Molecular diversity of visual pigments in Stomatopoda (Crustacea)

Full-length transcriptome reveals the circularly polarized light response-related molecular genetic characteristics of Oratosquilla oratoria

The mantis shrimp is the only animal that can recognize circularly polarized light (CPL), but its molecular genetic characteristics are unclear. Multi-tissue level full-length (FL) transcriptome sequencing of Oratosquilla oratoria, a representative widely distributed mantis shrimp, was performed in the present study. We used comparative transcriptomics to explore the critical genes of O. oratoria selected by CPL and the GNβ gene associated with CPL signal transduction was hypothesized to be positively selected. Furthermore, the FL transcriptomes of O. oratoria compound eyes under five light conditions were sequenced and used to detect alternative splicing (AS). The ASs associated with CPL recognition mainly occurred in the LWS, ARR and TRPC regions. The number of FL transcripts with AS events and annotation information also provided evidence that O. oratoria could recognize LCPL. Additionally, 51 sequences belonging to the LWS, UV and Peropsin gene families were identified based on conserved 7tm domains. The LWS, UV and Peropsin opsins have similar 3D structures with seven domains across the cell membrane and conserved KSLRTPSN, DRY, and QAKK motifs. In conclusion, these results are undoubtedly valuable for perfecting the vision theory of O. oratoria and other mantis shrimp.

How Oratosquilla oratoria compound eye response to the polarization of light: In the perspective of vision genes and related proteins

The special rhabdom structure of the mid-band ommatidium in compound eye contributes to the mantis shrimp being the only animal species known to science that can recognize circularly polarized light (CPL). Although the number of mid-band ommatidium of Oratosquilla oratoria is reduced, the mid-band ommatidium still has orthogonal geometric interleaved rhabdom and short oval distal rhabdom, which may mean that the O. oratoria has weakened circular polarized light vision (CPLV). Here we explored the molecular mechanisms of how O. oratoria response to the polarization of light. Based on the specific expression patterns of vision-related functional genes and proteins, we suggest that the order of light response by O. oratoria compound eye was first natural light, then left-circularly polarized light (LCPL), linearly polarized light, right-circularly polarized light (RCPL) and dark. Meanwhile, we found that the expression levels of vision-related functional genes and proteins in O. oratoria compound eye under RCPL were not significantly different from those in DL, which may imply that O. oratoria cannot respond to RCPL. Furthermore, the response of LCPL is likely facilitated by the differential expression of opsin and microvilli - related functional genes and proteins (arrestin and sodium-coupled neutral amino acid transporter). In conclusion, this study systematically illustrated for the first time how O. oratoria compound eye response to the polarization of light at the genetic level, and it can improve the visual ecological theory behind polarized light vision evolution.

Increasing complexity of opsin expression across stomatopod development

Stomatopods are well studied for their unique visual systems, which can consist of up to 16 different photoreceptor types and 33 opsin proteins expressed in the adults of some species. The light-sensing abilities of larval stomatopods are comparatively less well understood with limited information about the opsin repertoire of these early-life stages. Early work has suggested that larval stomatopods may not possess the extensive light detection abilities found in their adult counterparts. However, recent studies have shown that these larvae may have more complex photosensory systems than previously thought. To examine this idea at the molecular level, we characterized the expression of putative light-absorbing opsins across developmental stages, from embryo to adult, in the stomatopod species Pullosquilla thomassini using transcriptomic methods with a special focus on ecological and physiological transition periods. Opsin expression during the transition from the larval to the adult stage was further characterized in the species Gonodactylaceus falcatus. Opsin transcripts from short, middle, and long wavelength-sensitive clades were found in both species, and analysis of spectral tuning sites suggested differences in absorbance within these clades. This is the first study to document the changes in opsin repertoire across development in stomatopods, providing novel evidence for light detection across the visual spectrum in larvae.

Investigation of the ultrastructures and retinal arrangements of larval stomatopod eyes

Though the transparent apposition eyes of larval stomatopod crustaceans lack most of the unique retinal specializations known from their adult counterparts, increasing evidence suggests that these tiny pelagic organisms possess their own version of retinal complexity. In this paper, we examined the structural organization of larval eyes in six species of stomatopod crustaceans across three stomatopod superfamilies using transmission electron microscopy. The primary focus was to examine retinular cell arrangement of the larval eyes and characterize the presence of an eighth retinular cell (R8), which is typically responsible for UV vision in crustaceans. For all species investigated, we identified R8 photoreceptor cells positioned distal to the main rhabdom of R1-7 cells. This is the first evidence that R8 photoreceptor cells exist in larval stomatopod retinas, and among the first identified in any larval crustacean. Considering recent studies that identified UV sensitivity in larval stomatopods, we propose that this sensitivity is driven by this putative R8 photoreceptor cell. Additionally, we identified a potentially unique crystalline cone structure in each of the species examined, the function of which is still not understood.

The diversity of invertebrate visual opsins spanning Protostomia, Deuterostomia, and Cnidaria

Across eumetazoans, the ability to perceive and respond to visual stimuli is largely mediated by opsins, a family of proteins belonging to the G protein-coupled receptor (GPCR) superclass. Lineage-specific gains and losses led to a striking diversity in the numbers, types, and spectral sensitivities conferred by visual opsin gene expression. Here, we review the diversity of visual opsins and differences in opsin gene expression from well-studied protostome, invertebrate deuterostome, and cnidarian groups. We discuss the functional significance of opsin expression differences and spectral tuning among lineages. In some cases, opsin evolution has been linked to the detection of relevant visual signals, including sexually selected color traits and host plant features. In other instances, variation in opsins has not been directly linked to functional or ecological differences. Overall, the array of opsin expression patterns and sensitivities across invertebrate lineages highlight the diversity of opsins in the eumetazoan ancestor and the labile nature of opsins over evolutionary time.

Crustacean conundrums: a review of opsin diversity and evolution

Knowledge of crustacean vision is lacking compared to the more well-studied vertebrates and insects. While crustacean visual systems are typically conserved morphologically, the molecular components (i.e. opsins) remain understudied. This review aims to characterize opsin diversity across crustacean lineages for an integrated view of visual system evolution. Using publicly available data from 95 species, we identified opsin sequences and classified them by clade. Our analysis produced 485 putative visual opsins and 141 non-visual opsins. The visual opsins were separated into six clades: long wavelength sensitive (LWS), middle wavelength sensitive (MWS) 1 and 2, short wavelength or ultraviolet sensitive (SWS/UVS) and a clade of thecostracan opsins, with multiple LWS and MWS opsin copies observed. The SWS/UVS opsins were relatively conserved in most species. The crustacean classes Cephalocarida, Remipedia and Hexanauplia exhibited reduced visual opsin diversity compared to others, with the malacostracan decapods having the highest opsin diversity. Non-visual opsins were identified from all investigated classes except Cephalocarida. Additionally, a novel clade of non-visual crustacean-specific, R-type opsins (Rc) was discovered. This review aims to provide a framework for future research on crustacean vision, with an emphasis on the need for more work in spectral characterization and molecular analysis. This article is part of the theme issue 'Understanding colour vision: molecular, physiological, neuronal and behavioural studies in arthropods'.

