The chromosome-scale reference genome for the pinfish (Lagodon rhomboides) provides insights into their evolutionary and demographic history

The pinfish (Lagodon rhomboides) is an ecologically, economically, and culturally relevant member of the family Sparidae, playing crucial roles in the marine food webs of the western Atlantic Ocean and Gulf of Mexico. Despite their high abundance and ecological importance, there is a scarcity of genomic resources for this species. We assembled and annotated a chromosome-scale genome for the pinfish, resulting in a highly contiguous 785 Mb assembly of 24 scaffolded chromosomes. The high-quality assembly contains 98.9% complete BUSCOs and shows strong synteny to other chromosome-scale genomes of fish in the family Sparidae, with a limited number of large-scale genomic rearrangements. Leveraging this new genomic resource, we found evidence of significant expansions of dietary gene families over the evolutionary history of the pinfish, which may be associated with an ontogenetic shift from carnivory to herbivory seen in this species. Estimates of historical patterns of population demography using this new reference genome identified several periods of population growth and contraction which were associated with ancient climatic shifts and sea level changes. This genome serves as a valuable reference for future studies of population genomics and differentiation and provides a much-needed genomic resource for this western Atlantic sparid.

Dynamic colour change as a signalling tool in bluelined goatfish (Upeneicthtys lineatus)

Many animal species can rapidly change their body colouration and patterning, but often the ecological drivers of such changes are unknown. Here, we explored dynamic colour change in the bluelined goatfish, Upeneichthys lineatus, a temperate marine teleost species. Upeneichthus lineatus can change in a matter of seconds, from a uniform white colour to display prominent, vertical, dark red stripes. Initial observations suggested that rapid colour change in U. lineatus was associated with feeding and may act as a signal to both conspecifics and heterospecifics that are frequently observed to follow feeding goatfish. Field observations of the colour and behaviour of individual U. lineatus were collected to (1) document the repertoire of behaviours that U. lineatus displays and categorise associated colour patterns; (2) quantify the speed of dynamic colour change; (3) establish the context in which U. lineatus changes colour and pattern; and (4) test whether the behaviour of follower fishes is influenced by colour patterning or specific behaviours of the focal goatfish. We found that U. lineatus changed colouration from white to the red banded pattern in less than 10 s. The key driver of rapid colour change in U. lineatus was feeding, particularly when the fish fed with its head buried in sediment. Conspecific followers were most likely to be white in colour and adopt searching behaviour, regardless of the focal fish colour or behaviour. Other species of follower fish spent significantly more time following U. lineatus that were displaying dark red stripes when searching or eating, implying the red stripes may be an interspecific signalling mechanism. Our findings indicate that rapid colour change in teleost fish may be used for social communication and may provide U. lineatus with increased protection from predation when feeding via a safety-in-numbers approach.

Developing and adult reef fish show rapid light-induced plasticity in their visual system

The visual capabilities of fish are optimized for their ecology and light environment over evolutionary time. Similarly, fish vision can adapt to regular changes in light conditions within their lifetime, e.g., ontogenetic or seasonal variation. However, we do not fully understand how vision responds to irregular short-term changes in the light environment, e.g., algal blooms and light pollution. In this study, we investigated the effect of short-term exposure to unnatural light conditions on opsin gene expression and retinal cell densities in juvenile and adult diurnal reef fish (convict surgeonfish; Acanthurus triostegus). Results revealed phenotypic plasticity in the retina across ontogeny, particularly during development. The most substantial differences at both molecular and cellular levels were found under constant dim light, while constant bright light and simulated artificial light at night had a lesser effect. Under dim light, juveniles and adults increased absolute expression of the cone opsin genes, sws2a, rh2c and lws, within a few days and juveniles also decreased densities of cones, inner nuclear layer cells and ganglion cells. These changes potentially enhanced vision under the altered light conditions. Thus, our study suggests that plasticity mainly comes into play when conditions are extremely different to the species' natural light environment, i.e., a diurnal fish in "constant night". Finally, in a rescue experiment on adults, shifts in opsin expression were reverted within 24 h. Overall, our study showed rapid, reversible light-induced changes in the retina of A. triostegus, demonstrating phenotypic plasticity in the visual system of a reef fish throughout life.

