Mechanisms of wavelength tuning in the rod opsins of deep-sea fishes

An EvoDevo Study of Salmonid Visual Opsin Dynamics and Photopigment Spectral Sensitivity

Salmonids are ideal models as many species follow a distinct developmental program from demersal eggs and a large yolk sac to hatching at an advanced developmental stage. Further, these economically important teleosts inhabit both marine- and freshwaters and experience diverse light environments during their life histories. At a genome level, salmonids have undergone a salmonid-specific fourth whole genome duplication event (Ss4R) compared to other teleosts that are already more genetically diverse compared to many non-teleost vertebrates. Thus, salmonids display phenotypically plastic visual systems that appear to be closely related to their anadromous migration patterns. This is most likely due to a complex interplay between their larger, more gene-rich genomes and broad spectrally enriched habitats; however, the molecular basis and functional consequences for such diversity is not fully understood. This study used advances in genome sequencing to identify the repertoire and genome organization of visual opsin genes (those primarily expressed in retinal photoreceptors) from six different salmonids [Atlantic salmon (Salmo salar), brown trout (Salmo trutta), Chinook salmon (Oncorhynchus tshawytcha), coho salmon (Oncorhynchus kisutch), rainbow trout (Oncorhynchus mykiss), and sockeye salmon (Oncorhynchus nerka)] compared to the northern pike (Esox lucius), a closely related non-salmonid species. Results identified multiple orthologues for all five visual opsin classes, except for presence of a single short-wavelength-sensitive-2 opsin gene. Several visual opsin genes were not retained after the Ss4R duplication event, which is consistent with the concept of salmonid rediploidization. Developmentally, transcriptomic analyzes of Atlantic salmon revealed differential expression within each opsin class, with two of the long-wavelength-sensitive opsins not being expressed before first feeding. Also, early opsin expression in the retina was located centrally, expanding dorsally and ventrally as eye development progressed, with rod opsin being the dominant visual opsin post-hatching. Modeling by spectral tuning analysis and atomistic molecular simulation, predicted the greatest variation in the spectral peak of absorbance to be within the Rh2 class, with a ∼40 nm difference in λ max values between the four medium-wavelength-sensitive photopigments. Overall, it appears that opsin duplication and expression, and their respective spectral tuning profiles, evolved to maximize specialist color vision throughout an anadromous lifecycle, with some visual opsin genes being lost to tailor marine-based vision.

Ancient whale rhodopsin reconstructs dim-light vision over a major evolutionary transition: Implications for ancestral diving behavior

Cetaceans are fully aquatic mammals that descended from terrestrial ancestors, an iconic evolutionary transition characterized by adaptations for underwater foraging via breath-hold diving. Although the evolutionary history of this specialized behavior is challenging to reconstruct, coevolving sensory systems may offer valuable clues. The dim-light visual pigment, rhodopsin, which initiates phototransduction in the rod photoreceptors of the eye, has provided insight into the visual ecology of depth in several aquatic vertebrate lineages. Here, we use ancestral sequence reconstruction and protein resurrection experiments to quantify light-activation metrics in rhodopsin pigments from ancestors bracketing the cetacean terrestrial-to-aquatic transition. By comparing multiple reconstruction methods on a broadly sampled cetartiodactyl species tree, we generated highly robust ancestral sequence estimates. Our experimental results provide direct support for a blue-shift in spectral sensitivity along the branch separating cetaceans from terrestrial relatives. This blue-shift was 14 nm, resulting in a deep-sea signature (λ_max = 486 nm) similar to many mesopelagic-dwelling fish. We also discovered that the decay rates of light-activated rhodopsin increased in ancestral cetaceans, which may indicate an accelerated dark adaptation response typical of deeper-diving mammals. Because slow decay rates are thought to help sequester cytotoxic photoproducts, this surprising result could reflect an ecological trade-off between rod photoprotection and dark adaptation. Taken together, these ancestral shifts in rhodopsin function suggest that some of the first fully aquatic cetaceans could dive into the mesopelagic zone (>200 m). Moreover, our reconstructions indicate that this behavior arose before the divergence of toothed and baleen whales.

Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering

The first member and eponym of the rhodopsin family was identified in the 1930s as the visual pigment of the rod photoreceptor cell in the animal retina. It was found to be a membrane protein, owing its photosensitivity to the presence of a covalently bound chromophoric group. This group, derived from vitamin A, was appropriately dubbed retinal. In the 1970s a microbial counterpart of this species was discovered in an archaeon, being a membrane protein also harbouring retinal as a chromophore, and named bacteriorhodopsin. Since their discovery a photogenic panorama unfolded, where up to date new members and subspecies with a variety of light-driven functionality have been added to this family. The animal branch, meanwhile categorized as type-2 rhodopsins, turned out to form a large subclass in the superfamily of G protein-coupled receptors and are essential to multiple elements of light-dependent animal sensory physiology. The microbial branch, the type-1 rhodopsins, largely function as light-driven ion pumps or channels, but also contain sensory-active and enzyme-sustaining subspecies. In this review we will follow the development of this exciting membrane protein panorama in a representative number of highlights and will present a prospect of their extraordinary future potential.

Additive and epistatic effects influence spectral tuning in molluscan retinochrome opsin

The relationship between genotype and phenotype is nontrivial due to often complex molecular pathways that make it difficult to unambiguously relate phenotypes to specific genotypes. Photopigments, an opsin apoprotein bound to a light-absorbing chromophore, present an opportunity to directly relate the amino acid sequence to an absorbance peak phenotype (λmax). We examined this relationship by conducting a series of site-directed mutagenesis experiments of retinochrome, a non-visual opsin, from two closely related species: the common bay scallop, Argopecten irradians, and the king scallop, Pecten maximus. Using protein folding models, we identified three amino acid sites of likely functional importance and expressed mutated retinochrome proteins in vitro. Our results show that the mutation of amino acids lining the opsin binding pocket are responsible for fine spectral tuning, or small changes in the λmax of these light sensitive proteins Mutations resulted in a blue or red shift as predicted, but with dissimilar magnitudes. Shifts ranged from a 16 nm blue shift to a 12 nm red shift from the wild-type λmax. These mutations do not show an additive effect, but rather suggests the presence of epistatic interactions. This work highlights the importance of binding pocket shape in the evolution of spectral tuning and builds on our ability to relate genotypic changes to phenotypes in an emerging model for opsin functional analysis.

Molecular evolution and depth-related adaptations of rhodopsin in the adaptive radiation of cichlid fishes in Lake Tanganyika

The visual sensory system is essential for animals to perceive their environment and is thus under strong selection. In aquatic environments, light intensity and spectrum differ primarily along a depth gradient. Rhodopsin (RH1) is the only opsin responsible for dim‐light vision in vertebrates and has been shown to evolve in response to the respective light conditions, including along a water depth gradient in fishes. In this study, we examined the diversity and sequence evolution of RH1 in virtually the entire adaptive radiation of cichlid fishes in Lake Tanganyika, focusing on adaptations to the environmental light with respect to depth. We show that Tanganyikan cichlid genomes contain a single copy of RH1. The 76 variable amino acid sites detected in RH1 across the radiation were not uniformly distributed along the protein sequence, and 31 of these variable sites show signals of positive selection. Moreover, the amino acid substitutions at 15 positively selected sites appeared to be depth‐related, including three key tuning sites that directly mediate shifts in the peak spectral sensitivity, one site involved in protein stability and 11 sites that may be functionally important on the basis of their physicochemical properties. Among the strongest candidate sites for deep‐water adaptations are two known key tuning sites (positions 292 and 299) and three newly identified variable sites (37, 104 and 290). Our study, which is the first comprehensive analysis of RH1 evolution in a massive adaptive radiation of cichlid fishes, provides novel insights into the evolution of RH1 in a freshwater environment.

