Circuit mechanisms for colour vision in zebrafish

A standardized nomenclature for the rods and cones of the vertebrate retina

Vertebrate photoreceptors have been studied for well over a century, but a fixed nomenclature for referring to orthologous cell types across diverse species has been lacking. Instead, photoreceptors have been variably-and often confusingly-named according to morphology, presence/absence of 'rhodopsin', spectral sensitivity, chromophore usage, and/or the gene family of the opsin(s) they express. Here, we propose a unified nomenclature for vertebrate rods and cones that aligns with the naming systems of other retinal cell classes and that is based on the photoreceptor type's putative evolutionary history. This classification is informed by the functional, anatomical, developmental, and molecular identities of the neuron as a whole, including the expression of deeply conserved transcription factors required for development. The proposed names will be applicable across all vertebrates and indicative of the widest possible range of properties, including their postsynaptic wiring, and hence will allude to their common and species-specific roles in vision. Furthermore, the naming system is open-ended to accommodate the future discovery of as-yet unknown photoreceptor types.

Comparative transcriptomic insights into the evolution of vertebrate photoreceptor types

To explore the molecular similarities and potential evolutionary origins of vertebrate photoreceptor types, we analyzed single-cell and -nucleus transcriptomic atlases from six vertebrate species: zebrafish, chicken, lizard, opossum, ground squirrel, and human. Comparative analyses identified conserved transcriptional signatures for the five ancestral photoreceptor types: red, blue, green, and UV cones, as well as rods. We further identified and validated molecular markers of the principal and accessory members of the tetrapod double cone. Comparative transcriptomics suggests that the principal member originated from ancestral red cones, although the origin of the accessory member is less clear. The gene expression variation among cone types mirrors their spectral order (red → green → blue → UV). We find that rods are highly dissimilar to all cone types, suggesting that rods may have diverged prior to the spectral diversification of cones.

Protocol to perform ex vivo electroretinography on adult zebrafish

Ex vivo electroretinography (ERG) provides insight into the health and functionality of retinal cells, the integrity of phototransduction, and the visual cycle and allows for the direct application of pharmaceuticals to the retinal tissues. Here, we present a protocol for performing ex vivo ERG on adult zebrafish. We describe steps for zebrafish tissue dissection, mounting tissues, and assembling and connecting cassettes. We then detail procedures for running the Diagnosys software and processing and analyzing the resulting data.

Damsels in Disguise: Development of Ultraviolet Sensitivity and Colour Patterns in Damselfishes (Pomacentridae)

Damselfishes (Pomacentridae) are widespread and highly abundant on tropical coral reefs. They exhibit diverse body colouration within and between the ~250 species and across ontogenetic stages. In addition to human-visible colours (i.e., 400-700 nm), most adult damselfishes reflect ultraviolet (UV, 300-400 nm) colour patches. UV sensitivity and UV colour signals are essential for feeding and form the basis for a secret communication channel invisible to the many UV-blind predatory fish on the reef; however, how these traits develop across ontogenetic stages and their distribution across the damselfish family is poorly characterised. Here, we used UV photography, phylogenetic reconstructions of opsin genes, and differential gene expression analysis (DGE) of retinal samples to investigate the development of UV vision and colour patterns in three ontogenetic stages (pre-settlement larval, juvenile, and adult) of 11 damselfish species. Using DGE, we found similar gene expression between juveniles and adults, which strongly differed from larvae. All species and all stages expressed at least one UV-sensitive sws1 opsin gene. However, UV body colour patterns only started to appear at the juvenile stage. Moreover, Pomacentrus species displayed highly complex UV body patterns that were correlated with the expression of two sws1 copies. This could mean that some damselfishes can discriminate colours that change only in their UV component. We demonstrate dramatic shifts in both UV sensitivity and UV colouration across the development stages of damselfish while highlighting the importance of considering ontogeny when studying the coevolution of visual systems and colour signals.