Colour vision in stomatopod crustaceans

The stomatopod crustaceans, or mantis shrimps, are colourful marine invertebrate predators. Their unusual compound eyes have dorsal and ventral regions resembling typical crustacean apposition designs separated by a unique region called the midband that consists of from two to six parallel rows of ommatidia. In species with six-row midbands, the dorsal four rows are themselves uniquely specialized for colour analysis. Rhabdoms of ommatidia in these rows are longitudinally divided into three distinct regions: an apical ultraviolet (UV) receptor, a shorter-wavelength middle tier receptor and a longer-wavelength proximal tier receptor. Each of the total of 12 photoreceptors has a different spectral sensitivity, potentially contributing to a colour-vision system with 12 channels. Mantis shrimps can discriminate both human-visible and UV colours, but with limited precision compared to other colour-vision systems. Here, we review the structure and function of stomatopod colour vision, examining the types of receptors present in a species, the spectral tuning of photoreceptors both within and across species, the neural analysis of colour and the genetics underlying the multiple visual pigments used for colour vision. Even today, after many decades of research into the colour vision of stomatopods, much of its operation and its use in nature remain a mystery. This article is part of the theme issue 'Understanding colour vision: molecular, physiological, neuronal and behavioural studies in arthropods'.

Molecular advances to study the function, evolution and spectral tuning of arthropod visual opsins

Visual opsins of vertebrates and invertebrates diversified independently and converged to detect ultraviolet to long wavelengths (LW) of green or red light. In both groups, colour vision largely derives from opsin number, expression patterns and changes in amino acids interacting with the chromophore. Functional insights regarding invertebrate opsin evolution have lagged behind those for vertebrates because of the disparity in genomic resources and the lack of robust in vitro systems to characterize spectral sensitivities. Here, we review bioinformatic approaches to identify and model functional variation in opsins as well as recently developed assays to measure spectral phenotypes. In particular, we discuss how transgenic lines, cAMP-spectroscopy and sensitive heterologous expression platforms are starting to decouple genotype–phenotype relationships of LW opsins to complement the classical physiological-behavioural-phylogenetic toolbox of invertebrate visual sensory studies. We illustrate the use of one heterologous method by characterizing novel LW Gq opsins from 10 species, including diurnal and nocturnal Lepidoptera, a terrestrial dragonfly and an aquatic crustacean, expressing them in HEK293T cells, and showing that their maximum absorbance spectra (λ_max) range from 518 to 611 nm. We discuss the advantages of molecular approaches for arthropods with complications such as restricted availability, lateral filters, specialized photochemistry and/or electrophysiological constraints.

This article is part of the theme issue ‘Understanding colour vision: molecular, physiological, neuronal and behavioural studies in arthropods’.

The diversity of opsins in Lake Baikal amphipods (Amphipoda: Gammaridae)

BACKGROUND

Vision is a crucial sense for the evolutionary success of many animal groups. Here we explore the diversity of visual pigments (opsins) in the transcriptomes of amphipods (Crustacea: Amphipoda) and conclude that it is restricted to middle (MWS) and long wavelength-sensitive (LWS) opsins in the overwhelming majority of examined species.

RESULTS

We evidenced (i) parallel loss of MWS opsin expression in multiple species (including two independently evolved lineages from the deep and ancient Lake Baikal) and (ii) LWS opsin amplification (up to five transcripts) in both Baikal lineages. The number of LWS opsins negatively correlated with habitat depth in Baikal amphipods. Some LWS opsins in Baikal amphipods contained MWS-like substitutions, suggesting that they might have undergone spectral tuning.

CONCLUSIONS

This repeating two-step evolutionary scenario suggests common triggers, possibly the lack of light during the periods when Baikal was permanently covered with thick ice and its subsequent melting. Overall, this observation demonstrates the possibility of revealing climate history by following the evolutionary changes in protein families.

Illuminating the impact of diel vertical migration on visual gene expression in deep-sea shrimp

Diel vertical migration (DVM) of marine animals represents one of the largest migrations on our planet. Migrating fauna are subjected to a variety of light fields and environmental conditions that can have notable impacts on sensory mechanisms, including an organism's visual capabilities. Among deep-sea migrators are oplophorid shrimp that vertically migrate hundreds of metres to feed in shallow waters at night. These species also have bioluminescent light organs that emit light during migrations to aid in camouflage. The organs have recently been shown to contain visual proteins (opsins) and genes that infer light sensitivity. Knowledge regarding the impacts of vertical migratory behaviour, and fluctuating environmental conditions, on sensory system evolution is unknown. In this study, the oplophorid Systellaspis debilis was either collected during the day from deep waters or at night from relatively shallow waters to ensure sampling across the vertical distributional range. De novo transcriptomes of light-sensitive tissues (eyes/photophores) from the day/night specimens were sequenced and analysed to characterize opsin diversity and visual/light interaction genes. Gene expression analyses were also conducted to quantify expression differences associated with DVM. Our results revealed an expanded opsin repertoire among the shrimp and differential opsin expression that may be linked to spectral tuning during the migratory process. This study sheds light on the sensory systems of a bioluminescent invertebrate and provides additional evidence for extraocular light sensitivity. Our findings further suggest opsin co-expression and subsequent fluctuations in opsin expression may play an important role in diversifying the visual responses of vertical migrators.

Exceptional diversity of opsin expression patterns in Neogonodactylus oerstedii (Stomatopoda) retinas

Stomatopod crustaceans possess some of the most complex animal visual systems, including at least 16 spectrally distinct types of photoreceptive units (e.g., assemblages of photoreceptor cells). Here we fully characterize the set of opsin genes expressed in retinal tissues and determine expression patterns of each in the stomatopod Neogonodactylus oerstedii Using a combination of transcriptome and RACE sequencing, we identified 33 opsin transcripts expressed in each N. oerstedii eye, which are predicted to form 20 long-wavelength-sensitive, 10 middle-wavelength-sensitive, and three UV-sensitive visual pigments. Observed expression patterns of these 33 transcripts were highly unusual in five respects: 1) All long-wavelength and short/middle-wavelength photoreceptive units expressed multiple opsins, while UV photoreceptor cells expressed single opsins; 2) most of the long-wavelength photoreceptive units expressed at least one middle-wavelength-sensitive opsin transcript; 3) the photoreceptors involved in spatial, motion, and polarization vision expressed more transcripts than those involved in color vision; 4) there is a unique opsin transcript that is expressed in all eight of the photoreceptive units devoted to color vision; and 5) expression patterns in the peripheral hemispheres of the eyes suggest visual specializations not previously recognized in stomatopods. Elucidating the expression patterns of all opsin transcripts expressed in the N. oerstedii retina reveals the potential for previously undocumented functional diversity in the already complex stomatopod eye and is a first step toward understanding the functional significance of the unusual abundance of opsins found in many arthropod species' visual systems.

