Multiple Ecological Axes Drive Molecular Evolution of Cone Opsins in Beloniform Fishes.

Ecological and evolutionary transitions offer an excellent opportunity to examine the molecular basis of adaptation. Fishes of the order Beloniformes include needlefishes, flyingfishes, halfbeaks, and allies, and comprise over 200 species occupying a wide array of habitats-from the marine epipelagic zone to tropical rainforest rivers. These fishes also exhibit a diversity of diets, including piscivory, herbivory, and zooplanktivory. We investigated how diet and habitat affected the molecular evolution of cone opsins, which play a key role in bright light and colour vision and are tightly linked to ecology and life history. We analyzed a targeted-capture dataset to reconstruct the evolutionary history of beloniforms and assemble cone opsin sequences. We implemented codon-based clade models of evolution to examine how molecular evolution was affected by habitat and diet. We found high levels of positive selection in medium- and long-wavelength beloniform opsins, with piscivores showing increased positive selection in medium-wavelength opsins and zooplanktivores showing increased positive selection in long-wavelength opsins. In contrast, short-wavelength opsins showed purifying selection. While marine/freshwater habitat transitions have an effect on opsin molecular evolution, we found that diet plays a more important role. Our study suggests that evolutionary transitions along ecological axes produce complex adaptive interactions that affect patterns of selection on genes that underlie vision.

Unstable environmental conditions constrain the fine-tune between opsin sensitivity and underwater light in an Amazon forest stream fish.

Visual adaptations can stem from variations in amino acid composition, chromophore utilization, and differential opsin gene expression levels, enabling individuals to adjust their light sensitivity to environmental lighting conditions. In stable environments, adaptations often involve amino acid substitutions, whereas in unstable conditions, differential gene expression may be a more relevant mechanism. Amazon forest streams present diverse underwater lighting conditions and experience short-term water colour fluctuations. In these environments, it is less likely for genetic and amino acid sequences to undergo modifications that tailor opsin proteins to the prevailing lighting conditions, particularly in species having several copies of the same gene. The sailfin tetra, Crenuchus spilurus, inhabits black and clear water Amazon forest streams. The long-wavelength sensitivity (LWS) is an important component for foraging and courtship. Here, we investigated LWS opsin genes in the sailfin tetra. Three copies of LWS1 and two copies of LWS2 genes were found. The maximum absorbance wavelength (λmax) estimated from the amino acid sequences of LWS1 genes exhibited variation among the different copies. In contrast, the copies of LWS2 genes showed identical expected λmax values. Although the amino acid positions affecting λmax varied among LWS genes, they remained consistent among populations living in different water colours. The relative expression levels of LWS genes differed between gene copies. While not formally tested, our results suggest that in fluctuating environments, visual adaptations may primarily stem from alterations in gene expression profiles and/or chromophore usage rather than precise genetic tuning of protein light sensitivity to environmental lighting conditions.

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.

Impact of blur on clinical and occupational colour vision test results.

PURPOSE: To evaluate whether colour vision normal (CVN) adults pass two Fletcher-Evans (CAM) lantern tests and to investigate the impact of imposed blur on Ishihara, CAM lantern and computerised colour discrimination test (colour assessment and diagnosis test [CAD] and Cambridge colour test [CCT]) results. METHODS: In a pilot experiment, 20 (16 CVN and 4 colour vision deficient [CVD]) participants with normal VA were tested with the CAM lantern. In the main experiment, the impact of imposed dioptric blur (up to +8.00 D) on visual acuity and the Ishihara test, CAM lantern, CAD and CCT was assessed for 15 CVN participants. RESULTS: CVN participants can fail the CAM lantern, with specificity of 81.25% (aviation mode) and 75% (clinical mode), despite following the test requirements of participants having at least 0.18 logMAR (6/9) in the better eye. With blur, test accuracy was affected. As expected, significant detrimental effects of blur on test results were found for logMAR VA and CAM lantern (aviation) with +1.00 D or higher. Ishihara, CAD and CCT results were not detrimentally affected until +8.00 D. Yellow-blue discrimination was more affected by blur for the CAD than the CCT, which was not explained by the different colour spaces used or vectors tested. CONCLUSION: False-positive findings on lantern colour vision tests with small apertures are likely to be increased in patients with blur due to uncorrected refractive error or ocular and visual pathway disease. Other colour vision tests with larger stimuli are more robust to blur.