Methylmercury-induced visual deficits involve loss of GABAergic cells in the zebrafish embryo retina

Methylmercury (MeHg) is a neurotoxicant with adverse effects on visual systems from fish to man. Clinical signs of visual deficits including color-vision alterations, visual field constriction and blindness have been frequently identified in patients and affected animals following acute and chronic exposure to MeHg. However, it is still unclear whether MeHg causes developmental defects in the eye. We performed here an experimental study to analyze retinal cells expressing gamma-aminobutyric acid (GABA) of MeHg-exposed zebrafish embryos and combined this with a deep RNA-seq analysis. Exposure of zebrafish embryos to MeHg (10-30 μg/L) from 4 to 96 h post fertilization (hpf) resulted in significantly decreased number of GABAergic neurons located in the ganglion cells layer (GCL) and inner nuclear layer (INL). Twenty μg MeHg/L abolished the color preference characterized in larval zebrafish aged 5 days post fertilization (dpf), and impaired optomotor response (OMR) in larval zebrafish at 6 dpf. The genes playing a role in retinal cell redox homeostasis, steroid hormone and folate biosynthesis, lysosome activity and necroptosis were enriched in MeHg-treated eyes. The expression patterns of genes encoding opsin and genes involved in phototransduction were altered in the eye by MeHg. Our experimental findings show that MeHg disturbs the retinal cells development by interfering with the cell differentiation and cellular homeostasis, which in turn may lead to visual deficits in the larval zebrafish.

Behavioural and transgenerational effects of artificial light at night (ALAN) of varying spectral compositions in zebrafish (Danio rerio)

Artificial light at night (ALAN) can disrupt the natural behaviour, physiology, and circadian rhythms of organisms exposed to it, and therefore presents a significant and widespread ecological concern. ALAN typically comprises a wide range of wavelengths, and different wavelengths have different effects on circadian clocks. In the animals investigated thus far, short and middle wavelengths are intensely involved in synchronisation and entrainment, but we still have a poor understanding of how different wavelengths might affect behaviour when animals are exposed to ALAN, in particular whether some wavelengths are disproportionally detrimental. This experiment examined the direct and transgenerational effects of 10 different wavelength treatments of ALAN on behaviour in zebrafish (Danio rerio), a diurnally active model organism. Across a 10-day period, female zebrafish were exposed to either a monochromatic wavelength, white light ALAN, or to a control treatment, and the individual impacts of each treatment on locomotion and anxiety-like behaviours were examined both for solitary fish and fish in groups. We found the strongest impact at short wavelengths (365 to 470 nm), with individuals and groups of zebrafish showing more anxiety-like behaviour after fewer nights of ALAN exposure relative to the other wavelengths. Furthermore, F1 offspring born from ALAN-exposed mothers displayed less frequent movement and shorter movement distances despite never being exposed to ALAN themselves, regardless of the spectral treatment. Our results highlight both the specific and broad-spectrum potential for ALAN to cause disruption to locomotion in adult zebrafish and their offspring.

Ontogeny of Thyroid Hormone Signaling in the Retina of Zebrafish: Effects of Thyroidal Status on Retinal Morphology, Cell Survival, and Color Preference

The retina is crucial for converting light into neuronal signals for visual perception. Understanding the retina's structure, function, and development is essential for vision research. It is known that the thyroid hormone (TH) receptor type beta 2 (TRβ2) is a key element in the regulation of cone differentiation in the retina, but other elements of TH signaling, such as transporters and enzyme deiodinases, have also been implicated in retinal cell development and survival. In the present study, we investigated the expression profile of genes involved in TH signaling and analyzed the impact of thyroidal status on retinal morphology, opsin expression, cell death/proliferation profile, as well as color preference behavior during the early retina development of zebrafish larvae. mRNA expression analysis on dissected whole eyes revealed that TH signaling elements gradually increase during eye development, with dio3b being the component that shows the most dramatic change. Mutations generated by CRISPR/CAS9 in the dio3b gene, but not in the thrb gene, modifies the structure of the retina. Disruption in TH level reduces the cell number of the ganglion cell layer, increases cell death, and modifies color preference, emphasizing the critical importance of precise TH regulation by its signaling elements for optimal retinal development and function.

