Proximate and ultimate causes of variable visual sensitivities: Insights from cichlid fish radiations

Robust Sensory Traits Across Light Habitats: Visual Signals but Not Receptors Vary in Centrarchids Inhabiting Distinct Photic Environments

Visual communication in fish is often shaped by their light environment, which influences both sensory (e.g., eye size, opsin gene expression) and signalling traits (e.g., body reflectance). This study explores the phenotypic variation in the visual communication traits of six species of centrarchids (Centrarchidae) inhabiting two contrasting light environments. We measured morphological, molecular and signalling traits to determine their variation across photic conditions. Our findings reveal significant interspecific variation in sensory traits but no consistent phenotypic variation between light environments. Centrarchids showed robust visual systems with green-sensitive rh2 and red-sensitive lws opsin genes representing the main chromatic channels, with their expression remaining largely unaffected between distinct light habitats. We also found significant molecular evolution in the visual opsin genes, although these changes were not associated with environmental conditions. However, body reflectance displayed species-specific responses to environmental conditions, suggesting that signalling traits may be more flexible than sensory traits. Overall, our results challenge the generality of the current paradigm in visual ecology, which portrays visual systems in fish as highly tunable owing to photic conditions. Our study highlights the potential evolutionary or developmental constraints on centrarchid visual systems and their implications for adaptability to various habitats and novel environmental threats.

Differential Regulation of Opsin Gene Expression in Response to Internal and External Stimuli

Determining how internal and external stimuli interact to determine developmental trajectories of traits is a challenge that requires the integration of different subfields of biology. Internal stimuli, such as hormones, control developmental patterns of phenotypic changes, which might be modified by external environmental cues (e.g. plasticity). Thyroid hormone (TH) modulates the timing of opsin gene expression in developing Midas cichlid fish (Amphilophus citrinellus). Moreover, fish reared in red light accelerate this developmental timing compared to fish reared in white light. Hence, we hypothesized that plasticity caused by variation in light conditions has coopted the TH signaling pathway to induce changes in opsin gene expression. We treated Midas cichlids with TH and crossed this treatment with two light conditions, white and red. We observed that not only opsin expression responded similarly to TH and red light but also that, at high TH levels, there is limited capacity for light-induced plasticity. Transcriptomic analysis of the eye showed that genes in the TH pathway were affected by TH, but not by light treatments. Coexpression network analyses further suggested that response to light was independent of the response to TH manipulations. Taken together, our results suggest independent mechanisms mediating development and plasticity during development of opsin gene expression, and that responses to environmental stimuli may vary depending on internal stimuli. This conditional developmental response to external factors depending on internal ones (e.g. hormones) might play a fundamental role in the patterns of phenotypic divergence observed in Midas cichlids and potentially other organisms.

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.

Influence of ambient water coloration on habitat and conspecific choice in the female Lake Malawi cichlid, Metriaclima zebra

Female cichlid fish living in African great lakes are known to have sensory systems that are adapted to ambient light environments. These sensory system adaptations are hypothesized to have influenced the evolution of the diverse male nuptial coloration. In rock-dwelling Lake Malawi mbuna cichlids, however, the extent to which ambient light environments influence female sensory systems and potentially associated male nuptial coloration remains unknown. Yet, the ubiquitous blue flank coloration and UV reflection of male mbuna cichlids suggest the potential impacts of the blue-shifted ambient light environment on these cichlid's visual perception and male nuptial coloration in the shallow water depth in Lake Malawi. In the present study, we explored whether and how the sensory bias of females influences intersexual communication in the mbuna cichlid, Metriaclima zebra. A series of choice experiments in various light environments showed that M. zebra females 1) have a preference for the blue-shifted light environment, 2) prefer to interact with males in blue-shifted light environments, 3) do not show a preference between dominant and subordinate males in full-spectrum, long-wavelength filtered, and short-wavelength filtered light environments, and 4) show a "reversed" preference for subordinate males in the UV-filtered light environment. These results suggest that the visual perception of M. zebra females may be biased to the ambient light spectra in their natural habitat by local adaptation and that this sensory bias may influence the evolution of blue and UV reflective patterns in male nuptial coloration.

Turbidity drives plasticity in the eyes and brains of an African cichlid

Natural variation in environmental turbidity correlates with variation in the visual sensory system of many fishes, suggesting that turbidity may act as a strong selective agent on visual systems. Since many aquatic systems experience increased turbidity due to anthropogenic perturbations, it is important to understand the degree to which fish can respond to rapid shifts in their visual environment, and whether such responses can occur within the lifetime of an individual. We examined whether developmental exposure to turbidity (clear, <5 NTU; turbid, ∼9 NTU) influenced the size of morphological structures associated with vision in the African blue-lip cichlid Pseudocrenilabrus multicolor. Parental fish were collected from two sites (clear swamp, turbid river) in western Uganda. F1 broods from each population were split and reared under clear and turbid rearing treatments until maturity. We measured morphological traits associated with the visual sensory system (eye diameter, pupil diameter, axial length, brain mass, optic tectum volume) over the course of development. Age was significant in explaining variation in visual traits even when standardized for body size, suggesting an ontogenetic shift in the relative size of eyes and brains. When age groups were analyzed separately, young fish reared in turbid water grew larger eyes than fish reared in clear conditions. Population was important in the older age category, with swamp-origin fish having relatively larger eyes and optic lobes relative to river-origin fish. Plastic responses during development may be important for coping with a more variable visual environment associated with anthropogenically induced turbidity.

Developmental and environmental plasticity in opsin gene expression in Lake Victoria cichlid fish

In many organisms, sensory abilities develop and evolve according to the changing demands of navigating, foraging, and communication across different environments and life stages. Teleost fish inhabit heterogeneous light environments and exhibit a large diversity in visual system properties among species. Cichlids are a classic example of this diversity; visual system variation is generated by different tuning mechanisms that involve both genetic factors and phenotypic plasticity. Here, we document the developmental progression of visual pigment gene expression in Lake Victoria cichlids and test if these patterns are influenced by variation in light conditions. We reared two sister species of Pundamilia to adulthood in two distinct visual conditions that resemble the light environments that they naturally inhabit in Lake Victoria. We also included interspecific first-generation hybrids. We focused on the four opsins that are expressed in Pundamilia adults (using real-time quantitative polymerase chain reaction (RT-qPCR)) (SWS2B, SWS2A, RH2A, and LWS) at 17 time points. We find that opsin expression profiles progress from shorter-wavelength sensitive opsins to longer-wavelength sensitive opsins with increasing age, in both species and their hybrids. The developmental trajectories of opsin expression also responded plastically to the visual conditions. Developmental and environmental plasticity in opsin expression may provide an important stepping stone in the evolution of cichlid visual system diversity.