Development of dim-light vision in the nocturnal reef fish family Holocentridae II: retinal morphology

Ontogenetic changes in the habitats and lifestyles of animals are often reflected in their visual systems. Coral reef fishes start life in the shallow open ocean but inhabit the reef as juveniles and adults. Alongside this change in habitat, some species also change lifestyles and become nocturnal. However, it is not fully understood how the visual systems of nocturnal reef fishes develop and adapt to these significant ecological shifts over their lives. Therefore, we used a histological approach to examine visual development in the nocturnal coral reef fish family, Holocentridae. We examined seven representative species spanning both subfamilies, Holocentrinae (squirrelfishes) and Myripristinae (soldierfishes). Pre-settlement larvae showed strong adaptation for photopic vision with high cone densities and had also started to develop a multibank retina (i.e., multiple rod layers), with up to two rod banks present. At reef settlement, holocentrids showed increased investment in their scotopic visual system, with higher rod densities and higher summation of rods onto the ganglion cell layer. By adulthood, they had well-developed scotopic vision with a highly rod-dominated multibank retina comprising 5-17 rod banks and enhanced summation of rods onto the ganglion cell layer. Lastly, the ecological demands of the two subfamilies were similar throughout their lives, yet their visual systems differed after settlement, with Myripristinae showing a more pronounced investment in scotopic vision than Holocentrinae. Thus, it is likely that both ecology and phylogeny contribute to the development of the holocentrid visual system.

Development of dim-light vision in the nocturnal reef fish family Holocentridae I: retinal gene expression

Developmental changes to the visual systems of animals are often associated with ecological shifts. Reef fishes experience a change in habitat between larval life in the shallow open ocean to juvenile and adult life on the reef. Some species also change their lifestyle over this period and become nocturnal. While these ecological transitions are well documented, little is known about the ontogeny of nocturnal reef fish vision. Here, we used transcriptomics to investigate visual development in 12 representative species from both subfamilies, Holocentrinae (squirrelfishes) and Myripristinae (soldierfishes), in the nocturnal coral reef fish family, Holocentridae. Results revealed that the visual systems of holocentrids are initially well adapted to photopic conditions with pre-settlement larvae having high levels of cone opsin gene expression and a broad cone opsin gene repertoire (8 genes). At reef settlement, holocentrids started to invest more in their scotopic visual system, and compared with adults, showed upregulation of genes involved in cell differentiation/proliferation. By adulthood, holocentrids had well developed scotopic vision with high levels of rod opsin gene expression, reduced cone opsin gene expression and repertoire (1–4 genes) and upregulated phototransduction genes. Finally, although the two subfamilies shared similar ecologies across development, their visual systems diverged after settlement, with Myripristinae investing more in scotopic vision than Holocentrinae. Hence, both ecology and phylogeny are likely to determine the development of the holocentrid visual system.

Summary: Coral reef fishes in the family Holocentridae remodel their retina at the molecular level to adapt to a nocturnal lifestyle during development.

Chromosome-level assembly of southern catfish (silurus meridionalis) provides insights into visual adaptation to nocturnal and benthic lifestyles

The Southern catfish (Silurus meridionalis) is a nocturnal and benthic freshwater fish endemic to the Yangtze River and its tributaries. In this study, we constructed a chromosome-level draft genome of S. meridionalis using 69.7-Gb Nanopore long reads and 49.5-Gb Illumina short reads. The genome assembly was 741.2 Mb in size with a contig N50 of 13.19 Mb. An additional 116.4 Gb of Bionano and 77.4 Gb of Hi-C data were applied to assemble contigs into scaffolds and further into 29 chromosomes, resulting in a 738.9-Mb genome with a scaffold N50 of 28.04 Mb. A total of 22,965 protein-coding genes were predicted from the genome with 22,519 (98.06%) genes functionally annotated. Comparative genomic and transcriptomic analyses revealed a rod-dominated visual system which was responsible for scotopic vision. The absence of cone opsins SWS1 and SWS2 resulted in the lack of ultraviolet and blue violet sensitivity. Mutations at key amino acid sites of RH1.1, RH1.2 and RH2 resulted in spectral tuning good for dim light vision and narrow colour vision. A higher expression level of rod phototransduction genes than that of cone genes and higher rod-to-cone ratio led to higher optical sensitivity under dim light conditions. In addition, analysis of the genes involved in eye morphogenesis and development revealed the loss of some conserved noncoding elements, which might be associated with the small eyes in catfish. Together, our study provides important clues for the adaptation of the catfish visual system to the nocturnal and benthic lifestyles. The draft genome of S. meridionalis represents a valuable resource for studies of the molecular mechanisms of ecological adaptation.

