Daniel I. Speiser

A Chiton Uses Aragonite Lenses to Form Images

Hundreds of ocelli are embedded in the dorsal shell plates of certain chitons. These ocelli each contain a pigment layer, retina, and lens, but it is unknown whether they provide chitons with spatial vision. It is also unclear whether chiton lenses are made from proteins, like nearly all biological lenses, or from some other material. Electron probe X-ray microanalysis and X-ray diffraction revealed that the chiton Acanthopleura granulata has the first aragonite lenses ever discovered. We found that these lenses allow A. granulatas ocelli to function as small camera eyes with an angular resolution of about 9°-12°. Animals responded to the sudden appearance of black, overhead circles with an angular size of 9°, but not to equivalent, uniform decreases in the downwelling irradiance. Our behavioral estimates of angular resolution were consistent with estimates derived from focal length and receptor spacing within the A. granulata eye. Behavioral trials further indicated that A. granulatas eyes provide the same angular resolution in both air and water. We propose that one of the two refractive indices of the birefringent chiton lens places a focused image on the retina in air, whereas the other does so in water.

Understanding the dermal light sense in the context of integrative photoreceptor cell biology.

While the concept of a dermal light sense has existed for over a century, little progress has been made in our understanding of the mechanisms underlying dispersed photoreception and the evolutionary histories of dispersed photoreceptor cells. These cells historically have been difficult to locate and positively identify, but modern molecular techniques, integrated with existing behavioral, morphological, and physiological data, will make cell identification easier and allow us to address questions of mechanism and evolution. With this in mind, we propose a new classification scheme for all photoreceptor cell types based on two axes, cell distribution (aggregated vs. dispersed) and position within neural networks (first order vs. high order). All photoreceptor cells fall within one of four quadrants created by these axes: aggregated/high order, dispersed/high order, aggregated/first order, or dispersed/first order. This new method of organization will help researchers make objective comparisons between different photoreceptor cell types. Using integrative data from four major phyla (Mollusca, Cnidaria, Echinodermata, and Arthropoda), we also provide evidence for three hypotheses for dispersed photoreceptor cell function and evolution. First, aside from echinoderms, we find that animals often use dispersed photoreceptor cells for tasks that do not require spatial vision. Second, although there are both echinoderm and arthropod exceptions, we find that dispersed photoreceptor cells generally lack morphological specializations that either enhance light gathering or aid in the collection of directional information about light. Third, we find that dispersed photoreceptor cells have evolved a number of times in Metazoa and that most dispersed photoreceptor cells have likely evolved through the co-option of existing phototransduction cascades. Our new classification scheme, combined with modern investigative techniques, will help us address these hypotheses in great detail and generate new hypothesis regarding the function and evolution of dispersed photoreceptor cells.

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

BackgroundTools 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.ResultsWe 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/).ConclusionsOur 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.

Multifunctionality of chiton biomineralized armor with an integrated visual system

A set of strong eyes Although many biological tissues serve more than one purpose, rarely are they optimized to do multiple tasks well. When you try to optimize for one functionality, it comes at the expense of another. Li et al. investigated the biomineralized armor of the small mollusc chiton Acanthopleura granulata. The armor appears to be optimized for both mechanical strength and for image capture by hundreds of integral aragonite-based lenses. Science, this issue p. 952 Chiton armor shows both mechanical strength and optical functionality. Nature provides a multitude of examples of multifunctional structural materials in which trade-offs are imposed by conflicting functional requirements. One such example is the biomineralized armor of the chiton Acanthopleura granulata, which incorporates an integrated sensory system that includes hundreds of eyes with aragonite-based lenses. We use optical experiments to demonstrate that these microscopic lenses are able to form images. Light scattering by the polycrystalline lenses is minimized by the use of relatively large, crystallographically aligned grains. Multiscale mechanical testing reveals that as the size, complexity, and functionality of the integrated sensory elements increase, the local mechanical performance of the armor decreases. However, A. granulata has evolved several strategies to compensate for its mechanical vulnerabilities to form a multipurpose system with co-optimized optical and structural functions.

The last common ancestor of most bilaterian animals possessed at least 9 opsins.