Visual opsin gene expression evolution in the adaptive radiation of cichlid fishes of Lake Tanganyika

Tuning the visual sensory system to the ambient light is essential for survival in many animal species. This is often achieved through duplication, functional diversification, and/or differential expression of visual opsin genes. Here, we examined 753 new retinal transcriptomes from 112 species of cichlid fishes from Lake Tanganyika to unravel adaptive changes in gene expression at the macro-evolutionary and ecosystem level of one of the largest vertebrate adaptive radiations. We found that, across the radiation, all seven cone opsins-but not the rhodopsin-rank among the most differentially expressed genes in the retina, together with other vision-, circadian rhythm-, and hemoglobin-related genes. We propose two visual palettes characteristic of very shallow- and deep-water living species, respectively, and show that visual system adaptations along two major ecological axes, macro-habitat and diet, occur primarily via gene expression variation in a subset of cone opsin genes.

Molecular Mechanisms Underlying Vertebrate Adaptive Evolution: A Systematic Review

Adaptive evolution is a process in which variation that confers an evolutionary advantage in a specific environmental context arises and is propagated through a population. When investigating this process, researchers have mainly focused on describing advantageous phenotypes or putative advantageous genotypes. A recent increase in molecular data accessibility and technological advances has allowed researchers to go beyond description and to make inferences about the mechanisms underlying adaptive evolution. In this systematic review, we discuss articles from 2016 to 2022 that investigated or reviewed the molecular mechanisms underlying adaptive evolution in vertebrates in response to environmental variation. Regulatory elements within the genome and regulatory proteins involved in either gene expression or cellular pathways have been shown to play key roles in adaptive evolution in response to most of the discussed environmental factors. Gene losses were suggested to be associated with an adaptive response in some contexts. Future adaptive evolution research could benefit from more investigations focused on noncoding regions of the genome, gene regulation mechanisms, and gene losses potentially yielding advantageous phenotypes. Investigating how novel advantageous genotypes are conserved could also contribute to our knowledge of adaptive evolution.

Developmental changes of opsin gene expression in ray-finned fishes (Actinopterygii)

Fish often change their habitat and trophic preferences during development. Dramatic functional differences between embryos, larvae, juveniles and adults also concern sensory systems, including vision. Here, we focus on the photoreceptors (rod and cone cells) in the retina and their gene expression profiles during development. Using comparative transcriptomics on 63 species, belonging to 23 actinopterygian orders, we report general developmental patterns of opsin expression, mostly suggesting an increased importance of the rod opsin ( RH1 ) gene and the long-wavelength-sensitive cone opsin, and a decreasing importance of the shorter wavelength-sensitive cone opsin throughout development. Furthermore, we investigate in detail ontogenetic changes in 14 selected species (from Polypteriformes, Acipenseriformes, Cypriniformes, Aulopiformes and Cichliformes), and we report examples of expanded cone opsin repertoires, cone opsin switches (mostly within RH2 ) and increasing rod : cone ratio as evidenced by the opsin and phototransduction cascade genes. Our findings provide molecular support for developmental stage-specific visual palettes of ray-finned fishes and shifts between, which most likely arose in response to ecological, behavioural and physiological factors.

Contribution of opsins and chromophores to cone pigment variation across populations of Lake Victoria cichlids

Adaptation to heterogeneous sensory environments has been implicated as a key parameter in speciation. Cichlid fish are a textbook example of divergent visual adaptation, mediated by variation in the sequences and expression levels of cone opsin genes (encoding the protein component of visual pigments). In some vertebrates including fish, visual sensitivity is also tuned by the ratio of vitamin A₁ /A₂ -derived chromophores (i.e., the light-sensitive component of the visual pigment bound to the opsin protein), where higher proportions of A₂ cause a more red-shifted wavelength absorbance. This study explores the variation in chromophore ratios across multiple cichlid populations in Lake Victoria, using as a proxy the expression of the gene Cyp27c1, which has been shown to regulate the conversion of vitamin A₁ into vitamin A₂ in several vertebrates. This study focuses on sympatric Pundamilia cichlids, where species with blue or red male coloration co-occur at multiple islands but occupy different depths and consequently different visual habitats. In the red species, we found higher cyp27c1 expression in populations from turbid waters than from clear waters, but there was no such pattern in the blue species. Across populations, differences between the sympatric species in cyp27c1 expression had a consistent relationship with species differences in opsin expression patterns, but the red/blue identity reversed between clear and turbid waters. To assess the contribution of heritable vs. environmental causes of variation, we tested whether light manipulations induce a change in cyp27c1 expression in the laboratory. We found that cyp27c1 expression was not influenced by experimental light conditions, suggesting that the observed variation in the wild is due to genetic differences. Nonetheless, compared to other cichlid species, cyp27c1 is expressed at very low levels in Pundamilia, suggesting that it may not be relevant for visual adaptation in this species. Conclusively, establishing the biological importance of this variation requires testing of actual A₁ /A₂ ratios in the eye, as well as its consequences for visual performance.

Oca2 targeting using CRISPR/Cas9 in the Malawi cichlid Astatotilapia calliptera

Identifying genetic loci underlying trait variation provides insights into the mechanisms of diversification, but demonstrating causality and characterizing the role of genetic loci requires testing candidate gene function, often in non-model species. Here we establish CRISPR/Cas9 editing in Astatotilapia calliptera, a generalist cichlid of the remarkably diverse Lake Malawi radiation. By targeting the gene oca2 required for melanin synthesis in other vertebrate species, we show efficient editing and germline transmission. Gene edits include indels in the coding region, probably a result of non-homologous end joining, and a large deletion in the 3' untranslated region due to homology-directed repair. We find that oca2 knock-out A. calliptera lack melanin, which may be useful for developmental imaging in embryos and studying colour pattern formation in adults. As A. calliptera resembles the presumed generalist ancestor of the Lake Malawi cichlids radiation, establishing genome editing in this species will facilitate investigating speciation, adaptation and trait diversification in this textbook radiation.