The visual ecology of Holocentridae, a nocturnal coral reef fish family with a deep-sea-like multibank retina

The visual systems of teleost fishes usually match their habitats and lifestyles. Since coral reefs are bright and colourful environments, the visual systems of their diurnal inhabitants have been more extensively studied than those of nocturnal species. In order to fill this knowledge gap, we conducted a detailed investigation of the visual system of the nocturnal reef fish family Holocentridae. Results showed that the visual system of holocentrids is well adapted to their nocturnal lifestyle with a rod-dominated retina. Surprisingly, rods in all species were arranged into 6-17 well-defined banks, a feature most commonly found in deep-sea fishes, that may increase the light sensitivity of the eye and/or allow colour discrimination in dim light. Holocentrids also have the potential for dichromatic colour vision during the day with the presence of at least two spectrally different cone types: single cones expressing the blue-sensitive SWS2A gene, and double cones expressing one or two green-sensitive RH2 genes. Some differences were observed between the two subfamilies, with Holocentrinae (squirrelfish) having a slightly more developed photopic visual system than Myripristinae (soldierfish). Moreover, retinal topography of both ganglion cells and cone photoreceptors showed specific patterns for each cell type, likely highlighting different visual demands at different times of the day, such as feeding. Overall, their well-developed scotopic visual systems and the ease of catching and maintaining holocentrids in aquaria, make them ideal models to investigate teleost dim-light vision and more particularly shed light on the function of the multibank retina and its potential for dim-light colour vision.

Description of the egg cases and juvenile colouration in two catsharks of the genus Atelomycterus (Carcharhiniformes: Scyliorhinidae)

Descriptions of egg cases and hatchlings of the Bali catshark Atelomycterus baliensis and the Australian marbled catshark Atelomycterus macleayi are provided. Comparisons are made with two of their congeners, banded sand catshark Atelomycterus fasciatus and coral catshark Atelomycterus marmoratus. The Atelomycterus egg cases have the same general morphology, i.e., elongate with anterior and posterior waists, a depressed and truncate anterior end sometimes with attachment fibres, a medially tapered posterior end with two horns sometimes terminating in short, tightly curled tendrils and four respiratory fissures (one at each left corner on opposing sides). Morphometric measurements taken of the egg cases of the four species differed significantly when subjected to multivariate analysis, with unique characters enabling distinction between them. The morphological characters that best distinguished the Atelomycterus species from each other were anterior border width, posterior waist width and posterior case width. Thus, egg case morphology could be used to distinguish the egg cases of the four Atelomycterus species examined, consistent with other studies on scyliorhinid and pentanchid egg cases. Colouration of A. baliensis and A. macleayi juveniles was similar to that of other Atelomycterus juveniles in being pale with a series of dark-brown distinct dorsal saddles along the body, blotches and sometimes with a low number of small dark spots.

Body size determines eyespot size and presence in coral reef fishes

Numerous organisms display conspicuous eyespots. These eye-like patterns have been shown to effectively reduce predation by either deflecting strikes away from nonvital organs or by intimidating potential predators. While investigated extensively in terrestrial systems, determining what factors shape eyespot form in colorful coral reef fishes remains less well known. Using a broadscale approach we ask: How does the size of the eyespot relate to the actual eye, and at what size during ontogeny are eyespots acquired or lost? We utilized publicly available images to generate a dataset of 167 eyespot-bearing reef fish species. We measured multiple features relating to the size of the fish, its eye, and the size of its eyespot. In reef fishes, the area of the eyespot closely matches that of the real eye; however, the eyespots "pupil" is nearly four times larger than the real pupil. Eyespots appear at about 20 mm standard length. However, there is a marked decrease in the presence of eyespots in fishes above 48 mm standard length; a size which is tightly correlated with significant decreases in documented mortality rates. Above 75-85 mm, the cost of eyespots appears to outweigh their benefit. Our results identify a "size window" for eyespots in coral reef fishes, which suggests that eyespot use is strictly body size-dependent within this group.

