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

Diversity and Molecular Evolution of Nonvisual Opsin Genes across Environmental, Developmental, and Morphological Adaptations in Frogs

Nonvisual opsins are transmembrane proteins expressed in the eyes and other tissues of many animals. When paired with a light-sensitive chromophore, nonvisual opsins form photopigments involved in various nonvisual, light-detection functions including circadian rhythm regulation, light-seeking behaviors, and seasonal responses. Here, we investigate the molecular evolution of nonvisual opsin genes in anuran amphibians (frogs and toads). We test several evolutionary hypotheses including the predicted loss of nonvisual opsins due to nocturnal ancestry and potential functional differences in nonvisual opsins resulting from environmental light variation across diverse anuran ecologies. Using whole-eye transcriptomes of 81 species, combined with genomes, multitissue transcriptomes, and independently annotated genes from an additional 21 species, we identify which nonvisual opsins are present in anuran genomes and those that are also expressed in the eyes, compare selective constraint among genes, and test for potential adaptive evolution by comparing selection between discrete ecological classes. At the genomic level, we recovered all 18 ancestral vertebrate nonvisual opsins, indicating that anurans demonstrate the lowest documented amount of opsin gene loss among ancestrally nocturnal tetrapods. We consistently found expression of 14 nonvisual opsins in anuran eyes and detected positive selection in a subset of these genes. We also found shifts in selective constraint acting on nonvisual opsins in frogs with differing activity periods, habitats, distributions, life histories, and pupil shapes, which may reflect functional adaptation. Although many nonvisual opsins remain poorly understood, these findings provide insight into the diversity and evolution of these genes across anurans, filling an important gap in our understanding of vertebrate opsins and setting the stage for future research on their functional evolution across taxa.

Diversity and Evolution of Frog Visual Opsins: Spectral Tuning and Adaptation to Distinct Light Environments

Visual systems adapt to different light environments through several avenues including optical changes to the eye and neurological changes in how light signals are processed and interpreted. Spectral sensitivity can evolve via changes to visual pigments housed in the retinal photoreceptors through gene duplication and loss, differential and coexpression, and sequence evolution. Frogs provide an excellent, yet understudied, system for visual evolution research due to their diversity of ecologies (including biphasic aquatic-terrestrial life cycles) that we hypothesize imposed different selective pressures leading to adaptive evolution of the visual system, notably the opsins that encode the protein component of the visual pigments responsible for the first step in visual perception. Here, we analyze the diversity and evolution of visual opsin genes from 93 new eye transcriptomes plus published data for a combined dataset spanning 122 frog species and 34 families. We find that most species express the four visual opsins previously identified in frogs but show evidence for gene loss in two lineages. Further, we present evidence of positive selection in three opsins and shifts in selective pressures associated with differences in habitat and life history, but not activity pattern. We identify substantial novel variation in the visual opsins and, using microspectrophotometry, find highly variable spectral sensitivities, expanding known ranges for all frog visual pigments. Mutations at spectral-tuning sites only partially account for this variation, suggesting that frogs have used tuning pathways that are unique among vertebrates. These results support the hypothesis of adaptive evolution in photoreceptor physiology across the frog tree of life in response to varying environmental and ecological factors and further our growing understanding of vertebrate visual evolution.

Insights into the adaptive evolution of chromosome and essential traits through chromosome-level genome assembly of Gekko japonicus

Gekko japonicus possesses flexible climbing and detoxification abilities under insectivorous habits. Still, the evolutionary mechanisms behind these traits remain unclarified. This study presents a chromosome-level G. japonicus genome, revealing that its evolutionary breakpoint regions were enriched with specific repetitive elements and defense response genes. Gene families unique to G. japonicus and positively selected genes are mainly enriched in immune, sensory, and nervous pathways. Expansion of bitter taste receptor type 2 primarily in insectivorous species could be associated with toxin clearance. Detox cytochrome P450 in G. japonicus has undergone more birth and death processes than biosynthesis-type P450 genes. Proline, cysteine, glycine, and serine in corneous beta proteins of G. japonicus might influence flexibility and setae adhesiveness. Certain thermosensitive transient receptor potential channels under relaxed purifying selection or positive selection in G. japonicus might enhance adaptation to climate change. This genome assembly offers insights into the adaptive evolution of gekkotans.