Thyroid hormone tinkering elicits integrated phenotypic changes potentially explaining rapid adaptation of color vision in cichlid fish

Vision is critical for most vertebrates, including fish. One challenge that aquatic habitats pose is the high variability in spectral properties depending on depth and the inherent optical properties of the water. By altering opsin gene expression and chromophore usage, cichlid fish modulate visual sensitivities to maximize sensory input from the available light in their respective habitat. Thyroid hormone (TH) has been proposed to play a role in governing adaptive diversification in visual sensitivity in Nicaraguan Midas cichlids, which evolved in less than 4000 generations. As suggested by indirect measurements of TH levels (i.e., expression of deiodinases), populations adapted to short wavelength light in clear lakes have lower TH levels than ones inhabiting turbid lakes enriched in long-wavelength light. We experimentally manipulated TH levels by exposing 2-week-old Midas cichlids to exogenous TH or a TH inhibitor and measured opsin gene expression and chromophore usage (via cyp27c1 expression). Although exogenous TH induces long-wavelength sensitivity by changing opsin gene expression and chromophore usage in a concerted manner, TH-inhibited fish exhibit a visual phenotype with sensitivities shifted to shorter wavelengths. Tinkering with TH levels in eyes results in concerted phenotypic changes that can provide a rapid mechanism of adaptation to novel light environments.

Visual gene expression reveals a cone to rod developmental progression in deep-sea fishes

Vertebrates use cone cells in the retina for colour vision and rod cells to see in dim light. Many deep-sea fishes have adapted to their environment to have only rod cells in the retina, while both rod and cone genes are still preserved in their genomes. As deep-sea fish larvae start their lives in the shallow, and only later submerge to the depth, they have to cope with diverse environmental conditions during ontogeny. Using a comparative transcriptomic approach in 20 deep-sea fish species from eight teleost orders, we report on a developmental cone-to-rod switch. While adults mostly rely on rod opsin (RH1) for vision in dim light, larvae almost exclusively express middle-wavelength-sensitive ("green") cone opsins (RH2) in their retinas. The phototransduction cascade genes follow a similar ontogenetic pattern of cone- followed by rod-specific gene expression in most species, except for the pearleye and sabretooth (Aulopiformes), in which the cone cascade remains dominant throughout development. By inspecting the whole genomes of five deep-sea species (four of them sequenced within this study: Idiacanthus fasciola, Chauliodus sloani; Stomiiformes; Coccorella atlantica, and Scopelarchus michaelsarsi; Aulopiformes), we found that deep-sea fish possess one or two copies of the rod RH1 opsin gene, and up to seven copies of the cone RH2 opsin genes in their genomes, while other cone opsin classes have been mostly lost. Our findings hence provide molecular evidence for a limited opsin gene repertoire and a conserved vertebrate pattern whereby cone photoreceptors develop first and rod photoreceptors are added only at later developmental stages.

Chromosome-level assembly of southern catfish (silurus meridionalis) provides insights into visual adaptation to nocturnal and benthic lifestyles

The Southern catfish (Silurus meridionalis) is a nocturnal and benthic freshwater fish endemic to the Yangtze River and its tributaries. In this study, we constructed a chromosome-level draft genome of S. meridionalis using 69.7-Gb Nanopore long reads and 49.5-Gb Illumina short reads. The genome assembly was 741.2 Mb in size with a contig N50 of 13.19 Mb. An additional 116.4 Gb of Bionano and 77.4 Gb of Hi-C data were applied to assemble contigs into scaffolds and further into 29 chromosomes, resulting in a 738.9-Mb genome with a scaffold N50 of 28.04 Mb. A total of 22,965 protein-coding genes were predicted from the genome with 22,519 (98.06%) genes functionally annotated. Comparative genomic and transcriptomic analyses revealed a rod-dominated visual system which was responsible for scotopic vision. The absence of cone opsins SWS1 and SWS2 resulted in the lack of ultraviolet and blue violet sensitivity. Mutations at key amino acid sites of RH1.1, RH1.2 and RH2 resulted in spectral tuning good for dim light vision and narrow colour vision. A higher expression level of rod phototransduction genes than that of cone genes and higher rod-to-cone ratio led to higher optical sensitivity under dim light conditions. In addition, analysis of the genes involved in eye morphogenesis and development revealed the loss of some conserved noncoding elements, which might be associated with the small eyes in catfish. Together, our study provides important clues for the adaptation of the catfish visual system to the nocturnal and benthic lifestyles. The draft genome of S. meridionalis represents a valuable resource for studies of the molecular mechanisms of ecological adaptation.

Genetic basis for variation in the number of cephalic pores in a hybrid zone between closely related species of goby, Gymnogobius breunigii and Gymnogobius castaneus

Populations or species exploiting different habitats can differ in sensory perception as a result of divergent adaptation. In bony fish, the water current is perceived via neuromasts, the end organ of the lateral line system. Although fish in different habitats are known to vary in neuromasts, we know little about the genetic basis for such variation. Here, we investigate the genetic basis for variation in supraorbital neuromasts in a hybrid zone between the Japanese gobies Gymnogobius breunigii and Gymnogobius castaneus. The former has supraorbital canal neuromasts with six cephalic pores, whereas the latter has only superficial neuromasts with no canals or pores in the supraorbital region. Our genomic analysis showed that G. breunigii and G. castaneus occur mainly in the lower and mid/upper reaches, respectively. In a river in northern Japan, hybrids were found at the sites between the habitats of the two species. These hybrids exhibited anomalies of cephalic pores. Using this hybrid zone, we conducted genome-wide association studies and identified one locus significantly associated with the number of pores. Genomic cline analysis in the hybrid zone demonstrated that this locus exhibited a higher introgression rate compared with the genomic background, indicating the possibility of adaptive introgression.