Colour perception develops throughout childhood with increased risk of deficiencies in children born prematurely.

AIM: To quantify the impact of prematurity on chromatic discrimination throughout childhood, from 2 to 15 years of age. METHODS: We recruited two cohorts of children, as part of the TrackAI Project, an international project with seven different study sites: a control group of full-term children with normal visual development and a group of children born prematurely. All children underwent a complete ophthalmological exam and an assessment of colour discrimination along the three colour axes: deutan, protan and trytan using a DIVE device with eye tracking technology. RESULTS: We enrolled a total of 1872 children (928 females and 944 males) with a mean age of 6.64 years. Out of them, 374 were children born prematurely and 1498 were full-term controls. Using data from all the children born at term, reference normative curves were plotted for colour discrimination in every colour axis. Pre-term children presented worse colour discrimination than full-term in the three colour axes (p < 0.001). Even after removing from the comparison, all pre-term children with any visual disorder colour discrimination outcomes remained significantly worse than those from full-term children. CONCLUSION: While colour perception develops throughout the first years of life, children born pre-term face an increased risk for colour vision deficiencies.

The construction of genetics teaching resources related to colour blindness and their application in genetics teaching.

Red-green colour blindness is a classic example for the teaching of X-linked recessive inheritance in genetics course. However, there are lots of types of color vision deficiencies besides red-green colour blindness. Different color vision deficiencies caused by different genes may have different modes of inheritance. In recent years, many research achievements on colour blindness have been made. These achievements could be used as teaching resources in genetics course. Here, we summarize the construction of genetics teaching resources related to colour blindness and their application in genetics teaching in several chapters such as introduction, cellular and molecular basis of genetics, sex-linked inheritance, chromosomal aberration, gene mutation and advances in genetics. Teacher could use the resources in class or after class with different teaching methods such as questioning teaching method and task method. It may expand students' academic horizons and inspire students' interest in genetics besides grasping basic genetic knowledge.

Influence of colour vision on attention to, and impression of, complex aesthetic images.

Humans exhibit colour vision variations due to genetic polymorphisms, with trichromacy being the most common, while some people are classified as dichromats. Whether genetic differences in colour vision affect the way of viewing complex images remains unknown. Here, we investigated how people with different colour vision focused their gaze on aesthetic paintings by eye-tracking while freely viewing digital rendering of paintings and assessed individual impressions through a decomposition analysis of adjective ratings for the images. Gaze-concentrated areas among trichromats were more highly correlated than those among dichromats. However, compared with the brief dichromatic experience with the simulated images, there was little effect of innate colour vision differences on impressions. These results indicate that chromatic information is instructive as a cue for guiding attention, whereas the impression of each person is generated according to their own sensory experience and normalized through one's own colour space.

Dim-light colour vision in the facultatively nocturnal Asian giant honeybee, Apis dorsata.

We discovered nocturnal colour vision in the Asian giant honeybee Apis dorsata-a facultatively nocturnal species-at mesopic light intensities, down to half-moon light levels (approx. 10-2 cd m-2). The visual threshold of nocturnality aligns with their reported nocturnal activity down to the same light levels. Nocturnal colour vision in A. dorsata is interesting because, despite being primarily diurnal, its colour vision capabilities extend into dim light, while the 'model' European honeybee Apis mellifera is reported to be colour-blind at twilight. By employing behavioural experiments with naturally nesting A. dorsata colonies, we show discrimination of the trained colour from other stimuli during the day, and significantly, even at night. Nocturnal colour vision in bees has so far only been reported in the obligately nocturnal carpenter bee Xylocopa tranquebarica. The discovery of colour vision in these two bee species, despite differences in the extent of their nocturnality and the limitations of their apposition compound eye optics, opens avenues for future studies on visual adaptations for dim-light colour vision, their role in pollination of flowers at night, and the effect of light pollution on nocturnal activity in A. dorsata, a ubiquitous pollinator in natural, agricultural and urban habitats in the Asian tropics and sub-tropics.

Why are biting flies attracted to blue objects?

