Comparative mitogenomic analysis of subterranean and surface amphipods (Crustacea, Amphipoda) with special reference to the family Crangonyctidae.

Mitochondrial genomes play important roles in studying genome evolution, phylogenetic analyses, and species identification. Amphipods (Class Malacostraca, Order Amphipoda) are one of the most ecologically diverse crustacean groups occurring in a diverse array of aquatic and terrestrial environments globally, from freshwater streams and lakes to groundwater aquifers and the deep sea, but we have a limited understanding of how habitat influences the molecular evolution of mitochondrial energy metabolism. Subterranean amphipods likely experience different evolutionary pressures on energy management compared to surface-dwelling taxa that generally encounter higher levels of predation and energy resources and live in more variable environments. In this study, we compared the mitogenomes, including the 13 protein-coding genes involved in the oxidative phosphorylation (OXPHOS) pathway, of surface and subterranean amphipods to uncover potentially different molecular signals of energy metabolism between surface and subterranean environments in this diverse crustacean group. We compared base composition, codon usage, gene order rearrangement, conducted comparative mitogenomic and phylogenomic analyses, and examined evolutionary signals of 35 amphipod mitogenomes representing 13 families, with an emphasis on Crangonyctidae. Mitogenome size, AT content, GC-skew, gene order, uncommon start codons, location of putative control region (CR), length of rrnL and intergenic spacers differed between surface and subterranean amphipods. Among crangonyctid amphipods, the spring-dwelling Crangonyx forbesi exhibited a unique gene order, a long nad5 locus, longer rrnL and rrnS loci, and unconventional start codons. Evidence of directional selection was detected in several protein-encoding genes of the OXPHOS pathway in the mitogenomes of surface amphipods, while a signal of purifying selection was more prominent in subterranean species, which is consistent with the hypothesis that the mitogenome of surface-adapted species has evolved in response to a more energy demanding environment compared to subterranean amphipods. Overall, gene order, locations of non-coding regions, and base-substitution rates points to habitat as an important factor influencing the evolution of amphipod mitogenomes.

Molecular Evolution of Malacostracan Short Wavelength Sensitive Opsins.

Investigations of the molecular mechanisms behind detection of short, and particularly ultraviolet, wavelengths in arthropods have relied heavily on studies from insects due to the relative ease of heterologous expression of modified opsin proteins in model organisms like Drosophila. However, species outside of the Insecta can provide information on mechanisms for spectral tuning as well as the evolutionary history of pancrustacean visual pigments. Here we investigate the basis of spectral tuning in malacostracan short wavelength sensitive (SWS) opsins using phylogenetic comparative methods. Tuning sites that may be responsible for the difference between ultraviolet (UV) and violet visual pigment absorbance in the Malacostraca are identified, and the idea that an amino acid polymorphism at a single site is responsible for this shift is shown to be unlikely. Instead, we suggest that this change in absorbance is accomplished through multiple amino acid substitutions. On the basis of our findings, we conducted further surveys to identify spectral tuning mechanisms in the order Stomatopoda where duplication of UV opsins has occurred. Ancestral state reconstructions of stomatopod opsins from two main clades provide insight into the amino acid changes that lead to differing absorption by the visual pigments they form, and likely contribute the basis for the wide array of UV spectral sensitivities found in this order.

Physiological and behavioral evidence for multiple spectral channels in the larval stomatopod visual system.