Diversity in visual sensitivity across Neotropical cichlid fishes via differential expression and intraretinal variation of opsin genes

The visual system of vertebrates has greatly contributed to our understanding of how different molecular mechanisms shape adaptive phenotypic diversity. Extensive work on African cichlid fishes has shown how variation in opsin gene expression mediates diversification as well as convergent evolution in colour vision. This trait has received less attention in Neotropical cichlids, the sister lineage to African cichlids, but the work done so far led to the conclusion that colour vision is much less variable in Neotropical species. However, as only few taxa have been investigated and as recent work found contradicting patterns, the diversity in meotropical cichlids might be greatly underestimated. Here, we survey patterns of opsin gene expression in 35 representative species of Neotropical cichlids, revealing much more variation than previously known. This diversity can be attributed to two main mechanisms: (i) differential expression of the blue-sensitive sws2a, the green-sensitive rh2a, and the red-sensitive lws opsin genes, and (ii) simultaneous expression of up to five opsin genes, instead of only three as commonly found, in a striking dorsoventral pattern across the retina. This intraretinal variation in opsin genes expression results in steep gradients in visual sensitivity that may represent a convergent adaptation to clear waters with broad light environments. These results highlight the role and flexibility of gene expression in generating adaptive phenotypic diversification.

Genome sequences of Tropheus moorii and Petrochromis trewavasae, two eco-morphologically divergent cichlid fishes endemic to Lake Tanganyika

With more than 1000 species, East African cichlid fishes represent the fastest and most species-rich vertebrate radiation known, providing an ideal model to tackle molecular mechanisms underlying recurrent adaptive diversification. We add high-quality genome reconstructions for two phylogenetic key species of a lineage that diverged about ~ 3-9 million years ago (mya), representing the earliest split of the so-called modern haplochromines that seeded additional radiations such as those in Lake Malawi and Victoria. Along with the annotated genomes we analysed discriminating genomic features of the study species, each representing an extreme trophic morphology, one being an algae browser and the other an algae grazer. The genomes of Tropheus moorii (TM) and Petrochromis trewavasae (PT) comprise 911 and 918 Mbp with 40,300 and 39,600 predicted genes, respectively. Our DNA sequence data are based on 5 and 6 individuals of TM and PT, and the transcriptomic sequences of one individual per species and sex, respectively. Concerning variation, on average we observed 1 variant per 220 bp (interspecific), and 1 variant per 2540 bp (PT vs PT)/1561 bp (TM vs TM) (intraspecific). GO enrichment analysis of gene regions affected by variants revealed several candidates which may influence phenotype modifications related to facial and jaw morphology, such as genes belonging to the Hedgehog pathway (SHH, SMO, WNT9A) and the BMP and GLI families.

Movement of transposable elements contributes to cichlid diversity

African cichlid fishes are a prime model for studying speciation mechanisms. Despite the development of extensive genomic resources, it has been difficult to determine which sources of genetic variation are responsible for cichlid phenotypic variation. One of their most variable phenotypes is visual sensitivity, with some of the largest spectral shifts among vertebrates. These shifts arise primarily from differential expression of seven cone opsin genes. By mapping expression quantitative trait loci (eQTL) in intergeneric crosses of Lake Malawi cichlids, we previously identified four causative genetic variants that correspond to indels in the promoters of either key transcription factors or an opsin gene. In this comprehensive study, we show that these indels are the result of the movement of transposable elements (TEs) that correlate with opsin expression variation across the Malawi flock. In tracking the evolutionary history of these particular indels, we found they are endemic to Lake Malawi, suggesting that these TEs are recently active and are segregating within the Malawi cichlid lineage. However, an independent indel has arisen at a similar genomic location in one locus outside of the Malawi flock. The convergence in TE movement suggests these loci are primed for TE insertion and subsequent deletions. Increased TE mobility may be associated with interspecific hybridization, which disrupts mechanisms of TE suppression. This might provide a link between cichlid hybridization and accelerated regulatory variation. Overall, our study suggests that TEs may be an important driver of key regulatory changes, facilitating rapid phenotypic change and possibly speciation in African cichlids.

Evolutionary dynamics of pre- and postzygotic reproductive isolation in cichlid fishes

Cichlid fishes are exceptionally species-rich, speciated at explosive rates and, hence, are a model system in speciation research. Yet, their reproductive isolating barriers have, so far, not been comprehensively studied. Here, we review current knowledge on pre- and postzygotic mechanisms in cichlids. While premating isolation is the norm in cichlids, its strength varies across lineages and with the geographical setting. Moreover, manipulations of ambient conditions tended to reduce assortative mating among closely related species, suggesting that premating isolation in cichlids is often fragile and context dependent. The observed lack of complete reproductive isolation is supported by past and present hybridization events that have contributed to diversity by creating novel allelic combinations. On the other hand, our meta-analysis highlights that intrinsic postzygotic isolation might accumulate faster than assumed. Mild forms of genetic incompatibilities, such as sex ratio distortion, can already be observed among closely related species. Therefore, cessation of gene flow by strong reproductive isolation in cichlids requires a combination of premating prezygotic isolation supplemented with intrinsic and extrinsic postzygotic barriers. Further, we suggest crucial next steps to improve our knowledge about reproductive barriers in cichlids to understand the evolutionary dynamics of pre- and postzygotic isolation mechanisms during adaptive radiations. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.

Tbx2a Modulates Switching of RH2 and LWS Opsin Gene Expression

Sensory systems are tuned by selection to maximize organismal fitness in particular environments. This tuning has implications for intraspecies communication, the maintenance of species boundaries, and speciation. Tuning of color vision largely depends on the sequence of the expressed opsin proteins. To improve tuning of visual sensitivities to shifts in habitat or foraging ecology over the course of development, many organisms change which opsins are expressed. Changes in this developmental sequence (heterochronic shifts) can create differences in visual sensitivity among closely related species. The genetic mechanisms by which these developmental shifts occur are poorly understood. Here, we use quantitative trait locus analyses, genome sequencing, and gene expression studies in African cichlid fishes to identify a role for the transcription factor Tbx2a in driving a switch between long wavelength sensitive (LWS) and Rhodopsin-like (RH2) opsin expression. We identify binding sites for Tbx2a in the LWS promoter and the highly conserved locus control region of RH2 which concurrently promote LWS expression while repressing RH2 expression. We also present evidence that a single change in Tbx2a regulatory sequence has led to a species difference in visual tuning, providing the first mechanistic model for the evolution of rapid switches in sensory tuning. This difference in visual tuning likely has important roles in evolution as it corresponds to differences in diet, microhabitat choice, and male nuptial coloration.

