Lens optical properties in the eyes of large marine predatory teleosts

New chromosome-scale genomes provide insights into marine adaptations of sea snakes (Hydrophis: Elapidae)

BACKGROUND

Sea snakes underwent a complete transition from land to sea within the last ~ 15 million years, yet they remain a conspicuous gap in molecular studies of marine adaptation in vertebrates.

RESULTS

Here, we generate four new annotated sea snake genomes, three of these at chromosome-scale (Hydrophis major, H. ornatus and H. curtus), and perform detailed comparative genomic analyses of sea snakes and their closest terrestrial relatives. Phylogenomic analyses highlight the possibility of near-simultaneous speciation at the root of Hydrophis, and synteny maps show intra-chromosomal variations that will be important targets for future adaptation and speciation genomic studies of this system. We then used a strict screen for positive selection in sea snakes (against a background of seven terrestrial snake genomes) to identify genes over-represented in hypoxia adaptation, sensory perception, immune response and morphological development.

CONCLUSIONS

We provide the best reference genomes currently available for the prolific and medically important elapid snake radiation. Our analyses highlight the phylogenetic complexity and conserved genome structure within Hydrophis. Positively selected marine-associated genes provide promising candidates for future, functional studies linking genetic signatures to the marine phenotypes of sea snakes and other vertebrates.

Movement behavior of swordfish provisions connectivity between the temperate and tropical southwest Pacific Ocean

Swordfish (Xiphias gladius) are a widely distributed (45°N-45°S) large pelagic fish targeted by fisheries worldwide. Swordfish that occur at high latitudes tend to disproportionately be large adults, so their movements have implications for population dynamics and fisheries management. In the southwest Pacific, little is known about this subset of the stock and existing evidence suggests limited movement from the subtropics into cooler high latitude waters. Here, we capitalize on the recent emergence of a recreational swordfish fishery off temperate southeast Australia to characterize movements of swordfish caught in the fishery with pop-up satellite archival transmitting tags. Data were recovered from tags deployed for 56-250 days on 11 swordfish (50-350 kg) tagged between 38 and 43°S in the western Tasman Sea. Five swordfish entered the Coral Sea (< 30°S), with four reaching north to 11-24°S, up to 3275 km away from location of capture. Behavior modelling suggests these four individuals rapidly transited north until encountering 23-27 °C water, at which point they lingered in the area for several months, consistent with spawning-related partial migration. One migrating swordfish still carrying a tag after the spawning season returned to ~ 120 km of its release location, suggesting site fidelity. Movements toward the central south Pacific were confined to two individuals crossing 165°E. Swordfish predominantly underwent normal diel vertical migration, descending into the mesopelagic zone at dawn (median daytime depth 494.9 m, 95% CI 460.4-529.5 m). Light attenuation predicted daytime depth, with swordfish rising by up to 195 m in turbid water. At night, swordfish were deeper during the full moon, median night-time depth 45.8 m (37.8-55.5) m versus 18.0 m (14.9-21.8) m at new moon. Modelling fine-scale (10 min^-1) swordfish depth revealed dynamic effects of moon phase varying predictably across time of night with implications for fisheries interactions. Studying highly migratory fishes near distribution limits allows characterization of the full range of movement phenotypes within a population, a key consideration for important fish stocks in changing oceans.

The Functional and Ecological Significance of Deep Diving by Large Marine Predators

Many large marine predators make excursions from surface waters to the deep ocean below 200 m. Moreover, the ability to access meso- and bathypelagic habitats has evolved independently across marine mammals, reptiles, birds, teleost fishes, and elasmobranchs. Theoretical and empirical evidence suggests a number of plausible functional hypotheses for deep-diving behavior. Developing ways to test among these hypotheses will, however, require new ways to quantify animal behavior and biophysical oceanographic processes at coherent spatiotemporal scales. Current knowledge gaps include quantifying ecological links between surface waters and mesopelagic habitats and the value of ecosystem services provided by biomass in the ocean twilight zone. Growing pressure for ocean twilight zone fisheries creates an urgent need to understand the importance of the deep pelagic ocean to large marine predators.