Larval stomatopods have generally been described as having a typical larval crustacean compound eye, which lacks the visual pigment diversity and morphological specializations of the well-studied stomatopod adult eye. However, recent work has suggested that larval stomatopod eyes are more complex than previously described. In this study, we provide physiological and behavioral evidence of at least three distinct photoreceptor classes in three species of larval stomatopods: Gonodactylellus n. sp., Gonodactylaceus falcatus and Pullosquilla n. sp. First, electroretinogram recordings were used to measure the spectral sensitivity of each species. Evidence for at least three spectral classes were identified in each: an ultraviolet, peaking at 340-376 nm; a short-wavelength blue, peaking at 455-464 nm; and a long-wavelength orange, peaking at 576-602 nm. Next, the behavioral response to light was investigated. We found that each species demonstrated positive phototactic responses to monochromatic stimuli across the UV-visible spectrum. In wavelength preference trials, distinct preferences among species were identified when different colored light stimuli were presented simultaneously. All species displayed a strong response to the UV stimulus, as well as responses to blue and orange stimuli, although at different response strengths, but no response to green. The results of this study demonstrate that larval stomatopods not only have multiple physiologically active spectral classes but they also display clear and distinct responses to wavelengths across the spectrum. We propose that the spectral classes demonstrated in each are related to visually guided ecological tasks of the larvae, which may differ between species.

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.

Ultraviolet vision in larval Neogonodactylus oerstedii.

Stomatopod crustaceans have among the most complex eyes in the animal kingdom, with up to 12 different color detection channels. The capabilities of these unique eyes include photoreception of ultraviolet (UV) wavelengths (<400 nm). UV vision has been well characterized in adult stomatopods but has not been previously demonstrated in the comparatively simpler larval eye. Larval stomatopod eyes are developmentally distinct from their adult counterpart and have been described as lacking the visual pigment diversity and morphological specializations found in adult eyes. However, recent studies have provided evidence that larval stomatopod eyes are more complex than previously thought and warrant closer investigation. Using electroretinogram recordings in live animals we found physiological evidence of blue- and UV-sensitive photoreceptors in larvae of the Caribbean stomatopod species Neogonodactylus oerstedii. Transcriptomes of individual larvae were used to identify the expression of three distinct UV opsin mRNA transcripts, which may indicate the presence of multiple UV spectral channels. This is the first paper to document UV vision in any larval stomatopod, expanding our understanding of the importance of UV sensitivity in plankton. Larval stomatopod eyes are more complex and more similar to adult eyes than expected, showing previously uncharacterized molecular diversity and physiological functions.

Scaling and development of elastic mechanisms: the tiny strikes of larval mantis shrimp.

Latch-mediated spring actuation (LaMSA) is used by small organisms to produce high acceleration movements. Mathematical models predict that acceleration increases as LaMSA systems decrease in size. Adult mantis shrimp use a LaMSA mechanism in their raptorial appendages to produce extremely fast strikes. Until now, however, it was unclear whether mantis shrimp at earlier life-history stages also strike using elastic recoil and latch mediation. We tested whether larval mantis shrimp (Gonodactylaceus falcatus) use LaMSA and, because of their smaller size, achieve higher strike accelerations than adults of other mantis shrimp species. Based on microscopy and kinematic analyses, we discovered that larval G. falcatus possess the components of, and actively use, LaMSA during their fourth larval stage, which is the stage of development when larvae begin feeding. Larvae performed strikes at high acceleration and speed (mean: 4.133×105 rad s-2, 292.7 rad s-1; 12 individuals, 25 strikes), which are of the same order of magnitude as for adults - even though adult appendages are up to two orders of magnitude longer. Larval strike speed (mean: 0.385 m s-1) exceeded the maximum swimming speed of similarly sized organisms from other species by several orders of magnitude. These findings establish the developmental timing and scaling of the mantis shrimp LaMSA mechanism and provide insights into the kinematic consequences of scaling limits in tiny elastic mechanisms.

Evolution under pressure and the adaptation of visual pigment compressibility in deep-sea environments.

Understanding the link between how proteins function in animals that live in extreme environments and selection on specific properties of amino acids has proved extremely challenging. Here we present the discovery of how the compressibility of opsin proteins in two evolutionarily distinct animal groups, teleosts and cephalopods, appears to be adapted to the high-pressure environment of the deep-sea. We report how in both groups, opsins in deeper living species are calculated to be less compressible. This is largely due to a common set of amino acid sites (bovRH# 159, 196, 213, 275) undergoing positive destabilizing selection in six of the twelve amino acid physiochemical properties that determine protein compressibility. This suggests a common evolutionary mechanism to reduce the adiabatic compressibility of opsin proteins. Intriguingly, the sites under selection are on the proteins' outer faces at locations known to be involved in opsin-opsin dimer interactions.

