Shifts in Selective Pressures on Snake Phototransduction Genes Associated with Photoreceptor Transmutation and Dim-Light Ancestry

Shifts in Selective Pressures on Snake Phototransduction Genes Associated with Photoreceptor Transmutation and Dim-Light Ancestry Ryan K. Schott,1 Alexander Van Nynatten,2 Daren C. Card,3 Todd A. Castoe,3 and Belinda S.W. Chang*,1,2 1 Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada 3 Department of Biology, University of Texas, Arlington, TX 2 Abstract The visual systems of snakes are heavily modified relative to other squamates, a condition often thought to reflect their fossorial origins. Further modifications are seen in caenophidian snakes, where evolutionary transitions between rod and cone photoreceptors, termed photoreceptor transmutations, have occurred in many lineages. Little previous work, however, has focused on the molecular evolutionary underpinnings of these morphological changes. To address this, we sequenced seven snake eye transcriptomes and utilized new whole-genome and targeted capture sequencing data. We used these data to analyze gene loss and shifts in selection pressures in phototransduction genes that may be associated with snake evolutionary origins and photoreceptor transmutation. We identified the surprising loss of rhodopsin kinase (GRK1), despite a low degree of gene loss overall and a lack of relaxed selection early during snake evolution. These results provide some of the first evolutionary genomic corroboration for a dim-light ancestor that lacks strong fossorial adaptations. Our results also indicate that snakes with photoreceptor transmutation experienced significantly different selection pressures from other reptiles. Significant positive selection was found primarily in cone-specific genes, but not rod-specific genes, contrary to our expectations. These results reveal potential molecular adaptations associated with photoreceptor transmutation and also highlight unappreciated functional differences between rod- and cone-specific phototransduction proteins. This intriguing example of snake visual system evolution illustrates how the underlying molecular components of a complex system can be reshaped in response to changing selection pressures. Article Key words: evolution of vision, reptile vision, eye transcriptomes, snake origins, visual transduction, photoreceptor evolution. Introduction Snakes are a diverse group of squamate reptiles that are fascinating due in part to their contested evolutionary origins. Early work suggested that snakes may have had an aquatic origin based on affinities with extinct marine squamates, such as mosasaurs and dolichosaurs (Nopcsa 1908; 1923; for review see Lee and Caldwell 2000). Walls (1940), however, noted that snake eyes were heavily modified compared with other squamates such that they contain no structural features that could identify them as being squamate, or even reptilian, eyes. Walls (1940) hypothesized that these changes were due to a fossorial phase during the early evolution of snakes that led to a degeneration of the eye, followed later by recolonization of terrestrial habitats that necessitated a re-evolution of eye structure and function. Although this view was supported by later studies (Bellairs and Underwood 1951; Rieppel 1988), a quantitative morphometric analysis of eye morphology by Caprette et al. (2004) indicated that snake eyes most closely resembled those of primitively aquatic vertebrates, supporting an aquatic origin for snakes. Similarly, phylogenetic and fossil evidence has provided mixed, and often contradictory, support for both hypotheses resulting in an ongoing debate on snake origins (Caldwell and Lee 1997; Lee 2005; Longrich et al. 2012; Hsiang et al. 2015; Sim~oes et al. 2015; Yi and Norell 2015; Lee et al. 2016). Beyond their implications for snake origins, snake eyes are also particularly interesting due to the predominance of allcone and all-rod retinas, a feature that is extremely rare in other vertebrate groups (Walls 1942; Underwood 1970; Schott, Muller, et al. 2016). Typical vertebrate retinas are duplex, containing both rod and cone photoreceptors, which are often identified based on their outer segment morphology (rod- or cone-shaped). Rods are much more photosensitive and less noisy (i.e., less spontaneous activation) than cones ß The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For Permissions, please e-mail: 1376 Mol. Biol. Evol. 35(6):1376–1389 doi:10.1093/molbev/msy025 Advance Access publication February 22, 2018 *Corresponding author: E-mail: . Associate editor: Tal Pupko Data associated with this study have been submitted to NCBI under Bioproject PRJNA432436 and the Dryad Digital Repository at https://doi.org/10.5061/dryad.r31js91. Raw sequence data were deposited in the NCBI Short Read Archive (SRA accession SRP132105) and coding sequences in the NCBI GenBank database (accessions in supplementary files 1 and 2, Supplementary Material online). Shifts in Selective Pressures on Snake Phototransduction Genes . doi:10.1093/molbev/msy025 Henophidian-type Duplex Retina Caenophidian-type Duplex Retina e.g., pythons, boas, sunbeam snakes e.g., crotalid vipers MBE Intermediate Retina All-cone Retina All-rod Retina e.g., viperid vipers, secretive colubrids e.g., diurnal colubrids and elapids e.g., nocturnal colubrids enabling vision in dim light, but have slow response and recovery kinetics causing them to saturate under bright light (Lamb 2013). Cones have much faster response and recovery times, and can respond over a wider range of intensities than rods; however, they are less sensitive and more noisy, making vision in dim light unreliable (Lamb 2010, 2013). Rod and cone photoreceptor cells differ in both their morphology and molecular components, and these contribute to their differences in physiology (for a review, see Ingram et al. 2016). Due to these differences in function, most vertebrates have both rods and cones enabling them to see under a range of natural light conditions. Only a few groups, most notably snakes and other squamate reptiles, have simplex retinas that contain only rods or only cones. Snakes in particular have a wide range of retinal compositions, including not only allcone and all-rod retinas but also retinas with photoreceptor morphologies that are intermediate between typical vertebrate rods and cones (Walls 1942; Underwood 1970). This diversity of retinal types and photoreceptor morphologies within snakes appears to be restricted to caenophidians, a taxonomically, ecologically, and phenotypically diverse lineage (Walls 1942; Greene 1997; Vidal et al. 2007). Although noncaenophidian snakes surveyed to date have retinas containing only reduced rods (scolecophidians), or simple duplex retinas with single cones and rods (“henophidian”-grade species, such as pythons and boas), caenophidians ha (...truncated)