Molecular bases of color vision in vertebrates

Evolutionary history limits species' ability to match colour sensitivity to available habitat light

The spectrum of light that an animal sees-from ultraviolet to far red light-is governed by the number and wavelength sensitivity of a family of retinal proteins called opsins. It has been hypothesized that the spectrum of light available in an environment influences the range of colours that a species has evolved to see. However, invertebrates and vertebrates use phylogenetically distinct opsins in their retinae, and it remains unclear whether these distinct opsins influence what animals see, or how they adapt to their light environments. Systematically using published visual sensitivity data from across animal phyla, we found that terrestrial animals are more sensitive to shorter and longer wavelengths of light than aquatic animals and that invertebrates are more sensitive to shorter wavelengths of light than vertebrates. Using phylogenetically controlled analyses, we found that closed and open canopy habitat species have different spectral sensitivities when comparing across the Metazoa and excluding habitat generalists, while deepwater animals are no more sensitive to shorter wavelengths of light than shallow-water animals. Our results suggest that animals do adapt to their light environment; however, the invertebrate-vertebrate evolutionary divergence may limit the degree to which animals can perform visual tuning.

Yield improvement of Gracilaria tenuistipitata by optimizing different aspects in coast of cox's bazar, Bangladesh

This research was designed to find out the effect of different factors such as influence of lunar cycle, harvesting interval, rope type and seeding gap on the production of G. tenuistipitata in coast of Cox’s Bazar. Duration of these experiments were sixty days and all the parameters were recorded fortnightly. Monitoring of water quality parameters indicated that salinity, temperature, transparency, pH and DO were suitable for seaweed cultivation. In determining lunar cycle effect, results envisaged that fresh yield was 14.43% increased when seeding and harvesting time was selected considering the moon cycle. Regarding the selection of harvesting interval, it was found that T₃ (30 days interval) was the best to harvest the seaweed whereas T₄ (40 days interval) showed decreasing trend in production. Our study also found that semi floating single line showed better yield performance compared to semi floating double line system. In case of influence on seeding gap, it has been found that 20 cm gap between two seed showed the highest yields followed by 10 cm, 30 cm and 40 cm, respectively. Overall, it can be concluded that yield of G. tenuistipitata in coast of Cox’s Bazar could be improved considering those factors.

Molecular models of human visual pigments: insight into the atomic bases of spectral tuning

The cycle of vision is a chain of biochemical reactions that occur after exposure of the pigments to the light. The known mechanisms of the transduction of the light pulse derive mainly from studies on bovine rhodopsin. The objective of this work is to construct molecular models of human rhodopsin and opsins, for which three-dimensional structures are not available, to analyze the retinal environment and identify the similarities and differences that characterize the human visual pigments. One of the main results of this work is the identification of Glu102 as the probable second counterion of the Schiff base in M opsin (green pigments) and L opsin (red pigments). Further, the analysis of the molecular models allows uncovering the molecular bases of the different absorption maxima of M and L opsins with respect to rhodopsin and S opsin. These differences appear to be due to both an increase in the polarity of the retinal environment and specific electrostatic interactions, which determine a reorganization of the electronic distribution of retinal by selectively stabilizing one of the two resonance forms.

Color tuning in short wavelength-sensitive human and mouse visual pigments: ab initio quantum mechanics/molecular mechanics studies

We have investigated the protonation state and photoabsorption spectrum of Schiff-base (SB) nitrogen bound 11-cis-retinal in human blue and mouse UV cone visual pigments as well as in bovine rhodopsin by hybrid quantum mechanical/molecular mechanical (QM/MM) calculations. We have employed both multireference (MRCISD+Q, MR-SORCI+Q, and MR-DDCI2+Q) and single reference (TD-B3LYP and RI-CC2) QM methods. The calculated ground-state and vertical excitation energies show that UV-sensitive pigments have deprotonated SB nitrogen, while violet-sensitive pigments have protonated SB nitrogen, in agreement with some indirect experimental evidence. A significant blue shift of the absorption maxima of violet-sensitive pigments relative to rhodopsins arises from the increase in bond length alternation of the polyene chain of 11-cis-retinal induced by polarizing fields of these pigments. The main counterion is Glu113 in both violet-sensitive vertebrate pigments and bovine rhodopsin. Neither Glu113 nor the remaining pigment has a significant influence on the first excitation energy of 11-cis-retinal in the UV-sensitive pigments that have deprotonated SB nitrogen. There is no charge transfer between the SB and beta-ionone terminals of 11-cis-retinal in the ground and first excited states.