Optic lobe organization in stomatopod crustacean species possessing different degrees of retinal complexity

Stomatopod crustaceans possess tripartite compound eyes; upper and lower hemispheres are separated by an equatorial midband of several ommatidial rows. The organization of stomatopod retinas is well established, but their optic lobes have been studied less. We used histological staining, immunolabeling, and fluorescent tracer injections to compare optic lobes in two 6-row midband species, Neogonodactylus oerstedii and Pseudosquilla ciliata, to those in two 2-row midband species, Squilla empusa and Alima pacifica. Compared to the 6-row species, we found structural differences in all optic neuropils in both 2-row species. Photoreceptor axons from 2-row midband ommatidia supply two sets of lamina cartridges; however, conspicuous spaces lacking lamina cartridges are observed in locations corresponding to where the cartridges of the upper four ommatidial rows of 6-row species would exist. The tripartite arrangement and enlarged projections containing fibers associated with the two rows of midband ommatidia can be traced throughout the entire optic lobe. However, 2-row species lack some features of medullar and lobular neuropils in 6-row species. Our results support the hypothesis that 2-row midband species are derived from a 6-row ancestor, and suggest specializations in the medulla and lobula found solely in 6-row species are important for color and polarization analysis.

Evolutionary ecology of opsin gene sequence, expression and repertoire

Linking molecular evolution to biological function is a long-standing challenge in evolutionary biology. Some of the best examples of this involve opsins, the genes that encode the molecular basis of light reception. In this issue of Molecular Ecology, three studies examine opsin gene sequence, expression and repertoire to determine how natural selection has shaped the visual system. First, Escobar-Camacho et al. () use opsin repertoire and expression in three Amazonian cichlid species to show that a shift in sensitivity towards longer wavelengths is coincident with the long-wavelength-dominated Amazon basin. Second, Stieb et al. () explore opsin sequence and expression in reef-dwelling damselfish and find that UV- and long-wavelength vision are both important, but likely for different ecological functions. Lastly, Suvorov et al. () study an expansive opsin repertoire in the insect order Odonata and find evidence that copy number expansion is consistent with the permanent heterozygote model of gene duplication. Together these studies emphasize the utility of opsin genes for studying both the local adaptation of sensory systems and, more generally, gene family evolution.

Sequence, Structure, and Expression of Opsins in the Monochromatic Stomatopod Squilla empusa

Most stomatopod crustaceans have complex retinas in their compound eyes, with up to 16 spectral types of photoreceptors, but members of the superfamily Squilloidea have much simpler retinas, thought to contain a single photoreceptor spectral class. In the Atlantic stomatopod Squilla empusa, microspectrophotometry shows that all photoreceptors absorb light maximally at 517 nm, indicating that a single visual pigment is present in all photoreceptors in the retina. However, six distinct, but partial, long wavelength sensitive (LWS) opsin transcripts, which encode the protein component of the visual pigment, have been previously isolated through RT-PCR. In order to investigate the spectral and functional differences among S. empusa's opsins, we used RT-PCR to complete the 3' end of sequences for five of the six expressed opsins. The extended sequences spanned from the first transmembrane (TM1) helix to the 3' end of the coding region. Using homology-based modeling, we predicted the three-dimensional structure of the amino acid translation of the S. empusa opsins. Based on these analyses, S. empusa LWS opsins share a high sequence identity in TM regions and in amino acids within 15 Å of the chromophore-binding lysine on TM helix 7 (TM7), suggesting that these opsins produce spectrally similar visual pigments in agreement with previous results. However, we propose that these spectrally similar opsins differ functionally, as there are non-conservative amino acid substitutions found in intracellular loop 2 (ICL2) and TM5/ICL3, which are critical regions for G-protein binding, and substitutions in extracellular regions suggest different chromophore attachment affinities. In situ hybridization of two of the opsins (Se5 and Se6) revealed strong co-expression in all photoreceptors in both midband and peripheral regions of the retina as well as in selected ocular and cerebral ganglion neuropils. These data suggest the expression of multiple opsins-likely spectrally identical, but functionally different-in multiple types of neuronal cells in S. empusa. This suggests that the multiple opsins characteristic of other stomatopod species may have similar functional specialization.

Molecular palaeontology illuminates the evolution of ecdysozoan vision

Colour vision is known to have arisen only twice-once in Vertebrata and once within the Ecdysozoa, in Arthropoda. However, the evolutionary history of ecdysozoan vision is unclear. At the molecular level, visual pigments, composed of a chromophore and a protein belonging to the opsin family, have different spectral sensitivities and these mediate colour vision. At the morphological level, ecdysozoan vision is conveyed by eyes of variable levels of complexity; from the simple ocelli observed in the velvet worms (phylum Onychophora) to the marvellously complex eyes of insects, spiders, and crustaceans. Here, we explore the evolution of ecdysozoan vision at both the molecular and morphological level; combining analysis of a large-scale opsin dataset that includes previously unknown ecdysozoan opsins with morphological analyses of key Cambrian fossils with preserved eye structures. We found that while several non-arthropod ecdysozoan lineages have multiple opsins, arthropod multi-opsin vision evolved through a series of gene duplications that were fixed in a period of 35-71 million years (Ma) along the stem arthropod lineage. Our integrative study of the fossil and molecular record of vision indicates that fossils with more complex eyes were likely to have possessed a larger complement of opsin genes.

Cerebral photoreception in mantis shrimp

The currently unsurpassed diversity of photoreceptors found in the eyes of stomatopods, or mantis shrimps, is achieved through a variety of opsin-based visual pigments and optical filters. However, the presence of extraocular photoreceptors in these crustaceans is undescribed. Opsins have been found in extraocular tissues across animal taxa, but their functions are often unknown. Here, we show that the mantis shrimp Neogonodactylus oerstedii has functional cerebral photoreceptors, which expands the suite of mechanisms by which mantis shrimp sense light. Illumination of extraocular photoreceptors elicits behaviors akin to common arthropod escape responses, which persist in blinded individuals. The anterior central nervous system, which is illuminated when a mantis shrimp's cephalothorax protrudes from its burrow to search for predators, prey, or mates, appears to be photosensitive and to feature two types of opsin-based, potentially histaminergic photoreceptors. A pigmented ventral eye that may be capable of color discrimination extends from the cerebral ganglion, or brain, against the transparent outer carapace, and exhibits a rapid electrical response when illuminated. Additionally, opsins and histamine are expressed in several locations of the eyestalks and cerebral ganglion, where any photoresponses could contribute to shelter-seeking behaviors and other functions.

