A "deep sea rhodopsin" in a mammal

The evolutionary history and spectral tuning of vertebrate visual opsins

Many animals depend on the sense of vision for survival. In eumetazoans, vision requires specialized, light-sensitive cells called photoreceptors. Light reaches the photoreceptors and triggers the excitation of light-detecting proteins called opsins. Here, we describe the story of visual opsin evolution from the ancestral bilaterian to the extant vertebrate lineages. We explain the mechanisms determining color vision of extant vertebrates, focusing on opsin gene losses, duplications, and the expression regulation of vertebrate opsins. We describe the sequence variation both within and between species that has tweaked the sensitivities of opsin proteins towards different wavelengths of light. We provide an extensive resource of wavelength sensitivities and mutations that have diverged light sensitivity in many vertebrate species and predict how these mutations were accumulated in each lineage based on parsimony. We suggest possible natural and sexual selection mechanisms underlying these spectral differences. Understanding how molecular changes allow for functional adaptation of animals to different environments is a major goal in the field, and therefore identifying mutations affecting vision and their relationship to photic selection pressures is imperative. The goal of this review is to provide a comprehensive overview of our current understanding of opsin evolution in vertebrates.

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.

New Insight Into Visual Adaptation in the Mudskipper Cornea: From Morphology to the Cornea-Related COL8A2 Gene

Much research has focused on visual system evolution in bony fishes. The capacity of visual systems to perceive and respond to external signals is integral to evolutionary success. However, integrated research on the mechanisms of adaptive evolution based on corneal structure and related genes remains limited. In this study, scanning electron microscopy (SEM) was used to assess the microstructure and adaptation of corneal epithelial cells. Then, the evolution of the cornea-related COL8A2 gene was investigated. We found various projections (microridges, microplicae, microholes, and microvilli) on the corneal epithelial cells of amphibious mudskippers. Compared with those of fully aquatic fishes, these microstructures were considered adaptations to the variable environments experienced by amphibious mudskippers, as they can resist dryness in terrestrial environments and infection in aquatic environments. Moreover, strong purifying selection was detected for COL8A2. In addition, some specific amino acid substitution sites were also identified in the COL8A2 sequence in mudskippers. Interestingly, the evolutionary rate of the COL8A2 gene was significantly and positively correlated with maximum diving depth in our dataset. Specifically, with increasing diving depth, the evolutionary rate of the COL8A2 gene seemed to gradually accelerate. The results indicated that the cornea of bony fishes has evolved through adaptation to cope with the different diving depths encountered during the evolutionary process, with the corneal evolution of the amphibious mudskipper group showing a unique pattern.

Convergent Phenotypic Evolution of Rhodopsin for Dim-Light Sensing across Deep-Diving Vertebrates

Rhodopsin comprises an opsin attached to a retinal chromophore and is the only visual pigment conferring dim-light vision in vertebrates. On activation by photons, the retinal group becomes detached from the opsin, which is then inactive until it is recharged. Of all vertebrate species, those that dive face unique visual challenges, experiencing rapid decreases in light level and hunting in near darkness. Here, we combine sequence analyses with functional assays to show that the rhodopsin pigments of four divergent lineages of deep-diving vertebrates have undergone convergent increases in their retinal release rate. We compare gene sequences and detect parallel amino acids between penguins and diving mammals and perform mutagenesis to show that a single critical residue fully explains the observed increases in retinal release rate in both the emperor penguin and beaked whale. At the same time, we find that other shared sites have no significant effect on retinal release, implying that convergence does not always signify adaptive significance. We propose that accelerated retinal release confers rapid rhodopsin recharging, enabling the visual systems of diving species to adjust quickly to changing light levels as they descend through the water column. This contrasts with nocturnal species, where adaptation to darkness has been attributed to slower retinal release rates.