Sensory genes and mate choice: Evidence that duplications, mutations, and adaptive evolution alter variation in mating cue genes and their receptors

Fascinating new data, revealed through gene sequencing, comparative genomics, and genetic engineering, precisely establish which genes are involved in mate choice and mating activity--behaviors that are surprisingly understudied from a genetic perspective. Discussed here are some of the recently identified visual and chemosensory genes that are involved in mate choice and mating behavior. These genes' products are involved in the production, transmission, and receipt of crucial sensory mate-choice cues that affect fitness. This review exposes newfound evidence that alternative splicing, gene-expression pattern changes, and molecular genetic variation in sensory genes are crucial for both intra- and interspecific mate choice and mating success. Many sensory genes have arisen through gene duplications, and data amassed from studies conducted at scales ranging from individual genes to genomic comparisons show that strong, positive Darwinian selection acts on several mating-related genes and that these genes evolve rapidly.

The role of eyespots as anti-predator mechanisms, principally demonstrated in the Lepidoptera

Eyespots are found in a variety of animals, in particular lepidopterans. The role of eyespots as antipredator mechanisms has been discussed since the 19th Century, with two main hypotheses invoked to explain their occurrence. The first is that large, centrally located eyespots intimidate predators by resembling the eyes of the predators' own enemies; the second, though not necessarily conflicting, hypothesis is that small, peripherally located eyespots function as markers to deflect the attacks of predators to non-vital regions of the body. A third possibility is also proposed; that eyespots intimidate predators merely because they are novel or rarely encountered salient features. These hypotheses are reviewed, with special reference given to avian predators, since these are likely to be the principal visually hunting predators of the lepidopterans considered. Also highlighted is the necessity to consider the potential influence of sexual selection on lepidopteran wing patterns, and the genetics and development of eyespot formation.

Evolutionary analysis of rhodopsin and cone pigments: connecting the three-dimensional structure with spectral tuning and signal transfer

Extensive sequence data and structural sampling of expressed proteins from different species lead to the idea that entire molecules or specific domain folds belong to large superfamilies of proteins. A subset of G protein-coupled receptors, one of the largest families involved in cellular signaling, rod and cone opsins are involved in phototransduction in photoreceptor cells. Here, the evolutionary analysis of opsin sequences and structures predicts key residues involved in the transmission of the signal from the binding site of the chromophore to the cytoplasmic surface and residues that are involved in the spectral tuning of opsins to short wavelengths of light.

Olive green or chestnut brown?

Reflectance and spectral power functions are poor predictors of color experiences. Only in completely relativized conditions (single observer, non-metameric set of stimuli, and single set of viewing conditions) is the relationship close. Variation in reflectance of Munsell chips experienced by color-normal observers as having a unique green hue encompasses approximately sixty percent of the complete range of hues falling under the category “green”; and in recent determinations of unique hues, ranges of yellow and green as well as green and blue unique hues overlap.

Why not color physicalism without color absolutism?

We make three points. First, the concept of productance value that the authors propose in their defense of color physicalism fails to do the work for which it is intended. Second, the authors fail to offer an adequate physicalist account of what they call the hue-magnitudes. Third, their answer to the problem of individual differences faces serious difficulties.

Color realism and color illusions

As demonstrated by several example displays, color illusions challenge color realism, because they involve a one-to-many reflectance-to-color mapping. Solving this problem by differentiating between veridical and illusory colors corresponding to the same reflectance is hampered because of the lack of an appropriate criterion. However, the difference between veridical and illusory color perception can still be maintained.

Have Byrne & Hilbert answered Hardin's challenge?

I argue that Byrne & Hilbert (B&H) have not answered Hardin's objection to physicalism about color concerning the unitary-binary structure of the colors for two reasons. First, their account of unitary-binary structure seems unsatisfactory. Second, pace B&H, there are no physicalistically acceptable candidates to be the hue-magnitudes. I conclude with a question about the justification of physicalism about color.

Perceptual variation, realism, and relativization, or: How I learned to stop worrying and love variations in color vision

In many cases of variation in color vision, there is no nonarbitrary way of choosing between variants. Byrne & Hilbert insist that there is an unknown standard for choosing, whereas eliminativists claim that all the variants are erroneous. A better response relativizes colors to perceivers, thereby providing a color realism that avoids the need to choose between variants.

Can a physicalist notion of color provide any insight into the nature of color perception?

Byrne & Hilbert (B&H) conceive of color perception as the representation of a physical property “out there.” In our view, their approach does not only have various internal problems, but is also apt to becloud both the intricate and still poorly understood role that “color” plays within perceptual architecture, and the complex coupling to the “external world” of the perceptual system as an entirety. We propose an alternative perspective, which avoids B&H's misleading dichotomy between a purely subjective and a realist conception of “color.”

