The Evolution of Vertebrate Color Vision

Imaging Approaches to Investigate Pathophysiological Mechanisms of Brain Disease in Zebrafish

Zebrafish has become an essential model organism in modern biomedical research. Owing to its distinctive features and high grade of genomic homology with humans, it is increasingly employed to model diverse neurological disorders, both through genetic and pharmacological intervention. The use of this vertebrate model has recently enhanced research efforts, both in the optical technology and in the bioengineering fields, aiming at developing novel tools for high spatiotemporal resolution imaging. Indeed, the ever-increasing use of imaging methods, often combined with fluorescent reporters or tags, enable a unique chance for translational neuroscience research at different levels, ranging from behavior (whole-organism) to functional aspects (whole-brain) and down to structural features (cellular and subcellular). In this work, we present a review of the imaging approaches employed to investigate pathophysiological mechanisms underlying functional, structural, and behavioral alterations of human neurological diseases modeled in zebrafish.

Genome-wide identification and expression patterns of opsin genes during larval development in Chinese perch (Siniperca chuatsi)

Vision is important for fish to forage food and fishes express opsin genes to receive visual signals. Chinese perch (Siniperca chuatsi) larvae prey on other fish species larvae at firstfeeding but donoteat any zooplankton, the expression of opsin genes in S. chuatsilarvae is unknown. In this study, we conducted a whole-genome analysis and demonstrated that S. chuatsihave5cone opsin genes (sws1, sws2Aα, sws2Aβ, rh2and lws)and 2 rod opsin genes (rh1and rh1-exorh). The syntenicanalysisshowedthe flanking genes ofall opsin genes were conserved during fish evolution, but the ancestorof S. chuatsimightlost some opsin gene copies duringtheevolution.The phylogeneticanalysisshowed sws1of S. chuatsiwas closest to those of Lates calcariferwhich had a truncated sws1gene; the sws2Aα, sws2Aβ,lws,rh2,rh1 andrh1-exorh of S. chuatsihad a closer relationship with those of Percomorpha fishes.Importantly, results of in situhybridization showed the sws1 opsingene,which is related to forage zooplankton,had extremely low levelexpression in retinaat early stages.Surprisingly, the rh2 opsin gene had a high level expression at firstfeeding stage. The sws2Aα, sws2Aβand lwshad a little expression at early stages but the lwsshowed a increasing trend with larval development, rh1 opsin gene expression appeared at15 dph. In thisstudy, we found a specialpattern of visual opsin genes expression in S. chuatsi, it might influence the larval first feeding and feeding habit.

Making a bat: The developmental basis of bat evolution

Bats are incredibly diverse, both morphologically and taxonomically. Bats are the only mammalian group to have achieved powered flight, an adaptation that is hypothesized to have allowed them to colonize various and diverse ecological niches. However, the lack of fossils capturing the transition from terrestrial mammal to volant chiropteran has obscured much of our understanding of bat evolution. Over the last 20 years, the emergence of evo-devo in non-model species has started to fill this gap by uncovering some developmental mechanisms at the origin of bat diversification. In this review, we highlight key aspects of studies that have used bats as a model for morphological adaptations, diversification during adaptive radiations, and morphological novelty. To do so, we review current and ongoing studies on bat evolution. We first investigate morphological specialization by reviewing current knowledge about wing and face evolution. Then, we explore the mechanisms behind adaptive diversification in various ecological contexts using vision and dentition. Finally, we highlight the emerging work into morphological novelties using bat wing membranes.

Plasticity in perception: insights from color vision deficiencies

Inherited color vision deficiencies typically result from a loss or alteration of the visual photopigments absorbing light and thus impact the very first step of seeing. There is growing interest in how subsequent steps in the visual pathway might be calibrated to compensate for the altered receptor signals, with the possibility that color coding and color percepts might be less severely impacted than the receptor differences predict. These compensatory adjustments provide important insights into general questions about sensory plasticity and the sensory and cognitive processes underlying how we experience color.

Developmental duration as an organizer of the evolving mammalian brain: scaling, adaptations, and exceptions