Sensory Transduction in Photoreceptors and Olfactory Sensory Neurons: Common Features and Distinct Characteristics

The past decades have seen tremendous progress in our understanding of the function of photoreceptors and olfactory sensory neurons, uncovering the mechanisms that determine their properties and, ultimately, our ability to see and smell. This progress has been driven to a large degree by the powerful combination of physiological experimental tools and genetic manipulations, which has enabled us to identify the main molecular players in the transduction cascades of these sensory neurons, how their properties affect the detection and discrimination of stimuli, and how diseases affect our senses of vision and smell. This review summarizes some of the common and unique features of photoreceptors and olfactory sensory neurons that make these cells so exciting to study.

Photoreceptor Diversification Accompanies the Evolution of Anthozoa

Anthozoan corals are an ecologically important group of cnidarians, which power the productivity of reef ecosystems. They are sessile, inhabit shallow, tropical oceans and are highly dependent on sun- and moonlight to regulate sexual reproduction, phototaxis, and photosymbiosis. However, their exposure to high levels of sunlight also imposes an increased risk of UV-induced DNA damage. How have these challenging photic environments influenced photoreceptor evolution and function in these animals? To address this question, we initially screened the cnidarian photoreceptor repertoire for Anthozoa-specific signatures by a broad-scale evolutionary analysis. We compared transcriptomic data of more than 36 cnidarian species and revealed a more diverse photoreceptor repertoire in the anthozoan subphylum than in the subphylum Medusozoa. We classified the three principle opsin classes into distinct subtypes and showed that Anthozoa retained all three classes, which diversified into at least six subtypes. In contrast, in Medusozoa, only one class with a single subtype persists. Similarly, in Anthozoa, we documented three photolyase classes and two cryptochrome (CRY) classes, whereas CRYs are entirely absent in Medusozoa. Interestingly, we also identified one anthozoan CRY class, which exhibited unique tandem duplications of the core functional domains. We next explored the functionality of anthozoan photoreceptors in the model species Exaiptasia diaphana (Aiptasia), which recapitulates key photo-behaviors of corals. We show that the diverse opsin genes are differentially expressed in important life stages common to reef-building corals and Aiptasia and that CRY expression is light regulated. We thereby provide important clues linking coral evolution with photoreceptor diversification.

Evolutionary ecology of the visual opsin gene sequence and its expression in turbot (Scophthalmus maximus)

Background

As flatfish, turbot undergo metamorphosis as part of their life cycle. In the larval stage, turbot live at the ocean surface, but after metamorphosis they move to deeper water and turn to benthic life. Thus, the light environment differs greatly between life stages. The visual system plays a great role in organic evolution, but reports of the relationship between the visual system and benthic life are rare. In this study, we reported the molecular and evolutionary analysis of opsin genes in turbot, and the heterochronic shifts in opsin expression during development.

Results

Our gene synteny analysis showed that subtype RH2C was not on the same gene cluster as the other four green-sensitive opsin genes (RH2) in turbot. It was translocated to chromosome 8 from chromosome 6. Based on branch-site test and spectral tuning sites analyses, E122Q and M207L substitutions in RH2C, which were found to be under positive selection, are closely related to the blue shift of optimum light sensitivities. And real-time PCR results indicated the dominant opsin gene shifted from red-sensitive (LWS) to RH2B1 during turbot development, which may lead to spectral sensitivity shifts to shorter wavelengths.

Conclusions

This is the first report that RH2C may be an important subtype of green opsin gene that was retained by turbot and possibly other flatfish species during evolution. Moreover, E122Q and M207L substitutions in RH2C may contribute to the survival of turbot in the bluish colored ocean. And heterochronic shifts in opsin expression may be an important strategy for turbot to adapt to benthic life.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01837-2.

The deep sea is a hot spot of fish body shape evolution

Deep-sea fishes have long captured our imagination with striking adaptations to life in the mysterious abyss, raising the possibility that this cold, dark ocean region may be a key hub for physiological and functional diversification. We explore this idea through an analysis of body shape evolution across ocean depth zones in over 3000 species of marine teleost fishes. We find that the deep ocean contains twice the body shape disparity of shallow waters, driven by elevated rates of evolution in traits associated with locomotion. Deep-sea fishes display more frequent adoption of forms suited to slow and periodic swimming, whereas shallow living species are concentrated around shapes conferring strong, sustained swimming capacity and manoeuvrability. Our results support long-standing impressions of the deep sea as an evolutionary hotspot for fish body shape evolution and highlight that factors like habitat complexity and ecological interactions are potential drivers of this adaptive diversification.

Not just shades of grey: life is full of colour for the ocellate river stingray (Potamotrygon motoro)

Previous studies have shown that marine stingrays have the anatomical and physiological basis for colour vision, with cone spectral sensitivity in the blue to green range of the visible spectrum. Behavioural studies on Glaucostegus typus also showed that blue and grey can be perceived and discriminated. The present study is the first to assess visual opsin genetics in the ocellate river stingray (Potamotrygon motoro) and test whether individuals perceive colour in two alternative forced choice experiments. Retinal transcriptome profiling using RNA-Seq and quantification demonstrated the presence of lws and rh2 cone opsin genes and a highly expressed single rod (rh1) opsin gene. Spectral tuning analysis predicted these vitamin A1-based visual photopigments to exhibit spectral absorbance maxima at 461 nm (rh2), 496 nm (rh1) and 555 nm (lws); suggesting the presence of dichromacy in this species. Indeed, P. motoro demonstrates the potential to be equally sensitive to wavelengths from 380 to 600 nm of the visible spectrum. Behavioural results showed that red and green plates, as well as blue and yellow plates, were readily discriminated based on colour; however, brightness differences also played a part in the discrimination of blue and yellow. Red hues of different brightness were distinguished significantly above chance level from one another. In conclusion, the genetic and behavioural results support prior data on marine stingrays. However, this study suggests that freshwater stingrays of the family Potamotrygonidae may have a visual colour system that has ecologically adapted to a riverine habitat.