An account of color without a subject?

While color realism is endorsed, Byrne & Hilbert's (B&H's) case for it stretches the notion of “physical property” beyond acceptable bounds. It is argued that a satisfactory account of color should do much more to respond to antirealist intuitions that flow from the specificity of color experience, and a pointer to an approach that does so is provided.

Color realism redux

Our reply is in three parts. The first part concerns some foundational issues in the debate about color realism. The second part addresses the many objections to the version of physicalism about color (“productance physicalism”) defended in the target article. The third part discusses the leading alternative approaches and theories endorsed by the commentators.

Orange laser beams are not illusory: The need for a plurality of “real” color ontologies

Reflectance physicalism only provides a partial picture of the ontology of color. Byrne & Hilbert’ account is unsatisfactory because the replacement of reflectance functions by productance functions is ad hoc, unclear, and only leads to new problems. Furthermore, the effects of color contrast and differences in illumination are not really taken seriously: Too many “real” colors are tacitly dismissed as illusory, and this for arbitrary reasons. We claim that there cannot be an all-embracing ontology for color.

Color nominalism, pluralistic realism, and color science

Byrne & Hilbert are right that it might be an objective fact that a particular tomato is unique red, but wrong that it cannot simultaneously be yellowish-red (not only objectively, but from somebody else's point of view). Sensory categorization varies among organisms, slightly among conspecifics, and sharply across taxa. There is no question of truth or falsity concerning choice of categories, only of utility and disutility. The appropriate framework for color categories is Nominalism and Pluralistic Realism.

Perceptual variation and access to colors

To identify the set of reflectances that constitute redness, the authors must first determine which surfaces are red. They do this by relying on widespread agreement among us. However, arguments based on the possible ways in which humans would perceive colors show that mere widespread agreement among us is not a satisfactory way to determine which surfaces are red.

Parallels between hearing and seeing support physicalism

There are 2,000 hair cells in the cochlea, but only three cones in the retina. This disparity can be understood in terms of the differences between the physical characteristics of the auditory signal (discrete excitations and resonances requiring many narrowly tuned receptors) and those of the visual signal (smooth daylight excitations and reflectances requiring only a few broadly tuned receptors). We argue that this match supports the physicalism of color and timbre.

Surreptitious substitution

In this commentary I argue that Byrne & Hilbert commit a number of philosophical solecisms: They beg the question of “realism,” they take the phenomenon and the theoretical model to be the same thing, and they surreptitiously substitute data sets for the life-world.

Clarifying the problem of color realism

“The problem of color realism” as defined in the first section of the target article, is crucial to the argument laid out by Byrne & Hilbert. They claim that the problem of color realism “does not concern, at least in the first instance, color language or color concepts” (sect. 1.1). I argue that this claim is misconceived and that a different characterisation of the problem, and some of their preliminary assumptions makes their positive proposal less appealing.

Ecological considerations support color physicalism

We argue that any theory of color physicalism must include consideration of ecological interactions. Ecological and sensorimotor contingencies resulting from relative surface motion and observer motion give rise to measurable effects on the spectrum of light reflecting from surfaces. These contingencies define invariant manifolds in a sensory-spatial space, which is the physical underpinning of all subjective color experiences.

Confusion of sensations and their physical correlates

The authors favor a “color realism” theory that considers colors to be physical properties residing in objects that reflect, emit, or transmit light. It is opposed to the theory that colors are sensations or visual experiences. This commentary suggests that both theories are correct, and that context usually indicates which of these dual aspects is being considered.

True color only exists in the eye of the observer

The colors we perceive are the outcome of an attempt to meaningfully order the spectral information from the environment. These colors are not the result of a straightforward mapping of a physical property to a sensation, but arise from an interaction between our environment and our visual system. Thus, although one may infer from a surface’ reflectance characteristics that it will be perceived as “colored,” true colors only arise by virtue of the interaction of the reflected light with the eye (and brain) of an observer.

Color and content

Those who identify colours with physical properties need to say how the content of colour experiences relate to their favoured identifications. This is because it is not plausible to hold that colour experiences represent things as having the physical properties in question. I sketch how physical realists about colour might tackle this item of unfinished business.

“Color realism” shows a subjectivist' mode of thinking

Byrne & Hilbert (B&H) assert that reflectances embody the reality of color, but metamerism smears the authors' “real” color categories into uselessness. B&H ignore this problem, possibly because they implicitly adopt a sort of subjectivism, whereby an object is defined by the percepts (or more generally by the measurements) it engenders. Subjectivism is unwieldy, and hence prone to such troubles.