Visual system diversity in coral reef fishes

Coral reefs are one of the most species rich and colourful habitats on earth and for many coral reef teleosts, vision is central to their survival and reproduction. The diversity of reef fish visual systems arises from variations in ocular and retinal anatomy, neural processing and, perhaps most easily revealed by, the peak spectral absorbance of visual pigments. This review examines the interplay between retinal morphology and light environment across a number of reef fish species, but mainly focusses on visual adaptations at the molecular level (i.e. visual pigment structure). Generally, visual pigments tend to match the overall light environment or micro-habitat, with fish inhabiting greener, inshore waters possessing longer wavelength-shifted visual pigments than open water blue-shifted species. In marine fishes, particularly those that live on the reef, most species have between two (likely dichromatic) to four (possible tetrachromatic) cone spectral sensitivities and a single rod for crepuscular vision; however, most are trichromatic with three spectral sensitivities. In addition to variation in spectral sensitivity number, spectral placement of the absorbance maximum (λ_max) also has a surprising degree of variability. Variation in ocular and retinal anatomy is also observed at several levels in reef fishes but is best represented by differences in arrangement, density and distribution of neural cell types across the retina (i.e. retinal topography). Here, we focus on the seven reef fish families most comprehensively studied to date to examine and compare how behaviour, environment, activity period, ontogeny and phylogeny might interact to generate the exceptional diversity in visual system design that we observe.

Habitat light sets the boundaries for the rapid evolution of cichlid fish vision, while sexual selection can tune it within those limits

Cichlid fishes' famous diversity in body coloration is accompanied by a highly diverse and complex visual system. Although cichlids possess an unusually high number of seven cone opsin genes, they express only a subset of these during their ontogeny, accounting for their astonishing interspecific variation in visual sensitivities. Much of this diversity is thought to have been shaped by natural selection as cichlids inhabit a variety of habitats with distinct light environments. Also, sexual selection might have contributed to the observed visual diversity, and sexual dimorphism in coloration potentially co-evolved with sexual dimorphism in opsin expression. We investigated sex-specific opsin expression of several cichlids from Africa and the Neotropics and collected and integrated data sets on sex-specific body coloration, species-specific visual sensitivities, lens transmission and habitat light properties for some of them. We comparatively analysed this wide range of molecular and ecological data, illustrating how integrative approaches can address specific questions on the factors and mechanisms driving diversification, and the evolution of cichlid vision in particular. We found that both sexes expressed opsins at the same levels-even in sexually dimorphic cichlid species-which argues against coevolution of sexual dichromatism and differences in sex-specific visual sensitivity. Rather, a combination of environmental light properties and body coloration shaped the diversity in spectral sensitivities among cichlids. We conclude that although cichlids are particularly colourful and diverse and often sexually dimorphic, it would appear that natural rather than sexual selection is a more powerful force driving visual diversity in this hyperdiverse lineage.

The round goby genome provides insights into mechanisms that may facilitate biological invasions

Background

The invasive benthic round goby (Neogobius melanostomus) is the most successful temperate invasive fish and has spread in aquatic ecosystems on both sides of the Atlantic. Invasive species constitute powerful in situ experimental systems to study fast adaptation and directional selection on short ecological timescales and present promising case studies to understand factors involved the impressive ability of some species to colonize novel environments. We seize the unique opportunity presented by the round goby invasion to study genomic substrates potentially involved in colonization success.

Results

We report a highly contiguous long-read-based genome and analyze gene families that we hypothesize to relate to the ability of these fish to deal with novel environments. The analyses provide novel insights from the large evolutionary scale to the small species-specific scale. We describe expansions in specific cytochrome P450 enzymes, a remarkably diverse innate immune system, an ancient duplication in red light vision accompanied by red skin fluorescence, evolutionary patterns of epigenetic regulators, and the presence of osmoregulatory genes that may have contributed to the round goby’s capacity to invade cold and salty waters. A recurring theme across all analyzed gene families is gene expansions.

Conclusions

The expanded innate immune system of round goby may potentially contribute to its ability to colonize novel areas. Since other gene families also feature copy number expansions in the round goby, and since other Gobiidae also feature fascinating environmental adaptations and are excellent colonizers, further long-read genome approaches across the goby family may reveal whether gene copy number expansions are more generally related to the ability to conquer new habitats in Gobiidae or in fish.

Electronic supplementary material

The online version of this article (10.1186/s12915-019-0731-8) contains supplementary material, which is available to authorized users.

Visual adaptation could aid sympatric speciation in a deep crater lake

Allopatric speciation was originally suggested to be the primary mechanism of animal speciation (Mayr, 1942; Figure 1). During allopatric speciation, populations diverge when gene flow is reduced across significant biogeographic barriers. Sympatric speciation, where species diverge while inhabiting the same location, was thought to be essentially impossible. However, the advent of theoretical models followed by new experimental evidence made sympatric speciation more plausible (Via, 2001). The cichlid fishes of Barombi Mbo, a small crater lake in western Cameroon, became one of the most widely accepted examples of sympatric speciation (Schliewen, Tautz, & Paabo, 1994). Although the phylogenetic history of this clade is not quite as simple as originally thought, it remains one of the best examples of sympatric speciation (Richards, Poelstra, & Martin, 2018). However, little is known about the molecular mechanisms contributing to the splitting of these species in situ. In a From the Cover article in this issue of Molecular Ecology, Musilova et al. (2019) focus on the diversity of visual systems among these fishes. They identify genetic changes associated with several aspects of visual adaptation that may have contributed to the ecological specialization and sympatric speciation of cichlids in this lake.

A detailed investigation of the visual system and visual ecology of the Barrier Reef anemonefish, Amphiprion akindynos

Vision plays a major role in the life of most teleosts, and is assumingly well adapted to each species ecology and behaviour. Using a multidisciplinary approach, we scrutinised several aspects of the visual system and ecology of the Great Barrier Reef anemonefish, Amphiprion akindynos, including its orange with white patterning, retinal anatomy and molecular biology, its symbiosis with anemones and sequential hermaphroditism. Amphiprion akindynos possesses spectrally distinct visual pigments and opsins: one rod opsin, RH1 (498 nm), and five cone opsins, SWS1 (370 nm), SWS2B (408 nm), RH2B (498 nm), RH2A (520 nm), and LWS (554 nm). Cones were arranged in a regular mosaic with each single cone surrounded by four double cones. Double cones mainly expressed RH2B (53%) in one member and RH2A (46%) in the other, matching the prevailing light. Single cones expressed SWS1 (89%), which may serve to detect zooplankton, conspecifics and the host anemone. Moreover, a segregated small fraction of single cones coexpressed SWS1 with SWS2B (11%). This novel visual specialisation falls within the region of highest acuity and is suggested to increase the chromatic contrast of Amphiprion akindynos colour patterns, which might improve detection of conspecifics.