Visual Opsin Diversity in Sharks and Rays

The diversity of color vision systems found in extant vertebrates suggests that different evolutionary selection pressures have driven specializations in photoreceptor complement and visual pigment spectral tuning appropriate for an animal's behavior, habitat, and life history. Aquatic vertebrates in particular show high variability in chromatic vision and have become important models for understanding the role of color vision in prey detection, predator avoidance, and social interactions. In this study, we examined the capacity for chromatic vision in elasmobranch fishes, a group that have received relatively little attention to date. We used microspectrophotometry to measure the spectral absorbance of the visual pigments in the outer segments of individual photoreceptors from several ray and shark species, and we sequenced the opsin mRNAs obtained from the retinas of the same species, as well as from additional elasmobranch species. We reveal the phylogenetically widespread occurrence of dichromatic color vision in rays based on two cone opsins, RH2 and LWS. We also confirm that all shark species studied to date appear to be cone monochromats but report that in different species the single cone opsin may be of either the LWS or the RH2 class. From this, we infer that cone monochromacy in sharks has evolved independently on multiple occasions. Together with earlier discoveries in secondarily aquatic marine mammals, this suggests that cone-based color vision may be of little use for large marine predators, such as sharks, pinnipeds, and cetaceans.

Exceptional diversity of opsin expression patterns in Neogonodactylus oerstedii (Stomatopoda) retinas

Stomatopod crustaceans possess some of the most complex animal visual systems, including at least 16 spectrally distinct types of photoreceptive units (e.g., assemblages of photoreceptor cells). Here we fully characterize the set of opsin genes expressed in retinal tissues and determine expression patterns of each in the stomatopod Neogonodactylus oerstedii Using a combination of transcriptome and RACE sequencing, we identified 33 opsin transcripts expressed in each N. oerstedii eye, which are predicted to form 20 long-wavelength-sensitive, 10 middle-wavelength-sensitive, and three UV-sensitive visual pigments. Observed expression patterns of these 33 transcripts were highly unusual in five respects: 1) All long-wavelength and short/middle-wavelength photoreceptive units expressed multiple opsins, while UV photoreceptor cells expressed single opsins; 2) most of the long-wavelength photoreceptive units expressed at least one middle-wavelength-sensitive opsin transcript; 3) the photoreceptors involved in spatial, motion, and polarization vision expressed more transcripts than those involved in color vision; 4) there is a unique opsin transcript that is expressed in all eight of the photoreceptive units devoted to color vision; and 5) expression patterns in the peripheral hemispheres of the eyes suggest visual specializations not previously recognized in stomatopods. Elucidating the expression patterns of all opsin transcripts expressed in the N. oerstedii retina reveals the potential for previously undocumented functional diversity in the already complex stomatopod eye and is a first step toward understanding the functional significance of the unusual abundance of opsins found in many arthropod species' visual systems.

Vision using multiple distinct rod opsins in deep-sea fishes

Vertebrate vision is accomplished through light-sensitive photopigments consisting of an opsin protein bound to a chromophore. In dim light, vertebrates generally rely on a single rod opsin [rhodopsin 1 (RH1)] for obtaining visual information. By inspecting 101 fish genomes, we found that three deep-sea teleost lineages have independently expanded their RH1 gene repertoires. Among these, the silver spinyfin (Diretmus argenteus) stands out as having the highest number of visual opsins in vertebrates (two cone opsins and 38 rod opsins). Spinyfins express up to 14 RH1s (including the most blueshifted rod photopigments known), which cover the range of the residual daylight as well as the bioluminescence spectrum present in the deep sea. Our findings present molecular and functional evidence for the recurrent evolution of multiple rod opsin-based vision in vertebrates.

Opsin-based photopigments expressed in the retina of a South American pit viper, Bothrops atrox (Viperidae)

Although much is known about the visual system of vertebrates in general, studies regarding vision in reptiles, and snakes in particular, are scarce. Reptiles display diverse ocular structures, including different types of retinae such as pure cone, mostly rod, or duplex retinas (containing both rods and cones); however, the same five opsin-based photopigments are found in many of these animals. It is thought that ancestral snakes were nocturnal and/or fossorial, and, as such, they have lost two pigments, but retained three visual opsin classes. These are the RH1 gene (rod opsin or rhodopsin-like-1) expressed in rods and two cone opsins, namely LWS (long-wavelength-sensitive) and SWS1 (short-wavelength-sensitive-1) genes. Until recently, the study of snake photopigments has been largely ignored. However, its importance has become clear within the past few years as studies reconsider Walls’ transmutation theory, which was first proposed in the 1930s. In this study, the visual pigments of Bothrops atrox (the common lancehead), a South American pit viper, were examined. Specifically, full-length RH1 and LWS opsin gene sequences were cloned, as well as most of the SWS1 opsin gene. These sequences were subsequently used for phylogenetic analysis and to predict the wavelength of maximum absorbance (λ_max) for each photopigment. This is the first report to support the potential for rudimentary color vision in a South American viper, specifically a species that is regarded as being nocturnal.

Rhodopsin gene evolution in early teleost fishes

Rhodopsin mediates an essential step in image capture and is tightly associated with visual adaptations of aquatic organisms, especially species that live in dim light environments (e.g., the deep sea). The rh1 gene encoding rhodopsin was formerly considered a single-copy gene in genomes of vertebrates, but increasing exceptional cases have been found in teleost fish species. The main objective of this study was to determine to what extent the visual adaptation of teleosts might have been shaped by the duplication and loss of rh1 genes. For that purpose, homologous rh1/rh1-like sequences in genomes of ray-finned fishes from a wide taxonomic range were explored using a PCR-based method, data mining of public genetic/genomic databases, and subsequent phylogenomic analyses of the retrieved sequences. We show that a second copy of the fish-specific intron-less rh1 is present in the genomes of most anguillids (Elopomorpha), Hiodon alosoides (Osteoglossomorpha), and several clupeocephalan lineages. The phylogenetic analysis and comparisons of alternative scenarios for putative events of gene duplication and loss suggested that fish rh1 was likely duplicated twice during the early evolutionary history of teleosts, with one event coinciding with the hypothesized fish-specific genome duplication and the other in the common ancestor of the Clupeocephala. After these gene duplication events, duplicated genes were maintained in several teleost lineages, whereas some were secondarily lost in specific lineages. Alternative evolutionary schemes of rh1 and comparison with previous studies of gene evolution are also reviewed.

Green-shifting of SWS2A opsin sensitivity and loss of function of RH2-A opsin in flounders, genus Verasper

We identified visual opsin genes for three flounder species, including the spotted halibut (Verasper variegatus), slime flounder (Microstomus achne), and Japanese flounder (Paralichthys olivaceus). Structure and function of opsins for the three species were characterized together with those of the barfin flounder (V. moseri) that we previously reported. All four flounder species possessed five basic opsin genes, including lws, sws1, sws2, rh1, and rh2. Specific features were observed in rh2 and sws2. The rh2-a, one of the three subtypes of rh2, was absent in the genome of V. variegatus and pseudogenized in V. moseri. Moreover, rh2-a mRNA was not detected in M. achne and P. olivaceus, despite the presence of a functional reading frame. Analyses of the maximum absorption spectra (λ_max) estimated by in vitro reconstitution indicated that SWS2A of M. achne (451.9 nm) and P. olivaceus (465.6 nm) were blue-sensitive, whereas in V. variegatus (485.4 nm), it was green-sensitive and comparable to V. moseri (482.3 nm). Our results indicate that although the four flounder species possess a similar opsin gene repertoire, the SWS2A opsin of the genus Verasper is functionally green-sensitive, while its overall structure remains conserved as a blue-sensitive opsin. Further, the rh2-a function seems to have been reduced during the evolution of flounders. λ_max values of predicted ancestral SWS2A of Pleuronectiformes and Pleuronectidae was 465.4 and 462.4 nm, respectively, indicating that these were blue-sensitive. Thus, the green-sensitive SWS2A is estimated to be arisen in ancestral Verasper genus. It is suggested that the sensitivity shift of SWS2A from blue to green may have compensated functional reduction in RH2-A.