Multichannel spectrometers in animals

Multispectral, hyperspectral, polarimetric, and other types of multichannel imaging spectrometers are coming into common use for a variety of applications, including remote sensing, material identification, forensics, and medical diagnosis. These instruments are often bulky and intolerant of field abuse, so designing compact, reliable, portable, and robust devices is a priority. In contrast to most engineering designs, animals have been building compact and robust multichannel imaging systems for millennia-their eyes. Biological sensors arise by evolution, of course, and are not designed 'for' a particular use; they exist because the creatures that were blessed with useful mutations were better able to survive and reproduce than their competitors. While this is an inefficient process for perfecting a sensor, it brings unexpected innovations and novel concepts into visual system design-concepts that may be useful in the inspiration of new engineered solutions to problematic challenges, like the ones mentioned above. Here, we review a diversity of multichannel visual systems from both vertebrate and invertebrate animals, considering the receptor molecules and cells, spectral sensitivity and its tuning, and some aspects of the higher-level processing systems used to shape spectral (and polarizational) channels in vision. The eyes of mantis shrimps are presented as potential models for biomimetic multichannel imaging systems. We end with a description of a bioinspired, newly developed multichannel spectral/polarimetric imaging system based on mantis shrimp vision that is highly adaptable to field application.

Comparative visual ecology of cephalopods from different habitats

Previous investigations of vision and visual pigment evolution in aquatic predators have focused on fish and crustaceans, generally ignoring the cephalopods. Since the first cephalopod opsin was sequenced in late 1980s, we now have data on over 50 cephalopod opsins, prompting this functional and phylogenetic examination. Much of this data does not specifically examine the visual pigment spectral absorbance position (λ_max) relative to environment or lifestyle, and cephalopod opsin functional adaptation and visual ecology remain largely unknown. Here we introduce a new protocol for photoreceptor microspectrophotometry (MSP) that overcomes the difficulty of bleaching the bistable visual pigment and that reveals eight coastal coleoid cephalopods to be monochromatic with λ_max varying from 484 to 505 nm. A combination of current MSP results, the λ_max values previously characterized using cephalopod retinal extracts (467–500 nm) and the corresponding opsin phylogenetic tree were used for systematic comparisons with an end goal of examining the adaptations of coleoid visual pigments to different light environments. Spectral tuning shifts are described in response to different modes of life and light conditions. A new spectral tuning model suggests that nine amino acid substitution sites may determine the direction and the magnitude of spectral shifts.

Intracellular Recordings of Spectral Sensitivities in Stomatopods: a Comparison across Species

Stomatopods (mantis shrimps) possess one of the most complex eyes in the world with photoreceptors detecting up to 12 different colors. It is not yet understood why stomatopods have almost four times the number of spectral photoreceptors compared with most other animals. It has, however, been suggested that these seemingly redundant photoreceptors could encode color through a new mechanism. Here we compare the spectral sensitivities across five species of stomatopods within the superfamily Gonodactyloidea using intracellular electrophysiological recordings. The results show that the spectral sensitivities across species of stomatopods are remarkably similar apart from some variation in the long-wavelength receptors. We relate these results to spectral sensitivity estimates previously obtained using microspectrophotometry and discuss the variation in the spectral sensitivity maxima (λmax) of the long-wavelength receptors in regard to the previous findings that stomatopods are able to tune their spectral sensitivities according to their respective light environment. We further discuss the similarities of the spectral sensitivities across species of stomatopods in regard to how color information might be processed by their visual systems.

Opsin Expression in the Central Nervous System of the Mantis Shrimp Neogonodactylus oerstedii

Visual pigments, each composed of an opsin protein covalently bound to a chromophore molecule, confer light sensitivity for vision. The eyes of some species of stomatopod crustaceans, or mantis shrimp, can express dozens of different opsin genes. The opsin diversity, along with spectral filters and unique tripartite eye structure, bestow upon stomatopods unusually complex visual systems. Although opsins are found in tissues outside typical image-forming eyes in other animals, extraocular opsin expression in stomatopods, animals well known for their diversity of opsins, was unknown. Caudal photoreception in the central nervous system of decapod crustaceans, a group closely related to stomatopod crustaceans, is thought to be opsin based. However, electrophysiological data suggest that stomatopods do not have caudal photoreceptors. In this study, we identified mRNAs that could encode four different opsins and several components of a potential G_q-mediated phototransduction pathway in the central nervous system of the Caribbean mantis shrimp Neogonodactylus oerstedii. The four opsins are abundantly expressed in the cerebral ganglion, or brain, with little or no expression in the remainder of the ventral nerve cord. Our data suggest that there are previously undiscovered cerebral photoreceptors in stomatopods.

Retention of duplicated long-wavelength opsins in mosquito lineages by positive selection and differential expression

Background

Opsins are light sensitive receptors associated with visual processes. Insects typically possess opsins that are stimulated by ultraviolet, short and long wavelength (LW) radiation. Six putative LW-sensitive opsins predicted in the yellow fever mosquito, Aedes aegypti and malaria mosquito, Anopheles gambiae, and eight in the southern house mosquito, Culex quinquefasciatus, suggest gene expansion in the Family Culicidae (mosquitoes) relative to other insects. Here we report the first detailed molecular and evolutionary analyses of LW opsins in three mosquito vectors, with a goal to understanding the molecular basis of opsin-mediated visual processes that could be exploited for mosquito control.

Results

Time of divergence estimates suggest that the mosquito LW opsins originated from 18 or 19 duplication events between 166.9/197.5 to 1.07/0.94 million years ago (MY) and that these likely occurred following the predicted divergence of the lineages Anophelinae and Culicinae 145–226 MY. Fitmodel analyses identified nine amino acid residues in the LW opsins that may be under positive selection. Of these, eight amino acids occur in the N and C termini and are shared among all three species, and one residue in TMIII was unique to culicine species. Alignment of 5′ non-coding regions revealed potential Conserved Non-coding Sequences (CNS) and transcription factor binding sites (TFBS) in seven pairs of LW opsin paralogs.

Conclusions

Our analyses suggest opsin gene duplication and residues possibly associated with spectral tuning of LW-sensitive photoreceptors. We explore two mechanisms - positive selection and differential expression mediated by regulatory units in CNS – that may have contributed to the retention of LW opsin genes in Culicinae and Anophelinae. We discuss the evolution of mosquito LW opsins in the context of major Earth events and possible adaptation of mosquitoes to LW-dominated photo environments, and implications for mosquito control strategies based on disrupting vision-mediated behaviors.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-017-0910-6) contains supplementary material, which is available to authorized users.