Color discrimination thresholds in a cichlid fish: Metriaclima benetos

Color vision is essential for animals as it allows them to detect, recognize and discriminate between colored objects. Studies analyzing color vision require an integrative approach, combining behavioral experiments, physiological models and quantitative analyses of photoreceptor stimulation. Here, we demonstrate, for the first time, the limits of chromatic discrimination in Metriaclima benetos, a rock-dwelling cichlid from Lake Malawi, using behavioral experiments and visual modeling. Fish were trained to discriminate between colored stimuli. Color discrimination thresholds were quantified by testing fish chromatic discrimination between the rewarded stimulus and distracter stimuli that varied in chromatic distance (ΔS). This was done under fluorescent lights alone and with additional violet lights. Our results provide two main outcomes. First, cichlid color discrimination thresholds correspond with predictions from the receptor noise limited (RNL) model but only if we assume a Weber fraction higher than the typical value of 5%. Second, cichlids may exhibit limited color constancy under certain lighting conditions as most individuals failed to discriminate colors when violet light was added. We further used the color discrimination thresholds obtained from these experiments to model color discrimination of actual fish colors and backgrounds under natural lighting for Lake Malawi. We found that, for M. benetos, blue is most chromatically contrasting against yellows and space-light, which might be important for discriminating male nuptial colorations and detecting males against the background. This study highlights the importance of lab-based behavioral experiments in understanding color vision and in parameterizing the assumptions of the RNL vision model for different species.

Geographic variation in opsin expression does not align with opsin genotype in Lake Victoria cichlid populations

Sensory adaptation to the local environment can contribute to speciation. Aquatic environments are well suited for studying this process: The natural attenuation of light through water results in heterogeneous light environments, to which vision-dependent species must adapt for communication and survival. Here, we study visual adaptation in sympatric Pundamilia cichlids from southeastern Lake Victoria. Species with blue or red male nuptial coloration co-occur at many rocky islands but tend to be depth-differentiated, entailing different visual habitats, more strongly at some islands than others. Divergent visual adaptation to these environments has been implicated as a major factor in the divergence of P. pundamilia and P. nyererei, as they show consistent differentiation in the long-wavelength-sensitive visual pigment gene sequence (LWS opsin). In addition to sequence variation, variation in the opsin gene expression levels may contribute to visual adaptation. We characterized opsin gene expression and LWS genotype across Pundamilia populations inhabiting turbid and clear waters, to examine how different mechanisms of visual tuning contribute to visual adaptation. As predicted, the short-wavelength-sensitive opsin (SWS2b) was expressed exclusively in a population from clear water. Contrary to prediction however, expression levels of the other opsins were species- and island-dependent and did not align with species differences in LWS genotype. Specifically, in two locations with turbid water, the shallow-water dwelling blue species expressed more LWS and less RH2A than the deeper-dwelling red species, while the opposite pattern occurred in the two locations with clear water. Visual modeling suggests that the observed distribution of opsin expression profiles and LWS genotypes does not maximize visual performance, implying the involvement of additional visual tuning mechanisms and/or incomplete adaptation.

OPEN RESEARCH BADGE

This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://hdl.handle.net/10411/I1IUUQ.

Reverting ontogeny: rapid phenotypic plasticity of colour vision in cichlid fish

Phenotypic plasticity, particularly during development, allows organisms to rapidly adjust to different environmental conditions. Yet, it is often unclear whether the extent and direction of plastic changes are restricted by an individual's ontogeny. Many species of cichlid fishes go through ontogenetic changes in visual sensitivity, from short to long wavelengths, by switching expression of cone opsin genes crucial for colour vision. During this progression, individuals often exhibit phenotypic plasticity to the ambient light conditions. However, it is commonly assumed that once an adult visual phenotype is reached, reverting to an earlier ontogenetic state with higher sensitivity at shorter wavelengths is not common. In this study, we experimentally demonstrate that four-month-old Midas cichlid fish (Amphilophus astorquii) show plasticity in single cone opsin expression after experiencing drastic changes in light conditions. Resulting shifts of visual sensitivity occurred presumably in an adaptive direction-towards shorter or longer wavelengths when exposed to short- or long-wavelength light, respectively. Single cone opsin expression changed within only a few days and went through a transitional phase of co-expression. When the environment was experimentally enriched in long-wavelength light, the corresponding change occurred gradually along a dorsoventral gradient within the retina. This plasticity allowed individuals to revert earlier ontogenetic changes and return to a more juvenile visual phenotype demonstrating previously unrecognized insights into temporal and spatial dynamics of phenotypic plasticity of the visual system in response to ambient light.

Evolutionary ecology of opsin gene sequence, expression and repertoire

Linking molecular evolution to biological function is a long-standing challenge in evolutionary biology. Some of the best examples of this involve opsins, the genes that encode the molecular basis of light reception. In this issue of Molecular Ecology, three studies examine opsin gene sequence, expression and repertoire to determine how natural selection has shaped the visual system. First, Escobar-Camacho et al. () use opsin repertoire and expression in three Amazonian cichlid species to show that a shift in sensitivity towards longer wavelengths is coincident with the long-wavelength-dominated Amazon basin. Second, Stieb et al. () explore opsin sequence and expression in reef-dwelling damselfish and find that UV- and long-wavelength vision are both important, but likely for different ecological functions. Lastly, Suvorov et al. () study an expansive opsin repertoire in the insect order Odonata and find evidence that copy number expansion is consistent with the permanent heterozygote model of gene duplication. Together these studies emphasize the utility of opsin genes for studying both the local adaptation of sensory systems and, more generally, gene family evolution.

Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

The hundreds of cichlid fish species in Lake Malawi constitute the most extensive recent vertebrate adaptive radiation. Here we characterize its genomic diversity by sequencing 134 individuals covering 73 species across all major lineages. The average sequence divergence between species pairs is only 0.1-0.25%. These divergence values overlap diversity within species, with 82% of heterozygosity shared between species. Phylogenetic analyses suggest that diversification initially proceeded by serial branching from a generalist Astatotilapia-like ancestor. However, no single species tree adequately represents all species relationships, with evidence for substantial gene flow at multiple times. Common signatures of selection on visual and oxygen transport genes shared by distantly related deep-water species point to both adaptive introgression and independent selection. These findings enhance our understanding of genomic processes underlying rapid species diversification, and provide a platform for future genetic analysis of the Malawi radiation.