Spectral tuning and deactivation kinetics of marine mammal melanopsins

In mammals, the photopigment melanopsin (Opn4) is found in a subset of retinal ganglion cells that serve light detection for circadian photoentrainment and pupil constriction (i.e., mydriasis). For a given species, the efficiency of photoentrainment and length of time that mydriasis occurs is determined by the spectral sensitivity and deactivation kinetics of melanopsin, respectively, and to date, neither of these properties have been described in marine mammals. Previous work has indicated that the absorbance maxima (λmax) of marine mammal rhodopsins (Rh1) have diversified to match the available light spectra at foraging depths. However, similar to the melanopsin λmax of terrestrial mammals (~480 nm), the melanopsins of marine mammals may be conserved, with λmax values tuned to the spectrum of solar irradiance at the water's surface. Here, we investigated the Opn4 pigments of 17 marine mammal species inhabiting diverse photic environments including the Infraorder Cetacea, as well as the Orders Sirenia and Carnivora. Both genomic and cDNA sequences were used to deduce amino acid sequences to identify substitutions most likely involved in spectral tuning and deactivation kinetics of the Opn4 pigments. Our results show that there appears to be no amino acid substitutions in marine mammal Opn4 opsins that would result in any significant change in λmax values relative to their terrestrial counterparts. We also found some marine mammal species to lack several phosphorylation sites in the carboxyl terminal domain of their Opn4 pigments that result in significantly slower deactivation kinetics, and thus longer mydriasis, compared to terrestrial controls. This finding was restricted to cetacean species previously found to lack cone photoreceptor opsins, a condition known as rod monochromacy. These results suggest that the rod monochromat whales rely on extended pupillary constriction to prevent photobleaching of the highly photosensitive all-rod retina when moving between photopic and scotopic conditions.

Three-dimensional space use during the bottom phase of southern elephant seal dives

BACKGROUND

In marine pelagic ecosystems, the spatial distribution of biomass is heterogeneous and dynamic. At large scales, physical processes are the main driving forces of biomass distribution. At fine scales, both biotic and abiotic parameters are likely to be key determinants in the horizontal and vertical distribution of biomass, with direct consequences on the foraging behaviour of diving predators. However, fine scale three-dimensional (3D) spatial interactions between diving predators and their prey are still poorly known.

RESULTS

We reconstructed and examined the patterns of southern elephant seals 3D path during the bottom phase of their dives, and related them to estimated prey encounter density. We found that southern elephant seal tracks at bottom are strongly dominated by a single horizontal direction. In high prey density areas, seals travelled shorter distances but their track remained strongly orientated according to a main linear direction. Horizontal, and more importantly, vertical deviations from this main direction, were related negatively to the estimated prey density. We found that prey encounter density decreased with diving depth but tended to be more predictable.

CONCLUSION

Southern elephant seal behaviour during the bottom phase of their dives suggest that the prey are dispersed and distributed into layers in which their density relates to the vertical spread of the layer. The linear trajectories performed by the elephant seals would allow to explore the largest volume of water, maximizing the opportunities of prey encounter, while travelling great horizontal distances.

Marine Bioluminescence: Measurement by a Classical Light Sensor and Related Foraging Behavior of a Deep Diving Predator

Bioluminescence is produced by a broad range of organisms for defense, predation or communication purposes. Southern elephant seal (SES) vision is adapted to low-intensity light with a peak sensitivity, matching the wavelength emitted by myctophid species, one of the main preys of female SES. A total of 11 satellite-tracked female SESs were equipped with a time-depth-light 3D accelerometer (TDR10-X) to assess whether bioluminescence could be used by SESs to locate their prey. Firstly, we demonstrated experimentally that the TDR10-X light sensor was sensitive enough to detect natural bioluminescence; however, we highlighted a low-distance detection of the sensor. Then, we linked the number of prey capture attempts (PCAs), assessed from accelerometer data, with the number of detected bioluminescence events. PCA was positively related to bioluminescence, which provides strong support that bioluminescence is involved in predator-prey interactions for these species. However, the limitations of the sensor did not allow us to discern whether bioluminescence (i) provided remote indication of the biological richness of the area to SES, (ii) was emitted as a mechanic reaction or (iii) was emitted as a defense mechanism in response to SES behavior.