Comparative transcriptomic insights into the evolutionary origin of the tetrapod double cone

The tetrapod double cone is a pair of tightly associated cones called the "principal" and the "accessory" member. It is found in amphibians, reptiles, and birds, as well as monotreme and marsupial mammals but is absent in fish and eutherian mammals. To explore the potential evolutionary origins of the double cone, we analyzed single-cell and -nucleus transcriptomic atlases of photoreceptors from six vertebrate species: zebrafish, chicken, lizard, opossum, ground squirrel, and human. Computational analyses separated the principal and accessory members in chicken and lizard, identifying molecular signatures distinguishing either member from single cones and rods in the same species. Comparative transcriptomic analyses suggest that both the principal and accessory originated from ancestral red cones. Furthermore, the gene expression variation among cone subtypes mirrors their spectral order (red → green → blue → UV), suggesting a constraint in their order of emergence during evolution. Finally, we find that rods are equally dissimilar to all cone types, suggesting that they emerged before the spectral diversification of cones.

Restoration of cone-circuit functionality in the regenerating adult zebrafish retina

Unlike humans, teleosts like zebrafish exhibit robust retinal regeneration after injury from endogenous stem cells. However, it is unclear if regenerating cone photoreceptors regain physiological function and integrate correctly into post-synaptic circuits. We used two-photon calcium imaging of living adult retina to examine photoreceptor responses before and after light-induced lesions. To assess functional recovery of cones and downstream outer retinal circuits, we exploited color opponency; UV cones exhibit intrinsic Off-response to blue light, but On-response to green light, which depends on feedback signals from outer retinal circuits. Accordingly, we assessed the presence and quality of Off- vs. On-responses and found that regenerated UV cones regain both Off-responses to short-wavelength and On-responses to long-wavelength light within 3 months after lesion. Therefore, physiological circuit functionality is restored in regenerated cone photoreceptors, suggesting that inducing endogenous regeneration is a promising strategy for human retinal repair.

"Why (Zebra)fish May Get Ulcers": Cognitive and Social Modulation of Stress in Fish

BACKGROUND

In the bestseller book "Why Zebras Don't Get Ulcers", Robert Sapolsky argues that animals do not suffer from stress-related diseases like humans because for them, stress is episodic, while humans in contrast suffer from chronic psychological stress. In particular, the idea that fish cannot experience psychological stress is still prevalent, partly due to the lack of a homologous brain area to the neocortex. However, emerging evidence suggests that teleosts can undergo psychological stress, defined as a subjective and perceptual experience of the stressor, and in recent years, the underlying mechanisms started to be unveiled.

SUMMARY

The occurrence of cognitive appraisal in the assessment of stressors has been demonstrated in fish, indicating that the subjective evaluation of stimulus valence and salience, rather than absolute intrinsic characteristics of the stimulus itself, play a key role in the activation of the stress response. Moreover, individual biases (i.e., cognitive bias) in the cognitive appraisal of stimuli have also been described in fish, with some individuals consistently evaluating ambiguous stimuli as positive (aka optimists) whereas other individuals (aka pessimists) appraise them as negative. As a result, optimists and pessimists show consistent differences in stress reactivity and susceptibility/resilience to disease. Finally, social context has also been shown to modulate the response to aversive stimuli with the behavior of conspecifics either buffering or enhancing the response (i.e., social buffering vs. social contagion).

KEY MESSAGES

Cognitive appraisal of stressors occurs in fish, implying that the stress response is modulated by a subjective and perceptual experience of the stressor. Moreover, interindividual consistent cognitive biases in the appraisal of stressors are also present in fish making some individuals more susceptible to stress-related diseases. Therefore, psychological stress has a health toll in fish, and psychologically stressed fish can potentially have ulcers.