Visual system diversity in coral reef fishes

Coral reefs are one of the most species rich and colourful habitats on earth and for many coral reef teleosts, vision is central to their survival and reproduction. The diversity of reef fish visual systems arises from variations in ocular and retinal anatomy, neural processing and, perhaps most easily revealed by, the peak spectral absorbance of visual pigments. This review examines the interplay between retinal morphology and light environment across a number of reef fish species, but mainly focusses on visual adaptations at the molecular level (i.e. visual pigment structure). Generally, visual pigments tend to match the overall light environment or micro-habitat, with fish inhabiting greener, inshore waters possessing longer wavelength-shifted visual pigments than open water blue-shifted species. In marine fishes, particularly those that live on the reef, most species have between two (likely dichromatic) to four (possible tetrachromatic) cone spectral sensitivities and a single rod for crepuscular vision; however, most are trichromatic with three spectral sensitivities. In addition to variation in spectral sensitivity number, spectral placement of the absorbance maximum (λ_max) also has a surprising degree of variability. Variation in ocular and retinal anatomy is also observed at several levels in reef fishes but is best represented by differences in arrangement, density and distribution of neural cell types across the retina (i.e. retinal topography). Here, we focus on the seven reef fish families most comprehensively studied to date to examine and compare how behaviour, environment, activity period, ontogeny and phylogeny might interact to generate the exceptional diversity in visual system design that we observe.

Seeing the rainbow: mechanisms underlying spectral sensitivity in teleost fishes

Among vertebrates, teleost eye diversity exceeds that found in all other groups. Their spectral sensitivities range from ultraviolet to red, and the number of visual pigments varies from 1 to over 40. This variation is correlated with the different ecologies and life histories of fish species, including their variable aquatic habitats: murky lakes, clear oceans, deep seas and turbulent rivers. These ecotopes often change with the season, but fish may also migrate between ecotopes diurnally, seasonally or ontogenetically. To survive in these variable light habitats, fish visual systems have evolved a suite of mechanisms that modulate spectral sensitivities on a range of timescales. These mechanisms include: (1) optical media that filter light, (2) variations in photoreceptor type and size to vary absorbance and sensitivity, and (3) changes in photoreceptor visual pigments to optimize peak sensitivity. The visual pigment changes can result from changes in chromophore or changes to the opsin. Opsin variation results from changes in opsin sequence, opsin expression or co-expression, and opsin gene duplications and losses. Here, we review visual diversity in a number of teleost groups where the structural and molecular mechanisms underlying their spectral sensitivities have been relatively well determined. Although we document considerable variability, this alone does not imply functional difference per se. We therefore highlight the need for more studies that examine species with known sensitivity differences, emphasizing behavioral experiments to test whether such differences actually matter in the execution of visual tasks that are relevant to the fish.

Intertidal gobies acclimate rate of luminance change for background matching with shifts in seasonal temperature

Rate of colour change and background matching capacity are important functional traits for avoiding predation and hiding from prey. Acute changes in environmental temperature are known to impact the rate at which animals change colour, and therefore may affect their survival. Many ectotherms have the ability to acclimate performance traits such as locomotion, metabolic rate and growth rate with changes in seasonal temperature. However, it remains unclear how other functional traits that are directly linked to behaviour and survival respond to long-term changes in temperature (within an individual's lifetime). We assessed whether the rate of colour change is altered by long-term changes in temperature (seasonal variation) and if rate of colour change can acclimate to seasonal thermal conditions. We used an intertidal rock-pool goby Bathygobius cocosensis, to test this and exposed individuals to representative seasonal mean temperatures (16 or 31°C, herein referred to cold- and warm-exposed fish respectively) for 9 weeks and then tested their rate of luminance change when placed on white and black backgrounds at acute test temperatures 16 and 31°C. We modelled rate of luminance change using the visual sensitives of a coral trout Plectropmus leopardus to determine how well gobies matched their backgrounds in terms of luminance contrast to a potential predator. After exposure to long-term seasonal conditions, the warm-exposed fish had faster rates of luminance change and matched their background more closely when tested at 31 than at 16°C. Similarly, the cold-exposed fish had faster rates of luminance change and matched their backgrounds more closely at 16°C than at 31°C. This demonstrates that rate of luminance change can be adjusted to compensate for long-term changes in seasonal temperature. This is the first study to show that animals can acclimate rate of colour change for background matching to seasonal thermal conditions. We also show that rapid changes in acute temperature reduce background matching capabilities. Stochastic changes in climate are likely to affect the frequency of predator-prey interactions which may have substantial knock-on effects throughout ecosystems.

