Integration between comparative biology and cellular/molecular biology has helped advance understanding of the structure, function and physiology of the vertebrate small heat shock proteins αA- and αB-crystallin. These proteins are expressed at high concentration in the eye lens where they contribute to transparency and refractive power. But they also function similarly to molecular chaperones by preventing the aggregation of denatured proteins that can cause opacities, or cataracts. α-crystallins also serve a number of other roles in and out of the lens that are still not completely understood. Comparative examination of α-crystallins and closely related small heat shock proteins from diverse taxa has helped provide insights into the proteins' three-dimensional shape and structure/function relationships. Until recently, no studies had examined the tissue specific expression or chaperone-like activity of α-crystallins from a non-mammalian vertebrate. I have been investigating the α-crystallins of the zebrafish, Danio rerio, as a first step towards utilizing the bony fishes as a model group for understanding the evolution of α-crystallin function. Zebrafish αA-crystallin displays similar structure and expression and increased chaperone-like activity compared to its human orthologue. Zebrafish αB-crystallin, however, has a truncated C-terminal extension, more limited expression and lower chaperone-like activity than its human orthologue. These data suggest that αA-crystallin physiological function may be conserved between zebrafish and mammals, while αB-crystallin physiological function has diverged. Understanding zebrafish α-crystallin physiology is necessary before this species can be used for developmental and genetic studies, and provides a foundation for further comparative studies.

The crystallins comprise 80–90% of the water-soluble proteins of the transparent, cellular, refractive eye lens and are responsible for its optical properties. Comparative studies have established that the crystallins are surprisingly diverse and often differ among species in a taxon-specific fashion. In general, the crystallins are derived from or identical to metabolic enzymes or stress (small heat shock) proteins that are expressed to a lesser extent in other tissues where they have non-refractive roles. We call the phenomenon of having the small heat shock protein or enzyme and lens crystallin encoded in the identical gene “gene sharing”; examples include small heat shock protein/αB-crystallin, α-enolase/τ-crystallin and argininosuccinate lyase/δ2-crystallin. Lens crystallins have evolved by gene sharing in vertebrates (all) and invertebrates (cephalopods, scallops, jellyfish). Similar cis-elements and transcription factors (including Pax6 among others) appear to unify lens expression of crystallin genes in vertebrates and mollusks (especially scallops). Instead of Pax6, cnidarians have a PaxB gene encoding a Pax2 DNA-binding paired domain and octapeptide, and a Pax6 homeodomain; PaxB appears important for ocellus (eye) development and crystallin gene expression in the cubomedusan jellyfish, Tridpedalia cystophora. Finally, we speculate on the basis of our current studies on Tripedalia that eyes and statocysts (associated with mechanoreceptors in many cnidarians and thus possibly ears in vertebrates) are evolutionarily related. Numerous examples indicate that gene sharing is widely used, consistent with changes in gene regulation being an evolutionary driving force for innovation of protein function.

Laboratory synthesis of ancestral proteins offers an intriguing opportunity to study the past directly. The development of Bayesian methods to infer ancestral sequences, combined with advances in models of molecular evolution, and synthetic gene technology make this an increasingly promising approach in evolutionary studies of molecular function. Visual pigments form the first step in the biochemical cascade of events in the retina in all animals known to possess visual capabilities. In vertebrates, the necessity of spanning a dynamic range of light intensities of many orders of magnitude has given rise to two different types of photoreceptors, rods specialized for dim-light conditions, and cones for daylight and color vision. These photoreceptors contain different types of visual pigment genes. Reviewed here are methods of inferring ancestral sequences, chemical synthesis of artificial ancestral genes in the laboratory, and applications to the evolution of vertebrate visual systems and the experimental recreation of an archosaur rod visual pigment. The ancestral archosaurs gave rise to several notable lineages of diapsid reptiles, including the birds and the dinosaurs, and would have existed over 200 MYA. What little is known of their physiology comes from fossil remains, and inference based on the biology of their living descendants. Despite its age, an ancestral archosaur pigment was successfully recreated in the lab, and showed interesting properties of its wavelength sensitivity that may have implications for the visual capabilities of the ancestral archosaurs in dim light.