Light wavelength modulates search behavior performance in zebrafish

Visual systems have evolved to discriminate between different wavelengths of light. The ability to perceive color, or specific light wavelengths, is important as color conveys crucial information about both biotic and abiotic features in the environment. Indeed, different wavelengths of light can drive distinct patterns of activity in the vertebrate brain, yet what remains incompletely understood is whether distinct wavelengths can invoke etiologically relevant behavioral changes. To address how specific wavelengths in the visible spectrum modulate behavioral performance, we use larval zebrafish and a stereotypic light-search behavior. Prior work has shown that the cessation of light triggers a transitional light-search behavior, which we use to interrogate wavelength-dependent behavioral modulation. Using 8 narrow spectrum light sources in the visible range, we demonstrate that all wavelengths induce motor parameters consistent with search behavior, yet the magnitude of search behavior is spectrum sensitive and the underlying motor parameters are modulated in distinct patterns across short, medium, and long wavelengths. However, our data also establishes that not all motor features of search are impacted by wavelength. To define how wavelength modulates search performance, we performed additional assays with alternative wavelengths, dual wavelengths, and variable intensity. Last, we also tested blind larvae to resolve which components of wavelength dependent behavioral changes potentially include signaling from non-retinal photoreception. These findings have important implications as organisms can be exposed to varying wavelengths in laboratory and natural settings and therefore impose unique behavioral outputs.

The vertebrate retina: a window into the evolution of computation in the brain

Animal brains are probably the most complex computational machines on our planet, and like everything in biology, they are the product of evolution. Advances in developmental and palaeobiology have been expanding our general understanding of how nervous systems can change at a molecular and structural level. However, how these changes translate into altered function - that is, into 'computation' - remains comparatively sparsely explored. What, concretely, does it mean for neuronal computation when neurons change their morphology and connectivity, when new neurons appear or old ones disappear, or when transmitter systems are slowly modified over many generations? And how does evolution use these many possible knobs and dials to constantly tune computation to give rise to the amazing diversity in animal behaviours we see today? Addressing these major gaps of understanding benefits from choosing a suitable model system. Here, I present the vertebrate retina as one perhaps unusually promising candidate. The retina is ancient and displays highly conserved core organisational principles across the entire vertebrate lineage, alongside a myriad of adjustments across extant species that were shaped by the history of their visual ecology. Moreover, the computational logic of the retina is readily interrogated experimentally, and our existing understanding of retinal circuits in a handful of species can serve as an anchor when exploring the visual circuit adaptations across the entire vertebrate tree of life, from fish deep in the aphotic zone of the oceans to eagles soaring high up in the sky.

Shy and Bold Fish Have the Same Preference for Light Color Selection

Personality, which matters for animal welfare, demonstrates behavioral differences. Light is one of the most important factors in aquaculture. However, how fish personality affects light color selection is unclear. In this study, we tested the personality of yellow catfish Pelteobagrus fulvidraco juveniles and then quantified the selective behaviors of different personalities under six light colors: violet (410-420 nm), yellow (580-590 nm), green (550-560 nm), red (620-630 nm), blue (470-480 nm), and white. The results showed that juveniles preferred the yellow and green light over the other colors of light, probably due to different reasons. The average cumulative dwell time in yellow (32.81 ± 5.22%), green (21.81 ± 3.58%), and red (26.36 ± 4.89%) lights was significantly longer than the other light colors, and the average visit frequency in green light (32.00 ± 4.93%) was the most. Juveniles had the longest total moved distance in green light. Moreover, the results demonstrated that shy and bold individuals had the same preference for the green light. Bold individuals could find the preferred light colors rapidly and make quick decisions for light color selection. After identifying the preferred light colors, bold individuals reduced the frequency of exploration. This study provides a theoretical basis for the welfare of juvenile yellow catfish in aquaculture.