Ancient and Recent Duplications Support Functional Diversity of Daphnia Opsins

Daphnia pulex has the largest known family of opsins, genes critical for photoreception and vision in animals. This diversity may be functionally redundant, arising from recent processes, or ancient duplications may have been preserved due to distinct functions and independent contributions to fitness. We analyzed opsins in D. pulex and its distant congener Daphnia magna. We identified 48 opsins in the D. pulex genome and 32 in D. magna. We inferred the complement of opsins in the last common ancestor of all Daphnia and evaluated the history of opsin duplication and loss. We further analyzed sequence variation to assess possible functional diversification among Daphnia opsins. Much of the opsin expansion occurred before the D. pulex-D. magna split more than 145 Mya, and both Daphnia lineages preserved most ancient opsins. More recent expansion occurred in pteropsins and long-wavelength visual opsins in both species, particularly D. pulex. Recent duplications were not random: the same ancestral genes duplicated independently in each modern species. Most ancient and some recent duplications involved differentiation at residues known to influence spectral tuning of visual opsins. Arthropsins show evidence of gene conversion between tandemly arrayed paralogs in functionally important domains. Intron-exon gene structure was generally conserved within clades inferred from sequences, although pteropsins showed substantial intron size variation. Overall, our analyses support the hypotheses that diverse opsins are maintained due to diverse functional roles in photoreception and vision, that functional diversification is both ancient and recent, and that multiple evolutionary processes have influenced different types of opsins.

Structural differences and differential expression among rhabdomeric opsins reveal functional change after gene duplication in the bay scallop, Argopecten irradians (Pectinidae)

Background

Opsins are the only class of proteins used for light perception in image-forming eyes. Gene duplication and subsequent functional divergence of opsins have played an important role in expanding photoreceptive capabilities of organisms by altering what wavelengths of light are absorbed by photoreceptors (spectral tuning). However, new opsin copies may also acquire novel function or subdivide ancestral functions through changes to temporal, spatial or the level of gene expression. Here, we test how opsin gene copies diversify in function and evolutionary fate by characterizing four rhabdomeric (G_q-protein coupled) opsins in the scallop, Argopecten irradians, identified from tissue-specific transcriptomes.

Results

Under a phylogenetic analysis, we recovered a pattern consistent with two rounds of duplication that generated the genetic diversity of scallop G_q-opsins. We found strong support for differential expression of paralogous G_q-opsins across ocular and extra-ocular photosensitive tissues, suggesting that scallop G_q-opsins are used in different biological contexts due to molecular alternations outside and within the protein-coding regions. Finally, we used available protein models to predict which amino acid residues interact with the light-absorbing chromophore. Variation in these residues suggests that the four G_q-opsin paralogs absorb different wavelengths of light.

Conclusions

Our results uncover novel genetic and functional diversity in the light-sensing structures of the scallop, demonstrating the complicated nature of G_q-opsin diversification after gene duplication. Our results highlight a change in the nearly ubiquitous shadow response in molluscs to a narrowed functional specificity for visual processes in the eyed scallop. Our findings provide a starting point to study how gene duplication may coincide with eye evolution, and more specifically, different ways neofunctionalization of G_q-opsins may occur.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0823-9) contains supplementary material, which is available to authorized users.

Ancient default activators of terminal photoreceptor differentiation in the pancrustacean compound eye: the homeodomain transcription factors Otd and Pph13

The origin of the Drosophila compound eye predates the ancestor of Pancrustacea, the arthropod clade that includes insects and Crustaceans. Recent studies in emerging model systems for pancrustacean development-the red flour beetle Tribolium castaneum and water flea Daphnia pulex-have begun to shed light on the evolutionary conservation of transcriptional mechanisms found for the Drosophila compound eye. Here, we discuss the conserved roles of the transcription factors Otd and Pph13, which complement each other in two terminal events of photoreceptor differentiation: rhabdomere morphogenesis and transcriptional default activation of opsin gene expression. The synthesis of these data allows us to frame an evolutionary developmental model of the earliest events that generated the wavelength-specific photoreceptor subtypes of pancrustacean compound eyes.

Sexual dimorphism in the compound eye of Heliconius erato: a nymphalid butterfly with at least five spectral classes of photoreceptor

Most butterfly families expand the number of spectrally-distinct photoreceptors in their compound eye by opsin gene duplications together with lateral filter pigments, however most nymphalid genera have limited diversity, with only three or four spectral types of photoreceptor. Here we examine the spatial pattern of opsin expression and photoreceptor spectral sensitivities in Heliconius erato, a nymphalid with duplicate ultraviolet opsin genes, UVRh1 and UVRh2. We find that the H. erato compound eye is sexually dimorphic. Females express the two UV opsin proteins in separate photoreceptors, but males do not express UVRh1. Intracellular recordings confirmed that females have three short wavelength-sensitive photoreceptors (λmax=356 nm, ∼390 nm and 470 nm), while males have two (λmax=390 nm and ∼470 nm). We also found two long wavelength-sensitive photoreceptors (green, λmax ∼555 nm, and red, λmax ∼600 nm), which express the same LW opsin. The red cell's shifted sensitivity is probably due to perirhabdomal filtering pigments. Sexual dimorphism of the UV-absorbing rhodopsins may reflect the females' need to discriminate conspecifics from co-mimics. Red-green color vision may be used to detect differences in red coloration on Heliconius wings, or for host-plant identification. Among nymphalids so far investigated, only H. erato is known to possess five spectral classes of photoreceptor; sexual dimorphism of the eye via suppression of one class of opsin (here UVRh1 in males) has not—to our knowledge—been reported in any animal.

Vision: two plus four equals six

Using two UV-sensitive visual pigments and the UV-filtering properties of four mycosporine-like amino acids, mantis shrimp create six spectrally distinct UV receptors. This is yet another example of the unique ways in which mantis shrimp have adapted to extract information from their visual world.

Extraordinary diversity of visual opsin genes in dragonflies

Dragonflies are colorful and large-eyed animals strongly dependent on color vision. Here we report an extraordinary large number of opsin genes in dragonflies and their characteristic spatiotemporal expression patterns. Exhaustive transcriptomic and genomic surveys of three dragonflies of the family Libellulidae consistently identified 20 opsin genes, consisting of 4 nonvisual opsin genes and 16 visual opsin genes of 1 UV, 5 short-wavelength (SW), and 10 long-wavelength (LW) type. Comprehensive transcriptomic survey of the other dragonflies representing an additional 10 families also identified as many as 15-33 opsin genes. Molecular phylogenetic analysis revealed dynamic multiplications and losses of the opsin genes in the course of evolution. In contrast to many SW and LW genes expressed in adults, only one SW gene and several LW genes were expressed in larvae, reflecting less visual dependence and LW-skewed light conditions for their lifestyle under water. In this context, notably, the sand-burrowing or pit-dwelling species tended to lack SW gene expression in larvae. In adult visual organs: (i) many SW genes and a few LW genes were expressed in the dorsal region of compound eyes, presumably for processing SW-skewed light from the sky; (ii) a few SW genes and many LW genes were expressed in the ventral region of compound eyes, probably for perceiving terrestrial objects; and (iii) expression of a specific LW gene was associated with ocelli. Our findings suggest that the stage- and region-specific expressions of the diverse opsin genes underlie the behavior, ecology, and adaptation of dragonflies.