Phylogenomics uncovers early hybridization and adaptive loci shaping the radiation of Lake Tanganyika cichlid fishes

Lake Tanganyika is the oldest and phenotypically most diverse of the three East African cichlid fish adaptive radiations. It is also the cradle for the younger parallel haplochromine cichlid radiations in Lakes Malawi and Victoria. Despite its evolutionary significance, the relationships among the main Lake Tanganyika lineages remained unresolved, as did the general timescale of cichlid evolution. Here, we disentangle the deep phylogenetic structure of the Lake Tanganyika radiation using anchored phylogenomics and uncover hybridization at its base, as well as early in the haplochromine radiation. This suggests that hybridization might have facilitated these speciation bursts. Time-calibrated trees support that the radiation of Tanganyika cichlids coincided with lake formation and that Gondwanan vicariance concurred with the earliest splits in the cichlid family tree. Genes linked to key innovations show signals of introgression or positive selection following colonization of lake habitats and species' dietary adaptations are revealed as major drivers of colour vision evolution. These findings shed light onto the processes shaping the evolution of adaptive radiations.

Convergent phenotypic evolution of the visual system via different molecular routes: How Neotropical cichlid fishes adapt to novel light environments

How predictable is evolution? This remains a fundamental but contested issue in evolutionary biology. When independent lineages colonize the same environment, we are presented with a natural experiment that allows us to ask if genetic and ecological differences promote species-specific evolutionary outcomes or whether species phenotypically evolve in a convergent manner in response to shared selection pressures. If so, are the molecular mechanisms underlying phenotypic convergence the same? In Nicaragua, seven species of cichlid fishes concurrently colonized two novel photic environments. Hence, their visual system represents a compelling model to address these questions, particularly since the adaptive value of phenotypic changes is well-understood. By analyzing retinal transcriptomes, we found that differential expression of genes responsible for color vision (cone opsins and cyp27c1) produced rapid and mostly convergent changes of predicted visual sensitivities. Notably, these changes occurred in the same direction in all species although there were differences in underlying gene expression patterns illustrating nonconvergence at the molecular level. Adaptive phenotypes evolved deterministically, even when species differ substantially in ecology and genetic variation. This provides strong evidence that phenotypic evolution of the visual system occurred in response to similar selective forces of the photic environment.

Reviewing guppy color vision: integrating the molecular and physiological variation in visual tuning of a classic system for sensory drive

Sensory drive predicts coevolution of mate choice signals with the sensory systems detecting those signals. Guppies are a classic model for sensory drive as mate preferences based on coloration differ across individuals and populations. A large body of work has identified variation in color vision, yet we lack a direct tie between how such variation in color vision influences variation in color preference. Here we bring together studies that have investigated guppy vision over the past 40 years to: (1) highlight our current understanding of where variation occurs in the guppy color vision pathway and (2) suggest future avenues of research into sources of visual system variation that could influence guppy color preference. This will allow researchers to design careful studies that couple measures of color preference with measures of visual system variation from the same individual or population. Such studies will finally provide important answers as to what sets the direction and speed of mate preference evolution via sensory drive.

Multichannel spectrometers in animals

Multispectral, hyperspectral, polarimetric, and other types of multichannel imaging spectrometers are coming into common use for a variety of applications, including remote sensing, material identification, forensics, and medical diagnosis. These instruments are often bulky and intolerant of field abuse, so designing compact, reliable, portable, and robust devices is a priority. In contrast to most engineering designs, animals have been building compact and robust multichannel imaging systems for millennia-their eyes. Biological sensors arise by evolution, of course, and are not designed 'for' a particular use; they exist because the creatures that were blessed with useful mutations were better able to survive and reproduce than their competitors. While this is an inefficient process for perfecting a sensor, it brings unexpected innovations and novel concepts into visual system design-concepts that may be useful in the inspiration of new engineered solutions to problematic challenges, like the ones mentioned above. Here, we review a diversity of multichannel visual systems from both vertebrate and invertebrate animals, considering the receptor molecules and cells, spectral sensitivity and its tuning, and some aspects of the higher-level processing systems used to shape spectral (and polarizational) channels in vision. The eyes of mantis shrimps are presented as potential models for biomimetic multichannel imaging systems. We end with a description of a bioinspired, newly developed multichannel spectral/polarimetric imaging system based on mantis shrimp vision that is highly adaptable to field application.

Short term colour vision plasticity on the reef: Changes in opsin expression under varying light conditions differ between ecologically distinct reef fish species

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 opsin genes, 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 shorter 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, Ostorhinchus cyanosoma, Ambon damselfish, Pomacentrus amboinensis, and Lemon damselfish, Pomacentrus moluccensis, 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 opsin expression changes in single cones generally occurred more rapidly than in double cones, and identified different responses of RH2 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.

Accelerated Evolution and Functional Divergence of the Dim Light Visual Pigment Accompanies Cichlid Colonization of Central America

Cichlids encompass one of the most diverse groups of fishes in South and Central America, and show extensive variation in life history, morphology, and colouration. While studies of visual system evolution in cichlids have focussed largely on the African rift lake species flocks, Neotropical cichlids offer a unique opportunity to investigate visual system evolution at broader temporal and geographic scales. South American cichlid colonization of Central America has likely promoted accelerated rates of morphological evolution in Central American lineages as they encountered reduced competition, renewed ecological opportunity, and novel aquatic habitats. To investigate whether such transitions have influenced molecular evolution of vision in Central American cichlids, we sequenced the dim-light rhodopsin gene in 101 Neotropical cichlid species, spanning the diversity of the clade. We find strong evidence for increased rates of evolution in Central American cichlid rhodopsin relative to South American lineages, and identify several sites under positive selection in rhodopsin that likely contribute to adaptation to different photic environments. We expressed a Neotropical cichlid rhodopsin protein invitro for the first time, and found that while its spectral tuning properties were characteristic of typical vertebrate rhodopsin pigments, the rate of decay of its active signalling form was much slower, consistent with dim light adaptation in other vertebrate rhodopsins. Using site-directed mutagenesis combined with spectroscopic assays, we found that a key amino acid substitution present in some Central American cichlids accelerates the rate of decay of active rhodopsin, which may mediate adaptation to clear water habitats.

