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 (Gq-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 Gq-opsins. We found strong support for differential expression of paralogous Gq-opsins across ocular and extra-ocular photosensitive tissues, suggesting that scallop Gq-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 Gq-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 Gq-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 Gq-opsins may occur

Review

Detecting the direction of image motion is a fundamental component of visual computation, essential for survival of the animal. However, at the level of individual photoreceptors, the direction in which the image is shifting is not explicitly represented. Rather, directional motion information needs to be extracted from the photoreceptor array by comparing the signals of neighboring units over time. The exact nature of this process as implemented in the visual system of the fruit fly Drosophila melanogaster has been studied in great detail, and much progress has recently been made in determining the neural circuits giving rise to directional motion information. The results reveal the following: (1) motion information is computed in parallel ON and OFF pathways. (2) Within each pathway, T4 (ON) and T5 (OFF) cells are the first neurons to represent the direction of motion. Four subtypes of T4 and T5 cells exist, each sensitive to one of the four cardinal directions. (3) The core process of direction selectivity as implemented on the dendrites of T4 and T5 cells comprises both an enhancement of signals for motion along their preferred direction as well as a suppression of signals for motion along the opposite direction. This combined strategy ensures a high degree of direction selectivity right at the first stage where the direction of motion is computed. (4) At the subsequent processing stage, tangential cells spatially integrate direct excitation from ON and OFF-selective T4 and T5 cells and indirect inhibition from bi-stratified LPi cells activated by neighboring T4/T5 terminals, thus generating flow-field-selective responses

Photoreception in Ambulacraria: A Comprehensive Approach

Non-directional photoreceptors are the evolutionary precursors of all animal eyes; they enable the monitoring of ambient light intensity and regulate feeding, movement and reproduction. While the first animals were most likely benthic, they evolved larval stages very early on, thus conquering a new ecological niche: the pelagic. In this realm, the evolutionary pressure to prey but not be preyed upon became stronger. This implied strong selection for better sensory systems, including photoreception. How were the photoreceptor systems of the earliest primary larvae arranged? Did this system mediate vertical migration, the largest movement of biomass on Earth? To try to answer these questions, I chose the pluteus larva of the sea urchin as a model. A comprehensive array of techniques was applied, covering levels of organization from genes to behaviour. The diversity of opsins in Ambulacraria (echinoderms plus hemichordates) has been surveyed to have the first phylogenetic context on this matter (Chapter 1). A nondirectional photoreceptor based on Go-opsins has been first described in an invertebrate larva of the deuterostome lineage (Chapter 2). A novel custom built behavioural set up was created to investigate the vertical migration of these pluteus larvae under different light conditions (Chapter 3). Based on these findings, a mechanistic model for understanding simple photodetection is proposed

Fly-inspired VLSI vision sensors

Journal ArticleEngineers have long looked to nature for inspiration. The diversity of life produced by five billion years of evolution provides countless existence proofs of organic machines with abilities that far surpass those of our own relatively crude automata. We have learned how to harness large amounts of energy and thus far exceed the capabilities of biological systems in some ways (e.g., supersonic flight, space travel, and global communications). However, biological information processing systems (i.e., brains) far outperform today's most advanced computers at tasks involving real-time pattern recognition and perception in complex, uncontrolled environments. If we take energy efficiency into account, the performance gap widens. The human brain dissipates 12 W of power, independent of mental activity. A modern microprocessor dissipates around 50 W, and is equivalent to a vanishingly small fraction of our brain's functionality

Octopus Senses: From Genes To Behavior

Octopuses are intelligent, soft-bodied animals, have complex nervous systems with remarkable cognitive abilities and keen senses that perform reliably in a variety of visual and chemo-tactile learning tasks for exploring and sensing the environment. They have the largest nervous system of any invertebrate, with 500 million neurons distributed centrally and peripherally throughout the body. The nervous system of common octopus (Octopus vulgaris), is comprised of central lobes surrounding the esophagus and a pair of optic lobes that together contain approximately a third of the neurons, with the remaining two-thirds distributed within the arms (e.g. in the large axial nerve cords that extends along the center of each of their eight arms). The most obvious characteristic feature of an octopus is its eight long and flexible arms, but these pose a great challenge for achieving the level of motor and sensory information processing necessary for their behaviors. In addition, octopuses have a significant number of lobes of the nervous system dedicated to visual, tactile, and chemosensory perception. In this study, I aimed to provide a comprehensive view on the genetic bases for the tactile form of olfaction, extraocular photoreception in the sucker, localization of photoreceptors molecules in the optic lobe of O. vulgaris, as well as to identify the major genes are involved in the adult neurogenesis and then the cognitive system in O. vulgaris. I have applied a developed whole-mount in situ hybridization, real-time qPCR, and bioinformatic methods, supported by behavioral evidences to provide a comprehensive view on these processes in O. vulgaris, highlight how genomic innovation translates into organismal organization novelties. Results achieved contributed to some extent, and promoted interest in this field