Abstract The opsin gene family encodes key proteins animals use to sense light and has expanded dramatically as it originated early in animal evolution. Understanding the origins of opsin diversity can offer clues to how separate lineages of animals have repurposed different opsin paralogs for different light-detecting functions. However, the more we look for opsins outside of eyes and from additional animal phyla, the more opsins we uncover, suggesting we still do not know the true extent of opsin diversity, nor the ancestry of opsin diversity in animals. To estimate the number of opsin paralogs present in both the last common ancestor of the Nephrozoa (bilaterians excluding Xenoacoelomorpha), and the ancestor of Cnidaria + Bilateria, we reconstructed a reconciled opsin phylogeny using sequences from 14 animal phyla, especially the traditionally poorly-sampled echinoderms and molluscs. Our analysis strongly supports a repertoire of at least nine opsin paralogs in the bilaterian ancestor and at least four opsin paralogs in the last common ancestor of Cnidaria + Bilateria. Thus, the kernels of extant opsin diversity arose much earlier in animal history than previously known. Further, opsins likely duplicated and were lost many times, with different lineages of animals maintaining different repertoires of opsin paralogs. This phylogenetic information can inform hypotheses about the functions of different opsin paralogs and can be used to understand how and when opsins were incorporated into complex traits like eyes and extraocular sensors.

Spectral sensitivity of the concave mirror eyes of scallops: potential influences of habitat, self-screening and longitudinal chromatic aberration

SUMMARY Scallop eyes contain two retinas, one proximal and one distal. Molecular evidence suggests that each retina expresses a different visual pigment. To test whether these retinas have different spectral sensitivities, we used microspectrophotometry to measure the absorption spectra of photoreceptors from the eyes of two different scallop species. Photoreceptors from the proximal and distal retinas of the sea scallop Placopecten magellanicus had absorption peak wavelengths (λmax) of 488±1 nm (mean ± s.e.m.; N=20) and 513±3 nm (N=26), respectively. Photoreceptors from the corresponding retinas of the bay scallop Argopecten irradians had λmax values of 506±1 nm (N=21) and 535±3 nm (N=14). Assuming that the proximal and distal receptors had equal absorption coefficients (kD=0.0067 μm–1), we found that self-screening within the scallop eye caused the proximal and distal receptors in P. magellanicus to have peak absorption at 490 and 520 nm, respectively, and the corresponding receptors in A. irradians to have peak absorption at 504 and 549 nm. We conclude that environment may influence the λmax of scallop visual pigments: P. magellanicus, generally found in blue oceanic water, has visual pigments that are maximally sensitive to shorter wavelengths than those found in A. irradians, which lives in greener inshore water. Scallop distal retinas may be sensitive to longer wavelengths of light than scallop proximal retinas to correct for either self-screening by the retinas or longitudinal chromatic aberration of the lens.

The shell-eyes of the chiton Acanthopleura granulata (Mollusca, Polyplacophora) use pheomelanin as a screening pigment

Certain species of chiton (Mollusca, Polyplacophora) have hundreds of small (< 100 µm) eyes embedded in their dorsal shell plates. These eyes each contain a retina, a layer of screening pigment, and a lens. Previously, we demonstrated that the eyes of chitons provide spatial vision. As in other camera-type eyes, the screening pigments in the eyes of chitons absorb off-axis light in order to preserve the contrast of images formed on the retina. Our results indicate that the red-brown, alkali-soluble screening pigment associated with the eyes of the chiton Acanthopleura granulata (Gmelin, 1791) is pheomelanin. Using high-performance liquid chromatography (HPLC) and MALDI-TOF mass spectroscopy, we find that degrading A. granulata’s screening pigment with alkaline hydrogen peroxide produces 6-(2-amino-2-carboxyethyl)-2-carboxy-4-hydroxybenzothiazole (BTCA), a diagnostic marker of pheomelanin. Chitons are the first molluscs demonstrated to use pheomelanin as a screening pigment in their eyes. Our results suggest that the image-forming eyes of chitons may have evolved separately from eyes that employ different types of screening pigment, such as those of most other invertebrates. Further, we hypothesize that change in the expression pattern of tyrosinase – an enzyme responsible for melanin synthesis in many other metazoans – may have contributed to the origin of screening pigments in chitons, a critical step in the evolution of their eyes.