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 21 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.

Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms.

BACKGROUND: Tools for high throughput sequencing and de novo assembly make the analysis of transcriptomes (i.e. the suite of genes expressed in a tissue) feasible for almost any organism. Yet a challenge for biologists is that it can be difficult to assign identities to gene sequences, especially from non-model organisms. Phylogenetic analyses are one useful method for assigning identities to these sequences, but such methods tend to be time-consuming because of the need to re-calculate trees for every gene of interest and each time a new data set is analyzed. In response, we employed existing tools for phylogenetic analysis to produce a computationally efficient, tree-based approach for annotating transcriptomes or new genomes that we term Phylogenetically-Informed Annotation (PIA), which places uncharacterized genes into pre-calculated phylogenies of gene families. RESULTS: We generated maximum likelihood trees for 109 genes from a Light Interaction Toolkit (LIT), a collection of genes that underlie the function or development of light-interacting structures in metazoans. To do so, we searched protein sequences predicted from 29 fully-sequenced genomes and built trees using tools for phylogenetic analysis in the Osiris package of Galaxy (an open-source workflow management system). Next, to rapidly annotate transcriptomes from organisms that lack sequenced genomes, we repurposed a maximum likelihood-based Evolutionary Placement Algorithm (implemented in RAxML) to place sequences of potential LIT genes on to our pre-calculated gene trees. Finally, we implemented PIA in Galaxy and used it to search for LIT genes in 28 newly-sequenced transcriptomes from the light-interacting tissues of a range of cephalopod mollusks, arthropods, and cubozoan cnidarians. Our new trees for LIT genes are available on the Bitbucket public repository ( http://bitbucket.org/osiris_phylogenetics/pia/ ) and we demonstrate PIA on a publicly-accessible web server ( http://galaxy-dev.cnsi.ucsb.edu/pia/ ). CONCLUSIONS: Our new trees for LIT genes will be a valuable resource for researchers studying the evolution of eyes or other light-interacting structures. We also introduce PIA, a high throughput method for using phylogenetic relationships to identify LIT genes in transcriptomes from non-model organisms. With simple modifications, our methods may be used to search for different sets of genes or to annotate data sets from taxa outside of Metazoa.

Characterization of visual pigments, oil droplets, lens and cornea in the whooping crane Grus americana.

Vision has been investigated in many species of birds, but few studies have considered the visual systems of large birds and the particular implications of large eyes and long-life spans on visual system capabilities. To address these issues we investigated the visual system of the whooping crane Grus americana (Gruiformes, Gruidae), which is one of only two North American crane species. It is a large, long-lived bird in which UV sensitivity might be reduced by chromatic aberration and entrance of UV radiation into the eye could be detrimental to retinal tissues. To investigate the whooping crane visual system we used microspectrophotometry to determine the absorbance spectra of retinal oil droplets and to investigate whether the ocular media (i.e. the lens and cornea) absorb UV radiation. In vitro expression and reconstitution was used to determine the absorbance spectra of rod and cone visual pigments. The rod visual pigments had wavelengths of peak absorbance (λmax) at 500 nm, whereas the cone visual pigment λmax values were determined to be 404 nm (SWS1), 450 nm (SWS2), 499 nm (RH2) and 561 nm (LWS), similar to other characterized bird visual pigment absorbance values. The oil droplet cut-off wavelength (λcut) values similarly fell within ranges recorded in other avian species: 576 nm (R-type), 522 nm (Y-type), 506 nm (P-type) and 448 nm (C-type). We confirm that G. americana has a violet-sensitive visual system; however, as a consequence of the λmax of the SWS1 visual pigment (404 nm), it might also have some UV sensitivity.

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.

Localization of multiple opsins in ocular and non-ocular tissues of deep-sea shrimps and the first evidence of co-localization in a rhabdomeric R8 cell (Caridea: Oplophoroidea).