From cryptic to colorful: Evolutionary decoupling of larval and adult color in butterflies

Many animals undergo complete metamorphosis, where larval forms change abruptly in adulthood. Color change during ontogeny is common, but there is little understanding of evolutionary patterns in these changes. Here, we use data on larval and adult color for 246 butterfly species (61% of all species in Australia) to test whether the evolution of color is coupled between life stages. We show that adults are more variable in color across species than caterpillars and that male adult color has lower phylogenetic signal. These results suggest that sexual selection is driving color diversity in male adult butterflies at a broad scale. Moreover, color similarities between species at the larval stage do not predict color similarities at the adult stage, indicating that color evolution is decoupled between young and adult forms. Most species transition from cryptic coloration as caterpillars to conspicuous coloration as adults, but even species with conspicuous caterpillars change to different conspicuous colors as adults. The use of high‐contrast coloration is correlated with body size in caterpillars but not adults. Taken together, our results suggest a change in the relative importance of different selective pressures at different life stages, resulting in the evolutionary decoupling of coloration through ontogeny.

Vision using multiple distinct rod opsins in deep-sea fishes

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

A detailed investigation of the visual system and visual ecology of the Barrier Reef anemonefish, Amphiprion akindynos

Vision plays a major role in the life of most teleosts, and is assumingly well adapted to each species ecology and behaviour. Using a multidisciplinary approach, we scrutinised several aspects of the visual system and ecology of the Great Barrier Reef anemonefish, Amphiprion akindynos, including its orange with white patterning, retinal anatomy and molecular biology, its symbiosis with anemones and sequential hermaphroditism. Amphiprion akindynos possesses spectrally distinct visual pigments and opsins: one rod opsin, RH1 (498 nm), and five cone opsins, SWS1 (370 nm), SWS2B (408 nm), RH2B (498 nm), RH2A (520 nm), and LWS (554 nm). Cones were arranged in a regular mosaic with each single cone surrounded by four double cones. Double cones mainly expressed RH2B (53%) in one member and RH2A (46%) in the other, matching the prevailing light. Single cones expressed SWS1 (89%), which may serve to detect zooplankton, conspecifics and the host anemone. Moreover, a segregated small fraction of single cones coexpressed SWS1 with SWS2B (11%). This novel visual specialisation falls within the region of highest acuity and is suggested to increase the chromatic contrast of Amphiprion akindynos colour patterns, which might improve detection of conspecifics.

Colours and colour vision in reef fishes: Past, present and future research directions

Many fishes, both freshwater or marine, have colour vision that may outperform humans. As a result, to understand the behavioural tasks that vision enables; including mate choice, feeding, agonistic behaviour and camouflage, we need to see the world through a fish's eye. This includes quantifying the variable light environment underwater and its various influences on vision. As well as rapid loss of light with depth, light attenuation underwater limits visual interaction to metres at most and in many instances, less than a metre. We also need to characterize visual sensitivities, fish colours and behaviours relative to both these factors. An increasingly large set of techniques over the past few years, including improved photography, submersible spectrophotometers and genetic sequencing, have taken us from intelligent guesswork to something closer to sensible hypotheses. This contribution to the special edition on the Ecology of Fish Senses under a shifting environment first reviews our knowledge of fish colour vision and visual ecology, past, present and very recent, and then goes on to examine how climate change may impinge on fish visual capability. The review is limited to mostly colour vision and to mostly reef fishes. This ignores a large body of work, both from other marine environments and freshwater systems, but the reef contains examples of many of the challenges to vision from the aquatic environment. It is also a concentrate of life, perhaps the most specious and complex on earth, suffering now catastrophically from the consequences of our lack of action on climate change. A clear course of action to prevent destruction of this habitat is the need to spend more time in it, in the study of it and sharing it with those not fortunate enough to see coral reefs first-hand. Sir David Attenborough on The Great Barrier Reef: "Do we really care so little about the Earth upon which we live that we don't wish to protect one of its greatest wonders from the consequences of our behaviours?"

Visual system development of the spotted unicornfish, Naso brevirostris (Acanthuridae)