Repeated Divergence in Opsin Gene Expression Mirrors Photic Habitat Changes in Rapidly Evolving Crater Lake Cichlid Fishes

AbstractSelection pressures differ along environmental gradients, and traits tightly linked to fitness (e.g., the visual system) are expected to track such variation. Along gradients, adaptation to local conditions might be due to heritable and nonheritable environmentally induced variation. Disentangling these sources of phenotypic variation requires studying closely related populations in nature and in the laboratory. The Nicaraguan lakes represent an environmental gradient in photic conditions from clear crater lakes to very turbid great lakes. From two old, turbid great lakes, Midas cichlid fish (Amphilophus cf. citrinellus) independently colonized seven isolated crater lakes of varying light conditions, resulting in a small adaptive radiation. We estimated variation in visual sensitivities along this photic gradient by measuring cone opsin gene expression among lake populations. Visual sensitivities observed in all seven derived crater lake populations shifted predictably in direction and magnitude, repeatedly mirroring changes in photic conditions. Comparing wild-caught and laboratory-reared fish revealed that 48% of this phenotypic variation is genetically determined and evolved rapidly. Decreasing intrapopulation variation as environments become spectrally narrower suggests that different selective landscapes operate along the gradient. We conclude that the power to predict phenotypic evolution along gradients depends on both the magnitude of environmental change and the selective landscape shape.

Ultraviolet vision in anemonefish improves colour discrimination

In many animals, ultraviolet (UV) vision guides navigation, foraging, and communication, but few studies have addressed the contribution of UV signals to colour vision, or measured UV discrimination thresholds using behavioural experiments. Here, we tested UV colour vision in an anemonefish (Amphiprion ocellaris) using a five-channel (RGB-V-UV) LED display. We first determined that the maximal sensitivity of the A. ocellaris UV cone was ∼386 nm using microspectrophotometry. Three additional cone spectral sensitivities had maxima at ∼497, 515 and ∼535 nm. We then behaviourally measured colour discrimination thresholds by training anemonefish to distinguish a coloured target pixel from grey distractor pixels of varying intensity. Thresholds were calculated for nine sets of colours with and without UV signals. Using a tetrachromatic vision model, we found that anemonefish were better (i.e. discrimination thresholds were lower) at discriminating colours when target pixels had higher UV chromatic contrast. These colours caused a greater stimulation of the UV cone relative to other cone types. These findings imply that a UV component of colour signals and cues improves their detectability, which likely increases the prominence of anemonefish body patterns for communication and the silhouette of zooplankton prey.

Ancestral photoreceptor diversity as the basis of visual behaviour

Animal colour vision is based on comparing signals from different photoreceptors. It is generally assumed that processing different spectral types of photoreceptor mainly serves colour vision. Here I propose instead that photoreceptors are parallel feature channels that differentially support visual-motor programmes like motion vision behaviours, prey capture and predator evasion. Colour vision may have emerged as a secondary benefit of these circuits, which originally helped aquatic vertebrates to visually navigate and segment their underwater world. Specifically, I suggest that ancestral vertebrate vision was built around three main systems, including a high-resolution general purpose greyscale system based on ancestral red cones and rods to mediate visual body stabilization and navigation, a high-sensitivity specialized foreground system based on ancestral ultraviolet cones to mediate threat detection and prey capture, and a net-suppressive system based on ancestral green and blue cones for regulating red/rod and ultraviolet circuits. This ancestral strategy probably still underpins vision today, and different vertebrate lineages have since adapted their original photoreceptor circuits to suit their diverse visual ecologies.