Diurnal biting flies are strongly attracted to blue objects. This behaviour is widely exploited for fly control, but its functional significance is debated. It is hypothesized that blue objects resemble animal hosts; blue surfaces resemble shaded resting places; and blue attraction is a by-product of attraction to polarized light. We computed the fly photoreceptor signals elicited by a large sample of leaf and animal integument reflectance spectra, viewed under open/cloudy illumination and under woodland shade. We then trained artificial neural networks (ANNs) to distinguish animals from leaf backgrounds, and shaded from unshaded surfaces, in order to find the optimal means of doing so based upon the sensory information available to a fly. After training, we challenged ANNs to classify blue objects used in fly control. Trained ANNs could make both discriminations with high accuracy. They discriminated animals from leaves based upon blue-green photoreceptor opponency and commonly misclassified blue objects as animals. Meanwhile, they discriminated shaded from unshaded stimuli using achromatic cues and never misclassified blue objects as shaded. We conclude that blue-green opponency is the most effective means of discriminating animals from leaf backgrounds using a fly's sensory information, and that blue objects resemble animal hosts through such mechanisms.

Misidentifying illuminant changes in natural scenes due to failures in relational colour constancy.

The colours of surfaces in a scene may not appear constant with a change in the colour of the illumination. Yet even when colour constancy fails, human observers can usually discriminate changes in lighting from changes in surface reflecting properties. This operational ability has been attributed to the constancy of perceived colour relations between surfaces under illuminant changes, in turn based on approximately invariant spatial ratios of cone photoreceptor excitations. Natural deviations in these ratios may, however, lead to illuminant changes being misidentified. The aim of this work was to test whether such misidentifications occur with natural scenes and whether they are due to failures in relational colour constancy. Pairs of scene images from hyperspectral data were presented side-by-side on a computer-controlled display. On one side, the scene underwent illuminant changes and on the other side, it underwent the same changes but with images corrected for any residual deviations in spatial ratios. Observers systematically misidentified the corrected images as being due to illuminant changes. The frequency of errors increased with the size of the deviations, which were closely correlated with the estimated failures in relational colour constancy.

Spectral sensitivity of retinal photoreceptors of tortricid moths is not tuned to diel activity period.

Leafrollers (Lepidoptera: Tortricidae) are a large family of small moths containing over 10,000 species, many of which are crop pests. Grapholita molesta, Lobesia botrana and Cydia pomonella adults are sexually active before, during and after sunset, respectively. We wanted to determine whether being active at different times of the day and night is associated with differences in their visual system. Spectral sensitivity (SS) was measured with electroretinograms and selective adaptation with green, blue and ultraviolet light. SS curves could be fitted with a triple nomogram template which indicated the existence of three photoreceptor classes peaking at 355, 440 and 525 nm. The retinae showed clear regionalization, with fewer blue receptors dorsally. No differences among species or between sexes were found. Intracellular recordings in C. pomonella also revealed three photoreceptor classes with sensitivities peaking at 355, 440 and 525 nm. The blue photoreceptors showed inhibitory responses in the green part of the spectrum, indicating the presence of a colour-opponent system. Flicker fusion frequency experiments showed that the response speed was similar between sexes and species and fused at around 100 Hz. Our results indicate that the three species have the ancestral insect retinal substrate for a trichromatic colour vision, based upon the UV, blue and green-sensitive photoreceptors, and lack any prominent adaptations related to being active under different light conditions.

Rapid measurement and machine learning classification of colour vision deficiency.

Colour vision deficiencies (CVDs) indicate potential genetic variations and can be important biomarkers of acquired impairment in many neuro-ophthalmic diseases. However, CVDs are typically measured with tests which possess high sensitivity for detecting the presence of a CVD but do not quantify its type or severity. In this study, we introduce Foraging Interactive D-prime (FInD), a novel computer-based, generalisable, rapid, self-administered vision assessment tool and apply it to colour vision testing. This signal detection theory-based adaptive paradigm computed test stimulus intensity from d-prime analysis. Stimuli were chromatic Gaussian blobs in dynamic luminance noise, and participants clicked on cells that contained chromatic blobs (detection) or blob pairs of differing colours (discrimination). Sensitivity and repeatability of FInD colour tasks were compared against the Hardy-Rand-Rittler and the Farnsworth-Munsell 100 hue tests in 19 colour-normal and 18 inherited colour-atypical, age-matched observers. Rayleigh colour match was also completed. Detection and discrimination thresholds were higher for atypical than for typical observers, with selective threshold elevations corresponding to unique CVD types. Classifications of CVD type and severity via unsupervised machine learning confirmed functional subtypes. FInD tasks reliably detect inherited CVDs, and may serve as valuable tools in basic and clinical colour vision science.