Neurodevelopmental duration plays a central role in the evolution of the retina and neocortex in mammals. In the diurnal primate eye and retina, it is necessary to scale the number of cones versus the number of rods with different exponents to defend their respective functions of spatial acuity and sensitivity in eyes of different sizes. The order of photoreceptor precursor specification, cones specified first, rods second, couples their respective cell numbers at maturity to the kinetics of embryonic stem cell proliferation. Different durations of retinogenesis change the ratio of rods to cones produced so as to defend both functions over a range of eye diameters. In the evolution of nocturnality, the same coupling of photoreceptor specification to neurogenesis is altered to fewer cones and many more rods in nocturnal eyes, by delaying the onset of retinogenesis. Similarly, the neocortex also shows coupling of the specification of laminar position with duration of neurogenesis. Overall, duration of neurogenesis directly predicts neocortex volume in most mammalian clades. In larger brains with longer neocortical neurogenesis, its organization changes progressively, differentiating the frontal pole from the occipital pole in volume of connectivity and number of neurons per unit column. This permits greater, hierarchically organized information abstraction with increasing neocortex volume. Exceptions do exist, however, in species of three separate taxa, marsupials, naked mole rats, and bats, which break the correlation of neurodevelopmental duration and brain size. Naked mole rats and bats both have small brains and unusual longevity, coupled with neurodevelopmental periods characteristic of much bigger-brained animals, raising the possibility that developmental duration and lifespan have some genetic or mechanistic control in common. The role of duration of development in mediating between the mechanistic levels of construction of retinal and cortical organization, and the different life histories associated with larger brains, such as duration of parental care, learning and overall longevity are discussed.

Diverse Cell Types, Circuits, and Mechanisms for Color Vision in the Vertebrate Retina

Synaptic interactions to extract information about wavelength, and thus color, begin in the vertebrate retina with three classes of light-sensitive cells: rod photoreceptors at low light levels, multiple types of cone photoreceptors that vary in spectral sensitivity, and intrinsically photosensitive ganglion cells that contain the photopigment melanopsin. When isolated from its neighbors, a photoreceptor confounds photon flux with wavelength and so by itself provides no information about color. The retina has evolved elaborate color opponent circuitry for extracting wavelength information by comparing the activities of different photoreceptor types broadly tuned to different parts of the visible spectrum. We review studies concerning the circuit mechanisms mediating opponent interactions in a range of species, from tetrachromatic fish with diverse color opponent cell types to common dichromatic mammals where cone opponency is restricted to a subset of specialized circuits. Distinct among mammals, primates have reinvented trichromatic color vision using novel strategies to incorporate evolution of an additional photopigment gene into the foveal structure and circuitry that supports high-resolution vision. Color vision is absent at scotopic light levels when only rods are active, but rods interact with cone signals to influence color perception at mesopic light levels. Recent evidence suggests melanopsin-mediated signals, which have been identified as a substrate for setting circadian rhythms, may also influence color perception. We consider circuits that may mediate these interactions. While cone opponency is a relatively simple neural computation, it has been implemented in vertebrates by diverse neural mechanisms that are not yet fully understood.

The evolution of eyes: major steps. The Keeler lecture 2017: centenary of Keeler Ltd

Ocular evolution is an immense topic, and I do not expect to cover all the details of this process in this manuscript. I will present some concepts about some of the major steps in the evolutionary process to stimulate your thinking about this interesting and complex topic. In the prebiotic soup, vision was not inevitable. Eyes were not preordained. Nor were their shapes, sizes, or current physiology. Sight is an evolutionary gift but it was not ineluctable. The existence of eyes is so basic to our profession that we often do not consider how and why vision appeared or evolved on earth at all. Although vision is a principal sensory modality for at least three major phyla and is present in three or four more phyla, there are other sensory mechanisms that could have been and were occasionally selected instead. Some animals rely on other sensory mechanisms such as audition, echolocation, or olfaction that are much more effective in their particular niche than would be vision. We may not believe those sensory mechanisms to be as robust as vision, but the creatures using those skills would argue otherwise. Why does vision exist at all? And why is it so dominant at least in the number of species that rely upon it for their principal sensory mechanism? How did vision begin? What were the important steps in the evolution of eyes? How did eyes differentiate along their various paths, and why?

[Color vision in animals : From color blind seals to tetrachromatic vision in birds]

BACKGROUND

The colors in which we see an object are not only dependent on the spectral composition of the reflected light but also represent an interpretation by our eyes and the trichromatic visual system.

OBJECTIVE

How do animals of other species see the world?

RESULTS

The majority of mammals do not have three but only two types of cones and therefore have dichromatic color vision. Marine mammals and some nocturnally active mammals even have only one type of cone and are completely color blind. In contrast, birds as well as many fish and reptiles see in the world in more color hues and with four types of cones. Many vertebrates, insects and crustaceans can see not only the spectrum perceived by us but also ultraviolet radiation as light.

CONCLUSION

In order to understand how animals of other species see the world, their visual systems must be understood and the animals must be tested in behavioral investigations.

Protanopia (red color-blindness) in medaka: a simple system for producing color-blind fish and testing their spectral sensitivity

BACKGROUND

Color perception is important for fish to survive and reproduce in nature. Visual pigments in the retinal photoreceptor cells are responsible for receiving light stimuli, but the function of the pigments in vivo has not been directly investigated in many animals due to the lack of color-blind lines and appropriate color-perception tests.

