we investigated the ability of three reef fish species that belong to two ecologically distinct families, yellow-striped cardinalfish (), Ambon damselfish () and lemon damselfish (), to alter opsin gene expression as an adaptation to short-term (weeks to months) changes of environmental light conditions, and attempted to characterize the underlying expression regulation principles. We report the ability for all species to alter opsin gene expression within months and even a few weeks, suggesting that opsin expression in adult reef fish is not static. Furthermore, we found that changes in opsin expression in single cones generally occurred more rapidly than in double cones, and identified different responses of opsin gene expression between the ecologically distinct reef fish families. Quantum catch correlation analysis suggested different regulation mechanisms for opsin expression dependent on gene class.

Animal visual systems adapt to environmental light on various timescales. In scotopic conditions, evolutionary time‐scale adaptations include spectral tuning to a narrower light spectrum, loss (or inactivation) of visual genes, and pure‐rod or rod‐dominated retinas. Some fishes inhabiting shallow coral reefs may show activity during the day and at night. It is unclear whether these fishes show adaptations typical of exclusively nocturnal or deep‐sea fishes, or of diurnally active shallow‐water species. Here, we investigated visual pigment diversity in cardinalfishes (Apogonidae). Most cardinalfishes are nocturnal foragers, yet they aggregate in multispecies groups in and around coral heads during the day, engaging in social and predator avoidance behaviours. We sequenced retinal transcriptomes of 28 species found on the Great Barrier Reef, assessed the diversity of expressed opsin genes and predicted the spectral sensitivities of resulting photopigments using sequence information. Predictions were combined with microspectrophotometry (MSP) measurements in seven cardinalfish species. Retinal opsin expression was rod opsin (RH1) dominated (>87%), suggesting the importance of scotopic vision. However, all species retained expression of multiple cone opsins also, presumably for colour vision. We found five distinct quantitative expression patterns among cardinalfishes, ranging from short‐wavelength‐shifted to long‐wavelength‐shifted. These results indicate that cardinalfishes are both well adapted to dim‐light conditions and have retained a sophisticated colour vision sense. Other reef fish families also show both nocturnal and diurnal activity while most are strictly one or the other. It will be interesting to compare these behavioural differences across different phylogenetic groups using the criteria and methods developed here.

16 17 1. Vertebrates exhibit diverse visual systems that vary in terms of morphology, number and 18 distribution of spectrally distinct photoreceptor types, visual opsin genes and gene 19 expression levels. 20 2. In fish, such adaptations are driven by two main factors: differences in the light environment 21 and behavioural tasks, including foraging, predator avoidance and mate selection. Whether 22 visual systems also adapt to small-scale spectral differences in light, between microhabitats, 23 is less clear. 243. We suggest that differences in microhabitat use by cardinalfishes (Apogonidae) on coral 25 reefs drive morphological and molecular adaptations in their visual systems. To test this, we 26 investigated diurnal microhabitat use in 17 cardinalfish species and assessed whether this 27 correlated with differences in visual opsin gene expression and eye morphology. 28 4. We found that cardinalfishes display six types of partitioning behaviours during the day, 29 ranging from specialists found exclusively in the water column to species that are always 30 hidden inside the reef matrix. 31 5. Using data on visual opsin gene expression previously characterized in this family, it was 32 discovered that species in exposed habitats had increased expression of the short-wavelength 33 sensitive violet opsin (SWS2B) and decreased expression of the dim-light active rod opsin 34 (RH1). Species of intermediate exposure, on the other hand, expressed opsins that are 35 mostly sensitive to the blue-green central part of the light spectrum (SWS2As and RH2s), 36while fishes entirely hidden in the reef substrate had an increased expression of the long-37 wavelength sensitive red opsin (LWS). 38 6. We found that eye size relative to body size significantly differed between cardinalfish 39 species, and relative eye size decreased with an increase in habitat exposure. 40 7. Retinal topography did not show co-adaptation with microhabitat use, but instead with 41 feeding mode. 42 8. We suggest that, although most cardinalfishes are nocturnal foragers, their visual systems 43 are also adapted to both the light intensity and the light spectrum of their preferred diurnal 44 microhabitat. 45 48 the molecular level. In fish, this diversity is mainly driven by differences in the availability of light 49