Elaborate Evaluation of Farnsworth Dichotomous D-15 Panel Test Can Help Differentiate between Best Vitelliform Macular Dystrophy and Autosomal Recessive Bestrophinopathy.

INTRODUCTION: The colour vision in bestrophinopathies has not been assessed in detail so far. The aim of this study was to explore the extent to which distinct types of bestrophinopathies differ in regard to colour vision deficiencies using Farnsworth Dichotomous D-15 and Lanthony Desaturated D-15 panel tests. METHODS: Both D-15 tests were performed in 52 eyes of 26 patients with Best vitelliform macular dystrophy (BVMD) and 10 eyes of 5 patients with autosomal recessive bestrophinopathy (ARB). Two methods were used for a quantitative assessment of the colour vision deficiencies: moment of inertia method and Bowman method. The following parameters were calculated: confusion angle, confusion index (C-index), selectivity index (S-index), total error score (TES), and colour confusion index (CCI). RESULTS: The median value of confusion angle for all stages of BVMD fell into a narrow range around 62, indicating normal results. The median confusion angle value was 57 in ARB patients within a very wide range down to -82, indicating non-specific deficits. These differences were statistically significant. Significantly abnormal C-index and CCI values were found only in ARB patients, being 2.0 and 1.49, respectively. The majority of parameters of D-15 tests were independent of the visual acuity in both bestrophinopathies. CONCLUSIONS: Elaborate evaluation of the D-15 panel tests might help establish a differential diagnosis between different bestrophinopathies, as the pattern of the colour vision loss is different between BVMD and ARB. The quantitative parameters of colour vision tests in bestrophinopathies are independent of the visual acuity.

AI-Assisted Cotton Grading: Active and Semi-Supervised Learning to Reduce the Image-Labelling Burden.

The assessment of food and industrial crops during harvesting is important to determine the quality and downstream processing requirements, which in turn affect their market value. While machine learning models have been developed for this purpose, their deployment is hindered by the high cost of labelling the crop images to provide data for model training. This study examines the capabilities of semi-supervised and active learning to minimise effort when labelling cotton lint samples while maintaining high classification accuracy. Random forest classification models were developed using supervised learning, semi-supervised learning, and active learning to determine Egyptian cotton grade. Compared to supervised learning (80.20-82.66%) and semi-supervised learning (81.39-85.26%), active learning models were able to achieve higher accuracy (82.85-85.33%) with up to 46.4% reduction in the volume of labelled data required. The primary obstacle when using machine learning for Egyptian cotton grading is the time required for labelling cotton lint samples. However, by applying active learning, this study successfully decreased the time needed from 422.5 to 177.5 min. The findings of this study demonstrate that active learning is a promising approach for developing accurate and efficient machine learning models for grading food and industrial crops.

Visual symptoms with Sofosbuvir in hepatitis C treatment - a case report from Pakistan.

Hepatitis C virus infection is one of the main causes of chronic liver disease worldwide. The highly efficacious direct-acting antiviral (DAA) drugs licensed for therapy have revolutionised the treatment and are reported to have few side effects. Sofosbuvir is a pan-genotypic DAA that acts by inhibition of the hepatitis C NS5B polymerase. It has shown high efficacy in combination with several other drugs with low toxicity, a high resistance barrier, and minimal drug interactions with other hepatitis C DAA drugs. We describe a first of its kind case from Pakistan with visual disturbances caused by Sofosbuvir. A temporal relationship was observed between the treatment initiation and the onset of visual disturbances. The aim of this case report is to draw attention to the unanticipated side effects of this relatively new class of drug that have not been reported previously.

Masking Colour Blindness: A Case Report.

Colour vision is an important aspect of visual function that might help individuals in doing daily activities. Some occupations require and test for good colour discrimination. We describe a case of a 20-year-old man who was referred to our centre to establish if he had colour vision deficiency (CVD). He had been tested for this twice as part of his assessment to enter the police force. At the first examination, he had normal colour vision, while the second examination revealed CVD, thus the patient was referred for confirmation. Colour vision tests using the Ishihara plates showed normal results with each eye, while a Roth test revealed an unspecified CVD in the right eye and deuteranopia in the left eye. During the evaluation, we noticed he was using a red-tinted contact lens in the right eye, and was wearing a red mask with transparent red plastic in the upper part. After removal of the contact lens and mask, he was asked to repeat the examinations and it revealed deuteranopia in both eyes. A tinted contact lens is a corrective device that can help to enhance colour discrimination in CVD subjects. However, in this case the tinted contact lens was used inappropriately to manipulate the colour vision examination. We highlight the case to raise awareness that the use of red contact lenses and red filters can mask CVD.