Bioluminescence is a prevalent phenomenon throughout the marine realm and is often the dominant source of light in mesophotic and aphotic depth horizons. Shrimp belonging to the superfamily Oplophoroidea are mesopelagic, perform diel vertical migration, and secrete a bright burst of bioluminescent mucous when threatened. Species in the family Oplophoridae also possess cuticular light-emitting photophores presumably for camouflage via counter-illumination. Many species within the superfamily express a single visual pigment in the retina, consistent with most other large-bodied mesopelagic crustaceans studied to date. Photophore-bearing species have an expanded visual opsin repertoire and dual-sensitivity visual systems, as evidenced by transcriptomes and electroretinograms. In this study, we used immunohistochemistry to describe opsin protein localization in the retinas of four species of Oplophoroidea and non-ocular tissues of Janicella spinicauda. Our results show that Acanthephyra purpurea (Acanthephyridae) retinas possess LWS-only photoreceptors, consistent with the singular peak sensitivity previously reported. Oplophoridae retinas contain two opsin clades (LWS and MWS) consistent with dual-sensitivity. Oplophorus gracilirostris and Systellaspis debilis have LWS in the proximal rhabdom (R1-7 cells) and MWS2 localized in the distal rhabdom (R8 cell). Surprisingly, Janicella spinicauda has LWS in the proximal rhabdom (R1-7) and co-localized MWS1 and MWS2 opsin paralogs in the distal rhabdom, providing the first evidence of co-localization of opsins in a crustacean rhabdomeric R8 cell. Furthermore, opsins were found in multiple non-ocular tissues of J. spinicauda, including nerve, tendon, and photophore. These combined data demonstrate evolutionary novelty and opsin duplication within Oplophoridae, with implications for visual ecology, evolution in mesophotic environments, and a mechanistic understanding of adaptive counter-illumination using photophore bioluminescence.

Secondary not subordinate: Opsin localization suggests possibility for color sensitivity in salticid secondary eyes.

The principal eyes of jumping spiders (Salticidae) integrate a dual-lens system, a tiered retinal matrix with multiple photoreceptor classes and muscular control of retinal movements to form high resolution images, extract color information, and dynamically evaluate visual scenes. While much work has been done to characterize these more complex principal anterior eyes, little work has investigated the three other pairs of simpler secondary eyes: the anterior lateral eye pair and two posterior (lateral and median) pairs of eyes. We investigated the opsin protein component of visual pigments in the eyes of three species of salticid using transcriptomics and immunohistochemistry. Based on characterization and localization of a set of three conserved opsins (Rh1 - green sensitive, Rh2 - blue sensitive, and Rh3 - ultraviolet sensitive) we have identified potential photoreceptors for blue light detection in the eyes of two out of three species: Menemerus bivittatus (Chrysillini) and Habrocestum africanum (Hasarinii). Additionally, the photoreceptor diversity of the secondary eyes exhibits more variation than previous estimates, particularly for the small, posterior median eyes previously considered vestigial in some species. In all three species investigated the lateral eyes were dominated by green-sensitive visual pigments (RH1 opsins), while the posterior median retinas were dominated by opsins forming short-wavelength sensitive visual pigments (e.g. RH2 and/or RH3/RH4). There was also variation among secondary eye types and among species in the distribution of opsins in retinal photoreceptors, particularly for the putatively blue-sensitive visual pigment formed from RH2. Our findings suggest secondary eyes have the potential for color vision, with observed differences between species likely associated with different ecologies and visual tasks.

Morphological and molecular description of the late-stage larvae of Alima Leach, 1817 (Crustacea: Stomatopoda) from Lizard Island, Australia.

Alima pacifica and A. orientalis are stomatopods commonly found at Lizard Island, Great Barrier Reef, Australia. There are currently no descriptions that link the larvae to the adult morphotype despite the frequent occurrence of the last larval stage of these two species. We used DNA barcoding of the cytochrome oxidase I (COI) gene to link the last stage larvae of A. pacifica and A. orientalis to the respective adult morphotype. Detailed morphological descriptions of the late larva of each species are provided and compared to other described last-stage Alima larvae. These data support previous studies that suggest paraphyly of the genus Alima.