Scallops visually respond to the size and speed of virtual particles

SUMMARY The unique eyes of scallops are abundant along the right and left valve mantle margins. These eyes form images by reflection off a concave spherical mirror, and give scallops an angular resolution of around 2°, far better than the 13–40° angular resolution provided by the eyes of other bivalves. It has been argued that bivalve mantle eyes primarily act as predator detectors, but behavioral studies have suggested that vision may serve additional purposes in scallops. By placing specimens of the bay scallop Argopecten irradians (Lamarck 1819) in a tank with 5–10 cm s–1 flow, showing them simulated images of moving particles, and recording their behavior, we tested whether visual cues may influence feeding behavior in these animals. We found that scallops opened their anterior mantle gapes significantly more often when they were shown 1.5×1.5 mm virtual particles (with angular sizes of 3.4°) than when they were shown 0.6×0.6 mm particles (1.4°; P<0.001) or no particles at all (P<0.05). We also found that scallops opened their anterior mantle gapes significantly more often when they were shown virtual particles moving at 2.5 cm s–1 (P<0.01) or 5 cm s–1 (P<0.05) than when they were shown particles moving at 10 cm s–1. Because scallops must open their anterior mantle gapes to feed, our findings suggest that these animals may visually detect the size and speed of moving particles and use this information to help identify favorable feeding conditions.

Eavesdropping on visual secrets

Private communication may benefit signalers by reducing the costs imposed by potential eavesdroppers such as parasites, predators, prey, or rivals. It is likely that private communication channels are influenced by the evolution of signalers, intended receivers, and potential eavesdroppers, but most studies only examine how private communication benefits signalers. Here, we address this shortcoming by examining visual private communication from a potential eavesdropper’s perspective. Specifically, we ask if a signaler would face fitness consequences if a potential eavesdropper could detect its signal more clearly. By integrating studies on private communication with those on the evolution of vision, we suggest that published studies find few taxon-based constraints that could keep potential eavesdroppers from detecting most hypothesized forms of visual private communication. However, we find that private signals may persist over evolutionary time if the benefits of detecting a particular signal do not outweigh the functional costs a potential eavesdropper would suffer from evolving the ability to detect it. We also suggest that all undetectable signals are not necessarily private signals: potential eavesdroppers may not benefit from detecting a signal if it co-occurs with signals in other more detectable sensory modalities. In future work, we suggest that researchers consider how the evolution of potential eavesdroppers’ sensory systems influences private communication. Specifically, we suggest that examining the fitness correlates and evolution of potential eavesdroppers can help (1) determine the likelihood that private communication channels are stable over evolutionary time, and (2) demonstrate that undetectable signals are private signals by showing that signalers benefit from a reduction in detection by potential eavesdroppers.

A Transcriptomic Analysis of Cave, Surface, and Hybrid Isopod Crustaceans of the Species Asellus aquaticus.

Cave animals, compared to surface-dwelling relatives, tend to have reduced eyes and pigment, longer appendages, and enhanced mechanosensory structures. Pressing questions include how certain cave-related traits are gained and lost, and if they originate through the same or different genetic programs in independent lineages. An excellent system for exploring these questions is the isopod, Asellus aquaticus. This species includes multiple cave and surface populations that have numerous morphological differences between them. A key feature is that hybrids between cave and surface individuals are viable, which enables genetic crosses and linkage analyses. Here, we advance this system by analyzing single animal transcriptomes of Asellus aquaticus. We use high throughput sequencing of non-normalized cDNA derived from the head of a surface-dwelling male, the head of a cave-dwelling male, the head of a hybrid male (produced by crossing a surface individual with a cave individual), and a pooled sample of surface embryos and hatchlings. Assembling reads from surface and cave head RNA pools yielded an integrated transcriptome comprised of 23,984 contigs. Using this integrated assembly as a reference transcriptome, we aligned reads from surface-, cave- and hybrid- head tissue and pooled surface embryos and hatchlings. Our approach identified 742 SNPs and placed four new candidate genes to an existing linkage map for A. aquaticus. In addition, we examined SNPs for allele-specific expression differences in the hybrid individual. All of these resources will facilitate identification of genes and associated changes responsible for cave adaptation in A. aquaticus and, in concert with analyses of other species, will inform our understanding of the evolutionary processes accompanying adaptation to the subterranean environment.