Foraging in the darkness of the Southern Ocean: influence of bioluminescence on a deep diving predator

How non-echolocating deep diving marine predators locate their prey while foraging remains mostly unknown. Female southern elephant seals (SES) (Mirounga leonina) have vision adapted to low intensity light with a peak sensitivity at 485 nm. This matches the wavelength of bioluminescence produced by a large range of marine organisms including myctophid fish, SES’s main prey. In this study, we investigated whether bioluminescence provides an accurate estimate of prey occurrence for SES. To do so, four SES were satellite-tracked during their post-breeding foraging trip and were equipped with Time-Depth-Recorders that also recorded light levels every two seconds. A total of 3386 dives were processed through a light-treatment model that detected light events higher than ambient level, i.e. bioluminescence events. The number of bioluminescence events was related to an index of foraging intensity for SES dives deep enough to avoid the influence of natural ambient light. The occurrence of bioluminescence was found to be negatively related to depth both at night and day. Foraging intensity was also positively related to bioluminescence both during day and night. This result suggests that bioluminescence likely provides SES with valuable indications of prey occurrence and might be a key element in predator-prey interactions in deep-dark marine environments.

Deep-sea and pelagic rod visual pigments identified in the mysticete whales

Our current understanding of the spectral sensitivities of the mysticete whale rod-based visual pigments is based on two species, the gray whale (Eschrichtius robustus) and the humpback whale (Megaptera novaeangliae) possessing absorbance maxima determined from difference spectra to be 492 and 497 nm, respectively. These absorbance maxima values are blueshifted relative to those from typical terrestrial mammals (≈500 nm) but are redshifted when compared to those identified in the odontocetes (479–484 nm). Although these mysticete species represent two of the four mysticete families, they do not fully represent the mysticete whales in terms of foraging strategy and underwater photic environments where foraging occurs. In order to better understand the spectral sensitivities of the mysticete whale rod visual pigments, we have examined the rod opsin genes from 11 mysticete species and their associated amino acid substitutions. Based on the amino acids occurring at positions 83, 292, and 299 along with the directly determined dark spectra from expressed odontocete and mysticete rod visual pigments, we have determined that the majority of mysticete whales possess deep-sea and pelagic like rod visual pigments with absorbance maxima between 479 and 484 nm. Finally, we have defined the five amino acid substitution events that determine the resulting absorbance spectra and associated absorbance maxima for the mysticete whale rod visual pigments examined here.

Basic mechanisms in pinniped vision

Pinnipeds are amphibious mammals. The amphibious lifestyle is challenging for all sensory systems including vision, and specific adaptations of the eyes have evolved in response to the changed requirements concerning vision in two optically very different media, water and air. The present review summarizes the information available on pinniped eyes with an emphasis on harbour seal vision for which most information is available to date. Recent studies in this species have improved the understanding of amphibious vision by reanalysing refraction, by studying corneal topography, and by measuring visual acuity as a function of ambient luminance. The harbour seal eye can be characterized as an eye that balances high resolution, supported by data on ganglion cell density and topography, and sensitivity. Furthermore, it was shown that seals have multifocal lenses, broad visual Welds, and distinct eye movement abilities. The mechanisms described here form the basis for future research on visually guided behaviour.

Visual pigments of marine carnivores: pinnipeds, polar bear, and sea otter

Rod and cone visual pigments of 11 marine carnivores were evaluated. Rod, middle/long-wavelength sensitive (M/L) cone, and short-wavelength sensitive (S) cone opsin (if present) sequences were obtained from retinal mRNA. Spectral sensitivity was inferred through evaluation of known spectral tuning residues. The rod pigments of all but one of the pinnipeds were similar to those of the sea otter, polar bear, and most other terrestrial carnivores with spectral peak sensitivities (lambda(max)) of 499 or 501 nm. Similarly, the M/L cone pigments of the pinnipeds, polar bear, and otter had inferred lambda(max) of 545 to 560 nm. Only the rod opsin sequence of the elephant seal had sensitivity characteristic of adaptation for vision in the marine environment, with an inferred lambda(max) of 487 nm. No evidence of S cones was found for any of the pinnipeds. The polar bear and otter had S cones with inferred lambda(max) of approximately 440 nm. Flicker-photometric ERG was additionally used to examine the in situ sensitivities of three species of pinniped. Despite the use of conditions previously shown to evoke cone responses in other mammals, no cone responses could be elicited from any of these pinnipeds. Rod photoreceptor responses for all three species were as predicted by the genetic data.