Broadbill swordfish (Xiphias gladius) foraging and vertical movements in the north-west Atlantic

The northern edge of Georges Bank is an important seasonal foraging habitat for swordfish (Xiphias gladius) in the North Atlantic, where aggregations support commercial pelagic longline and harpoon fisheries. Following a period of overfishing during the 1990s, the North Atlantic X. gladius stock underwent a period of recovery during the early 2000s and was considered rebuilt in 2009. We analysed stomach contents from X. gladius (n = 39) harvested by the Canadian harpoon fishery on Georges Bank in 2007 to characterize diet in this important foraging habitat. We used electronic tagging data from X. gladius (n = 6) on Georges Bank in 2005-2007 to assess vertical habitat preferences and associated prey composition within those zones. We also used stable isotope analysis (δ¹³ C and δ¹⁵ N) of X. gladius liver (n = 2) and common prey types (Paralepididae, Myctophidae, Merluccidae, Ommastrephidae) as a longer-term record of feeding. Stomach contents were co-dominated by Paralepididae [31.9% weight (W)] and Ommastrephidae (36.8%W) with secondary contributions from hake (Merluccidae, 6.5%W), Myctophidae (2.9%W) and Sebastidae (2.1%W). X. gladius displayed diel vertical migrations, descending to depths of 300-400 m during daytime followed by residence in surface waters at night. X. gladius liver δ¹⁵ N values were similar to or lower than values of primary stomach contents, likely due to bias of diet consumed in southerly waters with lower nitrogen isotope baselines prior to arrival on Georges Bank. Diet data are similar to results from historical studies from the late 1950s to the early 1980s. This apparent temporal stability to the underlying food web in this region may explain the high X. gladius site fidelity observed in electronic tagging studies and the consistent aggregation of these fish to this region.

Exposure to Crude Oil from the Deepwater Horizon Oil Spill Impairs Oil Avoidance Behavior without Affecting Olfactory Physiology in Juvenile Mahi-Mahi (Coryphaena hippurus)

The understanding of the detection threshold and behavioral response of fishes in response to crude oil is critical to predicting the effects of oil spills on wild fish populations. The Deepwater Horizon oil spill released approximately 4.9 million barrels of crude oil into the northern Gulf of Mexico in 2010, overlapping spatially and temporally with the habitat of many pelagic fish species. Yet, it is unknown whether highly migratory species, such as mahi-mahi (Coryphaena hippurus), might detect and avoid oil contaminated waters. We tested the ability of control and oil-exposed juvenile mahi-mahi (15-45 mm) to avoid two dilutions of crude oil in a two-channel flume. Control fish avoided the higher concentration (27.1 μg/L Σ₅₀PAH), while oil-exposed (24 h, 18.0 μg/L Σ₅₀PAH) conspecifics did not. Electro-olfactogram (EOG) data demonstrated that both control and oil-exposed (24 h, 14.5 μg/L Σ₅₀PAH) juvenile mahi-mahi (27-85 mm) could detect crude oil as an olfactory cue and that oil-exposure did not affect the EOG amplitude or duration in response to oil or other cues. These results show that a brief oil exposure impairs the ability of mahi-mahi to avoid oil and suggests that this alteration likely results from injury to higher order central nervous system processing rather than impaired olfactory physiology.