Spatial position and perceived color of objects

Visual percepts are called veridical when a “real” object can be identified as their cause, and illusions otherwise. The perceived position and color of a flashed object may be called veridical or illusory depending on which viewpoint one adopts. Since “reality” is assumed to be fixed (independent of viewpoint) in the definition of veridicality (or illusion), this suggests that “perceived” position and color are not properties of “real” objects.

Reflectance-to-color mappings depend critically on spatial context

In visual science, color is usually regarded as a subjective phenomenon. The relationship between the specific color experiences that are evoked by a visual scene and the physical properties of the surfaces viewed in that scene are complex and highly dependent on spatial context. There is no simple correspondence between experienced color and a stable class of physical reflectances.

Byrne and Hilbert's chromatic ether

Because our only access to color qualities is through their appearance, Byrne & Hilbert's insistence on a strict distinction between apparent colors and real colors leaves them without a principled way of determining when, if ever, we see colors as they really are.

Beautiful red squares

The reflectance types that Byrne & Hilbert identify with colors count as types only in a way that is more dependent on, and more relative to color perceivers, than their account suggests. Their account of perceptual content may be overly focused on input conditions and distal causes.

Perceptual objects may have nonphysical properties

Byrne & Hilbert defend color realism, which assumes that: (a) colors are properties of objects; (b) these objects are physical; hence, (c) colors are physical properties. I accept (a), agree that in a certain sense (b) can be defended, but reject (c). Colors are properties of perceptual objects – which also have underlying physical properties – but they are not physical properties.

Color as a material, not an optical, property

For all animals, color is an indicator of the substance and state of objects, for which purpose reflectance is just one among many relevant optical properties. This broader meaning of color is confirmed by linguistic evidence. Rather than reducing color to a simple physical property, it is more realistic to embrace its full phenomenology.

Productance physicalism and a posteriori necessity

The problem of nonreflectors perceived as colored is the central problem for Byrne & Hilbert's (B&H's) physicalism. Vision scientists and other interested parties need to consider the motivation for their account of “productance physicalism.” Is B&H's theory motivated by scientific concerns or by philosophical interests intended to preserve a physicalist account of color as a posteriori necessary?

In favor of an ecological account of color

Byrne & Hilbert understate the difficulties facing their version of color realism. We doubt that they can fix reflectance types and magnitudes in a way that does not invoke relations to perceivers. B&H's account, therefore, resembles the dispositional or ecological accounts that they dismiss. This is a good thing, for a dispositional account is promising if understood in an ecological framework.

Color as a factor analytic approximation to Nature

Color vision provides accurate measures of the phase and intensity of daylight, and also a means of discriminating between objects. Neither property implies that objects are colored.

Hue magnitudes and Revelation

Revelation, the thesis that the full intrinsic nature of colors is revealed to us by color experiences, is false in Byrne & Hilbert's (B&H's) view, but in an interesting and nonobvious way. I show what would make Revelation true, given B&H's account of colors, and then show why that situation fails to obtain, and why that is interesting.

Surface color perception in constrained environments

Byrne & Hilbert propose that color can be identified with explicit properties of physical surfaces. I argue that this claim must be qualified to take into account constraints needed to make recovery of surface color information possible. When these constraints are satisfied, then a biological visual system can establish a correspondence between perceived surface color and specific surface properties.

Color: A vision scientist's perspective

Vision scientists are interested in three diverse entities: physical stimuli, neural states, and consciously perceived colors, and in the mapping rules among the three. In this worldview, the three kinds of entities have coequal status, and views that attribute color exclusively to one or another of them, such as color realism, have no appeal.

Do metamers matter?

Metamerism is a rather common feature of objects. The authors see it as problematic because they are concerned with a special case: metamerism in standard conditions. Such metamerism does not, however, pose a problem for color realists. There is an apparent problem in cases of metameric light sources, but to see such metamers as problematic is to fail to answer Berkeley's challenge.

Imprecise color constancy versus color realism

Byrne & Hilbert's thesis, that color be associated with reflectance-type, is questioned on the grounds that it is far from clear that the human visual system is able to determine a surface's reflectance-type with sufficient accuracy. In addition, a (friendly) suggestion is made as to how to amend the definition of reflectance-type in terms of CIE (Commission Internationale de l'Eclairage) coordinates under a canonical illuminant.