Rhodopsin in the Dark Hot Sea: Molecular Analysis of Rhodopsin in a Snailfish, Careproctus rhodomelas, Living near the Deep-Sea Hydrothermal Vent

Visual systems in deep-sea fishes have been previously studied from a photobiological aspect; however, those of deep-sea fish inhabiting the hydrothermal vents are far less understood due to sampling difficulties. In this study, we analyzed the visual pigment of a deep-sea snailfish, Careproctus rhodomelas, discovered and collected only near the hydrothermal vents of oceans around Japan. Proteins were solubilized from the C. rhodomelas eyeball and subjected to spectroscopic analysis, which revealed the presence of a pigment characterized by an absorption maximum (λ_max) at 480 nm. Immunoblot analysis of the ocular protein showed a rhodopsin-like immunoreactivity. We also isolated a retinal cDNA encoding the entire coding sequence of putative C. rhodomelas rhodopsin (CrRh). HEK293EBNA cells were transfected with the CrRh cDNA and the proteins extracted from the cells were subjected to spectroscopic analysis. The recombinant CrRh showed the absorption maximum at 480 nm in the presence of 11-cis retinal. Comparison of the results from the eyeball extract and the recombinant CrRh strongly suggests that CrRh has an A₁-based 11-cis-retinal chromophore and works as a photoreceptor in the C. rhodomelas retina, and hence that C. rhodomelas responds to dim blue light much the same as other deep-sea fishes. Because hydrothermal vent is a huge supply of viable food, C. rhodomelas likely do not need to participate diel vertical migration and may recognize the bioluminescence produced by aquatic animals living near the hydrothermal vents.

Divergent positive selection in rhodopsin from lake and riverine cichlid fishes

Studies of cichlid evolution have highlighted the importance of visual pigment genes in the spectacular radiation of the African rift lake cichlids. Recent work, however, has also provided strong evidence for adaptive diversification of riverine cichlids in the Neotropics, which inhabit environments of markedly different spectral properties from the African rift lakes. These ecological and/or biogeographic differences may have imposed divergent selective pressures on the evolution of the cichlid visual system. To test these hypotheses, we investigated the molecular evolution of the dim-light visual pigment, rhodopsin. We sequenced rhodopsin from Neotropical and African riverine cichlids and combined these data with published sequences from African cichlids. We found significant evidence for positive selection using random sites codon models in all cichlid groups, with the highest levels in African lake cichlids. Tests using branch-site and clade models that partitioned the data along ecological (lake, river) and/or biogeographic (African, Neotropical) boundaries found significant evidence of divergent selective pressures among cichlid groups. However, statistical comparisons among these models suggest that ecological, rather than biogeographic, factors may be responsible for divergent selective pressures that have shaped the evolution of the visual system in cichlids. We found that branch-site models did not perform as well as clade models for our data set, in which there was evidence for positive selection in the background. One of our most intriguing results is that the amino acid sites found to be under positive selection in Neotropical and African lake cichlids were largely nonoverlapping, despite falling into the same three functional categories: spectral tuning, retinal uptake/release, and rhodopsin dimerization. Taken together, these results would imply divergent selection across cichlid clades, but targeting similar functions. This study highlights the importance of molecular investigations of ecologically important groups and the flexibility of clade models in explicitly testing ecological hypotheses.

The evolution and expression of the moth visual opsin family

Because visual genes likely evolved in response to their ambient photic environment, the dichotomy between closely related nocturnal moths and diurnal butterflies forms an ideal basis for investigating their evolution. To investigate whether the visual genes of moths are associated with nocturnal dim-light environments or not, we cloned long-wavelength (R), blue (B) and ultraviolet (UV) opsin genes from 12 species of wild-captured moths and examined their evolutionary functions. Strong purifying selection appeared to constrain the functions of the genes. Dark-treatment altered the levels of mRNA expression in Helicoverpa armigera such that R and UV opsins were up-regulated after dark-treatment, the latter faster than the former. In contrast, B opsins were not significantly up-regulated. Diel changes of opsin mRNA levels in both wild-captured and lab-reared individuals showed no significant fluctuation within the same group. However, the former group had significantly elevated levels of expression compared with the latter. Consequently, environmental conditions appeared to affect the patterns of expression. These findings and the proportional expression of opsins suggested that moths potentially possessed color vision and the visual system played a more important role in the ecology of moths than previously appreciated. This aspect did not differ much from that of diurnal butterflies.

Evolution and functional characterisation of melanopsins in a deep-sea chimaera (elephant shark, Callorhinchus milii)

Non-visual photoreception in mammals is primarily mediated by two splice variants that derive from a single melanopsin (OPN4M) gene, whose expression is restricted to a subset of retinal ganglion cells. Physiologically, this sensory system regulates the photoentrainment of many biological rhythms, such as sleep via the melatonin endocrine system and pupil constriction. By contrast, melanopsin exists as two distinct lineages in non-mammals, opn4m and opn4x, and is broadly expressed in a wide range of tissue types, including the eye, brain, pineal gland and skin. Despite these findings, the evolution and function of melanopsin in early vertebrates are largely unknown. We, therefore, investigated the complement of opn4 classes present in the genome of a model deep-sea cartilaginous species, the elephant shark (Callorhinchus milii), as a representative vertebrate that resides at the base of the gnathostome (jawed vertebrate) lineage. We reveal that three melanopsin genes, opn4m1, opn4m2 and opn4x, are expressed in multiple tissues of the elephant shark. The two opn4m genes are likely to have arisen as a result of a lineage-specific duplication, whereas “long” and “short” splice variants are generated from a single opn4x gene. By using a heterologous expression system, we suggest that these genes encode functional photopigments that exhibit both “invertebrate-like” bistable and classical “vertebrate-like” monostable biochemical characteristics. We discuss the evolution and function of these melanopsin pigments within the context of the diverse photic and ecological environments inhabited by this chimaerid holocephalan, as well as the origin of non-visual sensory systems in early vertebrates.