METHODS

In this study, we established a system for producing color-blind fish and testing their spectral sensitivity. First, we disrupted long-wavelength-sensitive (LWS) opsins of medaka (Oryzias latipes) using the CRISPR/Cas9 system to make red-color-blind lines. Single guide RNAs were designed using the consensus sequences between the paralogous LWSa and LWSb genes to simultaneously introduce double-frameshift mutations. Next, we developed a non-invasive and no-prior-learning test for spectral sensitivity by applying an optomotor response (OMR) test under an Okazaki Large Spectrograph (OLS), termed the O-O test. We constructed an electrical-rotary cylinder with black/white stripes, into which a glass aquarium containing one or more fish was placed under various monochromatic light conditions. The medaka were irradiated by the OLS every 10 nm, from wavelengths of 700 nm to 900 nm, and OMR was evaluated under each condition.

RESULTS

We confirmed that the lws ^- medaka were indeed insensitive to red light (protanopia). While the control fish responded to wavelengths of up to 830 nm (λ = 830 nm), the lws ^- mutants responded up to λ = 740 nm; however, this difference was not observed after adaptation to dark: both the control and lws ^- fish could respond up to λ = 820 ~ 830 nm.

CONCLUSIONS

These results suggest that the lws ^- mutants lost photopic red-cone vision, but retained scotopic rod vision. Considering that the peak absorption spectra (λ_max) of medaka LWSs are about 560 nm, but the light-adapted control medaka could respond behaviorally to light at λ = 830 nm, red-cone vision could cover an unexpectedly wide range of wavelengths, and behavioral tests could be an effective way to measure spectral sensitivity. Using the CRISPR/Cas9 and O-O systems, the establishment of various other color-blind lines and assessment of their spectra sensitivity could be expected to proceed in the future.

Opsin clines in butterflies suggest novel roles for insect photopigments

Opsins are ancient molecules that enable animal vision by coupling to a vitamin-derived chromophore to form light-sensitive photopigments. The primary drivers of evolutionary diversification in opsins are thought to be visual tasks related to spectral sensitivity and color vision. Typically, only a few opsin amino acid sites affect photopigment spectral sensitivity. We show that opsin genes of the North American butterfly Limenitis arthemis have diversified along a latitudinal cline, consistent with natural selection due to environmental factors. We sequenced single nucleotide (SNP) polymorphisms in the coding regions of the ultraviolet (UVRh), blue (BRh), and long-wavelength (LWRh) opsin genes from ten butterfly populations along the eastern United States and found that a majority of opsin SNPs showed significant clinal variation. Outlier detection and analysis of molecular variance indicated that many SNPs are under balancing selection and show significant population structure. This contrasts with what we found by analysing SNPs in the wingless and EF-1 alpha loci, and from neutral amplified fragment length polymorphisms, which show no evidence of significant locus-specific or genome-wide structure among populations. Using a combination of functional genetic and physiological approaches, including expression in cell culture, transgenic Drosophila, UV-visible spectroscopy, and optophysiology, we show that key BRh opsin SNPs that vary clinally have almost no effect on spectral sensitivity. Our results suggest that opsin diversification in this butterfly is more consistent with natural selection unrelated to spectral tuning. Some of the clinally varying SNPs may instead play a role in regulating opsin gene expression levels or the thermostability of the opsin protein. Lastly, we discuss the possibility that insect opsins might have important, yet-to-be elucidated, adaptive functions in mediating animal responses to abiotic factors, such as temperature or photoperiod.

Reduced density of geniculocortical terminals in foveal layer 4A in the macaque primary visual cortex: relationship to S-cone density

The S-cone system is closely linked to the perception of blue/yellow. The trichromatic system of Old-World monkeys and humans has relatively few S-cones in the fovea. In this study, we investigated the distribution of putative S-cone afferents in macaques primary visual cortex (V1) which form a characteristic honeycomb arrangement in layer 4A. It was hypothesized that if there were a low number of S-cone opponent projecting neurons in central vision then this would be seen as a reduction in afferents in foveal layer 4A. Recent studies have shown that the vesicular glutamate transporter 2 (VGlut2) is a marker for thalamic afferent terminals in cortex. The distribution of VGlut2-immunoreactive (-ir) terminals was studied in the foveal and perifoveal representation of V1. It was found that there was a substantial reduction in the terminal density in the foveal representation: the density was 5-6 times lower in the foveal V1 than in regions representing perifoveal eccentricities of 1°-2° and beyond. These findings may provide the cortical substrate of foveal tritanopia, the reduced blue perceptual ability for small fields in the center of gaze.