Insights into visual pigment adaptation and diversity from model ecological and evolutionary systems

Sensory systems provide valuable insight into the evolution of molecular mechanisms underlying organismal anatomy, physiology, and behaviour. Visual pigments, which mediate the first step in visual transduction, offer a unique window into the relationship between molecular variation and visual performance, and enhance our understanding of how ecology, life history, and physiology may shape genetic variation across a variety of organisms. Here we review recent work investigating vertebrate visual pigments from a number of perspectives. Opsin gene duplication, loss, differential expression, structural variation, and the physiological context in which they operate, have profoundly shaped the visual capabilities of vertebrates adapting to novel environments. We note the importance of conceptual frameworks in investigating visual pigment diversity in vertebrates, highlighting key examples including evolutionary transitions between different photic environments, major shifts in life history evolution and ecology, evolutionary innovations in visual system anatomy and physiology, as well as shifts in visually mediated behaviours and behavioural ecology. We emphasize the utility of studying visual pigment evolution in the context of these different perspectives, and demonstrate how the integrative approaches discussed in this review contribute to a better understanding of the underlying molecular processes mediating adaptation in sensory systems, and the contexts in which they occur.

Sensory Drive, Color, and Color Vision

Colors often appear to differ in arbitrary ways among related species. However, a fraction of color diversity may be explained because some signals are more easily perceived in one environment rather than another. Models show that not only signals but also the perception of signals should regularly evolve in response to different environments, whether these primarily involve detection of conspecifics or detection of predators and prey. Thus, a deeper understanding of how perception of color correlates with environmental attributes should help generate more predictive models of color divergence. Here, I briefly review our understanding of color vision in vertebrates. Then I focus on opsin spectral tuning and opsin expression, two traits involved in color perception that have become amenable to study. I ask how opsin tuning is correlated with ecological differences, notably the light environment, and how this potentially affects perception of conspecific colors. Although opsin tuning appears to evolve slowly, opsin expression levels are more evolutionarily labile but have been difficult to connect to color perception. The challenge going forward will be to identify how physiological differences involved in color vision, such as opsin expression levels, translate into perceptual differences, the selection pressures that have driven those differences, and ultimately how this may drive evolution of conspecific colors.

Behavioral color vision in a cichlid fish: Metriaclima benetos

Color vision is the capacity to discriminate color regardless of brightness. It is essential for many fish species as they rely on color discrimination for numerous ecological tasks. The study of color vision is important because it can unveil the mechanisms that shape coloration patterns, visual system sensitivities and, hence, visual signals. In order to better understand the mechanisms underlying color vision, an integrative approach is necessary. This usually requires combining behavioral, physiological and genetic experiments with quantitative modeling, resulting in a distinctive characterization of the visual system. Here, we provide new data on the color vision of a rock-dwelling cichlid from Lake Malawi: Metriaclima benetos. For this study we used a behavioral approach to demonstrate color vision through classical conditioning, complemented with modeling of color vision to estimate color contrast. For our experiments we took into account opsin coexpression and considered whether cichlids exhibit a dichromatic or a trichromatic visual system. Behavioral experiments confirmed color vision in M. benetos; most fish were significantly more likely to choose the trained over the distracter stimuli, irrespective of brightness. Our results are supported by visual modeling that suggests that cichlids are trichromats and achieve color vision through color opponency mechanisms, which are a result of three different photoreceptor channels. Our analyses also suggest that opsin coexpression can negatively affect perceived color contrast. This study is particularly relevant for research on the cichlid lineage because cichlid visual capabilities and coloration patterns are implicated in their adaptive radiation.

The opsin genes of amazonian cichlids

Vision is a critical sense for organismal survival with visual sensitivities strongly shaped by the environment. Some freshwater fishes with a Gondwanan origin are distributed in both South American rivers including the Amazon and African rivers and lakes. These different habitats likely required adaptations to murky and clear environments. In this study, we compare the molecular basis of Amazonian and African cichlid fishes' visual systems. We used next-generation sequencing of genomes and retinal transcriptomes to examine three Amazonian cichlid species. Genome assemblies revealed six cone opsin classes (SWS1, SWS2B, SWS2A, RH2B, RH2A and LWS) and rod opsin (RH1). However, the functionality of these genes varies across species with different pseudogenes found in different species. Our results support evidence of an RH2A gene duplication event that is shared across both cichlid groups, but which was probably followed by gene conversion. Transcriptome analyses show that Amazonian species mainly express three opsin classes (SWS2A, RH2A and LWS), which likely are a good match to the long-wavelength-oriented light environment of the Amazon basin. Furthermore, analysis of amino acid sequences suggests that the short-wavelength-sensitive genes (SWS2B, SWS2A) may be under selective pressures to shift their spectral properties to a longer-wavelength visual palette. Our results agree with the 'sensitivity hypothesis' where the light environment causes visual adaptation. Amazonian cichlid visual systems are likely adapting through gene expression, gene loss and possibly spectral tuning of opsin sequences. Such mechanisms may be shared across the Amazonian fish fauna.

Retinal specialization through spatially varying cell densities and opsin coexpression in cichlid fish

The distinct behaviours of animals and the varied habitats in which animals live place different requirements on their visual systems. A trade-off exists between resolution and sensitivity, with these properties varying across the retina. Spectral sensitivity, which affects both achromatic and chromatic (colour) vision, also varies across the retina, though the function of this inhomogeneity is less clear. We previously demonstrated spatially varying spectral sensitivity of double cones in the cichlid fish Metriaclima zebra owing to coexpression of different opsins. Here, we map the distributions of ganglion cells and cone cells and quantify opsin coexpression in single cones to show these also vary across the retina. We identify an area centralis with peak acuity and infrequent coexpression, which may be suited for tasks such as foraging and detecting male signals. The peripheral retina has reduced ganglion cell densities and increased opsin coexpression. Modeling of cichlid visual tasks indicates that coexpression might hinder colour discrimination of foraging targets and some fish colours. But, coexpression might improve contrast detection of dark objects against bright backgrounds, which might be useful for detecting predators or zooplankton. This suggests a trade-off between acuity and colour discrimination in the central retina versus lower resolution but more sensitive contrast detection in the peripheral retina. Significant variation in the pattern of coexpression among individuals, however, raises interesting questions about the selective forces at work.