Anatomy and dietary specialization influence sensory behaviour among sympatric primates.

Senses form the interface between animals and environments, and provide a window into the ecology of past and present species. However, research on sensory behaviours by wild frugivores is sparse. Here, we examine fruit assessment by three sympatric primates (Alouatta palliata, Ateles geoffroyi and Cebus imitator) to test the hypothesis that dietary and sensory specialization shape foraging behaviours. Ateles and Cebus groups are comprised of dichromats and trichromats, while all Alouatta are trichomats. We use anatomical proxies to examine smell, taste and manual touch, and opsin genotyping to assess colour vision. We find that the frugivorous spider monkeys (Ateles geoffroyi) sniff fruits most often, omnivorous capuchins (Cebus imitator), the species with the highest manual dexterity, use manual touch most often, and that main olfactory bulb volume is a better predictor of sniffing behaviour than nasal turbinate surface area. We also identify an interaction between colour vision phenotype and use of other senses. Controlling for species, dichromats sniff and bite fruits more often than trichromats, and trichromats use manual touch to evaluate cryptic fruits more often than dichromats. Our findings reveal new relationships among dietary specialization, anatomical variation and foraging behaviour, and promote understanding of sensory system evolution.

The gaze of a social monkey is perceptible to conspecifics and predators but not prey.

Eye gaze is an important source of information for animals, implicated in communication, cooperation, hunting and antipredator behaviour. Gaze perception and its cognitive underpinnings are much studied in primates, but the specific features that are used to estimate gaze can be difficult to isolate behaviourally. We photographed 13 laboratory-housed tufted capuchin monkeys (Sapajus [Cebus] apella) to quantify chromatic and achromatic contrasts between their iris, pupil, sclera and skin. We used colour vision models to quantify the degree to which capuchin eye gaze is discriminable to capuchins, their predators and their prey. We found that capuchins, regardless of their colour vision phenotype, as well as their predators, were capable of effectively discriminating capuchin gaze across ecologically relevant distances. Their prey, in contrast, were not capable of discriminating capuchin gaze, even under relatively ideal conditions. These results suggest that specific features of primate eyes can influence gaze perception, both within and across species.

Comparative psychophysics of Western honey bee (Apis mellifera) and stingless bee (Tetragonula carbonaria) colour purity and intensity perception.

Bees play a vital role as pollinators worldwide and have influenced how flower colour signals have evolved. The Western honey bee, Apis mellifera (Apini), and the Buff-tailed bumble bee, Bombus terrestris (Bombini) are well-studied model species with regard to their sensory physiology and pollination capacity, although currently far less is known about stingless bees (Meliponini) that are common in pantropical regions. We conducted comparative experiments with two highly eusocial bee species, the Western honey bee, A. mellifera, and the Australian stingless bee, Tetragonula carbonaria, to understand their colour preferences considering fine-scaled stimuli specifically designed for testing bee colour vision. We employed stimuli made of pigment powders to allow manipulation of single colour parameters including spectral purity (saturation) or colour intensity (brightness) of a blue colour (hue) for which both species have previously shown innate preferences. Both A. mellifera and T. carbonaria demonstrated a significant preference for spectrally purer colour stimuli, although this preference is more pronounced in honey bees than in stingless bees. When all other colour cues were tightly controlled, honey bees receiving absolute conditioning demonstrated a capacity to learn a high-intensity stimulus significant from chance expectation demonstrating some capacity of plasticity for this dimension of colour perception. However, honey bees failed to learn low-intensity stimuli, and T. carbonaria was insensitive to stimulus intensity as a cue. These comparative findings suggest that there may be some common roots underpinning colour perception in bee pollinators and how they interact with flowers, although species-specific differences do exist.

The Paton prize lecture 2021: A colourful experience leading to a reassessment of colour vision and its theories.

In this lecture, given in honour of Sir William Paton, a brilliant scientist and one of Britain's great patrons of biology, I give a personal account of the fundamental issues in colour vision that I have tackled since 1973, when I discovered a cortical zone lying outside the primary visual cortex that is rich in cells with chromatic properties. I do not provide an exhaustive review of colour vision but summarise how my views on colour vision and theories surrounding it have changed in light of that discovery.