Introduction to the Symposium “Molluscan Models: Advancing Our Understanding of the Eye”

Since the time of Darwin, the eye has been a subject of evolutionary and comparative biologists alike who were intrigued by the structural complexity and morphological diversity of eyes in nature. Much of what we know about the eye—development, structure, physiology, and function—has been determined from only a handful of model organisms, specifically the mouse and the fly. One major phylum in particular, the Mollusca, has been underutilized in investigating the evolution and development of the eye. This is surprising as molluscs display a myriad of eye types, such as simple pit eyes without any apparatus to focus images, compound eyes that superficially resemble the eyes of flies, camera-type eyes that are similar to vertebrate eyes, and eyes with mirrors, just to name a few. As a result, molluscan eyes comprise more morphological diversity than seen even in the largest animal phylum, the Arthropoda

Toward Developing Models to Study the Disease, Ecology, and Evolution of the Eye in Mollusca

Several invertebrate systems have been developed to study various aspects of the eye and eye disease including Drosophila, Planaria, Platynereis, and most recently, the cubozoan jellyfish Tripedalia; however, molluscs, the second largest metazoan phylum, so far have been underrepresented in eye research. This is surprising as mollusc systems offer opportunities to study visual processes that may be altered by disease, vision physiology, development of the visual system, behavior, and evolution. Malacologists have labored for over a century as morphologists, systematists, physiologists, and ecologists in order to understand the structural and functional diversity in molluscs at all levels of biological organization. Yet, malacologists have had little opportunity to interact with researchers whose interests are restricted to the biology and development of eyes as model systems as they tend not to publish in the same journals or attend the same meetings. In an effort to highlight the advantages of molluscan eyes as a model system and encourage greater collaboration among researchers, I provide an overview of molluscan eye research from these two perspectives: eye researchers whose interests involve the development, physiology, and disease of the eye and malacologists who study the complete organism in its natural environment. I discuss the developmental and genetic information available for molluscan eyes and the need to place this work in an evolutionary perspective. Finally, I discuss how synergy between these two groups will advance eye research, broaden research in both fields, and aid in developing new molluscan models for eye research

Congruence and Conflict Between Molecular and Reproductive Characters When Assessing Biological Diversity in the Western Fanshell Cyprogenia aberti (Bivalvia, Unionidae)

Organisms with complex life histories and unusual modes of genome inheritance can present challenges for phylogenetic reconstruction and accurate assessment of biological diversity. This is particularly true for freshwater bivalves in the family Unionidae because: (1) they have complex life cycles that include a parasitic larva and obligate fish host; (2) they possess both a male and female mitochondrial genome that is transmitted through doubly uniparental inheritance (DUI); and (3) they are found in riverine habitats with complex hydrogeological histories. Examination of mitochondrial DNA (mtDNA) sequences, conglutinate morphology, and host fish compatibility of the western fanshell Cyprogenia aberti (Conrad, 1850) revealed significant character variation across its range. Although variation was correlated among the different data sets and supports discrete groups, these groups did not always correspond to geographically isolated populations. Two discrete mtDNA clades exist sympatrically within most C. aberti populations, and these same clades are also diagnosed by at least one morphological character, egg color. The surprisingly high genetic distance (14.61%–20.19%) between the members of these sympatric clades suggests heritance infidelity of the two different mitochondrial genomes. This hypothesis was tested and falsified. More general patterns in geography were observed in host fish compatibility. Populations of C. aberti from the major river systems differed in their ability to utilize fish species as hosts. These differences in reproductive traits, which are presumably genetically based, suggest that these populations are not ecologically exchangeable with one another and represent biological diversity not previously recognized within Cyprogenia Agassiz, 1852

EnRICH: Extraction and Ranking using Integration and Criteria Heuristics

Background: High throughput screening technologies enable biologists to generate candidate genes at a rate that, due to time and cost constraints, cannot be studied by experimental approaches in the laboratory. Thus, it has become increasingly important to prioritize candidate genes for experiments. To accomplish this, researchers need to apply selection requirements based on their knowledge, which necessitates qualitative integration of heterogeneous data sources and filtration using multiple criteria. A similar approach can also be applied to putative candidate gene relationships. While automation can assist in this routine and imperative procedure, flexibility of data sources and criteria must not be sacrificed. A tool that can optimize the trade-off between automation and flexibility to simultaneously filter and qualitatively integrate data is needed to prioritize candidate genes and generate composite networks from heterogeneous data sources. Results: We developed the java application, EnRICH (Extraction and Ranking using Integration and Criteria Heuristics), in order to alleviate this need. Here we present a case study in which we used EnRICH to integrate and filter multiple candidate gene lists in order to identify potential retinal disease genes. As a result of this procedure, a candidate pool of several hundred genes was narrowed down to five candidate genes, of which four are confirmed retinal disease genes and one is associated with a retinal disease state. Conclusions: We developed a platform-independent tool that is able to qualitatively integrate multiple heterogeneous datasets and use different selection criteria to filter each of them, provided the datasets are tables that have distinct identifiers (required) and attributes (optional). With the flexibility to specify data sources and filtering criteria, EnRICH automatically prioritizes candidate genes or gene relationships for biologists based on their specific requirements. Here, we also demonstrate that this tool can be effectively and easily used to apply highly specific user-defined criteria and can efficiently identify high quality candidate genes from relatively sparse datasets