Losing focus: how lens position and viewing angle affect the function of multifocal lenses in fishes

Light rays of different wavelengths are focused at different distances when they pass through a lens (longitudinal chromatic aberration [LCA]). For animals with color vision this can pose a serious problem, because in order to perceive a sharp image the rays must be focused at the shallow plane of the photoreceptor's outer segments in the retina. A variety of fish and tetrapods have been found to possess multifocal lenses, which correct for LCA by assigning concentric zones to correctly focus specific wavelengths. Each zone receives light from a specific beam entrance position (BEP) (the lateral distance between incoming light and the center of the lens). Any occlusion of incoming light at specific BEPs changes the composition of the wavelengths that are correctly focused on the retina. Here, we calculated the effect of lens position relative to the plane of the iris and light entering the eye at oblique angles on how much of the lens was involved in focusing the image on the retina (measured as the availability of BEPs). We used rotational photography of fish eyes and mathematical modeling to quantify the degree of lens occlusion. We found that, at most lens positions and viewing angles, there was a decrease of BEP availability and in some cases complete absence of some BEPs. Given the implications of these effects on image quality, we postulate that three morphological features (aphakic spaces, curvature of the iris, and intraretinal variability in spectral sensitivity) may, in part, be adaptations to mitigate the loss of spectral image quality in the periphery of the eyes of fishes.

The visual ecology of a deep-sea fish, the escolar Lepidocybium flavobrunneum (Smith, 1843)

Escolar (Lepidocybium flavobrunneum, family Gempylidae) are large and darkly coloured deep-sea predatory fish found in the cold depths (more than 200 m) during the day and in warm surface waters at night. They have large eyes and an overall low density of retinal ganglion cells that endow them with a very high optical sensitivity. Escolar have banked retinae comprising six to eight layers of rods to increase the optical path length for maximal absorption of the incoming light. Their retinae possess two main areae of higher ganglion cell density, one in the ventral retina viewing the dorsal world above (with a moderate acuity of 4.6 cycles deg(-1)), and the second in the temporal retina viewing the frontal world ahead. Electrophysiological recordings of the flicker fusion frequency (FFF) in isolated retinas indicate that escolar have slow vision, with maximal FFF at the highest light levels and temperatures (around 9 Hz at 23°C) which fall to 1-2 Hz in dim light or cooler temperatures. Our results suggest that escolar are slowly moving sit-and-wait predators. In dim, warm surface waters at night, their slow vision, moderate dorsal resolution and highly sensitive eyes may allow them to surprise prey from below that are silhouetted in the downwelling light.

Computational visual ecology in the pelagic realm

Visual performance and visual interactions in pelagic animals are notoriously hard to investigate because of our restricted access to the habitat. The pelagic visual world is also dramatically different from benthic or terrestrial habitats, and our intuition is less helpful in understanding vision in unfamiliar environments. Here, we develop a computational approach to investigate visual ecology in the pelagic realm. Using information on eye size, key retinal properties, optical properties of the water and radiance, we develop expressions for calculating the visual range for detection of important types of pelagic targets. We also briefly apply the computations to a number of central questions in pelagic visual ecology, such as the relationship between eye size and visual performance, the maximum depth at which daylight is useful for vision, visual range relations between prey and predators, counter-illumination and the importance of various aspects of retinal physiology. We also argue that our present addition to computational visual ecology can be developed further, and that a computational approach offers plenty of unused potential for investigations of visual ecology in both aquatic and terrestrial habitats.

Sturgeons, sharks, and rays have multifocal crystalline lenses and similar lens suspension apparatuses

Crystalline lenses with multiple focal lengths in monochromatic light (multifocal lenses) are present in many vertebrate groups. These lenses compensate for chromatic aberration and create well-focused color images. Stabilization of the lens within the eye and the ability to adjust focus are further requirements for vision in high detail. We investigated the occurrence of multifocal lenses by photorefractometry and lens suspension structures by light and electron microscopy in sturgeons (Acipenseriformes, Chondrostei) as well as sharks and rays (Elasmobranchii, Chondrichthyes). Multifocal lenses were found in two more major vertebrate groups, the Chondrostei represented by Acipenseriformes and Chondrichthyes represented by Elasmobranchii. The lens suspension structures of sturgeons, sharks, and rays are more complex than described previously. The lens is suspended by many delicate suspensory fibers in association with a ventral papilla in all groups studied. The arrangements of the suspensory fibers are most similar between sturgeons and sharks. In rays, the lens is suspended by a smaller ventral papilla and the suspensory fibers are arranged more concentrically to the lens.