Ontogenetic changes of the visual system are often correlated to shifts in habitat and feeding behaviour of animals. Coral reef fishes begin their lives in the pelagic zone and then migrate to the reef. This habitat transition frequently involves a change in diet and light environment as well as major morphological modifications. The spotted unicornfish, Naso brevirostris, is known to shift diet from zooplankton to algae and back to mainly zooplankton when transitioning from larval to juvenile and then to adult stages. Concurrently, N. brevirostris also moves from an open pelagic to a coral-associated habitat before migrating up in the water column when reaching adulthood. Using retinal mapping techniques, we discovered that the distribution and density of ganglion and photoreceptor cells in N. brevirostris mostly changes during the transition from the larval to the juvenile stage, with only minor modifications thereafter. Similarly, visual gene (opsin) expression based on RNA sequencing, although qualitatively similar between stages (all fishes mainly expressed the same three cone opsins; SWS2B, RH2B, RH2A), also showed the biggest quantitative difference when transitioning from larvae to juveniles. The juvenile stage in particular seems mismatched with its reef-associated ecology, which may be due to this stage only lasting a fraction of the lifespan of these fishes. Hence, the visual ontogeny found in N. brevirostris is very different from the progressive changes found in other reef fishes calling for a thorough analysis of visual system development of the reef fish community.

The adaptive value of camouflage and colour change in a polymorphic prawn

Camouflage has been a textbook example of natural selection and adaptation since the time of the earliest evolutionists. However, aside from correlational evidence and studies using artificial dummy prey, experiments directly showing that better camouflaged prey to predator vision are at reduced risk of attack are lacking. Here, we show that the level of camouflage achieved through colour adjustments towards the appearance of seaweed habitats is adaptive in reducing predation pressure in the prawn Hippolyte obliquimanus. Digital image analysis and visual modelling of a fish predator (seahorse) predicted that brown prawns would be imperfectly concealed against both brown and red seaweed respectively, whereas pink prawns should be well camouflaged only in red weed. Predation trials with captive seahorses (Hippocampus reidi), coupled with high-speed video analyses, closely matched model predictions: predation rates were similar for brown prawns between seaweed types, but pink individuals were attacked significantly less on red than brown weed. Our work provides some of the clearest direct evidence to date that colour polymorphism and colour change provides a clear adaptive advantage for camouflage, and also highlights how this can be asymmetric across morphs and habitats (i.e. dependent on the specific background-morph combination).

Insights into visual pigment adaptation and diversity from model ecological and evolutionary systems

Sensory systems provide valuable insight into the evolution of molecular mechanisms underlying organismal anatomy, physiology, and behaviour. Visual pigments, which mediate the first step in visual transduction, offer a unique window into the relationship between molecular variation and visual performance, and enhance our understanding of how ecology, life history, and physiology may shape genetic variation across a variety of organisms. Here we review recent work investigating vertebrate visual pigments from a number of perspectives. Opsin gene duplication, loss, differential expression, structural variation, and the physiological context in which they operate, have profoundly shaped the visual capabilities of vertebrates adapting to novel environments. We note the importance of conceptual frameworks in investigating visual pigment diversity in vertebrates, highlighting key examples including evolutionary transitions between different photic environments, major shifts in life history evolution and ecology, evolutionary innovations in visual system anatomy and physiology, as well as shifts in visually mediated behaviours and behavioural ecology. We emphasize the utility of studying visual pigment evolution in the context of these different perspectives, and demonstrate how the integrative approaches discussed in this review contribute to a better understanding of the underlying molecular processes mediating adaptation in sensory systems, and the contexts in which they occur.

Why UV vision and red vision are important for damselfish (Pomacentridae): structural and expression variation in opsin genes

Coral reefs belong to the most diverse ecosystems on our planet. The diversity in coloration and lifestyles of coral reef fishes makes them a particularly promising system to study the role of visual communication and adaptation. Here, we investigated the evolution of visual pigment genes (opsins) in damselfish (Pomacentridae) and examined whether structural and expression variation of opsins can be linked to ecology. Using DNA sequence data of a phylogenetically representative set of 31 damselfish species, we show that all but one visual opsin are evolving under positive selection. In addition, selection on opsin tuning sites, including cases of divergent, parallel, convergent and reversed evolution, has been strong throughout the radiation of damselfish, emphasizing the importance of visual tuning for this group. The highest functional variation in opsin protein sequences was observed in the short- followed by the long-wavelength end of the visual spectrum. Comparative gene expression analyses of a subset of the same species revealed that with SWS1, RH2B and RH2A always being expressed, damselfish use an overall short-wavelength shifted expression profile. Interestingly, not only did all species express SWS1 - a UV-sensitive opsin - and possess UV-transmitting lenses, most species also feature UV-reflective body parts. This suggests that damsels might benefit from a close-range UV-based 'private' communication channel, which is likely to be hidden from 'UV-blind' predators. Finally, we found that LWS expression is highly correlated to feeding strategy in damsels with herbivorous feeders having an increased LWS expression, possibly enhancing the detection of benthic algae.