Evolutionary tinkering with visual photoreception

Eyes have evolved many times, and arthropods and vertebrates share transcription factors for early development. Moreover, the photochemistry of vision in all eyes employs an opsin and the isomerization of a retinoid from the 11-cis to the all-trans configuration. The opsins, however, have associated with several different G proteins, initiating hyperpolarizing and depolarizing conductance changes at the photoreceptor membrane. Beyond these obvious instances of homology, much of the evolutionary story is one of tinkering, producing a great variety of morphological forms and variation within functional themes. This outcome poses a central issue in the convergence of evolutionary and developmental biology: what are the heritable features in the later stages of development that give natural selection traction in altering phenotypic outcomes? This paper discusses some results of evolutionary tinkering where this question arises and, in some cases, where the reasons for particular outcomes and the role of adaptation may not be understood. Phenotypic features include: the exploitation of microvilli in rhabdomeric photoreceptors for detecting the plane of polarized light; different instances of retinoid in the visual pigment; examples of the many uses of accessory pigments in tuning the spectral sensitivity of photoreceptors; selection of opsins in tuning sensitivity in aquatic environments; employing either reflection or refraction in the optics of compound eyes; the multiple ways of constructing images in compound eyes; and the various ways of regenerating 11-cis retinals to maintain visual sensitivity. Evolution is an irreversible process, but tinkering may recover some lost functions, albeit by new mutational routes. There is both elegance and intellectual coherence to the natural processes that produce such variety and functional complexity. But marginalizing the teaching of evolution in public education is a continuing social and political problem that contributes to the reckless capacity of humans to alter the planet without trying to understand how nature works.

The opsin shift and mechanism of spectral tuning in rhodopsin

Molecular dynamics simulations and combined quantum mechanical and molecular mechanical calculations have been performed to investigate the mechanism of the opsin shift and spectral tuning in rhodopsin. A red shift of -980 cm(-1) was estimated in the transfer of the chromophore from methanol solution environment to the protonated Schiff base (PSB)-binding site of the opsin. The conformational change from a 6-s-cis-all-trans configuration in solution to the 6-s-cis-11-cis conformer contributes additional -200 cm(-1), and the remaining effects were attributed to dispersion interactions with the aromatic residues in the binding site. An opsin shift of 2100 cm(-1) was obtained, in reasonable accord with experiment (2730 cm(-1)). Dynamics simulations revealed that the 6-s-cis bond can occupy two main conformations for the β-ionone ring, resulting in a weighted average dihedral angle of about -50°, which may be compared with the experimental estimate of -28° from solid-state NMR and Raman data. We investigated a series of four single mutations, including E113D, A292S, T118A, and A269T, which are located near the PSB, along the polyene chain of retinal and close to the ionone ring. The computational results on absorption energy shift provided insights into the mechanism of spectral tuning, which involves all means of electronic structural effects, including the stabilization or destabilization of either the ground or the electronically excited state of the retinal PSB.

Identification and characterization of visual pigments in caecilians (Amphibia: Gymnophiona), an order of limbless vertebrates with rudimentary eyes

In comparison with the other amphibian orders, the Anura (frogs) and Urodela (salamanders), knowledge of the visual system of the snake-like Gymnophiona (caecilians) is relatively sparse. Most caecilians are fossorial with, as far as is known any surface activity occurring mainly at night. They have relatively small, poorly developed eyes and might be expected to possess detectable changes in the spectral sensitivity of their visual pigments. Microspectrophotometry was used to determine the spectral sensitivities of the photoreceptors in three species of caecilian, Rhinatrema bivittatum, Geotrypetes seraphini and Typhlonectes natans. Only rod opsin visual pigment, which may be associated with scotopic (dim light) vision when accompanied by other 'rod-specific' components of the phototransduction cascade, was found to be present. Opsin sequences were obtained from the eyes of two species of caecilian, Ichthyophis cf. kohtaoensis and T. natans. These rod opsins were regenerated in vitro with 11-cis retinal to give pigments with spectral sensitivity peaks close to 500 nm. No evidence for cone photoreception, associated with diurnal and colour vision, was detected using molecular and physiological methods. Additionally, visual pigments are short-wavelength shifted in terms of the maximum absorption of light when compared with other amphibian lineages.

The evolution of irradiance detection: melanopsin and the non-visual opsins

Circadian rhythms are endogenous 24 h cycles that persist in the absence of external time cues. These rhythms provide an internal representation of day length and optimize physiology and behaviour to the varying demands of the solar cycle. These clocks require daily adjustment to local time and the primary time cue (zeitgeber) used by most vertebrates is the daily change in the amount of environmental light (irradiance) at dawn and dusk, a process termed photoentrainment. Attempts to understand the photoreceptor mechanisms mediating non-image-forming responses to light, such as photoentrainment, have resulted in the discovery of a remarkable array of different photoreceptors and photopigment families, all of which appear to use a basic opsin/vitamin A-based photopigment biochemistry. In non-mammalian vertebrates, specialized photoreceptors are located within the pineal complex, deep brain and dermal melanophores. There is also strong evidence in fish and amphibians for the direct photic regulation of circadian clocks in multiple tissues. By contrast, mammals possess only ocular photoreceptors. However, in addition to the image-forming rods and cones of the retina, there exists a third photoreceptor system based on a subset of melanopsin-expressing photosensitive retinal ganglion cells (pRGCs). In this review, we discuss the range of vertebrate photoreceptors and their opsin photopigments, describe the melanopsin/pRGC system in some detail and then finally consider the molecular evolution and sensory ecology of these non-image-forming photoreceptor systems.

Individual variation in rod absorbance spectra correlated with opsin gene polymorphism in sand goby (Pomatoschistus minutus)

Rod absorbance spectra, characterized by the wavelength of peak absorbance(λmax) were related to the rod opsin sequences of individual sand gobies (Pomatoschistus minutus) from four allopatric populations[Adriatic Sea (A), English Channel (E), Swedish West Coast (S) and Baltic Sea(B)]. Rod λmax differed between populations in a manner correlated with differences in the spectral light transmission of the respective water bodies [λmax: (A)≈503 nm; (E and S)≈505–506 nm; (B)≈508 nm]. A distinguishing feature of B was the wide within-population variation of λmax (505.6–511.3 nm). The rod opsin gene was sequenced in marked individuals whose rod absorbance spectra had been accurately measured. Substitutions were identified using EMBL/GenBank X62405 English sand goby sequence as reference and interpreted using two related rod pigments, the spectrally similar one of the Adriatic P. marmoratus (λmax≈507 nm) and the relatively red-shifted Baltic P. microps(λmax≈515 nm) as outgroups. The opsin sequence of all E individuals was identical to that of the reference, whereas the S and B fish all had the substitution N151N/T or N151T. The B fish showed systematic within-population polymorphism, the sequence of individuals withλ max at 505.6–507.5 nm were identical to S, but those with λmax at 509–511.3 nm additionally had F261F/Y. The substitution F261Y is known to red-shift the rod pigment and was found in all P. microps. We propose that ambiguous selection pressures in the Baltic Sea and/or gene flow from the North Sea preserves polymorphism and is phenotypically evident as a wide variation in λmax.