Convergent evolution of dim light vision in owls and deep-diving whales

Animals with enhanced dim-light sensitivity are at higher risk of light-induced retinal degeneration when exposed to bright light conditions.1,2,3,4 This trade-off is mediated by the rod photoreceptor sensory protein, rhodopsin (RHO), and its toxic vitamin A chromophore by-product, all-trans retinal.5,6,7,8 Rod arrestin (Arr-1) binds to RHO and promotes sequestration of excess all-trans retinal,9,10 which has recently been suggested as a protective mechanism against photoreceptor cell death.2,11 We investigated Arr-1 evolution in animals at high risk of retinal damage due to periodic bright-light exposure of rod-dominated retinas. Here, we find the convergent evolution of enhanced Arr-1/RHO all-trans-retinal sequestration in owls and deep-diving whales. Statistical analyses reveal a parallel acceleration of Arr-1 evolutionary rates in these lineages, which is associated with the introduction of a rare Arr-1 mutation (Q69R) into the RHO-Arr-1 binding interface. Using in vitro assays, we find that this single mutation significantly enhances RHO-all-trans-retinal sequestration by ∼30%. This functional convergence across 300 million years of evolutionary divergence suggests that Arr-1 and RHO may play an underappreciated role in the photoprotection of the eye, with potentially vast clinical significance.

The genomic basis of temporal niche evolution in a diurnal rodent

Patterns of diel activity-how animals allocate their activity throughout the 24-h daily cycle-play key roles in shaping the internal physiology of an animal and its relationship with the external environment.1,2,3,4,5 Although shifts in diel activity patterns have occurred numerous times over the course of vertebrate evolution,6 the genomic correlates of such transitions remain unknown. Here, we use the African striped mouse (Rhabdomys pumilio), a species that transitioned from the ancestrally nocturnal diel niche of its close relatives to a diurnal one,7,8,9,10,11 to define patterns of naturally occurring molecular variation in diel niche traits. First, to facilitate genomic analyses, we generate a chromosome-level genome assembly of the striped mouse. Next, using transcriptomics, we show that the switch to daytime activity in this species is associated with a realignment of daily rhythms in peripheral tissues with respect to the light:dark cycle and the central circadian clock. To uncover selection pressures associated with this temporal niche shift, we perform comparative genomic analyses with closely related rodent species and find evidence of relaxation of purifying selection on striped mouse genes in the rod phototransduction pathway. In agreement with this, electroretinogram measurements demonstrate that striped mice have functional differences in dim-light visual responses compared with nocturnal rodents. Taken together, our results show that striped mice have undergone a drastic change in circadian organization and provide evidence that the visual system has been a major target of selection as this species transitioned to a novel temporal niche.

Evolutionary analyses of visual opsin genes in frogs and toads: Diversity, duplication, and positive selection

Among major vertebrate groups, anurans (frogs and toads) are understudied with regard to their visual systems, and little is known about variation among species that differ in ecology. We sampled North American anurans representing diverse evolutionary and life histories that likely possess visual systems adapted to meet different ecological needs. Using standard molecular techniques, visual opsin genes, which encode the protein component of visual pigments, were obtained from anuran retinas. Additionally, we extracted the visual opsins from publicly available genome and transcriptome assemblies, further increasing the phylogenetic and ecological diversity of our dataset to 33 species in total. We found that anurans consistently express four visual opsin genes (RH1, LWS, SWS1, and SWS2, but not RH2) even though reported photoreceptor complements vary widely among species. The proteins encoded by these genes showed considerable sequence variation among species, including at sites known to shift the spectral sensitivity of visual pigments in other vertebrates and had conserved substitutions that may be related to dim-light adaptation. Using molecular evolutionary analyses of selection (dN/dS) we found significant evidence for positive selection at a subset of sites in the dim-light rod opsin gene RH1 and the long wavelength sensitive cone opsin LWS. The function of sites inferred to be under positive selection are largely unknown, but a few are likely to affect spectral sensitivity and other visual pigment functions based on proximity to previously identified sites in other vertebrates. We also found the first evidence of visual opsin duplication in an amphibian with the duplication of the LWS gene in the African bullfrog, which had distinct LWS copies on the sex chromosomes suggesting the possibility of sex-specific visual adaptation. Taken together, our results indicate that ecological factors, such as habitat and life history, as well as behavior, may be driving changes to anuran visual systems.