Ultraviolet filters in stomatopod crustaceans: diversity, ecology, and evolution

Stomatopod crustaceans employ unique ultraviolet (UV) optical filters in order to tune the spectral sensitivities of their UV-sensitive photoreceptors. In the stomatopod species Neogonodactylus oerstedii, we previously found four filter types, produced by five distinct mycosporine-like amino acid pigments in the crystalline cones of their specialized midband ommatidial facets. This UV-spectral tuning array produces receptors with at least six distinct spectral sensitivities, despite expressing only two visual pigments. Here we present a broad survey of these UV filters across the stomatopod order, examining their spectral absorption properties in twenty-one species from seven families in four superfamilies. We found that UV filters are present in three of the four superfamilies, and evolutionary character reconstruction implies that at least one class of UV filter was present in the ancestor of all modern stomatopods. Additionally, postlarval stomatopods were observed to produce the UV filters simultaneously alongside development of the adult eye. The absorbance properties of the filters are consistent within a species; however, between species we found a great deal of diversity, both in the number of filters, and in their spectral absorbance characteristics. This diversity correlates with the habitat depth ranges of these species, suggesting that species living in shallow, UV-rich environments may tune their UV spectral sensitivities more aggressively. We also found additional, previously unrecognized UV filter types in the crystalline cones of the peripheral eye regions of some species, indicating the possibility for even greater stomatopod visual complexity than previously thought.

Phylogenetic and transcriptomic analyses reveal the evolution of bioluminescence and light detection in marine deep-sea shrimps of the family Oplophoridae (Crustacea: Decapoda)

Bioluminescence is essential to the survival of many organisms, particularly in the deep sea where light is limited. Shrimp of the family Oplophoridae exhibit a remarkable mechanism of bioluminescence in the form of a secretion used for predatory defense. Three of the ten genera possess an additional mode of bioluminescence in the form of light-emitting organs called photophores. Phylogenetic analyses can be useful for tracing the evolution of bioluminescence, however, the few studies that have attempted to reconcile the relationships within Oplophoridae have generated trees with low-resolution. We present the most comprehensive phylogeny of Oplophoridae to date, with 90% genera coverage using seven genes (mitochondrial and nuclear) across 30 oplophorid species. We use our resulting topology to trace the evolution of bioluminescence within Oplophoridae. Previous studies have suggested that oplophorid visual systems may be tuned to differentiate the separate modes of bioluminescence. While all oplophorid shrimp possess a visual pigment sensitive to blue-green light, only those bearing photophores have an additional pigment sensitive to near-ultraviolet light. We attempt to characterize opsins, visual pigment proteins essential to light detection, in two photophore-bearing species (Systellaspis debilis and Oplophorus gracilirostris) and make inferences regarding their function and evolutionary significance.

Out of the blue: the evolution of horizontally polarized signals in Haptosquilla (Crustacea, Stomatopoda, Protosquillidae)

The polarization of light provides information that is used by many animals for a number of different visually guided behaviours. Several marine species, such as stomatopod crustaceans and cephalopod molluscs, communicate using visual signals that contain polarized information, content that is often part of a more complex multi-dimensional visual signal. In this work, we investigate the evolution of polarized signals in species of Haptosquilla, a widespread genus of stomatopod, as well as related protosquillids. We present evidence for a pre-existing bias towards horizontally polarized signal content and demonstrate that the properties of the polarization vision system in these animals increase the signal-to-noise ratio of the signal. Combining these results with the increase in efficacy that polarization provides over intensity and hue in a shallow marine environment, we propose a joint framework for the evolution of the polarized form of these complex signals based on both efficacy-driven (proximate) and content-driven (ultimate) selection pressures.

Filtering and polychromatic vision in mantis shrimps: themes in visible and ultraviolet vision

Stomatopod crustaceans have the most complex and diverse assortment of retinal photoreceptors of any animals, with 16 functional classes. The receptor classes are subdivided into sets responsible for ultraviolet vision, spatial vision, colour vision and polarization vision. Many of these receptor classes are spectrally tuned by filtering pigments located in photoreceptors or overlying optical elements. At visible wavelengths, carotenoproteins or similar substances are packed into vesicles used either as serial, intrarhabdomal filters or lateral filters. A single retina may contain a diversity of these filtering pigments paired with specific photoreceptors, and the pigments used vary between and within species both taxonomically and ecologically. Ultraviolet-filtering pigments in the crystalline cones serve to tune ultraviolet vision in these animals as well, and some ultraviolet receptors themselves act as birefringent filters to enable circular polarization vision. Stomatopods have reached an evolutionary extreme in their use of filter mechanisms to tune photoreception to habitat and behaviour, allowing them to extend the spectral range of their vision both deeper into the ultraviolet and further into the red.

The evolution of complexity in the visual systems of stomatopods: insights from transcriptomics

Stomatopod crustaceans have complex visual systems containing up to 16 different spectral classes of photoreceptors, more than described for any other animal. A previous molecular study of this visual system focusing on the expression of opsin genes found many more transcripts than predicted on the basis of physiology, but was unable to fully document the expressed opsin genes responsible for this diversity. Furthermore, questions remain about how other components of phototransduction cascades are involved. This study continues prior investigations by examining the molecular function of stomatopods' visual systems using new whole eye 454 transcriptome datasets from two species, Hemisquilla californiensis and Pseudosquilla ciliata. These two species represent taxonomic diversity within the order Stomatopoda, as well as variations in the anatomy and physiology of the visual system. Using an evolutionary placement algorithm to annotate the transcriptome, we identified the presence of nine components of the stomatopods' G-protein-coupled receptor (GPCR) phototransduction cascade, including two visual arrestins, subunits of the heterotrimeric G-protein, phospholipase C, transient receptor potential channels, and opsin transcripts. The set of expressed transduction genes suggests that stomatopods utilize a Gq-mediated GPCR-signaling cascade. The most notable difference in expression between the phototransduction cascades of the two species was the number of opsin contigs recovered, with 18 contigs found in retinas of H. californiensis, and 49 contigs in those of P. ciliata. Based on phylogenetic placement and fragment overlap, these contigs were estimated to represent 14 and 33 expressed transcripts, respectively. These data expand the known opsin diversity in stomatopods to clades of arthropod opsins that are sensitive to short wavelengths and ultraviolet wavelengths and confirm the results of previous studies recovering more opsin transcripts than spectrally distinct types of photoreceptors. Many of the recovered transcripts were phylogenetically placed in an evolutionary clade of crustacean opsin sequences that is rapidly expanding as the visual systems from more species are investigated. We discuss these results in relation to the emerging pattern, particularly in crustacean visual systems, of the expression of multiple opsin transcripts in photoreceptors of the same spectral class, and even in single photoreceptor cells.

