Daily activity patterns influence retinal morphology, signatures of selection, and spectral tuning of opsin genes in colubrid snakes

Hauzman et al. BMC Evolutionary Biology (2017) 17:249 DOI 10.1186/s12862-017-1110-0 RESEARCH ARTICLE Open Access Daily activity patterns influence retinal morphology, signatures of selection, and spectral tuning of opsin genes in colubrid snakes E. Hauzman1,2* , D. M. O. Bonci1,2, E. Y. Suárez-Villota3,4, M. Neitz5 and D. F. Ventura1,2 Abstract Background: Morphological divergences of snake retinal structure point to complex evolutionary processes and adaptations. The Colubridae family has a remarkable variety of retinal structure that can range from all-cone and all-rod to duplex (cone/rod) retinas. To explore whether nocturnal versus diurnal activity is responsible for constraints on molecular evolution and plays a role in visual opsin spectral tuning of colubrids, we carried out molecular evolution analyses of the visual opsin genes LWS, RH1, and SWS1 from 17 species and performed morphological analyses. Results: Phylogenetic reconstructions of the RH1 and LWS recovered major clades characterized by primarily diurnal or primarily nocturnal activity patterns, in contrast with the topology for SWS1, which is very similar to the species tree. We found stronger signals of purifying selection along diurnal and nocturnal lineages for RH1 and SWS1, respectively. A blue-shift of the RH1 spectral peak is associated with diurnal habits. Spectral tuning of cone opsins did not differ among diurnal and nocturnal species. Retinas of nocturnal colubrids had many rows of photoreceptor nuclei, with large numbers of rods, labeled by wheat germ agglutinin (WGA), and two types of cones: large cones sensitive to long/medium wavelengths (L/M) and small cones sensitive to ultra-violet/violet wavelengths (UV/VS). In contrast, retinas of diurnal species had only one row of photoreceptor nuclei, with four types of cones: large and double L/M cones, small UV/VS cones, and a second group of small cones, labeled by WGA. Conclusions: For LWS gene, selection tests did not confirm different constraints related to activity pattern. For SWS1, stronger purifying selection in nocturnal lineages indicates divergent evolutionary pressures related to the activity pattern, and the importance of the short wavelength sensitivity at low light condition. Activity pattern has a clear influence on the signatures of selection and spectral tuning of RH1, with stronger purifying selection in diurnal lineages, which indicates selective pressure to preserve rhodopsin structure and function in pure-cone retinas. We suggest that the presence of four cone types in primarily diurnal colubrids might be related to the gain of color discrimination capacity. Keywords: Serpents, Retina, Visual pigments, Circadian activity pattern, dN/dS, Visual ecology * Correspondence: 1 Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, Av. Professor Mello Moraes 1721 Bloco A Sala D9 – Butantã, São Paulo, SP CEP 05508-030, Brazil 2 Instituto Israelita de Ensino e Pesquisa Albert Einstein, São Paulo, Brazil Full list of author information is available at the end of the article © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Hauzman et al. BMC Evolutionary Biology (2017) 17:249 Background Recent studies are bringing new light on the nature and evolution of the visual system of snakes [1–6]. After a long period of neglect, snake retinas, and more specifically, their visual pigments and opsin genes, have aroused new interest regarding their features and evolution [1–9]. The suborder Serpentes comprises a highly diversified group of vertebrates, with more than 3500 living species that inhabit a great diversity of ecological niches and exhibit distinct activity patterns, with diurnal, crepuscular and nocturnal species [10–13]. Most vertebrate visual systems have two distinct types of photoreceptor cells, rods and cones, that constitute, respectively, the rod system, which is highly sensitive to light and is responsible for nocturnal (scotopic) vision, and the cone system, which is responsible for mediating high visual acuity and color discrimination in photopic conditions [14–16]. Snakes retinal anatomies are very diverse and were classified based on their photoreceptor morphology as all-cone, all-rod or duplex retinas (cones/rods), with up to three types of cones and a rod [3, 7–9, 17–22]. Most nocturnal snakes have rod-dominated retinas and many diurnal species from the Caenophidia group (“advanced” or “higher” snakes) have pure-cone retinas [1, 7–9, 17–22]. On the other hand, some strictly nocturnal caenophidian snakes have no cone-like photoreceptor, but three rod-like cone classes [7, 8]. In a classic comparative study on the vertebrate retinas, Gordon Walls [7, 8] proposed that cones and rods could be interchangeable in a process he called “transmutation”. In this theory, Walls suggested, in reference to squamate reptiles, that some retinas with rods and cones had originated from pure-cone retinas of a diurnal ancestor, with the conversion of some of the cones into rods, as an adaptation to nocturnal activity (for more detail, see [3, 4, 6]). Recently, molecular analyses of the opsin genes were performed in Python regius and Xenopeltis unicolor, two nocturnal henophidian snakes. Three of the five major classes of visual opsin genes of vertebrates are expressed in the retinas of both species: the rhodopsin gene RH1 in rods, the short wavelength sensitive SWS1 in small singles cones, and the long wavelength sensitive LWS in large single cones [1]. The two remaining typical vertebrate cone opsin genes, RH2 and SWS2, sensitive to middle and short wavelengths, respectively, are not expressed in henophidian retinas and the authors suggested that they might have been lost in the ancestor of extant snakes. Subsequent studies on caenophidian snakes confirmed the absence of the RH2 and SWS2 opsin genes [2, 23] and the expression of the same three opsin genes (LWS, RH1, and SWS1) in retinas of most of the diurnal and nocturnal species studies so far [2–6]. These findings strongly suggest that the ancestral snake had functional copies of the three visual pigment genes Page 2 of 14 and provides evidence of at least some degree of scotopic vision in ancestral snakes [2, 5]. The expression of the rhodopsin RH1 visual pigment in pure-cone retinas of diurnal snakes is intriguing and has stimulated new investigations on the specific function and physiolo (...truncated)