Eye-Transcriptome and Genome-Wide Sequencing for Scolecophidia: Implications for Inferring the Visual System of the Ancestral Snake

Molecular genetic data have recently been incorporated in attempts to reconstruct the ecology of the ancestral snake, though this has been limited by a paucity of data for one of the two main extant snake taxa, the highly fossorial Scolecophidia. Here we present and analyze vision genes from the first eye-transcriptomic and genome-wide data for Scolecophidia, for Anilios bicolor, and A. bituberculatus, respectively. We also present immunohistochemistry data for retinal anatomy and visual opsin-gene expression in Anilios. Analyzed in the context of 19 lepidosaurian genomes and 12 eye transcriptomes, the new genome-wide and transcriptomic data provide evidence for a much more reduced visual system in Anilios than in non-scolecophidian (=alethinophidian) snakes and in lizards. In Anilios, there is no evidence of the presence of 7 of the 12 genes associated with alethinophidian photopic (cone) phototransduction. This indicates extensive gene loss and many of these candidate gene losses occur also in highly fossorial mammals with reduced vision. Although recent phylogenetic studies have found evidence for scolecophidian paraphyly, the loss in Anilios of visual genes that are present in alethinophidians implies that the ancestral snake had a better-developed visual system than is known for any extant scolecophidian.

Inside the head of snakes: influence of size, phylogeny, and sensory ecology on endocranium morphology

Environmental properties, and the behavioral habits of species impact sensory cues available for foraging, predator avoidance and inter/intraspecific communication. Consequently, relationships have been discovered between the sensory ecology and brain morphology in many groups of vertebrates. However, these types of studies have remained scare on snake. Here, we investigate the link between endocranial shape and the sensory-related ecology of snakes by comparing 36 species of snakes for which we gathered six sensory-ecology characteristics. We use µCT scanning and 3D geometric morphometrics to compare their endocranium in a phylogenetically informed context. Our results demonstrate that size is a major driver of endocranial shape, with smaller species tending to maximize endocranial volume using a more bulbous shape, while larger species share an elongate endocranial morphology. Phylogeny plays a secondary role with more derived snakes diverging the most in endocranial shape, compared to other species. The activity period influences the shape of the olfactory and optic tract, while the foraging habitat impacts the shape of the cerebellum and cranial nerve regions: structures involved in orientation, equilibrium, and sensory information. However, we found that endocranial morphology alone is not sufficient to predict the activity period of a species without prior knowledge of its phylogenetic relationship. Our results thus demonstrate the value of utilizing endocranial shape as complementary information to size and volume in neurobiological studies.

Recreated Ancestral Opsin Associated with Marine to Freshwater Croaker Invasion Reveals Kinetic and Spectral Adaptation

Rhodopsin, the light-sensitive visual pigment expressed in rod photoreceptors, is specialized for vision in dim-light environments. Aquatic environments are particularly challenging for vision due to the spectrally dependent attenuation of light, which can differ greatly in marine and freshwater systems. Among fish lineages that have successfully colonized freshwater habitats from ancestrally marine environments, croakers are known as highly visual benthic predators. In this study, we isolate rhodopsins from a diversity of freshwater and marine croakers and find that strong positive selection in rhodopsin is associated with a marine to freshwater transition in South American croakers. In order to determine if this is accompanied by significant shifts in visual abilities, we resurrected ancestral rhodopsin sequences and tested the experimental properties of ancestral pigments bracketing this transition using in vitro spectroscopic assays. We found the ancestral freshwater croaker rhodopsin is redshifted relative to its marine ancestor, with mutations that recapitulate ancestral amino acid changes along this transitional branch resulting in faster kinetics that are likely to be associated with more rapid dark adaptation. This could be advantageous in freshwater due to the redshifted spectrum and relatively narrow interface and frequent transitions between bright and dim-light environments. This study is the first to experimentally demonstrate that positively selected substitutions in ancestral visual pigments alter protein function to freshwater visual environments following a transition from an ancestrally marine state and provides insight into the molecular mechanisms underlying some of the physiological changes associated with this major habitat transition.