Expression dynamics and protein localization of rhabdomeric opsins in Platynereis larvae

The larval stages of polychaete annelids are often responsive to light and can possess one to six eyes. The early trochophore larvae of the errant annelid Platynereis dumerilii have a single pair of ventral eyespots, whereas older nectochaete larvae have an additional two pairs of dorsal eyes that will develop into the adult eyes. Early Platynereis trochophores show robust positive phototaxis starting on the first day of development. Even though the mechanism of phototaxis in Platynereis early trochophore larvae is well understood, no photopigment (opsin) expression has yet been described in this stage. In late trochophore larvae, a rhabdomeric-type opsin, r-opsin1, expressed in both the eyespots and the adult eyes has already been reported. Here, we identify another Platynereis rhabdomeric opsin, r-opsin3, that is expressed in a single photoreceptor in the eyespots in early trochophores, suggesting that it mediates early larval phototaxis. We also show that r-opsin1 and r-opsin3 are expressed in adjacent photoreceptor cells in the eyespots in later stages, indicating that a second eyespot-photoreceptor differentiates in late trochophore larvae. Using serial transmission electron microscopy (TEM), we identified and reconstructed both photoreceptors and a pigment cell in the late larval eyespot. We also characterized opsin expression in the adult eyes and found that the two opsins co-express there in several photoreceptor cells. Using antibodies recognizing r-opsin1 and r-opsin3 proteins, we demonstrate that both opsins localize to the rhabdomere in all six eyes. In addition, we found that r-opsin1 mRNA is localized to, and translated in, the projections of the adult eyes. The specific changes we describe in opsin transcription and translation and in the cellular complement suggest that the six larval eyes undergo spectral and functional maturation during the early planktonic phase of the Platynereis life cycle.

Parallel reduction in expression, but no loss of functional constraint, in two opsin paralogs within cave populations of Gammarus minus (Crustacea: Amphipoda)

Background

Gammarus minus, a freshwater amphipod living in the cave and surface streams in the eastern USA, is a premier candidate for studying the evolution of troglomorphic traits such as pigmentation loss, elongated appendages, and reduced eyes. In G. minus, multiple pairs of genetically related, physically proximate cave and surface populations exist which exhibit a high degree of intraspecific morphological divergence. The morphology, ecology, and genetic structure of these sister populations are well characterized, yet the genetic basis of their morphological divergence remains unknown.

Results

We used degenerate PCR primers designed to amplify opsin genes within the subphylum Crustacea and discovered two distinct opsin paralogs (average inter-paralog protein divergence ≈ 20%) in the genome of three independently derived pairs of G. minus cave and surface populations. Both opsin paralogs were found to be related to other crustacean middle wavelength sensitive opsins. Low levels of nucleotide sequence variation (< 1% within populations) were detected in both opsin genes, regardless of habitat, and dN/dS ratios did not indicate a relaxation of functional constraint in the cave populations with reduced or absent eyes. Maximum likelihood analyses using codon-based models also did not detect a relaxation of functional constraint in the cave lineages. We quantified expression level of both opsin genes and found that the expression of both paralogs was significantly reduced in all three cave populations relative to their sister surface populations.

Conclusions

The concordantly lowered expression level of both opsin genes in cave populations of G. minus compared to sister surface populations, combined with evidence for persistent purifying selection in the cave populations, is consistent with an unspecified pleiotropic function of opsin proteins. Our results indicate that phototransduction proteins such as opsins may have retained their function in cave-adapted organisms because they may play a pleiotropic role in other important processes that are unrelated to vision.

Opsin evolution and expression in arthropod compound eyes and ocelli: insights from the cricket Gryllus bimaculatus

Background

Opsins are key proteins in animal photoreception. Together with a light-sensitive group, the chromophore, they form visual pigments which initiate the visual transduction cascade when photoactivated. The spectral absorption properties of visual pigments are mainly determined by their opsins, and thus opsins are crucial for understanding the adaptations of animal eyes. Studies on the phylogeny and expression pattern of opsins have received considerable attention, but our knowledge about insect visual opsins is still limited. Up to now, researchers have focused on holometabolous insects, while general conclusions require sampling from a broader range of taxa. We have therefore investigated visual opsins in the ocelli and compound eyes of the two-spotted cricket Gryllus bimaculatus, a hemimetabolous insect.

Results

Phylogenetic analyses place all identified cricket sequences within the three main visual opsin clades of insects. We assign three of these opsins to visual pigments found in the compound eyes with peak absorbances in the green (515 nm), blue (445 nm) and UV (332 nm) spectral range. Their expression pattern divides the retina into distinct regions: (1) the polarization-sensitive dorsal rim area with blue- and UV-opsin, (2) a newly-discovered ventral band of ommatidia with blue- and green-opsin and (3) the remainder of the compound eye with UV- and green-opsin. In addition, we provide evidence for two ocellar photopigments with peak absorbances in the green (511 nm) and UV (350 nm) spectral range, and with opsins that differ from those expressed in the compound eyes.

Conclusions

Our data show that cricket eyes are spectrally more specialized than has previously been assumed, suggesting that similar adaptations in other insect species might have been overlooked. The arrangement of spectral receptor types within some ommatidia of the cricket compound eyes differs from the generally accepted pattern found in holometabolous insect taxa and awaits a functional explanation. From the opsin phylogeny, we conclude that gene duplications, which permitted differential opsin expression in insect ocelli and compound eyes, occurred independently in several insect lineages and are recent compared to the origin of the eyes themselves.

The Spalt family transcription factor Sall3 regulates the development of cone photoreceptors and retinal horizontal interneurons

The mammalian retina is a tractable model system for analyzing transcriptional networks that guide neural development. Spalt family zinc-finger transcription factors play a crucial role in photoreceptor specification in Drosophila, but their role in mammalian retinal development has not been investigated. In this study, we show that that the spalt homolog Sall3 is prominently expressed in developing cone photoreceptors and horizontal interneurons of the mouse retina and in a subset of cone bipolar cells. We find that Sall3 is both necessary and sufficient to activate the expression of multiple cone-specific genes, and that Sall3 protein is selectively bound to the promoter regions of these genes. Notably, Sall3 shows more prominent expression in short wavelength-sensitive cones than in medium wavelength-sensitive cones, and that Sall3 selectively activates expression of the short but not the medium wavelength-sensitive cone opsin gene. We further observe that Sall3 regulates the differentiation of horizontal interneurons, which form direct synaptic contacts with cone photoreceptors. Loss of function of Sall3 eliminates expression of the horizontal cell-specific transcription factor Lhx1, resulting in a radial displacement of horizontal cells that partially phenocopies the loss of function of Lhx1. These findings not only demonstrate that Spalt family transcription factors play a conserved role in regulating photoreceptor development in insects and mammals, but also identify Sall3 as a factor that regulates terminal differentiation of both cone photoreceptors and their postsynaptic partners.

The molecular basis of mechanisms underlying polarization vision

The underlying mechanisms of polarization sensitivity (PS) have long remained elusive. For rhabdomeric photoreceptors, questions remain over the high levels of PS measured experimentally. In ciliary photoreceptors, and specifically cones, little direct evidence supports any type of mechanism. In order to promote a greater interest in these fundamental aspects of polarization vision, we examined a varied collection of studies linking membrane biochemistry, protein-protein interactions, molecular ordering and membrane phase behaviour. While initially these studies may seem unrelated to polarization vision, a common narrative emerges. A surprising amount of evidence exists demonstrating the importance of protein-protein interactions in both rhabdomeric and ciliary photoreceptors, indicating the possible long-range ordering of the opsin protein for increased PS. Moreover, we extend this direction by considering how such protein paracrystalline organization arises in all cell types from controlled membrane phase behaviour and propose a universal pathway for PS to occur in both rhabdomeric and cone photoreceptors.

