Visual Pigments, Ocular Filters and the Evolution of Snake Vision

Visual Pigments, Ocular Filters and the Evolution of Snake Vision Bruno F. Sim~oes,*,1 Filipa L. Sampaio,1 Ronald H. Douglas,2 Ullasa Kodandaramaiah,3 Nicholas R. Casewell,4 Robert A. Harrison,4 Nathan S. Hart,5 Julian C. Partridge,6 David M. Hunt,6,7 and David J. Gower*,1 1 Department of Life Sciences, The Natural History Museum, London, United Kingdom Department of Optometry and Visual Science, City University London, London, United Kingdom 3 School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, India 4 Alistair Reid Venom Research Unit, Liverpool School of Tropical Medicine, Liverpool, United Kingdom 5 Department of Biological Sciences, Macquarie University, North Ryde, NSW, Australia 6 School of Animal Biology and the Oceans Institute, The University of Western Australia, Perth, WA, Australia 7 Lions Eye Institute, University of Western Australia, Perth, Australia 2 Abstract Much of what is known about the molecular evolution of vertebrate vision comes from studies of mammals, birds and fish. Reptiles (especially snakes) have barely been sampled in previous studies despite their exceptional diversity of retinal photoreceptor complements. Here, we analyze opsin gene sequences and ocular media transmission for up to 69 species to investigate snake visual evolution. Most snakes express three visual opsin genes (rh1, sws1, and lws). These opsin genes (especially rh1 and sws1) have undergone much evolutionary change, including modifications of amino acid residues at sites of known importance for spectral tuning, with several tuning site combinations unknown elsewhere among vertebrates. These changes are particularly common among dipsadine and colubrine “higher” snakes. All three opsin genes are inferred to be under purifying selection, though dN/dS varies with respect to some lineages, ecologies, and retinal anatomy. Positive selection was inferred at multiple sites in all three opsins, these being concentrated in transmembrane domains and thus likely to have a substantial effect on spectral tuning and other aspects of opsin function. Snake lenses vary substantially in their spectral transmission. Snakes active at night and some of those active by day have very transmissive lenses, whereas some primarily diurnal species cut out shorter wavelengths (including UVA). In terms of retinal anatomy, lens transmission, visual pigment spectral tuning and opsin gene evolution the visual system of snakes is exceptionally diverse compared with all other extant tetrapod orders. Introduction The fundamentals of vertebrate vision have been particularly well studied in terms of the molecular basis of photoreception and phototransduction. A cornerstone of this is knowledge of the photosensitivity of visual pigments, members of the large family of G-protein-coupled-receptor (GPCR) proteins, which share a common arrangement of an opsin protein linked to a chromophore derived from vitamin A (Wald 1968). Visual pigments play a core role in photon detection and color vision and they are a leading example of how gene duplications (Dulai et al. 1999) and changes in amino acid sequences (Yokoyama 2008), type of chromophore (vitamin A1 or A2: Enright et al. 2015) and gene expression (Hofmann and Carleton 2009; Carleton et al. 2010) underlie adaptations to differing ecological and behavioral selection pressures. Visual opsins in some vertebrates have been studied intensely over the past 20 years, to the extent that changes in specific (“spectral tuning”) amino acid sites ß The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: Mol. Biol. Evol. 33(10):2483–2495 doi:10.1093/molbev/msw148 Advance Access publication August 16, 2016 2483 Fast Track Animal vision has become one of the best examples of the power of integrative biology. A great deal is known about the anatomy of eyes at many levels, but much is also known about how eyes function and have evolved, including aspects of the physiology underlying photon capture, spectral sensitivity, signal transduction and propagation, and the identity of several key genes and proteins. Indeed, vision is one of the best characterized of all biological sensory systems. In addition, selective pressures can often be determined from physical first principles, allowing the identification and quantification of many aspects of the evolution of eyes (Land 1981; Nilsson 1996). In general, vision in vertebrates is especially well studied, and studies of the evolution of their visual pigments have been able to both identify evolutionary changes, and to ascribe such changes to adaptive evolutionary processes (Hughes 2008). Article Key words: ocular media, sensory evolution, photoreception, Serpentes, spectral tuning, vision. *Corresponding author: E-mail: ; . Associate editor: Nicholas Vidal MBE Sim~ oes et al. . doi:10.1093/molbev/msw148 2484 spectacle have been reported only twice (Hart et al. 2012; van Doorn and Sivak 2015). Given the anatomical diversity of snake retinal photoreceptors and the relative lack of previous studies, we address the following major questions: (1) What are the major patterns in the diversity and molecular evolution of snake visual opsins? (2) Is the diversity in snake retinal photoreceptor anatomy, visual opsin and ocular media transmission linked in a predictable way? (3) To what extent is snake visual opsin spectral tuning and/or opsin molecular evolution explained by major shifts in ecology and/or retinal anatomy? (4) Do snakes present diversity in visual opsins beyond that known for other major groups of vertebrates, mirroring the diversity of their ocular morphology? Here, we report the largest data set of visual opsin genes in reptiles to date, covering the major types of snake retinal anatomy and taxonomic and ecological diversity. We also report data on the spectral transmission of important components of the ocular media (lens and spectacle) of a subset of these snakes. We find that although the vast majority of snakes retain three of the visual opsin genes likely to have been present in the ancestral snake, these have undergone considerable diversification through functionally important amino acid substitutions. Notably, many of these substitutions are unreported in other vertebrate groups. There are also changes in the transmission of the lens, particularly with respect to the filtering of short wavelengths that will significantly affect overall spectral sensitivities. Snakes are an important system for understanding of the evolution of the vertebrate visual system. Materials and Methods Taxon Sampling and Sample Storage Snakes were acquired through fieldwork, the Liverpool School of Tropical Medicine, from hobbyists and the commercial trade. Our sampling (supplementary table S1, Supplementary Material online) aimed to maximize taxonomic (p (...truncated)