The molecular genetic dissection of Drosophila eye development led to the exciting discovery of a surprisingly large panel of genes and gene activities, which are functionally conserved across phyla. Little effort has yet been made towards pinpointing non-conserved gene functions in the developing Drosophila eye. This neglects the fact that Drosophila visual system development is a highly derived process. The comparative analysis of Drosophila eye development within insects can be expected to enhance resolution and accuracy of between phyla comparisons of eye development, and to reveal molecular developmental changes that facilitated the evolutionary transition from hemimetabolous to holometabolous insect development. Here we review aspects of early Drosophila eye development, which are likely to have diverged from the situation in more primitive insects, as indicated by results from work in the flour beetle Tribolium castaneum and the grasshopper Schistocerca americana.

Eyes serve as models to understand the evolution of complex traits, with broad implications for the origins of evolutionary novelty. Discussions of eye evolution are relevant at many taxonomic levels, especially within arthropods where compound eye distribution is perplexing. Either compound eyes were lost numerous times or very similar eyes evolved separately in multiple lineages. Arthropod compound eye homology is possible, especially between crustaceans and hexapods, which have very similar eye facets and may be sister taxa. However, judging homology only on similarity requires subjective decisions. Regardless of whether compound eyes were present in a common ancestor of arthropods or crustaceans hexapods, recent phylogenetic evidence suggests that the compound eyes, today present in myodocopid ostracods (Crustacea), may have been absent in ostracod ancestors. This pattern is inconsistent with phylogenetic homology. Multiple losses of ostracod eyes are an alternative hypothesis that is statistically improbable and without clear cause. One possible evolutionary process to explain the lack of phylogenetic homology of ostracod compound eyes is that eyes may evolve by switchback evolution, where genes for lost structures remain dormant and are re-expressed much later in evolution.

The evolutionary mechanisms responsible for the loss of eyes in cave animals are still unresolved. Hypotheses invoking natural selection or neutral mutation have been advanced to explain eye regression. Here we describe comparative molecular and developmental studies in the teleost Astyanax mexicanus that shed new light on this problem. A. mexicanus is a single species consisting of a sighted surface-dwelling form (surface fish) and many blind cave-dwelling forms (cavefish) from different caves. We first review the evolutionary relationships of Astyanax cavefish populations and conclude that eye degeneration may have evolved multiple times. We then compare the mechanisms of eye degeneration in different cavefish populations. We describe the results of experiments showing that programmed cell death of the lens plays a key role in controlling eye degeneration in these cavefish populations. We also show that Pax6 gene expression and fate determination in the optic primordia are modified similarly in different cavefish populations, probably due to hyperactive midline signaling. We discuss the contributions of the comparative developmental approach toward resolving the evolutionary mechanisms of eye degeneration. A new hypothesis is presented in which both natural selection and neutral mutation are proposed to have roles in cavefish eye degeneration.

Jellyfish belong to one of the oldest extant animal phyla, the Cnidaria. The first Cnidaria appear in the fossil record 600 million years ago, preceeding the Cambrian explosion. They are an extremely successful group present in all marine environments and some freshwater environments. In contrast to many animal phyla in which vision is a primary sense Cnidarians do not, generally, employ image forming eyes. One small class stands alone: the Cubozoa. Cubomedusae are commonly known as box jellyfish. They possess image forming eyes (Coates et al., 2001) which certainly evolved independently from other metazoans. Cubomedusae therefore offer a unique perspective on the evolution of image forming eyes. This literature review collects, into one place, what is known about: the multiple eye types of box jellyfish, cubomedusan life history and ecology, and the sensory and neural systems of box jellyfish. Here I discuss how these features set cubomedusae apart from scyphomedusae and hydromedusae. Knowledge in these areas is sparse; the work done to date inspires increased efforts.

Visual pigments, the molecules in photoreceptors that initiate the process of vision, are inherently dichroic, differentially absorbing light according to its axis of polarization. Many animals have taken advantage of this property to build receptor systems capable of analyzing the polarization of incoming light, as polarized light is abundant in natural scenes (commonly being produced by scattering or reflection). Such polarization sensitivity has long been associated with behavioral tasks like orientation or navigation. However, only recently have we become aware that it can be incorporated into a high-level visual perception akin to color vision, permitting segmentation of a viewed scene into regions that differ in their polarization. By analogy to color vision, we call this capacity polarization vision. It is apparently used for tasks like those that color vision specializes in: contrast enhancement, camouflage breaking, object recognition, and signal detection and discrimination. While color is very useful in terrestrial or shallow-water environments, it is an unreliable cue deeper in water due to the spectral modification of light as it travels through water of various depths or of varying optical quality. Here, polarization vision has special utility and consequently has evolved in numerous marine species, as well as at least one terrestrial animal. In this review, we consider recent findings concerning polarization vision and its significance in biological signaling.