Opsin co-expression in Limulus photoreceptors: differential regulation by light and a circadian clock

A long-standing concept in vision science has held that a single photoreceptor expresses a single type of opsin, the protein component of visual pigment. However, the number of examples in the literature of photoreceptors from vertebrates and invertebrates that break this rule is increasing. Here, we describe a newly discovered Limulus opsin, Limulus opsin5, which is significantly different from previously characterized Limulus opsins, opsins1 and 2. We show that opsin5 is co-expressed with opsins1 and 2 in Limulus lateral and ventral eye photoreceptors and provide the first evidence that the expression of co-expressed opsins can be differentially regulated. We show that the relative levels of opsin5 and opsin1 and 2 in the rhabdom change with a diurnal rhythm and that their relative levels are also influenced by the animal's central circadian clock. An analysis of the sequence of opsin5 suggests it is sensitive to visible light (400-700 nm) but that its spectral properties may be different from that of opsins1 and 2. Changes in the relative levels of these opsins may underlie some of the dramatic day-night changes in Limulus photoreceptor function and may produce a diurnal change in their spectral sensitivity.

Evolution of anatomical and physiological specialization in the compound eyes of stomatopod crustaceans

Stomatopod crustaceans have complex and diverse visual systems. Among their many unique features are a specialized ommatidial region (the midband) that enables the eye to have multiple overlapping visual fields, as well as sets of spectral filters that are intercalated at two levels between tiers of photoreceptors involved in polychromatic color vision. Although the physiology and visual function of stomatopod eyes have been studied for many years, how these unique visual features originated and diversified is still an open question. In order to investigate how stomatopods have attained the current complexity in visual function, we have combined physiological and morphological information (e.g. number of midband rows, number of filters in the retina, and the spectral properties of filters) with new phylogenetic analyses of relationships among species based on nucleotide sequence data from two nuclear (18S and 28S rDNA) and two mitochondrial [16S and cytochrome oxidase I (COI)] genes. Based on our recovered phylogenetic relationships among species, we propose two new superfamilies within the Stomatopoda: Hemisquilloidea and Pseudosquillodea. Maximum likelihood ancestral state reconstructions indicate that ancestral stomatopod eyes contained six midband rows and four intrarhabdomal filters, illustrating that the visual physiological complexity originated early in stomatopod evolutionary history. While the two distal filters contain conservative sets of filter pigments, the proximal filters show more spectral diversity in filter types, particularly in midband row 2, and are involved in tuning the color vision system to the photic environment. In particular, a set of related gonodactyloid families (Gonodactylidae, Protosquillidae, Takuidae) inhabiting shallow, brightly lit coral reef waters contain the largest diversity of filter pigments, which are spectrally placed relative to the underlying photoreceptors to take advantage of the broad spectrum of light available in the environment.

Allelic variation in Malawi cichlid opsins: a tale of two genera

The role of sequence variation in the spectral tuning of color vision is well established in many systems. This includes the cichlids of Lake Victoria where sequence variation has been linked to environmental light gradients and speciation. The cichlids of Lake Malawi are a similar model for visual evolution, but the role of gene sequence variation in visual tuning between closely related species is unknown. This work describes such variation in multiple species of two rock-dwelling genera: Metriaclima and Labidochromis. Genomic DNA for seven cone opsin genes was sequenced and the structure of the opsin proteins was inferred. Retinal binding pocket polymorphisms were identified and compared to available data regarding spectral absorbance shifts. Sequence variation with known or potential effects on absorbance spectra were found in four genes: SWS1 (UV sensitive), SWS2B (violet sensitive), RH2Abeta (green sensitive), and LWS (red sensitive). Functional variation was distributed such that each genus had both a variable short-wavelength and long-wavelength sensitive opsin. This suggests spectral tuning is important at the margins of the cichlid visual spectrum. Further, there are two SWS1 opsin alleles that differ in sensitivity by 10 nm and are >2 MY divergent. One of these occurs in a haplotype block >1 kb. Potential haplotype blocks were found around the RH2 opsin loci. These data suggest that molecular diversification has resulted in functionally unique alleles and changes to the visual system. These data also suggest that opsin sequence variation tunes spectral sensitivities between closely related species and that the specific regions of spectral tuning are genus-specific.

Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach

BACKGROUND

Duplication and divergence of genes and genetic networks is hypothesized to be a major driver of the evolution of complexity and novel features. Here, we examine the history of genes and genetic networks in the context of eye evolution by using new approaches to understand patterns of gene duplication during the evolution of metazoan genomes. We hypothesize that 1) genes involved in eye development and phototransduction have duplicated and are retained at higher rates in animal clades that possess more distinct types of optical design; and 2) genes with functional relationships were duplicated and lost together, thereby preserving genetic networks. To test these hypotheses, we examine the rates and patterns of gene duplication and loss evident in 19 metazoan genomes, including that of Daphnia pulex - the first completely sequenced crustacean genome. This is of particular interest because the pancrustaceans (hexapods+crustaceans) have more optical designs than any other major clade of animals, allowing us to test specifically whether the high amount of disparity in pancrustacean eyes is correlated with a higher rate of duplication and retention of vision genes.

RESULTS

Using protein predictions from 19 metazoan whole-genome projects, we found all members of 23 gene families known to be involved in eye development or phototransduction and deduced their phylogenetic relationships. This allowed us to estimate the number and timing of gene duplication and loss events in these gene families during animal evolution. When comparing duplication/retention rates of these genes, we found that the rate was significantly higher in pancrustaceans than in either vertebrates or non-pancrustacean protostomes. Comparing patterns of co-duplication across Metazoa showed that while these eye-genes co-duplicate at a significantly higher rate than those within a randomly shuffled matrix, many genes with known functional relationships in model organisms did not co-duplicate more often than expected by chance.

CONCLUSIONS

Overall, and when accounting for factors such as differential rates of whole-genome duplication in different groups, our results are broadly consistent with the hypothesis that genes involved in eye development and phototransduction duplicate at a higher rate in Pancrustacea, the group with the greatest variety of optical designs. The result that these genes have a significantly high number of co-duplications and co-losses could be influenced by shared functions or other unstudied factors such as synteny. Since we did not observe co-duplication/co-loss of genes for all known functional modules (e.g. specific regulatory networks), the interactions among suites of known co-functioning genes (modules) may be plastic at the temporal scale of analysis performed here. Other factors in addition to gene duplication - such as cis-regulation, heterotopy, and co-option - are also likely to be strong factors in the diversification of eye types.