The Evolution of Cutaneous Senses in Marine Snakes (Hydrophiinae)

Front-fanged elapid snakes (subfamily: Hydrophiinae) have invaded marine habitats twice: the oviparous sea kraits that diverged approximately 18 million years ago and the viviparous sea snakes that diverged approximately six million years ago. Due to these recent marine transitions, marine hydrophiine snakes are embedded within closely-related and extant terrestrial lineages. Within this phylogenetic context, I investigated two questions concerning two cutaneous senses in marine snakes: 1) How has the sense of touch evolved in the transition from land to sea? and 2) How has a novel phototactic trait arisen in sea snakes? Marine snakes possess small scale organs (‘sensilla’) that are presumptive mechanoreceptors widely thought to be co-opted for detecting water motion (i.e. hydrodynamic reception in homoplasy with the lateral line of fish). To test this hypothesis and infer ancestral and derived functions for scale sensilla, I used morphological techniques (quadrate sampling, scanning electron microscopy) to quantify sensilla traits (number, density, area, coverage) among 19 species of terrestrial and marine elapids. After accounting for effects of allometry (head size) and phylogeny (shared descent), I used Bayesian analyses to reconstruct ancestral sensilla traits in sea kraits and sea snakes. I also characterised ultrastructure (histology, immunohistochemistry, transmission electron microscopy) of scale sensilla on the head and tail of two species of sea snakes, Aipysurus laevis and Hydrophis stokesii, which indicate interspecific variation but overall structural similarities with mechanosensory sensilla in terrestrial snakes. These results provide the first evidence for a mechanosensory function for scale sensilla among sea snakes, and a basis for further studies to test for physiological and behavioural responses to water motion among marine snakes. In addition to scale mechanoreceptors, many lineages of sea snakes have conspicuous scale protuberances (e.g. spines, rugosities) with various purportedly sensory and non-sensory adaptive functions. I examined the morphology (scanning electron microscopy, histology) of sexually-dimorphic scale protuberances in turtle-headed sea snakes, Emydocephalus annulatus. Taken together with behavioural data, these morphological results suggest complex mechanosensory roles related to courtship and mating behaviours in this species. Finally, I investigated the evolution and molecular basis of a novel phototactic trait in sea snakes. The movement of tail in response to light detection via the skin (‘tail phototaxis’) is a sensory trait shared by aquatic vertebrates with secretive habits, elongate bodies and paddle-shaped tails, i.e. hagfish, lamprey, aquatic amphibians and sea snakes. I conducted behavioural tests in eight species of sea snakes, developing a preliminary hypothesis for the evolutionary origin of this trait within a small clade of Aipysurus sea snakes. I also quantified tail damage in museum specimens to test whether the probability of sustaining tail injuries is influenced by tail phototactic ability in snakes. I then profiled skin transcriptomes of phototactic snakes to identify candidate phototaxis genes, which can be used to understand the parallel evolution of this trait among vertebrates. This thesis provides the basis for future research on the sensory ecology and evolution of marine snakes. The integrative methods employed speaks to power of these approaches in resolving fundamental questions in evolutionary biology, particularly how novel traits can arise from existing variation.Thesis (Ph.D.) -- University of Adelaide, School of Biological Sciences, 201

The molecular basis of circadian and seasonal rhythms in the blue mussel Mytilus edulis