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.

Genomic Comparisons Reveal Selection Pressure and Functional Variation Between Nutritional Endosymbionts of Cave-Adapted and Epigean Hawaiian Planthoppers.

Planthoppers in the family Cixiidae (Hemiptera: Auchenorrhyncha: Fulgoromorpha) harbor a diverse set of obligate bacterial endosymbionts that provision essential amino acids and vitamins that are missing from their plant-sap diet. "Candidatus Sulcia muelleri" and "Ca. Vidania fulgoroidea" have been associated with cixiid planthoppers since their origin within the Auchenorrhyncha, whereas "Ca. Purcelliella pentastirinorum" is a more recent endosymbiotic acquisition. Hawaiian cixiid planthoppers occupy diverse habitats including lava tube caves and shrubby surface landscapes, which offer different nutritional resources and environmental constraints. Genomic studies have focused on understanding the nutritional provisioning roles of cixiid endosymbionts more broadly, yet it is still unclear how selection pressures on endosymbiont genes might differ between cixiid host species inhabiting such diverse landscapes, or how variation in selection might impact symbiont evolution. In this study, we sequenced the genomes of Sulcia, Vidania, and Purcelliella isolated from both surface and cave-adapted planthopper hosts from the genus Oliarus. We found that nutritional biosynthesis genes were conserved in Sulcia and Vidania genomes in inter- and intra-host species comparisons. In contrast, Purcelliella genomes retain different essential nutritional biosynthesis genes between surface- and cave-adapted planthopper species. Finally, we see the variation in selection pressures on symbiont genes both within and between host species, suggesting that strong coevolution between host and endosymbiont is associated with different patterns of molecular evolution on a fine scale that may be associated with the host diet.

Shedding new light on opsin evolution.

Opsin proteins are essential molecules in mediating the ability of animals to detect and use light for diverse biological functions. Therefore, understanding the evolutionary history of opsins is key to understanding the evolution of light detection and photoreception in animals. As genomic data have appeared and rapidly expanded in quantity, it has become possible to analyse opsins that functionally and histologically are less well characterized, and thus to examine opsin evolution strictly from a genetic perspective. We have incorporated these new data into a large-scale, genome-based analysis of opsin evolution. We use an extensive phylogeny of currently known opsin sequence diversity as a foundation for examining the evolutionary distributions of key functional features within the opsin clade. This new analysis illustrates the lability of opsin protein-expression patterns, site-specific functionality (i.e. counterion position) and G-protein binding interactions. Further, it demonstrates the limitations of current model organisms, and highlights the need for further characterization of many of the opsin sequence groups with unknown function.

The Gluopsins: Opsins without the Retinal Binding Lysine.

Opsins allow us to see. They are G-protein-coupled receptors and bind as ligand retinal, which is bound covalently to a lysine in the seventh transmembrane domain. This makes opsins light-sensitive. The lysine is so conserved that it is used to define a sequence as an opsin and thus phylogenetic opsin reconstructions discard any sequence without it. However, recently, opsins were found that function not only as photoreceptors but also as chemoreceptors. For chemoreception, the lysine is not needed. Therefore, we wondered: Do opsins exists that have lost this lysine during evolution? To find such opsins, we built an automatic pipeline for reconstructing a large-scale opsin phylogeny. The pipeline compiles and aligns sequences from public sources, reconstructs the phylogeny, prunes rogue sequences, and visualizes the resulting tree. Our final opsin phylogeny is the largest to date with 4956 opsins. Among them is a clade of 33 opsins that have the lysine replaced by glutamic acid. Thus, we call them gluopsins. The gluopsins are mainly dragonfly and butterfly opsins, closely related to the RGR-opsins and the retinochromes. Like those, they have a derived NPxxY motif. However, what their particular function is, remains to be seen.

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'.