Green light stimulates somatic growth in the barfin flounder Verasper moseri

We examined the effects of different light wavelengths-blue, green, and red-on the somatic growth of the barfin flounder Verasper moseri, a flatfish. The light sources used were fluorescent lamps and a combination of daylight and fluorescent lamps that produced ambient light. These light sources were filtered using blue, green, or red filters. During the experiments, the fish were reared in indoor tanks with running seawater of natural temperature and fed with commercial pellets twice daily until satiety. The tanks were white in color. Fish were exposed to constant light emitted from the fluorescent lamps (9:15, light:dark; 08:00-17:00, light) for 14 weeks from October or September to January or to ambient light with a 14-week natural photoperiod from September to December. The wavelengths that were filtered from the fluorescent lamp light modified the growth of the fish, i.e., fish reared under green or blue light exhibited a greater total length (TL; P<0.01) and body weight (BW; P<0.01) than those reared under red light. In contrast, in the case of fish exposed to filtered ambient light, fish reared under green light exhibited a greater TL (P<0.01) and BW (P<0.01) than fish exposed to other wavelengths-blue-, red-, and nonfiltered ambient light. Our results indicate that flounder growth was modified by certain wavelengths, namely, green and red light, which had growth-stimulating and growth-inhibiting effects, respectively.

The effect of elevated hydrostatic pressure on the spectral absorption of deep-sea fish visual pigments

The effect of hydrostatic pressure (0.1-54 MPa, equivalent to pressures experienced by fish from the ocean's surface to depths of ca. 5,400 m) on visual pigment absorption spectra was investigated for rod visual pigments extracted from the retinae of 12 species of deep-sea fish of diverse phylogeny and habitat. The wavelength of peak absorption (lambda(max)) was shifted to longer wavelengths by an average of 1.35 nm at 40 MPa (a pressure approximately equivalent to average ocean depth) relative to measurements made at one atmosphere (ca. 0.1 MPa), but with little evidence of a change in absorbance at the lambda(max). We conclude that previous lambda(max) measurements of deep-sea fish visual pigments, made at a pressure close to 0.1 MPa, provide a good indication of lambda(max) values at higher pressures when considering the ecology of vision in the deep-sea. Although not affecting the spectral sensitivity of the animal to any important degree, the observed shift in lambda(max) may be of interest in the context of understanding opsin-chromophore interaction and spectral tuning of visual pigments.

Visual pigment absorbance and spectral sensitivity of the Mysis relicta species group (Crustacea, Mysida) in different light environments

Visual-pigment absorbance spectra and eye spectral sensitivities were examined in eight populations of opossum shrimp from different light environments. Four Finnish populations, two from the Baltic Sea and two from freshwater lakes, represent Mysis relicta, sensu stricto. The sibling species M. salemaai and M. diluviana are represented by, respectively, two Baltic Sea populations and two populations from freshwater lakes in Idaho, USA. In M. relicta, the visual pigments of the two lake populations were similar (lambda(max)=554.3+/-0.8 nm and 556.4+/-0.4 nm), but significantly red-shifted compared with the sea populations (at 529 and 535 nm) and with M. salemaai (at 521 and 525 nm). All these pigments had only A2 chromophore and the lake/sea difference indicates adaptive evolution of the opsin. In M. diluviana, lambda(max) varied in the range 505-529 nm and the shapes of spectra suggested varying A1/A2 chromophore proportions, with pure A1 in the 505 nm animals. Eye sensitivity spectra were flatter and peaked at longer wavelengths than the relevant visual-pigment templates, but declined with the same slope beyond ca. 700 nm. The deviations from visual-pigment spectra can be explained by ocular light filters based on three types of identified screening pigments.

Parallelism of amino acid changes at the RH1 affecting spectral sensitivity among deep-water cichlids from Lakes Tanganyika and Malawi

Many examples of the appearance of similar traits in different lineages are known during the evolution of organisms. However, the underlying genetic mechanisms have been elucidated in very few cases. Here, we provide a clear example of evolutionary parallelism, involving changes in the same genetic pathway, providing functional adaptation of RH1 pigments to deep-water habitats during the adaptive radiation of East African cichlid fishes. We determined the RH1 sequences from 233 individual cichlids. The reconstruction of cichlid RH1 pigments with 11-cis-retinal from 28 sequences showed that the absorption spectra of the pigments of nine species were shifted toward blue, tuned by two particular amino acid replacements. These blue-shifted RH1 pigments might have evolved as adaptations to the deep-water photic environment. Phylogenetic evidence indicates that one of the replacements, A292S, has evolved several times independently, inducing similar functional change. The parallel evolution of the same mutation at the same amino acid position suggests that the number of genetic changes underlying the appearance of similar traits in cichlid diversification may be fewer than previously expected.

Polymorphism of the rod visual pigment between allopatric populations of the sand goby (Pomatoschistus minutus): a microspectrophotometric study

Absorbance spectra were measured by microspectrophotometry in retinal rods of sand gobies (Pomatoschistus minutus) from four allopatric populations (Baltic Sea, Swedish west coast, English Channel and Adriatic Sea). Mean (+/- S.E.M.) wavelengths of maximum absorbance (lambda(max)) were 508.3+/-0.5 nm, 505.4+/-0.2 nm, 506.2+/-0.3 nm and 503.0+/-0.3 nm, respectively. Pairwise comparison between the populations (post-ANOVA Scheffe's test) shows that each of the lambda(max) differences, except that between the Swedish west coast and the English Channel, is statistically significant (P<0.05). The shapes of the absorbance spectra indicated that the pigments were A1 rhodopsins with no measurable admixture of the A2 chromophore. Thus, the differences indicate polymorphism in the protein part (opsin) of the pigment. Convolution of A1 templates for lambda(max) values 508.3 nm and 503.0 nm with quantum spectra of the downwelling light at two locations at the south-west coast of Finland indicated that a 13-19% improvement in quantum catch would accrue in the Baltic environment from the 5.3 nm red-shift of the rod pigment of Baltic compared with Adriatic sand gobies.

Adaptive color vision in Pullosquilla litoralis (Stomatopoda, Lysiosquilloidea) associated with spectral and intensity changes in light environment

Some stomatopod crustacean species that inhabit a range of habitat depths have color vision systems that adapt to changes in ambient light conditions. To date, this change in retinal function has been demonstrated in species within the superfamily Gonodactyloidea in response to varying the spectral range of light. Intrarhabdomal filters in certain ommatidia within the specialized midband of the eye change spectrally, modifying the sensitivity of underlying photoreceptors to match the spectrum of available light. In the present study, we utilized Pullosquilla litoralis, a member of the superfamily Lysiosquilloidea that also has a wide depth range. Individuals were placed within one of three light treatments: (1) full-spectrum, high-intensity 'white' light, (2) narrow-spectrum 'blue' light and (3) full-spectrum, reduced-intensity 'gray' light. After 3 months, the intrarhabdomal filters in Row 3 ommatidia of the midband in blue- and gray-light-treated animals were short-wavelength shifted by 10-20 nm compared with homologous filters in animals in white-light treatments. These spectral changes increase the relative sensitivity of associated photoreceptors in animals that inhabit environments where light spectral range or intensity is reduced. The adaptable color vision system of stomatopods may allow animals to make the best use of the ambient light occurring at their habitat regardless of depth. The major controlling element of the plasticity in lysiosquilloid stomatopod color vision appears to be light intensity rather than spectral distribution.