Exposure to regular environmental oscillations such as day/night have allowed organisms to evolve biological mechanisms to adaptively anticipate and prepare for rhythmic environmental change. A network of gene-protein interactions between clock genes and their proteins comprise the molecular clock mechanism at the heart of regulating biological rhythms. Though this is an endogenous and self-regulating system, elements of this network can be entrained by exogenous biotic and abiotic factors. This synchronisation process between environmental cycles and endogenous rhythms is facilitated by cues like light and temperature, which influence clock gene expression patterns.Marine bivalves often inhabit intertidal habitats under the influence of numerous oscillating environmental conditions, though little is known about how they regulate their biological timekeeping. In this thesis, we investigate the molecular regulation of biological rhythms in the ecologically and commercially important blue mussel, M. edulis, over different timeframes. For the first time in this species, we isolate and characterise a number of clock genes (Clk, Cry1, ROR/HR3, Per and Rev-erb) and clock-associated genes (ARNT, Timeout-like and aaNAT). Rhythmic clock gene expression is demonstrated in the absence of light cues, indicative of endogenous clock control. Differential expression of Cry1 expression between males and females under the same conditions indicates sex-specific regulation and/or function. In addition, diurnal temperature cycles modulated the otherwise rhythmic expression of Rev-erb to constant levels demonstrating an interaction of temperature with clock function. Instances of seasonal clock mRNA expression differences were found, in addition to a number of other putative seasonal genes, indicating a possible mechanism by which seasonal cues can inform rhythmic biological processes.Understanding the influence of environmental cues on the molecular clock is essential in predicting the outcomes of future environmental change on fundamental rhythmic processes, in particular the impacts of decoupled environmental cues on the already highly dynamic and stressful intertidal zone

Octopus skin ‘sight’ and the evolution of dispersed, dermal light sensing in Mollusca

We now know that co-option, or reuse of ancestral components, plays a prominent role in the evolution of emergent systems, like the reuse of gene regulatory networks in the evolution of developmental programs for morphology. Do the evolutionary origins of animal behaviors show evidence of modular reuse that we find at other levels of biological organization? I found that the skin of Octopus bimaculoides is intrinsically light sensitive, and that bright light causes colored chromatophore organs in octopus skin to expand, even without input from the central brain or eyes. Because this Light-Activated Chromatophore Expansion (or LACE) behavior relies on evolutionary novel chromatophore organs, LACE is also an evolutionary novelty. As such, I can pinpoint its origin in evolutionary time and ask whether the ability of mollusc skin to sense light existed prior to the evolution of cephalopod chromatophores and LACE. I found expression of the same r-opsin based phototransduction genes in both O. bimaculoides eyes and skin, and the spectral sensitivity of LACE closely matches that of the r-opsin in octopus eyes, consistent with the hypothesis that r-opsin phototransduction underlies LACE. The r-opsin phototransduction cascade can be traced back to at least the last common ancestor of bilaterians, so did the reuse of the cascade in octopus skin arise before, in time with, or after the evolution of cephalopod chromatophores? After surveying 28 mollusc mantle transcriptomes for opsins, I found that r-opsin cascade genes are expressed across the molluscs, from multiple species in each of the major mollusc classes, and an ancestral state reconstruction suggests that the last common ancestor of molluscs expressed r-opsin in its mantle. Taken together, these results suggest that the evolution of LACE required co-option of an ancient phototransduction module, and that like the evolution of development and other emergent systems, reuse may play a fundamental role in the macroevolution of animal behaviors

Circadian clock and light input system in the sea urchin larva

A circadian clock is an endogenous time-keeping mechanism that synchronizes several biological processes with local environment. In metazoans the circadian system is driven by a regulatory network of so called ―clock‖ genes interconnected in transcriptional-translational feedback loops that generate rhythmicity at mRNA and protein level. Sea urchin and its molecular tools can facilitate the comprehension of the evolution of the time-keeping mechanism in bilaterians. For this purpose we identified and analysed the expression of orthologous clock genes in the sea urchin larvae. Genome survey identifies almost all canonical clock genes known in protostomes and deuterostomes, with exception of period, indicating that the last common ancestor of all bilaterians already had a complex clock toolkit. Quantitative gene expression data reveal that the circadian clock begins to oscillate consistently in the free-living larva. Sp_vcry and sp_tim mRNA cycle in both light/dark (LD) and free running (DD) conditions; several other genes consistently show oscillation in LD condition only; while, neither sp_clock, nor sp_bmal have rhythmic expression. Interestingly, in-situ hybridization of key sea urchin clock genes together with cell markers (e.g. serotonin) suggest the presence of two types of light perceiving cells in the apical region of the larva: serotoninergic cells expressing sp_dcry and no-serotoninergic cells expressing sp_opsin3.2. Furthermore, functional analysis was performed to discern linkages in the regulatory network of clock genes. In larvae entrained to light/dark cycles, knockdown of sp_dcry induces arrythmicity in the expression of itself, reduction of amplitude of oscillation in sp_vcry, and reduction of amplitude of oscillation and lower levels of expression in sp_tim. Knockdown of sp_opsin3.2 reduces levels of expression of sp_hlf; and sp_vcry knockdown induces arrythmicity in sp_tim. Importantly, our study highlights differences in the architecture and gene regulation of the sea urchin larval circadian clock compared to other metazoan clocks