Eye size in North American watersnakes (genus Nerodia) correlates with variation in feeding ecology

Visual acuity and sensitivity positively correlate to eye size in vertebrates, and eye size relates to the ecology of colubrid snakes. We investigated whether eye morphology of North American colubrids of the genus Nerodia correlates with ecology as well. Although all members of the genus utilize aquatic habits, they differ widely in the proportion of anurans they eat. We specifically tested whether eye size and placement is associated with the proportion of frogs in the diet to determine whether these two aspects of eye morphology relate to feeding ecology. Using phylogenetic comparative methods, we found a significantly positive association between eye size and the proportion of anurans eaten by Nerodia species. Although the evidence is equivocal, the anterior placement of relatively small eyes in one species may also enhance anurophagy. Although eye size may improve a snake’s ability to feed on frogs, eye size must compete with other selective forces on head shape in trade-offs that may also influence eye size.

Functional evolution of vertebrate sensory receptors

Sensory receptors enable animals to perceive their external world, and functional properties of receptors evolve to detect the specific cues relevant for an organism's survival. Changes in sensory receptor function or tuning can directly impact an organism's behavior. Functional tests of receptors from multiple species and the generation of chimeric receptors between orthologs with different properties allow for the dissection of the molecular basis of receptor function and identification of the key residues that impart functional changes in different species. Knowledge of these functionally important sites facilitates investigation into questions regarding the role of epistasis and the extent of convergence, as well as the timing of sensory shifts relative to other phenotypic changes. However, as receptors can also play roles in non-sensory tissues, and receptor responses can be modulated by numerous other factors including varying expression levels, alternative splicing, and morphological features of the sensory cell, behavioral validation can be instrumental in confirming that responses observed in heterologous systems play a sensory role. Expression profiling of sensory cells and comparative genomics approaches can shed light on cell-type specific modifications and identify other proteins that may affect receptor function and can provide insight into the correlated evolution of complex suites of traits. Here we review the evolutionary history and diversity of functional responses of the major classes of sensory receptors in vertebrates, including opsins, chemosensory receptors, and ion channels involved in temperature-sensing, mechanosensation and electroreception.

Adaptations and evolutionary trajectories of the snake rod and cone photoreceptors

Most vertebrates have duplex retinas, with two classes of photoreceptors, rods and cones. In the group of Snakes, however, distinct patterns of retinal morphology are associated with transitions between diurnal-nocturnal habits and reflect important adaptations of their visual system. Pure-cone, pure-rod and duplex retinas were described in different species, and this variability led Gordon Walls (1934) to formulate the transmutation theory, which suggests that rods and cones are not fixed entities, but can assume transitional states. Three opsin genes are expressed in retinas of most snake species, lws, rh1, and sws1, and recent studies have shown that the rhodopsin gene, rh1, is expressed in pure-cone retinas of diurnal snakes. This expression raised many questions about the nature of transmutation and functional aspects of the rhodopsin in a cone-like photoreceptor. Extreme differences in the retinal architecture of diurnal and nocturnal snakes also highlight the complexity of adaptations of their visual structures, which might have contributed to the adaptive radiation of this group and will be discussed in this review.

Phosphorylation at Serine 21 in G protein-coupled receptor kinase 1 (GRK1) is required for normal kinetics of dark adaption in rod but not cone photoreceptors