Allocating structure to function: the strong links between neuroplasticity and natural selection

A central question in brain evolution is how species-typical behaviors, and the neural function-structure mappings supporting them, can be acquired and inherited. Advocates of brain modularity, in its different incarnations across scientific subfields, argue that natural selection must target domain-dedicated, separately modifiable neural subsystems, resulting in genetically-specified functional modules. In such modular systems, specification of neuron number and functional connectivity are necessarily linked. Mounting evidence, however, from allometric, developmental, comparative, systems-physiological, neuroimaging and neurological studies suggests that brain elements are used and reused in multiple functional systems. This variable allocation can be seen in short-term neuromodulation, in neuroplasticity over the lifespan and in response to damage. We argue that the same processes are evident in brain evolution. Natural selection must preserve behavioral functions that may co-locate in variable amounts with other functions. In genetics, the uses and problems of pleiotropy, the re-use of genes in multiple networks have been much discussed, but this issue has been sidestepped in neural systems by the invocation of modules. Here we highlight the interaction between evolutionary and developmental mechanisms to produce distributed and overlapping functional architectures in the brain. These adaptive mechanisms must be robust to perturbations that might disrupt critical information processing and action selection, but must also recognize useful new sources of information arising from internal genetic or environmental variability, when those appear. These contrasting properties of "robustness" and "evolvability" have been discussed for the basic organization of body plan and fundamental cell physiology. Here we extend them to the evolution and development, "evo-devo," of brain structure.

Non-invasive measurement of frog skin reflectivity in high spatial resolution using a dual hyperspectral approach

BACKGROUND

Most spectral data for the amphibian integument are limited to the visible spectrum of light and have been collected using point measurements with low spatial resolution. In the present study a dual camera setup consisting of two push broom hyperspectral imaging systems was employed, which produces reflectance images between 400 and 2500 nm with high spectral and spatial resolution and a high dynamic range.

METHODOLOGY/PRINCIPAL FINDINGS

We briefly introduce the system and document the high efficiency of this technique analyzing exemplarily the spectral reflectivity of the integument of three arboreal anuran species (Litoria caerulea, Agalychnis callidryas and Hyla arborea), all of which appear green to the human eye. The imaging setup generates a high number of spectral bands within seconds and allows non-invasive characterization of spectral characteristics with relatively high working distance. Despite the comparatively uniform coloration, spectral reflectivity between 700 and 1100 nm differed markedly among the species. In contrast to H. arborea, L. caerulea and A. callidryas showed reflection in this range. For all three species, reflectivity above 1100 nm is primarily defined by water absorption. Furthermore, the high resolution allowed examining even small structures such as fingers and toes, which in A. callidryas showed an increased reflectivity in the near infrared part of the spectrum.

CONCLUSION/SIGNIFICANCE

Hyperspectral imaging was found to be a very useful alternative technique combining the spectral resolution of spectrometric measurements with a higher spatial resolution. In addition, we used Digital Infrared/Red-Edge Photography as new simple method to roughly determine the near infrared reflectivity of frog specimens in field, where hyperspectral imaging is typically difficult.

True blue: S-opsin is widely expressed in different animal species

Colour vision in animals is an interesting, fascinating subject. In this study, we examined a wide variety of species for expression of S-opsin (blue sensitive) and M-/L-opsin (green-red sensitive) in retinal cones using two novel monoclonal antibodies specific for peptides from human opsins. Mouse, rat and hare did not express one of the investigated epitopes, but we could clearly prove existence of cones through peanut agglutinin labelling. Retinas of guinea pig, dog, wolf, marten, cat, roe deer, pig and horse were positive for S-opsin, but not for M-/L-opsin. Nevertheless all these species are clearly at least dichromats, because we could detect further S-opsin negative cones by labelling with cone arrestin specific antibody. In contrast, pheasant and char had M-/L-opsin positive cones, but no S-opsin expressing cones. Sheep, cattle, monkey, men, pigeon, duck and chicken were positive for both opsins. Visual acuity analyzed through density of retinal ganglion cells revealed least visual discrimination by horses and highest resolution in pheasant and pigeon. Most mammals studied are dichromats with visual perception similar to red-green blind people.

Evidence of abundant purifying selection in humans for recently acquired regulatory functions

Although only 5% of the human genome is conserved across mammals, a substantially larger portion is biochemically active, raising the question of whether the additional elements evolve neutrally or confer a lineage-specific fitness advantage. To address this question, we integrate human variation information from the 1000 Genomes Project and activity data from the ENCODE Project. A broad range of transcribed and regulatory nonconserved elements show decreased human diversity, suggesting lineage-specific purifying selection. Conversely, conserved elements lacking activity show increased human diversity, suggesting that some recently became nonfunctional. Regulatory elements under human constraint in nonconserved regions were found near color vision and nerve-growth genes, consistent with purifying selection for recently evolved functions. Our results suggest continued turnover in regulatory regions, with at least an additional 4% of the human genome subject to lineage-specific constraint.