The molecular basis for spectral tuning of rod visual pigments in deep-sea fish

Most species of deep-sea fish possess of a rod-only retina with a pigment that is generally shortwave shifted in λmax towards the blue region of the spectrum. In addition, the λmax values of different species tend to cluster at particular points in the spectrum. In this study, the rod opsin gene sequences from 28 deep-sea fish species drawn from seven different Orders are compared. The λmax values of the rod pigments vary from approximately 520 nm to &lt;470 nm, with the majority lying between 490 nm and 477 nm. The 520 nm pigment in two species of dragon fish is associated with a Phe261Tyr substitution, whereas the shortwave shifts of the pigments in the other 26 species are accountable by substitutions at a further eight sites (83, 122, 124, 132, 208, 292, 299 and 300). Clustering of λmax values does not, however, involve a common subset of these substitutions in the different species. A phylogenetic analysis predicts that the pigment in the ancestral species would have had a λmax of approximately 480 nm. A total of 27 changes is required to generate the pattern of substitutions seen in the different species, with many sites undergoing multiple changes.

A structural role for Asp83 in the photoactivation of rhodopsin

Asp83 is a highly conserved residue in the second transmembrane domain of visual pigments and many members of other G protein-coupled receptor subfamilies. Upon illumination, the rod visual pigment rhodopsin proceeds through various intermediate states (Batho<-->BSI<-->Lumi<-->Meta I<-->Meta II). Meta II represents the active state of rhodopsin, which binds and activates the G protein transducin. Evidence has been presented that Asp83 participates in the formation of Meta II and undergoes a change in H-bonding. To investigate whether this role of Asp83 requires its proton-donating capacity and/or its H-bonding capability, we constructed the mutants D83C and D83N. Both mutants appear to effectively activate transducin, indicating that Asp83 is not essential for signal transduction. Differential effects of the mutations D83C and D83N are observed in the spectral properties and the pH sensitivity of the Meta I-->Meta II transition. In general, D83C behaves much more like wild-type than D83N. We conclude that the structural role of Asp83 also involves the acidic nature of its carboxyl group. In addition, the participation in Meta II formation of Cys83 in D83C manifests itself as a change in the vibrational properties of the sulfhydryl group, demonstrating that the -SH group can be used as a non-invasive probe for local structural changes.

The ecology of visual pigments

The visual systems of vertebrates have adapted to function in photic environments ranging from the broad spectrum of full sunlight to almost total darkness, including the restricted spectral ranges found in different coloured aquatic environments. Such adaptations are immediately obvious at the level of retinal photoreceptors. The basic vertebrate photoreceptor pattern consists of rods and four spectrally distinct classes of cone that span the spectrum from the near ultraviolet to the far red. This arrangement is found in many diurnal species including shallow-living teleosts, reptiles and birds, but is noticeably absent in mammals. In freshwater teleosts the visual pigments may be porphyropsins which have maximum sensitivities displaced to longer wavelengths than their equivalent rhodopsins. Water acts as a monochromator, so that with increasing depth the spectral range of the ambient light is restricted, primarily at long wavelengths. Therefore, at depth the down-welling daylight is not only attenuated in intensity, but is restricted to a narrow spectral band centred around 470 nm. Closely related species that live at increasing depths show a loss of long-wave-sensitive cones and a displacement of the maximum sensitivities of middle-wave-sensitive cones and rods to shorter wavelengths. Such species offer a natural model for determining specific amino acids in opsin responsible for the spectral tuning of these middle-wave-sensitive pigments.

Colour tuning mechanisms of visual pigments

Spectral tuning by visual pigments involves modulation of physical properties of the 11-cis-retinylidene protonated Schiff base (PSB) chromophore by amino acid side chains in and around the chromophore-binding pocket. Specific molecular contacts between the chromophore and the amino acid side chains of the opsin chromophore-binding pocket have been determined recently using an interdisciplinary approach consisting of site-directed mutagenesis, optical and vibrational spectroscopy, and molecular graphics modelling. These studies provide insight into the mechanism of spectral tuning among visual pigments. In blue pigments a majority of the opsin shift is caused by polar amino acid side chains arrayed about the PSB to increase the energy gap between the ground (S0) and excited states (S1). In addition, a specific tyrosine near the chromophore ring causes a decrease in solvent polarizability. Other amino acid residues alter the binding pocket structure to strengthen electrostatic interaction between the PSB and its counterion and/or solvent dipoles. In the green and red pigments, the work of Kochendoerfer et al (1997; Biochemistry 26:6577-6587) demonstrates that local structural perturbations at the PSB or elsewhere are not responsible for spectral tuning. Instead, the green-to-red opsin shift is best explained by dipolar side chains near the chromophore ring that lower the transition energy that occurs upon electronic excitation by affecting the change in electric dipole moment. In summary, the absorption maximum of a visual pigment is primarily regulated by the interaction of the chromophore charge distribution with dipolar residues in its opsin chromophore-binding pocket. The work presented in this paper is reported in greater detail in Lin et al.

Spectral tuning of a circadian photopigment in a subterranean 'blind' mammal (Spalax ehrenbergi)

The atrophied subcutaneous eyes of Spalax ehrenbergi (the blind mole rat) express a long wavelength sensitive (LWS) cone opsin. Our data provide strong evidence that this photopigment is spectrally tuned to enhance photon capture in the red light environment of the eye. Furthermore, novel mechanisms appear partially responsible for this sensory fine-tuning. These data support the hypothesis that the LWS opsin of Spalax acts as a functional photopigment and that it is not a 'residue' of the pre-subterranean visual system. As the eye of Spalax has only one known function, the entrainment of circadian rhythms to environmental light, the LWS photopigment is implicated in this task. These results, together with our recent findings that rod and cone photopigments are not required for murine photoentrainment, suggest that multiple photopigments (classical and novel) mediate the effects of light on the mammalian circadian system.

Visual pigments and oil droplets in the retina of a passerine bird, the canary Serinus canaria: microspectrophotometry and opsin sequences

The visual receptors of the passeriform bird Serinus canaria, the canary, have been examined microspectrophotometrically and the sequences of the opsins determined. Rods have a maximum absorbance (lambda max) at 506 nm. Four spectral classes of single cone are present: long-wave-sensitive (LWS) containing a photopigment with lambda max at 569 nm, middle-wave-sensitive (MWS) with lambda max at 505 nm, short-wave-sensitive (SWS) with lambda max at 442 nm, and ultraviolet-sensitive (UVS) with lambda max at about 366 nm. Double cones possess the 569-nm pigment in both members. Typical combinations of photopigment and oil droplet occur in most cone classes. An ambiguity exists in the oil droplet of the single LWS cones. In some birds, LWS cones are paired with an R-type droplet, whereas in the majority of canaries the LWS pigment is paired with a droplet similar to the P-type of double cones. Mechanisms of spectral tuning within each opsin class are discussed.