Why pinnipeds don't echolocate

Odontocete cetaceans have evolved a highly advanced system of active biosonar. It has been hypothesized that other groups of marine animals, such as the pinnipeds, possess analogous sound production, reception, and processing mechanisms that allow for underwater orientation using active echolocation. Despite sporadic investigation over the past 30 years, the accumulated evidence in favor of the pinniped echolocation hypothesis is unconvincing. We argue that an advanced echolocation system is unlikely to have evolved in pinnipeds primarily because of constraints imposed by the obligate amphibious functioning of the pinniped auditory system. As a result of these constraints, pinnipeds have not developed highly acute, aquatic, high frequency sound production or reception systems required for underwater echolocation. Instead, it appears that pinnipeds have evolved enhanced visual, tactile, and passive listening skills. The evolutionary refinement of alternative sensory systems allows pinnipeds to effectively forage, navigate, and avoid predators under water despite the lack of active biosonar capabilities.

Hunting behavior of a marine mammal beneath the antarctic fast Ice

The hunting behavior of a marine mammal was studied beneath the Antarctic fast ice with an animal-borne video system and data recorder. Weddell seals stalked large Antarctic cod and the smaller subice fish Pagothenia borchgrevinki, often with the under-ice surface for backlighting, which implies that vision is important for hunting. They approached to within centimeters of cod without startling the fish. Seals flushed P. borchgrevinki by blowing air into subice crevices or pursued them into the platelet ice. These observations highlight the broad range of insights that are possible with simultaneous recordings of video, audio, three-dimensional dive paths, and locomotor effort.

Pupillometry in seals and sea lions: ecological implications

Phocid and otariid pinnipeds forage almost exclusively under water, where observing them is difficult. As a result, little is known of how their senses are used while diving to locate and capture prey. In this study we used pupillometric methods to describe the relative visual abilities of three pinniped species: the northern elephant seal (Mirounga angustirostris), the harbor seal (Phoca vitulina), and the California sea lion (Zalophus californianus). The range of pupillary area and lower limit of pupillary adjustment were determined for each species. The northern elephant seal exhibited the largest range of pupillary area of the species examined. Furthermore, the elephant seal's pupil was found to reach maximum size only under extremely dim conditions. Both the harbor seal and California sea lion exhibited maximum pupillary dilation in conditions several log units brighter. These results indicate that the elephant seal's visual system is designed to function in dimmer conditions and to respond to greater changes in light levels than those of the harbor seal and sea lion. Such findings support the hypothesis that the visual systems of these pinnipeds are adapted for use in their respective foraging environments, and thus suggest that the visual sense is probably an important sensory modality used to locate and capture prey while diving.

Adaptations of visual pigments to the photic environment of the deep sea

This is a summary of studies that bear on the problems of the adaptation of visual pigments to the photic environment of the deep sea. The results suggest that the spectral absorption of these retinal pigments is shifted toward the blue in order to match the dim, blue-green downwelling light and/or the bioluminescence of organisms that are critical to the life of the species. Through such a spectral match, greater visual sensitivity is achieved for life in the special photic condition of their habitat. This adaptation has been found for chimaerid fishes, for elasmobranchs, for teleosts, for mammals, and for certain crustaceans and cephalopods. The most convincing evidence for such an adaptive match has been found in teleosts that have red-emitting photophores. In these fishes a photopigment with absorbance shifted toward the red has been found by extraction and microspectrophotometry. A few exceptions to this idea of an adaptive match have appeared in the literature, the cone pigments, especially, being examples of such offset pigments. The malacosteid fishes have been shown to have a red-shifted retinal pigment with 11-cis-3-dehydroretinal as the chromophore and some invertebrates have also adopted this molecule to adjust the spectral absorption to the photic environment or to the bioluminescence. These studies are beginning to reveal that visual biochemistry is basically the same in vertebrates and invertebrates and that the visual pigment protein arose early in phylogeny and has been retained, with appropraite modifications, to the present.