From water to land: Evolution of photoreceptor circuits for vision in air

When vertebrates first conquered the land, they encountered a visual world that was radically distinct from that of their aquatic ancestors. Fish exploit the strong wavelength-dependent interactions of light with water by differentially feeding the signals from up to 5 spectral photoreceptor types into distinct behavioural programmes. However, above the water the same spectral rules do not apply, and this called for an update to visual circuit strategies. Early tetrapods soon evolved the double cone, a still poorly understood pair of new photoreceptors that brought the "ancestral terrestrial" complement from 5 to 7. Subsequent nonmammalian lineages differentially adapted this highly parallelised retinal input strategy for their diverse visual ecologies. By contrast, mammals shed most ancestral photoreceptors and converged on an input strategy that is exceptionally general. In eutherian mammals including in humans, parallelisation emerges gradually as the visual signal traverses the layers of the retina and into the brain.

Imaging the voltage of neurons distributed across entire brains of larval zebrafish

Neurons interact in networks distributed throughout the brain. Although much effort has focused on whole-brain calcium imaging, recent advances in genetically encoded voltage indicators (GEVIs) raise the possibility of imaging voltage of neurons distributed across brains. To achieve this, a microscope must image at high volumetric rate and signal-to-noise ratio. We present a remote scanning light-sheet microscope capable of imaging GEVI-expressing neurons distributed throughout entire brains of larval zebrafish at a volumetric rate of 200.8 Hz. We measured voltage of ∼1/3 of the neurons of the brain, distributed throughout. We observed that neurons firing at different times during a sequence were located at different brain locations, for sequences elicited by a visual stimulus, which mapped onto locations throughout the optic tectum, as well as during stimulus-independent bursts, which mapped onto locations in the cerebellum and medulla. Whole-brain voltage imaging may open up frontiers in the fundamental operation of neural systems.

Birds multiplex spectral and temporal visual information via retinal On- and Off-channels

In vertebrate vision, early retinal circuits divide incoming visual information into functionally opposite elementary signals: On and Off, transient and sustained, chromatic and achromatic. Together these signals can yield an efficient representation of the scene for transmission to the brain via the optic nerve. However, this long-standing interpretation of retinal function is based on mammals, and it is unclear whether this functional arrangement is common to all vertebrates. Here we show that male poultry chicks use a fundamentally different strategy to communicate information from the eye to the brain. Rather than using functionally opposite pairs of retinal output channels, chicks encode the polarity, timing, and spectral composition of visual stimuli in a highly correlated manner: fast achromatic information is encoded by Off-circuits, and slow chromatic information overwhelmingly by On-circuits. Moreover, most retinal output channels combine On- and Off-circuits to simultaneously encode, or multiplex, both achromatic and chromatic information. Our results from birds conform to evidence from fish, amphibians, and reptiles which retain the full ancestral complement of four spectral types of cone photoreceptors.

The multi-level regulation of clownfish metamorphosis by thyroid hormones

Most marine organisms have a biphasic life cycle during which pelagic larvae transform into radically different juveniles. In vertebrates, the role of thyroid hormones (THs) in triggering this transition is well known, but how the morphological and physiological changes are integrated in a coherent way with the ecological transition remains poorly explored. To gain insight into this question, we performed an integrated analysis of metamorphosis of a marine teleost, the false clownfish (Amphiprion ocellaris). We show how THs coordinate a change in color vision as well as a major metabolic shift in energy production, highlighting how it orchestrates this transformation. By manipulating the activity of liver X regulator (LXR), a major regulator of metabolism, we also identify a tight link between metabolic changes and metamorphosis progression. Strikingly, we observed that these regulations are at play in the wild, explaining how hormones coordinate energy needs with available resources during the life cycle.

Trade-off between coding efficiency and color space in outer retinal circuits with colored oil droplets

To enhance color vision, animals adapt diverse strategies according to their environmental conditions. For instance, zebrafish use clever retinal circuits to encode spectral information in aquatic environments. Other species, such as birds, develop colored oil droplets to expand their plethora of distinguishable colors. Studies on these species provide insights into each strategy. Nevertheless, there is no data on retinas using both strategies simultaneously. In this work, we combine our knowledge of colored oil droplets and circuits for efficient spectral coding in different species to explore the outcome of retinas exhibiting both strategies simultaneously. Our findings suggest the existence of a trade-off between coding efficiency and color-space area in zebrafish-like retinal circuits. More specifically, we find that spectral encoding becomes compromised with the presence of colored oil droplets while the accessible color space expands significantly.