Spectral tuning in salamander visual pigments studied with dihydroretinal chromophores

In visual pigments, opsin proteins regulate the spectral absorption of a retinal chromophore by mechanisms that change the energy level of the excited electronic state relative to the ground state. We have studied these mechanisms by using photocurrent recording to measure the spectral sensitivities of individual red rods and red (long-wavelength-sensitive) and blue (short-wavelength-sensitive) cones of salamander before and after replacing the native 3-dehydro 11-cis retinal chromophore with retinal analogs: 11-cis retinal, 3-dehydro 9-cis retinal, 9-cis retinal, and 5,6-dihydro 9-cis retinal. The protonated Schiff's bases of analogs with unsaturated bonds in the ring had broader spectra than the same chromophores bound to opsins. Saturation of the bonds in the ring reduced the spectral bandwidths of the protonated Schiff's bases and the opsin-bound chromophores and made them similar to each other. This indicates that torsion of the ring produces spectral broadening and that torsion is limited by opsin. Saturating the 5,6 double bond in retinal reduced the perturbation of the chromophore by opsin in red and in blue cones but not in red rods. Thus an interaction between opsin and the chromophoric ring shifts the spectral maxima of the red and blue cone pigments, but not that of the red rod pigment.

Enhanced retinal longwave sensitivity using a chlorophyll-derived photosensitiser in Malacosteus niger, a deep-sea dragon fish with far red bioluminescence

Through partial bleaching of both visual pigment extracts and cell suspensions we show that the deep-sea stomiid Malacosteus niger, which produces far red bioluminescence, has two visual pigments within its retina which form a rhodopsin/porphyropsin pigment pair with lambda max values around 520 and 540 nm, but lacks the very longwave sensitive visual pigments (lambda max > 550 nm) observed in two other red light producing stomiids. The presence of only a single opsin gene in the M. niger genome was confirmed by molecular and cladistic analysis. To compensate for its apparently reduced longwave sensitivity compared to related species, the outer segments of M. niger contain additional pigments, which we identify as a mixture of defarnesylated and demetallated derivatives of bacteriochlorophylls c and d, that are used as a photosensitiser to enhance its sensitivity to longwave radiation.

Adaptive evolution of color vision of the Comoran coelacanth (Latimeria chalumnae)

The coelacanth, a "living fossil," lives near the coast of the Comoros archipelago in the Indian Ocean. Living at a depth of about 200 m, the Comoran coelacanth receives only a narrow range of light, at about 480 nm. To detect the entire range of "color" at this depth, the coelacanth appears to use only two closely related paralogous RH1 and RH2 visual pigments with the optimum light sensitivities (lambdamax) at 478 nm and 485 nm, respectively. The lambdamax values are shifted about 20 nm toward blue compared with those of the corresponding orthologous pigments. Mutagenesis experiments show that each of these coadapted changes is fully explained by two amino acid replacements.

Molecular evolution of trichromacy in primates

Although trichromacy in Old and New World primates is based on three visual pigments with spectral peaks in the violet (SW, shortwave), green (MW, middlewave) and yellow-green (LW, longwave) regions of the spectrum, the underlying genetic mechanisms differ. The SW pigment is encoded in both cases by an autosomal gene and, in Old World primates, the MW and LW pigments by separate genes on the X chromosome. In contrast, there is a single polymorphic X-linked gene in most New World primates with three alleles coding for spectrally distinct pigments. The one reported exception to this rule is the New World howler monkey that follows the Old World system of separate LW and MW genes. A comparison of gene sequences in these different genetic systems indicates that the duplication that gave rise to the separate MW and LW genes of Old World primates is more ancient than that in the howler monkey. In addition, the amino acid sequences of the two howler monkey pigments show similarities to the pigments encoded by the polymorphic gene of other New World primates. It would appear therefore that the howler monkey gene duplication arose after the split between New and Old World primates and was generated by an unequal crossover that placed two different forms of the New World polymorphic gene on to a single chromosome. In contrast, the lack of identity at variable sites within the New and Old World systems argues for the origin of the separate genes in Old World primates by the duplication of a single form of the gene followed by divergence to give spectrally distinct LW and MW pigments. In contrast, the similarity in amino acid variation across the tri-allelic system of New World primates indicates that this polymorphism had a single origin in New World primates. A striking feature of all these pigments is the use of a common set of substitutions at three amino acid sites to achieve the spectral shift from MW at around 530 nm to LW at around 560 nm. The separate origin of the trichromacy in New and Old World primates would indicate that the selection of these three sites is the result of convergent evolution, perhaps as a consequence of visual adaptation in both cases to foraging for yellow and orange fruits against a green foliage.

The eyes of deep-sea fish. I: Lens pigmentation, tapeta and visual pigments

Deep-sea fish, defined as those living below 200 m, inhabit a most unusual photic environment, being exposed to two sources of visible radiation; very dim downwelling sunlight and bioluminescence, both of which are, in most cases, maximal at wavelengths around 450-500 nm. This paper summarises the reflective properties of the ocular tapeta often found in these animals, the pigmentation of their lenses and the absorption characteristics of their visual pigments. Deep-sea tapeta usually appear blue to the human observer, reflecting mainly shortwave radiation. However, reflection in other parts of the spectrum is not uncommon and uneven tapetal distribution across the retina is widespread. Perhaps surprisingly, given the fact that they live in a photon limited environment, the lenses of some deep-sea teleosts are bright yellow, absorbing much of the shortwave part of the spectrum. Such lenses contain a variety of biochemically distinct pigments which most likely serve to enhance the visibility of bioluminescent signals. Of the 195 different visual pigments characterised by either detergent extract or microspectrophotometry in the retinae of deep-sea fishes, ca. 87% have peak absorbances within the range 468-494 nm. Modelling shows that this is most likely an adaptation for the detection of bioluminescence. Around 13% of deep-sea fish have retinae containing more than one visual pigment. Of these, we highlight three genera of stomiid dragonfishes, which uniquely produce far red bioluminescence from suborbital photophores. Using a combination of longwave-shifted visual pigments and in one species (Malacosteus niger) a chlorophyll-related photosensitizer, these fish have evolved extreme red sensitivity enabling them to see their own bioluminescence and giving them a private spectral waveband invisible to other inhabitants of the deep-ocean.

Mechanisms of spectral tuning in blue cone visual pigments. Visible and raman spectroscopy of blue-shifted rhodopsin mutants

Spectral tuning by visual pigments involves the modulation of the physical properties of the chromophore (11-cis-retinal) by amino acid side chains that compose the chromophore-binding pocket. We identified 12 amino acid residues in the human blue cone pigment that might induce the required green-to-blue opsin shift. The simultaneous substitution of nine of these sites in rhodopsin (M86L, G90S, A117G, E122L, A124T, W265Y, A292S, A295S, and A299C) shifted the absorption maximum from 500 to 438 nm, accounting for 2,830 cm-1, or 80%, of the opsin shift between rhodopsin and the blue cone pigment. Raman spectroscopy of mutant pigments shows that the dielectric character and architecture of the chromophore-binding pocket are specifically altered. An increase in the number of dipolar side chains near the protonated Schiff base of retinal increases the ground-excited state energy gap via long range dipole-dipole Coulomb interaction. In addition, the W265Y substitution causes a decrease in solvent polarizability near the chromophore ring structure. Finally, two substitutions on transmembrane helix 3 (A117G and E122L) act in combination with the other substitutions to alter the binding-pocket structure, resulting in stronger interaction of the protonated Schiff base group with the surrounding dipolar groups and the counterion. Taken together, these results identify the amino acid side chains and the underlying physical mechanisms responsible for a majority of the opsin shift in blue visual pigments.