The effects of light adaptation on flicker fusion frequency were examined in the photoreceptors of 13 species of deep-sea crustaceans. Light adaptation produced a significant increase in the maximum critical flicker fusion frequency (CFF_max) in 7 species—all 6 species of euphausiids in the study, and 1 species of oplophorid (Group 1). This is the first example of an increase in temporal resolution due to light adaptation in a deep-sea species. In the other six species—2 oplophorids, 1 pandalid, 1 pasiphaeid, 1 penaeid and 1 sergestid (Group 2)—light adaptation had no effect, or resulted in a decrease in the flicker fusion frequency. The mean dark-adapted CFF_max of the Group 1 species was significantly higher, and the mean response latency significantly lower, than those of the Group 2 species. Possible explanations for these differences include the activity and bioluminescence mode of preferred prey items, as well as the retention of larval/juvenile adaptations in adult eyes.

Diurnal and nocturnal hawkmoths (Sphingidae, Lepidoptera) have three spectral types of receptor sensitive to ultraviolet, blue and green light. As avid flower visitors and pollinators, they use olfactory and visual cues to find and recognise flowers. Moths of the diurnal species Macroglossum stellatarum and the nocturnal species Deilephila elpenor, Hyles lineata and Hyles gallii use and learn the colour of flowers. Nocturnal species can discriminate flowers at starlight intensities when humans and honeybees are colour-blind. M. stellatarum can use achromatic, intensity-related cues if colour cues are absent, and this is probably also true for D. elpenor. Both species can recognise colours even under a changed illumination colour.

While transparency, cryptic coloration, and counterillumination are all highly successful cryptic strategies for pelagic species, they become less effective when confronted with varying optical conditions. Transparent species are susceptible to detection by reflections from their body surface, particularly at shallow depths. Colored and mirrored species are vulnerable to detection when viewed from certain angles, or at certain times of day. Counterilluminating species must cope with the changes in the angular distribution and spectra of downwelling light at different depths. In all cases the vulnerabilities are more pronounced at shallow depths and essentially negligible at depths greater than 200 m. The results suggest interesting adaptations both for crypsis (e.g., anti-reflection coatings, variable coloration, variable filters for photophores) and for visual detection (e.g., circling, crepuscular predation), all of which are potentially fruitful topics for future research.

The fundamental dichotomy between incoherent (phase independent) and coherent (phase dependent) light scattering provides the best criterion for a classification of biological structural color production mechanisms. Incoherent scattering includes Rayleigh, Tyndall, and Mie scattering. Coherent scattering encompasses interference, reinforcement, thin-film reflection, and diffraction. There are three main classes of coherently scattering nanostructures—laminar, crystal-like, and quasi-ordered. Laminar and crystal-like nanostructures commonly produce iridescence, which is absent or less conspicuous in quasi-ordered nanostructures. Laminar and crystal-like arrays have been analyzed with methods from thin-film optics and Bragg's Law, respectively, but no traditional methods were available for the analysis of color production by quasi-ordered arrays. We have developed a tool using two-dimensional (2D) Fourier analysis of transmission electron micrographs (TEMs) that analyzes the spatial variation in refractive index (available from the authors). This Fourier tool can examine whether light scatterers are spatially independent, and test whether light scattering can be characterized as predominantly incoherent or coherent. The tool also provides a coherent scattering prediction of the back scattering reflectance spectrum of a biological nanostructure. Our applications of the Fourier tool have falsified the century old hypothesis that the non-iridescent structural colors of avian feather barbs and skin are produced by incoherent Rayleigh or Tyndall scattering. 2D Fourier analysis of these quasi-ordered arrays in bird feathers and skin demonstrate that these non-iridescent colors are produced by coherent scattering. No other previous examples of biological structural color production by incoherent scattering have been tested critically with either analysis of scatterer spatial independence or spectrophotometry. The Fourier tool is applied here for the first time to coherent scattering by a laminar array from iridescent bird feather barbules (Nectarinia) to demonstrate the efficacy of the technique on thin films. Unlike previous physical methods, the Fourier tool provides a single method for the analysis of coherent scattering by a diversity of nanostructural classes. This advance will facilitate the study of the evolution of nanostructural classes from one another and the evolution of nanostructure itself. The article concludes with comments on the emerging role of photonics in research on biological structural colors, and the future directions in development of the tool.