A unique advantage for giant eyes in giant squid

Giant and colossal deep-sea squid (Architeuthis and Mesonychoteuthis) have the largest eyes in the animal kingdom [1, 2], but there is no explanation for why they would need eyes that are nearly three times the diameter of those of any other extant animal. Here we develop a theory for visual detection in pelagic habitats, which predicts that such giant eyes are unlikely to evolve for detecting mates or prey at long distance but are instead uniquely suited for detecting very large predators, such as sperm whales. We also provide photographic documentation of an eyeball of about 27 cm with a 9 cm pupil in a giant squid, and we predict that, below 600 m depth, it would allow detection of sperm whales at distances exceeding 120 m. With this long range of vision, giant squid get an early warning of approaching sperm whales. Because the sonar range of sperm whales exceeds 120 m [3-5], we hypothesize that a well-prepared and powerful evasive response to hunting sperm whales may have driven the evolution of huge dimensions in both eyes and bodies of giant and colossal squid. Our theory also provides insights into the vision of Mesozoic ichthyosaurs with unusually large eyes.

Evolution of the vertebrate beaded filament protein, Bfsp2; comparing the in vitro assembly properties of a "tailed" zebrafish Bfsp2 to its "tailless" human orthologue

In bony fishes, Bfsp2 orthologues are predicted to possess a C-terminal tail domain, which is absent from avian, amphibian and mammalian Bfsp2 sequences. These sequences, are however, not conserved between fish species and therefore questions whether they have a functional role. For other intermediate filament proteins, the C-terminal tail domain is important for both filament assembly and regulating interactions between filaments. We confirm that zebrafish has a single Bfsp2 gene by radiation mapping. Two transcripts (bfsp2α and bfsp2β) are produced by alternative splicing of the last exon. Using a polyclonal antibody specific to a tridecameric peptide in the C-terminal tail domain common to both zebrafish Bfsp2 splice variants, we have confirmed its expression in zebrafish lens fibre cells. We have also determined the in vitro assembly properties of zebrafish Bfsp2α and conclude that the C-terminal sequences are required to regulate not only the diameter and uniformity of the in vitro assembly filaments, but also their filament-filament associations in vitro. Therefore we conclude zebrafish Bfsp2α is a functional orthologue conforming more closely to the conventional domain structure of intermediate filament proteins. Data mining of the genome databases suggest that the loss of this tail domain could occur in several stages leading eventually to completely tailless orthologues, such as human BFSP2.

Adaptation in the optical properties of the crystalline lens in the eyes of the Lessepsian migrant Siganus rivulatus

Vision is an important source of information for many animals. The crystalline lens plays a central role in the visual pathway and hence the ecology of fishes. In this study, we tested whether the different light regimes in the Mediterranean and Red Seas have an effect on the optical properties of the lenses in the rivulated rabbitfish, Siganus rivulatus. This species has migrated through the Suez Canal from the Red Sea and established a vital population in the Mediterranean Sea. Longitudinal spherical aberration curves and focal lengths of the fish lenses were measured by laser scans and compared between the two populations. In addition, rivulated rabbitfish from the Mediterranean Sea were exposed to colored light (yellow, green and blue) and unfiltered light for periods of 1 or 13 days to test for short-term adjustments. Lens focal length was significantly longer (3%) in the Rea Sea population. The shorter focal length of the Mediterranean population can be explained as an adaptation to the dimmer light environment, as this difference makes the Mediterranean eyes 5% more sensitive than the eyes of the Red Sea population. The difference may be due to genetic differences or, more likely, adaptive developmental plasticity. Short-term regulatory mechanisms do not seem to be involved.