Timely recovery of the light response in photoreceptors requires efficient inactivation of photoactivated rhodopsin. This process is initiated by phosphorylation of its carboxyl terminus by G protein-coupled receptor kinase 1 (GRK1). Previously, we showed that GRK1 is phosphorylated in the dark at Ser21 in a cAMP-dependent manner and dephosphorylated in the light. Results in vitro indicate that dephosphorylation of Ser21 increases GRK1 activity, leading to increased phosphorylation of rhodopsin. This creates the possibility of light-dependent regulation of GRK1 activity and its efficiency in inactivating the visual pigment. To address the functional role of GRK1 phosphorylation in rods and cones in vivo, we generated mutant mice in which Ser21 is substituted with alanine (GRK1-S21A), preventing dark-dependent phosphorylation of GRK1. GRK1-S21A mice had normal retinal morphology, without evidence of degeneration. The function of dark-adapted GRK1-S21A rods and cones was also unaffected, as demonstrated by the normal amplitude and kinetics of their responses obtained by ex vivo and in vivo ERG recordings. In contrast, rod dark adaptation following exposure to bright bleaching light was significantly delayed in GRK1-S21A mice, suggesting that the higher activity of this kinase results in enhanced rhodopsin phosphorylation and therefore delays its regeneration. In contrast, dark adaptation of cones was unaffected by the S21A mutation. Taken together, these data suggest that rhodopsin phosphorylation/dephosphorylation modulates the recovery of rhodopsin to the ground state and rod dark adaptation. They also reveal a novel role for cAMP-dependent phosphorylation of GRK1 in regulating the dark adaptation of rod but not cone photoreceptors.

Transcriptomic data support a nocturnal bottleneck in the ancestor of gecko lizards

Gecko lizards are a species-rich clade of primarily-nocturnal squamate reptiles. In geckos, adaptations to nocturnality have dramatically reshaped the eye. Perhaps the most notable change is the loss of rod cells in the retina and subsequent "transmutation" of cones into a rod-like morphology and physiology. While many studies have noted the absence of some rod-specific genes, such as the visual pigment Rhodopsin (RH1), these studies have focused on just a handful of species that are nested deep in the gecko phylogeny. Thus, it is not clear whether these changes arose through convergence, are homologous and ubiquitous across geckos, or restricted to a subset of species. Here, we used de novo eye transcriptomes from five gecko species, and genomes from two additional gecko species, representing the breadth of extant gecko diversity (i.e. 4 of the 7 gecko families, spanning the deepest divergence of crown Gekkota), to show that geckos lost expression of almost the entire suite of necessary rod-cell phototransduction genes in the eye, distinct from all other squamate reptiles. Geckos are the first vertebrate group to have lost their complete rod-cell expression pathway, not just the visual pigment. In addition, all sampled species have also lost expression of the cone-opsin SWS2 visual pigment. These results strongly suggest a single loss of rod cells and subsequent cone-to-rod transmutation that occurred prior to the diversification of extant geckos.

Characterization of the melanopsin gene (Opn4x) of diurnal and nocturnal snakes

BACKGROUND

A number of non-visual responses to light in vertebrates, such as circadian rhythm control and pupillary light reflex, are mediated by melanopsins, G-protein coupled membrane receptors, conjugated to a retinal chromophore. In non-mammalian vertebrates, melanopsin expression is variable within the retina and extra-ocular tissues. Two paralog melanopsin genes were classified in vertebrates, Opn4x and Opn4m. Snakes are highly diversified vertebrates with a wide range of daily activity patterns, which raises questions about differences in structure, function and expression pattern of their melanopsin genes. In this study, we analyzed the melanopsin genes expressed in the retinas of 18 snake species from three families (Viperidae, Elapidae, and Colubridae), and also investigated extra-retinal tissue expression.

RESULTS

Phylogenetic analysis revealed that the amplified gene belongs to the Opn4x group, and no expression of the Opn4m was found. The same paralog is expressed in the iris, but no extra-ocular expression was detected. Molecular evolutionary analysis indicated that melanopsins are evolving primarily under strong purifying selection, although lower evolutionary constraint was detected in snake lineages (ω = 0.2), compared to non-snake Opn4x and Opn4m (ω = 0.1). Statistical analysis of selective constraint suggests that snake phylogenetic relationships have driven stronger effects on melanopsin evolution, than the species activity pattern. In situ hybridization revealed the presence of melanopsin within cells in the outer and inner nuclear layers, in the ganglion cell layer, and intense labeling in the optic nerve.

CONCLUSIONS

The loss of the Opn4m gene and extra-ocular photosensitive tissues in snakes may be associated with a prolonged nocturnal/mesopic bottleneck in the early history of snake evolution. The presence of melanopsin-containing cells in all retinal nuclear layers indicates a globally photosensitive retina, and the expression in classic photoreceptor cells suggest a regionalized co-expression of melanopsin and visual opsins.