Molecular evolution of the cone visual pigments in the pure rod-retina of the nocturnal gecko, Gekko gekko

We have isolated a full-length cDNA encoding a putative ultraviolet (UV)-sensitive visual pigment of the Tokay gecko (Gekko gekko). This clone has 57 and 59% sequence similarities to the gecko RH2 and MWS pigment genes, respectively, but it shows 87% similarity to the UV pigment gene of the American chameleon (Anolis carolinensis). The evolutionary rates of amino acid replacement are significantly higher in the three gecko pigments than in the corresponding chameleon pigments. The accelerated evolutionary rates reflect not only the transition from cones to rods in the retina but also the blue-shift in the absorption spectra of the gecko pigments.

The molecular genetics and evolution of red and green color vision in vertebrates

To better understand the evolution of red-green color vision in vertebrates, we inferred the amino acid sequences of the ancestral pigments of 11 selected visual pigments: the LWS pigments of cave fish (Astyanax fasciatus), frog (Xenopus laevis), chicken (Gallus gallus), chameleon (Anolis carolinensis), goat (Capra hircus), and human (Homo sapiens);and the MWS pigments of cave fish, gecko (Gekko gekko), mouse (Mus musculus), squirrel (Sciurus carolinensis), and human. We constructed these ancestral pigments by introducing the necessary mutations into contemporary pigments and evaluated their absorption spectra using an in vitro assay. The results show that the common ancestor of vertebrates and most other ancestors had LWS pigments. Multiple regression analyses of ancestral and contemporary MWS and LWS pigments show that single mutations S180A, H197Y, Y277F, T285A, A308S, and double mutations S180A/H197Y shift the lambda(max) of the pigments by -7, -28, -8, -15, -27, and 11 nm, respectively. It is most likely that this "five-sites" rule is the molecular basis of spectral tuning in the MWS and LWS pigments during vertebrate evolution.

Adaptive evolution of the African and Indonesian coelacanths to deep-sea environments

We have PCR amplified and sequenced the rhodopsin (RH1) and evolutionarily closely related RH2 genes of the Indonesian coelacanth, now referred to as Latimeria menadoensis. When the RH1 and RH2 coding sequences are constructed, expressed in cultured cells, and reconstituted with 11-cis-retinal, the resulting visual pigments have wavelengths of maximal absorption (lambda(max)) of 485 and 479 nm, respectively. These lambda(max) values are identical to those of the African coelacanth, Latimeria chalumnae, showing that the Indonesian coelacanths also detect a narrow range of color. Statistical analyses show that the adaptation of the coelacanths toward the deep-sea started as early as 200 million years ago.

Molecular evolution of color vision of zebra finch

We have isolated and sequenced the RH1(Tg), RH2(Tg), SWS2(Tg), and LWS(Tg) opsin cDNAs from zebra finch retinas. Upon binding to 11-cis-retinal, these opsins regenerate the corresponding photosensitive molecules, visual pigments. The absorption spectra of visual pigments have a broad bell shape, with the peak being called lambda(max). Previously, SWS1(Tg) opsin cDNA was isolated from zebra finch retinal RNA, expressed in cultured COS1 cells, reconstituted with 11-cis-retinal, and the lambda(max) of the resulting visual pigment was shown to be 359nm. Here, the lambda(max) values of the RH1(Tg), RH2(Tg), SWS2(Tg), and LWS(Tg) pigments are determined to be 501, 505, 440, and 560nm, respectively. Molecular evolutionary analyses suggest that specific amino acid replacements in the SWS1 and SWS2 pigments, resulting from accelerated evolution, must have been responsible for their functional divergences among the avian pigments.

Molecular evolution of vertebrate visual pigments

Dramatic improvement of our understanding of the genetic basis of vision was brought by the molecular characterization of the bovine rhodopsin gene and the human rhodopsin and color opsin genes (Nathans and Hogness, 1983; Nathans et al., 1984, 1986a,b). The availability of cDNA clones from these studies has facilitated the isolation of retinal and nonretinal opsin genes and cDNA clones from a large variety of species. Today, the number of genomic and cDNA clones of opsin genes isolated from different vertebrate species exceeds 100 and is increasing rapidly. The opsin gene sequences reveal the importance of the origin and differentiation of various opsins and visual pigments. To understand the molecular genetic basis of spectral tuning of visual pigments, it is essential to establish correlations between a series of the sequences of visual pigments and their lambda(max) values. The potentially important amino acid changes identified in this way have to be tested whether they are in fact responsible for the lambda(max)-shifts using site-directed mutagenesis and cultured cells. A major goal of molecular evolutionary genetics is to understand the molecular mechanisms involved in functional adaptations of organisms to different environments, including the mechanisms of the regulation of the spectral absorption. Therefore, both molecular evolutionary analyses of visual pigments and vision science have an important common goal.