Both novelty and conspicuousness influence selection by mammalian predators on the colour pattern of Plethodon cinereus (Urodela: Plethodontidae)

Predators influence the evolution of color pattern in prey species, yet how these selective forces might differ among predators is rarely considered. In particular, prey color patterns that indicate unpalatability to some predator species may not carry the same signal for other predators. We test several hypotheses of selection on patterning between mammal predators and the polymorphic salamander Plethodon cinereus, which, under an avian visual system appears as a mimic of the toxic newt Notophthalmus viridescens. We fit each hypothesis against field observations of mammalian attacks on salamander clay replicas. We then develop a novel analytical procedure that enables the combination of multiple non-exclusive models in a likelihood framework. We find that mammals do not follow any single hypothesis proposed, including the hypothesis of mimicry. Instead, mammals in this system use visual cues while foraging to avoid unfamiliar, novel prey and attack conspicuous prey. We propose that mammals may help to maintain color pattern polymorphism within populations of P. cinereus by avoiding novel, unfamiliar color morphs. Additionally, selective pressures from multiple predators and variation in predator communities among sites may contribute to the maintenance of color polymorphism within and among localities in this salamander species

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

Trends in the sand: directional evolution in the shell shape of recessing scallops (Bivalvia: Pectinidae)

Directional evolution is one of the most compelling evolutionary patterns observed in macroevolution. Yet, despite its importance, detecting such trends in multivariate data remains a challenge. In this study, we evaluate multivariate evolution of shell shape in 93 bivalved scallop species, combining geometric morphometrics and phylogenetic comparative methods. Phylomorphospace visualization described the history of morphological diversification in the group; revealing that taxa with a recessing life habit were the most distinctive in shell shape, and appeared to display a directional trend. To evaluate this hypothesis empirically, we extended existing methods by characterizing the mean directional evolution in phylomorphospace for recessing scallops. We then compared this pattern to what was expected under several alternative evolutionary scenarios using phylogenetic simulations. The observed pattern did not fall within the distribution obtained under multivariate Brownian motion, enabling us to reject this evolutionary scenario. By contrast, the observed pattern was more similar to, and fell within, the distribution obtained from simulations using Brownian motion combined with a directional trend. Thus, the observed data are consistent with a pattern of directional evolution for this lineage of recessing scallops. We discuss this putative directional evolutionary trend in terms of its potential adaptive role in exploiting novel habitats

The Last Common Ancestor of Most Bilaterian Animals Possessed at Least Nine Opsins

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

Rates of morphological evolution, asymmetry and morphological integration of shell shape in scallops

Rates of morphological evolution vary across different taxonomic groups, and this has been proposed as one of the main drivers for the great diversity of organisms on Earth. Of the extrinsic factors pertaining to this variation, ecological hypotheses feature prominently in observed differences in phenotypic evolutionary rates across lineages. But complex organisms are inherently modular, comprising distinct body parts that can be differentially affected by external selective pressures. Thus, the evolution of trait covariation and integration in modular systems may also play a prominent role in shaping patterns of phenotypic diversity. Here we investigate the role ecological diversity plays in morphological integration, and the tempo of shell shape evolution and of directional asymmetry in bivalved scallops.Overall, the shape of both valves and the magnitude of asymmetry of the whole shell (difference in shape between valves) are traits that are evolving fast in ecomorphs under strong selective pressures (gliders, recessers and nestling), compared to low rates observed in other ecomorphs (byssal-attaching, free-living and cementing). Given that different parts of an organism can be under different selective pressures from the environment, we also examined the degree of evolutionary integration between the valves as it relates to ecological shifts. We find that evolutionary morphological integration is consistent and surprisingly high across species, indicating that while the left and right valves of a scallop shell are diversifying in accordance with ecomorphology, they are doing so in a concerted fashion.Our study on scallops adds another strong piece of evidence that ecological shifts play an important role in the tempo and mode of morphological evolution. Strong selective pressures from the environment, inferred from the repeated evolution of distinct ecomorphs, have influenced the rate of morphological evolution in valve shape and the magnitude of asymmetry between valves. Our observation that morphological integration of the valves making up the shell is consistently strong suggests tight developmental pathways are responsible for the concerted evolution of these structures while environmental pressures are driving whole shell shape. Finally, our study shows that directional asymmetry in shell shape among species is an important aspect of scallop macroevolution.Emma Sherratt, Jeanne M. Serb and Dean C. Adam

Convergent and parallel evolution in life habit of the scallops (Bivalvia: Pectinidae)

We employed a phylogenetic framework to identify patterns of life habit evolution in the marine bivalve family Pectinidae. Specifically, we examined the number of independent origins of each life habit and distinguished between convergent and parallel trajectories of life habit evolution using ancestral state estimation. We also investigated whether ancestral character states influence the frequency or type of evolutionary trajectories