Amacrine cells differentially balance zebrafish color circuits in the central and peripheral retina

The vertebrate inner retina is driven by photoreceptors whose outputs are already pre-processed; in zebrafish, outer retinal circuits split "color" from "grayscale" information across four cone-photoreceptor types. It remains unclear how the inner retina processes incoming spectral information while also combining cone signals to shape grayscale functions. We address this question by imaging the light-driven responses of amacrine cells (ACs) and bipolar cells (BCs) in larval zebrafish in the presence and pharmacological absence of inner retinal inhibition. We find that ACs enhance opponency in some bipolar cells while at the same time suppressing pre-existing opponency in others, so that, depending on the retinal region, the net change in the number of color-opponent units is essentially zero. To achieve this "dynamic balance," ACs counteract intrinsic color opponency of BCs via the On channel. Consistent with these observations, Off-stratifying ACs are exclusively achromatic, while all color-opponent ACs stratify in the On sublamina.

Seeing Picasso: an investigation into the visual system of the triggerfish Rhinecanthus aculeatus

Vision is used by animals to find food and mates, avoid predators, defend resources and navigate through complex habitats. Behavioural experiments are essential for understanding animals' perception but are often challenging and time-consuming; therefore, using species that can be trained easily for complex tasks is advantageous. Picasso triggerfish, Rhinecanthus aculeatus, have been used in many behavioural studies investigating vision and navigation. However, little is known about the molecular and anatomical basis of their visual system. We addressed this knowledge gap here and behaviourally tested achromatic and chromatic acuity. In terms of visual opsins, R. aculeatus possessed one rod opsin gene (RH1) and at least nine cone opsins: one violet-sensitive SWS2B gene, seven duplicates of the blue-green-sensitive RH2 gene (RH2A, RH2B, RH2C1-5) and one red-sensitive LWS gene. However, only five cone opsins were expressed: SWS2B expression was consistent, while RH2A, RH2C-1 and RH2C-2 expression varied depending on whether fish were sampled from the field or aquaria. Levels of LWS expression were very low. Using fluorescence in situ hybridisation, we found SWS2B was expressed exclusively in single cones, whereas RH2A and RH2Cs were expressed in opposite double cone members. Anatomical resolution estimated from ganglion cell densities was 6.8 cycles per degree (cpd), which was significantly higher than values obtained from behavioural testing for black-and-white achromatic stimuli (3.9 cpd) and chromatic stimuli (1.7-1.8 cpd). These measures were twice as high as previously reported. This detailed information on their visual system will help inform future studies with this emerging focal species.

Visual Function is Gradually Restored During Retina Regeneration in Adult Zebrafish

In comparison to mammals, zebrafish are able to regenerate many organs and tissues, including the central nervous system (CNS). Within the CNS-derived neural retina, light lesions result in a loss of photoreceptors and the subsequent activation of Müller glia, the retinal stem cells. Müller glia-derived progenitors differentiate and eventually restore the anatomical tissue architecture within 4 weeks. However, little is known about how light lesions impair vision functionally, as well as how and to what extent visual function is restored during the course of regeneration, in particular in adult animals. Here, we applied quantitative behavioral assays to assess restoration of visual function during homeostasis and regeneration in adult zebrafish. We developed a novel vision-dependent social preference test, and show that vision is massively impaired early after lesion, but is restored to pre-lesion levels within 7 days after lesion. Furthermore, we employed a quantitative optokinetic response assay with different degrees of difficulty, similar to vision tests in humans. We found that vision for easy conditions with high contrast and low level of detail, as well as color vision, was restored around 7–10 days post lesion. Vision under more demanding conditions, with low contrast and high level of detail, was regained only later from 14 days post lesion onwards. Taken together, we conclude that vision based on contrast sensitivity, spatial resolution and the perception of colors is restored after light lesion in adult zebrafish in a gradual manner.