Functional Shifts in Bat Dim-Light Visual Pigment Are Associated with Differing Echolocation Abilities and Reveal Molecular Adaptation to Photic-Limited Environments

Bats are excellent models for studying the molecular basis of sensory adaptation. In Chiroptera, a sensory trade-off has been proposed between the visual and auditory systems, though the extent of this association has yet to be fully examined. To investigate whether variation in visual performance is associated with echolocation, we experimentally assayed the dim-light visual pigment rhodopsin from bat species with differing echolocation abilities. While spectral tuning properties were similar among bats, we found that the rate of decay of their light-activated state was significantly slower in a nonecholocating bat relative to species that use distinct echolocation strategies, consistent with a sensory trade-off hypothesis. We also found that these rates of decay were remarkably slower compared with those of other mammals, likely indicating an adaptation to dim light. To examine whether functional changes in rhodopsin are associated with shifts in selection intensity upon bat Rh1 sequences, we implemented selection analyses using codon-based likelihood clade models. While no shifts in selection were identified in response to diverse echolocation abilities of bats, we detected a significant increase in the intensity of evolutionary constraint accompanying the diversification of Chiroptera. Taken together, this suggests that substitutions that modulate the stability of the light-activated rhodopsin state were likely maintained through intensified constraint after bats diversified, being finely tuned in response to novel sensory specializations. Our study demonstrates the power of combining experimental and computational approaches for investigating functional mechanisms underlying the evolution of complex sensory adaptations.

The transcriptome of the veiled chameleon (Chamaeleo calyptratus): A resource for studying the evolution and development of vertebrates

PURPOSE

The veiled chameleon (Chamaeleo calyptratus) is an emerging model system for studying functional morphology and evolutionary developmental biology (evo-devo). Chameleons possess body plans that are highly adapted to an arboreal life style, featuring laterally compressed bodies, split hands/ft for grasping, a projectile tongue, turreted independently moving eyes, and a prehensile tail. Despite being one of the most phenotypically divergent clades of tetrapods, genomic resources for chameleons are severely lacking.

METHODS

To address this lack of resources, we used RNAseq to generate 288 million raw Illumina sequence reads from four adult tissues (male and female eyes and gonads) and whole embryos at three distinct developmental stages. We used these data to assemble a largely complete de novo transcriptome consisting of only 82 952 transcripts. In addition, a majority of assembled transcripts (67%) were successfully annotated.

RESULTS

We then demonstrated the utility of these data in the context of studying visual system evolution by examining the content of veiled chameleon opsin genes to show that chameleons possess all five ancestral tetrapod opsins.

CONCLUSION

We present this de novo, annotated, multi-tissue transcriptome assembly for the Veiled Chameleon, Chamaeleo calyptratus, as a resource to address a range of evolutionary and developmental questions. The associated raw reads and final annotated transcriptome assembly are freely available for use on NCBI and Figshare, respectively.

Molecular Adaptations for Sensing and Securing Prey and Insight into Amniote Genome Diversity from the Garter Snake Genome

Colubridae represents the most phenotypically diverse and speciose family of snakes, yet no well-assembled and annotated genome exists for this lineage. Here, we report and analyze the genome of the garter snake, Thamnophis sirtalis, a colubrid snake that is an important model species for research in evolutionary biology, physiology, genomics, behavior, and the evolution of toxin resistance. Using the garter snake genome, we show how snakes have evolved numerous adaptations for sensing and securing prey, and identify features of snake genome structure that provide insight into the evolution of amniote genomes. Analyses of the garter snake and other squamate reptile genomes highlight shifts in repeat element abundance and expansion within snakes, uncover evidence of genes under positive selection, and provide revised neutral substitution rate estimates for squamates. Our identification of Z and W sex chromosome-specific scaffolds provides evidence for multiple origins of sex chromosome systems in snakes and demonstrates the value of this genome for studying sex chromosome evolution. Analysis of gene duplication and loss in visual and olfactory gene families supports a dim-light ancestral condition in snakes and indicates that olfactory receptor repertoires underwent an expansion early in snake evolution. Additionally, we provide some of the first links between secreted venom proteins, the genes that encode them, and their evolutionary origins in a rear-fanged colubrid snake, together with new genomic insight into the coevolutionary arms race between garter snakes and highly toxic newt prey that led to toxin resistance in garter snakes.