Spectral inference reveals principal cone-integration rules of the zebrafish inner retina

Retinal bipolar cells integrate cone signals at dendritic and axonal sites. The axonal route, involving amacrine cells, remains largely uncharted. However, because cone types differ in their spectral sensitivities, insights into bipolar cells' cone integration might be gained based on their spectral tunings. We therefore recorded in vivo responses of bipolar cell presynaptic terminals in larval zebrafish to widefield but spectrally resolved flashes of light and mapped the results onto spectral responses of the four cones. This "spectral circuit mapping" allowed explaining ∼95% of the spectral and temporal variance of bipolar cell responses in a simple linear model, thereby revealing several notable integration rules of the inner retina. Bipolar cells were dominated by red-cone inputs, often alongside equal sign inputs from blue and green cones. In contrast, UV-cone inputs were uncorrelated with those of the remaining cones. This led to a new axis of spectral opponency where red-, green-, and blue-cone "Off" circuits connect to "natively-On" UV-cone circuits in the outermost fraction of the inner plexiform layer-much as how key color opponent circuits are established in mammals. Beyond this, and despite substantial temporal diversity that was not present in the cones, bipolar cell spectral tunings were surprisingly simple. They either approximately resembled both opponent and non-opponent spectral motifs already present in the cones or exhibited a stereotyped non-opponent broadband response. In this way, bipolar cells not only preserved the efficient spectral representations in the cones but also diversified them to set up a total of six dominant spectral motifs, which included three axes of spectral opponency.

Ancestral circuits for vertebrate color vision emerge at the first retinal synapse

For color vision, retinal circuits separate information about intensity and wavelength. In vertebrates that use the full complement of four “ancestral” cone types, the nature and implementation of this computation remain poorly understood. Here, we establish the complete circuit architecture of outer retinal circuits underlying color processing in larval zebrafish. We find that the synaptic outputs of red and green cones efficiently rotate the encoding of natural daylight in a principal components analysis–like manner to yield primary achromatic and spectrally opponent axes, respectively. Blue cones are tuned to capture most remaining variance when opposed to green cones, while UV cone present a UV achromatic axis for prey capture. We note that fruitflies use essentially the same strategy. Therefore, rotating color space into primary achromatic and chromatic axes at the eye’s first synapse may thus be a fundamental principle of color vision when using more than two spectrally well-separated photoreceptor types.

Distinct synaptic transfer functions in same-type photoreceptors

Many sensory systems use ribbon-type synapses to transmit their signals to downstream circuits. The properties of this synaptic transfer fundamentally dictate which aspects in the original stimulus will be accentuated or suppressed, thereby partially defining the detection limits of the circuit. Accordingly, sensory neurons have evolved a wide variety of ribbon geometries and vesicle pool properties to best support their diverse functional requirements. However, the need for diverse synaptic functions does not only arise across neuron types, but also within. Here we show that UV-cones, a single type of photoreceptor of the larval zebrafish eye, exhibit striking differences in their synaptic ultrastructure and consequent calcium to glutamate transfer function depending on their location in the eye. We arrive at this conclusion by combining serial section electron microscopy and simultaneous 'dual-colour' two-photon imaging of calcium and glutamate signals from the same synapse in vivo. We further use the functional dataset to fit a cascade-like model of the ribbon synapse with different vesicle pool sizes, transfer rates, and other synaptic properties. Exploiting recent developments in simulation-based inference, we obtain full posterior estimates for the parameters and compare these across different retinal regions. The model enables us to extrapolate to new stimuli and to systematically investigate different response behaviours of various ribbon configurations. We also provide an interactive, easy-to-use version of this model as an online tool. Overall, we show that already on the synaptic level of single-neuron types there exist highly specialised mechanisms which are advantageous for the encoding of different visual features.